bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical Note: Characterization of custom 3D printed multimodality imaging phantoms
Authors: Bieniosek Matthew F. , Lee Brian J. , Levin Craig S. 
Published: September 2015

Purpose:Imaging phantoms are important tools for researchers and technicians, but they can be costly and difficult to customize. Three dimensional (3D) printing is a widely available rapid prototyping technique that enables the fabrication of objects with 3D computer generated geometries. It is ideal for quickly producing customized, low cost, multimodal, reusable imaging phantoms. This work validates the use of 3D printed phantoms by comparing CT and PET scans of a 3D printed phantom and a commercial “Micro Deluxe” phantom. This report also presents results from a customized 3D printed PET/MRI phantom, and a customized high resolution imaging phantom with sub‐mm features.Methods:CT and PET scans of a 3D printed phantom and a commercial Micro Deluxe (Data Spectrum Corporation, USA) phantom with 1.2, 1.6, 2.4, 3.2, 4.0, and 4.8 mm diameter hot rods were acquired. The measured PET and CT rod sizes, activities, and attenuation coefficients were compared. A PET/MRI scan of a custom 3D printed phantom with hot and cold rods was performed, with photon attenuation and normalization measurements performed with a separate 3D printed normalization phantom. X‐ray transmission scans of a customized two level high resolution 3D printed phantom with sub‐mm features were also performed.Results:Results show very good agreement between commercial and 3D printed micro deluxe phantoms with less than 3% difference in CT measured rod diameter, less than 5% difference in PET measured rod diameter, and a maximum of 6.2% difference in average rod activity from a 10 min, 333 kBq/ml (9 μCi/ml) Siemens Inveon (Siemens Healthcare, Germany) PET scan. In all cases, these differences were within the measurement uncertainties of our setups. PET/MRI scans successfully identified 3D printed hot and cold rods on PET and MRI modalities. X‐ray projection images of a 3D printed high resolution phantom identified features as small as 350 μm wide.Conclusions:This work shows that 3D printed phantoms can be functionally equivalent to commercially available phantoms. They are a viable option for quickly distributing and fabricating low cost, customized phantoms.
Physical Activity and Lung Cancer: A Case-Control Study in Brazil
Authors: Brizio Maria Laura Resem , Hallal Pedro C. , Lee I-Min , Domingues Marlos Rodrigues 
Published: September 2015

Background:The aim of this study was to investigate the association between lifetime physical activity and risk of lung cancer.Methods:A case-control study was conducted in southern Brazil. Case subjects were recruited from oncology services of 4 hospitals. Control subjects were selected from the same hospitals, but from different services (traumatology and emergency). Both case subjects (n = 81) and control subjects (n = 168) were interviewed using a questionnaire about sociodemographic characteristics, anthropometric information and family history of cancer. Control subjects were matched to case subjects according to sex and age (± 5 years). Detailed information on smoking was collected. Physical activity was measured using the Lifetime Physical Activity Questionnaire.Results:Of the case subjects, 89% were either current or former smokers; among control subjects, this value was 57%. Participants in the second, third, and fourth quartiles of all-domains physical activity had odds ratios of 0.54 (95% CI, 0.21–1.40), 0.25 (95% CI, 0.08–0.72), and 0.24 (95% CI, 0.07–0.83) for lung cancer, compared with the lowest quartile, after adjusting for confounding. In the fully adjusted models, leisure-time physical activity was not associated with lung cancer risk.Conclusion:Lifetime all-domains physical activity may reduce the risk of lung cancer.
Exercise on Prescription: A Cross-sectional Study With Self-reported Outcome
Authors: Pedersen Helene Buch , Helmer-Nielsen Morten , Dieperink Karin Brochstedt , Østergaard Birte 
Published: September 2015

Background:Exercise on prescription (EOP) is an attempt to increase physical activity among sedentary adults with signs of lifestyle diseases. Until now, no studies have focused on patients with chronic diseases and how they assess the long-term effect of participating in EOP consisting of supervised interventions of different intensities. This study aimed to describe and compare self-reported physical activity in the long term among participants in 3 EOP modules of different intensities.Methods:A cross-sectional survey was conducted among 1152 former participants in EOP between July 2005 and May 2007 in 2 Danish counties. Physical activity was measured as number of days with a minimum 30 minutes of moderate/vigorous activity.Results:Seventy-five percent (n = 854) returned the questionnaire. Of these, 36% reported being physically active ≥ 5 days/week. Comparing leisure-time activities before EOP 29% was sedentary vs. 15% (P < 0 .01) after, moderate + hard leisure-time activities was 7% before vs. 19% after EOP (P < 0 .01). Time postintervention did not influence the numbers reporting to be physical active negatively.Conclusions:This study in community-dwelling adults with chronic diseases participating in EOP finds that approximately one-third reported being physically active in the long term postintervention, but no differences between the modalities were found.
Comparison of Subjective and Objective Measures of Sedentary Behavior Using the Yale Physical Activity Survey and Accelerometry in Patients With Rheumatoid Arthritis
Authors: Gilbert Abigail L. , Lee Jungwha , Ma Madeleine , Semanik Pamela A. , DiPietro Loretta , Dunlop Dorothy D. , Chang Rowland W. 
Published: September 2015

