bluuebunny/crossref_metadata_2025_split huggingface dataset:
AIM1 promoter hypermethylation as a predictor of decreased risk of recurrence following radical prostatectomy
Authors: Rosenbaum Eli , Begum Shahnaz , Brait Mariana , Zahurak Marianna , Maldonado Leonel , Mangold Leslie A. , Eisenberger Mario A. , Epstein Jonathan I. , Partin Alan W. , Sidransky David , Hoque Mohammad O. 
Published: December 2011

AbstractPURPOSETo evaluate the prognostic significance of six epigenetic biomarkers (AIM1, CDH1, KIF1A, MT1G, PAK3, and RBM6 promoter hypermethlation) in a homogeneous group of prostate cancer patients, following radical prostatectomy (RP).PATIENTS AND METHODSBiomarker analyses were performed retrospectively on tumors from 95 prostate cancer patients all with a Gleason score of 3 + 4 = 7 and a minimum follow‐up period of 8 years. Using Quantitative Methylation Specific PCR (QMSP), we analyzed the promoter region of six genes in primary prostate tumor tissues. Time to any progression was the primary endpoint and development of metastatic disease and/or death from prostate cancer was a secondary endpoint. The association of clinicopathological and biomolecular risk factors to recurrence was performed using the Log‐rank test and Cox proportional hazards model for multivariate analysis. To identify independent prognostic factors, a stepwise selection method was used.RESULTSAt a median follow‐up time of 10 years, 48 patients (50.5%) had evidence of recurrence: Biochemical/PSA relapse, metastases, or death from prostate cancer. In the final multivariate analysis for time to progression, the significant factors were: Older age, HR = 0.95 (95% CI: 0.91, 1.0) (P = 0.03), positive lymph nodes HR = 2.11 (95% CI: 1.05, 4.26) (P = 0.04), and decreased hypermethylation of AIM1 HR = 0.45 (95% CI: 0.2, 1.0) (P = 0.05).CONCLUSIONSMethylation status of AIM1 in the prostate cancer specimen may predict for time to recurrence in Gleason 3 + 4 = 7 patients undergoing prostatectomy. These results should be validated in a larger and unselected cohort. Prostate 72:1133–1139, 2012. © 2011 Wiley Periodicals, Inc.
Atomic-level stress and induced growth of wurtzite zinc oxide using molecular dynamics simulation
Authors: Hong Zheng-Han , Fang Te-Hua , Hwang Shun-Fa 
Published: December 2011

Abstract
Molecular dynamics is used to simulate the film growth process of zinc oxide (ZnO) deposited on a ZnO substrate. In the work, the Buckingham-type interatomic potential is modelled to describe the interaction of Zn–O atoms. The effects of incident energy and substrate temperature on the layer coverage function, radial distribution function and residual stress are investigated. Results show that the crystal growth of the deposition film is a symmetric wurtzite lattice along the [0 0 0 1] direction due to charge transformation. Epitaxial-like growth only occurs at very low incident energies, while the intermixing process could start from an incident energy of 3 eV. The average stress of the Zn layer is a compressive stress that is close to zero. However, the average mean biaxial stress and the normal stress of the O layer are −4.49 GPa and −3.07 GPa, respectively. The simulation results are compared with experimental results available in the literature.
PGAP: pan-genomes analysis pipeline
Authors: Zhao Yongbing , Wu Jiayan , Yang Junhui , Sun Shixiang , Xiao Jingfa , Yu Jun 
Published: December 2011

Abstract
Summary: With the rapid development of DNA sequencing technology, increasing bacteria genome data enable the biologists to dig the evolutionary and genetic information of prokaryotic species from pan-genome sight. Therefore, the high-efficiency pipelines for pan-genome analysis are mostly needed. We have developed a new pan-genome analysis pipeline (PGAP), which can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of functional genes, species evolution analysis and function enrichment analysis of gene clusters. PGAP's performance has been evaluated on 11 Streptococcus pyogenes strains.
Availability:PGAP is developed with Perl script on the Linux Platform and the package is freely available from http://pgap.sf.net.
Contact: junyu@big.ac.cn; xiaojingfa@big.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
The structure of LsrB from Yersinia pestis complexed with autoinducer-2
Authors: Kavanaugh Jeffrey S. , Gakhar Lokesh , Horswill Alexander R. 
Published: December 2011

