bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short time-series microarray analysis: Methods and challenges
Authors: Wang Xuewei , Wu Ming , Li Zheng , Chan Christina 
Published: July 2008

Abstract
The detection and analysis of steady-state gene expression has become routine. Time-series microarrays are of growing interest to systems biologists for deciphering the dynamic nature and complex regulation of biosystems. Most temporal microarray data only contain a limited number of time points, giving rise to short-time-series data, which imposes challenges for traditional methods of extracting meaningful information. To obtain useful information from the wealth of short-time series data requires addressing the problems that arise due to limited sampling. Current efforts have shown promise in improving the analysis of short time-series microarray data, although challenges remain. This commentary addresses recent advances in methods for short-time series analysis including simplification-based approaches and the integration of multi-source information. Nevertheless, further studies and development of computational methods are needed to provide practical solutions to fully exploit the potential of this data.
Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers
Authors: Naxerova Kamila , Bult Carol J , Peaston Anne , Fancher Karen , Knowles Barbara B , Kasif Simon , Kohane Isaac S 
Published: July 2008

Abstract
Background
In recent years, the molecular underpinnings of the long-observed resemblance between neoplastic and immature tissue have begun to emerge. Genome-wide transcriptional profiling has revealed similar gene expression signatures in several tumor types and early developmental stages of their tissue of origin. However, it remains unclear whether such a relationship is a universal feature of malignancy, whether heterogeneities exist in the developmental component of different tumor types and to which degree the resemblance between cancer and development is a tissue-specific phenomenon.

Results
We defined a developmental landscape by summarizing the main features of ten developmental time courses and projected gene expression from a variety of human tumor types onto this landscape. This comparison demonstrates a clear imprint of developmental gene expression in a wide range of tumors and with respect to different, even non-cognate developmental backgrounds. Our analysis reveals three classes of cancers with developmentally distinct transcriptional patterns. We characterize the biological processes dominating these classes and validate the class distinction with respect to a new time series of murine embryonic lung development. Finally, we identify a set of genes that are upregulated in most cancers and we show that this signature is active in early development.

Conclusion
This systematic and quantitative overview of the relationship between the neoplastic and developmental transcriptome spanning dozens of tissues provides a reliable outline of global trends in cancer gene expression, reveals potentially clinically relevant differences in the gene expression of different cancer types and represents a reference framework for interpretation of smaller-scale functional studies.
Five-Gene Model to Predict Survival in Mantle-Cell Lymphoma Using Frozen or Formalin-Fixed, Paraffin-Embedded Tissue
Authors: Hartmann Elena , Fernàndez Verònica , Moreno Victor , Valls Joan , Hernández Luis , Bosch Francesc , Abrisqueta Pau , Klapper Wolfram , Dreyling Martin , Hoster Eva , Müller-Hermelink Hans Konrad , Ott German , Rosenwald Andreas , Campo Elías 
Published: July 2008

Purpose Despite the common underlying translocation t(11;14) involving cyclin D1 that is present in nearly all cases of mantle-cell lymphoma (MCL), the clinical course of the disease is highly variable. The aim of the present study was to develop a quantitative gene expression–based model to predict survival in newly diagnosed patients with MCL that involves a minimum number of genes and is applicable to fresh-frozen and formalin-fixed, paraffin-embedded (FFPE) tumor samples. Patients and Methods The expression of 33 genes with potential prognostic and pathogenetic impact in MCL was analyzed using quantitative reverse-transcription polymerase chain reactions (qRT-PCR) in a low-density array format in frozen tumor samples from 73 patients with MCL. Multivariate Cox methods and stepwise algorithms were applied to build gene expression-based survival predictors. An optimized five-gene model was subsequently applied to FFPE tumor samples from 13 patients with MCL from the initial series and to 42 independent MCL samples. Results The optimized survival predictor was composed of the five genes RAN, MYC, TNFRSF10B, POLE2, and SLC29A2 and was validated for application in FFPE tissue samples. It allowed the survival prediction of patients with MCL with widely disparate clinical outcome and was superior to the immunohistochemical marker Ki-67, an established prognostic factor in MCL. Conclusion We here present a validated qRT-PCR–based test for survival prediction in patients with MCL that is applicable to fresh frozen as well as to FFPE tissue specimens. This test may prove useful to guide individualized treatment approaches for patients with MCL.
Survival Patterns Among Lymphoma Patients With a Family History of Lymphoma
Authors: Anderson Lesley A. , Pfeiffer Ruth M. , Rapkin Joshua S. , Gridley Gloria , Mellemkjaer Lene , Hemminki Kari , Björkholm Magnus , Caporaso Neil E. , Landgren Ola 
Published: July 2008

