bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tropical and Subtropical Meridional Latent Heat Transports by Disturbances to the Zonal Mean and Their Role in the General Circulation
Authors: Shaw Tiffany A. , Pauluis Olivier 
Published: February 2012

Abstract
The spectrum of meridional latent heat transport in the tropics and subtropics by disturbances to the zonal mean during all seasons is analyzed. The transport is divided into stationary and transient planetary- and subplanetary-scale eddy contributions.
The stationary transport is largest in the subtropical lower troposphere and dominates the overall transport during summer. It is of planetary scale and the zonal scale of the transport corresponds to the number of subtropical anticyclones. The transient transport is large from the surface up to the midtroposphere and from the tropics to subpolar latitudes. It is dominated by the subplanetary-scale contribution during all seasons. Westward (eastward)- propagating waves dominate the transport in the tropics (subtropics and midlatitudes). The analysis reveals that, while the total eddy meridional latent heat transport is seamless from the deep tropics to the pole, it represents the sum of transport by distinct dynamical features.
The role of the eddy meridional latent heat transport in the moist isentropic circulation is assessed using the statistical transformed Eulerian mean formulation, which converts the eddy transports into streamfunctions. The addition of the eddy latent heat streamfunction to the Eulerian mean plus eddy sensible heat streamfunction increases the mass transport by a factor of 2–3 in the subtropics and midlatitudes. The eddy transport is found to dominate the transport across the subtropical boundary. During Northern Hemisphere summer there is virtually no circulation in the absence of eddy latent heat transport. The results highlight the important role of latent heat transport by subtropical anticyclones and tropical and baroclinic waves in the general circulation.
Effect of Touch Screen Button Size and Spacing on Touch Characteristics of Users With and Without Disabilities
Authors: Sesto Mary E. , Irwin Curtis B. , Chen Karen B. , Chourasia Amrish O. , Wiegmann Douglas A. 
Published: February 2012

Objective: The aim of this study was to investigate the effect of button size and spacing on touch characteristics (forces, impulses, and dwell times) during a digit entry touch screen task. A secondary objective was to investigate the effect of disability on touch characteristics. Background: Touch screens are common in public settings and workplaces. Although research has examined the effect of button size and spacing on performance, the effect on touch characteristics is unknown. Method: A total of 52 participants ( n = 23, fine motor control disability; n = 14, gross motor control disability; n = 15, no disability) completed a digit entry task. Button sizes varied from 10 mm to 30 mm, and button spacing was 1 mm or 3 mm. Results: Touch characteristics were significantly affected by button size. The exerted peak forces increased 17% between the largest and the smallest buttons, whereas impulses decreased 28%. Compared with the fine motor and nondisabled groups, the gross motor group had greater impulses (98% and 167%, respectively) and dwell times (60% and 129%, respectively). Peak forces were similar for all groups. Conclusion: Button size but not spacing influenced touch characteristics during a digit entry task. The gross motor group had significantly greater dwell times and impulses than did the fine motor and nondisabled groups. Application: Research on touch characteristics, in conjunction with that on user performance, can be used to guide human computer interface design strategies to improve accessibility of touch screen interfaces. Further research is needed to evaluate the effect of the exerted peak forces and impulses on user performance and fatigue.
Use Patterns Among Early Adopters of Adaptive Cruise Control
Authors: Xiong Huimin , Boyle Linda Ng , Moeckli Jane , Dow Benjamin R. , Brown Timothy L. 
Published: February 2012

