bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of the thorax‐to‐abdomen breathing ratio for breathing motion modeling
Authors: White Benjamin M. , Zhao Tianyu , Lamb James , Bradley Jeffrey D. , Low Daniel A. 
Published: May 2013

Purpose:The purpose of this study was to develop a methodology to quantitatively measure the thorax‐to‐abdomen breathing ratio from a 4DCT dataset for breathing motion modeling and breathing motion studies.Methods:The thorax‐to‐abdomen breathing ratio was quantified by measuring the rate of cross‐sectional volume increase throughout the thorax and abdomen as a function of tidal volume. Twenty‐six 16‐slice 4DCT patient datasets were acquired during quiet respiration using a protocol that acquired 25 ciné scans at each couch position. Fifteen datasets included data from the neck through the pelvis. Tidal volume, measured using a spirometer and abdominal pneumatic bellows, was used as breathing‐cycle surrogates. The cross‐sectional volume encompassed by the skin contour when compared for each CT slice against the tidal volume exhibited a nearly linear relationship. A robust iteratively reweighted least squares regression analysis was used to determine η(i), defined as the amount of cross‐sectional volume expansion at each sliceiper unit tidal volume. The sum Ση(i) throughout all slices was predicted to be the ratio of the geometric expansion of the lung and the tidal volume; 1.11. The Xiphoid process was selected as the boundary between the thorax and abdomen. The Xiphoid process slice was identified in a scan acquired at mid‐inhalation. The imaging protocol had not originally been designed for purposes of measuring the thorax‐to‐abdomen breathing ratio so the scans did not extend to the anatomy with η(i) = 0. Extrapolation of η(i)–η(i) = 0 was used to include the entire breathing volume. The thorax and abdomen regions were individually analyzed to determine the thorax‐to‐abdomen breathing ratios. There were 11 image datasets that had been scanned only through the thorax. For these cases, the abdomen breathing component was equal to 1.11 − Ση(i) where the sum was taken throughout the thorax.Results:The average Ση(i) for thorax and abdomen image datasets was found to be 1.20 ± 0.17, close to the expected value of 1.11. The thorax‐to‐abdomen breathing ratio was 0.32 ± 0.24. The average Ση(i) was 0.26 ± 0.14 in the thorax and 0.93 ± 0.22 in the abdomen. In the scan datasets that encompassed only the thorax, the average Ση(i) was 0.21 ± 0.11.Conclusions:A method to quantify the relationship between abdomen and thoracic breathing was developed and characterized.
Full Genome Sequence of an Avian Influenza H5N1 Virus Isolated from the Environment in Hunan Province, China
Authors: Wang Ba , Zhang Hongbo , Chen Quanjiao , Chen Ze 
Published: May 2013

ABSTRACT
We isolated an avian influenza virus A/environment/Hunan/3/2011(H5N1) from a body of water in Hunan, China. The nucleotide sequence of the virus shares 95% homology with H5N1 from the east Asia region. Phylogenetic analysis indicates that its HA gene belongs to clade 2.3.2.1 and that other internal genes present different recombination features.
Genome Sequence of Ex-Afghanistan Crimean-Congo Hemorrhagic Fever Virus SCT Strain, from an Imported United Kingdom Case in October 2012
Authors: Chamberlain John , Atkinson Barry , Logue Christopher H. , Latham Jennie , Newman Edmund N. C. , Hewson Roger 
Published: May 2013

ABSTRACT
Crimean-Congo hemorrhagic fever (CCHF) virus is a serious human pathogen causing severe hemorrhagic disease with a fatality rate of up to approximately 30%. We have determined the viral genomic sequence from an isolate that caused a fatal case of imported CCHF in the United Kingdom in October 2012.
Draft Genome Sequence of the Steroid Degrader Rhodococcus ruber Strain Chol-4
Authors: Fernández de las Heras Laura , Alonso Sergio , de la Vega de León Antonio , Xavier Daniela , Perera Julián , Navarro Llorens Juana María 
Published: May 2013

