bluuebunny/crossref_metadata_2025_split huggingface dataset:
Observed Local and Remote Influences of Vegetation on the Atmosphere across North America Using a Model-Validated Statistical Technique That First Excludes Oceanic Forcings*
Authors: Wang Fuyao , Notaro Michael , Liu Zhengyu , Chen Guangshan 
Published: September 2013

Abstract
The observed local and nonlocal influences of vegetation on the atmosphere across North America are quantified after first removing the oceanic impact. The interaction between vegetation and the atmosphere is dominated by forcing from the atmosphere, making it difficult to extract the forcing from vegetation. Furthermore, the atmosphere is not only influenced by vegetation but also the oceans, so in order to extract the vegetation impact, the oceanic forcing must first be excluded. This study identified significant vegetation impact in two climatically and ecologically unique regions: the North American monsoon region (NAMR) and the North American boreal forest (NABF). A multivariate statistical method, a generalized equilibrium feedback assessment, is applied to extract vegetation influence on the atmosphere. The statistical method is validated using a dynamical experiment for the NAMR in a fully coupled climate model, the Community Climate System Model, version 3.5 (CCSM3.5).
The observed influence of NAMR vegetation on the atmosphere peaks in June–August and is primarily attributed to both roughness and hydrological feedbacks. Elevated vegetation amount increases evapotranspiration and surface roughness, which leads to a local decline in sea level pressure and generates an atmospheric teleconnection response. This atmospheric response leads to moister and cooler (drier and warmer) conditions over the western and central United States (Gulf states). The observed influence of the NABF on the atmosphere peaks in March–May, related to a thermal feedback. Enhanced vegetation greenness increases the air temperature locally. The atmosphere tends to form a positive Pacific–North American (PNA)-like pattern, and this anomalous atmospheric circulation and associated moisture advection lead to moister (drier) conditions in the western (eastern) United States.
Fitting Parametric Vortices to Aliased Doppler Velocities Scanned from Hurricanes
Authors: Xu Qin , Jiang Yuan , Liu Liping 
Published: September 2013

AbstractAn alias-robust least squares method that produces less errors than established methods is developed to produce reference radial velocities for automatically correcting raw aliased Doppler velocities scanned from hurricanes. This method estimates the maximum tangential velocity VM and its radial distance RM from the hurricane vortex center by fitting a parametric vortex model directly to raw aliased velocities at and around each selected vertical level. In this method, aliasing-caused zigzag discontinuities in the relationship between the observed and true radial velocities are formulated into the cost function by applying an alias operator to the entire analysis-minus-observation term to ensure the cost function to be smooth and concave around the global minimum. Simulated radar velocity observations are used to examine the cost function geometry around the global minimum in the space of control parameters (VM, RM). The results show that the global minimum point can estimate the true (VM, RM) approximately if the hurricane vortex center location is approximately known and the hurricane core and vicinity areas are adequately covered by the radar scans, and the global minimum can be found accurately by an efficient descent algorithm as long as the initial guess is in the concave vicinity of the global minimum. The method is used with elaborated refinements for automated dealiasing, and this utility is highlighted by an example applied to severely aliased radial velocities scanned from a hurricane.
Patient-Reported Outcomes Following Flexible Sigmoidoscopy Screening for Colorectal Cancer in a Demonstration Screening Programme in the Uk
Authors: Robb Kathryn A. , Lo Siu Hing , Power Emily , Kralj-Hans Ines , Edwards Robert , Vance Maggie , Von Wagner Christian , Atkin Wendy , Wardle Jane 
Published: September 2013

