bluuebunny/crossref_metadata_2025_split huggingface dataset:
A protein network-guided screen for cell cycle regulators in Drosophila
Authors: Guest Stephen T , Yu Jingkai , Liu Dongmei , Hines Julie A , Kashat Maria A , Finley Russell L 
Published: May 2011

Abstract

Background
Large-scale RNAi-based screens are playing a critical role in defining sets of genes that regulate specific cellular processes. Numerous screens have been completed and in some cases more than one screen has examined the same cellular process, enabling a direct comparison of the genes identified in separate screens. Surprisingly, the overlap observed between the results of similar screens is low, suggesting that RNAi screens have relatively high levels of false positives, false negatives, or both.

Results
We re-examined genes that were identified in two previous RNAi-based cell cycle screens to identify potential false positives and false negatives. We were able to confirm many of the originally observed phenotypes and to reveal many likely false positives. To identify potential false negatives from the previous screens, we used protein interaction networks to select genes for re-screening. We demonstrate cell cycle phenotypes for a significant number of these genes and show that the protein interaction network is an efficient predictor of new cell cycle regulators. Combining our results with the results of the previous screens identified a group of validated, high-confidence cell cycle/cell survival regulators. Examination of the subset of genes from this group that regulate the G1/S cell cycle transition revealed the presence of multiple members of three structurally related protein complexes: the eukaryotic translation initiation factor 3 (eIF3) complex, the COP9 signalosome, and the proteasome lid. Using a combinatorial RNAi approach, we show that while all three of these complexes are required for Cdk2/Cyclin E activity, the eIF3 complex is specifically required for some other step that limits the G1/S cell cycle transition.

Conclusions
Our results show that false positives and false negatives each play a significant role in the lack of overlap that is observed between similar large-scale RNAi-based screens. Our results also show that protein network data can be used to minimize false negatives and false positives and to more efficiently identify comprehensive sets of regulators for a process. Finally, our data provides a high confidence set of genes that are likely to play key roles in regulating the cell cycle or cell survival.
The best practice for preparation of samples from FTA®cards for diagnosis of blood borne infections using African trypanosomes as a model system
Authors: Ahmed Heba A , MacLeod Ewan T , Hide Geoff , Welburn Susan C , Picozzi Kim 
Published: May 2011

Abstract

Background
Diagnosis of blood borne infectious diseases relies primarily on the detection of the causative agent in the blood sample. Molecular techniques offer sensitive and specific tools for this although considerable difficulties exist when using these approaches in the field environment. In large scale epidemiological studies, FTA®cards are becoming increasingly popular for the rapid collection and archiving of a large number of samples. However, there are some difficulties in the downstream processing of these cards which is essential for the accurate diagnosis of infection. Here we describe recommendations for the best practice approach for sample processing from FTA®cards for the molecular diagnosis of trypanosomiasis using PCR.

Results
A comparison of five techniques was made. Detection from directly applied whole blood was less sensitive (35.6%) than whole blood which was subsequently eluted from the cards using Chelex®100 (56.4%). Better apparent sensitivity was achieved when blood was lysed prior to application on the FTA cards (73.3%) although this was not significant. This did not improve with subsequent elution using Chelex®100 (73.3%) and was not significantly different from direct DNA extraction from blood in the field (68.3%).

Conclusions
Based on these results, the degree of effort required for each of these techniques and the difficulty of DNA extraction under field conditions, we recommend that blood is transferred onto FTA cards whole followed by elution in Chelex®100 as the best approach.
Breaking evolutionary and pleiotropic constraints in mammals: On sloths, manatees and homeotic mutations
Authors: Varela-Lasheras Irma , Bakker Alexander J , van der Mije Steven D , Metz Johan AJ , van Alphen Joris , Galis Frietson 
Published: May 2011

Abstract
Background
Mammals as a rule have seven cervical vertebrae, except for sloths and manatees. Bateson proposed that the change in the number of cervical vertebrae in sloths is due to homeotic transformations. A recent hypothesis proposes that the number of cervical vertebrae in sloths is unchanged and that instead the derived pattern is due to abnormal primaxial/abaxial patterning.

