bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative molecular analysis ofBursaphelenchus vallesianus, a wood‐inhabiting nematode isolated from declining pine trees in theCzechRepublic
Authors: Marek M. , Zouhar M. , Douda O. , Gaar V. , Ryšánek P. 
Published: May 2013

TheBursaphelenchusgenus (Nematoda:Parasitaphelenchidae) comprises mostly wood‐inhabiting nematodes that feed on various tree‐colonizing fungi. One species of the genus,B. xylophilus, has been proven as an agent causing pine wilt disease (PWD). However, involvement of otherBursaphelenchusspecies in thePWDremains enigmatic. In the current paper, comparative molecular analysis is performed based on nuclear ribosomalDNA(rDNA) ofB. vallesianus, a species that was recently isolated from pine trees (Pinus sylvestris) exhibiting wilting and declining symptoms in theCzechRepublic. Sequencing of the nuclear‐encodedITS1–5·8S–ITS2 rDNAregion confirmed previous taxonomic conclusions based on morphology. Evolutionary reconstructions resulted in a phylogenetic tree, where theCzech isolate ofB. vallesianusoccupied a common clade together with other species belonging to the so‐calledB. sexdentatigroup. Unexpectedly, comprehensive analysis of the sequence data revealed a genetic variation distinguishing theCzech isolate ofB. vallesianusfrom all other species of theB. sexdentatigroup. This dissimilarity consists of the presence of a four nucleotide exchange found in the 5·8S rRNA‐coding gene. The newly identified genetic variation appears to affect the 5·8S rRNAfolding, as deduced from secondary structure models. Additionally, it is shown that for the first time, to the authors’ knowledge, both bursaphelenchid internal transcribed spacers (ITS1 andITS2) fold into the multibranched closed loops. While theITS2 closed loop is formed with help of canonical 5·8S‐28SrRNApairing, theITS1 forms the thermodynamically stable closed loop with no support of flanking rRNAsequences. The current information on bursaphelenchidITSrDNAsequence diversity and structure is further discussed.
Validation of SAPS3 admission score and its customization for use in Korean intensive care unit patients: A prospective multicentre study
Authors: Lim So Yeon , Koh Shin Ok , Jeon Kyeongman , Na Sungwon , Lim Chae‐Man , Choi Won‐Il , Lee Young‐Joo , Kim Seok Chan , Chon Gyu Rak , Kim Je Hyeong , Kim Jae Yeol , Lim Jaemin , Rhee Chin Kook , Park Sunghoon , Kim Ho Cheol , Lee Jin Hwa , Lee Ji Hyun , Park Jisook , Koh Younsuck , Suh Gee Young ,   The Validation of Simplified acute physiology score 3 in Korean Intensive care unit (VSKI) study group,   Korean Study group on Respiratory Failure (KOSREF)
Published: May 2013

AbstractBackground and objectiveTo externally validate the simplified acute physiology score 3 (SAPS3) and to customize it for use in Korean intensive care unit (ICU) patients.MethodsThis is a prospective multicentre cohort study involving 22 ICUs from 15 centres throughout Korea. The study population comprised patients who were consecutively admitted to participating ICUs from 1 July 2010 to 31 January 2011.ResultsA total of 4617 patients were enrolled. ICU mortality was 14.3%, and hospital mortality was 20.6%. The patients were randomly assigned into one of two cohorts: a development (n = 2309) or validation (n = 2308) cohort. In the development cohort, the general SAPS3 had good discrimination (area under the receiver operating characteristics curve = 0.829), but poor calibration (Hosmer–Lemeshow goodness‐of‐fit test H = 123.06, P < 0.001, C = 118.45, P < 0.001). The Australasia SAPS3 did not improve calibration (H = 73.53, P < 0.001, C = 70.52, P < 0.001). Customization was achieved by altering the logit of the original SAPS3 equation. The new equation for Korean ICU patients was validated in the validation cohort, and demonstrated both good discrimination (area under the receiver operating characteristics curve = 0.835) and good calibration (H = 4.61, P = 0.799, C = 5.67, P = 0.684).ConclusionsGeneral and regional Australasia SAPS3 admission scores showed poor calibration for use in Korean ICU patients, but the prognostic power of the SAPS3 was significantly improved by customization. Prediction models should be customized before being used to predict mortality in different regions of the world.
Multiple tubulins: evolutionary aspects and biological implications
Authors: Breviario Diego , Gianì Silvia , Morello Laura 
Published: May 2013