Background:Sedentary behavior is associated with increased risk of functional decline and disability. Individuals with rheumatoid arthritis (RA) spend more time sedentary than healthy adults. Self-reported assessment of sedentary behavior has not been well-developed in this patient population.Methods:172 adults with RA wore an accelerometer for 7 days and completed a modified version of the Yale Physical Activity Survey (YPAS). YPAS-derived sedentary estimates included 1) daily sitting categories (<3, 3 to 6, 6 to 8, >8 hours/day), 2) continuous daily sedentary time calculated by subtracting hours spent sleeping or in physical activity from a 24-hour day, and 3) rank order of YPAS-derived continuous daily sedentary time. Each estimate was compared with objective accelerometer-derived sedentary time using linear regression and Bland-Altman analysis.Results:A significant relationship was observed between accelerometer-derived sedentary time and all 3 estimates. Bland-Altman plot demonstrated systematic bias, however Bland-Altman plot of rank-order demonstrated that the ranked YPAS-derived continuous estimate was an unbiased predictor of ranked accelerometer sedentary time though limits of agreement were wide.Conclusions:This patient-reported approach using the YPAS shows promise to be a useful tool to identify the most sedentary patients. Providing a practical and accurate tool may increase the frequency sedentary behavior is assessed by clinicians.
Cryo-EM shows the polymerase structures and a nonspooled genome within a dsRNA virus
Authors: Liu Hongrong , Cheng Lingpeng 
Published: September 2015

Caught in the act of copying
The genomes of double-stranded RNA (dsRNA) viruses consist of about a dozen dsRNA segments enclosed by a protein coat. Inside the host cell, the coat remains intact, and the dsRNAs have to replicate within the coat. Liu and Cheng used cryo–electron microscopy of cypovirus particles to catch the dsRNAs in the act of being copied. The structures revealed that the RNA formed a liquid-crystalline array on which viral enzymes carry out multiple rounds of transcription to replicate the viral genome.

Science
, this issue p.
1347
Draft Genome Sequence of Non-Vibrio parahaemolyticus Acute Hepatopancreatic Necrosis Disease Strain KC13.17.5, Isolated from Diseased Shrimp in Vietnam
Authors: Kondo Hidehiro , Van Phan Thi , Dang Lua T. , Hirono Ikuo 
Published: September 2015

ABSTRACT

A strain of
Vibrio
(KC13.17.5) causing acute hepatopancreatic necrosis disease (AHPND) in shrimp in northern Vietnam was isolated. Normally, AHPND is caused by
Vibrio parahaemolyticus
, but the genomic sequence of the strain indicated that it belonged to
Vibrio harveyi
. The sequence data included plasmid-like sequences and putative virulence genes.
Complete DNA Sequence of Pseudomonas syringae pv. actinidiae, the Causal Agent of Kiwifruit Canker Disease
Authors: Templeton Matthew D. , Warren Benjamin A. , Andersen Mark T. , Rikkerink Erik H. A. , Fineran Peter C. 
Published: September 2015

ABSTRACT

Pseudomonas syringae
pv. actinidiae is the causal agent of bacterial canker of kiwifruit, a disease that has rapidly spread worldwide. We have fully sequenced and assembled the chromosomal and plasmid DNA from
P. syringae
pv. actinidiae ICMP 18884 using the PacBio RS II platform.
Draft Genome Sequences of the Fish Pathogen Vibrio harveyi Strains VH2 and VH5
Authors: Castillo Daniel , D’Alvise Paul , Middelboe Mathias , Gram Lone , Liu Siyang , Kalatzis Panos G. , Kokkari Constantina , Katharios Pantelis 
Published: September 2015

