bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relative power and sample size analysis on gene expression profiling data
Authors: van Iterson M , 't Hoen PAC , Pedotti P , Hooiveld GJEJ , den Dunnen JT , van Ommen GJB , Boer JM , Menezes RX 
Published: September 2009

AbstractBackgroundWith the increasing number of expression profiling technologies, researchers today are confronted with choosing the technology that has sufficient power with minimal sample size, in order to reduce cost and time. These depend on data variability, partly determined by sample type, preparation and processing. Objective measures that help experimental design, given own pilot data, are thus fundamental.ResultsRelative power and sample size analysis were performed on two distinct data sets. The first set consisted of Affymetrix array data derived from a nutrigenomics experiment in which weak, intermediate and strong PPARαagonists were administered to wild-type and PPARα-null mice. Our analysis confirms the hierarchy of PPARα-activating compounds previously reported and the general idea that larger effect sizes positively contribute to the average power of the experiment. A simulation experiment was performed that mimicked the effect sizes seen in the first data set. The relative power was predicted but the estimates were slightly conservative. The second, more challenging, data set describes a microarray platform comparison study using hippocampalδC-doublecortin-like kinase transgenic mice that were compared to wild-type mice, which was combined with results from Solexa/Illumina deep sequencing runs. As expected, the choice of technology greatly influences the performance of the experiment. Solexa/Illumina deep sequencing has the highest overall power followed by the microarray platforms Agilent and Affymetrix. Interestingly, Solexa/Illumina deep sequencing displays comparable power across all intensity ranges, in contrast with microarray platforms that have decreased power in the low intensity range due to background noise. This means that deep sequencing technology is especially more powerful in detecting differences in the low intensity range, compared to microarray platforms.ConclusionPower and sample size analysis based on pilot data give valuable information on the performance of the experiment and can thereby guide further decisions on experimental design. Solexa/Illumina deep sequencing is the technology of choice if interest lies in genes expressed in the low-intensity range. Researchers can get guidance on experimental design using our approach on their own pilot data implemented as a BioConductor package, SSPAhttp://bioconductor.org/packages/release/bioc/html/SSPA.html.
Identification and characterization of miRNAs expressed in the bovine ovary
Authors: Hossain Md Munir , Ghanem Nasser , Hoelker Michael , Rings Franca , Phatsara Chirawath , Tholen Ernst , Schellander Karl , Tesfaye Dawit 
Published: September 2009

Abstract

Background
MicroRNAs are the major class of gene-regulating molecules playing diverse roles through sequence complementarity to target mRNAs at post-transcriptional level. Tightly regulated expression and interaction of a multitude of genes for ovarian folliculogenesis could be regulated by these miRNAs. Identification of them is the first step towards understanding miRNA-guided gene regulation in different biological functions. Despite increasing efforts in miRNAs identification across various species and diverse tissue types, little is known about bovine ovarian miRNAs. Here, we report the identification and characterization of miRNAs expressed in the bovine ovary through cloning, expression analysis and target prediction.

Results
The miRNA library (5'-independent ligation cloning method), which was constructed from bovine ovary in this study, revealed cloning of 50 known and 24 novel miRNAs. Among all identified miRNAs, 38 were found to be new for bovine and were derived from 43 distinct loci showing characteristic secondary structure. While 22 miRNAs precursor loci were found to be well conserved in more than one species, 16 were found to be bovine specific. Most of the miRNAs were cloned multiple times, in which let-7a, let-7b, let-7c, miR-21, miR-23b, miR-24, miR-27a, miR-126 and miR-143 were cloned 10, 28, 13, 4, 11, 7, 6, 4 and 11 times, respectively. Expression analysis of all new and some annotated miRNAs in different intra-ovarian structures and in other multiple tissues showed that some were present ubiquitously while others were differentially expressed among different tissue types. Bta-miR-29a was localized in the follicular cells at different developmental stages in the cyclic ovary. Bio-informatics prediction, screening and Gene Ontology analysis of miRNAs targets identified several biological processes and pathways underlying the ovarian function.

