bluuebunny/crossref_metadata_2025_split huggingface dataset:
A mouse embryonic stem cell bank for inducible overexpression of human chromosome 21 genes
Authors: De Cegli Rossella , Romito Antonio , Iacobacci Simona , Mao Lei , Lauria Mario , Fedele Anthony O , Klose Joachim , Borel Christelle , Descombes Patrick , Antonarakis Stylianos E , di Bernardo Diego , Banfi Sandro , Ballabio Andrea , Cobellis Gilda 
Published: June 2010

Abstract
Background
Dosage imbalance is responsible for several genetic diseases, among which Down syndrome is caused by the trisomy of human chromosome 21.

Results
To elucidate the extent to which the dosage imbalance of specific human chromosome 21 genes perturb distinct molecular pathways, we developed the first mouse embryonic stem (ES) cell bank of human chromosome 21 genes. The human chromosome 21-mouse ES cell bank includes, in triplicate clones, 32 human chromosome 21 genes, which can be overexpressed in an inducible manner. Each clone was transcriptionally profiled in inducing versus non-inducing conditions. Analysis of the transcriptional response yielded results that were consistent with the perturbed gene's known function. Comparison between mouse ES cells containing the whole human chromosome 21 (trisomic mouse ES cells) and mouse ES cells overexpressing single human chromosome 21 genes allowed us to evaluate the contribution of single genes to the trisomic mouse ES cell transcriptome. In addition, for the clones overexpressing the Runx1 gene, we compared the transcriptome changes with the corresponding protein changes by mass spectroscopy analysis.

Conclusions
We determined that only a subset of genes produces a strong transcriptional response when overexpressed in mouse ES cells and that this effect can be predicted taking into account the basal gene expression level and the protein secondary structure. We showed that the human chromosome 21-mouse ES cell bank is an important resource, which may be instrumental towards a better understanding of Down syndrome and other human aneuploidy disorders.
Use of Bisphosphonates and Risk of Postmenopausal Breast Cancer
Authors: Rennert Gad , Pinchev Mila , Rennert Hedy S. 
Published: June 2010

Purpose Bisphosphonates are commonly used for the treatment of osteoporosis and for prevention and treatment of skeletal lesions due to malignancy. However, the association between the use of bisphosphonates and the risk of developing breast cancer has not been reported. Patients and Methods The Breast Cancer in Northern Israel Study is a population-based case-control study in northern Israel of patients with breast cancer and age-, clinic-, and ethnic-group matched controls. Use of bisphosphonates was assessed in 4,039 postmenopausal patients and controls, members of Clalit Health Services, using pharmacy records. Results The use of bisphosphonates for longer than 1 year before diagnosis, but not for shorter than 1 year, was associated with a significantly reduced relative risk of breast cancer (odds ratio [OR], 0.61; 95% CI, 0.50 to 0.76). This association remained significant after adjustment for age, fruit, and vegetable consumption, sports activity, family history of breast cancer, ethnic group, body mass index, use of calcium supplements, hormone replacement therapy use, number of pregnancies, months of breast feeding, and age at first pregnancy (OR, 0.72; 95% CI, 0.57 to 0.90). Breast cancer risk did not change further if bisphosphonates were used for more years. Breast tumors identified in bisphosphonates users were more often estrogen receptor positive and less often poorly differentiated. Conclusion The use of bisphosphonates for longer than 1 year was associated with a 28% relative reduction in the risk of postmenopausal breast cancer. Tumors developing under bisphosphonates treatment tended to have a favorable prognostic factors profile.
Adoption of Adjuvant Chemotherapy for Non–Small-Cell Lung Cancer: A Population-Based Outcomes Study
Authors: Booth Christopher M. , Shepherd Frances A. , Peng Yingwei , Darling Gail E. , Li Gavin , Kong Weidong , Mackillop William J. 
Published: June 2010