SummaryPlant tubulin is a dimeric protein that contributes to formation of microtubules, major intracellular structures that are involved in the control of fundamental processes such as cell division, polarity of growth, cell‐wall deposition, intracellular trafficking and communications. Because it is a structural protein whose function is confined to the role of microtubule formation, tubulin may be perceived as an uninteresting gene product, but such a perception is incorrect. In fact, tubulin represents a key molecule for studying fundamental biological issues such as (i) microtubule evolution (also with reference to prokaryotic precursors and the formation of cytomotive filaments), (ii) protein structure with reference to the various biochemical features of members of theFstZ/tubulin superfamily, (iii) isoform variations contributed by the existence of multi‐gene families and various kinds of post‐translational modifications, (iv) anti‐mitotic drug interactions and mode of action, (v) plant and cell symmetry, as determined using a series of tubulin mutants, (vi) multiple and sophisticated mechanisms of gene regulation, and (vii) intron molecular evolution. In this review, we present and discuss many of these issues, and offer an updated interpretation of the multi‐tubulin hypothesis.
Cotton GhCKI disrupts normal male reproduction by delaying tapetum programmed cell death via inactivating starch synthase
Authors: Min Ling , Zhu Longfu , Tu Lili , Deng Fenglin , Yuan Daojun , Zhang Xianlong 
Published: May 2013

SummaryAnther infertility under high temperature (HT) conditions is a critical factor contributing to yield loss in cotton (Gossypium hirsutum). Using large‐scale expression profile sequencing, we studied the effect of HT on cotton anther development. Our analysis revealed that altered carbohydrate metabolism or disrupted tapetal programmed cell death (PCD) underlie anther sterility. Expression of the Gossypium hirsutum casein kinase I (GhCKI) gene, which encodes a homolog of casein kinase I (CKI), was induced in an HT‐sensitive cotton line after exposure to HT. As mammalian homologs of GhCKI are involved in inactivation of glycogen synthase and the regulation of apoptosis, GhCKI may be considered a target gene for improving anther fertility under HT conditions. Our studies suggest that GhCKI exhibits starch synthase kinase activity, increases glucose content in early‐stage buds and activates the accumulation of abscisic acid, thereby disturbing the balance of reactive oxygen species and eventually disrupting tapetal PCD, leading to anther abortion or indehiscence. These results indicate that GhCKI may be a key regulator of tapetal PCD and anther dehiscence, with the potential to facilitate regulation of HT tolerance in crops.
Trafficking of molecules between parasitic plants and their hosts
Authors: Aly R 
Published: May 2013

SummaryParasitic plants have evolved various methods of invading host plants. Some invade aerial parts, whereas others invade the roots to obtain necessary nutrients for their development. Phelipanche and Orobanche spp. (broomrapes) and Cuscuta spp. (dodders) are holoparasitic plants that subsist on roots and shoots, respectively, of a variety of agricultural crops. These weeds are able to connect directly with the vascular system of the host, thereby acquiring the water, minerals and carbohydrates necessary for their own growth and reproduction. This exploitation by parasitic plants often causes severe losses in yield quality and quantity of host crops. The key to an effective means for controlling parasitic plants lies in the development of resistant crops, supported by an improved understanding of broomrape and dodder biology. The haustoria formed at the junctions of parasite and host open the way for translocation of a variety of molecules and macromolecules from the host to the parasite. At the same time, however, the haustoria also open opportunities for the development of methods to control parasitic plants. This review will summarise the current knowledge on translocation of siRNAs, mRNAs, viruses, sugars, proteins and herbicides from host to parasitic plants and the potential significance of such molecules to the parasite. Improved understanding of the molecular exchange between host plants and their parasites is expected to lead to the development of state‐of‐the‐art, effective approaches to parasitic weed management.
Progressive cone beam CT dose control in image‐guided radiation therapy
Authors: Yan Hao , Zhen Xin , Cerviño Laura , Jiang Steve B. , Jia Xun 
Published: May 2013

