bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterising the Strain and Temperature Fields in a Surrogate Bone Material Subject to Power Ultrasonic Excitation
Authors: Wang D. , Lucas M. , Tanner K. E. 
Published: August 2013

ABSTRACTThe behaviour of the cancellous bone surrogate material, rigid polyurethane foam (PUF), subject to power ultrasonic vibration excitation has been studied, with the purpose of identifying a methodology to investigate the effects that ultrasonic surgical devices have on biological tissue materials. To characterise the vibrational response to ultrasonic excitation, non‐contact measurement of the full in‐plane displacement field of PUF plate specimens was performed by combining the use of an ultra‐high speed camera and 2D digital image correlation. To investigate the thermal response, an infrared camera was used in real time to detect the temperature field. The measured surface displacement and strain fields of the PUF specimens and the thermal response are compared with data from an analytical model, and two different finite element models using Abaqus and PZFlex. The close agreement between calculated and measured data provides initial confidence in the use of the models for predicting the effects of ultrasonic excitation on tissue materials. The measurement data demonstrate the success of the experimental method for measuring vibrational responses in a hard tissue surrogate material at the ultrasonic frequencies associated with power ultrasonic surgical devices.
AtMBP‐1, an alternative translation product of LOS2, affects abscisic acid responses and is modulated by the E3 ubiquitin ligase AtSAP5
Authors: Kang Miyoung , Abdelmageed Haggag , Lee Seonghee , Reichert Angelika , Mysore Kirankumar S. , Allen Randy D. 
Published: August 2013

SummaryThe LOS2 gene in Arabidopsis encodes an enolase with 72% amino acid sequence identity with human ENO1. In mammalian cells, the α‐enolase (ENO1) gene encodes both a 48 kDa glycolytic enzyme and a 37 kDa transcriptional suppressor protein that are targeted to different cellular compartments. The tumor suppressor c‐myc binding protein (MBP‐1), which is alternatively translated from the second start codon of ENO1 transcripts, is preferentially localized in nuclei while α‐enolase is found in the cytoplasm. We report here that an Arabidopsis MBP‐1‐like protein (AtMBP‐1) is alternatively translated from full‐length LOS2 transcripts using a second start codon. Like mammalian MBP‐1, this truncated form of LOS2 has little, if any, enolase activity, indicating that an intact N‐terminal region of LOS2 is critical for catalysis. AtMBP‐1 has a short half‐life in vivo and is stabilized by the proteasome inhibitor MG132, indicating that it is degraded via the ubiquitin‐dependent proteasome pathway. Arabidopsis plants that over‐express AtMBP‐1 are hypersensitive to abscisic acid (ABA) during seed germination and show defects in vegetative growth and lateral stem development. AtMBP‐1 interacts directly with the E3 ubiquitin ligase AtSAP5 and co‐expression of these proteins resulted in destabilization of AtMBP‐1 in vivo and abolished the developmental defects associated with AtMBP‐1 over‐expression. Thus, AtMBP‐1 is as a bona fide alternative translation product of LOS2. Accumulation of this factor is limited by ubiquitin‐dependent destabilization, apparently mediated by AtSAP5.
A unified statistical framework for material decomposition using multienergy photon counting x‐ray detectors
Authors: Choi Jiyoung , Kang Dong‐Goo , Kang Sunghoon , Sung Younghun , Ye Jong Chul 
Published: August 2013

Purpose:Material decomposition using multienergy photon counting x‐ray detectors (PCXD) has been an active research area over the past few years. Even with some success, the problem of optimal energy selection and three material decomposition including malignant tissue is still on going research topic, and more systematic studies are required. This paper aims to address this in a unified statistical framework in a mammographic environment.Methods:A unified statistical framework for energy level optimization and decomposition of three materials is proposed. In particular, an energy level optimization algorithm is derived using the theory of the minimum variance unbiased estimator, and an iterative algorithm is proposed for material composition as well as system parameter estimation under the unified statistical estimation framework. To verify the performance of the proposed algorithm, the authors performed simulation studies as well as real experiments using physical breast phantom andex vivo breast specimen. Quantitative comparisons using various performance measures were conducted, and qualitative performance evaluations for ex vivo breast specimen were also performed by comparing the ground‐truth malignant tissue areas identified by radiologists.Results:Both simulation and real experiments confirmed that the optimized energy bins by the proposed method allow better material decomposition quality. Moreover, for the specimen thickness estimation errors up to 2 mm, the proposed method provides good reconstruction results in both simulation and realex vivo breast phantom experiments compared to existing methods.Conclusions:The proposed statistical framework of PCXD has been successfully applied for the energy optimization and decomposition of three material in a mammographic environment. Experimental results using the physical breast phantom andex vivo specimen support the practicality of the proposed algorithm.
Genome Sequence of the Autotrophic Acetogen
Clostridium autoethanogenum
JA1-1 Strain DSM 10061, a Producer of Ethanol from Carbon Monoxide
Authors: Bruno-Barcena José M. , Chinn Mari S. , Grunden Amy M. 
Published: August 2013

