bluuebunny/crossref_metadata_2025_split huggingface dataset:
Xanthomonas campestris pv. campestris (cause of black rot of crucifers) in the genomic era is still a worldwide threat to brassica crops
Authors: Vicente Joana G. , Holub Eric B. 
Published: October 2012

SummaryBackgroundXanthomonas campestris pv. campestris (Xcc) (Pammel) Dowson is a Gram‐negative bacterium that causes black rot, the most important disease of vegetable brassica crops worldwide. Intensive molecular investigation of Xcc is gaining momentum and several whole genome sequences are available.TaxonomyBacteria; Phylum Proteobacteria; Class Gammaproteobacteria; Order Xanthomonadales; Family Xanthomonadacea; Genus Xanthomonas; Species X. campestris.Host range and symptomsXcc can cause disease in a large number of species of Brassicaceae (ex‐Cruciferae), including economically important vegetable Brassica crops and a number of other cruciferous crops, ornamentals and weeds, including the model plant Arabidopsis thaliana. Black rot is a systemic vascular disease. Typical disease symptoms include V‐shaped yellow lesions starting from the leaf margins and blackening of the veins.Race structure, pathogenesis and epidemiologyCollections of Xcc isolates have been differentiated into physiological races based on the response of several brassica species lines. Black rot is a seed‐borne disease. The disease is favoured by warm, humid conditions and can spread rapidly from rain dispersal and irrigation water.Disease controlThe control of black rot is difficult and relies on the use of pathogen‐free planting material and the elimination of other potential inoculum sources (infected crop debris and cruciferous weeds). Major gene resistance is very rare in B. oleracea (brassica C genome). Resistance is more readily available in other species, including potentially useful sources of broad‐spectrum resistance in B. rapa and B. carinata (A and BC genomes, respectively) and in the wild relative A. thaliana.GenomeThe reference genomes of three isolates have been released. The genome consists of a single chromosome of approximately 5 100 000 bp, with a GC content of approximately 65% and an average predicted number of coding DNA sequences (CDS) of 4308.Important genes identifiedThree different secretion systems have been identified and studied in Xcc. The gene clusters xps and xcs encode a type II secretion system and xps genes have been linked to pathogenicity. The role of the type IV secretion system in pathogenicity is still uncertain. The hrp gene cluster encodes a type III secretion system that is associated with pathogenicity. An inventory of candidate effector genes has been assembled based on homology with known effectors. A range of other genes have been associated with virulence and pathogenicity, including the rpf, gum and wxc genes involved in the regulation of the synthesis of extracellular degrading enzymes, xanthan gum and lipopolysaccharides.Useful websitehttp://www.xanthomonas.org/
Estimating primaries by sparse inversion, a generalized approach
Authors: Ypma F.H.C. , Verschuur D.J. 
Published: October 2012

ABSTRACTFor an accurate interpretation of seismic data, multiple‐free data are of great value. Removing surface multiples and interbed multiples proves to be challenging in many cases. The nowadays widely used method of Surface‐Related Multiple Elimination (SRME) has lately been redefined as a full‐waveform inversion process, resulting in the method of Estimation of Primaries by Sparse Inversion (EPSI). The new method is shown to be more accurate than the former method in several situations, because it estimates primaries such that they, together with their multiples, explain the input data. Its main advantage is that the minimum energy assumption in traditional multiple subtraction is avoided. The SRME methodology has been extended to the case of internal multiples by several authors, however, the involved subtraction of predicted multiples is probably even more challenging than for the surface‐multiple case. Therefore, in this paper the EPSI method is generalized to remove both surface and interbed multiples. As in previous implementations of internal multiple removal based on data‐driven convolution, the newly proposed scheme requires some knowledge about the subsurface: the data should be divided into (macro) layers and appropriate time windows must be selected. The method is tested on two 2D synthetic datasets to prove its viability. Furthermore, application to a 2D field dataset showed improved accuracy compared to conventional prediction and subtraction.
Changing use of camera traps in mammalian field research: habitats, taxa and study types
Authors: McCallum Jamie 
Published: October 2012