ABSTRACT

The whole-genome shotgun sequence of
Rhodococcus ruber
strain Chol-4 is presented here. This organism was shown to be able to grow using many steroids as the sole carbon and energy sources. These sequence data will help us to further explore the metabolic abilities of this versatile degrader.
Complete Nucleotide Sequence of Canine Distemper Virus CDV-PS, Isolated from Dogs in China
Authors: Yi Li , Xu Hongli , Wang Jianke , Cheng Yuening , Zhang Hailing , Yan Xijun , Cheng Shipeng 
Published: May 2013

ABSTRACT
A new strain of canine distemper virus, CDV-PS, has been isolated from dogs in China, and its complete genome has been sequenced and analyzed. The phylogenetic analysis suggests that CDV-PS belongs to the Asia-1 cluster and has low identity to the vaccine strain.
Complete Genome Sequence of
Xanthomonas citri
subsp.
citri
Strain A
w
12879, a Restricted-Host-Range Citrus Canker-Causing Bacterium
Authors: Jalan Neha , Kumar Dibyendu , Yu Fahong , Jones Jeffrey B. , Graham James H. , Wang Nian 
Published: May 2013

ABSTRACT

Xanthomonas citri
subsp.
citri
causes citrus canker. The Asiatic strain has a broad host range, whereas the Wellington variant has a restricted host range. Here, we present the complete genome of
X. citri
subsp.
citri
strain A
W
12879. This study lays the foundation to further characterize the mechanisms for virulence and host range of
X. citri
.
Complete Genome Sequence of
Marinobacter
sp. BSs20148
Authors: Song Lai , Ren Lufeng , Li Xingang , Yu Dan , Yu Yong , Wang Xumin , Liu Guiming 
Published: May 2013

ABSTRACT

Marinobacter
sp. BSs20148 was isolated from marine sediment collected from the Arctic Ocean at a water depth of 3,800 m. Here we report the complete genome sequence of
Marinobacter
sp. BSs20148. This genomic information will facilitate the study of the physiological metabolism, ecological roles, and evolution of the
Marinobacter
species.
Draft Genome Sequence of Cesiribacter andamanensis Strain AMV16
T
, Isolated from a Soil Sample from a Mud Volcano in the Andaman Islands, India
Authors: Shivaji Sisinthy , Ara Sreenivas , Begum Zareena , Srinivas T. N. R. , Singh Aditya , Kumar Pinnaka Anil 
Published: May 2013

ABSTRACT

Here we report the 4.75-Mb genome of
Cesiribacter andamanensis
strain AMV16
T
, isolated from a soil sample from a mud volcano in the Andaman Islands, India.
Testing for boosting at the Paralympic games: policies, results and future directions
Authors: Blauwet Cheri A , Benjamin-Laing Harry , Stomphorst Jaap , Van de Vliet Peter , Pit-Grosheide Pia , Willick Stuart E 
Published: May 2013

Background‘Boosting’ is defined as the intentional induction of autonomic dysreflexia (AD) by athletes with a spinal cord injury (SCI) at or above the level of T6 for the purpose of improving sports performance. Boosting has been shown to confer up to a 9.7% improvement in race time. Additionally, to compete in a hazardous dysreflexic state, whether intentional or unintentional, would present an extreme health risk to the athlete. For these reasons, the International Paralympic Committee strictly bans the practice of boosting, and has developed a protocol to test for its presence.MethodsTesting was performed at three major international Paralympic events. Education regarding the dangers of AD was provided to athletes and team staff. Testing was conducted on athletes from the relevant sport classes: Athletics (wheelchair racing classes T51/T52/T53) and Handcycling (H1). Key parameters included the athlete's demographics (gender, country of origin), classification and blood pressure measurements. An extremely elevated blood pressure was considered to be a proxy maker for AD, and a systolic blood pressure of ≥180 mm Hg was considered a positive test.ResultsA total of 78 tests for the presence of AD were performed during the three games combined. No athlete tested positive. The number of athletes tested, by classification, was: 6 in Athletics T51, 47 in Athletics T52, 9 in Athletics T53 and 16 in Handcycling H1. Of those tested, the average systolic and diastolic blood pressures were 135 mm Hg (range 98–178) and 82 mm Hg (range 44–112), respectively. All athletes were compliant with testing. No athletes were withdrawn from competition due to the presence of AD.DiscussionTesting for the presence of AD in paralympic athletes with SCI prior to competition has been carried out for the first time at three major international paralympic competitions. There have been no positive tests thus far. Knowledge gained during these early testing experiences will be used to guide ongoing refinement of the testing protocol and the development of further educational initiatives.
Criminal prosecution of a male partner for sexual transmission of infectious diseases: the views of educated people living in Togo
Authors: Kpanake Lonzozou , Patassi Akouda , Mullet Étienne 
Published: May 2013