Results
We test the detailed predictions derived from both hypotheses for the skeletal patterns in sloths and manatees for both hypotheses. We find strong support for Bateson's homeosis hypothesis. The observed vertebral and rib patterns cannot be explained by changes in primaxial/abaxial patterning. Vertebral patterns in sloths and manatees are similar to those in mice and humans with abnormal numbers of cervical vertebrae: incomplete and asymmetric homeotic transformations are common and associated with skeletal abnormalities. In sloths the homeotic vertebral shift involves a large part of the vertebral column. As such, similarity is greatest with mice mutant for genes upstream of Hox.

Conclusions
We found no skeletal abnormalities in specimens of sister taxa with a normal number of cervical vertebrae. However, we always found such abnormalities in conspecifics with an abnormal number, as in many of the investigated dugongs. These findings strongly support the hypothesis that the evolutionary constraints on changes of the number of cervical vertebrae in mammals is due to deleterious pleitropic effects. We hypothesize that in sloths and manatees low metabolic and activity rates severely reduce the usual stabilizing selection, allowing the breaking of the pleiotropic constraints. This probably also applies to dugongs, although to a lesser extent.
High mobility group box 1 (HMGB1) and anti-HMGB1 antibodies and their relation to disease characteristics in systemic lupus erythematosus
Authors: Abdulahad Deena A , Westra Johanna , Bijzet Johannes , Limburg Pieter C , Kallenberg Cees GM , Bijl Marc 
Published: May 2011

Abstract
Introduction
High Mobility Group Box 1 (HMGB1) is a nuclear non-histone protein. HMGB1, which is secreted by inflammatory cells and passively released from apoptotic and necrotic cells, may act as a pro-inflammatory mediator. As apoptotic cells accumulate in systemic lupus erythematosus (SLE), HMGB1 levels might be increased in SLE. HMGB1 may also serve as an autoantigen, leading to the production of anti-HMGB1 antibodies. In this study we determined levels of HMGB1 and anti-HMGB1 in SLE patients in comparison to healthy controls (HC) and analysed their relation with disease activity.

Methods
The study population consisted of 70 SLE patients and 35 age- and sex-matched HC. Thirty-three SLE patients had quiescent disease, the other 37 patients were selected for having active disease. Nineteen of these had lupus nephritis. HMGB1 levels were measured with both Western blot and ELISA. Anti-HMGB1 levels were measured by ELISA. Clinical and serological parameters were assessed according to routine procedures.

Results
HMGB1 levels in SLE patients could be measured reliably by Western blotting only, and were significantly increased compared to HC. During active disease HMGB1 levels increased, in particular in patients with renal involvement. Serum HMGB1 levels correlated with SLEDAI, proteinuria, and anti-dsDNA levels, and showed a negative correlation with complement C3. Anti-HMGB1 levels were significantly increased in SLE patients compared to HC, and positively correlated with HMGB1 levels.

Conclusions
Levels of HMGB1 in the sera of SLE patients, in particular in those with active renal disease, are increased. Serum HMGB1 levels are related to SLEDAI scores and proteinuria, as well as to levels of anti-HMGB1 antibodies. These findings suggest that besides HMGB1, HMGB1-anti-HMGB1 immune complexes play a role in the pathogenesis of SLE, in particular in patients with renal involvement.
Dynamic of oxidative and nitrosative stress markers during the convalescent period of stroke patients undergoing rehabilitation
Authors: Manolescu Bogdan Nicolae , Berteanu M , Oprea E , Chiriac N , Dumitru L , Vlădoiu S , Popa O , Ianăş O 
Published: May 2011

