bluuebunny/crossref_metadata_2025_split huggingface dataset:
Eccentricity dependent changes of density, spacing and packing arrangement of parafoveal cones
Authors: Lombardo Marco , Serrao Sebastiano , Ducoli Pietro , Lombardo Giuseppe 
Published: March 2013

AbstractPurposeTo investigate the distribution of cone density and spacing as well as the preferred packing arrangement of the cone mosaic as a function of retinal eccentricity.MethodsAn adaptive optics retinal camera (rtx1, www.imagine-eyes.com) was used to obtain images of the parafoveal cone mosaic in nineteen healthy volunteers. Cone density and spacing were estimated for each subject (both eyes) using a sampling window of 80 × 80 pixels, at 250‐, 450‐, 650‐ and 1100‐μm eccentricities from the fovea along the nasal and temporal retina of both eyes. The inter‐subject and intra‐subject variation of cone density and spacing were calculated via Coefficient of Variation (CoV). Cone packing arrangement was assessed using Voronoi analysis; calculations were done over 1024 × 128 pixels image sections of the cone mosaic across the horizontal meridian from 200‐ to 1050‐μm eccentricities.ResultsThe inter‐subject variation of parafoveal cone density ranged between 10% and 15% (p < 0.001) and the intra‐subject variation of cone density was lower than 8% in all subjects, except for two. The cone spacing values showed a moderate inter‐subject (CoV<7%; p < 0.001) and a low intra‐subject variation (CoV<4% in all subjects, except for two cases). In the parafoveal region, 40–50% of cones were hexagonally arranged; the percentage of non‐hexagonal Voronoi tiles increased at greater eccentricities.ConclusionThe use of multiple and complementary metric descriptors allows for a more detailed description of packing distribution and preferred arrangement of cone photoreceptors across the parafoveal retina.
Identification and differentiation of Phyllosticta species causing freckle disease of banana using high resolution melting (HRM) analysis
Authors: Wong M.‐H. , Henderson J. , Drenth A. 
Published: March 2013

Freckle disease of banana is caused by three closely related species of Phyllosticta, namely P. musarum, P. maculata and P. cavendishii. In this study, a high resolution melting (HRM) analysis assay was developed and its potential to identify these three fungal species is reported. The assay, which targets the ITS of the nuclear rDNA of the fungal species, generates three distinct melt profiles for the three Phyllosticta species. It is also able to distinguish a combination of up to three co‐infecting species by generating a deviant melt curve. Thirty‐five fungal cultures and infected herbarium leaf specimens, previously characterized using nucleotide sequencing as belonging to one of the three Phyllosticta species, were used for validation of the HRM analysis assay. The normalized curves generated differentiated all samples, with samples from each species correctly identified. The assay was further evaluated against 18 uncharacterized infected leaf specimens from various geographic locations and the results were verified by subsequent nucleotide sequencing. This HRM analysis assay allows rapid identification and differentiation of the three Phyllosticta species using a single primer pair in a one‐step closed‐tube system without labelled fluorescence probes. This novel assay format has potential for simultaneously identifying and differentiating other closely related species of plant pathogens, as well as the classification of infected historic specimens.
Expression and Localization of Vascular Endothelial Growth Factor and its Receptors in the Corpus Luteum During Oestrous Cycle in Water Buffaloes (Bubalus bubalis)
Authors: Chouhan VS , Panda RP , Yadav VP , Babitha V , Khan FA , Das GK , Gupta M , Dangi SS , Singh G , Bag S , Sharma GT , Berisha B , Schams D , Sarkar M 
Published: March 2013