PurposeGenetic factors are important in the etiology and pathogenesis of chronic lymphocytic leukemia (CLL), Hodgkin's lymphoma (HL), and non-Hodgkin's lymphoma (NHL). Only a few small studies have assessed clinical characteristics and prognosis for familial patients, with inconsistent findings.MethodsUsing population-based registries from Sweden and Denmark, 7,749 patients with CLL, 7,476 patients with HL, and 25,801 patients with NHL with linkable first-degree relatives were identified. Kaplan-Meier curves were constructed to compare survival in patients with lymphoma with and without a family history of lymphoma. The risk of dying was assessed using adjusted Cox proportional hazard models.ResultsWe found 85 patients with CLL (1.10%), 95 patients with HL (1.28%), and 206 patients with NHL (0.80%) with a family history of any lymphoma. Five-year mortality was similar for patients with CLL (hazard ratio [HR], 1.28; 95% CI, 0.95 to 1.72), HL (HR, 0.78; 95% CI, 0.49 to 1.25), and NHL (HR, 0.91; 95% CI, 0.74 to 1.12) versus without a family history of any lymphoma. Mortality was also similar for patients with versus without a family history of the same lymphoma. T-cell/anaplastic lymphoma patients with a family history of NHL had poorer outcome 5-years after diagnosis (HR, 5.38; 95% CI, 1.65 to 17.52). Results were similar for 10 years of follow-up.ConclusionWith the exception of T-cell/anaplastic lymphoma, survival patterns for patients with CLL, HL, and NHL with a family history of lymphoma were similar to those for sporadic patients, suggesting that most familial lymphomas do not have an altered clinical course. Our findings provide no evidence to modify therapeutic strategies for patients with CLL, HL, or NHL based solely on family history.
Microscopic Tumor Burden in Sentinel Lymph Nodes Predicts Synchronous Nonsentinel Lymph Node Involvement in Patients With Melanoma
Authors: Gershenwald Jeffrey E. , Andtbacka Robert H.I. , Prieto Victor G. , Johnson Marcella M. , Diwan A. Hafeez , Lee Jeffrey E. , Mansfield Paul F. , Cormier Janice N. , Schacherer Christopher W. , Ross Merrick I. 
Published: July 2008

PurposeWe and others have demonstrated that additional positive lymph nodes (LNs) are identified in only 8% to 33% of patients with melanoma who have positive sentinel LNs (SLNs) and undergo complete therapeutic LN dissection (cTLND). We sought to determine predictors of additional regional LN involvement in patients with positive SLNs.Patients and MethodsPatients with clinically node-negative melanoma who underwent SLN biopsy (1991 to 2003) and had positive SLNs were identified. Clinicopathologic factors, including extent of microscopic disease within SLNs, were evaluated as potential predictors of positive non-SLNs.ResultsOverall, 359 (16.3%) of the 2,203 patients identified had a positive SLN. Positive non-SLNs were identified in 48 (14.0%) of the 343 patients with positive SLNs who underwent cTLND. On univariate analysis, several measures of SLN microscopic tumor burden, one versus three or more SLNs harvested, tumor thickness more than 2 mm, age older than 50 years, and Clark level higher than III were predictive of positive non-SLNs; primary tumor ulceration and number of positive SLNs had no apparent impact. On multivariable logistic regression analysis, measures of SLN microscopic tumor burden were the most significant independent predictors of positive non-SLNs; tumor thickness more than 2 mm and number of SLNs harvested also predicted additional disease. A model was developed that stratified patients according to their risk for non-SLN involvement.ConclusionIn melanoma patients with positive SLNs, SLN tumor burden, primary tumor thickness, and number of SLNs harvested may be useful in identifying a group at low risk for positive non-SLNs and be spared the potential morbidity of a cTLND.
A cognitive model of peritraumatic dissociation
Authors: Wing Lun Lenora M. 
Published: July 2008