ObjectiveTo examine the views of educated people in Togo on the acceptability of criminal prosecution of a male partner for sexual transmission of infectious diseases (STIDs) to his female partner.Methods199 adults living in Kara, Togo judged acceptability of criminal prosecution for STID in 45 scenarios composed of combinations of five factors: (a) severity of disease; (b) awareness and communication of one's serological status; (c) partners’ marital status; (d) number of sexual partners the female partner has and (e) male partner's subsequent attitude (supportive or not).ResultsAcceptability was lower (a) when the male partner decided to take care of his female partner he had infected than when he decided to leave, (b) when both partners were informed but decided not to take precautions than when none of them was informed or when only the male partner was informed and (c) when the female partner has had several male sexual partners than when she has had only one. Two qualitatively different views were identified. For 66% of participants, when the male partner accepts to take care of his partner, he should not be sued, except when he did not disclose his serological status. For 34%, when both partners were informed, the male partner should not be sued, irrespective of other circumstances.ConclusionsRegarding criminal prosecution for STID, most people in the sample endorsed the position of the Joint United Nations Programme on HIV/AIDS that urges governments not to apply criminal law to cases where sexual partners disclosed their status or were not informed of it.
‘The intention may not be cruel… but the impact may be’: understanding legislators’ motives and wider public attitudes to a draft HIV Bill in Malawi
Authors: Stackpool-Moore Lucy 
Published: May 2013

ObjectivesThe law in relation to HIV has prominence in the formation and regulation of moral norms—in regard to human rights, and in regard to criminalisation, the policing of sexuality and intimate behaviours, and the production of stigma. The research focuses on the potential and impotence of the law to govern for, and enable, the human right to health in the context of HIV in Malawi.MethodsThis one-country qualitative case study (Malawi) action research involved data collection during a 6-month period (October 2010–March 2011). Datasets include interviews with law commissioners (n=10), opinion leaders (n=22), life story participants who were people living with and closely affected by HIV (n=20), reflections of the action research team (n=6), and a review of the proposed HIV and AIDS (Prevention and Management) Bill, legal and policy documents.ResultsThe analysis of the perspectives of the law commissioners, who formed the Special Law Commission and drafted the Bill, revealed that stigma was consciously invoked to delineate social norms and guide governance of notions of personal responsibility. The analysis of the perspectives of the life story participants, whose lives would be most directly impacted if these provisions came into force, reveals the extent to which the stigma associating criminality and HIV is falling on fertile ground through its engagement and generation of internalised stigma; unearthing an uneasy link between stigma and the law in response to HIV in Malawi.DiscussionThe results indicated that the proposed HIV Bill in Malawi manifests a tension between intention and impact. By incorporating criminal sanctions as part of the proposed HIV Bill, the lawmakers actively seek to use stigma to shape social attitudes and attempt to guide normative behaviour.
Integration of different sediment characteristics to discriminate between sources of coastal sediments
Authors: Guedes Alexandra , Murray Raymond C. , Ribeiro Helena , Rodrigues Andreia , Valentim Bruno , Sant’Ovaia Helena , Noronha Fernando 
Published: May 2013

Abstract
In order to investigate the effects of geological setting and the surrounding lithology on coastal sediment samples, four properties were analysed in a series of samples collected from different localities: colour determined by spectrophotometry; particle size distribution determined by laser granulometry; chemical composition determined by ICP-MS (inductively coupled plasma mass spectrometry); and low-field magnetic susceptibility determined using a susceptibility meter. A hierarchical cluster analysis was applied to ascertain the capacity of the different properties for discrimination between samples from the different geological settings.
The study reveals that colour analysis only allowed discrimination between different geographical areas; particle size distribution allowed separation between dune and beach samples; chemical composition allowed discrimination between both different geological settings and also between dune and beach sands; and, finally, the combination of magnetic susceptibility with colour and particle size distribution allowed for clear discrimination between geological settings, and between beach and sand dunes.
The studied samples are part of a larger and growing collection of data, and a more extensive evaluation will continue to be made for a more definitive assessment of the use of different characteristics for discrimination. So far, the results give confidence that it is meaningful to use these characteristics, especially when examined in combination, to distinguish between different locations.
Forensic provenance investigations of soil and sediment samples
Authors: Bowen A. M. , Caven E. A. 
Published: May 2013