Purpose Since 2004, several clinical trials have demonstrated that adjuvant chemotherapy (ACT) improves survival in patients with early-stage non–small-cell lung cancer (NSCLC). Here, we evaluate the uptake of ACT and its impact on outcomes in the general population of Ontario, Canada. Methods All patients diagnosed with NSCLC in Ontario from 2001 to 2006 who underwent surgical resection (n = 6,304) were identified using the Ontario Cancer Registry. We linked electronic records of treatment to the registry. We described uptake of ACT and compared survival of all patients with surgically resected NSCLC diagnosed from 2001 to 2003 with patients diagnosed from 2004 to 2006. As a proxy measure of ACT-related toxicity, we evaluated hospitalizations within 6 months of surgery. Results Demographic, disease, and treatment-related characteristics did not differ between the 2001 to 2003 and 2004 to 2006 study cohorts. Over the study period, the proportion of patients receiving ACT increased from 7% (192 of 2,950 patients) to 31% (1,032 of 3,354 patients; P < .001). The proportion of patients admitted to hospital within 6 months of surgery remained stable and (36% in the 2001 to 2003 cohort and 37% in the 2004 to 2006 cohort). However, within 2 years of surgery, there was a 33% reduction in the proportion of patients admitted to hospital with metastatic disease (P < .001). During the study period, there was a substantial improvement in 4-year survival among surgically resected patients, from 52.5% (2001 to 2003) to 56.1% (2004 to 2006; P = .001). Conclusion There has been a rapid uptake of ACT for NSCLC, which was not associated with an increased rate of hospitalization. The adoption of ACT was associated with a substantial improvement in overall survival, suggesting that the benefits seen in clinical trials are generalizable to the general population.
Analytical Performance of 4 Automated Assays for Measurement of Cystatin C
Authors: Li Jinong , Dunn Willard , Breaud Autumn , Elliott Debra , Sokoll Lori J , Clarke William 
Published: June 2010

BACKGROUND
We evaluated the analytical performance of 4 cystatin C assays (Siemens N Latex on BNII, Roche Tina-quant on Cobas c501, Genzyme on Cobas c501, and Tosoh ST AIA-PACK on Tosoh AIA-600II) according to guidelines published by the Clinical and Laboratory Standards Institute.

METHODS
We evaluated total imprecision, limit of detection, and limit of quantification for each assay using patient serum pools and linearity/recovery using serial dilutions of a patient serum pool with cystatin C–free serum. We compared patients (n = 102) using the Siemens assay as a comparison method.

RESULTS
All assays had limits of detection and quantification &lt;0.08 and &lt;0.39 mg/L, respectively. Total CVs were generally higher than the manufacturers' claims for all assays. The Roche assay overrecovered cystatin C, particularly at low concentrations (mean recovery 119%, 142% at 0.587 mg/L). Deming regression equations were y = 1.184x + 0.089, Sy|x = 0.246 for Genzyme; y = 0.937x + 0.231, Sy|x = 0.231 for Roche; and y = 1.010x + 0.216, Sy|x = 0.115 for Tosoh. The Genzyme assay appeared to report higher results than the Siemens assay, which is consistent with a higher reference interval specified by the manufacturer.

CONCLUSIONS
Although all assays were acceptable for clinical use, their diagnostic performances were not optimal. Limitations include imprecision greater than claimed, overrecovery for the Roche assay on low concentration samples, and differences in results for patient samples. The latter situation requires assay-specific cystatin C–based glomerular filtration rate prediction equations at least until calibration is standardized using the international cystatin C calibrator now being developed.
Evaluation of Oligonucleotide Sequence Capture Arrays and Comparison of Next-Generation Sequencing Platforms for Use in Molecular Diagnostics
Authors: Hoppman-Chaney Nicole , Peterson Lisa M , Klee Eric W , Middha Sumit , Courteau Laura K , Ferber Matthew J 
Published: June 2010

BACKGROUND
Next-generation DNA sequencing (NGS) techniques have the potential to revolutionize molecular diagnostics; however, a thorough evaluation of these technologies is necessary to ensure their performance meets or exceeds that of current clinical sequencing methods.

METHODS
We evaluated the NimbleGen Sequence Capture 385K Human Custom Arrays for enrichment of 22 genes. We sequenced each sample on both the Roche 454 Genome Sequencer FLX (GS-FLX) and the Illumina Genome Analyzer II (GAII) to compare platform performance.

RESULTS
Although the sequence capture method allowed us to rapidly develop a large number of sequencing assays, we encountered difficulty enriching G+C–rich regions. Although a high proportion of reads consistently mapped outside of the targeted regions, &gt;80% of targeted bases for the GAII and &gt;30% of bases for the GS-FLX were covered by a read depth of ≥20, and &gt;90% of bases for the GAII and &gt;80% of bases for the GS-FLX were covered by a read depth of ≥5. We observed discrepancies among sequence variants identified by the different platforms.

