bluuebunny/crossref_metadata_2025_split huggingface dataset:
The natural history and treatment outcome of blast phase BCR-ABL− myeloproliferative neoplasms
Authors: Tam Constantine S. , Nussenzveig Roberto M. , Popat Uday , Bueso-Ramos Carlos E. , Thomas Deborah A. , Cortes Jorge A. , Champlin Richard E. , Ciurea Stefan E. , Manshouri Taghi , Pierce Sherry M. , Kantarjian Hagop M. , Verstovsek Srdan 
Published: June 2008

Abstract
We analyzed the outcomes of 74 patients diagnosed with BCR-ABL− myeloproliferative neoplasms in blast phase receiving induction chemotherapy (55%), low-intensity therapy (16%), stem cell transplantation (SCT; 3%), or supportive care (26%). Median survival from the date of blastic transformation was 5 months. Patients receiving supportive therapy had a median survival of 6 weeks. Complete remission with or without blood recovery was achieved in 46% of patients receiving induction chemotherapy, but remissions were not durable with a median progression-free survival of only 5 months. Eight patients received SCT either as first therapy or after responding to antileukemia therapy. These patients had a markedly superior survival, with 73% alive at a median follow-up of 31 months. JAK2V617F kinetics were assessed in 16 patients: 0 of 4 negative patients became positive at transformation, and among 12 positive patients, 1 had an increase in JAK2V617F% at transformation, 7 had a substantial decrease, and 4 had stable levels. Myeloproliferative neoplasm blast phase is associated with a dismal prognosis. Responses to chemotherapy can be achieved but are not durable. Long-term survivors had all received SCT either as first therapy or in first remission.
Successful treatment of progressive cutaneous mastocytosis with imatinib in a 2-year-old boy carrying a somatic KIT mutation
Authors: Hoffmann Karl M. , Moser Andrea , Lohse Peter , Winkler Andreas , Binder Barbara , Sovinz Petra , Lackner Herwig , Schwinger Wolfgang , Benesch Martin , Urban Christian 
Published: June 2008

Abstract
Cutaneous mastocytosis (CM) in children is a usually benign skin disorder caused by mast cell proliferation. Progressive disease leading to systemic involvement and fatal outcomes has been described. C-kit receptor mutations have been identified as causative for CM, some of which potentially respond to imatinib treatment as described for patients with systemic mastocytosis. We report successful therapy of progressive CM with imatinib in a 23-month-old boy. KIT gene analysis revealed not only a somatic deletion of codon 419 in exon 8 (c.1255_1257delGAC) which responds to imatinib therapy, but also a novel germ line p. Ser840Asn substitution encoded by exon 18 in the c-kit kinase domain. Family history suggests this exchange does not affect receptor function or cause disease. Imatinib therapy was well tolerated, stopped symptoms and disease progression, and appeared to shorten the course of the disease. Imatinib could possibly represent a novel therapeutic option in patients with progressive CM.
Double feature selection and cluster analyses in mining of microarray data from cotton
Authors: Alabady Magdy S , Youn Eunseog , Wilkins Thea A 
Published: June 2008

Abstract

Background
Cotton fiber is a single-celled seed trichome of major biological and economic importance. In recent years, genomic approaches such as microarray-based expression profiling were used to study fiber growth and development to understand the developmental mechanisms of fiber at the molecular level. The vast volume of microarray expression data generated requires a sophisticated means of data mining in order to extract novel information that addresses fundamental questions of biological interest. One of the ways to approach microarray data mining is to increase the number of dimensions/levels to the analysis, such as comparing independent studies from different genotypes. However, adding dimensions also creates a challenge in finding novel ways for analyzing multi-dimensional microarray data.