ABSTRACT

Clostridium autoethanogenum
is an anaerobic, autotrophic acetogen that is capable of converting CO and CO
2
into ethanol and acetate. Here we report the draft genome sequence of
C. autoethanogenum
JA1-1 strain DSM 10061 (4.5 Mbp; G+C content, 37.5%) and the findings obtained from annotation of the genome sequence.
Draft Genome Sequence of Geobacillus kaustophilus GBlys, a Lysogenic Strain with Bacteriophage ϕOH2
Authors: Doi Katsumi , Mori Kazuki , Martono Hindra , Nagayoshi Yuko , Fujino Yasuhiro , Tashiro Kosuke , Kuhara Satoru , Ohshima Toshihisa 
Published: August 2013

ABSTRACT

Geobacillus kaustophilus
strain GBlys was isolated along with the bacteriophage ϕOH2, which infects
G. kaustophilus
NBRC 102445
T
. Here we present a draft sequence of this strain's genome, which consists of 216 contigs for a total of 3,541,481 bp, 3,679 predicted coding sequences, and a G+C content of 52.1%.
Genome Sequence of the Probiotic Strain Lactobacillus rhamnosus (Formerly Lactobacillus casei) LOCK900
Authors: Aleksandrzak-Piekarczyk Tamara , Koryszewska-Bagińska Anna , Bardowski Jacek 
Published: August 2013

ABSTRACT

Lactobacillus rhamnosus
LOCK900 fulfills the criteria required for probiotic strains. In this study, we report a whole-genome sequence of this isolate and compare it with other
L. rhamnosus
complete genome sequences already published.
MicroRNA-218 Inhibits Glioma Invasion, Migration, Proliferation, and Cancer Stem-like Cell Self-Renewal by Targeting the Polycomb Group Gene Bmi1
Authors: Tu Yanyang , Gao Xingchun , Li Gang , Fu Hualin , Cui Daxiang , Liu Hui , Jin Weilin , Zhang Yongsheng 
Published: August 2013

Abstract
Malignant gliomas are the most common central nervous system tumors and the molecular mechanism driving their development and recurrence is still largely unknown, limiting the treatment of this disease. Here, we show that restoring the expression of miR-218, a microRNA commonly downregulated in glioma, dramatically reduces the migration, invasion, and proliferation of glioma cells. Quantitative reverse transcription PCR and Western blotting analysis revealed that expression of the stem cell-promoting oncogene Bmi1 was decreased after overexpression of miR-218 in glioma cells. Mechanistic investigations defined Bmi1 as a functional downstream target of miR-218 through which miR-218 ablated cell migration and proliferation. We documented that miR-218 also blocked the self-renewal of glioma stem-like cells, consistent with the suggested role of Bmi1 in stem cell growth. Finally, we showed that miR-218 regulated a broad range of genes involved in glioma cell development, including Wnt pathways that suppress glioma cell stem-like qualities. Taken together, our findings reveal miR-218 as a tumor suppressor that prevents migration, invasion, proliferation, and stem-like qualities in glioma cells. Cancer Res; 73(19); 6046–55. ©2013 AACR.
Intraindividual Variation in One-Carbon Metabolism Plasma Biomarkers
Authors: Cope Elizabeth L. , Shrubsole Martha J. , Cohen Sarah S. , Cai Qiuyin , Wu Jie , Ueland Per Magne , Midttun Øivind , Sonderman Jennifer S. , Blot William J. , Signorello Lisa B. 
Published: August 2013