CONCLUSIONS
Although oligonucleotide arrays are quick and easy to develop, some problematic regions may evade capture, necessitating sequential redesigning for complete optimization. Neither sequencing technology was able to detect every variant identified by Sanger sequencing because of well-known drawbacks of the NGS technologies. The rapidly decreasing error rates and costs of these technologies, however, coupled with advancing bioinformatic capabilities, make them an attractive option for molecular diagnostics in the very near future.
Aurora kinases orchestrate mitosis; who are the players?
Authors: Molla Annie 
Published: June 2010

AbstractThe Aurora are a conserved family of serine/threonine kinases with essential functions in cell division. In mitosis, Aurora kinases are required for chromosome segregation, condensation and orientation in the metaphase plate, spindle assembly, and the completion of cytokinesis. This review presents the Aurora kinases, their partners and how their interactions impact on the different mitotic functions.
Desintegration und Interpretation: Weil-V2-Sätze an der Schnittstelle zwischen Syntax, Semantik und Pragmatik
Authors: Antomo Mailin , Steinbach Markus 
Published: June 2010

Abstract
In spoken varieties of German, causal adverbial clauses introduced by weil are frequently used with V2 order. Interestingly, weil-V2 clauses are not simply a colloquial variant of standard verb-final clauses, but have also many specific syntactic, semantic, and pragmatic properties. On the one hand, weil-V2 clauses differ systematically from their verb-final counterparts. While V2 clauses yield causal interpretations not available for the corresponding verb-final clauses, verb-final clauses show a higher degree of syntactic integration and syntactic flexibility than V2 clauses. On the other hand, weil-V2 clauses share crucial formal and functional properties with other kinds of embedded V2 clauses such as V2-complement clauses and V2-relative clauses. Weil-V2 clauses can therefore be subsumed under the notion of ‘embedded root phenomena’. In this paper, we develop an analysis that derives all syntactic, semantic, and pragmatic properties of weil-V2 clauses at the interfaces between syntax, semantics, and pragmatics from their paratactic syntactic structure and the assertional force potential triggered by V-to-C movement. The results of a questionnaire study provide independent empirical evidence for our analysis.
Immobilization of Cellulase and Hemicellulases on Porous Glass Beads
Authors: Mandali Pavani , Dalaly Basil K. 
Published: June 2010

Abstract
Experiments on immobilization of cellulase complex (cellulase, Novozymes) and enzyme complex (cellulases and hemicellulases, Novozymes) were performed on porous Siran™ beads using covalent and non-covalent bonding methods. Free enzyme complex was used for hydrolyzing various pretreated biomass such as corn stover, distillers dried grain with solubles, switch grass and blue stem grass. Maximum activity of enzyme complex was found with corn stover and was used as a substrate for measuring cellulase and hemicellulases activities. Protein loading for immobilized cellulase complex and enzyme complex on Siran™ carriers was found in the range of 10.776–18.000 % and 19.932–23.082 %, respectively. Activity loading for immobilized cellulase complex with avicel was in the range of 16.610–22.026 %. For enzyme complex, activity loading was found in the range of 43.558–61.222 %, 8.274–19.124 %, and 7.180–14.114 % with avicel, xylan, and corn stover as substrates, respectively. Recycling experiments for immobilized cellulase complex and enzyme complex were carried out using various substrates, and the residual enzyme activity was measured after the third cycle. Carbodiimide bonded cellulase complex retained more residual enzyme activity with avicel (49.460 %), which indicates a good cross linker for cellulase immobilization. The enzyme complex bonded to carbodiimide, and glutaraldehyde retained residual activity of 44.160 % with xylan and 73.230 % with corn stover, respectively. Recycling studies showed greater retention in residual enzyme activity with covalent bonded enzymes than non-covalent bonded enzymes. Glutaraldehyde and carbodiimide were found to be effective cross linkers for immobilizing both cellulase and hemicellulases in covalent bonding method.
Common Sense and Masonry Repair
Authors: Pashina Keith A. , Talafous Steven M. 
Published: June 2010