ABSTRACT

Vibrio harveyi
is an important marine pathogen that is responsible for vibriosis outbreaks in cultured fish and invertebrates worldwide. Here, we announce the draft genome sequences of
V. harveyi
strains VH2 and VH5, isolated from farmed juvenile
Seriola dumerili
during outbreaks of vibriosis in Crete, Greece.
Genome Sequence of Virgibacillus pantothenticus DSM 26
T
(ATCC 14576), a Mesophilic and Halotolerant Bacterium Isolated from Soil
Authors: Wang Jie-ping , Liu Bo , Liu Guo-hong , Chen De-ju , Zhu Yu-jing , Chen Zheng , Che Jian-mei 
Published: September 2015

ABSTRACT

Virgibacillus pantothenticus
DSM 26
T
is a Gram-positive, spore-forming, aerobic, mesophilic, and halotolerant bacterium. Here, we report its 4.76-Mb draft genome sequence, which is the first genome information of
V. pantothenticus
and will promote biological research and biotechnological application for the species.
Complete Genome Sequence of Hyperthermophilic Piezophilic Archaeon Palaeococcus pacificus DY20341
T
, Isolated from Deep-Sea Hydrothermal Sediments
Authors: Zeng Xiang , Jebbar Mohamed , Shao Zongze 
Published: September 2015

ABSTRACT

We report the genome sequence of
Palaeococcus pacificus
DY20341
T
, isolated from a sediment sample collected from eastern Pacific Ocean hydrothermal fields, which is the first report of a complete genome for a
Palaeococcus
species. The genome sequence will help to better understand differentiation phylogenetic relationships and evolution of several
Thermococcales
species.
Complete Genome Sequence of Campylobacter gracilis ATCC 33236
T
Authors: Miller William G. , Yee Emma 
Published: September 2015

ABSTRACT

The human oral pathogen
Campylobacter gracilis
has been isolated from periodontal and endodontal infections, and also from nonoral head, neck, or lung infections. This study describes the whole-genome sequence of the human periodontal isolate ATCC 33236
T
(=FDC 1084), which is the first closed genome for
C. gracilis
.
Visitors to ‘the northern playgrounds’: tourists and exploratory science in north Norway
Authors: Whalley W. Brian , Parkinson Anne F. 
Published: September 2015

Abstract

This paper outlines some significant visits made to north Norway by geologists and mountaineers from Britain and Ireland from the early to late nineteenth century. These visitors wrote up their travels and climbing experiences in a region in north Norway that was difficult to get to other than by sea: Øksfjordjøkelen and Lyngen. Early travellers revealed the sights of the fjord areas and thereby promoted the region for subsequent travellers. Leopold von Buch's
Travels though Norway and Lapland during the Years 1806, 1807, and 1808
probably prompted J. D. Forbes to visit and produce
Norway and Its Glaciers
and Archibald Geikie's
Geological Sketches at Home and Abroad
as part of the contemporary discussions about the ‘glacial theory’. In the latter years of the nineteenth century the British climbers William Cecil Slingsby and George Hastings, with local climber Josef Caspari, explored the Lyngen Peninsula. Elizabeth Main (Mrs Aubrey Le Blond) also climbed in Lyngen. As well as providing written summaries of their exploits, the early explorers included photographs in their books. Some of these images are helpful in the reconstruction of the glacierized landscapes at the end of the Little Ice Age. It is suggested that present-day travellers might leave their observations available, in digital media, for future investigators.
Histone Deacetylase HDAC8 Promotes Insulin Resistance and β-Catenin Activation in NAFLD-Associated Hepatocellular Carcinoma
Authors: Tian Yuan , Wong Vincent W.S. , Wong Grace L.H. , Yang Weiqin , Sun Hanyong , Shen Jiayun , Tong Joanna H.M. , Go Minnie Y.Y. , Cheung Yue S. , Lai Paul B.S. , Zhou Mingyan , Xu Gang , Huang Tim H.M. , Yu Jun , To Ka F. , Cheng Alfred S.L. , Chan Henry L.Y. 
Published: September 2015

