bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis on the clinical features of 22 basaloid squamous cell carcinoma of the lung
Authors: Wang Li C , Wang Lei , Kwauk Sabrina , Woo Jennifer A , Wu Li Q , Zhu Hong , Zhan Li Z , Sun Na L , Zhang Lei 
Published: January 2011

Abstract

Background
Basaloid squamous cell carcinoma of the lung is a rare and highly malignant tumor mostly observed in the proximal bronchi. Basaloid squamous cell carcinoma of the lung cases typically show rapid clinical progression, very poor prognosis and special pathological morphology. This project aimed to examine the clinical features of basaloid squamous cell carcinoma of the lung and the factors related to its prognosis; and to compare survival outcomes between basaloid squamous cell carcinoma and poorly differentiated squamous cell carcinomas (PDSC).

Methods
Between January 2004 and December 2008, pathological sections from basaloid squamous cell carcinoma and PDSC of the lung were collected and retrospectively analyzed at Tianjin Medical University Cancer Institute and Hospital. Data analysis was performed using Statistical Package for the Social Sciences (SPSS11.0). The Kaplan-Meier method was used to calculate the survival rate. Log-rank test was used to compare the differences in survival rate between the two groups. The factors influencing prognosis were analyzed using the Cox proportional hazard model.

Results
A total of 120 pathological sections were used in the analysis of this study-22 from basaloid squamous cell carcinoma cases and 98 from PDSC cases. Compared to the PDSC group, the basaloid squamous cell carcinoma group had a larger proportion of female patients (p = 0.001); however it had higher proportion of male smokers (p = 0.003). There were no statistically significant differences in survival rate between the two groups (χ2 = 1.200, p = 0.273). Additionally, prognosis of basaloid squamous cell carcinoma is significantly influenced by treatment mode and clinical stages of the tumor. The post-operation mortality hazard of patients treated with a combination chemotherapy and radiotherapy was 1.296 times higher than other treatment modes (p = 0.025). Increases in post-operation mortality hazard ratio were also associated with more advanced clinical stage of tumors (χ2 trend = 11.907, p = 0.000).

Conclusions
This study demonstrated that basaloid squamous cell carcinoma and PDSC have very similar clinical features, and there are no significant differences in survival rates between the two groups. Hence, we conclude that in the short term, the same clinical treatments and therapeutic modes can be administered to patients with basaloid squamous cell carcinoma and PDSC of the lung.
Initial characterization of the human central proteome
Authors: Burkard Thomas R , Planyavsky Melanie , Kaupe Ines , Breitwieser Florian P , Bürckstümmer Tilmann , Bennett Keiryn L , Superti-Furga Giulio , Colinge Jacques 
Published: January 2011

Abstract

Background
On the basis of large proteomics datasets measured from seven human cell lines we consider their intersection as an approximation of the human central proteome, which is the set of proteins ubiquitously expressed in all human cells. Composition and properties of the central proteome are investigated through bioinformatics analyses.

Results
We experimentally identify a central proteome comprising 1,124 proteins that are ubiquitously and abundantly expressed in human cells using state of the art mass spectrometry and protein identification bioinformatics. The main represented functions are proteostasis, primary metabolism and proliferation. We further characterize the central proteome considering gene structures, conservation, interaction networks, pathways, drug targets, and coordination of biological processes. Among other new findings, we show that the central proteome is encoded by exon-rich genes, indicating an increased regulatory flexibility through alternative splicing to adapt to multiple environments, and that the protein interaction network linking the central proteome is very efficient for synchronizing translation with other biological processes. Surprisingly, at least 10% of the central proteome has no or very limited functional annotation.

Conclusions
Our data and analysis provide a new and deeper description of the human central proteome compared to previous results thereby extending and complementing our knowledge of commonly expressed human proteins. All the data are made publicly available to help other researchers who, for instance, need to compare or link focused datasets to a common background.
Actinomadura meyerae osteitis following wound contamination with hay in a woman in France: a case report
Authors: Bonnet Emilie , Flecher Xavier , Paratte Sebastien , Argenson Jean-Noël , Raoult Didier , Fournier Pierre-Edouard 
Published: January 2011

Abstract

Introduction
Mycetoma is a chronic granulomatous infection caused by environmental fungi or bacteria. It affects dermal and subcutaneous tissues, with putative contiguous extension to muscles or bones. While common in tropical and subtropical areas, mycetoma is rare in Europe.

