bluuebunny/crossref_metadata_2025_split huggingface dataset:
Incremental Value of Pulmonary Function and Sputum DNA Image Cytometry in Lung Cancer Risk Prediction
Authors: Tammemagi Martin C. , Lam Stephen C. , McWilliams Annette M. , Sin Don D. 
Published: March 2011

Abstract
Lung cancer is the leading cause of cancer death worldwide. Accurate prediction of lung cancer risk is of value for individuals, clinicians, and researchers. The aims of this study were to characterize the associations between pulmonary function and sputum DNA image cytometry (SDIC) and lung cancer, and their contributions to risk prediction. During 1990 to 2007, 2,596 high-risk individuals were enrolled and followed prospectively for development of lung cancer (n = 139; median follow-up 7.7 years) in trials at the British Columbia Cancer Agency. At baseline, an epidemiologic questionnaire was administered, sputum was collected for aneuploidy measurement and spirometry was obtained. Multivariable logistic models were prepared including known lung cancer predictors (model 1), that additionally included percent-expected-forced expiratory volume in 1 second [forced expiratory volume in 1 second (FEV1%), model 2], and that additionally included SDIC (model 3). Prediction was assessed by evaluating discrimination (receiver operator characteristic area under the curve (ROC AUC)) and calibration. Net reclassification indices (NRI) were calculated with cutoff points for 8-year risks identifying low, intermediate, and high risk at 1.5% and 3%. Lung cancer risk increased with decline in FEV1%, but did so more for men than for women (interaction P &lt; 0.001). SDIC demonstrated a dose–response with lung cancer (P = 0.022). The ROC AUCs for models 1, 2, and 3 were 0.718 (95% CI: 0.671–0.765), 0.767 (95% CI: 0.725–0.809), and 0.773 (95% CI: 0.732–0.815), respectively. Model 2 versus 1 had a NRI of 12.6% (P &lt; 0.0001) and model 3 versus 2 had a NRI of 3.1% (P = 0.059). Spirometry and SDIC data substantially and minimally improved lung cancer prediction, respectively. Cancer Prev Res; 4(4); 552–61. ©2011 AACR.
A Conversation with Malcolm Pines
Authors: Tubert-Oklander Juan , Hernández-Tubert Reyna 
Published: March 2011

Part II: Group Analysis, Psycho-Analysis and Politics This second part of the conversation between the authors, Malcolm Pines and his wife, Iris, is much more variegated than the first. We move easily through several themes: the differences between group analysis in Britain and in the USA, the distinctive traits of group analysis, Malcolm’s contribution to its development, the contrast with psychoanalysis, politics, ethnology, Marxism, power, values, the Weltanschauung, terrorism, religion, the relationship between Malcolm and Iris, and a comparison of our respective points of view. The common thread that joins all these apparently disparate ideas is the flow of conversation, as in group analysis. The result is most valuable and fascinating, and worth preserving and sharing.
Imperfection and Disillusionment as Therapeutic Agents
Authors: Sargeant Rhona 
Published: March 2011

In the initial phase of group development the conductor strives hard to nurture the new analytic group in order that it survives as a whole through the early anxieties. The group develops a dependence on the group conductor, who tries to offer something close to perfection. However, during the middle phase this nurturing role needs to be reduced to allow the growth and creativity of the group to develop. In this article the concept of disillusionment or de-adaptation is borrowed from the individual analytic literature. In the middle phase of group development imperfections in the conductor are considered as therapeutic agents, necessary for the group to move to a more mature position where their own creativity can be discovered and the group can become owned by its members. Parallels between the group’s development and a child’s development are drawn.
LXR as a novel antithrombotic target
Authors: Spyridon Michael , Moraes Leonardo A. , Jones Chris I. , Sage Tanya , Sasikumar Parvathy , Bucci Giovanna , Gibbins Jonathan M. 
Published: March 2011