Objectives Flexible sigmoidoscopy (FS) screening for colorectal cancer will be introduced into the National Cancer Screening Programmes in England in 2013. Patient-reported outcome measures (PROMs) from trial participants indicate high acceptability and no adverse physical or psychological consequences, but this may not generalize to routine screening in the community. This study examined PROMs in a community-based FS screening programme. Methods Eligible adults aged 58–59 ( n = 2016) registered at 34 London general practices were mailed a National Health Service-endorsed invitation to attend FS screening. Pain and side-effects were assessed in a ‘morning-after’ questionnaire, and satisfaction was assessed in a three-month follow-up questionnaire. Anxiety, self-rated health and colorectal symptoms were assessed at prescreening and follow-up. Results In total, 1020 people attended screening and were included in the current analyses, of whom 913 (90%) returned the morning-after questionnaire, and 674 (66%) the follow-up questionnaire. The prescreening questionnaire had been completed by 751 (74%) of those who attended. The majority (87%) of respondents reported no pain or mild pain, and the most frequent side-effect (wind) was only experienced more than mildly by 16%. Satisfaction was extremely high, with 98% glad they had the test; 97% would encourage a friend to have it. From prescreening to follow-up there were no changes in anxiety or self-rated health, and the number of colorectal symptoms declined. Satisfaction and changes in wellbeing were not moderated by gender, deprivation, ethnicity or screening outcome. Conclusions PROMs indicate high acceptability of FS screening in 58–59 year olds, with no adverse effects on colorectal symptoms, health status or psychological wellbeing.
Integrating biomarker information within trials to evaluate treatment mechanisms and efficacy for personalised medicine
Authors: Dunn Graham , Emsley Richard , Liu Hanhua , Landau Sabine 
Published: September 2013

Background The development of personalised (stratified) medicine is intrinsically dependent on an understanding of treatment-effect mechanisms (effects on therapeutic targets that mediate the effect of the treatment on clinical outcomes). There is a need for clinical trial data for the joint evaluation of treatment efficacy, the utility of predictive markers as indicators of treatment efficacy, and the mediational mechanisms proposed as the explanation of these effects. Purpose (1) To review the problem of confounding (common causes) for the drawing of valid inferences concerning treatment-effect mechanisms, even when the data have been generated using a randomised controlled trial, and (2) to suggest and illustrate solutions to this problem of confounding. Results We illustrate the potential of the predictive biomarker stratified design, together with baseline measurement of all known prognostic markers, to enable us to evaluate both the utility of the predictive biomarker in such a stratification and, perhaps more importantly, to estimate how much of the treatment’s effect is actually explained by changes in the putative mediator. The analysis strategy involves the use of instrumental variable (IV) regression, using the treatment by predictive biomarker interaction as an IV – a refined, much more powerful, and (in the present context) subtle use of Mendelian randomisation. Conclusion Personalised (stratified) medicine and treatment-effect mechanisms evaluation are inextricably linked. Stratification without corresponding mechanisms evaluation lacks credibility. In the presence of mediator-outcome confounding, mechanisms evaluation is dependent on stratification for its validity. Both stratification and treatment-effect mediation can be evaluated using a biomarker stratified trial design together with detailed baseline measurement of all known prognostic biomarkers and other prognostic covariates. Direct and indirect (mediated) effects should be estimated through the use of IV methods (the IV being the predictive marker by treatment interaction) together with adjustments for all known prognostic markers (confounders) – the latter adjustments contributing to increased precision (as in a conventional analysis of treatment effects) rather than bias reduction.
Population structure of Wolbachia and cytoplasmic introgression in a complex of mosquito species
Authors: Dumas Emilie , Atyame Célestine M , Milesi Pascal , Fonseca Dina M , Shaikevich Elena V , Unal Sandra , Makoundou Patrick , Weill Mylène , Duron Olivier 
Published: September 2013