Case presentation
We describe a case of Actinomadura meyerae osteitis in a 49-year-old Caucasian woman who suffered a tibia open fracture contaminated with hay; to the best of our knowledge the first case of autochthonous A. meyerae infection reported in France. The bacterium was cultivated from a bone biopsy. Following surgical osteosynthesis and six months of treatment with cotrimoxazole, our patient made a full recovery.

Conclusion
Our case report suggests that A. meyerae is a potential agent of wound infection in farm workers in contact with hay.
Peritoneal mesothelioma in a woman who has survived for seven years: a case report
Authors: Pillai Krishna , Akhter Javed , Pourgholami Mohammad H , Morris David L 
Published: January 2011

Abstract

Introduction
Malignant peritoneal mesothelioma is a rare cancer with poor patient survival. Female gender has been identified as a positive prognostic factor. Recently, it has been suggested that the expression of estrogen receptor β in malignant mesothelioma leads to tumor suppression and a better prognosis.

Case presentation
We report the case of a 48-year-old Caucasian woman who is alive and disease-free seven years after the initial diagnosis and treatment of malignant peritoneal mesothelioma.

Conclusion
This patient's long survival may be attributable to a combination of factors, including minimal disease, complete cytoreductive surgery and hyperthermic intraperitoneal chemotherapy plus the estrogen receptor β positivity of the tumor.
A novel SNP analysis method to detect copy number alterations with an unbiased reference signal directly from tumor samples
Authors: Lisovich Alex , Chandran Uma R , Lyons-Weiler Maureen A , LaFramboise William A , Brown Ashley R , Jakacki Regina I , Pollack Ian F , Sobol Robert W 
Published: January 2011

Abstract

Background
Genomic instability in cancer leads to abnormal genome copy number alterations (CNA) as a mechanism underlying tumorigenesis. Using microarrays and other technologies, tumor CNA are detected by comparing tumor sample CN to normal reference sample CN. While advances in microarray technology have improved detection of copy number alterations, the increase in the number of measured signals, noise from array probes, variations in signal-to-noise ratio across batches and disparity across laboratories leads to significant limitations for the accurate identification of CNA regions when comparing tumor and normal samples.

Methods
To address these limitations, we designed a novel "Virtual Normal" algorithm (VN), which allowed for construction of an unbiased reference signal directly from test samples within an experiment using any publicly available normal reference set as a baseline thus eliminating the need for an in-lab normal reference set.

Results
The algorithm was tested using an optimal, paired tumor/normal data set as well as previously uncharacterized pediatric malignant gliomas for which a normal reference set was not available. Using Affymetrix 250K Sty microarrays, we demonstrated improved signal-to-noise ratio and detected significant copy number alterations using the VN algorithm that were validated by independent PCR analysis of the target CNA regions.

Conclusions
We developed and validated an algorithm to provide a virtual normal reference signal directly from tumor samples and minimize noise in the derivation of the raw CN signal. The algorithm reduces the variability of assays performed across different reagent and array batches, methods of sample preservation, multiple personnel, and among different laboratories. This approach may be valuable when matched normal samples are unavailable or the paired normal specimens have been subjected to variations in methods of preservation.
Genetic variation of ESR1 and its co-activator PPARGC1B is synergistic in augmenting the risk of estrogen receptor-positive breast cancer
Authors: Li Yuqing , Li Yi , Wedrén Sara , Li Guoliang , Charn Tze Howe , Desai Kartiki Vasant , Bonnard Carine , Czene Kamila , Humphreys Keith , Darabi Hatef , Einarsdóttir Kristjana , Heikkinen Tuomas , Aittomäki Kristiina , Blomqvist Carl , Chia Kee Seng , Nevanlinna Heli , Hall Per , Liu Edison T , Liu Jianjun 
Published: January 2011

Abstract
Introduction
Given the role of estrogen in breast carcinogenesis and the modification of estrogen receptor (ER) activity by its biochemical cofactors, we hypothesize that genetic variation within ER cofactor genes alters cellular response to estrogen exposure and consequently modifies the risk for ER-positive breast cancer.