The crystal structure of LsrB from Yersinia pestis complexed with autoinducer-2 (AI-2; space group P212121, unit-cell parameters a = 40.61, b = 61.03, c = 125.23 Å) has been solved by molecular replacement using the structure of LsrB from Salmonella typhimurium (PDB entry 1tjy) and refined to R = 0.180 (R
free = 0.213) at 1.75 Å resolution. The electron density for bound AI-2 and the stereochemistry of the AI-2-binding site are consistent with bound AI-2 adopting the (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran conformation, just as has been observed in the crystal structures of the Salmonella typhimurium and Sinorhizobium meliloti LsrB–AI-2 complexes.
Structure of the H107R variant of the extracellular domain of mouse NKR-P1A at 2.3 Å resolution
Authors: Kolenko Petr , Rozbeský Daniel , Vaněk Ondřej , Bezouška Karel , Hašek Jindřich , Dohnálek Jan 
Published: December 2011

The structure of the H107R variant of the extracellular domain of the mouse natural killer cell receptor NKR-P1A has been determined by X-ray diffraction at 2.3 Å resolution from a merohedrally twinned crystal. Unlike the structure of the wild-type receptor in space group I4122 with a single chain per asymmetric unit, the crystals of the variant belonged to space group I41 with a dimer in the asymmetric unit. Different degrees of merohedral twinning were detected in five data sets collected from different crystals. The mutation does not have a significant impact on the overall structure, but led to the binding of an additional phosphate ion at the interface of the molecules.
Light exposure and cell viability in fluorescence microscopy
Authors: SCHNECKENBURGER H. , WEBER P. , WAGNER M. , SCHICKINGER S. , RICHTER V. , BRUNS T. , STRAUSS W.S.L. , WITTIG R. 
Published: December 2011

SummaryTest systems for measuring cell viability in optical microscopy (based on colony formation ability or lysosomal integrity) were established and applied to native cells as well as to cells incubated with fluorescence markers or transfected with genes encoding for fluorescent proteins. Human glioblastoma and Chinese hamster ovary cells were irradiated by various light doses, and maximum doses where at least 90% of the cells survived were determined. These tolerable light doses were in the range between 25 J cm−2 and about 300 J cm−2 for native cells (corresponding to about 250−3000 s of solar irradiance and depending on the wavelength as well as on the mode of illumination, e.g. epi‐ or total internal reflection illumination) and decreased to values between 50 J cm−2 and less than 1 J cm−2 upon application of fluorescent markers, fluorescent proteins or photosensitizers. In high‐resolution wide field or laser scanning microscopy of single cells, typically 10−20 individual cell layers needed for reconstruction of a 3D image could be recorded with tolerable dose values. Tolerable light doses were also maintained in fluorescence microscopy of larger 3D samples, e.g. cell spheroids exposed to structured illumination, but may be exceeded in super‐resolution microscopy based on single molecule detection.
Biotin deficiency causes spontaneous cell death and activation of defense signaling
Authors: Li Jing , Brader Günter , Helenius Elina , Kariola Tarja , Palva E. Tapio 
Published: December 2011

SummaryIn addition to its essential metabolic functions, biotin has been suggested to play a critical role in regulating gene expression. The first committed enzyme in biotin biosynthesis in Arabidopsis, 7‐keto‐8‐aminopelargonic acid synthase, is encoded by At5g04620 (BIO4). We isolated a T‐DNA insertion mutant of BIO4 (bio4‐1) with a spontaneous cell death phenotype, which was rescued both by exogenous biotin and genetic complementation. The bio4‐1 plants exhibited massive accumulation of hydrogen peroxide and constitutive up‐regulation of a number of genes that are diagnostic for defense and reactive oxygen species signaling. The cell‐death phenotype was independent of salicylic acid and jasmonate signaling. Interestingly, the observed increase in defense gene expression was not accompanied by enhanced resistance to bacterial pathogens, which may be explained by uncoupling of defense gene transcription from accumulation of the corresponding protein. Characterization of biotinylated protein profiles showed a substantial reduction of both chloroplastic biotinylated proteins and a nuclear biotinylated polypeptide in the mutant. Our results suggest that biotin deficiency results in light‐dependent spontaneous cell death and modulates defense gene expression. The isolation and molecular characterization of the bio4‐1 mutant provides a valuable tool for elucidating new functions of biotin.
Renoprotective effect of erythropoietin in ischemia/reperfusion injury: Possible roles of the Akt/endothelial nitric oxide synthase‐dependent pathway
Authors: Oba Shigeyoshi , Suzuki Etsu , Nishimatsu Hiroaki , Kumano Shintaro , Hosoda Chihiro , Homma Yukio , Hirata Yasunobu 
Published: December 2011