Objective: The objective of this study was to investigate use patterns among early adopters of adaptive cruise control (ACC). Background: Extended use of ACC may influence a driver’s behavior in the long term, which can have unintended safety consequences. Method: The authors examined the use of a motion-based simulator by 24 participants (15 males and 9 females). Cluster analysis was performed on drivers’ use of ACC and was based on their gap settings, speed settings, number of warnings issued, and ACC disengaged. The data were then examined on the basis of driving performance measures and drivers’ subjective responses to trust in ACC, understanding of system operations, and driving styles. Driving performance measures included minimum time headway, adjusted minimum time to collision, and drivers’ reaction time to critical events. Results: Three groups of drivers were observed on the basis of risky behavior, moderately risky behavior, and conservative behavior. Drivers in the conservative group stayed farther behind the lead vehicle than did drivers in the other two groups. Risky drivers responded later to critical events and had more ACC warnings issued. Conclusion: Safety consequences with ACC may be more prevalent in some driver groups than others. The findings suggest that these safety implications are related to trust in automation, driving styles, understanding of system operations, and personalities. Application: Potential applications of this research include enhanced design for next-generation ACC systems and countermeasures to improve safe driving with ACC.
Supervisory Control of Multiple Robots
Authors: Chen Jessie Y. C. , Barnes Michael J. 
Published: February 2012

Objective: A military multitasking environment was simulated to examine the effects of an intelligent agent, RoboLeader, on the performance of robotics operators. Background: The participants’ task was to manage a team of ground robots with the assistance of RoboLeader, an intelligent agent capable of coordinating the robots and changing their routes on the basis of battlefield developments. Method: In the first experiment, RoboLeader was perfectly reliable; in the second experiment, RoboLeader’s recommendations were manipulated to be either false-alarm prone or miss prone, with a reliability level of either 60% or 90%. The visual density of the targeting environment was manipulated by the presence or absence of friendly soldiers. Results: RoboLeader, when perfectly reliable, was helpful in reducing the overall mission times. The type of RoboLeader imperfection (false-alarm vs. miss prone) affected operators’ performance of tasks involving visual scanning (target detection, route editing, and situation awareness). There was a consistent effect of visual density (clutter of the visual scene) for multiple performance measures. Participants’ attentional control and video gaming experience affected their overall multitasking performance. In both experiments, participants with greater spatial ability consistently outperformed their low-spatial-ability counterparts in tasks that required effective visual scanning. Conclusion: Intelligent agents, such as RoboLeader, can benefit the overall human-robot teaming performance. However, the effects of type of agent unreliability, tasking requirements, and individual differences have complex effects on human-agent interaction. Application: The current results will facilitate the implementation of robots in military settings and will provide useful data to designs of systems for multirobot control.
An analysis of measured and estimated creatinine clearance rates in normal weight, overweight, and obese patients with gynecologic cancers
Authors: Nelson Wendelin K , Formica Richard N , Cooper Dennis L , Schwartz Peter E , Rutherford Thomas J 
Published: February 2012

Study objective: Different equations used to estimate creatinine clearance (Clcr) in obese oncology patients can produce divergent estimated creatinine clearance values, which in turn can result in significantly different calculated carboplatin doses. Standardization of the calculation of creatinine clearance in patients of all body types is a desirable goal. The objective of our study was to examine the impact of increasing body mass index on the accuracy of creatinine clearance estimation methods and to determine the optimal equation for creatinine clearance estimation in the obese adult female cancer patient. Design: Retrospective data analysis. Patients: We compared the estimated creatinine clearance values produced by each of 11 equations to 24-hour creatinine clearance values measured in 119 adult female patients with gynecologic cancers grouped according to body composition. Measurements and main results: We applied simple linear regression and Tukey mean-difference analysis to assess the relationship between estimated creatinine clearance values produced by these equations and measured creatinine clearance values for each patient. The relationship between measured creatinine clearance and estimated creatinine clearance produced by all equations displayed lower linear regression R2 values and higher limits of agreement in obese patients than in nonobese groups. Agreement between measured and estimated creatinine clearance produced by the Cockcroft-Gault equation is sensitive to the particular weight parameter incorporated and is lowest using ideal weight or actual body weight. The Cockcroft-Gault equation incorporating an intermediate weight value reduced estimation bias. The Jelliffe equation produced the lowest R2 values. Conclusion: Available model equations are less reliable for predicting creatinine clearance in obese female cancer patients (body mass index >30) than in nonobese patients. A measured glomerular filtration rate or creatinine clearance value is most accurate in obese female cancer patients. When using Cockcroft-Gault equation for estimation in this patient population, however, an intermediate weight value (adjusted or modified-adjusted) rather than ideal or actual body weight should be used.
Getting a sense of the client: Working methods in the personal social services in Sweden
Authors: Perlinski Marek , Blom Björn , Morén Stefan 
Published: February 2012

