bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical Decision Rules to Improve the Detection of Adverse Drug Events in Emergency Department Patients
Authors: Hohl Corinne M. , Yu Eugenia , Hunte Garth S. , Brubacher Jeffrey R. , Hosseini Faegheh , Argent Chelsea P. , Chan Winnie W.Y. , Wiens Matthew O. , Sheps Samuel B. , Singer Joel
Published: June 2012

ACADEMIC EMERGENCY MEDICINE 2012; 19:640–649 © 2012 by the Society for Academic Emergency Medicine

Objectives:  Adverse drug events (ADEs) are unintended and harmful consequences of medication use. They are associated with high health resource use and cost. Yet, high levels of inaccuracy exist in their identification in clinical practice, with over one‐third remaining unidentified in the emergency department (ED). The study objective was to derive clinical decision rules (CDRs) that are sensitive for the detection of ADEs, allowing their systematic identification early in a patient’s hospital course.

Methods:  This was a prospective observational cohort study carried out in two Canadian tertiary care hospitals. Participants were adults presenting to the ED having ingested at least one prescription or over‐the‐counter medication within 2 weeks. Nurses and physicians evaluated patients for standardized clinical findings. A second evaluator performed interobserver assessments of predictor variables in a subset of patients. Pharmacists, who were blinded to the predictor variables, evaluated all patients for ADEs. An independent committee reviewed and adjudicated cases where the ADE assessment was uncertain or the pharmacist’s diagnosis differed from the physician’s working diagnosis. The primary outcome was an ADE that required a change in medical therapy, diagnostic testing, consultation, or hospital admission. CDRs were derived using kappa coefficients, chi‐square statistics, and recursive partitioning.

Results:  Among 1,591 patients, 131 (8.2%, 95% confidence interval [CI] = 7.0% to 9.7%) were diagnosed with the primary outcome. The following variables were associated with ADEs and were used to derive two CDRs: 1) presence of comorbid conditions, 2) antibiotic use within 7 days, 3) medication changes within 28 days, 4) age ≥80 years, 5) arrival by ambulance, 6) triage acuity, 7) recent hospital admission, 8) renal failure, and 9) use of three or more prescription medications. The more sensitive rule had a sensitivity of 96.7% (95% CI = 91.8% to 98.6%) and required 40.8% (95% CI = 37.7% to 42.9%) of patients to have medication review. The more specific rule had a sensitivity 90.8% (95% CI = 81.4% to 95.7%) and required 28.3% of patients to proceed to medication review.

Conclusions:  The authors derived CDRs that identified patients with ADEs with high sensitivity. These rules may improve the identification of ADEs early in a patient’s hospital course while limiting the number of patients requiring a detailed medication review.
Context dependency of nectar reward‐guided oviposition
Authors: Kessler Danny
Published: June 2012

Nectar is the most common floral reward used to recruit pollination services. Changes in nectar volume may affect not only pollination services, but also the attraction of antagonists such as herbivores, especially if the same insect species acts as herbivore and pollinator. Plants compete with each other for the best pollination services, at the same time employing various strategies to avoid herbivory. Datura wrightii Regel and Nicotiana attenuata Torr. ex Watson, two sympatric solanaceous species, compete for the same hawkmoth pollinator, Manduca quinquemaculata (Haworth) (Lepidoptera: Sphingidae), although standing nectar volume per flower differs 50‐fold (70 vs. 1.3 μl, respectively) between these species. This large difference may also result in differences in oviposition rates. I conducted a detailed analysis of diurnal changes in nectar volume and sugar concentration in field‐ and glasshouse‐grown D. wrightii and N. attenuata plants, and tested how well nectar production is buffered against the loss of large amounts of foliar tissue that frequently occurs due to M. quinquemaculata larval herbivory. I examined the influence of nectar volume on herbivore damage in the field and compared the results with previously published data from N. attenuata which were collected simultaneously. Oviposition by M. quinquemaculata moths increased significantly in D. wrightii plants whose nectar volume had been experimentally increased five‐fold compared to untreated control plants, and correlated with the numbers of flowers per plant in native populations. The results suggest that a hawkmoth mother may use standing nectar volume of a potential host plant to estimate its size, and possibly health, to make the optimal decision for her progeny. This mode of assessment, however, is apparently not used with another plant species, as other more herbivory‐related cues, such as olfaction or vision, are more influential in determining oviposition rates on other plant species. Yet within a plant species, regulating nectar volume strongly influences future herbivory.
Renal aspects of thalassaemia a changing paradigm
Authors: Bhandari Sunil , Galanello Renzo
Published: June 2012

Beta‐thalassaemia is characterised by progressive anaemia necessitating regular blood transfusions to sustain life. With the advent of effective chelating agents that can reduce the iron burden and extend patients' survival, renal disease, as in other ageing populations, has become more prevalent. In recent years, chronic kidney disease (CKD) has become overwhelming; indeed, approximately 8% or 6 million people of the UK population has evidence of CKD. Several factors, which occur in patients with thalassaemia, account for the relative explosion of renal disease in the general population including increasing age, diabetes, hypertension and the advent of novel measures of renal function facilitating early detection of kidney disease. In addition, some patients with thalassaemia develop renal tubular dysfunction related to the disease itself, the effects of iron overload and the effects of chelator therapy, while other patients have an increased creatinine clearance leading to hyperfiltration. More recently, there is a noticeable increasing prevalence of impaired renal function and proteinuria because of several putative factors including chelators. We review current data on the potential mechanisms leading to renal abnormalities seen in patients with thalassaemia, the potential effects of iron loading within the kidney and the potential renal effects of chelator therapy. This article gives a speculative account of possible mechanisms and theories to consider providing pause for thought and direct future research in this area.
Receptor‐type tyrosine phosphatase ligands: looking for the needle in the haystack
Authors: Mohebiany Alma N. , Nikolaienko Roman M. , Bouyain Samuel , Harroch Sheila
Published: June 2012