Results
Mining of independent microarray studies from Pima and Upland (TM1) cotton using double feature selection and cluster analyses identified species-specific and stage-specific gene transcripts that argue in favor of discrete genetic mechanisms that govern developmental programming of cotton fiber morphogenesis in these two cultivated species. Double feature selection analysis identified the highest number of differentially expressed genes that distinguish the fiber transcriptomes of developing Pima and TM1 fibers. These results were based on the finding that differences in fibers harvested between 17 and 24 day post-anthesis (dpa) represent the greatest expressional distance between the two species. This powerful selection method identified a subset of genes expressed during primary (PCW) and secondary (SCW) cell wall biogenesis in Pima fibers that exhibits an expression pattern that is generally reversed in TM1 at the same developmental stage. Cluster and functional analyses revealed that this subset of genes are primarily regulated during the transition stage that overlaps the termination of PCW and onset of SCW biogenesis, suggesting that these particular genes play a major role in the genetic mechanism that underlies the phenotypic differences in fiber traits between Pima and TM1.

Conclusion
The novel application of double feature selection analysis led to the discovery of species- and stage-specific genetic expression patterns, which are biologically relevant to the genetic programs that underlie the differences in the fiber phenotypes in Pima and TM1. These results promise to have profound impacts on the ongoing efforts to improve cotton fiber traits.
Gait analysis does not correlate with clinical and MR imaging parameters in patients with symptomatic lumbar spinal stenosis
Authors: Zeifang Felix , Schiltenwolf Marcus , Abel Rainer , Moradi Babak 
Published: June 2008

Abstract

Background
Parameters of MR imaging play a pivotal role in diagnosing lumbar spinal stenosis (LSS), and serve as an important tool in clinical decision-making. Despite the importance of MR imaging, little is known about the correlation between MRI parameters, objective gait analysis, and clinical presentation of patients with lumbar spinal stenosis.

Methods
Sixty-three patients from our clinic with symptomatic lumbar spinal stenosis leading to neurogenic claudication were included in this study in accordance with clearly defined inclusion and exclusion criteria. Clinical parameters, the depression status (CES-D), the subjective functional back capacity (FFbH-R), and the absolute walking distance (treadmill gait analysis) were quantitatively evaluated in correlation with morphological data from radiographs and MRI scans, in order to determine the coherence of spinal canal narrowing and clinical affliction.

Results
Sixty-three consecutive paents with a median age of 68 years and a mean Body Mass Index (BMI) of 28 were included in the study. The mean FFbH-R score displayed a value of 44 percent. The depression status scored an average of 13.6. Objectively measured walking distances showed a mean value of 172 m until patients stopped due to leg pain. A significant difference was found between the objectively measured and the subjectively estimated walking distance. The mean cross-sectional area of the dural tube at L1/2 was 113 mm2, at L2/3 94 mm2, at L3/4 73 mm2, at L4/5 65 mm2, and at L5/S1 93 mm2. The mean overall cross sectional area of the dural tube of all segments did not correlate with the objectively measured walking distance. However, bivariate analysis found that the BMI (tau b = -0.194), functional back capacity (tau b = -0.225), and the cross sectional area of the dural tube at L1/2 (tau b = -0.188) correlated significantly with the objectively measured walking distance.

Conclusion
According to the results of this study MRI findings failed to show a major clinical relevance when evaluating the walking distance in patients with lumbar spinal stenosis and, therefore, should be treated with some caution as a predictor of walking distance. In determining the disease pattern of spinal stenosis functional back capacity and BMI might play a more active role than previously thought.
A model-based time-reversal of left ventricular motion improves cardiac motion analysis using tagged MRI data
Authors: Alrefae Tareq , Smirnova Irina V , Cook Larry T , Bilgen Mehmet 
Published: June 2008

Abstract

Background
Myocardial motion is an important observable for the assessment of heart condition. Accurate estimates of ventricular (LV) wall motion are required for quantifying myocardial deformation and assessing local tissue function and viability. Harmonic Phase (HARP) analysis was developed for measuring regional LV motion using tagged magnetic resonance imaging (tMRI) data. With current computer-aided postprocessing tools including HARP analysis, large motions experienced by myocardial tissue are, however, often intractable to measure. This paper addresses this issue and provides a solution to make such measurements possible.