Methods
We genotyped 790 tagging SNPs within 60 ER cofactor genes in 1,257 cases and 1,464 controls from Sweden and in 2,215 cases and 1,265 controls from Finland, and tested their associations with either ER-positive or ER-negative breast cancer.

Results
Seven SNPs showed consistent association with ER-positive breast cancer in the two independent samples, and six of them were located within PPARGC1B, encoding an ER co-activator, with the strongest association at rs741581 (odds ratio = 1.41, P = 4.84 × 10-5) that survived Bonferroni correction for multiple testing in the combined ER-positive breast cancer sample (Pcorrected = 0.03). Moreover, we also observed significant synergistic interaction (P
interaction
= 0.008) between the genetic polymorphisms within PPARGC1B and ESR1 in ER-positive breast cancer. By contrast, no consistent association was observed in ER-negative breast cancer. Furthermore, we found that administration of estrogen in the MCF-7 cell line induced PPARGC1B expression and enhanced occupancies of ER and RNA polymerase II within the region of SNP association, suggesting the upregulation of PPARGC1B expression by ESR1 activation.

Conclusions
Our study revealed that DNA polymorphisms of PPARGC1B, coding a bona fide ER co-activator, are associated with ER-positive breast cancer risk. The feed-forward transcriptional regulatory loop between PPARGC1B and ESR1 further augments their protein interaction, which provides a plausible mechanistic explanation for the synergistic genetic interaction between PPARGC1B and ESR1 in ER-positive breast cancer. Our study also highlights that biochemically and genomically informed candidate gene studies can enhance the discovery of interactive disease susceptibility genes.
Effect of erythropoietin on level of circulating endothelial progenitor cells and outcome in patients after acute ischemic stroke
Authors: Yip Hon-Kan , Tsai Tzu-Hsien , Lin Hung-Sheng , Chen Shu-Fang , Sun Cheuk-Kwan , Leu Steve , Yuen Chun-Man , Tan Teng-Yeow , Lan Min-Yu , Liou Chia-Wei , Lu Cheng-Hsien , Chang Wen-Neng 
Published: January 2011

Abstract
Introduction
Erythropoietin (EPO) enhances the circulating level of endothelial progenitor cells (EPCs), which has been reported to be associated with prognostic outcome in ischemic stroke (IS) patients. The aim of this study was to evaluate the time course of circulating EPC level and the impact of EPO therapy on EPC level and clinical outcome in patients after acute IS.

Methods
In total, 167 patients were prospectively randomized to receive either EPO therapy (group 1) (5,000 IU each time, subcutaneously) at 48 h and 72 h after acute IS, or serve as placebo (group 2). The circulating level of EPCs (double-stained markers: CD31/CD34 (E1), CD62E/CD34 (E2) and KDR/CD34 (E3)) was determined using flow cytometry at 48 h and on days 7 and 21 after IS. EPC level was also evaluated once in 60 healthy volunteers.

Results
Circulating EPC (E1 to E3) level at 48 h after IS was remarkably higher in patients than in control subjects (P < 0.02). At 48 h and on Day 7 after IS, EPC (E1 to E3) level did not differ between groups 1 and 2 (all P > 0.1). However, by Day 21, EPC (E1 to E3) level was significantly higher in group 1 than in group 2 (all P < 0.03). Additionally, 90-day recurrent stroke rate was notably lower in group 1 compared with group 2 (P = 0.022). Multivariate analysis demonstrated that EPO therapy (95% confidence interval (CI), 0.153 to 0.730; P = 0.006) and EPC (E3) (95% CI, 0.341 to 0.997; P = 0.049) levels were significantly and independently predictive of a reduced 90-day major adverse neurological event (MANE) (defined as recurrent stroke, National Institutes of Health Stroke scale ≥8, or death).

Conclusions
EPO therapy significantly improved circulating EPC level and 90-day MANE.

