bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Surrogate Ensemble Study of Climate Reconstruction Methods: Stochasticity and Robustness
Authors: Christiansen Bo , Schmith T. , Thejll P. 
Published: August 2008

Abstract
Reconstruction of the earth’s surface temperature from proxy data is an important task because of the need to compare recent changes with past variability. However, the statistical properties and robustness of climate reconstruction methods are not well known, which has led to a heated discussion about the quality of published reconstructions. In this paper a systematic study of the properties of reconstruction methods is presented. The methods include both direct hemispheric-mean reconstructions and field reconstructions, including reconstructions based on canonical regression and regularized expectation maximization algorithms. The study will be based on temperature fields where the target of the reconstructions is known. In particular, the focus will be on how well the reconstructions reproduce low-frequency variability, biases, and trends.
A climate simulation from an ocean–atmosphere general circulation model of the period a.d. 1500–1999, including both natural and anthropogenic forcings, is used. However, reconstructions include a large element of stochasticity, and to draw robust statistical interferences, reconstructions of a large ensemble of realistic temperature fields are needed. To this end a novel technique has been developed to generate surrogate fields with the same temporal and spatial characteristics as the original surface temperature field from the climate model. Pseudoproxies are generated by degrading a number of gridbox time series. The number of pseudoproxies and the relation between the pseudoproxies and the underlying temperature field are determined realistically from Mann et al.
It is found that all reconstruction methods contain a large element of stochasticity, and it is not possible to compare the methods and draw conclusions from a single or a few realizations. This means that very different results can be obtained using the same reconstruction method on different surrogate fields. This might explain some of the recently published divergent results.
Also found is that the amplitude of the low-frequency variability in general is underestimated. All methods systematically give large biases and underestimate both trends and the amplitude of the low-frequency variability. The underestimation is typically 20%–50%. The shape of the low-frequency variability, however, is well reconstructed in general.
Some potential in validating the methods on independent data is found. However, to gain information about the reconstructions’ ability to capture the preindustrial level it is necessary to consider the average level in the validation period and not the year-to-year correlations. The influence on the reconstructions of the number of proxies, the type of noise used to generate the proxies, the strength of the variability, as well as the effect of detrending the data prior to the calibration is also reported.
Marginal Sea Overflows and the Upper Ocean Interaction
Authors: Kida Shinichiro , Yang Jiayan , Price James F. 
Published: August 2008

Abstract
Marginal sea overflows and the overlying upper ocean are coupled in the vertical by two distinct mechanisms—by an interfacial mass flux from the upper ocean to the overflow layer that accompanies entrainment and by a divergent eddy flux associated with baroclinic instability. Because both mechanisms tend to be localized in space, the resulting upper ocean circulation can be characterized as a β plume for which the relevant background potential vorticity is set by the slope of the topography, that is, a topographic β plume.
The entrainment-driven topographic β plume consists of a single gyre that is aligned along isobaths. The circulation is cyclonic within the upper ocean (water columns are stretched). The transport within one branch of the topographic β plume may exceed the entrainment flux by a factor of 2 or more.
Overflows are likely to be baroclinically unstable, especially near the strait. This creates eddy variability in both the upper ocean and overflow layers and a flux of momentum and energy in the vertical. In the time mean, the eddies accompanying baroclinic instability set up a double-gyre circulation in the upper ocean, an eddy-driven topographic β plume. In regions where baroclinic instability is growing, the momentum flux from the overflow into the upper ocean acts as a drag on the overflow and causes the overflow to descend the slope at a steeper angle than what would arise from bottom friction alone.
Numerical model experiments suggest that the Faroe Bank Channel overflow should be the most prominent example of an eddy-driven topographic β plume and that the resulting upper-layer transport should be comparable to that of the overflow. The overflow-layer eddies that accompany baroclinic instability are analogous to those observed in moored array data. In contrast, the upper layer of the Mediterranean overflow is likely to be dominated more by an entrainment-driven topographic β plume. The difference arises because entrainment occurs at a much shallower location for the Mediterranean case and the background potential vorticity gradient of the upper ocean is much larger.
“You Could Be Doing Brain Surgery”: Gifted Girls Becoming Teachers
Authors: Willard-Holt Colleen 
Published: August 2008

