bluuebunny/crossref_metadata_2025_split huggingface dataset:
Grid artifact reduction for direct digital radiography detectors based on rotated stationary grids with homomorphic filtering
Authors: Kim Dong Sik , Lee Sanggyun 
Published: May 2013

Purpose:Grid artifacts are caused when using the antiscatter grid in obtaining digital x‐ray images. In this paper, research on grid artifact reduction techniques is conducted especially for the direct detectors, which are based on amorphous selenium.Methods:In order to analyze and reduce the grid artifacts, the authors consider a multiplicative grid image model and propose a homomorphic filtering technique. For minimal damage due to filters, which are used to suppress the grid artifacts, rotated grids with respect to the sampling direction are employed, and min‐max optimization problems for searching optimal grid frequencies and angles for given sampling frequencies are established. The authors then propose algorithms for the grid artifact reduction based on the band‐stop filters as well as low‐pass filters.Results:The proposed algorithms are experimentally tested for digital x‐ray images, which are obtained from direct detectors with the rotated grids, and are compared with other algorithms. It is shown that the proposed algorithms can successfully reduce the grid artifacts for direct detectors.Conclusions:By employing the homomorphic filtering technique, the authors can considerably suppress the strong grid artifacts with relatively narrow‐bandwidth filters compared to the normal filtering case. Using rotated grids also significantly reduces the ringing artifact. Furthermore, for specific grid frequencies and angles, the authors can use simple homomorphic low‐pass filters in the spatial domain, and thus alleviate the grid artifacts with very low implementation complexity.
Complete Closed Genome Sequences of Mannheimia haemolytica Serotypes A1 and A6, Isolated from Cattle
Authors: Harhay Gregory P. , Koren Sergey , Phillippy Adam M. , McVey D. Scott , Kuszak Jennifer , Clawson Michael L. , Harhay Dayna M. , Heaton Michael P. , Chitko-McKown Carol G. , Smith Timothy P. L. 
Published: May 2013

ABSTRACT

Mannheimia haemolytica
is a respiratory pathogen affecting cattle and related ruminants worldwide.
M. haemolytica
is commonly associated with bovine respiratory disease complex (BRDC), a polymicrobial multifactorial disease. We present the first two complete closed genome sequences of this species, determined using an automated assembly pipeline requiring no manual finishing.
Complete Genome Sequence of West Nile Virus Isolated from Alappuzha District, Kerala, India
Authors: Balakrishnan Anukumar , Butte Datta K. , Jadhav Santhosh M. 
Published: May 2013

ABSTRACT

West Nile virus belongs to the
Flaviviridae
family, transmitted by vector mosquitoes. Here, we reported the complete genome sequence of West Nile virus isolated from human samples during an acute encephalitis outbreak in Kerala, India. Phylogenetic analysis revealed that the virus genome clusters into genetic lineage 1, clade 1a.
Genome Sequence of Bacillus subtilis MB73/2, a Soil Isolate Inhibiting the Growth of Plant Pathogens
Dickeya
spp. and Rhizoctonia solani
Authors: Krzyzanowska Dorota M. , Iwanicki Adam , Ossowicki Adam , Obuchowski Michał , Jafra Sylwia 
Published: May 2013

ABSTRACT

Bacillus subilis
MB73/2 is a Gram-positive bacterium isolated in Poland from a meadow soil sample. When tested
in vitro
, the strain shows strong antagonism toward plant pathogens—the soft rot-causing bacteria
Dickeya
spp. and the crown rot fungus
Rhizoctonia solani
. Here, we present the genome sequence of MB73/2.
Draft Genome Sequence of Curtobacterium flaccumfaciens Strain UCD-AKU (Phylum
Actinobacteria
)
Authors: Flanagan Jennifer C. , Lang Jenna M. , Darling Aaron E. , Eisen Jonathan A. , Coil David A. 
Published: May 2013

ABSTRACT

Here we present the draft genome of an actinobacterium,
Curtobacterium flaccumfaciens
strain UCD-AKU, isolated from a residential carpet. The genome assembly contains 3,692,614 bp in 130 contigs. This is the first member of the
Curtobacterium
genus to be sequenced.
Complete Genome Sequence of a Novel Reassortant H3N6 Avian Influenza Virus Isolated from Domestic Green-Winged Teal
Authors: Xiong Chaochao , Liu Qian , Chen Quanjiao , Yao Yanfeng , Wang Huadong , Chen Jianjun 
Published: May 2013