AbstractLiver X receptors (LXRs) are transcription factors involved in the regulation of cholesterol homeostasis. LXR ligands have athero-protective properties independent of their effects on cholesterol metabolism. Platelets are involved in the initiation of atherosclerosis and despite being anucleate express nuclear receptors. We hypothesized that the athero-protective effects of LXR ligands could be in part mediated through platelets and therefore explored the potential role of LXR in platelets. Our results show that LXR-β is present in human platelets and the LXR ligands, GW3965 and T0901317, modulated nongenomically platelet aggregation stimulated by a range of agonists. GW3965 caused LXR to associate with signaling components proximal to the collagen receptor, GPVI, suggesting a potential mechanism of LXR action in platelets that leads to diminished platelet responses. Activation of platelets at sites of atherosclerotic lesions results in thrombosis preceding myocardial infarction and stroke. Using an in vivo model of thrombosis in mice, we show that GW3965 has antithrombotic effects, reducing the size and the stability of thrombi. The athero-protective effects of GW3965, together with its novel antiplatelet/thrombotic effects, indicate LXR as a potential target for prevention of athero-thrombotic disease.
How I treat warfarin-associated coagulopathy in patients with intracerebral hemorrhage
Authors: Goodnough Lawrence Tim , Shander Aryeh 
Published: March 2011

Abstract
Intracerebral hemorrhage in patients with warfarin-associated coagulopathy is an increasingly common life-threatening condition that requires emergent management. The evolution of therapeutic options in this setting, as well as recently published guidelines, has resulted in some heterogeneity in recommendations by professional societies. This heterogeneity can be attributed to lack of evidence-based support for plasma therapy; the variability in availability of prothrombin complex concentrates; the variability in the coagulation factor levels and contents of prothrombin complex concentrates; ambiguity about the optimal dose and route of administration of vitamin K; and the lack of standardized clinical care pathways, particularly in community hospitals, for the management of these critical care patients. In this review, we summarize the relevant literature about these controversies and present recommendations for management of patients with warfarin-associated coagulopathy and intracerebral hemorrhage.
Bone marrow-derived cells serve as proangiogenic macrophages but not endothelial cells in wound healing
Authors: Okuno Yuji , Nakamura-Ishizu Ayako , Kishi Kazuo , Suda Toshio , Kubota Yoshiaki 
Published: March 2011

AbstractBone marrow-derived cells (BMDCs) contribute to postnatal vascular growth by differentiating into endothelial cells or secreting angiogenic factors. However, the extent of their endothelial differentiation highly varies according to the angiogenic models used. Wound healing is an intricate process in which the skin repairs itself after injury. As a process also observed in cancer progression, neoangiogenesis into wound tissues is profoundly involved in this healing process, suggesting the contribution of BMDCs. However, the extent of the differentiation of BMDCs to endothelial cells in wound healing is unclear. In this study, using the green fluorescent protein-bone marrow chim-eric experiment and high resolution confocal microscopy at a single cell level, we observed no endothelial differentiation of BMDCs in 2 acute wound healing models (dorsal excisional wound and ear punch) and a chronic wound healing model (decubitus ulcer). Instead, a major proportion of BMDCs were macrophages. Indeed, colony-stimulating factor 1 (CSF-1) inhibition depleted approximately 80% of the BMDCs at the wound healing site. CSF-1–mutant (CSF-1op/op) mice showed significantly reduced neoangiogenesis into the wound site, supporting the substantial role of BMDCs as macrophages. Our data show that the proangiogenic effects of macrophages, but not the endothelial differentiation, are the major contribution of BMDCs in wound healing.
MRCQuant- an accurate LC-MS relative isotopic quantification algorithm on TOF instruments
Authors: Haskins William E , Petritis Konstantinos , Zhang Jianqiu 
Published: March 2011

Abstract

Background
Relative isotope abundance quantification, which can be used for peptide identification and differential peptide quantification, plays an important role in liquid chromatography-mass spectrometry (LC-MS)-based proteomics. However, several major issues exist in the relative isotopic quantification of peptides on time-of-flight (TOF) instruments: LC peak boundary detection, thermal noise suppression, interference removal and mass drift correction. We propose to use the Maximum Ratio Combining (MRC) method to extract MS signal templates for interference detection/removal and LC peak boundary detection. In our method, MRCQuant, MS templates are extracted directly from experimental values, and the mass drift in each LC-MS run is automatically captured and compensated. We compared the quantification accuracy of MRCQuant to that of another representative LC-MS quantification algorithm (msInspect) using datasets downloaded from a public data repository.