Abstract
Camera traps are automated cameras, triggered by movements, used to collect photographic evidence of the presence of animals in field research. I asked whether the use of camera traps in mammalian field research is distributed evenly and increasing equally in a range of habitats, taxa and study types. I aimed to understand where camera traps are used and for what purposes.
I identified the population of papers published since 1994 in which camera trap methodology was used. I then explored the population for defined habitats, taxa and study types. I tested the derived data for growth and distribution. Over 96% of the population of camera trap papers identified were focused on mammalian species.
Between 1994 and 2011, the use of camera traps for mammalian research increased: 73% of 414 studies were published after 2005. Over time, equipment has become more sophisticated, reliable, flexible, cost‐effective and easy to deploy, and there have been other methodological advances.
Growth in the number of mammal‐related camera trap studies was matched by an expansion in the taxa studied and in study types. The most studied taxon is the order Carnivora; forests are the most studied habitat. No single study type dominates, although there are more population density studies than any other. Camera trap studies are focused on a limited number of habitats and taxa due to their particular strengths and the characteristics of the species that they are used to investigate.
Developments such as infrared illumination and triggering, greater battery life, improved lenses, digital storage capacity, miniaturization, video and real‐time links will enable camera traps to be used for an increasing range of habitats, taxa and study types and will reinforce their growing value in the areas in which they currently predominate.
In vitro evaluation of topical biocide and antimicrobial susceptibility of Staphylococcus pseudintermedius from dogs
Authors: Valentine Becky K. , Dew Walter , Yu Anthony , Weese J. Scott 
Published: October 2012

Background –  Staphylococcus pseudintermedius is an important canine pathogen, and the emergence and widespread dissemination of meticillin‐resistant strains (MRSP) is of significant concern. Multidrug‐resistant infections may require alternative approaches, such as the use of topical therapy. There is minimal information about the in vitro susceptibility of meticillin‐susceptible S. pseudintermedius (MSSP) and MRSP to biocides and topical antimicrobials.Hypothesis/Objectives –  The hypothesis was that clinical isolates of MSSP and MRSP would not have universal susceptibility to topical biocides and antimicrobials. The goal of this study was to assess the susceptibility of a collection of S. pseudintermedius isolates to selected antimicrobials and biocides.Animals –  The study was performed on clinical isolates of MSSP and MRSP from dogs with skin and soft tissue infections collected throughout North America between 2006 and 2008.Methods –  The minimal inhibitory concentrations (MICs) of chlorhexidine digluconate, benzalkonium chloride, triclosan, accelerated hydrogen peroxide, geranium oil, tea tree oil and grapefruit seed extract were tested for 25 MRSP and 25 MSSP isolates from dogs using the agar dilution method. The MICs of fusidic acid, bacitracin and mupirocin were determined using Etests.Results –  Triclosan demonstrated excellent activity against all bacterial isolates, with no growth at the lowest concentration evaluated (MIC ≤ 0.5 μg/mL). Conversely, grapefruit seed extract did not inhibit growth at the highest concentration tested (MIC > 3.84 μg/mL). All isolates were susceptible to mupirocin, fusidic acid and bacitracin. There were no significant differences noted in the range, MIC50 or MIC90 between MSSP and MRSP isolates.Conclusions and clinical importance –  While isolates were susceptible to most of the tested compounds, universal susceptibility to all compounds with potential antimicrobial activity cannot be assumed, and specific testing is required.
Capability of different non‐nutritive feed additives on improving productive and physiological traits of broiler chicks fed diets with or without aflatoxin during the first 3 weeks of life
Authors: Attia Y. A. , Allakany H. F. , Abd Al‐Hamid A. E. , Al‐Saffar A. A. , Hassan R. A. , Mohamed N. A. 
Published: October 2012