Objectives:  It has been reported that erythropoietin protects the kidneys from ischemia/reperfusion injury. In the present study, we examined the role of Akt and endothelial nitric oxide synthase in the protective effect of erythropoietin on ischemia/reperfusion injury of the kidney.Methods:  Erythropoietin was injected in the peritoneal space of ICR mice after ischemia/reperfusion injury and its effect was assessed by measuring blood urea nitrogen and creatinine, and by histological analysis. Phosphorylation of Akt and endothelial nitric oxide synthase was examined by western blot analysis. Endothelial nitric oxide synthase gene null mice were also used to examine the role of endothelial nitric oxide synthase in the renoprotective effect of erythropoietin.Results:  Erythropoietin administration significantly inhibited the increase in blood urea nitrogen and creatinine after ischemia/reperfusion injury compared with control mice. Accordingly, erythropoietin administration significantly ameliorated the histological damages, including apoptotic cell death. Erythropoietin significantly stimulated phosphorylation of Akt and endothelial nitric oxide synthase in the kidneys. When endothelial nitric oxide synthase gene null mice were subjected to ischemia/reperfusion injury, erythropoietin did not significantly suppress the increase in blood urea nitrogen or creatinine.Conclusions:  Erythropoietin seems to activate the Akt/endothelial nitric oxide synthase‐dependent pathway in the kidneys. This pathway might be implicated in the renoprotective effect of erythropoietin in the ischemia/reperfusion injury model.
Ablation and Pacing: Improving Brain Perfusion and Cognitive Function in Patients with Atrial Fibrillation and Uncontrolled Ventricular Rates
Authors: EFIMOVA IRINA , EFIMOVA NATALIYA , CHERNOV VLADIMIR , POPOV SERGEY , LISHMANOV YURI 
Published: December 2011

Background:
The aim of our study was to determine if ablation and pacing improved brain perfusion (BP) and cognitive function (CF) in patients with medically refractory rapidly conducted atrial fibrillation (Med Refr RCAF).
Methods and Results:
The study included 17 patients with Med Refr RCAF (average age 55.3 ± 4.5 years). All patients underwent brain single photon emission computed tomography scanning with 99mTc‐hexamethylpropylene amine oxime and comprehensive neuropsychological testing before and after 3 months following pacemaker implantation. The BP was significantly lower in all regions in patients with Med Refr RCAF compared with the control group. The greatest BP decrease was revealed in the inferior frontal (P = 0.002) and posterior parietal (P = 0.024) brain regions. These patients showed cognitive deficit in 94%. There was a direct correlation between BP and CF parameters. Ablation followed by pacemaker implantation had a positive effect on BP and CF in all patients with Med Refr RCAF. Thus, BP increased in the right inferior frontal (P = 0.01), in the left superior frontal (P = 0.007), and in the left temporal (P = 0.005) cortex. These patients demonstrated improvements in immediate and delayed verbal memory, immediate and delayed visual memory, abstract mentation, attention, psychomotor speed, as well as in learning.
Conclusions:
Patients with atrial fibrillation and rapid ventricular rates refractory to medical treatment have marked signs of brain hypoperfusion and impaired CF. Ablation and pacing improve left ventricular systolic function, thereby increasing BP and improving CF. (PACE 2011;1–7)
dRTA and hemolytic anemia: first detailed description of SLC4A1 A858D mutation in homozygous state
Authors: Fawaz Naglaa A. , Beshlawi Ismail O. , Al Zadjali Shoaib , Al Ghaithi Hamed K. , Elnaggari Mohamed A. , Elnour Ibtisam , Wali Yasser A. , Al‐Said Bushra B. , Rehman Jalil U. , Pathare Anil V. , Knox‐Macaulay Huxley , Alkindi Salam S. 
Published: December 2011