Reversible protein phosphorylation plays a pivotal role in intercellular communication. Together with protein tyrosine kinases, protein tyrosine phosphatases (PTPs) are involved in the regulation of key cellular processes by controlling the phosphorylation levels of diverse effectors. Among PTPs, receptor‐like protein tyrosine phosphatases (RPTPs) are involved in important developmental processes, particularly in the formation of the nervous system. Until recently, few ligands had been identified for RPTPs, making it difficult to grasp the effects these receptors have on cellular processes, as well as the mechanisms through which their functions are mediated. However, several potential RPTP ligands have now been identified to provide us with unparalleled insights into RPTP function. In this review, we focus on the nature and biological outcomes of these extracellular interactions between RPTPs and their associated ligands.
Amino acid sensing mechanisms: an Achilles heel in cancer?
Authors: Lamb Richard F.
Published: June 2012

The act of increasing mass, either in non‐dividing cells or in dividing cells seeking to provide new material for daughter cells, depends upon the continued presence of extracellular nutrients in order to conserve mass. For amino acid nutrients, it appears that their insufficiency for new protein synthesis is actively monitored by both prokaryotic and eukaryotic cells, eliciting appropriate cellular responses that may depend not only on bulk nutrient supply, but also on the abundance of specific amino acids.
An unusual tandem‐domain rhodanese harbouring two active sites identified in Desulfitobacterium hafniense
Authors: Prat Laure , Maillard Julien , Rohrbach‐Brandt Emmanuelle , Holliger Christof
Published: June 2012

The rhodanese protein domain is common throughout all kingdoms of life and is characterized by an active site cysteine residue that is able to bind sulfane sulfur and catalyse sulfur transfer. No unique function has been attributed to rhodanese‐domain‐containing proteins, most probably because of their diversity at both the level of sequence and protein domain architecture. In this study, we investigated the biochemical properties of an unusual rhodanese protein, PhsE, from Desulfitobacterium hafniense strain TCE1 which we have previously shown to be massively expressed under anaerobic respiration with tetrachloroethene. The peculiarity of the PhsE protein is its domain architecture which is constituted of two rhodanese domains each with an active site cysteine. The N‐terminal rhodanese domain is preceded by a lipoprotein signal peptide anchoring PhsE on the outside of the cytoplasmic membrane. In vitro sulfur‐transferase activity of recombinant PhsE variants was measured for both domains contrasting with other tandem‐domain rhodaneses in which usually only the C‐terminal domain has been found to be active. The genetic context of phsE shows that it is part of a six‐gene operon displaying homology with gene clusters encoding respiratory molybdoenzymes of the PhsA/PsrA family, possibly involved in the reduction of sulfur compounds. Our data suggest, however, that the presence of sulfide in the medium is responsible for the high expression of PhsE in Desulfitobacterium, where it could play a role in the sulfur homeostasis of the cell.
Secondary alcohol dehydrogenase catalyzes the reduction of exogenous acetone to 2‐propanol in Trichomonas vaginalis
Authors: Sutak Robert , Hrdy Ivan , Dolezal Pavel , Cabala Radomir , Sedinová Miroslava , Lewin Joern , Harant Karel , Müller Miklos , Tachezy Jan
Published: June 2012

Secondary alcohols such as 2‐propanol are readily produced by various anaerobic bacteria that possess secondary alcohol dehydrogenase (S‐ADH), although production of 2‐propanol is rare in eukaryotes. Specific bacterial‐type S‐ADH has been identified in a few unicellular eukaryotes, but its function is not known and the production of secondary alcohols has not been studied. We purified and characterized S‐ADH from the human pathogen Trichomonas vaginalis. The kinetic properties and thermostability of T. vaginalis S‐ADH were comparable with bacterial orthologues. The substantial activity of S‐ADH in the parasite’s cytosol was surprising, because only low amounts of ethanol and trace amounts of secondary alcohols were detected as metabolic end products. However, S‐ADH provided the parasite with a high capacity to scavenge and reduce external acetone to 2‐propanol. To maintain redox balance, the demand for reducing power to metabolize external acetone was compensated for by decreased cytosolic reduction of pyruvate to lactate and by hydrogenosomal metabolism of pyruvate. We speculate that hydrogen might be utilized to maintain cytosolic reducing power. The high activity of Tv‐S‐ADH together with the ability of T. vaginalis to modulate the metabolic fluxes indicate efficacious metabolic responsiveness that could be advantageous for rapid adaptation of the parasite to changes in the host environment.
Effect of Acticoat® and Cutinova Hydro® on wound healing
Authors: Arıcan Mustafa , Hatipoglu Fatih , Uyaroglu Aysen , Ozdemir Ozgur , Ozkan Kadircan
Published: June 2012