Purpose. Interacting cognitive subsystems (ICS; Barnard & Teasdale, 1991) is presented as a framework for understanding the impact of perceptual problems in peritraumatic dissociation.Methods. This paper analyses two peritraumatic dissociation symptoms, attention being drawn to stimuli and the experience of time slowing. ICS is described. Information processes in peritraumatic dissociation are analysed.Results. Peritraumatic dissociative symptoms are conceptualized as problems with early processing of sensory information that result from problems of sensory feature binding.Discussion. These problems are discussed in relation to experiences of fragmented memories in trauma within the context of ICS. A role for mindful attention in psychological therapy is raised.
National Academy of Clinical Biochemistry Laboratory Medicine Practice Guidelines for Use of Tumor Markers in Clinical Practice: Quality Requirements1
Authors: Sturgeon Catharine M , Hoffman Barry R , Chan Daniel W , Ch'ng Soo-Ling , Hammond Elizabeth , Hayes Daniel F , Liotta Lance A , Petricoin Emmanuel F , Schmitt Manfred , Semmes O John , Söletormos Györg , van der Merwe Elena , Diamandis Eleftherios P 
Published: July 2008

Abstract
Background: This report presents updated National Academy of Clinical Biochemistry Laboratory Medicine Practice Guidelines summarizing quality requirements for the use of tumor markers.
Methods: One subcommittee developed guidelines for analytical quality relevant to serum and tissue-based tumor markers in current clinical practice. Two other subcommittees formulated recommendations particularly relevant to the developing technologies of microarrays and mass spectrometry.
Results: Prerequisites for optimal use of tumor markers in routine practice include formulation of the correct clinical questions to ensure selection of the appropriate test, adherence to good clinical and laboratory practices (e.g., minimization of the risk of incorrect patient and/or specimen identification, tube type, or timing), use of internationally standardized and well-characterized methods, careful adherence to manufacturer instructions, and proactive and timely reactions to information derived from both internal QC and proficiency-testing specimens. Highly desirable procedures include those designed to minimize the risk of the reporting of erroneous results attributable to interferences such as heterophilic antibodies or hook effects, to facilitate the provision of informative clinical reports (e.g., cumulative and/or graphical reports, appropriately derived reference intervals, and interpretative comments), and when possible to integrate these reports with other patient information through electronic health records. Also mandatory is extensive validation encompassing all stages of analysis before introduction of new technologies such as microarrays and mass spectrometry. Provision of high-quality tumor marker services is facilitated by dialogue involving researchers, diagnostic companies, clinical and laboratory users, and regulatory agencies.
Conclusions: Implementation of these recommendations, adapted to local practice, should encourage optimization of the clinical use of tumor markers.
Novel Immunoassay for Quantification of Brain Natriuretic Peptide and Its Precursor in Human Blood
Authors: Tamm Natalia N , Seferian Karina R , Semenov Alexander G , Mukharyamova Kadriya S , Koshkina Ekaterina V , Krasnoselsky Mihail I , Postnikov Alexander B , Serebryanaya Daria V , Apple Fred S , Murakami MaryAnn M , Katrukha Alexey G 
Published: July 2008

Abstract
Background: Brain natriuretic peptide (BNP) is an unstable molecule that can rapidly lose immunologic activity in blood. Conventional sandwich BNP immunoassays use 2 antibodies specific to 2 different epitopes. Larger distances between epitopes are associated with a greater probability of proteolysis sites being located between the antibody-binding sites, and thus such assays have an increased susceptibility to underdetect BNP because of the increased likelihood of proteolytic degradation. The purpose of our study was to develop a sandwich immunoassay for the precise quantification of BNP and BNP precursor (proBNP) in human blood that is not susceptible to proteolysis.
Methods: Mice were immunized with an immune complex consisting of monoclonal antibody (MAb) 24C5 (specific for BNP peptide 11–22) and the entire BNP molecule. The MAb used in our assay (Ab-BNP2) recognizes the immune complex but neither free BNP nor MAb 24C5.
Results: We used MAbs 24C5 and Ab-BNP2 to develop a new type of sandwich BNP assay (the “single-epitope sandwich assay”), which requires only a short BNP fragment (fragment 11–22) for immunodetection. This assay recognizes both BNP and proBNP with the same efficiency and sensitivity and demonstrates both considerably less susceptibility to antigen degradation and greater stability of the measured antigen than conventional sandwich BNP immunoassays.
Conclusions: We have developed this sensitive single-epitope sandwich assay for detecting BNP, proBNP, and their fragments in human blood. This assay appears promising for use in clinical studies to assist in triage, management, and outcomes assessment in heart failure patients.
Attributional Bias of Offenders in Rehabilitation Therapy Workers
Authors: Kyne Karen , Williams Mei Wah M. 
Published: July 2008