Abstract
In recent decades, the polarizing light microscope has been slowly phased out of the geology curricula of many universities in the United States. This is unfortunate, as the polarizing light microscope is an instrument that is particularly well suited to overcoming problems typically encountered in forensic scenarios. Its versatility makes it uniquely powerful in provenance investigations in which sample size is limited and sample history is unknown. The polarizing light microscope can be used to determine the source rock type(s) of a sample of unconsolidated grains, either based on the mineral assemblage present in the sample or on properties observed for individual mineral grains or lithic fragments. Biological particles including pollen, spores, diatoms and botanical macerals can be identified and used to constrain the possible source of a sample. In addition, individual particles observed in the sample (geological, biological or anthropogenic) can be isolated and re-mounted for subsequent analyses that are useful for provenance determination. The inferences made can be used to produce maps illustrating potential source regions by means of geographical information systems (GIS). Several examples are provided to illustrate the various capabilities of the polarizing light microscope and its contributions to forensic soil analysis, specifically in forensic provenance investigations.
Instrumental neutron activation analysis (INAA) and forensic applications
Authors: Eby G. N. 
Published: May 2013

Abstract
Instrumental neutron activation analysis (INAA) is a non-destructive analytical technique that can be applied to a wide range of materials. The method requires no pretreatment of the sample, various geometries can be used and as many as 40 elements can be determined at the ppb–ppm level, depending on the characteristics of the specific sample. The method has been used in a number of forensic applications, such as identifying the source of ammunition, gunshot residue, arsenic in hair and the source of cigarettes. In this contribution, INAA is applied to characterizing ceramics, maple syrups and grasses, and based on the data it is possible to distinguish between various types of ceramics, sources of maple syrup and the geographical/geological locations of grass samples. As an example of an environmental forensic application, it is shown that a tree-ring record can be used to map the history of environmental pollution associated with a zinc smelter. Additional applications involve characterizing the products of nuclear detonations and the provenance of diamonds.
G-CSF Receptor Positive Neuroblastoma Subpopulations Are Enriched in Chemotherapy-Resistant or Relapsed Tumors and Are Highly Tumorigenic
Authors: Hsu Danielle M. , Agarwal Saurabh , Benham Ashley , Coarfa Cristian , Trahan Denae N. , Chen Zaowen , Stowers Paris N. , Courtney Amy N. , Lakoma Anna , Barbieri Eveline , Metelitsa Leonid S. , Gunaratne Preethi , Kim Eugene S. , Shohet Jason M. 
Published: May 2013

Abstract
Neuroblastoma is a neural crest-derived embryonal malignancy, which accounts for 13% of all pediatric cancer mortality, primarily due to tumor recurrence. Therapy-resistant cancer stem cells are implicated in tumor relapse, but definitive phenotypic evidence of the existence of these cells has been lacking. In this study, we define a highly tumorigenic subpopulation in neuroblastoma with stem cell characteristics, based on the expression of CSF3R, which encodes the receptor for granulocyte colony-stimulating factor (G-CSF). G-CSF receptor positive (aka G-CSFr+ or CD114+) cells isolated from a primary tumor and the NGP cell line by flow cytometry were highly tumorigenic and capable of both self-renewal and differentiation to progeny cells. CD114+ cells closely resembled embryonic and induced pluripotent stem cells with respect to their profiles of cell cycle, miRNA, and gene expression. In addition, they reflect a primitive undifferentiated neuroectodermal/neural crest phenotype revealing a developmental hierarchy within neuroblastoma tumors. We detected this dedifferentiated neural crest subpopulation in all established neuroblastoma cell lines, xenograft tumors, and primary tumor specimens analyzed. Ligand activation of CD114 by the addition of exogenous G-CSF to CD114+ cells confirmed intact STAT3 upregulation, characteristic of G-CSF receptor signaling. Together, our data describe a novel distinct subpopulation within neuroblastoma with enhanced tumorigenicity and a stem cell–like phenotype, further elucidating the complex heterogeneity of solid tumors such as neuroblastoma. We propose that this subpopulation may represent an additional target for novel therapeutic approaches to this aggressive pediatric malignancy. Cancer Res; 73(13); 4134–46. ©2013 AACR.
Connective Tissue Growth Factor Activates Pluripotency Genes and Mesenchymal–Epithelial Transition in Head and Neck Cancer Cells
Authors: Chang Cheng-Chi , Hsu Wen-Hao , Wang Chen-Chien , Chou Chun-Hung , Kuo Mark Yen-Ping , Lin Been-Ren , Chen Szu-Ta , Tai Shyh-Kuan , Kuo Min-Liang , Yang Muh-Hwa 
Published: May 2013