ContentsThe aim of this study was to document the expression and localization of VEGF system comprising of VEGF isoforms (VEGF 120, VEGF 164 and VEGF 188) and their receptors (VEGFR1 and VEGFR2) in buffalo corpus luteum (CL) obtained from different stages of the oestrous cycle. Real‐time RT‐PCR (qPCR), Western blot and immunohistochemistry were applied to investigate mRNA expression, protein expression and localization of examined factors. In general, all the components of VEGF system (the VEGF isoforms and their receptors) were found in the water buffalo CL during the oestrous cycle. The mRNA as well as protein expression of VEGF system was highest during the early and mid‐luteal phase, which later steadily decreased (p < 0.05) after day 10 to reach the lowest level in regressed CL. As demonstrated by immunohistochemistry, VEGF protein was localized predominantly in luteal cells; however, VEGFR1 and VEGFR2 were localized in luteal cells as well as in endothelial cells. In conclusion, the dynamics of expression and localization of VEGF system in buffalo corpora lutea during the luteal phase were demonstrated in this study, indicating the possible role of VEGF system in the regulation of luteal angiogenesis and proliferation of luteal as well as endothelial cells through their non‐angiogenic function.
Integrated spatiotemporal analysis for automatic contrast agent inflow detection on angiography and fluoroscopy during transcatheter aortic valve implantation
Authors: Liao Rui , You Wei , Liu Yinxiao , Yan Michelle , John Matthias , Shea Steven 
Published: March 2013

Purpose:In this paper, the authors propose an integrated spatial and temporal analysis for automatic detection of contrast agent inflow at the aortic root on fluoroscopic and angiographic sequences during transcatheter aortic valve implantation procedures as a means to automatically trigger registration of 3D aortic models.Methods:The proposed contrast agent inflow detection method is based on a contrast feature curve, calculated using histogram analysis and a likelihood ratio test. Several image preprocessing steps are performed to enhance the properties of the contrast feature curve. For sequences with a dominant peak on its contrast feature curve, a cascaded classifier is then applied to differentiate the contrast‐enhanced aorta from contrast‐enhanced balloons. Finally, a multilayer classifier based on sparse Gabor features is used to recognize sequences containing a faint contrast‐enhanced aorta.Results:The algorithm was evaluated using 105 sequences consisting of more than 12 000 frames, and achieved a detection accuracy of 99.1% (100% sensitivity and 98.5% specificity). The computation time for a typical sequence of 150 frames was ∼1 s on a single‐core Dell PC with a 1 GHz Intel Xeon processor and 2 GB of RAM.Conclusions:The authors developed a novel, automatic method for contrast agent inflow detection on x‐ray sequences. With the achieved efficiency and accuracy, the proposed method is potentially feasible for clinical use as it facilitates a seamless workflow in utilizing patient‐specific 3D models to provide anatomical details during transcatheter aortic valve implantation procedures.
Small-Sized Circular Genomes Similar to Genome of Porcine Circovirus 2
Authors: Luo Wei , Zhao Dun , Yu Xing-Long , Ge Meng , Li Run-Cheng , Jiang Da-Liang 
Published: March 2013

ABSTRACT

Circular genomes smaller than and similar to the genome of porcine circovirus 2 were obtained from pig tissues along with the full-length genome of porcine circovirus 2. The 922-, 839-, and 617-nucleotide-long genomes exhibit high homology to the
rep
gene plus the origin of replication sequence of porcine circovirus 2.
Draft Genome Sequence of Clostridium ultunense Strain Esp, a Syntrophic Acetate-Oxidizing Bacterium
Authors: Manzoor Shahid , Müller Bettina , Niazi Adnan , Bongcam-Rudloff Erik , Schnürer Anna 
Published: March 2013

ABSTRACT

Clostridium ultunense
strain Esp belongs to the functional group of syntrophic acetate-oxidizing bacteria (SAOB), which have been identified as key organisms for efficient biogas production from protein-rich materials. Genome analysis and comparative genomics might aid us to define physiological features that are essential for maintaining this particular syntrophic lifestyle.
Draft Genome Sequence of Rhodococcus triatomae Strain BKS 15-14
Authors: Kumar Shailesh , Bala Monu , Raghava Gajendra Pal Singh , Mayilraj Shanmugam 
Published: March 2013