AbstractAttribution theory was used to provide a conceptual analysis of how personal responsibility and blame are ascribed to fictional male and female offenders. Thirty drug and alcohol counsellors participated in the study; half read a description of a crime committed by a female and the other half read the same description of the crime but committed by a male. Counsellors rated the offence in terms of the attributional domains of internality, control, and stability and then listed potential treatment targets. Offender sex influenced differentially attribution of blame with counsellors tending to attribute less blame to an offender of the same gender. This effect was particularly pronounced in the case of female counsellors.
A practical approach to instrument selection, evaluation, basic financial management and implementation in pathology and research
Authors: Mina Ashraf , Favaloro Emmanuel J. , Koutts Jerry 
Published: July 2008

AbstractIn response to increasingly complex demands in terms of productivity and budgets, there is a critical need to avoid mistakes during instrument selection that will be financially costly, and adversely affect customers, staff, productivity and test turnaround time. As there is no “one size fits all”, guidelines must be appropriate to permit informed decision making. A Medline search was conducted to assess background knowledge in this area, using the terms “laboratory instrument selection” and “laboratory instrument evaluation”. Searches returned over 800 articles, of which only seven were directly related to the topic of the search, with most outdated, and suggesting a paucity of appropriate information. Additional resources used included the American Association of Clinical Chemistry (AACC) website and the Internet. Appropriate criteria for instrument selection were established in the current report based on subjective and objective (technical) evaluations. Additionally, a sound and simple financial approach is also suggested to help in making informed decisions and avoid costly mistakes. We propose that such a process as outlined in our report will protect laboratories from making costly and avoidable mistakes in the acquisition of major equipment.Clin Chem Lab Med 2008;46:1223–9.
Attention-Deficit/Hyperactivity–Related Symptoms Among Children With Enterovirus 71 Infection of the Central Nervous System
Authors: Gau Susan Shur-Fen , Chang Luan-Yin , Huang Li-Min , Fan Tsui-Yen , Wu Yu-Yu , Lin Tzou-Yien 
Published: July 2008

BACKGROUND. No study has investigated the association between enterovirus 71 central nervous system infection and symptoms related to attention-deficit/hyperactivity disorder. In this study we evaluated attention-deficit/hyperactivity disorder–related symptoms and internalizing problems as long-term sequelae resulting from enterovirus 71 central nervous system infection in children.METHODS. We enrolled 86 children 4 to 16 years old with virus-culture–confirmed enterovirus 71 infection and central nervous system involvement diagnosed 3 to 7 years before the study and 172 control subjects, matched for age, gender, and parents’ education levels. Their mothers and teachers were asked to report on possible attention-deficit/hyperactivity disorder–related symptoms, and their mothers were asked to report on possible internalizing problems. All of the children previously infected with enterovirus 71 received intelligence tests.RESULTS. Forty-two (49%) of the children previously infected with enterovirus 71 had had viral meningitis; 35 (41%) had severe central nervous system involvement, such as encephalitis, poliomyelitis-like syndrome, or encephalomyelitis; and 9 (10%) had cardiopulmonary failure and central nervous system involvement. The children previously infected with enterovirus 71 had higher scores than matched control subjects on teacher- and mother-rated scales of inattention, hyperactivity-impulsivity, oppositional symptoms, and attention-deficit/hyperactivity disorder index. The rate of elevated attention-deficit/hyperactivity disorder–related symptoms among children with enterovirus 71 central nervous system infection was 20%, whereas that rate among matched control subjects was only 3%. They also had more internalizing problems. Their verbal and performance IQs, as well as verbal comprehension indices, were significantly inversely correlated with symptoms of inattention, hyperactivity-impulsivity, and attention-deficit/hyperactivity disorder index scores.CONCLUSIONS. Enterovirus 71 central nervous system infection may affect long-term regulation of attention and emotion and cause hyperactivity-impulsivity in children.
Vitellogenin as a biomarker for estrogenic effects in brown trout,Salmo trutta: Laboratory and field investigations
Authors: Bjerregaard Poul , Hansen Pernille R , Larsen Katrine J , Erratico Claudio , Korsgaard Bodil , Holbech Henrik 
Published: July 2008

