bluuebunny/crossref_metadata_2025_split huggingface dataset:
Grassroots literacy and the written record: Asbestos activism in South Africa
Authors: Trimbur John 
Published: September 2013

This article uses two key terms – ‘grassroots literacy’ and the ‘written record’ – to examine writing produced by the Asbestos Interest Group (AIG), a community organization in Kuruman, South Africa. The article considers the formation of theAIG's grassroots literacy in terms of the unequal distribution of semiotic resources in a stratified world system, with particular attention to how the allotment of the means of representation enables and constrains the capacity of texts to move across social locations. The article analyzes how theAIGnegotiates the paperwork of state, legal, and medical bureaucracies in compensation cases for asbestos‐related disease. It examines how theAIG's grassroots texts, such as monthly reports and handwritten/drawn maps, manage or not to circulate translocally, to take on semiotic mobility by making theAIG's interests known in the written record.Lekwalonyana le, le dirisa mareomagolo a mabedi – ‘go ruta baagi go buisa le go kwala’ le ‘rekoto e e kwadilweng’ – go lekola mokwalo o o tlhagisitsweng ke Abestos Interest Group (AIG), mogatlho wa set haba kwa Kuruman, Aforika Borwa. Lekwalonyana le, le sekaseka go tlhamiwa ga go ruta baagi go buisa le go kwala keAIGgo ya ka go aba ga tiriso ya didiriswa tsa matshwao ka mokgwa o o sa lekalekaneng mo bathong go lebeletswe thata mokgwa wa go aba ka kemedi e e kgotshang le go thibela bokgoni ba dipolelwana tse di kgonang go fitlhelela batho mo ba nnang. Lekwalonyana le, le sekaseka mokgwa oAIGe buisanang le tiro ya dikwalo tsa puso, tsa semolao le maparego a boitekanelo mo go neeleng ditlhapiso mo dikgetseng tse di amanang le abesetose e e tlholang bolwetsi jwa mafatlha. [Setswana]
Incidence and mortality trends for biliary tract cancers in Austria
Authors: Pinter Matthias , Hucke Florian , Zielonke Nadine , Waldhör Thomas , Trauner Michael , Peck‐Radosavljevic Markus , Sieghart Wolfgang 
Published: September 2013

AbstractBackground & AimsThe epidemiology of biliary tract cancers (BTC) varies between geographical regions and has changed over time globally. We investigated the incidence and mortality trends of patients diagnosed with BTC over a 20‐year period in Austria.MethodsPatients diagnosed with intrahepatic (iCCC)/extrahepatic cholangiocarcinoma (eCCC), ampullary carcinoma, gall bladder carcinoma (GBC), overlapping lesions or unspecified carcinomas of the biliary tract and liver were included. Data on age‐adjusted incidence were obtained from the Austrian National Cancer Registry which compiles data on all newly diagnosed cancers. Data on age‐adjusted mortality were obtained from the national death registry (Statistics Austria).ResultsBetween 1990 and 2009, 15201 patients were diagnosed with BTC (m/f=42/58%; mean age, 73 years). The median survival of all patients with BTC was 4.8 months with a 1‐/5‐year survival rate of 31%/10%. In iCCC, the incidence and mortality rates increased from 1990 to 2009 in both men and women while in eCCC, the incidence and mortality rates decreased over time in both sexes. In ampullary carcinoma, the incidence slightly decreased in men and remained stable in women. The mortality rate remained stable in both sexes. In GBC, the age‐adjusted incidence and mortality rates dramatically decreased in both sexes.ConclusionsGBC and iCCC were the most common entities amongst BTC. While incidence and mortality rates of iCCC increased in men and women over time, incidence and mortality rates of eCCC and GBC decreased in both sexes. Other carcinomas of the biliary tract i.e. ampullary carcinoma were rarely diagnosed.
Mortality and morbidity of very preterm infants in Romania: How are we doing?
Authors: Suciu Laura Mihaela , Puscasiu Lucian , Szabo Bela , Cucerea Manuela , Ognean Maria Livia , Oprea Ioan , Bell Edward F. 
Published: September 2013