Results
MRCQuant showed significant improvement in the number of accurately quantified peptides.

Conclusions
MRCQuant effectively addresses major issues in the relative quantification of LC-MS-based proteomics data, and it provides improved performance in the quantification of low abundance peptides.
Position and sequence conservation in Amniota of polymorphic enhancer HS1.2 within the palindrome of IgH 3'Regulatory Region
Authors: D'Addabbo Pietro , Scascitelli Moira , Giambra Vincenzo , Rocchi Mariano , Frezza Domenico 
Published: March 2011

AbstractBackgroundThe Immunoglobulin heavy chain (IgH) 3' Regulatory Region (3'RR), located at the 3' of the constant alpha gene, plays a crucial role in immunoglobulin production. In humans, there are 2 copies of the 3'RR, each composed of 4 main elements: 3 enhancers and a 20 bp tandem repeat. The single mouse 3'RR differs from the two human ones for the presence of 4 more regulative elements with the double copy of one enhancer at the border of a palindromic region.ResultsWe compared the 3'RR organization in genomes of vertebrates to depict the evolutionary history of the region and highlight its shared features. We found that in the 8 species in which the whole region was included in a fully assembled contig (mouse, rat, dog, rabbit, panda, orangutan, chimpanzee, and human), the shared elements showed synteny and a highly conserved sequence, thus suggesting a strong evolutionary constraint. In these species, the wide 3'RR (~30 kb in human) bears a large palindromic sequence, consisting in two ~3 kb complementary branches spaced by a ~3 kb sequence always including the HS1.2 enhancer. In mouse and rat, HS3 is involved by the palindrome so that one copy of the enhancer is present on each side. A second relevant feature of our present work concerns human polymorphism of the HS1.2 enhancer, associated to immune diseases in our species. We detected a similar polymorphism in all the studied Catarrhini (a primate parvorder). The polymorphism consists of multiple copies of a 40 bp element up to 12 in chimpanzees, 8 in baboons, 6 in macaque, 5 in gibbons, 4 in humans and orangutan, separated by stretches of Cytosine. We show specific binding of this element to nuclear factors.ConclusionsThe nucleotide sequence of the palindrome is not conserved among evolutionary distant species, suggesting pressures for the maintenance of two self-matching regions driving a three-dimensional structure despite of the inter-specific divergence at sequence level. The information about the conservation of the palindromic structure and the settling in primates of the polymorphic feature of HS1.2 show the relevance of these structures in the control and modulation of the Ig production through the formation of possible three-dimensional structures.
Genome-wide temporal-spatial gene expression profiling of drought responsiveness in rice
Authors: Wang Di , Pan Yajiao , Zhao Xiuqin , Zhu Linghua , Fu Binying , Li Zhikang 
Published: March 2011

Abstract
Background
Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. The transcriptome from leaf, root, and young panicle at three developmental stages was comparatively analyzed combined with bioinformatics exploring drought stress related cis-elements.

Results
There were 5,284 genes detected to be differentially expressed under drought stress. Most of these genes were tissue- or stage-specific regulated by drought. The tissue-specific down-regulated genes showed distinct function categories as photosynthesis-related genes prevalent in leaf, and the genes involved in cell membrane biogenesis and cell wall modification over-presented in root and young panicle. In a drought environment, several genes, such as GA2ox, SAP15, and Chitinase III, were regulated in a reciprocal way in two tissues at the same development stage. A total of 261 transcription factor genes were detected to be differentially regulated by drought stress. Most of them were also regulated in a tissue- or stage-specific manner. A cis-element containing special CGCG box was identified to over-present in the upstream of 55 common induced genes, and it may be very important for rice plants responding to drought environment.