SummaryAn experiment was conducted to determine whether some non‐nutritive feed additives (NNFA) could block the adverse effects of aflatoxin (AF) on growth performance and physiological parameters of Cobb broilers throughout the period from 1 to 21 day of age. There were eight treatments consisting of two levels of AF at 0 and 200 ppb and four NNFA within each AF level. These additives included mannan oligosaccharides (MOS) at 2 g/kg diet, hydrated sodium calcium aluminosilicate (HSCAS) at 2 g/kg diet and Lactobacillus acidophilus (Lac) at 2 g/kg diet. At 21 day of age, five chickens of each treatment were slaughtered to study dressing percentage and relative weight of inner organs and glands. AF had a significant negative effect on body weight gain (BWG), and feed intake, while impairing feed conversion ratio (FCR). Aflatoxin significantly increased percentage liver, lymphocyte (%), monocyte (%), serum triglyceride level, and the aspartate aminotransferase (AST), and alanine aminotransferase (ALT), concentrations while decreasing dressing percentage, intestinal percentage, white blood cells (WBCs), red blood cells (RBCs), haemoglobin (Hgb), packed cell volume (PCV), heterophil (%), heterophil/lymphocyte ratio, total serum protein and serum albumin. Aflatoxin adversely affected the morphology of the liver, bursa and the thymus. There was a significant interaction between AF and NNFA on the relative weights of liver, heart and intestine. Lac completely blocked the negative effects of AF on the percentage liver and the heart and partially on the intestine. In conclusion, Lac was most effective in reversing the adverse effects of AF on growth and FCR and on the percentage, functions and morphology of the liver. Hydrated sodium calcium aluminosilicate also improved the economic traits of broilers but was less effective than Lac and more effective than MOS.
What is the predictor of prolonged operative time during laparoscopic radical prostatectomy?
Authors: Kaneko Gou , Miyajima Akira , Yazawa Satoshi , Yuge Kazuyuki , Kikuchi Eiji , Asanuma Hiroshi , Nakagawa Ken , Oya Mototsugu 
Published: October 2012

ObjectivesTo study the impact of high body mass index and large prostate weight on operative time of laparoscopic radical prostatectomy.MethodsA retrospective analysis of medical records from patients who had undergone extraperitoneal laparoscopic radical prostatectomy by a single surgeon at our institution between September 2008 and April 2011 was carried out. For each case, the following parameters were recorded: age, body mass index, prostate weight, cross‐section area of the Retzius space, and history of previous lower abdominal surgery, repeated prostate biopsy and neoadjuvant hormone therapy. The laparoscopic radical prostatectomy procedure was divided into seven surgical steps: (i) port insertion and lymph node dissection; (ii) endopelvic fascia incision; (iii) dorsal vein complex ligation; (iv) prostate dissection from bladder neck; (v) dissection of seminal vesicles and vas deferens; (vi) prostate dissection from rectum; and (vii) vesicourethral anastomosis. The overall operative time and the duration of each surgical step were retrieved. Potential predictors of prolonged total operative time and prolonged duration of a step were assessed by multivariate logistic regression analysis.ResultsA total of 152 patients were analyzed. High body mass index (≥25.0 kg/m2) and prostate weight were independent predictors of prolonged total operative time. High body mass index was an independent predictor of prolonged step 1, 3, 4, 5 and 6. Prostate weight was an independent predictor of prolonged step 2, 5 and 6. A history of previous lower abdominal surgery was a predictor of prolonged step 1.ConclusionsHigh body mass index and high prostate weight are independent predictors of prolonged total operative time in extraperitoneal laparoscopic radical prostatectomy. Although high body mass index seems to affect most of the surgical steps of the procedure, prostate weight mainly impacts the dissection close to the prostate, as enlarged prostate results in a narrower working space.
Exploring Counterurbanisation in a Post‐Socialist Context: Case of theCzechRepublic
Authors: Šimon Martin 
Published: October 2012

AbstractUrban‐rural research in post‐socialist countries has focused on urban transformation, the impact of international migration and the spread of suburbanisation; little attention has been paid to counterurban migration. The aim of this article is to propose a typology of counterurban migration strategies based on quantitative research in rural areas in theCzechRepublic. Firstly, the article discusses the differences and similarities of counterurbanisation in western and post‐socialist countries by bringing together counterurbanisation and post‐socialist research literature. Secondly, detailed information about the counterurbanisation migration stream is provided on the basis of extensive field research. Thirdly, the article presents four basic types of counterurbanisation migration strategies, two lifestyle‐oriented types and two economic‐oriented types, based on household motivation, preferences and household employment location. The research demonstrates both general and specific features of counterurbanisation stream in theCzechRepublic.
CHAPERONIN 20 mediates iron superoxide dismutase (FeSOD) activity independent of its co‐chaperonin role in Arabidopsis chloroplasts
Authors: Kuo W. Y. , Huang C. H. , Liu A. C. , Cheng C. P. , Li S. H. , Chang W. C. , Weiss C. , Azem A. , Jinn T. L. 
Published: October 2012