• Summary: This article presents a study of working methods used by social workers within the personal social services (PSS), in their work with clients. The study is part of a larger research project with the aim of describing and analysing how specialized respectively integrated forms of organizations in the PSS condition social workers’ interventions and client effects (outcomes). The study was carried out in three Swedish municipalities with different organizational models. Two of those represent ‘extremes’ as they have pure specialized (divided in different types of units) respectively integrated (generic) organizations. The third municipality has chosen a middle way with an organization that combines aspects of the two other models. All social workers within the PSS in those three municipalities were included in the study. • Findings: Our findings among other things show 1) that the use of unspecific methods dominates, 2) that several methods that are reported as specific are definitely not specific, 3) that specific methods often are used in free and unspecific ways, 4) that there seems to be a compensating movement (regarding use of methods) with the aim of evening out limitations in the formal PSS organizations, 5) that there are two relatively large groups of method users: ‘improvisers’ and ‘eclecticists’. • Applications: One can neither understand the use of working methods in social work with clients by studying the methods as such nor by studying the evidence base of different methods. Social workers consider their relationships to clients and the clients’ trust as much more important (in order to achieve results) than any particular method. The use of methods is mirroring the social workers’ readiness before, and planned adaptation to, different types of situations.
Midcourse correction to a clinical trial when the event rate is underestimated: the Look AHEAD (Action for Health in Diabetes) Study
Authors: Brancati Frederick L , Evans Mary , Furberg Curt D , Geller Nancy , Haffner Steven , Kahn Steven E , Kaufmann Peter G , Lewis Cora E , Nathan David M , Pitt Bertram , Safford Monika M ,   on behalf of the Look AHEAD Study Group
Published: February 2012

The Look AHEAD (Action for Health in Diabetes) Study is a long-term clinical trial that aims to determine the cardiovascular disease (CVD) benefits of an intensive lifestyle intervention (ILI) in obese adults with type 2 diabetes. The study was designed to have 90% statistical power to detect an 18% reduction in the CVD event rate in the ILI Group compared to the Diabetes Support and Education (DSE) Group over 10.5 years of follow-up. The original power calculations were based on an expected CVD rate of 3.125% per year in the DSE group; however, a much lower-than-expected rate in the first 2 years of follow-up prompted the Data and Safety Monitoring Board (DSMB) to recommend that the Steering Committee undertake a formal blinded evaluation of these design considerations. The Steering Committee created an Endpoint Working Group (EPWG) that consisted of individuals masked to study data to examine relevant issues. The EPWG considered two primary options: (1) expanding the definition of the primary endpoint and (2) extending follow-up of participants. Ultimately, the EPWG recommended that the Look AHEAD Steering Committee approve both strategies. The DSMB accepted these modifications, rather than recommending that the trial continue with inadequate statistical power. Trialists sometimes need to modify endpoints after launch. This decision should be well justified and should be made by individuals who are fully masked to interim results that could introduce bias. This article describes this process in the Look AHEAD study and places it in the context of recent articles on endpoint modification and recent trials that reported endpoint modification.
Infusion of statistical science in comparative effectiveness research
Authors: Morton Sally C , Ellenberg Jonas H 
Published: February 2012