In this study, the effects of the wound‐covering materials, Acticoat® and Cutinova Hydro®, on wound healing have been studied in rabbit models with open and tissue‐lost wounds with full‐thickness flank excisions. Rabbits were used as subjects with three groups of four rabbits each, and trial periods of 7, 14 and 21{\uns}days. Four circular wounds, of 1.5 cm diameter were made two on the right (one of them control) and two on the left (one of them control) of the dorsal sides of the abdomen. Acticoat® and Cutinova Hydro® were applied on the wounds with suture for a period of 21 days and one each placed on the right and left sides as control with gauze. Biopsy specimens were taken from the animals at the end of the research period to check the length of the epithelium, epithelial thickness, size of wounds, wound granulation tissue formation and histopathological evaluation for clarity. The Acticoat® group showed better healing and scar formation compared to the Cutinova Hydro® group by macroscopic examination. Epithelial wound length and clarity in terms of statistical difference occurred on day 21 (P <0.05); while the length of the wound epithelium decreased patency, epithelial thickness on days~7, 14 and 21, showed no statistical differences (P >0.05). As a result, the Acticoat® wound dressing was determined as a more reliable for the early wound healing. This study has shown the short‐term clinical benefits of hydroactive, polyurethane dressings in the management of acute wounds. However, longer periods of wound healing procedure should be planned for reliable and safe results of wound dressing. It has also been concluded that microbiological analyses should be included for more robust and reliable comparisons.
Influence of Carbon Content on Surface Quality of Solid‐State Sintered SiC Ceramics
Authors: Gao Jianqin , Chen Jian , Liu Guiling , Yan Yongjie , Huang Zhengren
Published: June 2012

Influence of carbon content on surface quality of solid‐state sintered
SiC
ceramics with nearly full density was first investigated. Comparison study was carried out with varying carbon contents of 2, 3, and 6 wt%, respectively. Investigation on surface morphology using atomic force microscope reveals that residual carbon presents as protuberances on the polished surface. The surface quality of the polished samples was improved by decreasing carbon content, and with 2 wt% carbon, the surface quality can reach 0.7 nm rms surface roughness after polishing. It offers a material‐design approach to improve surface quality of solid‐state sintered
SiC
ceramics.
Effects of Major Water Quality Variables on Shrimp Production in Inland, Low‐Salinity Ponds in Alabama
Authors: Prapaiwong Naparat , Boyd Claude E.
Published: June 2012

Common water quality variables in nine, inland low‐salinity shrimp ponds in Alabama exhibited wide variation in concentrations among ponds and over time. Shrimp performance also varied considerably among ponds in 2008 as follows: survival, 16–128%; production, 928–5950 kg/ha; feed conversion ratio (FCR), 1.18–2.89. Measured water quality variables were not at concentrations high enough to be lethal to shrimp; but water temperature, dissolved oxygen, carbon dioxide, total ammonia nitrogen, calcium, and magnesium were occasionally outside optimum ranges for shrimp production and may have stressed shrimp. Survival and production both were positively correlated (P < 0.05) with increasing concentrations of methyl orange alkalinity, total alkalinity, and calcium hardness. Negative correlations (P < 0.05) between production and higher pH and water temperature may have resulted from lower water temperature and pH during final days of the crop in ponds harvested in October rather than from an actual effect of temperature and pH on growth. Nevertheless, those variables that were outside optimal ranges or correlated with shrimp survival or growth should be further investigated to ascertain whether or not excursions outside optimum ranges are harmful and to determine if observed correlations are causal.
The Scale‐up of Spotted Rose Snapper, Lutjanus guttatus, Larval Rearing at Mazatlan, Mexico
Authors: Alvarez‐Lajonchère L. , Abdo de la Parra M. I. , Rodríguez Ibarra L. E. , Velasco Blanco G. , Puello‐Cruz A. C. , González Rodríguez B. , Ibarra‐Soto A. , Ibarra Castro L.
Published: June 2012

The scale‐up of spotted rose snapper, Lutjanus guttatus, larval rearing is described. Fertilized eggs (480,000) were obtained from a 1‐d harvest of a natural spawning captive broodstock acclimatized for 1 yr and 6 mo in two fiberglass tanks (18 m3). Fourteen hours after spawning, 89.6% of the collected eggs were floating, of which 96.2% were transparent with live embryos. Incubation at 25–26 C lasted 21 h, with 90.2 ± 2.1% hatching percentage of normal larvae. The percentage of viable larvae at 48 h after hatching was 79.7 ± 1.9%. Initial stocking density was 10.4 ± 1.0 larvae/L 2 days after hatching (d.p.h.). A total of 22,600 juveniles (1256 ± 170 juveniles/m3) were harvested from six 3‐m3 cylindrical fiberglass tanks. Average survival was 12.1 ± 1.1%. Final mean length and weight were 5.5 ± 0.05 cm and 2.24 ± 0.04 g, respectively. Growth expressed in total length was TL = 2.1476e0.0543t (R2 = 0.9911). Final mean biomass and condition factor were 2.8 kg/m3, 12.3% and 1.346. General length‐weight ratio was W = 0.05460 LT2.2306.
Impact of pregnancy on health‐related quality of life of patients with inflammatory bowel disease
Authors: ANANTHAKRISHNAN Ashwin N , ZADVORNOVA Yelena , NAIK Amar S , ISSA Mazen , PERERA Lilani P
Published: June 2012

Objective

To examine the impact of pregnancy on health‐related quality of life (HRQoL) of women with inflammatory bowel disease (IBD).

Methods

This was a retrospective study in a tertiary referral center and included women with ≥2 short inflammatory bowel disease questionnaire (SIBDQ) scores obtained during their pregnancy. Regression models were used to identify independent factors influencing SIBDQ scores and changes of SIBDQ scores at different time points.