AbstractBackgroundBirth before 28 weeks of gestation is associated with high mortality and morbidity. The purpose of this study was to examine characteristics associated with in‐hospital mortality and morbidity among extremely low‐birthweight neonates admitted to three tertiary care centers in Romania.MethodsThe study was conducted in three Romanian hospitals with level‐III neonatal intensive care units. We studied singleton live births at the established Romanian limit of viability (i.e., 25–28 weeks' gestational age) born between January 2007 and December 2010 (n = 227). Infants born in non‐level‐III facilities transferred to these three centers were included in our study (n = 39). Descriptive and multivariate statistical analyses were used to describe the population and examine outcomes and risk factors.ResultsDuring the study period, 62 neonates (27.3%) were delivered at 25 weeks, 56 (24.7%) were delivered at 26 weeks, 56 (24.7%) at 27 weeks, and 53 (23.3%) at 28 weeks. Overall in‐hospital mortality was 65% (from 85% at 25 weeks to 35% at 28 weeks). The rates for major morbidities were necrotizing enterocolitis 8.8%, bronchopulmonary dysplasia 12.5%, and retinopathy of prematurity (stage higher than 2) 26.2%.ConclusionsDuring 2007–2010, in‐hospital survival of infants admitted to three neonatal intensive care units in Romania was 35% and ranged from 14% at 25 weeks to 64% at 28 weeks.
A validation study to find highly correlated parameters with visual assessment for clinical evaluation of cosmetic anti‐cellulite products
Authors: Yoo Mi Ae , Seo Young Kyoung , Ryu Ja Hyun , Back Ji Hwoon , Koh Jae Sook 
Published: September 2013

Background/purposeThere has been growing interest in cellulite on parts of the body; however, no objective assessment has been specifically established. This study aims to demonstrate an optimized method by comparing the existing assessments of cellulite.MethodsIn Test 1, for subjects of 20 healthy females who have cellulite, we measured volume and roughness of cellulite using fringe projection method, roughness using replica method, dermo‐subcutaneous interface length and subcutaneous thickness using ultrasonography and skin temperature using infrared ray, elasticity and blood flow. In Test 2, we applied an anti‐cellulite cosmetic to 28 subjects for 6 weeks and observed if they have any changes.ResultsIn Test 1, the effective parameter that is the most correlated with visual assessment was volume of skin measured using fringe projection method (r = 0.780). Dermo‐subcutaneous interface length (r = 0.355) and subcutaneous thickness (r = 0.502) measured using ultrasonography followed in order. In Test 2, after applying a tested product, the correlation coefficient of volume of skin, of dermo‐subcutaneous interface length and of subcutaneous thickness are 0.409 (P = 0.000), 0.275 (P = 0.016) and 0.311 (P = 0.012) respectively.ConclusionWe conclude that visual assessment, volume of skin (cavities), dermo‐subcutaneous interface length and subcutaneous thickness are optimized methods for assessing an effect of cosmetics on cellulite.
Dispute Settlement at the WTO: Impacts of a No Deal in the US‐Brazil Cotton Dispute
Authors: Lakatos Csilla , Walmsley Terrie 
Published: September 2013

AbstractOn the day before Brazil was to start imposing retaliatory sanctions against the United States in the WTO dispute settlement case regarding unfair domestic and export upland cotton subsidies, the parties have reached a preliminary concession aimed at settling this eight‐year‐long trade dispute. In this paper, we explore the economywide impacts of a no deal with specific emphasis on intellectual property retaliation in a computable general equilibrium framework. As awarded by a WTO dispute settlement panel, Brazil would have been entitled to $591 million in retaliatory sanctions in goods sectors and $238 million in intellectual property sanctions. We find that retaliation by Brazil would have led to welfare gains for all countries except the United States. Most importantly, however, had Brazil not been allowed to retaliate in the form of suspension of intellectual property rights, the impact of trade retaliation alone would have been negative for both Brazil and the United States, a case of shooting oneself in the foot to shoot at the other person's foot.
Muscle afferents and cardiorespiratory control: the Birmingham connection
Authors: White Michael J. 
Published: September 2013

New findings
What is the topic of this review?
This brief review describes the work of Professor John Coote and colleagues at the University of Birmingham, which has contributed to understanding of the role of muscle afferent involvement in cardiorespiratory control in exercise.
What advances does it highlight?
The seminal findings of John Coote's early work are highlighted, as well as more recent developments in the field, especially the role of muscle afferents in the control of human ventilation during exercise.
Through the work of John Coote, research into the role of muscle afferent involvement in cardiorespiratory control has had strong links with Birmingham since the late 1960s. This brief review gives an historical background to John's early work and how his research and mentorship of colleagues continues to have a profound influence on the field today.
Evaluation of motion correction methods in human brain PET imaging—A simulation study based on human motion data
Authors: Jin Xiao , Mulnix Tim , Gallezot Jean‐Dominique , Carson Richard E. 
Published: September 2013