Abstract
Interest in the relationship between one-carbon metabolism (OCM) and carcinogenesis is intensifying, leading to increased use of related biomarkers as measures of exposure. Little is known, however, about the intraindividual variation in these markers and whether or not the use of a single measure is appropriate for assessing exposure–disease relationships in epidemiologic studies. We evaluated the intraindividual variation in plasma concentrations of 19 OCM biomarkers in a sample of 147 African American and 68 non-Hispanic white participants from the Southern Community Cohort Study who donated blood samples and responded to questionnaires at two time points from 2005 to 2008. Weighted kappa coefficients (κ) were calculated to assess the agreement between quartile assignments based on the repeated measures. Adjusted intraclass correlation coefficients (ICC) were also used to assess the consistency of the two measurements. Most (16/19) OCM biomarkers showed a moderate or better agreement for quartile assignment at the two time points, with only methionine, methionine sulfoxide, and cystathionine having κ ≤ 0.40. The median-adjusted ICC across the 19 biomarkers was 0.60. Reproducibility was highest for flavin mononucleotide [ICC = 0.84, 95% confidence interval (CI), 0.79–0.87] and lowest for methionine and its oxidative product methionine sulfoxide (ICC = 0.22, 95% CI 0.09–0.34; ICC = 0.20, 95% CI 0.07–0.32, respectively). Overall, the intraindividual variation in OCM biomarkers was similar for African Americans and whites and for males and females. Our results suggest that with the exception of methionine and methionine sulfoxide, OCM biomarkers generally have good intraindividual reproducibility and can be considered as reliable exposure measures in epidemiologic studies. Cancer Epidemiol Biomarkers Prev; 22(10); 1894–9. ©2013 AACR.
Melanoma Genetic Counseling and Test Reporting Improve Screening Adherence Among Unaffected Carriers 2 Years Later
Authors: Aspinwall Lisa G. , Taber Jennifer M. , Leaf Samantha L. , Kohlmann Wendy , Leachman Sancy A. 
Published: August 2013

AbstractBackground: A major goal of predictive genetic testing for melanoma is to promote early detection to reduce mortality. This study evaluated the long-term impact of melanoma genetic test reporting and counseling on screening adherence.Methods: This study assessed adherence to recommendations for annual total body skin examinations (TBSE) and monthly skin self-examinations (SSE) among 37 members of Utah CDKN2A/p16 kindreds (10 unaffected carriers, 11 affected carriers, and 16 unaffected noncarriers; response rate = 64.9% of eligible participants).Results: Two years following test reporting, adherence to annual TBSE among unaffected carriers increased from 40% to 70%. However, unaffected noncarriers' adherence decreased from 56% to 13%. Affected carriers reported TBSEs at both assessments (91% and 82%, respectively). Monthly SSE frequency remained highly variable in all patient groups: at 2 years, 29.7% reported monthly SSEs, 27.0% reported more frequent self-examinations, and 43.2% reported underscreening. However, SSE quality improved significantly: participants checked more body sites at 2 years than at baseline, especially feet, shoulders, legs, and genitals. Perceived logistic barriers to TBSEs (e.g., expensive, inconvenient) and SSEs (hard to remember, time-consuming) predicted lower adherence.Conclusions: Unaffected carriers reported increased TBSE adherence and thoroughness of SSEs 2 years following melanoma genetic test reporting, suggesting clinical benefit in this modest sample. Unaffected noncarriers reported comparable gains in SSE thoroughness, but decreased TBSEs.Impact: Melanoma genetic counseling and test reporting may improve adherence among unaffected carrier members of p16 families. Further interventions to reduce logistic barriers and to promote continued screening adherence among unaffected noncarrier family members may be needed. Cancer Epidemiol Biomarkers Prev; 22(10); 1687–97. ©2013 AACR.
Human Breast Cancer Cells Harboring a Gatekeeper T798M Mutation in HER2 Overexpress EGFR Ligands and Are Sensitive to Dual Inhibition of EGFR and HER2
Authors: Rexer Brent N. , Ghosh Ritwik , Narasanna Archana , Estrada Mónica Valeria , Chakrabarty Anindita , Song Youngchul , Engelman Jeffrey A. , Arteaga Carlos L. 
Published: August 2013