Conclusion
Results of this study suggest the presence of miRNAs in the bovine ovary, thereby elucidate their potential role in regulating diverse molecular and physiological pathways underlying the ovarian functionality. This information will give insights into bovine ovarian miRNAs, which can be further characterized for their role in follicular development and female fertility as well.
Revisiting the Plasmodium falciparum RIFIN family: from comparative genomics to 3D-model prediction
Authors: Bultrini Emanuele , Brick Kevin , Mukherjee Srayanta , Zhang Yang , Silvestrini Francesco , Alano Pietro , Pizzi Elisabetta 
Published: September 2009

Abstract

Background
Subtelomeric RIFIN genes constitute the most abundant multigene family in Plasmodium falciparum. RIFIN products are targets for the human immune response and contribute to the antigenic variability of the parasite. They are transmembrane proteins grouped into two sub-families (RIF_A and RIF_B). Although recent data show that RIF_A and RIF_B have different sub-cellular localisations and possibly different functions, the same structural organisation has been proposed for members of the two sub-families. Despite recent advances, our knowledge of the regulation of RIFIN gene expression is still poor and the biological role of the protein products remain obscure.

Results
Comparative studies on RIFINs in three clones of P. falciparum (3D7, HB3 and Dd2) by Multidimensional scaling (MDS) showed that gene sequences evolve differently in the 5'upstream, coding, and 3'downstream regions, and suggested a possible role of highly conserved 3' downstream sequences. Despite the expected polymorphism, we found that the overall structure of RIFIN repertoires is conserved among clones suggesting a balance between genetic drift and homogenisation mechanisms which guarantees emergence of novel variants but preserves the functionality of genes. Protein sequences from a bona fide set of 3D7 RIFINs were submitted to predictors of secondary structure elements. In contrast with the previously proposed structural organisation, no signal peptide and only one transmembrane helix were predicted for the majority of RIF_As. Finally, we developed a strategy to obtain a reliable 3D-model for RIF_As. We generated 265 possible structures from 53 non-redundant sequences, from which clustering and quality assessments selected two models as the most representative for putative RIFIN protein structures.

Conclusion
First, comparative analyses of RIFIN repertoires in different clones of P. falciparum provide insights on evolutionary mechanisms shaping the multigene family. Secondly, we found that members of the two sub-families RIF_As and RIF_Bs have different structural organization in accordance with recent experimental results. Finally, representative models for RIF_As have an "Armadillo-like" fold which is known to promote protein-protein interactions in diverse contexts.
Early detection of breast cancer: benefits and risks of supplemental breast ultrasound in asymptomatic women with mammographically dense breast tissue. A systematic review
Authors: Nothacker Monika , Duda Volker , Hahn Markus , Warm Mathias , Degenhardt Friedrich , Madjar Helmut , Weinbrenner Susanne , Albert Ute-Susann 
Published: September 2009