Summary

Iron superoxide dismutases (FeSODs; FSDs) are primary antioxidant enzymes in Arabidopsis thaliana chloroplasts. The stromal FSD1 conferred the only detectable FeSOD activity, whereas the thylakoid membrane‐ and nucleoid‐co‐localized FSD2 and FSD3 double mutant showed arrested chloroplast development.

FeSOD requires cofactor Fe for its activity, but its mechanism of activation is unclear. We used reversed‐phase high‐performance liquid chromatography (HPLC), gel filtration chromatography, LC‐MS/MS, protoplast transient expression and virus‐induced gene silencing (VIGS) analyses to identify and characterize a factor involved in FeSOD activation.

We identified the chloroplast‐localized co‐chaperonin CHAPERONIN 20 (CPN20) as a mediator of FeSOD activation by direct interaction. The relationship between CPN20 and FeSOD was confirmed by in vitro experiments showing that CPN20 alone could enhance FSD1, FSD2 and FSD3 activity. The in vivo results showed that CPN20‐overexpressing mutants and mutants with defective co‐chaperonin activity increased FSD1 activity, without changing the chaperonin CPN60 protein level, and VIGS‐induced downregulation of CPN20 also led to decreased FeSOD activity.

Our findings reveal that CPN20 can mediate FeSOD activation in chloroplasts, a role independent of its known function in the chaperonin system.
Microvascular protection is essential for successful neuroprotection in stroke
Authors: Gursoy‐Ozdemir Yasemin , Yemisci Muge , Dalkara Turgay 
Published: October 2012

AbstractCurrently, the best way of neuroprotection for acute ischemic stroke appears to be restoration of blood flow to the ischemic area by thrombolysis. Unfortunately, a short therapeutic time window as well as thrombolysis‐induced bleeding and edema limit the use of recanalization therapies. Here, we review the evidence suggesting that ischemia/reperfusion‐induced microvascular injury plays a critical role in determining tissue survival after recanalization in focal cerebral ischemia by disrupting the blood–brain barrier integrity and promoting microcirculatory clogging. Among many complex mechanisms of the ischemia–reperfusion injury, overproduction of oxygen and nitrogen radicals on the microvascular wall appears to significantly contribute to these pathological processes. These developments bring about the exciting possibility that effective suppression of oxidative/nitrative stress during pharmacological or interventional re‐opening of the occluded artery may significantly improve the outcome of recanalization therapies in stroke patients by improving microcirculatory reflow as well as by preventing hemorrhagic conversion and vasogenic edema. They also point to the critical (but partly neglected) importance of the microcirculation in neuroprotection.
Novel therapeutic strategies targeting innate immune responses and early inflammation after stroke
Authors: Shichita Takashi , Ago Tetsuro , Kamouchi Masahiro , Kitazono Takanari , Yoshimura Akihiko , Ooboshi Hiroaki 
Published: October 2012

AbstractPost‐ischemic inflammation is an essential step in the progression of ischemic stroke. This review focuses on the function of infiltrating immune cells, macrophages, and T cells, in ischemic brain injury. The brain is a sterile organ; however, the activation of Toll‐like receptor (TLR) 2 and TLR4 is pivotal in the beginning of post‐ischemic inflammation. Some endogenous TLR ligands are released from injured brain cells, including high mobility group box 1 and peroxiredoxin family proteins, and activate the infiltrating macrophages and induce the expression of inflammatory cytokines. Following this step, T cells also infiltrate into the ischemic brain and mediate post‐ischemic inflammation in the delayed phase. Various cytokines from helper T cells and γδT cells function as neurotoxic (IL‐23/IL‐17, IFN‐γ) or neuroprotective (IL‐10, IL‐4) mediators. Novel neuroprotective strategies should therefore be developed through more detailed understanding of this process and the regulation of post‐ischemic inflammation.
Mitochondrial biogenesis contributes to ischemic neuroprotection afforded by LPS pre‐conditioning
Authors: Anne Stetler R. , Leak Rehana K. , Yin Wei , Zhang Lili , Wang Suping , Gao Yanqin , Chen Jun 
Published: October 2012