Abstract
Purpose: Mutations in receptor tyrosine kinase (RTK) genes can confer resistance to receptor-targeted therapies. A T798M mutation in the HER2 oncogene has been shown to confer resistance to the tyrosine kinase inhibitor (TKI) lapatinib. We studied the mechanisms of HER2-T798M–induced resistance to identify potential strategies to overcome that resistance.
Experimental Design: HER2-T798M was stably expressed in BT474 and MCF10A cells. Mutant cells and xenografts were evaluated for effects of the mutation on proliferation, signaling, and tumor growth after treatment with combinations of inhibitors targeting the EGFR/HER2/HER3/PI3K axis.
Results: A low 3% allelic frequency of the T798M mutant shifted 10-fold the IC50 of lapatinib. In mutant-expressing cells, lapatinib did not block basal phosphorylation of HER2, HER3, AKT, and ERK1/2. In vitro kinase assays showed increased autocatalytic activity of HER2-T798M. HER3 association with PI3K p85 was increased in mutant-expressing cells. BT474-T798M cells were also resistant to the HER2 antibody trastuzumab. These cells were sensitive to the pan-PI3K inhibitors BKM120 and XL147 and the irreversible HER2/EGFR TKI afatinib but not the MEK1/2 inhibitor CI-1040, suggesting continued dependence of the mutant cells on ErbB receptors and downstream PI3K signaling. BT474-T798M cells showed increased expression of the EGFR ligands EGF, TGFα, amphiregulin, and HB-EGF. Addition of the EGFR neutralizing antibody cetuximab or lapatinib restored trastuzumab sensitivity of BT474-T798M cells and xenografts, suggesting that increased EGFR ligand production was causally associated with drug resistance.
Conclusions: Simultaneous blockade of HER2 and EGFR should be an effective treatment strategy against HER2 gene–amplified breast cancer cells harboring T798M mutant alleles. Clin Cancer Res; 19(19); 5390–401. ©2013 AACR.
Maternal Hypercholesterolemia in Pregnancy Associates With Umbilical Vein Endothelial Dysfunction
Authors: Leiva Andrea , de Medina Camila Diez , Salsoso Rocío , Sáez Tamara , San Martín Sebastián , Abarzúa Fernando , Farías Marcelo , Guzmán-Gutiérrez Enrique , Pardo Fabián , Sobrevia Luis 
Published: August 2013

Objective—

Human pregnancy that courses with maternal supraphysiological hypercholesterolemia (MSPH) correlates with atherosclerotic lesions in fetal arteries. It is known that hypercholesterolemia associates with endothelial dysfunction in adults, a phenomenon where nitric oxide (NO) and arginase are involved. However, nothing is reported on potential alterations in the fetoplacental endothelial function in MSPH. The aim of this study was to determine whether MSPH alters fetal vascular reactivity via endothelial arginase/urea and
l
-arginine transport/NO signaling pathways.

Approach and Results—

Total cholesterol <280 mg/dL was considered as maternal physiological hypercholesterolemia (n=46 women) and ≥280 mg/dL as MSPH (n=28 women). Maternal but not fetal total cholesterol and low-density lipoprotein-cholesterol levels were elevated in MSPH. Umbilical veins were used for vascular reactivity assays (wire myography), and primary cultures of umbilical vein endothelial cells to determine arginase, endothelial NO synthase (eNOS), and human cationic amino acid transporter 1 and human cationic amino acid transporter 2A/B expression and activity. MSPH reduced calcitonine gene–related peptide-umbilical vein relaxation and increased intima/media ratio (histochemistry), as well as reduced eNOS activity (
l
-citrulline synthesis from
l
-arginine, eNOS phosphorylation/dephosphorylation), but increased arginase activity and arginase II protein abundance. Arginase inhibition increased eNOS activity and
l
-arginine transport capacity without altering human cationic amino acid transporter 1 or human cationic amino acid transporter 2A/B protein abundance in maternal physiological hypercholesterolemia and MSPH.

Conclusions—
MSPH is a pathophysiological condition altering umbilical vein reactivity because of fetal endothelial dysfunction associated with arginase and eNOS signaling imbalance. We speculate that elevated maternal circulating cholesterol is a factor leading to fetal endothelial dysfunction, which could have serious consequences to the growing fetus.
Overexpression of Catalase in Vascular Smooth Muscle Cells Prevents the Formation of Abdominal Aortic Aneurysms
Authors: Parastatidis Ioannis , Weiss Daiana , Joseph Giji , Taylor W. Robert 
Published: August 2013

Objective—

Elevated levels of oxidative stress have been reported in abdominal aortic aneurysms (AAA), but which reactive oxygen species promotes the development of AAA remains unclear. Here, we investigate the effect of hydrogen peroxide (H
2
O
2
)–degrading enzyme catalase on the formation of AAA.

Approach and Results—

AAA were induced with the application of calcium chloride (CaCl
2
) on mouse infrarenal aortas. The administration of PEG-catalase, but not saline, attenuated the loss of tunica media and protected against AAA formation (0.91±0.1 versus 0.76±0.09 mm). Similarly, in a transgenic mouse model, catalase overexpression in the vascular smooth muscle cells preserved the thickness of tunica media and inhibited aortic dilatation by 50% (0.85±0.14 versus 0.57±0.08 mm). Further studies showed that injury with CaCl
2
decreased catalase expression and activity in the aortic wall. Pharmacological administration or genetic overexpression of catalase restored catalase activity and subsequently decreased matrix metalloproteinase activity. In addition, a profound reduction in inflammatory markers and vascular smooth muscle cell apoptosis was evident in aortas of catalase-overexpressing mice. Interestingly, as opposed to infusion of PEG-catalase, chronic overexpression of catalase in vascular smooth muscle cells did not alter the total aortic H
2
O
2
levels.