AbstractBackgroundMammographic screening alone will miss a certain fraction of malignancies, as evidenced by retrospective reviews of mammograms following a subsequent screening. Mammographic breast density is a marker for increased breast cancer risk and is associated with a higher risk of interval breast cancer, i.e. cancer detected between screening tests. The purpose of this review is to estimate risks and benefits of supplemental breast ultrasound in women with negative mammographic screening with dense breast tissue.MethodsA systematic search and review of studies involving mammography and breast ultrasound for screening of breast cancer was conducted. The search was performed for the period 1/2000-8/2008 within the data source of PubMed, DARE, and Cochrane databases. Inclusion and exclusion criteria were determined prospectively, and the Oxford evidence classification system for diagnostic studies was used for evidence level. The parameters biopsy rate, positive predictive value (PPV) for biopsy, cancer yield for breast ultrasound alone, and carcinoma detection rate by breast density were extracted or constructed.ResultsThe systematic search identified no randomized controlled trials or systematic reviews, six cohort studies of intermediate level of evidence (3b) were found. Only two of the studies included adequate follow-up of subjects with negative or benign findings. Supplemental breast ultrasound after negative mammographic screening permitted diagnosis of primarily invasive carcinomas in 0.32% of women in breast density type categories 2-4 of the American College of Radiology (ACR); mean tumor size for those identified was 9.9 mm, 90% with negative lymph node status. Most detected cancers occurred in mammographically dense breast ACR types 3 and 4. Biopsy rates were in the range 2.3%-4.7%, with PPV of 8.4-13.7% for those biopsied due to positive ultrasound, or about one third of the PPV of biopsies due to mammography. Limitations: The study populations included wide age ranges, and the application to women age 50-69 years as proposed for mammographic screening could result in less striking benefit. Further validation studies should employ a uniform assessment system such as BI-RADS and report not only PPV, but also negative predictive value, sensitivity and specificity.ConclusionSupplemental breast ultrasound in the population of women with mammographically dense breast tissue (ACR 3 and 4) permits detection of small, otherwise occult, breast cancers. Potential adverse impacts for women in this intermediate risk group are associated with an increased biopsy rate.
Using vital statistics to estimate the population-level impact of osteoporotic fractures on mortality based on death certificates, with an application to France (2000-2004)
Authors: Ziadé Nelly , Jougla Eric , Coste Joël 
Published: September 2009

Abstract

Background
We developed a methodology using vital statistics to estimate the impact of osteoporotic fractures on the mortality of an entire population, and applied it to France for the period 2000-2004.

Methods
Current definitions of osteoporotic fractures were reviewed and their components identified. We used the International Classification of Diseases with national vital statistics data for the French adult population and performed cross-classifications between various components: age, sex, I-code (site) and E-code (mechanism of fracture). This methodology allowed identification of appropriate thresholds and categorization for each pertinent component.

Results
2,625,743 death certificates were analyzed, 2.2% of which carried a mention of fracture. Hip fractures represented 55% of all deaths from fracture. Both sexes showed a similar pattern of mortality rates for all fracture sites, the rate increased with age from the age of 70 years. The E-high-energy code (present in 12% of death certificates with fractures) was found to be useful to rule-out non-osteoporotic fractures, and to correct the overestimation of mortality rates. Using this methodology, the crude number of deaths associated with fractures was estimated to be 57,753 and the number associated with osteoporotic fractures 46,849 (1.85% and 1.78% of all deaths, respectively).

Conclusion
Osteoporotic fractures have a significant impact on overall population mortality.
The Sam domain of the lipid phosphatase Ship2 adopts a common model to interact with Arap3-Sam and EphA2-Sam
Authors: Leone Marilisa , Cellitti Jason , Pellecchia Maurizio 
Published: September 2009

Abstract

Background
Sterile alpha motif (Sam) domains are small protein modules that can be involved in homotypic or heterotypic associations and exhibit different functions. Previous studies have demonstrated that the Sam domain of the lipid phosphatase Ship2 can hetero-dimerize with the Sam domain of the PI3K effector protein Arap3.

Results
Here, we determine the NMR solution structure of Arap3-Sam and implement a multidisciplinary approach consisting of NMR spectroscopy, ITC (Isothermal Titration Calorimetry), mutagenesis and molecular modeling studies to analyze the interaction between Ship2-Sam and Arap3-Sam. This work reveals that Arap3-Sam may associate with Ship2-Sam by adopting a binding mode common to other Sam domains. This binding mode is identical to what we have very recently observed for the association between Ship2-Sam and the Sam domain from the Ephrin A2 receptor.