Background Stroke patients have a redox imbalance, a consequence of both the cerebrovascular event and the associated pathological conditions. Our study was aimed to investigate the dynamic of some oxidative and nitrosative markers during the convalescent phase of postacute stroke patients undergoing rehabilitation. Methods We assessed thiol, advanced oxidation protein product, protein carbonyl, 3-nitro-l-tyrosine, ceruloplasmin and oxidized LDL concentrations, as well as gamma-glutamyltranspeptidase (GGT) activity in 20 patients at the beginning of the hospitalization and at the discharge moment, respectively, and 24 apparently healthy controls. Results We found significantly increased values for GGT ( P = 0.04), ceruloplasmin ( P = 0.01) and protein carbonyl ( P = 0.04) in stroke patients at the hospitalization moment when compared with healthy controls, while total thiols were significantly decreased ( P = 0.002). Rehabilitation was associated with a significant decrease of protein carbonyl ( P = 0.03) and oxidized LDL particle concentrations ( P = 0.03), as well as GGT activity ( P = 0.02). At the hospitalization moment, both GGT and ceruloplasmin were significantly negatively correlated with non-proteic thiols ( r = −0.44, P = 0.049, and r = −0.53, P = 0.015, respectively) and significantly positively with protein carbonyls ( r = +0.80, P < 0.001, and r = +0.69, P < 0.001, respectively) suggesting putative roles of GGT and ceruloplasmin in the redox imbalance. Conclusions These results highlight the existence of a redox imbalance in postacute stroke patients, and the possible benefits of an antioxidant-based therapy for the recovery of these patients.
Size Effect Related to Composite Toughness Characterization
Authors: Yotte Sylvie , Breysse Denys 
Published: May 2011

Abstract
This paper deals with toughness characterization of composite materials. In that case, Linearly Elastic Fracture Mechanics (LEFM) may not be effective because a damage zone develops at the notch tip during crack propagation. Experimental tests were carried out on two different series of homothetic specimens (Single Edge Notched Tensile and Steel Frame Assisted Tension). Data gathered for the tested sample sizes confirmed that LEFM cannot be used for toughness characterization. A macroscopic failure criterion was hence derived from experimental data. Acoustic emission data indicated fiber bridging as the main mechanism opposing crack propagation. The corresponding microscopic failure criterion is chosen to define a test-independent criterion. Cumulative statistical distributions of test-independent failure parameters were finally determined on the basis of all experimental results.
Derivation of Clinically Relevant Boundary Conditions Suitable for Evaluation of Chronic Impingement of Lumbar Total Disk Replacement: Application to Standard Development
Authors: Rundell S. A. , Day J. S. , Isaza J. , Siskey R. , MacDonald D. , Kurtz S. M. 
Published: May 2011

Abstract
Currently available standardized methods for evaluating the long-term wear of total disk replacements do not incorporate the effects of potential device impingement. Creation of a standard that incorporates device impingement is difficult without a thorough understanding of the associated biomechanical environment. Arbitrary modification of the currently available wear-test protocols to account for device impingement may add unnecessary cost, and potentially inaccurate, unrealistic results. Finite element models provide the ability to control variation and test for a wide range of parameters without the excessive time and monetary costs associated with cadaveric testing or wear simulations. However, careful validation and verification of these models is required in order to ensure predictability. Retrieved implants can be used to validate the clinical predictability of finite element models (FEMs). The objective of the current study was to quantify the ability of a previously developed FEM of the lumbar spine to predict polyethylene damage modes and impingement in actual clinical scenarios, and extract the loading and boundary conditions for implementation into a new lumbar TDR wear simulation standard. In order to achieve this objective, actual clinical scenarios, associated with retrieved implants, were modeled and simulated. We hypothesized that clinical damage modes, including both impingement and non-impingement scenarios, can be predicted using a FEM that incorporates case-specific clinical factors, anterior-posterior shear forces, coupled translations, and facet contact.
A Clustering Analysis Model for Golden Die Extractions Based on Wafer Acceptance Test at Semiconductor R&D Stage
Authors: Liu S. F. , Chen F. L. , Lin S. C. , Chang K. J. , Yu S. M. 
Published: May 2011