Methods
To improve the estimation performance of large cardiac motions while analyzing tMRI data sets, we propose a two-step solution. The first step involves constructing a model to describe average systolic motion of the LV wall within a subject group. The second step involves time-reversal of the model applied as a spatial coordinate transformation to digitally relax the contracted LV wall in the experimental data of a single subject to the beginning of systole. Cardiac tMRI scans were performed on four healthy rats and used for developing the forward LV model. Algorithms were implemented for preprocessing the tMRI data, optimizing the model parameters and performing the HARP analysis. Slices from the midventricular level were then analyzed for all systolic phases.

Results
The time-reversal operation derived from the LV model accounted for the bulk portion of the myocardial motion, which was the average motion experienced within the overall subject population. In analyzing the individual tMRI data sets, removing this average with the time-reversal operation left small magnitude residual motion unique to the case. This remaining residual portion of the motion was estimated robustly using the HARP analysis.

Conclusion
Utilizing a combination of the forward LV model and its time reversal improves the performance of motion estimation in evaluating the cardiac function.
Optimization of the hydrotesting sequence in tank farm construction using an adaptive genetic algorithm with stochastic preferential logic
Authors: Lancaster J , Cheng K 
Published: June 2008

In the construction of tank farms there is a requirement for the tanks to be hydrotested in order to verify that they are leak proof as well as proving the lack of differential settlement in the foundations. The tanks will be required to be filled to a predetermined level and then to maintain this loaded state for a certain period of time before being drained. In areas such as the Middle East, water for hydrotesting is not freely available as sea water is often not suitable for this purpose, so fresh water needs to be produced or transported to the construction site for this purpose. It is therefore of major benefit to the project to schedule the hydrotesting of the tanks in such a manner as to minimize the utilization of hydrotest water. This problem is a special case of the resource-constrained project scheduling problem (RCPSP) and in this research the fitness differential adaptive genetic algorithm previously developed by the authors has been modified to enable the solution of this real world problem. The algorithm has been ported from the original MATLAB code into Microsoft Project using Microsoft Visual Basic for Applications in order to provide a more user friendly, practical interface.
Safety of screening with Human papillomavirus testing for cervical cancer at three-year intervals in a high-risk population: experience from the LAMS study
Authors: Derchain S F , Sarian L O , Naud P , Roteli-Martins C , Longatto-Filho A , Tatti S , Branca M , Eržen M , Serpa-Hammes L , Matos J , Gontijo R C , Bragança J F , Lima T P , Maeda M Y S , Lörincz A , Dores G B , Costa S , Syrjänen S , Syrjänen K 
Published: June 2008

Objectives To assess whether human papillomavirus (HPV) testing is a safe enough approach to warrant extension of the screening intervals of baseline Papanicolaou (Pap)−/HPV− women in low-income settings. Methods Of the >1000 women prospectively followed up as part of the Latin American Screening (LAMS) Study in São Paulo, Campinas, Porto Alegre) and Buenos Aires, 470 women with both baseline cytology and Hybrid Capture 2 (HC2) results available were included in this analysis. These baseline Pap-negative and HC2− or HC2+ women were controlled at six-month intervals with colposcopy, HC2 and Pap to assess the cumulative risk of incident Pap smear abnormalities and their predictive factors. Results Of the 470 women, 324 (68.9%) were high-risk HPV (hrHPV) positive and 146 (31.1%) were negative. Having two or more lifetime sex partners (odds ratio [OR] = 2.63; 95% CI 1.70–3.51) and women using hormonal contraception (OR = 2.21; 95% CI 1.40–3.51) were at increased risk for baseline hrHPV infection. Baseline hrHPV+ women had a significantly increased risk of incident abnormal Pap smears during the follow-up. Survival curves deviate from each other starting at month 24 onwards, when hrHPV+ women start rapidly accumulating incident Pap smear abnormalities, including atypical squamous cells (ASC) or worse (log-rank; P < 0.001), low-grade squamous intraepithelial lesions (LSIL) or worse ( P < 0.001) and high-grade squamous intraepithelial lesions (HSIL) ( P = 0.03). Among the baseline hrHPV− women, the acquisition of incident hrHPV during the follow-up period significantly increased the risk of incident cytological abnormalities (hazard ratio = 3.5; 95% CI 1.1–11.7). Conclusion These data implicate that HPV testing for hrHPV types might be a safe enough approach to warrant extension of the screening interval of hrHPV−/Pap−women even in low-resource settings. Although some women will inevitably contract hrHPV, the process to develop HSIL will be long enough to enable their detection at the next screening round (e.g. after three years).
Probabilistic Cross-Species Inference of Orthologous Genomic Regions Created by Whole-Genome Duplication in Yeast
Authors: Conant Gavin C , Wolfe Kenneth H 
Published: June 2008