ABSTRACT

We report the 5.8-Mb genome sequence of
Rhodococcus triatomae
BKS 15-14, isolated from an ant hill soil sample, collected from Bhitarkanika Mangrove Reserve Forest, Odisha, India. The draft genome of strain BKS 15-14 consists of 5,824,349 bp, with a G+C content of 69%, 5,387 protein-coding genes, and 57 RNAs.
Advanced age influences the dynamic changes in circulating C-reactive protein following injury
Authors: Pinato David J , Bains Jasmeen , Irkulla Sashidhar , Pomroy Josh , Ujam Bedri , Gaze David , Mendall Michael A 
Published: March 2013

BackgroundThe concentration of C-reactive protein (CRP), a biomarker of systemic inflammation, is determined by genetic, clinical and demographic factors including gender, smoking and body mass index (BMI). The influence of age on CRP dynamic changes following insult has, however, been poorly characterised.MethodsWe used unilateral hernia repair as a model of standardised insult to investigate the influence of baseline demographic and clinico-pathological factors affecting the dynamic changes in CRP, interleukin (IL) 6 and tumour necrosis factor-α over a time course of 48 h following injury.ResultsWe derived CRP negativisation kinetics on 100 prospectively enrolled male subjects with mean age of 60.6 years (range 24–90 years) and mean BMI of 25.7 kg/m2(range 17.9–37 kg/m2). Patients who failed to normalise CRP to<10 mg/l at 48 h (n=74) were significantly older (p<0.001), had longer surgical times (p=0.05), higher waist/hip ratio (p=0.02). Multiple regression analysis confirmed age as the only independent predictor of delayed CRP normalisation (p=0.03). Persistent CRP elevation was associated with higher peak CRP values (p<0.001), higher IL-6 concentrations at 24 (p=0.01) and 48 h (p=0.03).ConclusionsCRP decline following insult is delayed in elderly patients as a result of unopposed IL-6 release. Age should be routinely incorporated in the assessment of CRP response to avoid misinterpretation of age-related delay in CRP clearance with ongoing systemic inflammation.
Developing a cumulative anatomic scoring system for military perineal and pelvic blast injuries
Authors: Mossadegh Somayyeh , Midwinter M , Parker P 
Published: March 2013

BackgroundImprovised explosive device (IED) yields in Afghanistan have increased resulting in more proximal injuries. The injury severity score (ISS) is an anatomic aggregate score of the three most severely injured anatomical areas but does not accurately predict severity in IED related pelvi-perineal trauma patients. A scoring system based on abbreviated injury score (AIS) was developed to reflect the severity of these injuries in order to better understand risk factors, develop a tool for future audit and improve performance.MethodUsing standard AIS descriptors, injury scales were constructed for the pelvis (1, minor to 6, maximal). The perineum was divided into anterior and posterior zones as relevant to injury patterns and blast direction with each soft tissue structure being allocated a score from its own severity scale. A cumulative score, from 1 to 36 for soft tissue, or a maximum of 42 if a pelvic fracture was involved, was created for all structures injured in the anterior and posterior zones.ResultsUsing this new scoring system, 77% of patients survived with a pelvi-perineal trauma score (PPTS) below 5. There was a significant increase in mortality, number of pelvic fractures and amputations with increase in score when comparing the first group (score 1–5) to the second group (score 6–10). For scores between 6 and 16 survival was 42% and 22% for scores between 17 and 21. In our cohort of 62 survivors, 1 patient with an IED related pelvi-perineal injury had a ‘theoretically un-survivable’ maximal ISS of 75 and survived, whereas there were no survivors with a PPTS greater than 22 but this group had no-one with an ISS of 75 suggesting ISS is not an accurate reflection of the true severity of pelvi-perineal blast injury.ConclusionsThis scoring system is the initial part of a more complex logistic regression model that will contribute towards a unique trauma scoring system to aid surgical teams in predicting fluid requirements and operative timelines. In austere environments, it may also help to prevent futile resuscitations. Better correlation between measurement of severity and outcome would aid performance improvement monitoring. In the longer term it will also allow benchmarking of current survival rates and comparisons in the future.
Dermatological manifestations and relationship to outcomes of patients admitted to a medical intensive care unit: a study from a tertiary care hospital in India
Authors: Agrawal Poonam , Peter John Victor , George Renu 
Published: March 2013