ABSTRACT

An avian influenza virus strain, A/domestic green-winged teal/Hunan/2036/2007(H3N6) (DGW-T2036), was isolated from healthy domestic green-winged teals (
Anas crecca
) in Hunan Province, South China. All eight gene segments of the isolate were sequenced. Genomic analysis demonstrated that this H3N6 virus is a novel reassortant avian influenza virus with a gene constellation originating from multiple ancestors.
Does physical activity during pregnancy adversely influence markers of the metabolic syndrome in adult offspring? A prospective study over two decades
Authors: Danielsen Inge , Granström Charlotta , Rytter Dorte , Hammer Bech Bodil , Brink Henriksen Tine , Vaag Allan Arthur , Olsen Sjurdur Frodi 
Published: May 2013

BackgroundIt is unknown whether physical activity during pregnancy (PA) has long-term impact on the metabolic profile of the offspring. We investigated associations of PA with markers of the metabolic syndrome (MS) in 20y old offspring.MethodsLongitudinal study where 965 pregnant women during 1988–1989 had four dimensions of PA assessed by questionnaires in gestation week 30: PA at work; leisure time PA, daily amount of walking-biking and sport participation. The following MS markers were assessed in the offspring (n=439): body mass index (BMI), waist circumference, blood pressure, homeostasis model assessment insulin resistance as well as fasting plasma glucose, triglycerides, cholesterol (high-density lipoprotein (HDL), low-density lipoprotein and total cholesterol), insulin and leptin levels.ResultsWalking-biking PA in pregnancy is associated with unchanged or subtle, adverse changes of distinct MS markers among offspring including lower levels of HDL cholesterol (ratio 0.95 (95% CI 0.92 to 0.98) per 1 h increment in walking-biking), a higher diastolic blood pressure (difference 1.12 (95% CI 0.03 to 2.20) mm Hg/1 h increment) and a higher BMI (ratio 1.03 (95% CI 1.01 to 1.05) per 1 h increment). In separate analyses in males, these associations persisted and additional adverse associations were found for triglycerides, systolic blood pressure, waist circumference and leptin. No associations were detected with other measures of PA.ConclusionsThe study did not substantiate any protective effects of PA in pregnancy. In contrast, data suggested that high amounts of daily walking-biking in pregnancy may have adverse effects on levels of HDL cholesterol, diastolic blood pressure and BMI in young adult offspring.
Preparing residents for future practice: report of a curriculum for electronic patient–doctor communication
Authors: Crotty Bradley H , Mostaghimi Arash , Landon Bruce E 
Published: May 2013

Abstract

Objectives
Patients frequently use secure web portals to access their medical record and communicate with their doctors, though few institutions currently train residents for electronic communication. We sought to develop a curriculum for secure messaging between patients and resident physicians, and to assess resident attitudes before and after the curriculum.

Methods
In 2011, we developed a curriculum for patient–doctor secure messaging using a web-based patient portal within an internal medicine residency programme. We asked all residents to perform a self-assessment of skills, and report attitudes toward electronic communication at the beginning and end of the experience (9 months apart). We enrolled residents who practiced at the hospital-based clinic site into the patient portal, and recorded usage statistics.

Results
The completed survey response rate was 108/159 (68%). At baseline, 57% of residents had used traditional email with patients, and most residents felt that the portal would increase work for providers but benefit patients. Postintervention questionnaires demonstrated no significant changes among all respondents, but residents who used the portal perceived improvements in care. Most residents were concerned about professional liability. More residents felt comfortable writing electronic messages to patients after the curriculum (80% to 91%, p=0.01).

Conclusions
Implementing a patient web portal and secure messaging in a residency clinic is feasible and may improve the work and educational experience of trainees. Residents were initially sceptical of secure messaging being an additional burden to their work, but this was not realised among residents who used the portal.
Female sex workers incarcerated in New York City jails: prevalence of sexually transmitted infections and associated risk behaviors
Authors: Parvez Farah , Katyal Monica , Alper Howard , Leibowitz Ruth , Venters Homer 
Published: May 2013