Purpose:Cone beam CT (CBCT) in image‐guided radiotherapy (IGRT) offers a tremendous advantage for treatment guidance. The associated imaging dose is a clinical concern. One unique feature of CBCT‐based IGRT is that the same patient is repeatedly scanned during a treatment course, and the contents of CBCT images at different fractions are similar. The authors propose a progressive dose control (PDC) scheme to utilize this temporal correlation for imaging dose reduction.Methods:A dynamic CBCT scan protocol, as opposed to the static one in the current clinical practice, is proposed to gradually reduce the imaging dose in each treatment fraction. The CBCT image from each fraction is processed by a prior‐image based nonlocal means (PINLM) module to enhance its quality. The increasing amount of prior information from previous CBCT images prevents degradation of image quality due to the reduced imaging dose. Two proof‐of‐principle experiments have been conducted using measured phantom data and Monte Carlo simulated patient data with deformation.Results:In the measured phantom case, utilizing a prior image acquired at 0.4 mAs, PINLM is able to improve the image quality of a CBCT acquired at 0.2 mAs by reducing the noise level from 34.95 to 12.45 HU. In the synthetic patient case, acceptable image quality is maintained at four consecutive fractions with gradually decreasing exposure levels of 0.4, 0.1, 0.07, and 0.05 mAs. When compared with the standard low‐dose protocol of 0.4 mAs for each fraction, an overall imaging dose reduction of more than 60% is achieved.Conclusions:PINLM‐PDC is able to reduce CBCT imaging dose in IGRT utilizing the temporal correlations among the sequence of CBCT images while maintaining the quality.
The Clinical Viewpoint: Definitions, Limitations of RECIST, Practical Considerations of Measurement
Authors: Villaruz Liza C. , Socinski Mark A. 
Published: May 2013

Abstract
In selecting an endpoint in clinical trial design, it is important to consider that the endpoint is both reliably measured and clinically meaningful. As such, overall survival (OS) has traditionally been considered the most clinically relevant and convincing endpoint in clinical trial design as long as it is accompanied by preservation in quality of life. However, progression-free survival (PFS) is increasingly more prominent in clinical trial design because of feasibility issues (smaller sample sizes and shorter follow-up). PFS has the advantage of taking into account not only responsive disease, but stable disease as well, an issue of particular importance in the relapsed and refractory setting in which therapies are often associated with a minimal to nil response but may still confer a survival advantage. Finally, PFS has a significant advantage in molecularly selected populations, in whom OS advantages are difficult to detect due to the effects of crossover. With an understanding of the limitations and biases that are introduced with PFS as a primary endpoint, we believe that PFS is not only a viable but also a necessary alternative to OS in assessing the efficacy of selected novel-targeted therapies in molecularly defined cancer populations. Ultimately, the selection of a clinical trial endpoint should not be based on a one-size-fits all approach; rather, it should be based on the specifics of the therapeutic strategy being tested and the population under study. Clin Cancer Res; 19(10); 2629–36. ©2013 AACR.
The Imaging Viewpoint: How Imaging Affects Determination of Progression-Free Survival
Authors: Sullivan Daniel Carl , Schwartz Lawrence H. , Zhao Binsheng 
Published: May 2013

Abstract
Tumor measurements on computed tomgoraphic or MRI scans and/or the appearance of new lesions on any of a variety of imaging studies including positron emission tomographic scans are key determinants for assessing progression-free survival as an endpoint in many clinical trials of therapies for solid tumors. Test–retest tumor measurement reproducibility may vary considerably across serial scans on the same patient unless rigorous attention is paid to standardization of image acquisition parameters and unless measurements are made by trained, experienced observers using validated objective methods. Target lesion selection also must be done with care to choose lesions that are or will be reproducibly measurable. Likewise, new lesions will be missed or misinterpreted on follow-up imaging studies unless those imaging studies are obtained using techniques suitable for detecting early, small lesions. Reader variability is clearly a major component of the problem. The increasing availability of semiautomatic image processing algorithms will help ameliorate that issue. In addition, an array of internationally accepted guidelines, standards, and accreditation programs now exist to help address these problems. Clin Cancer Res; 19(10); 2621–8. ©2013 AACR.
Impact of Onset-to-Reperfusion Time on Stroke Mortality
Authors: Mazighi Mikael , Chaudhry Saqib A. , Ribo Marc , Khatri Pooja , Skoloudik David , Mokin Maxim , Labreuche Julien , Meseguer Elena , Yeatts Sharon D. , Siddiqui Adnan H. , Broderick Joseph , Molina Carlos A. , Qureshi Adnan I. , Amarenco Pierre 
Published: May 2013

Background—
Onset-to-reperfusion time has been reported to be associated with clinical prognosis. However, its impact on mortality remained to be assessed. Using a collaborative pooled analysis, we examined whether early mortality after successful endovascular treatment is time dependent.