Abstract
The growing epidemic of obesity, which causes nonalcoholic fatty liver disease (NAFLD) and the more severe phenotype nonalcoholic steatohepatitis (NASH), has paralleled the increasing incidence of hepatocellular carcinoma (HCC). Accumulating evidence demonstrates that overnutrition and metabolic pathways can trigger modifications of DNA and histones via deregulation of chromatin modifiers, resulting in aberrant transcriptional activity. However, the epigenetic regulation of HCC development in NAFLD remains obscure. Here, we uncover key epigenetic regulators using both dietary and genetic obesity-promoted HCC models through quantitative expression profiling and characterize the oncogenic activities of histone deacetylase HDAC8 in NAFLD-associated hepatocarcinogenesis. HDAC8 is directly upregulated by the lipogenic transcription factor SREBP-1 where they are coexpressed in dietary obesity models of NASH and HCC. Lentiviral-mediated HDAC8 attenuation in vivo reversed insulin resistance and reduced NAFLD-associated tumorigenicity. HDAC8 modulation by genetic and pharmacologic approaches inhibited p53/p21-mediated apoptosis and G2–M phase cell-cycle arrest and stimulated β-catenin–dependent cell proliferation. Mechanistically, HDAC8 physically interacted with the chromatin modifier EZH2 to concordantly repress Wnt antagonists via histone H4 deacetylation and H3 lysine 27 trimethylation. In human NAFLD-associated HCC, levels of SREBP-1, HDAC8, EZH2, H4 deacetylation, H3K27me3, and active β-catenin were all correlated positively in tumors compared with nontumor tissues. Overall, our findings show how HDAC8 drives NAFLD-associated hepatocarcinogenesis, offering a novel epigenetic target to prevent or treat HCC in obese patients. Cancer Res; 75(22); 4803–16. ©2015 AACR.
Early Prediction of Cancer Progression by Depth-Resolved Nanoscale Mapping of Nuclear Architecture from Unstained Tissue Specimens
Authors: Uttam Shikhar , Pham Hoa V. , LaFace Justin , Leibowitz Brian , Yu Jian , Brand Randall E. , Hartman Douglas J. , Liu Yang 
Published: September 2015

Abstract
Early cancer detection currently relies on screening the entire at-risk population, as with colonoscopy and mammography. Therefore, frequent, invasive surveillance of patients at risk for developing cancer carries financial, physical, and emotional burdens because clinicians lack tools to accurately predict which patients will actually progress into malignancy. Here, we present a new method to predict cancer progression risk via nanoscale nuclear architecture mapping (nanoNAM) of unstained tissue sections based on the intrinsic density alteration of nuclear structure rather than the amount of stain uptake. We demonstrate that nanoNAM detects a gradual increase in the density alteration of nuclear architecture during malignant transformation in animal models of colon carcinogenesis and in human patients with ulcerative colitis, even in tissue that appears histologically normal according to pathologists. We evaluated the ability of nanoNAM to predict “future” cancer progression in patients with ulcerative colitis who did and did not develop colon cancer up to 13 years after their initial colonoscopy. NanoNAM of the initial biopsies correctly classified 12 of 15 patients who eventually developed colon cancer and 15 of 18 who did not, with an overall accuracy of 85%. Taken together, our findings demonstrate great potential for nanoNAM in predicting cancer progression risk and suggest that further validation in a multicenter study with larger cohorts may eventually advance this method to become a routine clinical test. Cancer Res; 75(22); 4718–27. ©2015 AACR.
Predictive Value of Cytokines and Immune Activation Biomarkers in AIDS-Related Non-Hodgkin Lymphoma Treated with Rituximab plus Infusional EPOCH (AMC-034 trial)
Authors: Epeldegui Marta , Lee Jeannette Y. , Martínez Anna C. , Widney Daniel P. , Magpantay Larry I. , Regidor Deborah , Mitsuyasu Ronald , Sparano Joseph A. , Ambinder Richard F. , Martínez-Maza Otoniel 
Published: September 2015

AbstractPurpose: The aims of this study were to determine whether pretreatment plasma levels of cytokines and immune activation-associated molecules changed following treatment for AIDS-NHL with rituximab plus infusional EPOCH, and to determine whether pretreatment levels of these molecules were associated with response to treatment and/or survival.Experimental Design: We quantified plasma levels of B-cell activation-associated molecules (sCD27, sCD30, and sCD23) and cytokines (IL6, IL10, and CXCL13) before and after the initiation of treatment in persons with AIDS-NHL (n = 69) in the AIDS Malignancies Consortium (AMC) 034 study, which evaluated treatment of AIDS-NHL with EPOCH chemotherapy and rituximab.Results: Treatment resulted in decreased plasma levels of some of these molecules (CXCL13, sCD27, and sCD30), with decreased levels persisting for one year following the completion of treatment. Lower levels of CXCL13 before treatment were associated with complete responses following lymphoma therapy. Elevated levels of IL6 pretreatment were associated with decreased overall survival, whereas higher IL10 levels were associated with shorter progression-free survival (PFS), in multivariate analyses. Furthermore, patients with CXCL13 or IL6 levels higher than the median levels for the NHL group, as well as those who had detectable IL10, had lower overall survival and PFS, in Kaplan–Meier analyses.Conclusions: These results indicate that CXCL13, IL6, and IL10 have significant potential as prognostic biomarkers for AIDS-NHL. Clin Cancer Res; 22(2); 328–36. ©2015 AACR.
MYC, Metabolism, and Cancer
Authors: Stine Zachary E. , Walton Zandra E. , Altman Brian J. , Hsieh Annie L. , Dang Chi V. 
Published: September 2015