AbstractThe sensitivity of juvenile brown trout towards estrogenic chemicals (17β-estradiol [E2], estrone [E1], 17α-ethinyles-tradiol [EE2], 4-tert-octylphenol [OP], and n-butylparaben [BP]) was tested in laboratory experiments with plasma and liver vitellogenin concentrations as endpoints. Vitellogenin concentrations were also assessed in juvenile brown trout collected in streams affected by agricultural runoff and discharges from scattered houses in the open land. In the laboratory, juvenile brown trout were exposed to the chemicals in flow-through tanks for 7 to 12 d and concentration–response relationships for the induction of vitellogenin synthesis were obtained. The actual exposure concentrations were determined by liquid chromatography–mass spectrometry. The median plasma vitellogenin concentration in first year control brown trout reared in recirculated groundwater was 165 ng/ml with 783 ng/ml as the highest value. The median effective concentration (EC50) values for vitellogenin induction (based on plasma concentrations) were 3.7 ng EE2/L, 15 ng E2/L, 88 ng E1/L, 68 μg BP/L, and 7 μg OP/L. Median effective concentrations derived from liver vitellogenin concentrations were similar. The 166 brown trout caught in the field were mainly first and second year fish and a few third year fish. Plasma vitellogenin concentrations were below 1,000 ng/L in 146 of the fish, between 1,000 ng/L and 4,234 ng/L in 19 fish and 5.3 × 106 ng/L in one male fish. Vitellogenin concentrations did not differ between first and second year fish, but were elevated in third year fish. The data may indicate that juvenile (&lt;2 years) trout with plasma vitellogenin concentrations above 1,000 ng/ml have had their vitellogenin synthesis induced by exposure to estrogens in the environment. Plasma and liver vitellogenin concentrations were closely correlated in brown trout with elevated vitellogenin concentrations. It is noteworthy, however, that exposure to synthetic estrogens (EE2, BP, and OP) resulted in higher liver concentrations (for the same plasma concentration) than exposure to the natural estrogens E1 and E2.
Impact of Diabetes and Its Treatment on Cognitive Function Among Adolescents Who Participated in the Diabetes Control and Complications Trial
Authors: Musen Gail , Jacobson Alan M. , Ryan Christopher M. , Cleary Patricia A. , Waberski Barbara H. , Weinger Katie , Dahms William , Bayless Meg , Silvers Nancy , Harth Judith , White Neil ,   the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) Research Group
Published: July 2008

OBJECTIVE—The purpose of this study was to evaluate whether severe hypoglycemia or intensive therapy affects cognitive performance over time in a subgroup of patients who were aged 13–19 years at entry in the Diabetes Control and Complications Trial (DCCT).
RESEARCH DESIGN AND METHODS—This was a longitudinal study involving 249 patients with type 1 diabetes who were between 13 and 19 years old when they were randomly assigned in the DCCT. Scores on a comprehensive battery of cognitive tests obtained during the Epidemiology of Diabetes Interventions and Complications follow-up study, ∼18 years later, were compared with baseline performance. We assessed the effects of the original DCCT treatment group assignment, mean A1C values, and frequency of severe hypoglycemic events on eight domains of cognition.
RESULTS—There were a total of 294 reported episodes of coma or seizure. Neither frequency of hypoglycemia nor previous treatment group was associated with decline on any cognitive domain. As in a previous analysis of the entire study cohort, higher A1C values were associated with declines in the psychomotor and mental efficiency domain (P &lt; 0.01); however, the previous finding of improved motor speed with lower A1C values was not replicated in this subgroup analysis.
CONCLUSIONS—Despite relatively high rates of severe hypoglycemia, cognitive function did not decline over an extended period of time in the youngest cohort of patients with type 1 diabetes.