Purpose:Motion correction in PET has become more important as system resolution has improved. The purpose of this study was to evaluate the accuracy of event‐by‐event and frame‐based MC methods in human brain PET imaging.Methods:Motion compensated image reconstructions were performed with static and dynamic simulated high resolution research tomograph data with frame‐based image reconstructions, using a range of measured human head motion data. Image intensities in high‐contrast regions of interest (ROI) and parameter estimates in tracer kinetic models were assessed to evaluate the accuracy of the motion correction methods.Results:Given accurate motion data, event‐by‐event motion correction can reliably correct for head motions. The average ROI intensities and the kinetic parameter estimatesVT and BPND were comparable to the true values. The frame‐based motion correction methods with correctly aligned attenuation map using the average of externally acquired motion data or motion data derived from image registration give comparable quantitative accuracy. For large intraframe (>5 mm) motion, the frame‐based methods produced ∼9% bias in ROI intensities, ∼5% in VT, and ∼10% in BPND estimates. In addition, in real studies that lack a ground truth, the normalized weighted residual sum of squared difference is a potential figure‐of‐merit to evaluate the accuracy of motion correction methods.Conclusions:The authors conclude that frame‐based motion correction methods are accurate when the intraframe motion is less than 5 mm and when the attenuation map is accurately aligned. Given accurate motion data, event‐by‐event motion correction can reliably correct for head motion in human brain PET studies.
Revisit of combined parallel‐beam/cone‐beam or fan‐beam/cone‐beam imaging
Authors: Zeng Gengsheng L. 
Published: September 2013

Purpose:This aim of this paper is to revisit the parallel‐beam/cone‐beam or fan‐beam/cone‐beam imaging configuration, and to investigate whether this configuration has any advantages.Methods:Twenty years ago, it was suggested to simultaneously use a parallel‐beam (or a fan‐beam) collimator and a cone‐beam collimator to acquire single photon emission computed tomography data. The motivation was that the parallel‐beam (or the fan‐beam) collimator can provide sufficient sampling, while the cone‐beam collimator is able to provide higher photon counts. Even with higher total counts, this hybrid system does not give significant improvement (if any) in terms of image noise and artifacts reduction. If a conventional iterative maximum‐likelihood expectation‐maximization algorithm is used to reconstruct the image, the resultant reconstruction may be worse than the parallel‐beam‐only (or fan‐beam‐only) system. This paper uses the singular value decomposition (SVD) analysis to explain this phenomenon.Results:The SVD results indicate that the parallel‐beam‐only and the fan‐beam‐only system outperform the combined systems.Conclusions:The optimal imaging system does not necessary to be the one that generates the projections with highest signal‐to‐noise ratio and best resolution.
Predicting pathologic tumor response to chemoradiotherapy with histogram distances characterizing longitudinal changes in 18F‐FDG uptake patterns
Authors: Tan Shan , Zhang Hao , Zhang Yongxue , Chen Wengen , D'Souza Warren D. , Lu Wei 
Published: September 2013

Purpose:A family of fluorine‐18 (18F)‐fluorodeoxyglucose (18F‐FDG) positron‐emission tomography (PET) features based on histogram distances is proposed for predicting pathologic tumor response to neoadjuvant chemoradiotherapy (CRT). These features describe the longitudinal change of FDG uptake distribution within a tumor.Methods:Twenty patients with esophageal cancer treated with CRT plus surgery were included in this study. All patients underwent PET/CT scans before (pre‐) and after (post‐) CRT. The two scans were first rigidly registered, and the original tumor sites were then manually delineated on the pre‐PET/CT by an experienced nuclear medicine physician. Two histograms representing the FDG uptake distribution were extracted from the pre‐ and the registered post‐PET images, respectively, both within the delineated tumor. Distances between the two histograms quantify longitudinal changes in FDG uptake distribution resulting from CRT, and thus are potential predictors of tumor response. A total of 19 histogram distances were examined and compared to both traditional PET response measures and Haralick texture features. Receiver operating characteristic analyses and Mann‐Whitney U test were performed to assess their predictive ability.Results:Among all tested histogram distances, seven bin‐to‐bin and seven crossbin distances outperformed traditional PET response measures using maximum standardized uptake value (AUC = 0.70) or total lesion glycolysis (AUC = 0.80). The seven bin‐to‐bin distances were:L2 distance (AUC = 0.84), χ2 distance (AUC = 0.83), intersection distance (AUC = 0.82), cosine distance (AUC = 0.83), squared Euclidean distance (AUC = 0.83), L1 distance (AUC = 0.82), and Jeffrey distance (AUC = 0.82). The seven crossbin distances were: quadratic‐chi distance (AUC = 0.89), earth mover distance (AUC = 0.86), fast earth mover distance (AUC = 0.86), diffusion distance (AUC = 0.88), Kolmogorov‐Smirnov distance (AUC = 0.88), quadratic form distance (AUC = 0.87), and match distance (AUC = 0.84). These crossbin histogram distance features showed slightly higher prediction accuracy than texture features on post‐PET images.Conclusions:The results suggest that longitudinal patterns in18F‐FDG uptake characterized using histogram distances provide useful information for predicting the pathologic response of esophageal cancer to CRT.
Predicting diagnostic error in radiology via eye‐tracking and image analytics: Preliminary investigation in mammography
Authors: Voisin Sophie , Pinto Frank , Morin‐Ducote Garnetta , Hudson Kathleen B. , Tourassi Georgia D. 
Published: September 2013