Abstract

Aim
To determine the prevalence of dermatological manifestations in intensive care unit (ICU) patients and assess its impact on outcomes.

Methods
This was a prospective cohort study of 1013 ICU patients admitted between December 2009 and April 2011. Patients were categorised following an initial screening (within 48 h) and subsequent daily review as those with dermatological manifestations in association with multisystem disorder (category 1), occurring due to treatment or critical illness (category 2), coincidental lesions (category 3) or primary dermatological conditions needing intensive care (category 4). Outcomes included mortality, duration of ventilation and hospitalisation. Factors associated with mortality were explored using univariate and multivariate analyses.

Results
Dermatological manifestations were observed in 427 (42.2%) patients, predominantly of categories 1 (n=159) and 2 (n=160). Common aetiologies were infections (39.3%) and mechanical, thermal or physical injuries (32.8%). Primary dermatological conditions (n=33) included 21 patients with cutaneous infections, 3 with angioedema, 2 each with pemphigus, toxic epidermal necrolysis and psoriasis, and 1 each with Stevens–Johnson syndrome, drug hypersensitivity syndrome and crusted scabies. The presence of cutaneous lesions increased mortality risk (OR 1.56, 95% CI 1.20 to 2.03) and significantly (p&lt;0.001) prolonged ventilation and hospitalisation. Mortality was higher (p&lt;0.001) in patients in categories 4 (65.6%) and 2 (57.5%) compared to those without manifestations (35.5%). After adjusting for age, Acute Physiology And Chronic Health Evaluation II (APACHE-II) score, ventilation and dialysis, the association between dermatological manifestations and mortality was insignificant (OR 1.37, 95% CI 0.97 to 1.95).

Conclusions
Dermatological manifestations are common in ICU patients. Their presence may impact mortality and duration of ventilation and hospitalisation.
Endothelial Cell Protein C Receptor Opposes Mesothelioma Growth Driven by Tissue Factor
Authors: Keshava Shiva , Sahoo Sanghamitra , Tucker Torry A. , Idell Steven , Rao L. Vijaya Mohan , Pendurthi Usha R. 
Published: March 2013

Abstract
The procoagulant protein tissue factor (F3) is a powerful growth promoter in many tumors, but its mechanism of action is not well understood. More generally, it is unknown whether hemostatic factors expressed on tumor cells influence tissue factor-mediated effects on cancer progression. In this study, we investigated the influence of tissue factor, endothelial cell protein C receptor (EPCR, PROCR), and protease activated receptor-1 (PAR1, F2R) on the growth of malignant pleural mesothelioma (MPM), using human MPM cells that lack or express tissue factor, EPCR or PAR1, and an orthotopic nude mouse model of MPM. Intrapleural administration of MPM cells expressing tissue factor and PAR1 but lacking EPCR and PAR2 (F2RL1) generated large tumors in the pleural cavity. Suppression of tissue factor or PAR1 expression in these cells markedly reduced tumor growth. In contrast, tissue factor overexpression in nonaggressive MPM cells that expressed EPCR and PAR1 with minimal levels of tissue factor did not increase their limited tumorigenicity. More importantly, ectopic expression of EPCR in aggressive MPM cells attenuated their growth potential, whereas EPCR silencing in nonaggressive MPM cells engineered to overexpress tissue factor increased their tumorigenicity. Immunohistochemical analyses revealed that EPCR expression in tumor cells reduced tumor cell proliferation and enhanced apoptosis. Overall, our results enlighten the mechanism by which tissue factor promotes tumor growth through PAR1, and they show how EPCR can attenuate the growth of tissue factor-expressing tumor cells. Cancer Res; 73(13); 3963–73. ©2013 AACR.
RETRACTED: Collagen Prolyl Hydroxylases Are Essential for Breast Cancer Metastasis
Authors: Gilkes Daniele M. , Chaturvedi Pallavi , Bajpai Saumendra , Wong Carmen C. , Wei Hong , Pitcairn Stephen , Hubbi Maimon E. , Wirtz Denis , Semenza Gregg L. 
Published: March 2013