Conclusion
Our studies further clarify the structural features that are relevant for Sam-Sam interactions involving Ship2 and give additional hints that could be used for the identification of new molecules able to selectively inhibit Sam-Sam associations.
Adherence to anti-tuberculosis treatment among pulmonary tuberculosis patients: a qualitative and quantitative study
Authors: Xu Weiguo , Lu Wei , Zhou Yang , Zhu Limei , Shen Hongbing , Wang Jianming 
Published: September 2009

Abstract

Background
Tuberculosis (TB) patients have difficulty following a long-term treatment regimen. Efforts to improve treatment outcomes require better understanding of adherence as a complex behavioral issue and of the particular barriers to and facilitators of patient adherence.

Methods
This study was carried out in Jiangsu Province of China with both quantitative and qualitative approaches. For the quantitative study, 780 sputum-smear positive TB patients consecutively registered since 2006 in 13 counties (districts) were queried with a structured questionnaire. Patients who had missed 10% of their total prescribed doses of TB drugs were deemed as non-adherent. Risks for non-adherence were estimated by computing odds ratios (ORs) and their 95% confidence intervals (95% CIs) using a logistic regression model. We also invited 20 TB patients and 10 local health workers for in-depth interviews. We then used content analysis based on this qualitative study to explore factors associated with non-adherence.

Results
The proportion of non-adherence among 670 patients was 12.2%. Univariate analysis showed that patients, who were illiterate, divorced/widowed, lacked health insurance and were migrants, were more likely to be non-adherent. The crude ORs(95%CIs) were 2.38(1.37-4.13), 2.42(1.30-4.52), 1.89(1.07-3.32) and 1.98(1.03-3.83), respectively. The risk of non-adherence was lower among patients whose treatment was given under direct observation by village doctors or regular home visits by health workers, with ORs (95% CIs) of 0.19(0.10-0.36) and 0.23(0.10-0.51), respectively. In multivariate analysis, factors associated with non-adherence included illiteracy (OR: 2.42; 95% CI: 1.25-4.67) and direct observation by village doctors (OR: 0.23; 95% CI: 0.11-0.45). The in-depth interviews indicated that financial burdens and extra medical expenditures, adverse drug reactions, and social stigma were additional potential factors accounted for non-adherence.

Conclusion
More importance should be given to treatment adherence under the current TB control program. Heavy financial burdens, lack of social support, adverse drug reactions and personal factors are associated with non-adherence. Direct observation and regular home visits by health workers appear to reduce the risk of non-adherence. More patient-centered interventions and greater attention to structural barriers are needed to improve treatment adherence.
Visualizing fusion of pseudotyped HIV-1 particles in real time by live cell microscopy
Authors: Koch Peter , Lampe Marko , Godinez William J , Müller Barbara , Rohr Karl , Kräusslich Hans-Georg , Lehmann Maik J 
Published: September 2009

Abstract

Background
Most retroviruses enter their host cells by fusing the viral envelope with the plasma membrane. Although the protein machinery promoting fusion has been characterized extensively, the dynamics of the process are largely unknown.

Results
We generated human immunodeficiency virus-1 (HIV-1) particles pseudotyped with the envelope (Env) protein of ecotropic murine leukemia virus eMLV to study retrovirus entry at the plasma membrane using live-cell microscopy. This Env protein mediates highly efficient pH independent fusion at the cell surface and can be functionally tagged with a fluorescent protein. To detect fusion events, double labeled particles carrying one fluorophor in Env and the other in the matrix (MA) domain of Gag were generated and characterized. Fusion events were defined as loss of Env signal after virus-cell contact. Single particle tracking of >20,000 individual traces in two color channels recorded 28 events of color separation, where particles lost the Env protein, with the MA layer remaining stable at least for a short period. Fourty-five events were detected where both colors were lost simultaneously. Importantly, the first type of event was never observed when particles were pseudotyped with a non-fusogenic Env.