Abstract
During the research and development (R&D) stage of semiconductor fabrication, the R&D engineers make a lot of effort to identify golden dice that meet simulated performance of circuit design. With feedback from wafer acceptance test (WAT) data of the golden dice, the efficiency of process window analysis can be further improved. However, it is difficult for current practices to select golden dice due to limited time and cost concerns. In this research, an analytical model is proposed to analyze WAT data during the R&D stage of semiconductor fabrication to assist R&D engineers in resolving these critical issues. WAT data are collected and utilized to classify dice on a wafer and similar golden dice are then identified based on pre-defined golden dice. Similar golden dice can provide much more important feedback from WAT data, and the efficiency of process window analysis can then be improved. Real WAT data at the R&D stage during semiconductor fabrication were collected from a famous semiconductor manufacturing company and were experimented through the presented methodology. Experimental results show that the presented model can successfully extract representative similar golden dice within clusters. With advice from R&D engineers, the representative similar golden dice extracted from this work are sufficient for subsequent process window analysis.
“—wie ihn uns Meister Dürer gemalt!”: Contest, Myth, and Prophecy in Wagner's Die Meistersinger von Nürnberg
Authors: Goehr Lydia 
Published: May 2011

Abstract
Wagner introduced into the very first scene of his opera Die Meistersinger von Nürnberg a brief description of an image of David slaying Goliath. He attributed the image to Albrecht Dürer. But did Dürer actually produce this image? To answer the question, this essay assumes the form of a “had I but known” mystery story to explore the mythological and theological foundations of Wagner's opera of contest, myth, and prophecy. The quest for Dürer's image is set against three contests: between Apollo and Marsyas; between the arts of music, poetry, and painting; and between composers, painters, and poets. The essay draws upon these contests to make explicit the unfolding of a drama that begins with an image in which the old King David of the harp is displaced by a young King David of the sword. The question is: who exactly is the young David?
Testicular size development and reproductive hormones in boys and adult males with Noonan syndrome: a longitudinal study
Authors: Ankarberg-Lindgren Carina , Westphal Otto , Dahlgren Jovanna 
Published: May 2011

ObjectiveTo characterise changes in testicular size and reproductive hormones and to investigate the aetiology of delayed puberty and impaired fertility in males with Noonan syndrome (NS).DesignIn this study, 12 males with NS were longitudinally followed from pre/early puberty until adulthood. Of the 12 males, ten had no medical history other than NS and were divided into two groups, undescended testes (UT), and descended testes (DT) and compared with a reference population.MethodsHormone concentrations in serum were determined by immunoassays and testicular volume was measured using an orchidometer.ResultsBefore puberty, reproductive hormone levels were within the expected range in almost all cases. In some cases, LH, FSH and testosterone and oestradiol (E2) concentrations started to increase during puberty and inhibin B and anti-Müllerian hormone (AMH) declined to subnormal levels. Most of the boys studied had small testes that, in the majority of cases, progressed to normal size in adulthood. No difference in reproductive hormones was observed between the UT and DT groups either during puberty or at adulthood. However, as adults, males with NS had higher LH (5.7 vs 4.0 U/l, P<0.01), FSH (7.1 vs 2.5 U/l, P<0.001), testosterone (18.7 vs 15.6 nmol/l, P<0.01) and E2 (66 vs 46 pmol/l, P<0.001) levels and lower AMH (33 vs 65 pmol/l, P<0.01) and inhibin B (median 108 vs 187 pg/ml, P<0.01) levels than the reference population.ConclusionsIn NS males, both Sertoli and Leydig cell dysfunction is common with reproductive hormone levels deteriorating progressively to adulthood.
Motivations of Orthodontic Residents in Canada and the United States to Treat Patients with Craniofacial Anomalies, Cleft Lip/Palate, and Special Needs
Authors: Noble James , Schroth Robert J. , Hechter Frank J. , Huminicki Amanda , Wiltshire William A. 
Published: May 2011