Results

A total of 32 women (23 CD, 9 UC) with a mean age at pregnancy of 29.4 years and a mean disease duration of 7.8 years were included in the study. The mean pre‐pregnancy SIBDQ score in our cohort was 49, which was significantly lower than the values during (55, P < 0.001) and post‐pregnancy (53, P = 0.01). The score during pregnancy directly correlated with the pre‐pregnancy SIBDQ score (correlation co‐efficient 0.50, P = 0.003). Half of the patients had a ≥7‐point increase in SIBDQ scores during pregnancy. Change in SIBDQ scores during pregnancy was inversely related to the pre‐pregnancy score (−0.47, 95% CI −0.75 to −0.20) and changes in disease activity during pregnancy (−1.80, 95% CI −0.75 to −0.20).

Conclusions

Half of the pregnant women with IBD in our cohort experienced improvement in their HRQoL. Pre‐pregnancy HRQoL is predictive of HRQoL during pregnancy, supporting the need for optimizing disease activity prior to conception.
Herbicide cycling has diverse effects on evolution of resistance in Chlamydomonas reinhardtii
Authors: Lagator Mato , Vogwill Tom , Colegrave Nick , Neve Paul
Published: June 2012

Cycling pesticides has been proposed as a means of retarding the evolution of resistance, but its efficacy has rarely been empirically tested. We evolved populations of
Chlamydomonas reinhardtii in the presence of three herbicides: atrazine, glyphosate and carbetamide. Populations were exposed to a weekly, biweekly and triweekly cycling between all three pairwise combinations of herbicides and continuously to each of the three herbicides. We explored the impacts of herbicide cycling on the rate of resistance evolution, the level of resistance selected, the cost of resistance and the degree of generality (cross‐resistance) observed. Herbicide cycling resulted in a diversity of outcomes: preventing evolution of resistance for some combinations of herbicides, having no impacts for others and increasing rates of resistance evolution in some instances. Weekly cycling of atrazine and carbetamide resulted in selection of a generalist population. This population had a higher level of resistance, and this generalist resistance was associated with a cost. The level of resistance selected did not vary amongst other regimes. Costs of resistance were generally highest when cycling was more frequent. Our data suggest that the effects of herbicide cycling on the evolution of resistance may be more complex and less favourable than generally assumed.
Engaging Communities in Education and Research: PBRNs, AHEC, and CTSA
Authors: Westfall John M. , Ingram Beth , Navarro Daniel , Magee Deidre , Niebauer Linda , Zittleman Linda , Fernald Douglas , Pace Wilson
Published: June 2012

Background: Community engagement has become a prominent element in medical research and is an important component of the Clinical and Translational Science Awards program. Area Health Education Centers engage communities in education and workforce development.

Methods: Engaging Communities in Education and Research (ECER) is a successful collaboration among the Colorado Area Health Education Center (AHEC), the Colorado Clinical Translational Science Institute, and Shared Network of Collaborative Ambulatory Practices and Partners—Colorado’s practice‐based research collaborative. The ECER Conference is an annual conference of community members, health care providers, clinical preceptors, AHEC board members, university faculty, primary care investigators, program administrators, and community organization leaders.

Results: Over 1,000 people have participated in the ECER Conference representing all regions of Colorado. Several projects from the “new ideas” breakout session have been developed and completed. Six‐month follow‐up provided evidence of numerous new collaborations, campus‐community partnerships, and developing research projects. Several new collaborations highlight the long‐term nature of building on relationships started at the ECER Conference.

Discussion and Conclusion: ECER has been a successful collaboration to develop and support campus‐community collaborations in Colorado. Although seemingly just a simple 3‐day conference, we have found that this event has lead to many important partnerships. Clin Trans Sci 2012; Volume #: 1–9
Use of chemicals and biological products in Asian aquaculture and their potential environmental risks: a critical review
Authors: Rico Andreu , Satapornvanit Kriengkrai , Haque Mohammad M. , Min Jiang , Nguyen Phuong T. , Telfer Trevor C. , van den Brink Paul J.
Published: June 2012

Over the past few decades, Asian aquaculture production has intensified rapidly through the adoption of technological advances, and the use of a wide array of chemical and biological products to control sediment and water quality and to treat and prevent disease outbreaks. The use of chemicals in aquaculture farms has raised environmental concerns owing to their potential impacts on downstream aquatic ecosystems. Currently little is known about the environmental fate and effects of the chemicals used in Asian aquaculture. Consequently, we reviewed recent information on the use of chemical and biological products in the most important Asian aquaculture producing countries and briefly summarize their main potential environmental impacts. We provide an overview of the main factors controlling the use of these chemicals and describe the international risk assessment guidelines available for aquaculture chemicals. Finally, data gaps and research needs for their implementation in Asian countries are discussed. Our review aims to form a basis for developing environmental risk assessment studies of the chemicals used in Asian aquaculture.
Non‐thermal Nanoelectroablation of UV‐induced Murine Melanomas Stimulates an Immune Response
Authors: Nuccitelli Richard , Tran Kevin , Lui Kaying , Huynh Joanne , Athos Brian , Kreis Mark , Nuccitelli Pamela , De Fabo Edward C.
Published: June 2012