Conclusions—
The data suggest that a reduction in aortic wall catalase activity can predispose to AAA formation. Restoration of catalase activity in the vascular wall enhances aortic vascular smooth muscle cell survival and prevents AAA formation primarily through modulation of matrix metalloproteinase activity.
Human secondary lymphoid organs typically contain polyclonally-activated proliferating regulatory T cells
Authors: Peters Jorieke H. , Koenen Hans J. P. M. , Fasse Esther , Tijssen Henk J. , IJzermans Jan N. M. , Groenen Patricia J. T. A. , Schaap Nicolaas P. M. , Kwekkeboom Jaap , Joosten Irma 
Published: August 2013

Key Points
The majority of suppressive Tregs in human secondary lymphoid organs are activated, produce cytokines, and proliferate. Human lymphoid organs may provide a platform for in vivo expansion of infused Tregs and subsequent tissue-directed homing.
Costs of tuberculosis disease in the European Union: a systematic analysis and cost calculation
Authors: Diel Roland , Vandeputte Joris , de Vries Gerard , Stillo Jonathan , Wanlin Maryse , Nienhaus Albert 
Published: August 2013

Without better vaccines it is unlikely that tuberculosis (TB) will ever be eliminated. An investment of ∼€560 million is considered necessary to develop a new, effective vaccine in the European Union (EU). However, less is known about the costs of TB disease in the EU. We performed a systematic review of literature and institutional websites addressing the 27 EU members to summarise cost data. We searched MEDLINE, EMBASE and Cochrane bibliographies for relevant articles.Combining direct and indirect costs, we arrived at an average per-TB case costs in the original EU-15 states plus Cyprus, Malta and Slovenia of €10 282 for drug-susceptible TB, €57 213 for multidrug resistant (MDR)-TB and €170 744 for extensively drug resistant (XDR)-TB. In the remaining new EU states, costs amounted to €3427 for drug-susceptible TB and €24 166 for MDR-TB/XDR-TB. For the 70 340 susceptible TB cases, 1488 MDR-TB and 136 XDR-TB cases notified in 2011 costs of €536 890 315 accumulated in 2012. In the same year, the 103 104 disability-adjusted life years caused by these cases, when stated in monetary terms, amounted to a total of €5 361 408 000.Thus, the resulting economic burden of TB in the EU clearly outweighs the cost of investing in more efficient vaccines against TB.
Comparative analysis of non-coding RNAs in the antibiotic-producing Streptomyces bacteria
Authors: Moody Matthew J , Young Rachel A , Jones Stephanie E , Elliot Marie A 
Published: August 2013

Abstract

Background
Non-coding RNAs (ncRNAs) are key regulatory elements that control a wide range of cellular processes in all bacteria in which they have been studied. Taking advantage of recent technological innovations, we set out to fully explore the ncRNA potential of the multicellular, antibiotic-producing Streptomyces bacteria.

Results
Using a comparative RNA sequencing analysis of three divergent model streptomycetes (S. coelicolor, S. avermitilis and S. venezuelae), we discovered hundreds of novel cis-antisense RNAs and intergenic small RNAs (sRNAs). We identified a ubiquitous antisense RNA species that arose from the overlapping transcription of convergently-oriented genes; we termed these RNA species ‘cutoRNAs’, for c onvergent u nt ranslated o verlapping RNAs. Conservation between different classes of ncRNAs varied greatly, with sRNAs being more conserved than antisense RNAs. Many species-specific ncRNAs, including many distinct cutoRNA pairs, were located within antibiotic biosynthetic clusters, including the actinorhodin, undecylprodigiosin, and coelimycin clusters of S. coelicolor, the chloramphenicol cluster of S. venezuelae, and the avermectin cluster of S. avermitilis.

Conclusions
These findings indicate that ncRNAs, including a novel class of antisense RNA, may exert a previously unrecognized level of regulatory control over antibiotic production in these bacteria. Collectively, this work has dramatically expanded the ncRNA repertoire of three Streptomyces species and has established a critical foundation from which to investigate ncRNA function in this medically and industrially important bacterial genus.