ObjectivesSexually transmitted infections (STIs) are an important cause of morbidity among incarcerated women and female sex workers (FSW). Little is known about FSW incarcerated in New York City (NYC) jails. We reviewed jail health records to identify the STI and HIV prevalence among newly incarcerated FSW in NYC jails. We also examined the relationship of demographics and self-reported clinical and risk behaviour history with FSW status and compared FSW with non-FSW incarcerated women to identify FSW predictors and, guide NYC jail programme planning and policy.MethodsWe retrospectively reviewed routinely collected jail health record data to identify the prevalence of chlamydia (Ct), gonorrhoea (Ng) and HIV infection among women newly incarcerated in NYC jails in 2009–2010 (study period) and studied the relationship of STIs, demographics and self-reported clinical and risk behaviour history with FSW status.ResultsDuring the study period, 10 828 women were newly incarcerated in NYC jails. Of these, 10 115 (93%) women were tested for Ct and Ng; positivity was 6.2% (95% CI 5.7% to 6.7%) and 1.7% (95% CI 1.4% to 1.9%), respectively. Nine percent had HIV infection. Seven hundred (6.5%) were defined as FSW. FSW were more likely to have Ct (adjusted OR (AOR): 1.55; 95% CI 1.17 to 2.05; p<0.0001) but not Ng or HIV. FSW were more likely to report age 20–24 years, reside in boroughs other than Manhattan, ≥6 prior incarcerations, ≥2 incarcerations during the study period, condom use with current sex partners, multiple sex partners and current drug use.ConclusionsWomen incarcerated in NYC jails had high rates of Ct, Ng, and HIV infection. FSW were at higher risk for Ct than non-FSW incarcerated women. These findings are being used to design targeted interventions to identify FSW, provide clinical and preventive services in jail and coordinate care with community partners.
Characteristic atmosphere–ocean–solid earth interactions in the Antarctic coastal and marine environment inferred from seismic and infrasound recording at Syowa Station, East Antarctica
Authors: Kanao Masaki , Maggi Alessia , Ishihara Yoshiaki , Stutzmann Eleonore , Yamamoto Masa-Yuki , Toyokuni Genti 
Published: May 2013

Abstract
Several characteristic waves detected by seismographs in Antarctic stations have been recognized as originating from the physical interaction between the solid earth and the atmosphere–ocean–cryosphere system surrounding the Antarctic and may be used as a proxy for characterizing ocean wave climate. A Chaparral-type infrasound sensor was installed at Syowa Station (SYO; 39.6E, 69.0S), East Antarctica, in April 2008 during the International Polar Year (IPY2007–2008). Matching data are also available for this time period from the existing broadband seismic recorder located close by. Continuous infrasound data for 2008–2009 include background signals (microbaroms) with a broad peak in the wave period between the values of 4 and 10 s. Signals with the same period are recorded by the broadband seismograph at SYO (microseisms). This period band is identified as double-frequency microseisms/baroms (DFM). The DFM have relatively lower amplitudes during winter. We suggest that this is due to the sea-ice extent around the coast causing a decreased ocean loading effect. In contrast, the single frequency microseisms/baroms with a peak in period between 12 and 30 s are observed under storm conditions, particularly in winter. On the infrasound data, stationary signals are identified with harmonic overtones at a few Hertz to lowermost human audible band, which we suggest is due to local effects such as sea-ice cracking and vibration. Microseism measurements are a useful proxy for characterizing ocean wave climate, complementing other oceanographic and geophysical data. At SYO, continuous monitoring by both broadband seismograph and infrasound contributes to the Federation of Digital Seismographic Networks, the Comprehensive Nuclear-Test-Ban Treaty in the high southern latitudes and the Pan-Antarctic Observations System under the Scientific Committee on Antarctic Research.
Windows on Antarctic soil–landscape relationships: comparison across selected regions of Antarctica
Authors: Balks Megan R. , López-Martínez Jerónimo , Goryachkin Sergey V. , Mergelov Nikita S. , Schaefer Carlos E. G. R. , Simas Felipe N. B. , Almond Peter C. , Claridge Graeme G. C. , Mcleod Malcolm , Scarrow Joshua 
Published: May 2013