Conclusion
These results reveal rapid retroviral fusion at the plasma membrane and permit studies of the immediate post-fusion events.
Beneficial effect of the oxygen free radical scavenger amifostine (WR-2721) on spinal cord ischemia/reperfusion injury in rabbits
Authors: Chronidou Fany , Apostolakis Efstratios , Papapostolou Ioannis , Grintzalis Konstantinos , Georgiou Christos D , Koletsis Efstratios N , Karanikolas Menelaos , Papathanasopoulos Panagiotis , Dougenis Dimitrios 
Published: September 2009

Abstract

Background
Paraplegia is the most devastating complication of thoracic or thoraco-abdominal aortic surgery. During these operations, an ischemia-reperfusion process is inevitable and the produced radical oxygen species cause severe oxidative stress for the spinal cord. In this study we examined the influence of Amifostine, a triphosphate free oxygen scavenger, on oxidative stress of spinal cord ischemia-reperfusion in rabbits.

Methods
Eighteen male, New Zealand white rabbits were anesthetized and spinal cord ischemia was induced by temporary occlusion of the descending thoracic aorta by a coronary artery balloon catheter, advanced through the femoral artery. The animals were randomly divided in 3 groups. Group I functioned as control. In group II the descending aorta was occluded for 30 minutes and then reperfused for 75 min. In group III, 500 mg Amifostine was infused into the distal aorta during the second half-time of ischemia period. At the end of reperfusion all animals were sacrificed and spinal cord specimens were examined for superoxide radicals by an ultra sensitive fluorescent assay.

Results
Superoxide radical levels ranged, in group I between 1.52 and 1.76 (1.64 ± 0.10), in group II between 1.96 and 2.50 (2.10 ± 0.23), and in group III (amifostine) between 1.21 and 1.60 (1.40 ± 0.19) (p = 0.00), showing a decrease of 43% in the Group of Amifostine. A lipid peroxidation marker measurement ranged, in group I between 0.278 and 0.305 (0.296 ± 0.013), in group II between 0.427 and 0.497 (0.463 ± 0.025), and in group III (amifostine) between 0.343 and 0.357 (0.350 ± 0.007) (p < 0.00), showing a decrease of 38% after Amifostine administration.

Conclusion
By direct and indirect methods of measuring the oxidative stress of spinal cord after ischemia/reperfusion, it is suggested that intra-aortic Amifostine infusion during spinal cord ischemia phase, significantly attenuated the spinal cord oxidative injury in rabbits.
Between-day reliability of electromechanical delay of selected neck muscles during performance of maximal isometric efforts
Authors: Almosnino Sivan , Pelland Lucie , Pedlow Samuel V , Stevenson Joan M 
Published: September 2009

Abstract

Background
The purpose of this study was to assess the between-day reliability of the electromechanical delay (EMD) of selected neck muscles during the performance of maximal isometric contractions in five different directions.

Methods
Twenty-one physically active males participated in two testing sessions separated by seven to eight days. Using a custom-made fixed frame dynamometer, cervical force and surface electromyography (EMG) were recorded bilaterally from the splenius capitis, upper trapezius and sternocleidomastoid muscles during the performance of efforts in extension, flexion, left and right lateral bending, and protraction. The EMD was extracted using the Teager-Kaiser Energy Operator. Reliability indices calculated for each muscle in each testing direction were: the difference in scores between the two testing sessions and corresponding 95% confidence intervals, the standard error of measurement (SEM) and intra-class correlation coefficients (ICC).

Results
EMD values showed no evidence of systematic difference between the two testing sessions across all muscles and testing directions. The SEM for extension, flexion and lateral bending efforts ranged between 2.5 ms to 4.8 ms, indicating a good level of measurement precision. For protraction, SEM values were higher and considered to be imprecise for research and clinical purposes. ICC values for all muscles across all testing directions ranged from 0.23 to 0.79.

Conclusion
EMD of selected neck muscles can be measured with sufficient precision for the assessment of neck muscle function in an athletic population in the majority of directions tested.