Abstract
The presence of hypoxia and fibrosis within the primary tumor are two major risk factors for metastasis of human breast cancer. In this study, we demonstrate that hypoxia-inducible factor 1 activates the transcription of genes encoding collagen prolyl hydroxylases that are critical for collagen deposition by breast cancer cells. We show that expression of collagen prolyl hydroxylases promotes cancer cell alignment along collagen fibers, resulting in enhanced invasion and metastasis to lymph nodes and lungs. Finally, we establish the prognostic significance of collagen prolyl hydroxylase mRNA expression in human breast cancer biopsies and show that ethyl 3,4-dihydroxybenzoate, a prolyl hydroxylase inhibitor, decreases tumor fibrosis and metastasis in a mouse model of breast cancer. Cancer Res; 73(11); 3285–96. ©2013 AACR.
Elevated 4-Aminobiphenyl and 2,6-Dimethylaniline Hemoglobin Adducts and Increased Risk of Bladder Cancer among Lifelong Nonsmokers—The Shanghai Bladder Cancer Study
Authors: Tao Li , Day Billy W. , Hu Bibin , Xiang Yong-Bing , Wang Renwei , Stern Mariana C. , Gago-Dominguez Manuela , Cortessis Victoria K. , Conti David V. , Van Den Berg David , Pike Malcolm C. , Gao Yu-Tang , Yu Mimi C. , Yuan Jian-Min 
Published: March 2013

Abstract
Background: 4-Aminobiphenyl (ABP) is an established human bladder carcinogen, with tobacco smoke being a major source of human exposure. Other arylamine compounds, including 2,6-dimethylaniline (2,6-DMA), have been implicated as possible human bladder carcinogens. Hemoglobin adducts of 4-ABP and 2,6-DMA are validated biomarkers of exposure to those compounds in humans.
Methods: The Shanghai Bladder Cancer Study enrolled 581 incident bladder cancer cases and 604 population controls. Each participant was solicited for his/her history of tobacco use and other lifestyle factors and donation of blood and urine specimens. Red blood cell lysates were used to quantify both hemoglobin adducts of 4-ABP and 2,6-DMA. Urine samples were used to quantify total cotinine. ORs and 95% confidence intervals (CI) for bladder cancer were estimated using unconditional logistic regression methods.
Results: Among lifelong nonsmokers, ORs (95% CIs) of bladder cancer for low (below median of positive values) and high versus undetectable levels of 2,6-DMA hemoglobin adducts were 3.87 (1.39–10.75) and 6.90 (3.17–15.02), respectively (Ptrend &lt; 0.001). Similarly, among lifelong nonsmokers, ORs (95% CIs) of bladder cancer for third and fourth versus first/second quartiles of 4-ABP hemoglobin adducts was 1.30 (0.76–2.22) and 2.29 (1.23–4.24), respectively (Ptrend = 0.009). The two associations were independent of each other.
Conclusion: Hemoglobin adducts of 4-ABP and 2,6-DMA were significantly and independently associated with increased bladder cancer risk among lifelong nonsmokers in Shanghai, China.
Impact: The findings of the present study in China with previous data in Los Angeles, California strongly implicate arylamines as potential causal agents of human bladder cancer. Cancer Epidemiol Biomarkers Prev; 22(5); 937–45. ©2013 AACR.
A Systems Biology Framework Identifies Molecular Underpinnings of Coronary Heart Disease
Authors: Huan Tianxiao , Zhang Bin , Wang Zhi , Joehanes Roby , Zhu Jun , Johnson Andrew D. , Ying Saixia , Munson Peter J. , Raghavachari Nalini , Wang Richard , Liu Poching , Courchesne Paul , Hwang Shih-Jen , Assimes Themistocles L. , McPherson Ruth , Samani Nilesh J. , Schunkert Heribert ,   Coronary ARteryDIsease Genome wide Replication and Meta-analysis (CARDIoGRAM) Consortium, International Consortium for Blood Pressure GWAS (ICBP), Meng Qingying , Suver Christine , O’Donnell Christopher J. , Derry Jonathan , Yang Xia , Levy Daniel 
Published: March 2013