AbstractBackgroundThe maternally inherited bacteriumWolbachiaoften acts as a subtle parasite that manipulates insect reproduction, resulting potentially in reproductive isolation between host populations. Whilst distinctWolbachiastrains are documented in a group of evolutionarily closely related mosquitoes known as theCulex pipienscomplex, their impact on mosquito population genetics remains unclear. To this aim, we developed a PCR-RFLP test that discriminates the five knownWolbachiagroups found in this host complex. We further examined theWolbachiagenetic diversity, the variability in the coinherited host mitochondria and their partitioning among members of theCx. pipienscomplex, in order to assess the impact ofWolbachiaon host population structure.ResultsThere was a strong association betweenWolbachiaand mitochondrial haplotypes indicating a stable co-transmission in mosquito populations. Despite evidence that members of theCx. pipienscomplex are genetically distinct on the basis of nuclear DNA, the association ofWolbachiaand mtDNA with members of theCx. pipienscomplex were limited. TheWolbachia wPip-I group, by far the most common, was associated with divergentCx. pipiensmembers, includingCx. quinquefasciatus,Cx. pipiens pipiensformpipiensandCx. pipiens pipiensformmolestus. Four otherwPip groups were also found in mosquito populations and all were shared between diverseCx. pipiensmembers.ConclusionThis data overall supports the hypothesis thatwPip infections, and their allied mitochondria, are associated with regular transfers betweenCx. pipiensmembers rather than specific host associations. Overall, this is suggestive of a recent and likely ongoing cytoplasmic introgression through hybridization events across theCx. pipienscomplex.
Health risk appraisal in older people 6: factors associated with self-reported poor vision and uptake of eye tests in older people
Authors: Iliffe Steve , Kharicha Kalpa , Harari Danielle , Swift Cameron , Gillmann Gerhard , Stuck Andreas E 
Published: September 2013

Abstract

Background
Although free eye testing is available in the UK from a nation-wide network of optometrists, there is evidence of unrecognised, tractable vision loss amongst older people. A recent review identified this unmet need as a priority for further investigation, highlighting the need to understand public perceptions of eye services and barriers to service access and utilisation. This paper aims to identify risk factors for (1) having poor vision and (2) not having had an eyesight check among community-dwelling older people without an established ophthalmological diagnosis.

Methods
Secondary analysis of self-reported data from the ProAge trial. 1792 people without a known ophthalmological diagnosis were recruited from three group practices in London.

Results
Almost two in ten people in this population of older individuals without known ophthalmological diagnoses had self-reported vision loss, and more than a third of them had not had an eye test in the previous twelve months. In this sample, those with limited education, depressed mood, need for help with instrumental and basic activities of daily living (IADLs and BADLs), and subjective memory complaints were at increased risk of fair or poor self-reported vision. Individuals with basic education only were at increased risk for not having had an eye test in the previous 12 months (OR 1.52, 95% CI 1.17-1.98 p=0.002), as were those with no, or only one chronic condition (OR 1.850, 95% CI 1.382-2.477, p<0.001).

Conclusions
Self-reported poor vision in older people without ophthalmological diagnoses is associated with other functional losses, with no or only one chronic condition, and with depression. This pattern of disorders may be the basis for case finding in general practice. Low educational attainment is an independent determinant of not having had eye tests, as well as a factor associated with undiagnosed vision loss. There are other factors, not identified in this study, which determine uptake of eye testing in those with self-reported vision loss. Further exploration is needed to identify these factors and lead towards effective case finding.
Joint pain severity predicts premature discontinuation of aromatase inhibitors in breast cancer survivors
Authors: Chim Kannie , Xie Sharon X , Stricker Carrie T , Li Qing S , Gross Robert , Farrar John T , DeMichele Angela , Mao Jun J 
Published: September 2013

Abstract

Background
Premature discontinuation of aromatase inhibitors (AIs) in breast cancer survivors compromises treatment outcomes. We aimed to evaluate whether patient-reported joint pain predicts premature discontinuation of AIs.

Methods
We conducted a retrospective cohort study of postmenopausal women with breast cancer on AIs who had completed a survey about their symptom experience on AIs with specific measurements of joint pain. The primary outcome was premature discontinuation of AIs, defined as stopping the medication prior to the end of prescribed therapy. Multivariate Cox regression modeling was used to identify predictors of premature discontinuation.

Results
Among 437 patients who met eligibility criteria, 47 (11%) prematurely discontinued AIs an average of 29 months after initiation of therapy. In multivariate analyses, patient-reported worst joint pain score of 4 or greater on the Brief Pain Inventory (BPI) (Hazard Ratio [HR] 2.09, 95% Confidence Interval [CI] 1.14-3.80, P = 0.016) and prior use of tamoxifen (HR 2.01, 95% CI 1.09-3.70, P = 0.026) were significant predictors of premature discontinuation of AIs. The most common reason for premature discontinuation was joint pain (57%) followed by other therapy-related side effects (30%). While providers documented joint pain in charts for 82% of patients with clinically important pain, no quantitative pain assessments were noted, and only 43% provided any plan for pain evaluation or management.