AbstractMutations in the anion exchanger 1 (AE1) gene encoding the erythroid and kidney anion (chloride–bicarbonate) exchanger 1 may result in familial distal renal tubular acidosis (dRTA) in association with membrane defect hemolytic anemia. Seven children presenting with hyperchloremic normal anion gap metabolic acidosis, failure to thrive, and compensated hemolytic anemia were studied. Analysis of red cell AE1/Band 3 surface expression by Eosin 5′‐maleimide (E5M) was performed in patients and their family members using flow cytometry. Genetic studies showed that all patients carried a common SLC4A1 mutation, c.2573C>A; p.Ala858Asp in exon 19, found as homozygous (A858D/A858D) mutation in the patients and heterozygous (A858D/N) in the parents. Analysis by flowcytometry revealed a single uniform fluorescence peak, with the mean channel fluorescence (MCF) markedly reduced in cases with homozygous mutation, along with a left shift of fluorescence signal but was only mildly reduced in the heterozygous state. Red cell morphology showed striking acanthocytosis in the homozygous state [patients] and only a mild acanthocytosis in heterozygous state [parents]. In conclusion, this is the first description of a series of homozygous cases with the A858D mutation. The E5M flowcytometry test is specific for reduction in the Band 3 membrane protein and was useful in conjunction with a careful morphological examination of peripheral blood smears in our patient cohort.
Mapping plant strategy types using remote sensing
Authors: Schmidtlein Sebastian , Feilhauer Hannes , Bruelheide Helge 
Published: December 2011

AbstractAimsThe three‐strategy (CSR) model proposed by Grime constitutes one of the most established systems for plant functional types. The primary strategies (competitive ability, adaptation to severe stress and adaptation to disturbance) relate to the productivity and level of disturbance at a given site. Accordingly, their change in space and time may serve as an illustration and measure of key processes such as succession, eutrophication and habitat shift. Here, we make use of the known links between the three primary strategies to traits with potential relevance for canopy reflectance, and test whether remote sensing is able to reproduce the spatial pattern of strategy types.LocationA raised bog and minerotrophic fen complex, Murnauer Moos, Germany.MethodsField data on the distribution of plant strategies in sample plots were regressed against canopy reflectance using partial least squares regression. The resulting models were validated and applied to airborne hyperspectral imagery on a per pixel basis. The resulting local maps for each strategy type and their combined representation in an RGB colour composite were interpreted in terms of plant species composition and environmental constraints.ResultsAll three primary strategy types could be mapped using remote sensing. Reflectance spectra related to competitive ability and adaptation to severe stress suggest that typical traits linked to these strategies exerted a direct influence. On the other hand, species with low cover values played a decisive role for the strength of the statistical relationship between reflectance and strategies. Because these species have a low impact on canopy reflectance, their contribution is better explained by their role as proxies for covarying variables such as the total cover of dead plant material.ConclusionsOur study demonstrates the potential to detect community strategy type composition using hyperspectral remote sensing, providing direct insights into spatial ecological patterns. By illustrating the exposure to stress, competition and disturbance, the derived maps of functional traits are potentially useful for applications in nature management and for the monitoring of functional shifts in ecosystems. As a next step, they can be easily combined into maps of functional diversity. Upcoming satellites with higher spectral resolution will improve access to this kind of spatial information.
Involvement of Perineuronal and Perisynaptic Extracellular Matrix in Alzheimer's Disease Neuropathology
Authors: Morawski Markus , Brückner Gert , Jäger Carsten , Seeger Gudrun , Matthews Russel T , Arendt Thomas 
Published: December 2011

AbstractBrain extracellular matrix (ECM) is organized in specific patterns assumed to mirror local features of neuronal activity and synaptic plasticity. Aggrecan‐based perineuronal nets (PNs) and brevican‐based perisynaptic axonal coats (ACs) form major structural phenotypes of ECM contributing to the laminar characteristics of cortical areas. In Alzheimer's disease (AD), the deposition of amyloid proteins and processes related to neurofibrillary degeneration may affect the integrity of the ECM scaffold. In this study we investigate ECM organization in primary sensory, secondary and associative areas of the temporal and occipital lobe. By detecting all major PN components we show that the distribution, structure and molecular properties of PNs remain unchanged in AD. Intact PNs occurred in close proximity to amyloid plaques and were even located within their territory. Counting of PNs revealed no significant alteration in AD. Moreover, neurofibrillary tangles never occurred in neurons associated with PNs. ACs were only lost in the core of amyloid plaques in parallel with the loss of synaptic profiles. In contrast, hyaluronan was enriched in the majority of plaques. We conclude that the loss of brevican is associated with the loss of synapses, whereas PNs and related matrix components resist disintegration and may protect neurons from degeneration.
Blocking the evolution of insecticide‐resistant malaria vectors with a microsporidian
Authors: Koella Jacob C. , Saddler Adam , Karacs Thomas P. S. 
Published: December 2011