Objective—
Genetic approaches have identified numerous loci associated with coronary heart disease (CHD). The molecular mechanisms underlying CHD gene–disease associations, however, remain unclear. We hypothesized that genetic variants with both strong and subtle effects drive gene subnetworks that in turn affect CHD.

Approach and Results—

We surveyed CHD-associated molecular interactions by constructing coexpression networks using whole blood gene expression profiles from 188 CHD cases and 188 age- and sex-matched controls. Twenty-four coexpression modules were identified, including 1 case-specific and 1 control-specific differential module (DM). The DMs were enriched for genes involved in B-cell activation, immune response, and ion transport. By integrating the DMs with gene expression–associated single-nucleotide polymorphisms and with results of genome-wide association studies of CHD and its risk factors, the control-specific DM was implicated as CHD causal based on its significant enrichment for both CHD and lipid expression–associated single-nucleotide polymorphisms. This causal DM was further integrated with tissue-specific Bayesian networks and protein–protein interaction networks to identify regulatory key driver genes. Multitissue key drivers (
SPIB
and
TNFRSF13C
) and tissue-specific key drivers (eg,
EBF1
) were identified.

Conclusions—
Our network-driven integrative analysis not only identified CHD-related genes, but also defined network structure that sheds light on the molecular interactions of genes associated with CHD risk.
Gene Expression Signatures of Coronary Heart Disease
Authors: Joehanes Roby , Ying Saixia , Huan Tianxiao , Johnson Andrew D. , Raghavachari Nalini , Wang Richard , Liu Poching , Woodhouse Kimberly A. , Sen Shurjo K. , Tanriverdi Kahraman , Courchesne Paul , Freedman Jane E. , O’Donnell Christopher J. , Levy Daniel , Munson Peter J. 
Published: March 2013

Objective—
To identify transcriptomic biomarkers of coronary heart disease (CHD) in 188 cases with CHD and 188 age- and sex-matched controls who were participants in the Framingham Heart Study.

Approach and Results—

A total of 35 genes were differentially expressed in cases with CHD versus controls at false discovery rate<0.5, including
GZMB
,
TMEM56
, and
GUK1
. Cluster analysis revealed 3 gene clusters associated with CHD, 2 linked to increased erythrocyte production and a third to reduced natural killer and T cell activity in cases with CHD. Exon-level results corroborated and extended the gene-level results. Alternative splicing analysis suggested that
GUK1
and 38 other genes were differentially spliced in cases with CHD versus controls. Gene Ontology analysis linked ubiquitination and T-cell–related pathways with CHD.

Conclusions—
Two bioinformatically defined groups of genes show consistent associations with CHD. Our findings are consistent with the hypotheses that hematopoesis is upregulated in CHD, possibly reflecting a compensatory mechanism, and that innate immune activity is disrupted in CHD or altered by its treatment. Transcriptomic signatures may be useful in identifying pathways associated with CHD and point toward novel therapeutic targets for its treatment and prevention.