This qualitative study focuses on messages to gifted girls about their choice of a career in teaching. Participants consisted of 18 female teachers identified as gifted. The methodology consisted of semistructured interviews and focus group discussions. Findings indicate that messages of discouragement toward a career in teaching were more numerous and more emphatic than were messages of encouragement. Despite this, these participants were content with and remained committed to teaching careers for the foreseeable future. Participants also mentioned a variety of ways in which their giftedness interacted with their teaching, for their own benefit and that of their students. Recommendations for counselors, teachers, and parents include providing information about the entire range of career options and carefully matching career pathways with the student's interests and dreams rather than the adult's preconceived notions of success or prestige. Putting the Research to Use: There is little question that our society desperately needs teachers who are gifted. Yet gifted students who express an interest in a teaching career are often discouraged by family members, friends, teachers, and counselors. Although it is appropriate to encourage gifted students to pursue careers that might be perceived by society as more prestigious than teaching, it is counterproductive to guide students into careers inconsistent with their interests and values. By the time they are in high school, students who are interested in teaching have often sought out opportunities to interact with children and have engaged in activities such as playing school. These activities indicate the desire to teach, a desire that should be taken seriously. As Delisle (1998, p. 21) put it, “My hope is that . . . we will lecture less and listen more, giving academic and career guidance based upon individual interest patterns rather than preordained societal benchmarks of success.” In addition, students should engage in discussions regarding ways in which their intellectual talents may be challenged in teaching to the benefit of all.
Graphical exploration of network meta-analysis data: the use of multidimensional scaling
Authors: Chung Hyoju , Lumley Thomas 
Published: August 2008

Background Evidence synthesis is increasingly being used to compare more than two treatments from multiple randomized trials. In a network of randomized comparisons, direct (head-to-head) evidence might be inconsistent with indirect evidence. However, the issue of potential incoherence of the network is not taken into account in statistical models with fixed treatment effects only, which are commonly employed in practice. Purpose We present a graphical method to summarize a network of randomized comparisons and to examine the incoherence of the network, without making any distributional assumptions. Methods At each treatment-pair level, the inverse variance method is used to pool results from multiple studies. We consider the magnitude of pairwise treatment contrasts as a measure of pairwise dissimilarity. We summarize a network of randomized comparisons as a dissimilarity matrix, and then apply weighted multidimensional scaling to the dissimilarity matrix. The weights are chosen according to the inverse variance method. We show that, with this weighting scheme, 1D multidimensional scaling configuration is closely related to a fixed effect model. Therefore, our interest is to explore a departure from 1D constraint. Results Two-dimensional multidimensional scaling configuration is useful to explore the incoherence of the network. Our method is illustrated with two published datasets. Limitations The weighting scheme in our multidimensional scaling setting is chosen to be optimal for independent treatment pairs. Pairwise differences within a multi-arm trial are correlated to one another and intrinsically coherent. Thus our weighting scheme may not apply to data with large numbers of multi-arm trials. Conclusions Multidimensional scaling provides a useful tool for investigators to visualize the network of randomized comparisons and to assess incoherence of the network. Clinical Trials 2008; 5: 301—307. http://ctj.sagepub.com
Determining optimal sample sizes for multi-stage randomized clinical trials using value of information methods
Authors: Willan Andrew , Kowgier Matthew 
Published: August 2008

Background Traditional sample size calculations for randomized clinical trials depend on somewhat arbitrarily chosen factors, such as Type I and II errors. An effectiveness trial (otherwise known as a pragmatic trial or management trial) is essentially an effort to inform decision-making, i.e., should treatment be adopted over standard? Taking a societal perspective and using Bayesian decision theory, Willan and Pinto (Stat. Med. 2005; 24:1791-1806 and Stat. Med. 2006; 25:720) show how to determine the sample size that maximizes the expected net gain, i.e., the difference between the cost of doing the trial and the value of the information gained from the results. Methods These methods are extended to include multi-stage adaptive designs, with a solution given for a two-stage design. The methods are applied to two examples. Results As demonstrated by the two examples, substantial increases in the expected net gain (ENG) can be realized by using multi-stage adaptive designs based on expected value of information methods. In addition, the expected sample size and total cost may be reduced. Limitations Exact solutions have been provided for the two-stage design. Solutions for higher-order designs may prove to be prohibitively complex and approximate solutions may be required. Conclusions The use of multi-stage adaptive designs for randomized clinical trials based on expected value of sample information methods leads to substantial gains in the ENG and reductions in the expected sample size and total cost. Clinical Trials 2008; 5: 289-300. http://ctj.sagepub.com
Feasibility of randomized controlled trials on seclusion and mechanical restraint
Authors: Bergk Jan , Einsiedler Beate , Steinert Tilman 
Published: August 2008