Purpose:The primary aim of the present study was to test the feasibility of predicting diagnostic errors in mammography by merging radiologists’ gaze behavior and image characteristics. A secondary aim was to investigate group‐based and personalized predictive models for radiologists of variable experience levels.Methods:The study was performed for the clinical task of assessing the likelihood of malignancy of mammographic masses. Eye‐tracking data and diagnostic decisions for 40 cases were acquired from four Radiology residents and two breast imaging experts as part of an IRB‐approved pilot study. Gaze behavior features were extracted from the eye‐tracking data. Computer‐generated and BIRADS images features were extracted from the images. Finally, machine learning algorithms were used to merge gaze and image features for predicting human error. Feature selection was thoroughly explored to determine the relative contribution of the various features. Group‐based and personalized user modeling was also investigated.Results:Machine learning can be used to predict diagnostic error by merging gaze behavior characteristics from the radiologist and textural characteristics from the image under review. Leveraging data collected from multiple readers produced a reasonable group model [area under the ROC curve (AUC) = 0.792 ± 0.030]. Personalized user modeling was far more accurate for the more experienced readers (AUC = 0.837 ± 0.029) than for the less experienced ones (AUC = 0.667 ± 0.099). The best performing group‐based and personalized predictive models involved combinations of both gaze and image features.Conclusions:Diagnostic errors in mammography can be predicted to a good extent by leveraging the radiologists’ gaze behavior and image content.
Fungal Diversity in Permafrost and Tallgrass Prairie Soils under Experimental Warming Conditions
Authors: Penton C. Ryan , StLouis Derek , Cole James R. , Luo Yiqi , Wu Liyou , Schuur E. A. G , Zhou Jizhong , Tiedje James M. 
Published: September 2013

ABSTRACTSoil fungi play a major role in terrestrial ecosystem functioning through interactions with soil structure, plants, micro- and mesofauna, and nutrient cycling through predation, pathogenesis, mutualistic, and saprotrophic roles. The diversity of soil fungi was assessed by sequencing their 28S rRNA gene in Alaskan permafrost and Oklahoma tallgrass prairie soils at experimental sites where the effect of climate warming is under investigation. A total of 226,695 reads were classified into 1,063 genera, covering 62% of the reference data set. Using the Bayesian Classifier offered by the Ribosomal Database Project (RDP) with 50% bootstrapping classification confidence, approximately 70% of sequences were returned as “unclassified” at the genus level, although the majority (∼65%) were classified at the class level, which provided insight into these lesser-known fungal lineages. Those unclassified at the genus level were subjected to BLAST analysis against the ARB-SILVA database, where ∼50% most closely matched nonfungal taxa. Compared to the more abundant sequences, a higher proportion of rare operational taxonomic units (OTU) were successfully classified to genera at 50% bootstrap confidence, indicating that the fungal rare biosphere in these sites is not composed of sequencing artifacts. There was no significant effect after 1 year of warming on the fungal community structure at both sites, except perhaps for a few minor members, but there was a significant effect of sample depth in the permafrost soils. Despite overall significant community structure differences driven by variations in OTU dominance, the prairie and permafrost soils shared 90% and 63% of all fungal sequences, respectively, indicating a fungal “seed bank” common between both sites.
Novel Method for Genomic Promoter Shuffling by Using Recyclable Cassettes
Authors: Tian Xuelei , Xu Xin , Xiao Wei 
Published: September 2013