Non‐thermal nanoelectroablation therapy completely ablates UV‐induced murine melanomas. C57/BL6‐HGF/SF transgenic mice were exposed to UV radiation as pups and began to develop visible melanomas 5–6 months later. We have treated 27 of these melanomas in 14 mice with nanosecond pulsed electric field (nsPEF) therapy delivering 2000 electric pulses each 100 ns long and 30 kV/cm at a rate of 5–7 pulses per second. All nanoelectroablated melanoma tumors began to shrink within a day after treatment and gradually disappeared over a period of 12–29 days. Pyknosis of nuclei was evident within 1 h of nsPEF treatment, and DNA fragmentation as detected by TUNEL staining was evident by 6 h after nsPEF treatment. In a melanoma allograft system, nsPEF treatment was superior to tumor excision at accelerating secondary tumor rejection in immune‐competent mice, suggesting enhanced stimulation of a protective immune response by nsPEF‐treated melanomas. This is supported by the presence of CD4+‐T cells within treated tumors as well as within untreated tumors located in mice with other melanomas that had been treated with nanoelectroablation at least 19 days earlier.
Willing or unwilling to share primary biodiversity data: results and implications of an international survey
Authors: Huang Xiaolei , Hawkins Bradford A. , Lei Fumin , Miller Gary L. , Favret Colin , Zhang Ruiling , Qiao Gexia
Published: June 2012

Biodiversity science and conservation increasingly depend on the sharing and integration of large amounts of data, but many researchers resist sharing their primary biodiversity data. We recently conducted an international survey to ascertain the attitudes, experiences, and expectations regarding biodiversity data sharing and archiving of researchers. The results show that whereas most respondents are willing to share article‐related biodiversity data, more than 60% of respondents are unwilling to share primary data before publishing. Results indicate an underdeveloped culture of data sharing and several major technological and operational barriers. A major concern for researchers is appropriate benefits from data sharing. Most respondents would accept data archiving policies of journals. Researchers also express concerns about how to easily and efficiently deal with data and data quality in public databases. Expectations for biodiversity databases include standardization of data format, user‐friendly data submission tools, formats for different types of data, and coordination among databases. The survey results provide suggestions for improving data sharing and archiving by individual scientists, organizations, journals, and databases.
HumanEscherichia colistrains of different geographical and time source: bacteriocin types and their gene sequences are population‐specific
Authors: Šmajs David , Čejková Darina , Micenková Lenka , Lima‐Bittencourt Claudia I. , Chartone‐Souza Edmar , Šmarda Jan , Nascimento Andréa M. A.
Published: June 2012

Bacteriocin production was tested in two sets ofEscherichia colistrains: one isolated in 1978 from healthy children of rubber tree tappers and Indians in Amazonia,Brazil (n = 35), and the second one isolated in 2004 from healthy adult volunteers in theMoravia region,CzechRepublic (n = 53). Although the occurrence of bacteriocin production was rather similar in both groups (54.3% and 43.4% respectively), the spectra of bacteriocin‐encoding determinants in both groups were different. Altogether, 12 different bacteriocin‐encoding determinants were found among the tested strains. The occurrence of colicinE1‐ andY‐genes was higher (P = 0.02 andP = 0.009 respectively) while the occurrence of microcinVgene was lower (P = 0.02) amongAmazonian strains compared withMoravian strains. The colicin‐encoding determinants of colicins Ia,M,YandE1 were amplified fromAmazonian andMoravian producer strains and sequenced, as were chromosomal 16SrRNA,gyrBandtonBgenes. While sequence alignments of chromosomal loci revealed no clusters with respect to geographical origin of strains, the colicin‐encoding genes were very similar among the strains of each origin but different between the two geographic groups.
A Finite Temperature Multiscale Interphase Zone Model and Simulations of Fracture
Authors: Liu Lisheng , Li Shaofan
Published: June 2012

In this work, an atomistic-based finite temperature multiscale interphase finite element method has been developed, and it has been applied to study fracture process of metallic materials at finite temperature. The coupled thermomechanical finite element formulation is derived based on continuum thermodynamics principles. The mesoscale constitutive relations and thermal conduction properties of materials are enriched by atomistic information of the underneath lattice microstructure in both bulk elements and interphase cohesive zone. This is accomplished by employing the Cauchy–Born rule, harmonic approximation, and colloidal crystal approximation. A main advantage of the proposed approach is its ability to capture the thermal conduction inside the material interface. The multiscale finite element procedure is performed to simulate an engineering nickel plate specimen with weak interfaces under uni-axial stretch. The simulation results indicate that the crack propagation is slowed down by thermal expansion, and a cooling region is found in the front of crack tip. These phenomena agree with related experimental results. The effect of different loading rates on fracture is also investigated.
Photoreflectance characteristics of chemical-bath-deposited-CdS layer in Cu(In,Ga)Se2 thin-film solar cells
Authors: Chung Yong-Duck , Cho Dae-Hyung , Choi Hae-Won , Park Soo-Jeong , Kim Ju-Hee , Ahn Byung-Jun , Song Jung-Hoon , Lee Kyu-Seok , Kim Jeha
Published: June 2012