AbstractAlthough alterations in mitochondrial dynamics are associated with cellular responses to injury, the functional role of these dynamic changes in ischemic neurons is underexplored. One of these dynamic responses to injury includes mitochondrial biogenesis. Various sublethal pre‐conditioning stimuli that induce an ischemic‐tolerant state [e.g., lipopolysaccharide (LPS)] may also induce mitochondrial biogenesis. Using neuron‐enriched cultures, we found that sublethal LPS pre‐conditioning induced both ischemic tolerance and markers of mitochondrial biogenesis with overlapping dose–response temporal kinetics. Sublethal LPS transiently increased the expression of critical components of the mitochondrial transcriptional machinery, including nuclear respiratory factor 1 (NRF1) and mitochondrial transcription factor A (TFAM), as well as mtDNA copy number, mitochondrial protein levels, and markers of functional mitochondria, such as increased cellular ATP content, citrate synthase activity, and maximal respiration capacity. Importantly, knockdown of TFAM abrogated both the induction of mitochondrial biogenesis and the neuroprotective pre‐conditioning effects of LPS. Several signaling pathways coordinated these events. AMPK inhibition suppressed NRF1 and TFAM expression by LPS, whereas PI3K/Akt signaling was necessary for the nuclear translocation of NRF1 and subsequent induction of TFAM. This is the first demonstration that LPS pre‐conditioning initiates multiple signaling pathways leading to mitochondrial biogenesis in neurons and that these dynamic changes contribute to ischemic tolerance.
Comparison of keratometry measurements using the Pentacam HR, the Orbscan IIz, and the TMS‐4 topographer
Authors: Tajbakhsh Zahra , Salouti Ramin , Nowroozzadeh Mohammad H , Aghazadeh‐Amiri Mohammad , Tabatabaee Seyedmehdi , Zamani Mohammad 
Published: October 2012

AbstractPurposeTo compare and evaluate the agreement between keratometry readings using three devices: the Pentacam HR, the Orbscan IIz, and the TMS‐4 topographer.MethodsIn this prospective comparative study, 115 eyes from 115 healthy refractive surgery candidates were sequentially examined using three devices. Fourier analysis was used to evaluate corneal astigmatism in these subjects. The outcome measures comprised steep and flat keratometry readings, corneal astigmatism, the mean keratometry reading, and the J0 and J45 components. Repeated‐measures analysis of variance (RM‐anova) and Bland–Altman plots with 95% limits of agreement were used to evaluate the difference between measurements.ResultsThe mean keratometry readings were 43.89 ± 1.51, 43.52 ± 1.48, and 43.79 ± 1.50 D using the TMS‐4 topographer, the Orbscan IIz, and the Pentacam HR, respectively (p < 0.001; RM‐anova). The mean keratometric astigmatism was 1.27 ± 0.87, 1.20 ± 0.86, and 1.21 ± 0.82 D using the TMS‐4 topographer, the Orbscan IIz, and the Pentacam HR, respectively (p = 0.007; RM‐anova). The J0 measurements were higher using the TMS‐4 topographer compared with the Orbscan IIz (p = 0.021; Bonferroni test). The mean, steep, and flat keratometry data were in better agreement using the TMS‐4 topographer and the Pentacam HR. In general, the Orbscan IIz device measured lower values than either the TMS‐4 topographer or the Pentacam HR. However, the corneal astigmatism measurements and the J0 component showed the best agreement using the TMS‐4 topographer and the Orbscan IIz.ConclusionsThe TMS‐4 topographer and the Pentacam HR produced similar readings and can be used interchangeably to measure simulated keratometry values in young, healthy eyes. To measure corneal astigmatism, the TMS‐4 topographer and the Orbscan IIz produced values that were similar and could be used interchangeably.