Abstract
This paper brings together topographic cross-section ‘windows’ from across Antarctica to illustrate soil–landscapes from the margins of the polar plateau in the Transantarctic Mountains and McMurdo Dry Valleys, through East Antarctic coastal areas, to the northern Antarctic Peninsula Region. Soils identified range from Gelisols in the Ross Sea Region, through Gelisols and Entisols in coastal East Antarctica, to a mixture of Gelisols, Entisols, Spodosols and Inceptisols in the northern Antarctic Peninsula Region where permafrost is not ubiquitous. The relative impacts of the soil-forming factors are considered. At a continental scale climate is the main driver of the differences observed between soils in different areas. At local scales strong soil–topographic relationships are observed. Organisms, time and parent material are dominant influences on soil properties only in relatively localized situations. Organisms dominate in areas of organic matter or guano accumulation and time is a dominant influence on exceptionally old upland surfaces in the McMurdo Dry Valleys. The US Department of Agriculture’s Soil Taxonomy gives a useful overall appraisal of Antarctic soils; however, for detailed work, there is a need to introduce some new categories at subgroup level to better capture the range of soils described.
Geological and palynological characterization of a river beach in Portugal for forensic purposes
Authors: Carvalho Áurea , Ribeiro Helena , Guedes Alexandra , Abreu Ilda , Noronha Fernando 
Published: May 2013

Abstract
Currently, it is important to use a combination of independent analytical techniques in order to reliably characterize between different samples of geological trace evidence in criminal investigations. Areínho beach, in the town of Vila Nova de Gaia (northern Portugal), is located on the southern bank of the Douro River. Although isolated, it is a very busy area during the summer and other seasons due to its popular water sports. The geology of the area is complex, with numerous different outcrops. In addition, there is a considerable variety of vegetation in the region, and many materials are transported by the Douro River and deposited in the area.
In order to characterize this beach for forensic purposes (both criminal and environmental), sediment samples were collected and analysed using a combination of geological techniques, namely colour, particle size distribution and mineralogy. These geological techniques were combined with a palynological assessment of the sediment samples. In addition, the surrounding vegetation was characterized and seasonal vegetation surveys were carried out.
In this study, the results obtained revealed homogeneous data throughout the profile in all the properties analysed. This research demonstrated that the combination of different, independent techniques used to characterize sediments from this river beach has the potential to contribute substantially to future forensic investigations.
Impact of Body Mass Index on the Risk of Colorectal Adenoma in a Metabolically Healthy Population
Authors: Yun Kyung Eun , Chang Yoosoo , Jung Hyun-Suk , Kim Chan-Won , Kwon Min-Jung , Park Sung Keun , Sung Eunju , Shin Hocheol , Park Hye Soon , Ryu Seungho 
Published: May 2013

Abstract
Metabolically healthy obese (MHO) states exist that seem to be protected from cardiovascular risks. Although obesity is a risk factor for colorectal adenoma (CRA), there has yet to be any study of the risks of CRA in MHO individuals. In this study, we compared CRA prevalence in MHO individuals versus metabolically healthy individuals who were normal in weight. This cross-sectional study involved 18,085 Korean adults (39.1 ± 6.7 years) who had a health checkup including a colonoscopy. High-risk CRA was defined as any adenoma over 1 cm, 3 or more adenomas, adenoma with a villous component, or high-grade dysplasia. Multinomial logistic regression models were used to measure the associations between body mass index (BMI) and the risk of low-risk and high-risk CRA. Low-risk and high-risk CRA were present in 9.3% and 1.4% of the study population, respectively. After adjusting for age, sex, smoking, drinking, exercise, family history of colorectal cancer, education, and use of analgesic and aspirin, compared with normal healthy individuals, the prevalence of low-risk and high-risk CRA was increased in MHO individuals [OR = 1.44; 95% confidence interval (CI), 1.23–1.69 and OR = 1.62; 95% CI, 1.09–2.41, respectively]. In fully adjusted models, the prevalence of low-risk and high-risk CRA was associated with increasing categories of BMI in a dose–response manner (P for trend &lt; 0.001 and 0.01, respectively). Thus, excess body weight, even in the absence of a metabolic unhealthy state, was found to be positively associated with increased presence of CRAs. Cancer Res; 73(13); 4020–7. ©2013 AACR.
Tumor MMP-1 Activates Endothelial PAR1 to Facilitate Vascular Intravasation and Metastatic Dissemination
Authors: Juncker-Jensen Anna , Deryugina Elena I. , Rimann Ivo , Zajac Ewa , Kupriyanova Tatyana A. , Engelholm Lars H. , Quigley James P. 
Published: May 2013