Background In psychiatry seclusion and mechanical restraint are most commonly used in the management of violence and self-directed aggression. Both interventions are considered as efficacious and indispensable. Yet, these measures can have deleterious effects on patients. The least restrictive alternative is recommended. Evidence about what kind of intervention is least restrictive is only scarcely available. Up to now, no randomized controlled trial (RCT) on this subject has been conducted. Purpose To describe ethical, methodological and legal problems of RCTs on coercive interventions and to suggest possible solutions. Methods Literature research on possible study designs, ethical considerations and legal regulations was conducted in PubMed. Results Corresponding to the procedures in emergency medicine informed consent can be obtained after the intervention when the patients are capable again. Informed consent refers only to participation in an interview and utilization of data. Randomization can be ethically approved, if exclusion criteria for randomization are defined. A comprehensive cohort study seems to be the most practicable study design. As primary outcome variable an assessment of subjective experiences of the patients' restrictions to human rights. Clinical Trials 2008; 5: 356—363. http://ctjsagepub.com
The Hip Impact Protection Project: design and methods
Authors: Barton Bruce A , Birge Stanley J , Magaziner Jay , Zimmerman Sheryl , Ball Linda , Brown Kathleen M , Kiel Douglas P 
Published: August 2008

Background Nearly 340,000 hip fractures occur each year in the U.S. With current demographic trends, the number of hip fractures is expected to double at least in the next 40 years. Purpose The Hip Impact Protection Project (HIP PRO) was designed to investigate the efficacy and safety of hip protectors in an elderly nursing home population. This paper describes the innovative clustered matched-pair research design used in HIP PRO to overcome the inherent limitations of clustered randomization. Methods Three clinical centers recruited 37 nursing homes to participate in HIP PRO. They were randomized so that the participating residents in that home received hip protectors for either the right or left hip. Informed consent was obtained from either the resident or the resident's responsible party. The target sample size was 580 residents with replacement if they dropped out, had a hip fracture, or died. One of the advantages of the HIP PRO study design was that each resident was his/her own case and control, eliminating imbalances, and there was no confusion over which residents wore pads (or on which hip). Limitations Generalizability of the findings may be limited. Adherence was higher in this study than in other studies because of: (1) the use of a run-in period, (2) staff incentives, and (3) the frequency of adherence assessments. The use of a single pad is not analogous to pad use in the real world and may have caused unanticipated changes in behavior. Fall assessment was not feasible, limiting the ability to analyze fractures as a function of falls. Finally, hip protector designs continue to evolve so that the results generated using this pad may not be applicable to other pad designs. However, information about factors related to adherence will be useful for future studies. Conclusions The clustered matched-pair study design avoided the major problem with previous cluster-randomized investigations of this question — unbalanced risk factors between the experimental group and the control group. Because each resident served as his/her own control, the effects of unbalanced risk factors on treatment effect were virtually eliminated. In addition, the use of frequent adherence assessments allowed us to study the effect of various demographic and environmental factors on adherence, which was vital for the assessment of efficacy. Clinical Trials 2008; 5: 347—355. http://ctj.sagepub.com
High Loosening Rate of the Moje Acamo Prosthesis for Treating Osteoarthritis of the Trapeziometacarpal Joint
Authors: HANSEN T. B. , VAINORIUS D. 
Published: August 2008

The Moje Acamo carpometacarpal (CMC) implant is an uncemented large ball-and-socket joint made of a ceramic material coated with a bioactive substance (Bioverit) for osseous fixation. Nine Moje Acamo CMC prostheses were implanted into nine patients with primary osteoarthritis of the thumb CMC joint. At 12 months, three implants had been revised because of progressing pain and osteolysis. In the remaining six patients, radiographs have shown progressive osteolysis around both implants in five patients. These poor results mean that we no longer perform this operation and we recommend close follow-up of all cases that have been performed.
Complex Extensor Tendon Injuries: Early Active Motion Following Single-Stage Reconstruction
Authors: KOUL A. R. , PATIL R. K. , PHILIP V. 
Published: August 2008

This study presents a retrospective evaluation of patients managed with single-stage repair following complex extensor tendon injuries. Over a 2-year period, 21 extensor tendons were reconstructed in 18 patients with complex hand injuries in zones V–VII. All eight patients needed soft tissue cover. Active mobilisation was started in the first week. Total active motion (TAM) at 4 weeks was a mean of 159° (SD 21.57) and at 6 weeks it was 202.6° (SD 13.26). Average TAM at 8 weeks was 223.8° (SD 16.46) and 249.5° (SD 14.38) at 12 weeks. Grip strength at 12 weeks and 6 months was around 75% and 90% of the contralateral normal hand in most of the patients. Single-stage reconstruction of complex extensor tendon injuries seems to reduce morbidity in terms of hospitalisation, and reduced cost of treatment. It also helps to achieve better functional outcome in the early postoperative period.
Stat5 regulates cellular iron uptake of erythroid cells via IRP-2 and TfR-1
Authors: Kerenyi Marc A. , Grebien Florian , Gehart Helmuth , Schifrer Manfred , Artaker Matthias , Kovacic Boris , Beug Hartmut , Moriggl Richard , Müllner Ernst W. 
Published: August 2008