Conclusion
Worst joint pain of 4 or greater on the BPI predicts premature discontinuation of AI therapy. Clinicians should monitor pain severity with quantitative assessments and provide timely management to promote optimal adherence to AIs.
Systematic screening of glycosylation- and trafficking-associated gene knockouts in Saccharomyces cerevisiaeidentifies mutants with improved heterologous exocellulase activity and host secretion
Authors: Wang Tzi-Yuan , Huang Chih-Jen , Chen Hsin-Liang , Ho Po-Chun , Ke Huei-Mien , Cho Hsing-Yi , Ruan Sz-Kai , Hung Kuo-Yen , Wang I-Li , Cai Ya-Wun , Sung Huang-Mo , Li Wen-Hsiung , Shih Ming-Che 
Published: September 2013

Abstract

Background
As a strong fermentator, Saccharomyces cerevisiae has the potential to be an excellent host for ethanol production by consolidated bioprocessing. For this purpose, it is necessary to transform cellulose genes into the yeast genome because it contains no cellulose genes. However, heterologous protein expression in S. cerevisiae often suffers from hyper-glycosylation and/or poor secretion. Thus, there is a need to genetically engineer the yeast to reduce its glycosylation strength and to increase its secretion ability.

Results

Saccharomyces cerevisiae gene-knockout strains were screened for improved extracellular activity of a recombinant exocellulase (PCX) from the cellulose digesting fungus Phanerochaete chrysosporium. Knockout mutants of 47 glycosylation-related genes and 10 protein-trafficking-related genes were transformed with a PCX expression construct and screened for extracellular cellulase activity. Twelve of the screened mutants were found to have a more than 2-fold increase in extracellular PCX activity in comparison with the wild type. The extracellular PCX activities in the glycosylation-related mnn10 and pmt5 null mutants were, respectively, 6 and 4 times higher than that of the wild type; and the extracellular PCX activities in 9 protein-trafficking-related mutants, especially in the chc1, clc1 and vps21 null mutants, were at least 1.5 times higher than the parental strains. Site-directed mutagenesis studies further revealed that the degree of N-glycosylation also plays an important role in heterologous cellulase activity in S. cerevisiae.

Conclusions
Systematic screening of knockout mutants of glycosylation- and protein trafficking-associated genes in S. cerevisiae revealed that: (1) blocking Golgi-to-endosome transport may force S. cerevisiae to export cellulases; and (2) both over- and under-glycosylation may alter the enzyme activity of cellulases. This systematic gene-knockout screening approach may serve as a convenient means for increasing the extracellular activities of recombinant proteins expressed in S. cerevisiae.
TLR9 signaling repressed tumor suppressor miR-7 expression through up-regulation of HuR in human lung cancer cells
Authors: Li Yong-Ju , Wang Chun-Hong , Zhou Ya , Liao Zheng-Yuan , Zhu Shun-Fei , Hu Yan , Chen Chao , Luo Jun-Min , Wen Zhen-Ke , Xu Lin 
Published: September 2013

Abstract

Background
Our recent evidence showed that Toll like receptor 9 (TLR9) signaling could enhance the growth and metastatic potential of human lung cancer cells through repressing microRNA-7 (miR-7) expression. Human antigen R (HuR) has been involved in stabilizing multiple mRNAs in cellular biology. However, whether HuR also contributed to the altered expression of miR-7 in TLR9 signaling stimulated human lung cancer cells remains to be elucidated.

Methods
The expression of HuR in human lung cancer 95D cells treated with TLR9 agonist CpG Oligonucleotides (ODNs) was detected by Real-time PCR and Western blot assay. To explore the possible role of HuR on miR-7 expression, eukaryotic expression vector encoding HuR was transiently transfected into 95D cells and then the expression of miR-7 was detected by Real-time PCR assay. Moreover, RNA interference, western blot, Real-time PCR, MTT assay, BrdU labeling, invasion assay and scratch assay were employed to examine the disrupt effect of HuR on miR-7 expression in human lung cancer cells treated with CpG ODNs. Finally, inhibitors for PI3K, Akt or Erk respectively, and western blot were performed to explore the possible signaling pathway related to HuR expression in CpG ODNs treated human lung cancer cells.