Methods and Results—

In a collaborative pooled analysis of 7 endovascular databases, we assessed the impact of onset-to-reperfusion time in large-artery occlusion (internal carotid artery or middle cerebral artery) on outcomes. Successful reperfusion was defined as complete or partial restoration of blood flow within 8 hours from symptom onset. Primary outcome was 90-day all-cause mortality. Secondary outcomes included 90-day favorable outcome (modified Rankin Scale score, 0–2), 90-day excellent outcome (modified Rankin Scale score, 0–1), and occurrence of any intracerebral hemorrhage within 24 to 36 hours after treatment. A total of 480 cases with successful reperfusion (median time, 285 minutes) contributed to the present pooled analysis (120 with internal carotid artery occlusion and 360 with isolated middle cerebral artery occlusion). Increasing onset-to-reperfusion time was associated with an increased rate of mortality and intracerebral hemorrhage and with a decreased rate of favorable and excellent outcomes, without heterogeneity across studies. The adjusted odds ratio for each 30-minute time increase was 1.21 (95% confidence interval, 1.09–1.34;
P
<0.001) for mortality, 0.79 (95% confidence interval, 0.72–0.87) for favorable outcome, 0.78 (95% confidence interval, 0.71–0.86) for excellent outcome, and 1.21 (95% confidence interval, 1.10–1.33) for intracerebral hemorrhage.

Conclusion—
Onset-to-reperfusion time affects mortality and favorable outcome and should be considered the main goal in acute stroke patient management.
Comparison of Monthly Temperature Extremes Simulated by CMIP3 and CMIP5 Models
Authors: Yao Yao , Luo Yong , Huang Jianbin , Zhao Zongci 
Published: May 2013

AbstractThe extreme monthly-mean temperatures simulated by 28 models in the fifth phase of the Coupled Model Intercomparison Project (CMIP5) are evaluated and compared with those from 24 models in the third phase of the Coupled Model Intercomparison Project (CMIP3). Comparisons with observations and reanalyses indicate that the models from both CMIP3 and CMIP5 perform well in simulating temperature extremes, which are expressed as 20-yr return values. When the climatological annual cycle is removed, the ensemble spread in CMIP5 is smaller than that in CMIP3. Benefitting from a higher resolution, the CMIP5 models perform better at simulating extreme temperatures on the local gridcell scale. The CMIP5 representative concentration pathway (RCP4.5) and CMIP3 B1 experiments project a similar change pattern in the near future for both warm and cold extremes, and the pattern is in agreement with that of the seasonal extremes. By the late twenty-first century, the changes in monthly temperature extremes projected under the three CMIP3 (B1, A1B, and A2) and two CMIP5 (RCP4.5 and RCP8.5) scenarios generally follow the changes in climatological annual cycles, which is consistent with previous studies on daily extremes. Compared with the CMIP3 ensemble, the CMIP5 ensemble shows a larger intermodel uncertainty with regard to the change in cold extremes in snow-covered regions. Enhanced changes in extreme temperatures that exceed the global mean warming are found in regions where the retreat of snow (or the soil moisture feedback effect) plays an important role, confirming the findings for daily temperature extremes.
Observational Evidence That Enhanced Subsidence Reduces Subtropical Marine Boundary Layer Cloudiness
Authors: Myers Timothy A. , Norris Joel R. 
Published: May 2013