Abstract
The epithelial–mesenchymal transition (EMT) is a key mechanism in both embryonic development and cancer metastasis. The EMT introduces stem-like properties to cancer cells. However, during somatic cell reprogramming, mesenchymal–epithelial transition (MET), the reverse process of EMT, is a crucial step toward pluripotency. Connective tissue growth factor (CTGF) is a multifunctional secreted protein that acts as either an oncoprotein or a tumor suppressor among different cancers. Here, we show that in head and neck squamous cell carcinoma (HNSCC), CTGF promotes the MET and reduces invasiveness. Moreover, we found that CTGF enhances the stem-like properties of HNSCC cells and increases the expression of multiple pluripotency genes. Mechanistic studies showed that CTGF induces c-Jun expression through αvβ3 integrin and that c-Jun directly activates the transcription of the pluripotency genes NANOG, SOX2, and POU5F1. Knockdown of CTGF in TW2.6 cells was shown to reduce tumor formation and attenuate E-cadherin expression in xenotransplanted tumors. In HNSCC patient samples, CTGF expression was positively correlated with the levels of CDH1, NANOG, SOX2, and POU5F1. Coexpression of CTGF and the pluripotency genes was found to be associated with a worse prognosis. These findings are valuable in elucidating the interplay between epithelial plasticity and stem-like properties during cancer progression and provide useful information for developing a novel classification system and therapeutic strategies for HNSCC. Cancer Res; 73(13); 4147–57. ©2013 AACR.
ETS Transcription Factor ESE1/ELF3 Orchestrates a Positive Feedback Loop That Constitutively Activates NF-κB and Drives Prostate Cancer Progression
Authors: Longoni Nicole , Sarti Manuela , Albino Domenico , Civenni Gianluca , Malek Anastasia , Ortelli Erica , Pinton Sandra , Mello-Grand Maurizia , Ostano Paola , D'Ambrosio Gioacchino , Sessa Fausto , Garcia-Escudero Ramon , Thalmann George N. , Chiorino Giovanna , Catapano Carlo V. , Carbone Giuseppina M. 
Published: May 2013

Abstract
Chromosomal translocations leading to deregulated expression of ETS transcription factors are frequent in prostate tumors. Here, we report a novel mechanism leading to oncogenic activation of the ETS factor ESE1/ELF3 in prostate tumors. ESE1/ELF3 was overexpressed in human primary and metastatic tumors. It mediated transforming phenotypes in vitro and in vivo and induced an inflammatory transcriptome with changes in relevant oncogenic pathways. ESE1/ELF3 was induced by interleukin (IL)-1β through NF-κB and was a crucial mediator of the phenotypic and transcriptional changes induced by IL-1β in prostate cancer cells. This linkage was mediated by interaction of ESE1/ELF3 with the NF-κB subunits p65 and p50, acting by enhancing their nuclear translocation and transcriptional activity and by inducing p50 transcription. Supporting these findings, gene expression profiling revealed an enrichment of NF-κB effector functions in prostate cancer cells or tumors expressing high levels of ESE1/ELF3. We observed concordant upregulation of ESE1/ELF3 and NF-κB in human prostate tumors that was associated with adverse prognosis. Collectively, our results define an important new mechanistic link between inflammatory signaling and the progression of prostate cancer. Cancer Res; 73(14); 4533–47. ©2013 AACR.