ABSTRACT

Genetic elements of interest can be introduced into the
Saccharomyces cerevisiae
genome via homologous recombination. The current method is to link such an element to a selectable marker gene to be integrated into the target locus. However, the marker gene in this method cannot be reused, which limits repeated manipulation of the yeast genome. An alternative method is to utilize a counterselectable gene, such as
URA3
, with flanking tandem repeats. After integration,
URA3
along with one copy of the repeat can be popped out via internal recombination, leaving behind one copy of the unwanted repeat. Here we describe a novel concept of genetic element shuffling in which the tandem repeats are made of the desired genetic element, so that after integration and popping out, only one copy of the element remains at the desired locus to function. As a proof of principle, we constructed three recyclable cassettes (

P
PGK1
-URA3-P
PGK1

,

P
GAL1
-URA3-P
GAL1

, and

P
tetO7
-URA3-P
tetO7

) and integrated them upstream of an engineered chromosomal

P
HIS3
-mCherry-Myc

locus. After promoter shuffling, the
mCherry-Myc
gene was regulated precisely as anticipated.
C
1
Metabolism in Corynebacterium glutamicum: an Endogenous Pathway for Oxidation of Methanol to Carbon Dioxide
Authors: Witthoff Sabrina , Mühlroth Alice , Marienhagen Jan , Bott Michael 
Published: September 2013

ABSTRACT

Methanol is considered an interesting carbon source in “bio-based” microbial production processes. Since
Corynebacterium glutamicum
is an important host in industrial biotechnology, in particular for amino acid production, we performed studies of the response of this organism to methanol. The
C. glutamicum
wild type was able to convert
13
C-labeled methanol to
13
CO
2
. Analysis of global gene expression in the presence of methanol revealed several genes of ethanol catabolism to be upregulated, indicating that some of the corresponding enzymes are involved in methanol oxidation. Indeed, a mutant lacking the alcohol dehydrogenase gene
adhA
showed a 62% reduced methanol consumption rate, indicating that AdhA is mainly responsible for methanol oxidation to formaldehyde. Further studies revealed that oxidation of formaldehyde to formate is catalyzed predominantly by two enzymes, the acetaldehyde dehydrogenase Ald and the mycothiol-dependent formaldehyde dehydrogenase AdhE. The Δ
ald
Δ
adhE
and Δ
ald
Δ
mshC
deletion mutants were severely impaired in their ability to oxidize formaldehyde, but residual methanol oxidation to CO
2
was still possible. The oxidation of formate to CO
2
is catalyzed by the formate dehydrogenase FdhF, recently identified by us. Similar to the case with ethanol, methanol catabolism is subject to carbon catabolite repression in the presence of glucose and is dependent on the transcriptional regulator RamA, which was previously shown to be essential for expression of
adhA
and
ald
. In conclusion, we were able to show that
C. glutamicum
possesses an endogenous pathway for methanol oxidation to CO
2
and to identify the enzymes and a transcriptional regulator involved in this pathway.
The Transfer-Messenger RNA-Small Protein B System Plays a Role in Avian Pathogenic Escherichia coli Pathogenicity
Authors: Mu Xiaohui , Huan Haixia , Xu Huiqing , Gao Qingqing , Xiong Liping , Gao Ruxia , Gao Song , Liu Xiufan 
Published: September 2013

ABSTRACT

Extraintestinal pathogenic
Escherichia coli
(ExPEC) is capable of colonizing outside of the intestinal tract and evolving into a systemic infection. Avian pathogenic
E. coli
(APEC) is a member of the ExPEC group and causes avian colibacillosis. Transfer-mRNA-small protein B (tmRNA-SmpB)-mediated
trans
-translation is a bacterial translational control system that directs the modification and degradation of proteins, the biosynthesis of which has stalled or has been interrupted, facilitating the rescue of ribosomes stalled at the 3′ ends of defective mRNAs that lack a stop codon. We found that disruption of one, or both, of the
smpB
or
ssrA
genes significantly decreased the virulence of the APEC strain E058, as assessed by chicken infection assays. Furthermore, the mutants were obviously attenuated in colonization and persistence assays. The results of quantitative real-time reverse transcription-PCR analysis indicated that the transcription levels of the transcriptional regulation gene
rfaH
and the virulence genes
kpsM
,
chuA
, and
iss
were significantly decreased compared to those of the wild-type strain. Macrophage infection assays showed that the mutant strains reduced the replication and/or survival ability in the macrophage HD11 cell line compared to that of the parent strain, E058. However, no significant differences were observed in ingestion by macrophages and in chicken serum resistance between the mutant and the wild-type strains. These data indicate that the tmRNA-SmpB system is important in the pathogenesis of APEC O2 strain E058.