Purpose We present a general introduction to comparative effectiveness research (CER) from a statistician’s viewpoint and focus on how statisticians can contribute to the methodology of CER. Conclusions The statistical science community needs to determine the priorities for methodological research in CER, in collaboration with our colleagues in the aligned medical fields. CER requires that we apply a new paradigm – a focus on the patient. The emphasis on the patient is driven by patients themselves, the federal government, and private payers, in addition to the fact that there is a rising chronic disease burden that is making patient populations more heterogeneous. The availability of new technology and data sources introduces not only complexity but also opportunity. Statistical scientists should rise to meet these new demands and develop optimal, statistically valid approaches to CER, just as they have in agriculture and clinical trials.
Periosteal Transplantation Combined with the Autologous Matrix-Induced Chondrogenesis (AMIC) Technique in Isolated Patellofemoral Osteoarthritis
Authors: Schüttler Stefan , Andjelkov Nenad 
Published: February 2012

Objective: Isolated cases of osteoarthritis of the knee represent a major clinical problem. A particular challenge is a case in which both articular surfaces are affected. Such is the case with the isolated form of patellofemoral osteoarthritis. Studies that describe methods for treating such conditions are few, and the results are not too promising. Methods: In this article, we present one such case of isolated patellofemoral osteoarthritis in which we used a new approach combining periosteal transplantation on one side and the autologous matrix-induced chondrogenesis (AMIC) technique on the other side. Results: The patient has improved, measured by the Knee injury and Osteoarthritis Outcome Score (KOOS) from 48 preoperatively to 77 at 1 year postoperatively (mean improvement) and measured by the Lysholm score from 45 preoperatively to 90 at 1 year postoperatively. Conclusion: This original approach has shown promising results in this patient and could be tested in a larger group of patients with the same type of osteoarthritis in order to estimate its real clinical value.
Cyclophosphamide-bortezomib-dexamethasone (CyBorD) produces rapid and complete hematologic response in patients with AL amyloidosis
Authors: Mikhael Joseph R. , Schuster Steven R. , Jimenez-Zepeda Victor H. , Bello Nancy , Spong Jacy , Reeder Craig B. , Stewart A. Keith , Bergsagel P. Leif , Fonseca Rafael 
Published: February 2012

Abstract
Cyclophosphamide, bortezomib, and dexamethasone (CyBorD) is highly effective in multiple myeloma. We treated patients with light chain amyloidosis (AL) before stem cell transplantation (ASCT), instead of ASCT in ineligible patients or as salvage. Treatment was a combination of bortezomib (1.5 mg/m2 weekly), cyclophosphamide (300 mg/m2 orally weekly), and dexamethasone (40 mg weekly). Seventeen patients received 2 to 6 cycles of CyBorD. Ten (58%) had symptomatic cardiac involvement, and 14 (82%) had 2 or more organs involved. Response occurred in 16 (94%), with 71% achieving complete hematologic response and 24% a partial response. Time to response was 2 months. Three patients originally not eligible for ASCT became eligible. CyBorD produces rapid and complete hematologic responses in the majority of patients with AL regardless of previous treatment or ASCT candidacy. It is well tolerated with few side effects. CyBorD warrants continued investigation as treatment for AL.
PANDAseq: paired-end assembler for illumina sequences
Authors: Masella Andre P , Bartram Andrea K , Truszkowski Jakub M , Brown Daniel G , Neufeld Josh D 
Published: February 2012

Abstract

Background
Illumina paired-end reads are used to analyse microbial communities by targeting amplicons of the 16S rRNA gene. Publicly available tools are needed to assemble overlapping paired-end reads while correcting mismatches and uncalled bases; many errors could be corrected to obtain higher sequence yields using quality information.

Results
PANDAseq assembles paired-end reads rapidly and with the correction of most errors. Uncertain error corrections come from reads with many low-quality bases identified by upstream processing. Benchmarks were done using real error masks on simulated data, a pure source template, and a pooled template of genomic DNA from known organisms. PANDAseq assembled reads more rapidly and with reduced error incorporation compared to alternative methods.