Trial registration number
ISRCTN: ISRCTN96340690
β2-Adrenergic Receptor Signaling in Osteoblasts Contributes to the Catabolic Effect of Glucocorticoids on Bone
Authors: Ma Yun , Nyman Jeffry S. , Tao Huan , Moss Heather H. , Yang Xiangli , Elefteriou Florent 
Published: January 2011

AbstractThe sympathetic nervous system is a physiological regulator of bone homeostasis. Autonomic nerves are indeed present in bone, bone cells express the β2-adrenergic receptors (β2AR), and pharmacological or genetic disruption of sympathetic outflow to bone induces bone gain in rodents. These recent findings implied that conditions that affect β2AR signaling in osteoblasts and/or sympathetic drive to bone may contribute to bone diseases. In this study, we show that dexamethasone stimulates the expression of the β2AR in differentiated primary calvarial osteoblasts, as measured by an increase in Adrβ2 mRNA and β2AR protein level after short-term dexamethasone treatment. Isoproterenol-induced cAMP accumulation and the expression of the β2AR target gene Rankl were also significantly increased after dexamethasone pretreatment, indicating that dexamethasone promotes the responsiveness of differentiated osteoblasts to adrenergic stimulation. These in vitro results led to the hypothesis that glucocorticoid-induced bone loss, provoked by increased endogenous or high-dose exogenous glucocorticoids given for the treatment of inflammatory diseases, might, at least in part, be mediated by increased sensitivity of bone-forming cells to the tonic inhibitory effect of sympathetic nerves on bone formation or their stimulatory effect on bone resorption. Supporting this hypothesis, both pharmacological and genetic β2AR blockade in mice significantly reduced the bone catabolic effect of high-dose prednisolone in vivo. This study emphasizes the importance of sympathetic nerves in the regulation of bone homeostasis and indicates that this neuroskeletal signaling axis can be modulated by hormones or drugs and contribute to enhance pathological bone loss.
N-dimensional animal energetic niches clarify behavioural options in a variable marine environment
Authors: Wilson Rory P. , McMahon Clive R. , Quintana Flavio , Frere Esteban , Scolaro Alejandro , Hays Graeme C. , Bradshaw Corey J. A. 
Published: January 2011

SUMMARYAnimals respond to environmental variation by exhibiting a number of different behaviours and/or rates of activity, which result in corresponding variation in energy expenditure. Successful animals generally maximize efficiency or rate of energy gain through foraging. Quantification of all features that modulate energy expenditure can theoretically be modelled as an animal energetic niche or power envelope; with total power being represented by the vertical axis and n-dimensional horizontal axes representing extents of processes that affect energy expenditure. Such an energetic niche could be used to assess the energetic consequences of animals adopting particular behaviours under various environmental conditions. This value of this approach was tested by constructing a simple mechanistic energetics model based on data collected from recording devices deployed on 41 free-living Magellanic penguins (Spheniscus magellanicus), foraging from four different colonies in Argentina and consequently catching four different types of prey. Energy expenditure was calculated as a function of total distance swum underwater (horizontal axis 1) and maximum depth reached (horizontal axis 2). The resultant power envelope was invariant, irrespective of colony location, but penguins from the different colonies tended to use different areas of the envelope. The different colony solutions appeared to represent particular behavioural options for exploiting the available prey and demonstrate how penguins respond to environmental circumstance (prey distribution), the energetic consequences that this has for them, and how this affects the balance of energy acquisition through foraging and expenditure strategy.
Stable isotopes of captive cetaceans (killer whales and bottlenose dolphins)
Authors: Caut Stéphane , Laran Sophie , Garcia-Hartmann Emmanuel , Das Krishna 
Published: January 2011