Objectives To determine the motivation of orthodontic residents in Canada and the United States to treat patients with cleft lip/palate (CLP), craniofacial anomalies (CFA), and special needs (SN). Methods In March 2009, an e-mail with a link to a 41-item survey was sent to all orthodontic residents in Canada and the United States (n = 944). Results Of 944 residents contacted, 339 viewed and 208 completed the survey (22.03%). Using a seven-point Likert scale, residents recognized the importance of treating patients with CLP/CFA/SN. When asked if they plan to treat patients with CLP/CFA/SN, 54.48% responded yes, 13.46% no, and 36.06% were unsure. A total of 38.05% said they would charge the same fee as a typical multiarch case, while 58.05% would charge more, and 60% of fourth-year residents would charge twice the fee. Of the respondents, 43.00% were aware of the established fellowship programs in CLP/CFA/SN. Canadian residents (67.9%) were more enthusiastic about completing a fellowship than Americans were. Of the respondents, 29.33% would complete a 1-year fellowship, while 70.67% would not. A total of 78.4% of male respondents and 77.4% of American residents indicated they would not pursue a fellowship. Conclusions Residents supported the importance of treating patients with CLP/CFA/SN, and more than 54% indicated they plan to treat these patients. Residents who indicated that they would not treat these patients sited limited experience and inadequate expertise as the reasons. Less than 30% indicated a willingness to pursue a fellowship program.
Experimental and Numerical Study of Steam Flooding in Fractured Porous Media
Authors: Ashrafi Mohammad , Souraki Yaser , Karimaie Hassan , Torsaeter Ole 
Published: May 2011

Abstract
Extra heavy oil and bitumen reservoirs constitute a huge proportion of total world oil reserves. Thermal recovery and steam based methods are the most widely used recovery methods in these kinds of reservoirs. Steam injection into fractured heavy oil reservoirs to recover matrix oil has been considered as an efficient EOR method. However, mechanism of steam injection is more complex in fractured reservoirs than in conventional reservoirs. Evaluation of steam injection in fractured porous media requires good understanding of the physical processes between rock and fluids in matrix and fracture. In fact recovery could be a combination of several mechanisms such as viscous forces, capillary imbibition, thermal expansion and gravity drainage.
This paper presents experimental and simulation study of steam flooding in fractured porous media that contains Athabasca heavy oil. Some PVT properties of Athabasca crude oil have been measured experimentally and simulation study was accomplished using a numerical thermal reservoir simulator. A single horizontal fracture and two surrounding matrix blocks have been defined to verify the performance of steam injection in a 20 cm long sandstone core with a permeability of 640 mD saturated with Athabasca heavy crude. Considering a fractured system, sensitivity analyses were focused on the effect of injection rate, fracture permeability and steam quality.
The most important conclusion is that there is an optimum steam temperature and quality for most efficient steam injection. The permeability of the fracture should be low considering both oil production and steam oil ratio (SOR), which is a measure of economy. Matrix permeability of 640 mD in sandstone core provides satisfactory recovery and SOR. Higher matrix permeability can cause very high SOR and affect the economy of the process. Results also clearly show that higher injection rate improve the oil recovery. However, SOR should also be considered at the same time. There is a trade-off between recovery and SOR. It is also clear that lower fracture width shows better recovery while causing high injection pressure at the inlet.
Applying Fractional Flow Theory to Determine CO2 Storage Capacity of a Deep Saline Aquifer
Authors: Ghanbarnezhad Rouzbeh , Lake Larry W. 
Published: May 2011

Abstract
In this paper, we introduce a novel technique to determine the storage capacity of a saline aquifer for CO2 trapped because of the capillary snap-off and dissolution. The capillary snap-off trapping and dissolution into the aqueous phase are two principal mechanisms of the CO2 sequestration in an intermediate time-scale. The CO2 storage capacity of aquifers provides a criterion to determine the best candidates.
However, conducting numerical simulations to assess the CO2 storage capacity of an aquifer is complex and time-consuming because of various trapping mechanisms acting simultaneously with various rates on different time scales. Further, these simulations require detailed inputs and hence are limited to site-specific study.
We adopt the notion of the optimal solvent-water-slug size and use the graphical solution of multiple geochemical front propagation and fractional flow theory to determine the largest (optimal) slug of injected CO2 trapped because of the capillary trapping and the dissolution. The optimal slug size is the CO2 storage capacity of the aquifer because injecting more than the optimum leads to production of injected CO2 and injecting below the optimum leaves the aquifer unfilled. The two cases represent overcapacity and under-capacity storage, respectively. We use numerical simulation to validate the accuracy of the predicted optimal slug size. Simulation results confirm the accuracy of the predicted values.
In practice, the proposed method provides an efficient screening method to assess the CO2 storage capacity of aquifers and significantly reduces the simulation costs.