AbstractErythropoiesis strictly depends on signal transduction through the erythropoietin receptor (EpoR)–Janus kinase 2 (Jak2)–signal transducer and activator of transcription 5 (Stat5) axis, regulating proliferation, differentiation, and survival. The exact role of the transcription factor Stat5 in erythropoiesis remained puzzling, however, since the first Stat5-deficient mice carried a hypomorphic Stat5 allele, impeding full phenotypical analysis. Using mice completely lacking Stat5—displaying early lethality—we demonstrate that these animals suffer from microcytic anemia due to reduced expression of the antiapoptotic proteins Bcl-xL and Mcl-1 followed by enhanced apoptosis. Moreover, transferrin receptor-1 (TfR-1) cell surface levels on erythroid cells were decreased more than 2-fold on erythroid cells of Stat5−/− animals. This reduction could be attributed to reduced transcription of TfR-1 mRNA and iron regulatory protein 2 (IRP-2), the major translational regulator of TfR-1 mRNA stability in erythroid cells. Both genes were demonstrated to be direct transcriptional targets of Stat5. This establishes an unexpected mechanistic link between EpoR/Jak/Stat signaling and iron metabolism, processes absolutely essential for erythropoiesis and life.
Exhaustive prediction of disease susceptibility to coding base changes in the human genome
Authors: Kulkarni Vinayak , Errami Mounir , Barber Robert , Garner Harold R 
Published: August 2008

Abstract

Background
Single Nucleotide Polymorphisms (SNPs) are the most abundant form of genomic variation and can cause phenotypic differences between individuals, including diseases. Bases are subject to various levels of selection pressure, reflected in their inter-species conservation.

Results
We propose a method that is not dependant on transcription information to score each coding base in the human genome reflecting the disease probability associated with its mutation. Twelve factors likely to be associated with disease alleles were chosen as the input for a support vector machine prediction algorithm. The analysis yielded 83% sensitivity and 84% specificity in segregating disease like alleles as found in the Human Gene Mutation Database from non-disease like alleles as found in the Database of Single Nucleotide Polymorphisms. This algorithm was subsequently applied to each base within all known human genes, exhaustively confirming that interspecies conservation is the strongest factor for disease association. For each gene, the length normalized average disease potential score was calculated. Out of the 30 genes with the highest scores, 21 are directly associated with a disease. In contrast, out of the 30 genes with the lowest scores, only one is associated with a disease as found in published literature. The results strongly suggest that the highest scoring genes are enriched for those that might contribute to disease, if mutated.

Conclusion
This method provides valuable information to researchers to identify sensitive positions in genes that have a high disease probability, enabling them to optimize experimental designs and interpret data emerging from genetic and epidemiological studies.
ProteoLens: a visual analytic tool for multi-scale database-driven biological network data mining
Authors: Huan Tianxiao , Sivachenko Andrey Y , Harrison Scott H , Chen Jake Y 
Published: August 2008

Abstract

Background
New systems biology studies require researchers to understand how interplay among myriads of biomolecular entities is orchestrated in order to achieve high-level cellular and physiological functions. Many software tools have been developed in the past decade to help researchers visually navigate large networks of biomolecular interactions with built-in template-based query capabilities. To further advance researchers' ability to interrogate global physiological states of cells through multi-scale visual network explorations, new visualization software tools still need to be developed to empower the analysis. A robust visual data analysis platform driven by database management systems to perform bi-directional data processing-to-visualizations with declarative querying capabilities is needed.

Results
We developed ProteoLens as a JAVA-based visual analytic software tool for creating, annotating and exploring multi-scale biological networks. It supports direct database connectivity to either Oracle or PostgreSQL database tables/views, on which SQL statements using both Data Definition Languages (DDL) and Data Manipulation languages (DML) may be specified. The robust query languages embedded directly within the visualization software help users to bring their network data into a visualization context for annotation and exploration. ProteoLens supports graph/network represented data in standard Graph Modeling Language (GML) formats, and this enables interoperation with a wide range of other visual layout tools. The architectural design of ProteoLens enables the de-coupling of complex network data visualization tasks into two distinct phases: 1) creating network data association rules, which are mapping rules between network node IDs or edge IDs and data attributes such as functional annotations, expression levels, scores, synonyms, descriptions etc; 2) applying network data association rules to build the network and perform the visual annotation of graph nodes and edges according to associated data values. We demonstrated the advantages of these new capabilities through three biological network visualization case studies: human disease association network, drug-target interaction network and protein-peptide mapping network.

Conclusion
The architectural design of ProteoLens makes it suitable for bioinformatics expert data analysts who are experienced with relational database management to perform large-scale integrated network visual explorations. ProteoLens is a promising visual analytic platform that will facilitate knowledge discoveries in future network and systems biology studies.