SUMMARY
There is currently a great deal of interest in using stable isotope methods to investigate diet, trophic level and migration in wild cetaceans. In order to correctly interpret the results stemming from these methods, it is crucial to understand how diet isotopic values are reflected in consumer tissues. In this study, we investigated patterns of isotopic discrimination between diet and blood constituents of two species of cetaceans (killer whale, Orcinus orca, and bottlenose dolphin, Tursiops truncatus) fed controlled diets over 308 and 312 days, respectively. Diet discrimination factors (Δ; mean ± s.d.) for plasma were estimated to Δ13C=2.3±0.6‰ and Δ15N=1.8±0.3‰, respectively, for both species and to Δ13C=2.7±0.3‰ and Δ15N=0.5±0.1‰ for red blood cells. Delipidation did not have a significant effect on carbon and nitrogen isotopic values of blood constituents, confirming that cetacean blood does not serve as a reservoir of lipids. In contrast, carbon isotopic values were higher in delipidated samples of blubber, liver and muscle from killer whales. The potential for conflict between fisheries and cetaceans has heightened the need for trophic information about these taxa. These results provide the first published stable isotope incorporation data for cetaceans, which are essential if conclusions are to be drawn on issues concerning trophic structures, carbon sources and diet reconstruction.
Egg yolk environment differentially influences physiological and morphological development of broiler and layer chicken embryos
Authors: Ho Dao H. , Reed Wendy L. , Burggren Warren W. 
Published: January 2011

SUMMARY
Maternal effects are important in epigenetic determination of offspring phenotypes during all life stages. In the chicken (Gallus gallus domesticus), transgenerational transfer of egg yolk factors may set the stage for morphological and physiological phenotypic differences observed among breeds. To investigate the effect of breed-specific yolk composition on embryonic broiler and layer chicken phenotypes, we employed an ex ovo, xenobiotic technique that allowed the transfer of broiler and layer chicken embryos from their natural yolks to novel yolk environments. Embryonic day two broiler embryos developing on broiler yolk culture medium (YCM) had significantly higher heart rates than layer embryos developing on layer YCM (176±7 beats min–1 and 147±7 beats min–1, respectively). Broiler embryos developing on layer YCM exhibited heart rates typical of layer embryos developing normally on layer YCM. However, layer embryo heart rates were not affected by development on broiler YCM. Unlike O2 consumption, development rate and body mass of embryos were significantly affected by exposure to different yolk types, with both broiler and layer embryos displaying traits that reflected yolk source rather than embryo genotype. Analysis of hormone concentrations of broiler and layer egg yolks revealed that testosterone concentrations were higher in broiler yolk (4.63±2.02 pg mg–1vs 3.32±1.92 pg mg–1), whereas triiodothyronine concentrations were higher in layer yolk (1.05±0.18 pg mg–1vs 0.46±0.22 pg mg–1). Thus, a complex synergistic effect of breed-specific genotype and yolk environment exists early in chicken development, with yolk thyroid hormone and yolk testosterone as potential mediators of the physiological and morphological effects.
The effect of substrate compliance on the biomechanics of gibbon leaps
Authors: Channon Anthony J. , Günther Michael M. , Crompton Robin H. , D'Août Kristiaan , Preuschoft Holger , Vereecke Evie E. 
Published: January 2011

SUMMARYThe storage and recovery of elastic strain energy in the musculoskeletal systems of locomoting animals has been extensively studied, yet the external environment represents a second potentially useful energy store that has often been neglected. Recent studies have highlighted the ability of orangutans to usefully recover energy from swaying trees to minimise the cost of gap crossing. Although mechanically similar mechanisms have been hypothesised for wild leaping primates, to date no such energy recovery mechanisms have been demonstrated biomechanically in leapers. We used a setup consisting of a forceplate and two high-speed video cameras to conduct a biomechanical analysis of captive gibbons leaping from stiff and compliant poles. We found that the gibbons minimised pole deflection by using different leaping strategies. Two leap types were used: slower orthograde leaps and more rapid pronograde leaps. The slower leaps used a wider hip joint excursion to negate the downward movement of the pole, using more impulse to power the leap, but with no increase in work done on the centre of mass. Greater hip excursion also minimised the effective leap distance during orthograde leaps. The more rapid leaps conversely applied peak force earlier in stance where the pole was effectively stiffer, minimising deflection and potential energy loss. Neither leap type appeared to usefully recover energy from the pole to increase leap performance, but the gibbons demonstrated an ability to best adapt their leap biomechanics to counter the negative effects of the compliant pole.