Conclusions
Genome-wide gene expression profiling revealed that most of the drought differentially expressed genes (DEGs) were under temporal and spatial regulation, suggesting a crosstalk between various development cues and environmental stimuli. The identification of the differentially regulated DEGs, including TF genes and unique candidate cis-element for drought responsiveness, is a very useful resource for the functional dissection of the molecular mechanism in rice responding to environment stress.
Seed-specific elevation of non-symbiotic hemoglobin AtHb1: beneficial effects and underlying molecular networks in Arabidopsis thaliana
Authors: Thiel Johannes , Rolletschek Hardy , Friedel Svetlana , Lunn John E , Nguyen Thuy H , Feil Regina , Tschiersch Henning , Müller Martin , Borisjuk Ljudmilla 
Published: March 2011

Abstract

Background
Seed metabolism is dynamically adjusted to oxygen availability. Processes underlying this auto-regulatory mechanism control the metabolic efficiency under changing environmental conditions/stress and thus, are of relevance for biotechnology. Non-symbiotic hemoglobins have been shown to be involved in scavenging of nitric oxide (NO) molecules, which play a key role in oxygen sensing/balancing in plants and animals. Steady state levels of NO are suggested to act as an integrator of energy and carbon metabolism and subsequently, influence energy-demanding growth processes in plants.

Results
We aimed to manipulate oxygen stress perception in Arabidopsis seeds by overexpression of the non-symbiotic hemoglobin AtHb1 under the control of the seed-specific LeB4 promoter. Seeds of transgenic AtHb1 plants did not accumulate NO under transient hypoxic stress treatment, showed higher respiratory activity and energy status compared to the wild type. Global transcript profiling of seeds/siliques from wild type and transgenic plants under transient hypoxic and standard conditions using Affymetrix ATH1 chips revealed a rearrangement of transcriptional networks by AtHb1 overexpression under non-stress conditions, which included the induction of transcripts related to ABA synthesis and signaling, receptor-like kinase- and MAP kinase-mediated signaling pathways, WRKY transcription factors and ROS metabolism. Overexpression of AtHb1 shifted seed metabolism to an energy-saving mode with the most prominent alterations occurring in cell wall metabolism. In combination with metabolite and physiological measurements, these data demonstrate that AtHb1 overexpression improves oxidative stress tolerance compared to the wild type where a strong transcriptional and metabolic reconfiguration was observed in the hypoxic response.

Conclusions

AtHb1 overexpression mediates a pre-adaptation to hypoxic stress. Under transient stress conditions transgenic seeds were able to keep low levels of endogenous NO and to maintain a high energy status, in contrast to wild type. Higher weight of mature transgenic seeds demonstrated the beneficial effects of seed-specific overexpression of AtHb1.
Identification of differentially expressed genes associated with semigamy in Pima cotton (Gossypium barbadenseL.) through comparative microarray analysis
Authors: Curtiss Jessica , Rodriguez-Uribe Laura , Stewart J McD , Zhang Jinfa 
Published: March 2011

Abstract

Background
Semigamy in cotton is a type of facultative apomixis controlled by an incompletely dominant autosomal gene (Se). During semigamy, the sperm and egg cells undergo cellular fusion, but the sperm and egg nucleus fail to fuse in the embryo sac, giving rise to diploid, haploid, or chimeric embryos composed of sectors of paternal and maternal origin. In this study we sought to identify differentially expressed genes related to the semigamy genotype by implementing a comparative microarray analysis of anthers and ovules between a non-semigametic Pima S-1 cotton and its doubled haploid natural isogenic mutant semigametic 57-4. Selected differentially expressed genes identified by the microarray results were then confirmed using quantitative reverse transcription PCR (qRT-PCR).

Results
The comparative analysis between isogenic 57-4 and Pima S-1 identified 284 genes in anthers and 1,864 genes in ovules as being differentially expressed in the semigametic genotype 57-4. Based on gene functions, 127 differentially expressed genes were common to both semigametic anthers and ovules, with 115 being consistently differentially expressed in both tissues. Nine of those genes were selected for qRT-PCR analysis, seven of which were confirmed. Furthermore, several well characterized metabolic pathways including glycolysis/gluconeogenesis, carbon fixation in photosynthetic organisms, sesquiterpenoid biosynthesis, and the biosynthesis of and response to plant hormones were shown to be affected by differentially expressed genes in the semigametic tissues.