Abstract
Identification of orthologous genes across species becomes challenging in the presence of a whole-genome duplication (WGD). We present a probabilistic method for identifying orthologs that considers all possible orthology/paralogy assignments for a set of genomes with a shared WGD (here five yeast species). This approach allows us to estimate how confident we can be in the orthology assignments in each genomic region. Two inferences produced by this model are indicative of purifying selection acting to prevent duplicate gene loss. First, our model suggests that there are significant differences (up to a factor of seven) in duplicate gene half-life. Second, we observe differences between the genes that the model infers to have been lost soon after WGD and those lost more recently. Gene losses soon after WGD appear uncorrelated with gene expression level and knockout fitness defect. However, later losses are biased toward genes whose paralogs have high expression and large knockout fitness defects, as well as showing biases toward certain functional groups such as ribosomal proteins. We suggest that while duplicate copies of some genes may be lost neutrally after WGD, another set of genes may be initially preserved in duplicate by natural selection for reasons including dosage.
Post-mating Gene Expression Profiles of Female Drosophila melanogaster in Response to Time and to Four Male Accessory Gland Proteins
Authors: McGraw Lisa A , Clark Andrew G , Wolfner Mariana F 
Published: June 2008

Abstract
In Drosophila melanogaster, the genetic and molecular bases of post-mating changes in the female's behavior and physiology are poorly understood. However, DNA microarray studies have demonstrated that, shortly after mating, transcript abundance of &gt;1700 genes is altered in the female's reproductive tract as well as in other tissues. Many of these changes are elicited by sperm and seminal fluid proteins (Acps) that males transfer to females. To further dissect the transcript-level changes that occur following mating, we examined gene expression profiles of whole female flies at four time points following copulation. We found that, soon after copulation ends, a large number of small-magnitude transcriptional changes occurred in the mated female. At later time points, larger magnitude changes were seen, although these occurred in a smaller number of genes. We then explored how four individual Acps (ovulin, Acp36DE, Acp29AB, and Acp62F) with unique functions independently affected gene expression in females shortly after mating. Consistent with their early and possibly local action within the female, ovulin and Acp36DE caused relatively few gene expression changes in whole bodies of mated females. In contrast, Acp29AB and Acp62F modulated a large number of transcriptional changes shortly after mating.
The Chromosomal Polymorphism Linked to Variation in Social Behavior in the White-Throated Sparrow (Zonotrichia albicollis) Is a Complex Rearrangement and Suppressor of Recombination
Authors: Thomas James W , Cáceres Mario , Lowman Joshua J , Morehouse Caroline B , Short Meghan E , Baldwin Erin L , Maney Donna L , Martin Christa L 
Published: June 2008