Abstract
The maintenance and restoration of masonry structures are often repetitive processes. Many of the problems encountered are very common. Many problems requiring maintenance and repair could have been mitigated or prevented with a little foresight and coordination during the design and construction period. Why is so much effort expended on “repairing the repairs”? This paper discusses how common mistakes occur and why. Many of the perceived restraints on the design and construction phases such as time, budget, level of craftsmanship, and material costs do and should affect the project. However, these constraints must be balanced against the functionality of the masonry, such as durability, structural stability, weather barrier, and aesthetics. Through real-life examples, this paper describes a simple repair of rehabilitation process that will lead to a successful project outcome: Long lasting, low maintenance masonry structures. It takes into account the owner’s needs, priorities, and budgetary, physical, and time constraints before any design development or repair begins. For comparison, unsuccessful project outcomes from actual projects will also be explored.
Fire ant alate wing motion data and numerical reconstruction
Authors: Gui L. , Fink T. , Cao Z , Sun D. , Seiner J.M , Streett D.A. 
Published: June 2010

Abstract
The wing motions of a male and a female fire ant alate, which beat their wings at 108 and 96 Hz, respectively, were captured with a stereo imaging system at a high frame rate of 8,000 frames per second. By processing the high-speed image frames, the three-dimensional wingtip positions and the wing surface orientation angles were determined with a high phase resolution, i.e. 74 and 83 phases per period for the male and the female, respectively. A numerical reconstruction of the stereo wingbeat images demonstrated that the data collected described almost all the details of the wing surface motion, so that further computational fluid dynamic simulations are possible for fire ant alate flight.
Tropical land‐cover change alters biogeochemical inputs to ecosystems in a Mexican montane landscape
Authors: Ponette-González A. G. , Weathers K. C. , Curran L. M. 
Published: June 2010

In tropical regions, the effects of land‐cover change on nutrient and pollutant inputs to ecosystems remain poorly documented and may be pronounced, especially in montane areas exposed to elevated atmospheric deposition. We examined atmospheric deposition and canopy interactions of sulfate‐sulfur (SO42−‐S), chloride (Cl−), and nitrate‐nitrogen (NO3−‐N) in three extensive tropical montane land‐cover types: clearings, forest, and coffee agroforest. Bulk and fog deposition to clearings was measured as well as throughfall (water that falls through plant canopies) ion fluxes in seven forest and five coffee sites. Sampling was conducted from 2005 to 2008 across two regions in the Sierra Madre Oriental, Veracruz, Mexico.Annual throughfall fluxes to forest and coffee sites ranged over 6–27 kg SO42−‐S/ha, 12–69 kg Cl−/ha, and 2–6 kg NO3−‐N/ha. Sulfate‐S in forest and coffee throughfall was higher or similar to bulk S deposition measured in clearings. Throughfall Cl− inputs, however, were consistently higher than Cl− amounts deposited to cleared areas, with net Cl− fluxes enhanced in evergreen coffee relative to semi‐deciduous forest plots. Compared to bulk nitrate‐N deposition, forest and coffee canopies retained 1–4 kg NO3−‐N/ha annually, reducing NO3−‐N inputs to soils. Overall, throughfall fluxes were similar to values reported for Neotropical sites influenced by anthropogenic emissions, while bulk S and N deposition were nine‐ and eightfold greater, respectively, than background wet deposition rates for remote tropical areas.Our results demonstrate that land‐cover type significantly alters the magnitude and spatial distribution of atmospheric inputs to tropical ecosystems, primarily through canopy‐induced changes in fog and dry deposition. However, we found that land cover interacts with topography and climate in significant ways to produce spatially heterogeneous patterns of anion fluxes, and that these factors can converge to create deposition hotspots. For land managers, this finding suggests that there is potential to identify species and ecosystems at risk of excess and increasing deposition in montane watersheds undergoing rapid transformation. Our data further indicate that montane ecosystems are vulnerable to air pollution impacts in this and similar tropical regions downwind of urban, industrial, and agricultural emission sources.
Similar cation exchange capacities among bryophyte species refute a presumed mechanism of peatland acidification
Authors: Soudzilovskaia N. A. , Cornelissen J. H. C. , During H. J. , van Logtestijn R. S. P. , Lang S. I. , Aerts R. 
Published: June 2010