Abstract
The MYC oncogene encodes a transcription factor, MYC, whose broad effects make its precise oncogenic role enigmatically elusive. The evidence to date suggests that MYC triggers selective gene expression amplification to promote cell growth and proliferation. Through its targets, MYC coordinates nutrient acquisition to produce ATP and key cellular building blocks that increase cell mass and trigger DNA replication and cell division. In cancer, genetic and epigenetic derangements silence checkpoints and unleash MYC's cell growth– and proliferation-promoting metabolic activities. Unbridled growth in response to deregulated MYC expression creates dependence on MYC-driven metabolic pathways, such that reliance on specific metabolic enzymes provides novel targets for cancer therapy.
Significance: MYC's expression and activity are tightly regulated in normal cells by multiple mechanisms, including a dependence upon growth factor stimulation and replete nutrient status. In cancer, genetic deregulation of MYC expression and loss of checkpoint components, such as TP53, permit MYC to drive malignant transformation. However, because of the reliance of MYC-driven cancers on specific metabolic pathways, synthetic lethal interactions between MYC overexpression and specific enzyme inhibitors provide novel cancer therapeutic opportunities. Cancer Discov; 5(10); 1024–39. ©2015 AACR.
Vitamin D Protects Against Atherosclerosis via Regulation of Cholesterol Efflux and Macrophage Polarization in Hypercholesterolemic Swine
Authors: Yin Kai , You Yong , Swier Vicki , Tang Lin , Radwan Mohamed M. , Pandya Amit N. , Agrawal Devendra K. 
Published: September 2015

Objective—
Prevalence of vitamin D (VD) deficiency and its association with the risk of cardiovascular disease prompted us to evaluate the effect of VD status on lipid metabolism and atherosclerosis in hypercholesterolemic microswine.

Approach and Results—

Yucatan microswine were fed with VD-deficient (0 IU/d), VD-sufficient (1000 IU/d), or VD-supplemented (3000 IU/d) high-cholesterol diet for 48 weeks. Serum lipids and 25(OH)-cholecalciferol levels were measured biweekly. Histology and biochemical parameters of liver and arteries were analyzed. Effect of 1,25(OH)
2
D
3
on cholesterol metabolism was examined in human hepatocyte carcinoma cell line (HepG2) and human monocytic cell line (THP-1) macrophage-derived foam cells. VD deficiency decreased plasma high-density lipoprotein levels, expression of liver X receptors, ATP-binding membrane cassette transporter A1, and ATP-binding membrane cassette transporter G1 and promoted cholesterol accumulation and atherosclerosis in hypercholesterolemic microswine. VD promoted nascent high-density lipoprotein formation in HepG2 cells via ATP-binding membrane cassette transporter A1–mediated cholesterol efflux. Cytochrome P450 (CYP)27B1 and VD receptor were predominantly present in the CD206
+
M2 macrophage foam cell–accumulated cores in coronary artery plaques. 1,25(OH)
2
D
3
increased the expression of liver X receptors, ATP-binding membrane cassette transporter A1, and ATP-binding membrane cassette transporter G1 and promoted cholesterol efflux in THP-1 macrophage–derived foam cells. 1,25(OH)
2
D
3
decreased intracellular free cholesterol and polarized macrophages to M2 phenotype with decreased expression of tumor necrosis factor-α, interleukin-1β, interleukin-6 under lipopolysaccharide stimulation. 1,25(OH)
2
D
3
markedly induced CYP27A1 expression via a VD receptor–dependent c-Jun N-terminal kinase (JNK) 1/2 signaling pathway and increased 27-hydroxycholesterol levels, which induced liver X receptors, ATP-binding membrane cassette transporter A1, and ATP-binding membrane cassette transporter G1 expression and stimulated cholesterol efflux that was inhibited by VD receptor antagonist and JNK1/2 signaling inhibitor in THP-1 macrophage–derived foam cell.

Conclusions—
VD protects against atherosclerosis in hypercholesterolemic swine via controlling cholesterol efflux and macrophage polarization via increased CYP27A1 activation.