Abstract
Intravasation, the active entry of primary tumor cells into the vasculature, remains the least studied step in the metastatic cascade. Protease-mediated escape and stromal invasion of tumor cells represent widely accepted processes leading up to the intravasation step. However, molecular factors that contribute directly to tumor cell vascular penetration have not been identified. In this study, the in vivo role of the collagenolytic protease, MMP-1, in cancer cell intravasation and metastasis was analyzed by using a highly disseminating variant of human HEp3 epidermoid carcinoma, HEp3-hi/diss. Although naturally acquired or experimentally induced MMP-1 deficiency substantially suppressed HEp3-hi/diss intravasation, supplementation of recombinant MMP-1 to MMP-1–silenced primary tumors restored their impaired vascular dissemination. Surprisingly, abrogation of MMP-1 production and activity did not significantly affect HEp3-hi/diss migration or matrix invasion, suggesting noncollagenolytic mechanisms underlying MMP-1–dependent cell intravasation. In support of such noncollagenolytic mechanisms, MMP-1 silencing in HEp3-hi/diss cells modulated the microarchitecture and integrity of the angiogenic vasculature in a novel microtumor model. Concomitantly, MMP-1 deficiency led to decreased levels of intratumoral vascular permeability, tumor cell intravasation, and metastatic dissemination. Taking advantage of PAR1 deficiency of HEp3-hi/diss cells, we further show that endothelial PAR1 is a putative nontumor-cell/nonmatrix target, activation of which by carcinoma-produced MMP-1 regulates endothelial permeability and transendothelial migration. The inhibitory effects of specific PAR1 antagonists in live animals have also indicated that the mechanisms of MMP-1–dependent vascular permeability in tumors involve endothelial PAR1 activation. Together, our findings mechanistically underscore the contribution of a tumor MMP-1/endothelial PAR1 axis to actual intravasation events manifested by aggressive carcinoma cells. Cancer Res; 73(14); 4196–211. ©2013 AACR.
Comparing Histone Deacetylase Inhibitor Responses in Genetically Engineered Mouse Lung Cancer Models and a Window of Opportunity Trial in Patients with Lung Cancer
Authors: Ma Tian , Galimberti Fabrizio , Erkmen Cherie P. , Memoli Vincent , Chinyengetere Fadzai , Sempere Lorenzo , Beumer Jan H. , Anyang Bean N. , Nugent William , Johnstone David , Tsongalis Gregory J. , Kurie Jonathan M. , Li Hua , DiRenzo James , Guo Yongli , Freemantle Sarah J. , Dragnev Konstantin H. , Dmitrovsky Ethan 
Published: May 2013

Abstract
Histone deacetylase inhibitor (HDACi; vorinostat) responses were studied in murine and human lung cancer cell lines and genetically engineered mouse lung cancer models. Findings were compared with a window of opportunity trial in aerodigestive tract cancers. In human (HOP62, H522, and H23) and murine transgenic (ED-1, ED-2, LKR-13, and 393P, driven, respectively, by cyclin E, degradation-resistant cyclin E, KRAS, or KRAS/p53) lung cancer cell lines, vorinostat reduced growth, cyclin D1, and cyclin E levels, but induced p27, histone acetylation, and apoptosis. Other biomarkers also changed. Findings from transgenic murine lung cancer models were integrated with those from a window of opportunity trial that measured vorinostat pharmacodynamic responses in pre- versus posttreatment tumor biopsies. Vorinostat repressed cyclin D1 and cyclin E expression in murine transgenic lung cancers and significantly reduced lung cancers in syngeneic mice. Vorinostat also reduced cyclin D1 and cyclin E expression, but increased p27 levels in post- versus pretreatment human lung cancer biopsies. Notably, necrotic and inflammatory responses appeared in posttreatment biopsies. These depended on intratumoral HDACi levels. Therefore, HDACi treatments of murine genetically engineered lung cancer models exert similar responses (growth inhibition and changes in gene expression) as observed in lung cancer cell lines. Moreover, enhanced pharmacodynamic responses occurred in the window of opportunity trial, providing additional markers of response that can be evaluated in subsequent HDACi trials. Thus, combining murine and human HDACi trials is a strategy to translate preclinical HDACi treatment outcomes into the clinic. This study uncovered clinically tractable mechanisms to engage in future HDACi trials. Mol Cancer Ther; 12(8); 1545–55. ©2013 AACR.