Conclusion
As the first report using microarray analysis, several important metabolic pathways affected by differentially expressed genes in the semigametic cotton genotype have been identified and described in detail. While these genes are unlikely to be the semigamy gene itself, the effects associated with expression changes in those genes do mimic phenotypic traits observed in semigametic plants. A more in-depth analysis of semigamy is necessary to understand its expression and regulation at the genetic and molecular level.
Coffee consumption and risk of cancers: a meta-analysis of cohort studies
Authors: Yu Xiaofeng , Bao Zhijun , Zou Jian , Dong Jie 
Published: March 2011

Abstract

Background
Coffee consumption has been shown to be associated with cancer of various sites in epidemiological studies. However, there is no comprehensive overview of the substantial body of epidemiologic evidence.

Methods
We searched MEDLINE, EMBASE, Science Citation Index Expanded and bibliographies of retrieved articles. Prospective cohort studies were included if they reported relative risks (RRs) and corresponding 95% confidence intervals (CIs) of various cancers with respect to frequency of coffee intake. We did random-effects meta-analyses and meta-regressions of study-specific incremental estimates to determine the risk of cancer associated with 1 cup/day increment of coffee consumption.

Results
59 studies, consisting of 40 independent cohorts, met the inclusion criteria. Compared with individuals who did not or seldom drink coffee per day, the pooled RR of cancer was 0.87 (95% CI, 0.82-0.92) for regular coffee drinkers, 0.89 (0.84-0.93) for low to moderate coffee drinkers, and 0.82 (0.74-0.89) for high drinkers. Overall, an increase in consumption of 1 cup of coffee per day was associated with a 3% reduced risk of cancers (RR, 0.97; 95% CI, 0.96-0.98). In subgroup analyses, we noted that, coffee drinking was associated with a reduced risk of bladder, breast, buccal and pharyngeal, colorectal, endometrial, esophageal, hepatocellular, leukemic, pancreatic, and prostate cancers.

Conclusions
Findings from this meta-analysis suggest that coffee consumption may reduce the total cancer incidence and it also has an inverse association with some type of cancers.
Age, period, and cohort analysis of regular dental care behavior and edentulism: A marginal approach
Authors: Li Kar-Yan , Wong May Chun Mei , Lam Kwok-Fai , Schwarz Eli 
Published: March 2011

Abstract

Background
To analyze the regular dental care behavior and prevalence of edentulism in adult Danes, reported in sequential cross-sectional oral health surveys by the application of a marginal approach to consider the possible clustering effect of birth cohorts.

Methods
Data from four sequential cross-sectional surveys of non-institutionalized Danes conducted from 1975-2005 comprising 4330 respondents aged 15+ years in 9 birth cohorts were analyzed. The key study variables were seeking dental care on an annual basis (ADC) and edentulism. For the analysis of ADC, survey year, age, gender, socio-economic status (SES) group, denture-wearing, and school dental care (SDC) during childhood were considered. For the analysis of edentulism, only respondents aged 35+ years were included. Survey year, age, gender, SES group, ADC, and SDC during childhood were considered as the independent factors. To take into account the clustering effect of birth cohorts, marginal logistic regressions with an independent correlation structure in generalized estimating equations (GEE) were carried out, with PROC GENMOD in SAS software.

Results
The overall proportion of people seeking ADC increased from 58.8% in 1975 to 86.7% in 2005, while for respondents aged 35 years or older, the overall prevalence of edentulism (35+ years) decreased from 36.4% in 1975 to 5.0% in 2005. Females, respondents in the higher SES group, in more recent survey years, with no denture, and receiving SDC in all grades during childhood were associated with higher probability of seeking ADC regularly (P < 0.05). The interaction of SDC and age (P < 0.0001) was significant. The probabilities of seeking ADC were even higher among subjects with SDC in all grades and aged 45 years or older. Females, older age group, respondents in earlier survey years, not seeking ADC, lower SES group, and not receiving SDC in all grades were associated with higher probability of being edentulous (P < 0.05).

Conclusions
With the use of GEE, the potential clustering effect of birth cohorts in sequential cross-sectional oral health survey data could be appropriately considered. The success of Danish dental health policy was demonstrated by a continued increase of regular dental visiting habits and tooth retention in adults because school dental care was provided to Danes in their childhood.