The authors have characterized the CdS layer in Cu(In,Ga)Se2 thin-film solar cells using photoreflectance (PR) spectroscopy and investigated its influence on the photovoltaic performance. The CdS layer was fabricated by chemical bath deposition with various concentrations of ammonia (1.0–3.0 M), thiourea (0.025–0.1 M), and Cd-salt (0.0004–0.003 M) as well as various thicknesses (30–90 nm). The PR transition energy in CdS increased from 2.282 to 2.366 eV as the thiourea concentration increased from 1.0 to 3.0 M, whereas it decreased as the thickness of CdS increased. The conversion efficiency depended on neither the ammonia and the Cd-salt concentrations nor the thickness of CdS, whereas it changed from 14.72% to 15.81% as the thiourea concentration decreases from 3.0 to 1.0 M.
Draft Genome Sequence of “Candidatus Hamiltonella defensa,” an Endosymbiont of the Whitefly Bemisia tabaci
Authors: Rao Qiong , Wang Shuang , Su Yun-Lin , Bing Xiao-Li , Liu Shu-Sheng , Wang Xiao-Wei
Published: June 2012

“
Candidatus
Hamiltonella defensa” is a facultative endosymbiont of the whitefly
Bemisia tabaci
. Herein, we report the first draft genome sequence of “
Candidatus
Hamiltonella defensa” from the invasive Mediterranean cryptic species of the
B. tabaci
complex. The 1.84-Mbp genome sequence comprises 404 contigs and contains 1,806 predicted protein-coding genes.
Draft Genome Sequence of Enterococcus faecium Strain LCT-EF90
Authors: Chang De , Zhu Yuanfang , Zou Yuanqiang , Fang Xiangqun , Li Tianzhi , Wang Junfeng , Guo Yinghua , Su Longxiang , Xia Jingjing , Yang Ruifu , Fang Chengxiang , Liu Changting
Published: June 2012

Enterococcus faecium
is an opportunistic human pathogen, found widely in the human gastrointestinal tract, and can also be isolated from a variety of plants, animals, insects, and other environmental sources. Here, we present the fine draft genome sequence of
E. faecium
LCT-EF90.
Draft Genome Sequence of Rhodococcus sp. Strain P14, a Biodegrader of High-Molecular-Weight Polycyclic Aromatic Hydrocarbons
Authors: Zhang Ying , Qin Fujun , Qiao Jing , Li Gangmin , Shen Chenghui , Huang Tongwang , Hu Zhong
Published: June 2012

The genus
Rhodococcus
is known for its ability to degrade various xenobiotic compounds.
Rhodococcus
sp. strain P14 isolated from crude oil-contaminated sediments can degrade mineral oil and polycyclic aromatic hydrocarbons (PAHs). The draft genome sequence of
Rhodococcus
sp. P14 was obtained using Solexa technology, which provided an invaluable genetic background for further investigation of the ability of P14 to degrade xenobiotic compounds.
Draft Genome Sequence of the Nitrogen-Fixing Symbiotic Bacterium Bradyrhizobium elkanii 587
Authors: de Souza Jackson Antônio Marcondes , Tieppo Eduardo , Magnani Giovana de Souza , Alves Lucia Maria Carareto , Cardoso Rodrigo Luís , Cruz Leonardo Magalhães , de Oliveira Lucas Ferrari , Raittz Roberto Tadeu , de Souza Emanuel Maltempi , Pedrosa Fábio de Oliveira , Lemos Eliana Gertrudes de Macedo
Published: June 2012

The draft sequence of the genome of
Bradyrhizobium elkanii
587 is presented. This was obtained using Illumina Next-Gen DNA sequencing combined with Sanger sequencing. Genes for the pathways involved in biological nitrogen fixation (the
nif
gene cluster),
nod
genes including
nodABC
, and genes for the type III protein secretion system (T3SS) are present.
Genome Sequence of Listeria monocytogenes 07PF0776, a Cardiotropic Serovar 4b Strain
Authors: McMullen P. David , Gillaspy Allison F. , Gipson Jenny , Bobo Linda D. , Skiest Daniel J. , Freitag Nancy E.
Published: June 2012

Listeria monocytogenes
is a food-borne bacterial pathogen commonly associated with serious invasive infections of the central nervous system or of the developing fetus. We present the genome sequence of
Listeria monocytogenes
07PF0776, a serovar 4b isolate from a human myocardial abscess that exhibits enhanced invasion of cardiac tissue.
The AlternativeTranslational Profile That Underlies the Immune-Evasive State of Persistence in Chlamydiaceae Exploits Differential Tryptophan Contents of the Protein Repertoire
Authors: Lo Chien-Chi , Xie Gary , Bonner Carol A. , Jensen Roy A.
Published: June 2012

One form of immune evasion is a developmental state called “persistence” whereby chlamydial pathogens respond to the host-mediated withdrawal of
l
-tryptophan (Trp). A sophisticated survival mode of reversible quiescence is implemented. A mechanism has evolved which suppresses gene products necessary for rapid pathogen proliferation but allows expression of gene products that underlie the morphological and developmental characteristics of persistence. This switch from one translational profile to an alternative translational profile of newly synthesized proteins is proposed to be accomplished by maximizing the Trp content of some proteins needed for rapid proliferation (e.g., ADP/ATP translocase, hexose-phosphate transporter, phosphoenolpyruvate [PEP] carboxykinase, the Trp transporter, the Pmp protein superfamily for cell adhesion and antigenic variation, and components of the cell division pathway) while minimizing the Trp content of other proteins supporting the state of persistence. The Trp starvation mechanism is best understood in the human-
Chlamydia trachomatis
relationship, but the similarity of up-Trp and down-Trp proteomic profiles in all of the pathogenic
Chlamydiaceae
suggests that Trp availability is an underlying cue relied upon by this family of pathogens to trigger developmental transitions. The biochemically expensive pathogen strategy of selectively increased Trp usage to guide the translational profile can be leveraged significantly with minimal overall Trp usage by (i) regional concentration of Trp residue placements, (ii) amplified Trp content of a single protein that is required for expression or maturation of multiple proteins with low Trp content, and (iii) Achilles'-heel vulnerabilities of complex pathways to high Trp content of one or a few enzymes.
Biology of the Heat Shock Response and Protein Chaperones: Budding Yeast (Saccharomyces cerevisiae) as a Model System
Authors: Verghese Jacob , Abrams Jennifer , Wang Yanyu , Morano Kevin A.
Published: June 2012