Results
Our data showed that TLR9 agonist CpG ODNs could induce the expression of HuR in human lung cancer cells. Moreover, overexpression of HuR could reduce the expression of miR-7 in lung cancer cells. Notably, down-regulation of HuR using RNA interference restored miR-7 expression in CpG ODNs treated lung cancer cells, accompanied by enhanced growth and metastatic potential. Finally, CpG ODNs could induce HuR expression through Akt pathway.

Conclusion
Our findings indicated that HuR could act as regulator in regulating TLR9 signaling associated biological effect in human lung cancer cells, which might be helpful for the understanding of the potential role of HuR in tumor biology.
A case of breast cancer in the axillary tail of Spence – enhanced magnetic resonance imaging and positron emission tomography for diagnostic differentiation and preoperative treatment decision
Authors: Okubo Mai , Tada Keiichiro , Niwa Takayoshi , Nishioka Kotoe , Tsuji Eiichi , Ogawa Toshihisa , Seto Yasuyuki 
Published: September 2013

AbstractBackgroundThe management of cancer in the axillary area depends on the etiology of the tumor.Case ReportA 37-year-old woman presented with a 2 cm mass in the axillary fossa. Core needle biopsy revealed adenocarcinoma. There were no abnormal breast findings on physical examination, mammography, or ultrasonography. However, enhanced magnetic resonance imaging (MRI) and positron emission tomography (PET) showed a segmentally-distributed, abnormal area in the upper-outer quadrant, continuous with the axillary mass. Samples of this area obtained by vacuum-assisted biopsy showed intraductal carcinoma. These findings indicated that the axillary lesion was a part of primary breast cancer originating from the axillary tail. Based on these results, the patient underwent total mastectomy with sentinel lymph node biopsy. Pathological examination of the specimen showed invasive ductal carcinoma accompanied by intraductal carcinoma extending up to 8.5 cm. Our case suggests that enhanced MRI and PET can provide useful preoperative information for the management of axillary breast lesions.
Proteomic analysis of seminal fluid from men exhibiting oxidative stress
Authors: Sharma Rakesh , Agarwal Ashok , Mohanty Gayatri , Du Plessis Stefan S , Gopalan Banu , Willard Belinda , Yadav Satya P , Sabanegh Edmund 
Published: September 2013

Abstract

Background
Seminal plasma serves as a natural reservoir of antioxidants. It helps to remove excessive formation of reactive oxygen species (ROS) and consequently, reduce oxidative stress. Proteomic profiling of seminal plasma proteins is important to understand the molecular mechanisms underlying oxidative stress and sperm dysfunction in infertile men.

Methods
This prospective study consisted of 52 subjects: 32 infertile men and 20 healthy donors. Once semen and oxidative stress parameters were assessed (ROS, antioxidant concentration and DNA damage), the subjects were categorized into ROS positive (ROS+) or ROS negative (ROS-). Seminal plasma from each group was pooled and subjected to proteomics analysis. In-solution digestion and protein identification with liquid chromatography tandem mass spectrometry (LC-MS/MS), followed by bioinformatics analyses was used to identify and characterize potential biomarker proteins.

Results
A total of 14 proteins were identified in this analysis with 7 of these common and unique proteins were identified in both the ROS+ and ROS- groups through MASCOT and SEQUEST analyses, respectively. Prolactin-induced protein was found to be more abundantly present in men with increased levels of ROS. Gene ontology annotations showed extracellular distribution of proteins with a major role in antioxidative activity and regulatory processes.

Conclusions
We have identified proteins that help protect against oxidative stress and are uniquely present in the seminal plasma of the ROS- men. Men exhibiting high levels of ROS in their seminal ejaculate are likely to exhibit proteins that are either downregulated or oxidatively modified, and these could potentially contribute to male infertility.