Fen–bog succession is accompanied by strong increases of carbon accumulation rates. We tested the prevailing hypothesis that living Sphagna have extraordinarily high cation exchange capacity (CEC) and therefore acidify their environment by exchanging tissue‐bound protons for basic cations in soil water. AsSphagnuminvasion in a peatland usually coincides with succession from a brown moss‐dominated alkaline fen to an acidic bog, the CEC of Sphagna is widely believed to play an important role in this acidification process. However,SphagnumCEC has never been compared explicitly to that of a wide range of other bryophyte taxa. Whether high CEC directly leads to the ability to acidify the environment in situ also remains to be tested.We screened 20 predominant subarctic bryophyte species, including fen brown mosses and bog Sphagna for CEC, in situ soil water acidification capacity (AC), and peat acid neutralizing capacity (ANC). All these bryophyte species possessed substantial CEC, which was remarkably similar for brown mosses and Sphagna. This refutes the commonly accepted idea of livingSphagnumCEC being responsible for peatland acidification, asSphagnum's ecological predecessors, brown mosses, can do the same job.SphagnumAC was several times higher than that of other bryophytes, suggesting that CE (cation exchange) sites of Sphagna in situ are not saturated with basic cations, probably due to the virtual absence of these cations in the bog water. Together, these results suggest that Sphagna can not realize their CEC in bogs, while fen mosses can do so in fens. The fen peat ANC was 65% higher than bog ANC, indicating that acidity released by brown mosses in the CE process was neutralized, maintaining an alkaline environment.We propose two successional pathways indicating boundaries for a fen–bog shift with respect to bryophyte CEC. In neither of them isSphagnumCE an important factor. We conclude that livingSphagnumCEC does not play any considerable role in the fen–bog shift. Alternatively, we propose that exclusively indirect effects ofSphagnumexpansion such as peat accumulation and subsequent blocking of upward alkaline soil water transport are keys to the fen–bog succession and therefore for bog‐associated carbon accumulation.
Periodontal Conditions in Elderly Men With and Without Osteoporosis or Osteopenia
Authors: Shum Irma , Leung Ping‐Chung , Kwok Anthony , Corbet Esmonde F. , Orwoll Eric S. , Phipps Kathy R. , Jin Lijian 
Published: June 2010

Background: The purpose of this case‐control study is to investigate the periodontal conditions in elderly men with and without osteoporosis or osteopenia and to determine their possible association with periodontal destruction.Methods: A total of 200 community‐dwelling Chinese males (age range: 69 to 78 years; mean ± SD age: 71.9 ± 3.3 years) were recruited from the Jockey Club Center for Osteoporosis Care and Control, The Chinese University of Hong Kong, including 67 subjects with osteoporosis, 66 subjects with osteopenia, and 67 age‐matched normal control subjects based on bone mineral density at the hip, spine, and whole body measured by dual‐energy x‐ray densitometry. All subjects were interviewed using questionnaires and received a full‐mouth periodontal examination.Results: Subjects with osteoporosis exhibited a significantly higher percentage of sites with clinical attachment loss (AL) ≥6 mm compared to subjects with osteopenia (P <0.05); subjects with osteoporosis also showed a greater percentage of sites with interproximal gingival recession (GR) ≥5 mm than did control subjects (P <0.05) after excluding smokers. Subjects with osteoporosis were more likely (odds ratio = 3.3; P <0.05) to exhibit interproximal GR ≥5 mm than were control subjects. Osteoporosis remained significantly associated with severe clinical AL and interproximal GR after adjusting for age, supragingival plaque, and number of teeth lost.Conclusion: This study suggests that osteoporosis is associated with severe clinical AL and interproximal GR in elderly Chinese men.
Crestal Bone–Level Changes Around Implants Placed in Post‐Extraction Sockets Augmented With Demineralized Freeze‐Dried Bone Allograft: A Retrospective Radiographic Study
Authors: Koutouzis Theofilos , Lundgren Tord 
Published: June 2010

Background: There is limited information regarding marginal crestal bone–level changes around implants placed in post‐extraction sockets augmented with demineralized freeze‐dried bone allograft (DFDBA). The aim of this study was to retrospectively compare bone‐level changes around implants placed in post‐extraction sockets augmented with DFDBA to implants placed in native bone.Methods: Records of 30 consecutive patients treated with dental implants placed in post‐extraction sockets augmented with DFDBA and 30 consecutive patients with implants placed in native bone were reviewed. For each implant, the radiographs from the surgical appointment were compared to those from the last follow‐up visit and evaluated regarding changes of marginal bone level over time.Results: The overall survival rate from baseline to the last follow‐up visit was 100% for both groups. The mean marginal bone loss was 0.15 mm for both groups for a mean follow‐up time of 12 months. There were no significant differences regarding the percentage of implants and implant surfaces demonstrating marginal bone loss.Conclusion: The present study indicates implants placed in post‐extraction sockets augmented with DFDBA exhibited minimal marginal bone loss similar to implants placed in native bone.