The eukaryotic heat shock response is an ancient and highly conserved transcriptional program that results in the immediate synthesis of a battery of cytoprotective genes in the presence of thermal and other environmental stresses. Many of these genes encode molecular chaperones, powerful protein remodelers with the capacity to shield, fold, or unfold substrates in a context-dependent manner. The budding yeastSaccharomyces cerevisiaecontinues to be an invaluable model for driving the discovery of regulatory features of this fundamental stress response. In addition, budding yeast has been an outstanding model system to elucidate the cell biology of protein chaperones and their organization into functional networks. In this review, we evaluate our understanding of the multifaceted response to heat shock. In addition, the chaperone complement of the cytosol is compared to those of mitochondria and the endoplasmic reticulum, organelles with their own unique protein homeostasis milieus. Finally, we examine recent advances in the understanding of the roles of protein chaperones and the heat shock response in pathogenic fungi, which is being accelerated by the wealth of information gained for budding yeast.
Viral Quasispecies Evolution
Authors: Domingo Esteban , Sheldon Julie , Perales Celia
Published: June 2012

Evolution of RNA viruses occurs through disequilibria of collections of closely related mutant spectra or mutant clouds termed viral quasispecies. Here we review the origin of the quasispecies concept and some biological implications of quasispecies dynamics. Two main aspects are addressed: (i) mutant clouds as reservoirs of phenotypic variants for virus adaptability and (ii) the internal interactions that are established within mutant spectra that render a virus ensemble the unit of selection. The understanding of viruses as quasispecies has led to new antiviral designs, such as lethal mutagenesis, whose aim is to drive viruses toward low fitness values with limited chances of fitness recovery. The impact of quasispecies for three salient human pathogens, human immunodeficiency virus and the hepatitis B and C viruses, is reviewed, with emphasis on antiviral treatment strategies. Finally, extensions of quasispecies to nonviral systems are briefly mentioned to emphasize the broad applicability of quasispecies theory.
OPTIMAL TENURING AND MAJOR COLLECTION TIMES FOR A GENERATIONAL GARBAGE COLLECTOR
Authors: ZHAO XUFENG , NAKAMURA SYOUJI , NAKAGAWA TOSHIO
Published: June 2012

It is an important problem to determine the tenuring collection time or major collection time to meet the pause time goal for a generational garbage collector. From such a viewpoint, this paper proposes two stochastic models based on the working schemes of a generational garbage collector: Garbage collections occur at a nonhomogeneous Poisson process. Minor collections are made when the garbage collector begins to work, tenuring collection is made at a planned time T or at the first collection time when surviving objects have exceeded K for the first model. Major collection is made at time T or at the Nth collection for the second model. Using the techniques of cumulative processes and reliability theory, expected cost rates are obtained, and optimal policies of tenuring and major collection times which minimize them are discussed analytically and computed numerically.
OPTIMAL DISCRETE-TIME PERIODIC REPLACEMENT POLICY FOR REPAIRABLE PRODUCTS UNDER FREE MINIMAL REPAIR WARRANTY
Authors: CHANG FU-MIN , CHIEN YU-HUNG
Published: June 2012

This paper presents the effects of a free minimal repair warranty (FMRW) on the periodic replacement policy under discrete operating circumstance. For the discrete-time periodic replacement policy, a product is preventively replaced at pre-specified operation cycles N, 2N, 3N, … (N = 1, 2, …). When the product fails, a minimal repair is performed at the time of failure and the failure rate is not disturbed by each repair. From the customer's perspective, the cost models are developed for both a warranted and a nonwarranted product, and the corresponding optimal periodic replacement policies are derived such that the long-run expected cost rates are minimized. Under the assumption of the discrete time increasing failure rate (IFR), the existence and uniqueness of the optimal N* are shown, and the impacts of a FMRW on the optimal replacement policies are investigated analytically. We found that the optimal N* for a warranted product should be adjusted toward the end of the warranty period.
DARK MATTER INTERFERENCE
Authors: DEL NOBILE EUGENIO , KOUVARIS CHRIS , SANNINO FRANCESCO , VIRKAJÄRVI JUSSI
Published: June 2012

We study different patterns of interference in WIMP-nuclei elastic scattering that can accommodate the DAMA and CoGeNT experiments via an isospin violating ratio fn/fp = -0.71. We study interference between the following pairs of mediators: Z and Z′, Z′ and Higgs, and two Higgs fields. We show under what conditions interference works. We also demonstrate that in the case of the two Higgs interference, an explanation of the DAMA/CoGeNT is consistent with electroweak baryogenesis scenarios based on two Higgs doublet models proposed in the past.
RESOURCE-FOCUSED TOOLCHAIN FOR RAPID PROTOTYPING OF EMBEDDED SYSTEMS
Authors: PENG SHAOLIN , PARSONS GREGORY , DEAN ALEXANDER G.
Published: June 2012