Abstract
Variation in social behavior and plumage in the white-throated sparrow (Zonotrichia albicollis) is linked to an inversion polymorphism on chromosome 2. Here we report the results of our comparative cytogenetic mapping efforts and population genetics studies focused on the genomic characterization of this balanced chromosomal polymorphism. Comparative chromosome painting and cytogenetic mapping of 15 zebra finch BAC clones to the standard (ZAL2) and alternative (ZAL2m) arrangements revealed that this chromosome is orthologous to chicken chromosome 3, and that at a minimum, ZAL2 and ZAL2m differ by a pair of included pericentric inversions that we estimate span at least 98 Mb. Population-based sequencing and genotyping of multiple loci demonstrated that ZAL2m suppresses recombination in the heterokaryotype and is evolving as a rare nonrecombining autosomal segment of the genome. In addition, we estimate that the first inversion within the ZAL2m arrangement originated 2.2 ± 0.3 million years ago. Finally, while previously recognized as a genetic model for the evolution of social behavior, we found that the ZAL2/ZAL2m polymorphism also shares genetic and phenotypic features with the mouse t complex and we further suggest that the ZAL2/ZAL2m polymorphism is a heretofore unrecognized model for the early stages of sex chromosome evolution.
In Search of the In Vivo Identity of Mesenchymal Stem Cells
Authors: da Silva Meirelles Lindolfo , Caplan Arnold I. , Nardi Nance Beyer 
Published: June 2008

Abstract
In spite of the advances in the knowledge of adult stem cells (ASCs) during the past few years, their natural activities in vivo are still poorly understood. Mesenchymal stem cells (MSCs), one of the most promising types of ASCs for cell-based therapies, are defined mainly by functional assays using cultured cells. Defining MSCs in vitro adds complexity to their study because the artificial conditions may introduce experimental artifacts. Inserting these results in the context of the organism is difficult because the exact location and functions of MSCs in vivo remain elusive; the identification of the MSC niche is necessary to validate results obtained in vitro and to further the knowledge of the physiological functions of this ASC. Here we show an analysis of the evidence suggesting a perivascular location for MSCs, correlating these cells with pericytes, and present a model in which the perivascular zone is the MSC niche in vivo, where local cues coordinate the transition to progenitor and mature cell phenotypes. This model proposes that MSCs stabilize blood vessels and contribute to tissue and immune system homeostasis under physiological conditions and assume a more active role in the repair of focal tissue injury. The establishment of the perivascular compartment as the MSC niche provides a basis for the rational design of additional in vivo therapeutic approaches. This view connects the MSC to the immune and vascular systems, emphasizing its role as a physiological integrator and its importance in tissue repair/regeneration.
Disclosure of potential conflicts of interest is found at the end of this article.
Reliability of Reservoir Parameters from History Matched Drill Stem Tests
Authors: Dixon Thomas N. , Seinfeld John H. , Startzman Richard A. , Chen W.H. 
Published: June 2008

Abstract
An important use of simulation is to determine reservoir properties by interpreting transient well tests. In general, this determination is carriedout by systematically varying reservoir properties until the pressures computed by the simulator match pressures measured during the well test â?" a procedure known as history matching. Reservoir properties determined by history matching are subject to error. Here we present a method of estimating this error. As an example, we studied the problem of estimating porosity and permeability in both a homogeneous reservoir and one in which damage is present in the vicinity of the well. Results presented indicate that the accuracy of calculated reservoir parameters depends on (1) the type of parameter estimated, (2) the number of parameters estimated, (3) the true value of the parameters and (4) the design of the well test.

Introduction
Research efforts in history-matching reservoir simulators have principally been directed toward improving and extending existing techniques with respect to decreasing computing time. Little attention has been paid, however, to the analysis of the accuracy of the parameter values from the history match. Without such an analysis, parameter estimates from history matching might be meaningless. The problem is to estimate errors in parameter values determined by history matching.
The theory that is presented in the Appendix is applicable in general to multiphase, two-dimensional simulators. However, as an illustration, we apply the theory to the well known radial form of the diffusion equation, describing the transient behavior of pressure in a radial, horizontal reservoir containing a single-phase fluid of small and constant compressibility. The equation allows for permeabilities to change with radial distance from a wellbore â?" a situation that might be encountered if damage is present. We assume that the reservoir is finite. Furthermore, we assume that the well produces at a constant rate for a certain time and then is shut in. Thus, both drawdown and buildup takes place. No wellbore storage effects are considered.