AbstractFinding a way to block the evolution insecticide resistance would be a major breakthrough for the control of malaria. We suggest that this may be possible by introducing a stress into mosquito populations that restores the sensitivity of genetically resistant mosquitoes and that decreases their longevity when they are not exposed to insecticide. We use a mathematical model to show that, despite the intense selection pressure imposed by insecticides, moderate levels of stress might tip the evolutionary balance between costs and benefits of resistance toward maintaining sensitivity. Our experimental work with the microsporidian parasite Vavraia culicis infecting two lines of resistant mosquitoes and a sensitive line suggests that it may indeed be possible to stress the mosquitoes in the required way. The mortality of resistant mosquitoes 24 h after exposure to the insecticide was up to 8.8 times higher in infected than in uninfected ones; if mosquitoes were not exposed to the insecticide, resistant mosquitoes infected by the microsporidian lived about half as long as uninfected ones and insecticide‐sensitive mosquitoes (with or without the parasite). Our results suggest that biopesticides or other insecticides that interfere with the expression of resistance may help to manage insecticide resistance in programs of malaria control.
Genetic and maternal effects on tail spine and body length in the invasive spiny water flea (Bythotrephes longimanus)
Authors: Miehls Andrea L. J. , Peacor Scott D. , McAdam Andrew G. 
Published: December 2011

AbstractInterest in the evolution of invasive species has grown in recent years, yet few studies have investigated sources of variation in invasive species traits experiencing natural selection. The spiny water flea, Bythotrephes longimanus, is an invasive zooplankton in the Great Lakes that exhibits seasonal changes in tail spine and body length consistent with natural selection. Evolution of Bythotrephes traits, however, depends on the presence and magnitude of quantitative genetic variation, which could change within or across years. Clonal analysis of wild‐captured Bythotrephes indicated that variance components for distal spine length were variable among but not within years. Spine length was always heritable but was not always influenced by maternal effects. In contrast, variance components for body length varied both within and among years, but likewise body length was always heritable and not always influenced by maternal effects. Results indicate that important Bythotrephes traits have heritable variation comparable to native species and other invasive species that would enable an evolutionary response to natural selection. This evolutionary capacity could contribute to the widespread success and dramatic effects of Bythotrephes invasion in systems with diverse biotic and abiotic conditions.
Defining Clinical Research Nursing Practice: Results of a Role Delineation Study
Authors: Bevans Margaret , Hastings Clare , Wehrlen Leslie , Cusack Georgie , Matlock Ann Marie , Miller‐Davis Claiborne , Tondreau Linda , Walsh Diane , Wallen Gwenyth R. 
Published: December 2011

AbstractClinical research nursing is a specialty nursing practice focused on the care of research subjects and implementation of clinical research. A five‐dimensional model (Clinical Practice [CP], Study Management, Care Coordination and Continuity, Contributing to the Science [CS], Human Subjects Protection) has been validated nationally to represent the domain of clinical research nursing practice. The purpose of this study was to describe the frequency and importance of activities within each dimension as performed by nurses in clinical research and to describe differences between roles. One thousand and four nurses from the NIH Intramural Campus in Bethesda, Maryland, were invited to participate in an anonymous web‐based survey. Participants (N = 412) were predominantly female (90%) with ≥11 years research experience (70%). Two hundred eighty‐eight respondents (70%) identified themselves as clinical research nurses (CRNs) and 74 (18%) as research nurse coordinators (RNCs). CP activities were reported most frequent and important whereas CS activities were least frequent and important. CRN and RNC activity frequency differed across all dimensions (p < 0.001) with CRNs reporting significantly higher levels of CP activities and significantly lower levels in other dimensions. Delineating specialty activities and practice across roles enhances the understanding of nurses’ role in clinical research and provides groundwork for role‐based training. Clin Trans Sci 2011; Volume 4: 421–427