Abstract
Conventional wisdom suggests that subsidence favors the presence of marine stratus and stratocumulus because regions of enhanced boundary layer cloudiness are observed to climatologically co-occur with regions of enhanced subsidence. Here it is argued that the climatological positive correlation between subsidence and cloudiness is not the result of a direct physical mechanism connecting the two. Instead, it arises because enhanced subsidence is typically associated with stronger temperature inversions capping the marine boundary layer, and stronger temperature inversions favor greater cloudiness. Through statistical analysis of satellite cloud data and meteorological reanalyses for the subsidence regime over tropical (30°S–30°N) oceans, it is shown that enhanced subsidence promotes reduced cloudiness for the same value of inversion strength and that a stronger inversion favors greater cloudiness for the same value of subsidence. Using a simple conceptual model, it is argued that enhanced subsidence leads to reduced cloud thickness, liquid water path, and cloud fraction by pushing down the top of the marine boundary layer. Moreover, a stronger inversion reduces entrainment drying and warming, thus leading to a more humid boundary layer and greater cloud thickness, liquid water path, and cloud fraction. These two mechanisms typically oppose each other for geographical and seasonal cloud variability because enhanced subsidence is usually associated with stronger inversions. If global warming results in stronger inversions but weaker subsidence, the two mechanisms could both favor increased subtropical low-level cloudiness.
Assimilation of Satellite Infrared Radiances and Doppler Radar Observations during a Cool Season Observing System Simulation Experiment
Authors: Jones Thomas A. , Otkin Jason A. , Stensrud David J. , Knopfmeier Kent 
Published: May 2013

Abstract
An observing system simulation experiment is used to examine the impact of assimilating water vapor–sensitive satellite infrared brightness temperatures and Doppler radar reflectivity and radial velocity observations on the analysis accuracy of a cool season extratropical cyclone. Assimilation experiments are performed for four different combinations of satellite, radar, and conventional observations using an ensemble Kalman filter assimilation system. Comparison with the high-resolution “truth” simulation indicates that the joint assimilation of satellite and radar observations reduces errors in cloud properties compared to the case in which only conventional observations are assimilated. The satellite observations provide the most impact in the mid- to upper troposphere, whereas the radar data also improve the cloud analysis near the surface and aloft as a result of their greater vertical resolution and larger overall sample size. Errors in the wind field are also significantly reduced when radar radial velocity observations were assimilated. Overall, assimilating both satellite and radar data creates the most accurate model analysis, which indicates that both observation types provide independent and complimentary information and illustrates the potential for these datasets for improving mesoscale model analyses and ensuing forecasts.
Contrast-enhanced US quantitatively detects changes of tumor perfusion in a murine breast cancer model during adriamycin chemotherapy
Authors: Wang Jian-wei , Cao Long-hui , Han Feng , Zheng Wei , Chen Yao , Li An-hua , Zhou Jian-hua 
Published: May 2013

Background Currently used morphologic criteria have limitations in assessing tumor response to chemotherapy because of the relatively slow tumor shrinkage as measured by conventional morphologic imaging. Functional imaging techniques show promising results in early assessment of tumor response to treatment. Purpose To quantitatively detect changes in tumor perfusion during chemotherapy with contrast-enhanced ultrasound. Material and Methods Twenty-three MCF-7 breast cancer bearing nude mice treated by either adriamycin ( n = 11) or sterile saline ( n = 12) were imaged before and after treatment with an ultrasound scanner after bolus injection of SonoVue. Regions of interest within the tumor were analyzed offline to determine perfusion parameters including peak enhancement (PE), area under the curve of wash-in (WiAUC), rise time (RT), wash-in rate (WiR), wash-in perfusion index (WiPI), and quality of fit (QOF). Hematoxylin and eosin was used to assess tumor cell density and immunohistochemical analysis was performed for evaluation of microvascular density (MVD). Results Treatment with adriamycin significantly reduced tumor growth in comparison to the control group ( P < 0.001). There was no significant difference in perfusion parameters before treatment. Treatment with adriamycin resulted in a significant decrease in PE, WiAUC, WiR, and WiPI in comparison with control group ( P < 0.01). The tumor cell density estimated by pathology slice was significantly lower in treated tumors than in control tumors after treatment ( P < 0.001). Immunohistochemistry showed significant decreases of MVD in treated tumors as compared with control tumors ( P < 0.001) after treatment. Conclusion Quantitative contrast-enhanced ultrasound can detect the change of tumor perfusion after chemotherapy, which may enable early assess tumor response to chemotherapy.