Conclusions
PANDAseq rapidly assembles sequences and scales to billions of paired-end reads. Assembly of control libraries showed a 4-50% increase in the number of assembled sequences over naïve assembly with negligible loss of "good" sequence.
CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences
Authors: Ding Yang , Lorenz William A , Chuang Jeffrey H 
Published: February 2012

Abstract

Background
It has been increasingly appreciated that coding sequences harbor regulatory sequence motifs in addition to encoding for protein. These sequence motifs are expected to be overrepresented in nucleotide sequences bound by a common protein or small RNA. However, detecting overrepresented motifs has been difficult because of interference by constraints at the protein level. Sampling-based approaches to solve this problem based on codon-shuffling have been limited to exploring only an infinitesimal fraction of the sequence space and by their use of parametric approximations.

Results
We present a novel O(N(log N)2)-time algorithm, CodingMotif, to identify nucleotide-level motifs of unusual copy number in protein-coding regions. Using a new dynamic programming algorithm we are able to exhaustively calculate the distribution of the number of occurrences of a motif over all possible coding sequences that encode the same amino acid sequence, given a background model for codon usage and dinucleotide biases. Our method takes advantage of the sparseness of loci where a given motif can occur, greatly speeding up the required convolution calculations. Knowledge of the distribution allows one to assess the exact non-parametric p-value of whether a given motif is over- or under- represented. We demonstrate that our method identifies known functional motifs more accurately than sampling and parametric-based approaches in a variety of coding datasets of various size, including ChIP-seq data for the transcription factors NRSF and GABP.

Conclusions
CodingMotif provides a theoretically and empirically-demonstrated advance for the detection of motifs overrepresented in coding sequences. We expect CodingMotif to be useful for identifying motifs in functional genomic datasets such as DNA-protein binding, RNA-protein binding, or microRNA-RNA binding within coding regions. A software implementation is available at http://bioinformatics.bc.edu/chuanglab/codingmotif.tar
Functional alleles of the flowering time regulator FRIGIDA in the Brassica oleraceagenome
Authors: Irwin Judith A , Lister Clare , Soumpourou Eleni , Zhang Yanwen , Howell Elaine C , Teakle Graham , Dean Caroline 
Published: February 2012

Abstract

Background
Plants adopt different reproductive strategies as an adaptation to growth in a range of climates. In Arabidopsis thaliana FRIGIDA (FRI) confers a vernalization requirement and thus winter annual habit by increasing the expression of the MADS box transcriptional repressor FLOWERING LOCUS C (FLC). Variation at FRI plays a major role in A. thaliana life history strategy, as independent loss-of-function alleles that result in a rapid-cycling habit in different accessions, appear to have evolved many times. The aim of this study was to identify and characterize orthologues of FRI in Brassica oleracea.

Results
We describe the characterization of FRI from Brassica oleracea and identify the two B. oleracea FRI orthologues (BolC.FRI.a and BolC.FRI.b). These show extensive amino acid conservation in the central and C-terminal regions to FRI from other Brassicaceae, including A. thaliana, but have a diverged N-terminus. The genes map to two of the three regions of B. oleracea chromosomes syntenic to part of A. thaliana chromosome 5 suggesting that one of the FRI copies has been lost since the ancient triplication event that formed the B. oleracea genome. This genomic position is not syntenic with FRI in A. thaliana and comparative analysis revealed a recombination event within the A. thaliana FRI promoter. This relocated A. thaliana FRI to chromosome 4, very close to the nucleolar organizer region, leaving a fragment of FRI in the syntenic location on A. thaliana chromosome 5. Our data show this rearrangement occurred after the divergence from A. lyrata. We explored the allelic variation at BolC.FRI.a within cultivated B. oleracea germplasm and identified two major alleles, which appear equally functional both to each other and A. thaliana FRI, when expressed as fusions in A. thaliana.

Conclusions
We identify the two Brassica oleracea FRI genes, one of which we show through A. thaliana complementation experiments is functional, and show their genomic location is not syntenic with A. thaliana FRI due to an ancient recombination event. This has complicated previous association analyses of FRI with variation in life history strategy in the Brassica genus.