This paper introduces the RaPTEX toolchain and its use for rapid prototyping and evaluation of embedded communication systems. This toolchain is unique for several reasons. First, by using static code analysis techniques, it is able to predict both the typical case and bounds for resource usage, such as computational, memory (both static and dynamic), and energy requirements. Second, it provides a graphical user interface with configurable software building blocks which allows easy creation and customization of protocol stacks. Third, it targets low-cost, low-energy hardware, allowing the creation of low-cost systems. We demonstrate the RaPTEX toolchain by evaluating different design options for an experimental ultrasonic communication system for biotelemetry in extremely shallow waters. The power, size, mass, and cost constraints of this application make it critical to pack as much processing into the available resources as possible. The RaPTEX toolchain analyzes resource use, enabling the system to safely operate closer to the edge of the resource envelope. The toolchain also helps users with the rapid prototyping of communication protocols by providing users with quick feedback on resource requirements. We demonstrate the use and output of the toolchain. We compare the accuracy of its predictions against measurements of the real hardware.
FROM LOCKS TO CORRECT AND EFFICIENT TRANSACTIONAL MEMORY
Authors: WANG CHENG , WU YOUFENG
Published: June 2012

Transactional memory addresses a number of important issues in lock-based parallel programs. Unfortunately, the semantics of transactions are different from those of critical sections defined by locks. The semantic differences make it difficult to correctly port existing lock-based programs to transaction-based programs. Experienced programmers accustomed to lock-based programming can easily make mistakes in transaction-based programming as parallel programs running correctly using locks can run incorrectly when critical sections are converted to using transactions. This problem becomes even more severe in porting lock-based programs to use the efficient software transactional memory. In this paper, we first identify three necessary properties in a program for the program execution using transactions to be equivalent to the program execution using locks. Assuming that the input lock-based program satisfies the necessary properties (i.e., a well-behaved parallel program), we next present a correctness condition to verify the transactional memory implementation in order for the program execution using transactions to be equivalent to the program execution using locks. Finally, we develop a correct and efficient software transactional memory implementation that satisfies the correctness condition so that locks in the well-behaved parallel programs can be converted to use the efficient software transactional memory easily and correctly.
CODE TRANSFORMATIONS FOR ENHANCING THE PERFORMANCE OF SPECULATIVELY PARALLEL THREADS
Authors: WANG SHENGYUE , YEW PEN-CHUNG , ZHAI ANTONIA
Published: June 2012

As technology advances, microprocessors that integrate multiple cores on a single chip are becoming increasingly common. How to use these processors to improve the performance of a single program has been a challenge. For general-purpose applications, it is especially difficult to create efficient parallel execution due to the complex control flow and ambiguous data dependences. Thread-level speculation and transactional memory provide two hardware mechanisms that are able to optimistically parallelize potentially dependent threads. However, a compiler that performs detailed performance trade-off analysis is essential for generating efficient parallel programs for these hardwares. This compiler must be able to take into consideration the cost of intra-thread as well as inter-thread value communication. On the other hand, the ubiquitous existence of complex, input-dependent control flow and data dependence patterns in general-purpose applications makes it impossible to have one technique optimize all program patterns. In this paper, we propose three optimization techniques to improve the thread performance: (i) scheduling instruction and generating recovery code to reduce the critical forwarding path introduced by synchronizing memory resident values; (ii) identifying reduction variables and transforming the code the minimize the serializing execution; and (iii) dynamically merging consecutive iterations of a loop to avoid stalls due to unbalanced workload. Detailed evaluation of the proposed mechanism shows that each optimization technique improves a subset but none improve all of the SPEC2000 benchmarks. On average, the proposed optimizations improve the performance by 7% for the set of the SPEC2000 benchmarks that have already been optimized for register-resident value communication.
TWISTED SYMMETRY AND NONCOMMUTATIVE FIELD THEORY
Authors: DIMITRIJEVIĆ MARIJA , JONKE LARISA
Published: June 2012

Although the meaning of twisted symmetry is still not fully understood, the twist approach has its advantages in the construction of field theories on noncommutative spaces. We discuss these advantages on the example of κ-Minkowski space-time. We construct the noncommutative U(1) gauge field theory. Especially the action is written as an integral of a maximal form, thus solving the cyclicity problem of the integral in κ-Minkowski. Using the Seiberg-Witten map to relate noncommutative and commutative degrees of freedom the effective action with the first order corrections in the deformation parameter is obtained.
KENAF/RECYCLED JUTE NATURAL FIBERS UNSATURATED POLYESTER COMPOSITES: WATER ABSORPTION/DIMENSIONAL STABILITY AND MECHANICAL PROPERTIES
Authors: OSMAN EKHLAS A. , VAKHGUELT ANATOLI , SBARSKI IGOR , MUTASHER SAAD A.
Published: June 2012

Effects of water absorption on the flexural properties of kenaf-unsaturated polyester composites and kenaf/recycled jute-unsaturated polyester composites were investigated. In the hybrid composites, the total fiber content was fixed to 20 wt%. In this 20 wt%, the addition of jute fiber varied from 0 to 75%, with increment of 25%. The result demonstrates the water absorption and the thickness swelling increased with increase in immersion time. Effects of water absorption on flexural properties of kenaf fiber composites can be reduced significantly with incorporation of recycled jute in composites formulation. The process of absorption of water was found to approach Fickian diffusion behavior for both kenaf composites and hybrid composites.