bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data
Authors: Pelz Carl R , Kulesz-Martin Molly , Bagby Grover , Sears Rosalie C 
Published: December 2008

AbstractBackgroundMicroarray technology has become very popular for globally evaluating gene expression in biological samples. However, non-linear variation associated with the technology can make data interpretation unreliable. Therefore, methods to correct this kind of technical variation are critical. Here we consider a method to reduce this type of variation applied after three common procedures for processing microarray data: MAS 5.0, RMA, and dChip®.ResultsWe commonly observe intensity-dependent technical variation between samples in a single microarray experiment. This is most common when MAS 5.0 is used to process probe level data, but we also see this type of technical variation with RMA and dChip®processed data. Datasets with unbalanced numbers of up and down regulated genes seem to be particularly susceptible to this type of intensity-dependent technical variation. Unbalanced gene regulation is common when studying cancer samples or genetically manipulated animal models and preservation of this biologically relevant information, while removing technical variation has not been well addressed in the literature. We propose a method based on using rank-invariant, endogenous transcripts as reference points for normalization (GRSN). While the use of rank-invariant transcripts has been described previously, we have added to this concept by the creation of a global rank-invariant set of transcripts used to generate a robust average reference that is used to normalize all samples within a dataset. The global rank-invariant set is selected in an iterative manner so as to preserve unbalanced gene expression. Moreover, our method works well as an overlay that can be applied to data already processed with other probe set summary methods. We demonstrate that this additional normalization step at the "probe set level" effectively corrects a specific type of technical variation that often distorts samples in datasets.ConclusionWe have developed a simple post-processing tool to help detect and correct non-linear technical variation in microarray data and demonstrate how it can reduce technical variation and improve the results of downstream statistical gene selection and pathway identification methods.
Development and validation of a gene expression oligo microarray for the gilthead sea bream (Sparus aurata)
Authors: Ferraresso Serena , Vitulo Nicola , Mininni Alba N , Romualdi Chiara , Cardazzo Barbara , Negrisolo Enrico , Reinhardt Richard , Canario Adelino VM , Patarnello Tomaso , Bargelloni Luca 
Published: December 2008

Abstract

Background
Aquaculture represents the most sustainable alternative of seafood supply to substitute for the declining marine fisheries, but severe production bottlenecks remain to be solved. The application of genomic technologies offers much promise to rapidly increase our knowledge on biological processes in farmed species and overcome such bottlenecks. Here we present an integrated platform for mRNA expression profiling in the gilthead sea bream (Sparus aurata), a marine teleost of great importance for aquaculture.

Results
A public data base was constructed, consisting of 19,734 unique clusters (3,563 contigs and 16,171 singletons). Functional annotation was obtained for 8,021 clusters. Over 4,000 sequences were also associated with a GO entry. Two 60mer probes were designed for each gene and in-situ synthesized on glass slides using Agilent SurePrint™ technology. Platform reproducibility and accuracy were assessed on two early stages of sea bream development (one-day and four days old larvae). Correlation between technical replicates was always > 0.99, with strong positive correlation between paired probes. A two class SAM test identified 1,050 differentially expressed genes between the two developmental stages. Functional analysis suggested that down-regulated transcripts (407) in older larvae are mostly essential/housekeeping genes, whereas tissue-specific genes are up-regulated in parallel with the formation of key organs (eye, digestive system). Cross-validation of microarray data was carried out using quantitative qRT-PCR on 11 target genes, selected to reflect the whole range of fold-change and both up-regulated and down-regulated genes. A statistically significant positive correlation was obtained comparing expression levels for each target gene across all biological replicates. Good concordance between qRT-PCR and microarray data was observed between 2- and 7-fold change, while fold-change compression in the microarray was present for differences greater than 10-fold in the qRT-PCR.

Conclusion
A highly reliable oligo-microarray platform was developed and validated for the gilthead sea bream despite the presently limited knowledge of the species transcriptome. Because of the flexible design this array will be able to accommodate additional probes as soon as novel unique transcripts are available.
The use of gamma-irradiation and ultraviolet-irradiation in the preparation of human melanoma cells for use in autologous whole-cell vaccines
Authors: Deacon Donna H , Hogan Kevin T , Swanson Erin M , Chianese-Bullock Kimberly A , Denlinger Chadrick E , Czarkowski Andrea R , Schrecengost Randy S , Patterson James W , Teague Mark W , Slingluff Craig L 
Published: December 2008

Abstract

Background
Human cancer vaccines incorporating autologous tumor cells carry a risk of implantation and subsequent metastasis of viable tumor cells into the patient who is being treated. Despite the fact that the melanoma cell preparations used in a recent vaccine trial (Mel37) were gamma-irradiated (200 Gy), approximately 25% of the preparations failed quality control release criteria which required that the irradiated cells incorporate 3H-thymidine at no more than 5% the level seen in the non-irradiated cells. We have, therefore, investigated ultraviolet (UV)-irradiation as a possible adjunct to, or replacement for gamma-irradiation.

Methods
Melanoma cells were gamma- and/or UV-irradiated. 3H-thymidine uptake was used to assess proliferation of the treated and untreated cells. Caspase-3 activity and DNA fragmentation were measured as indicators of apoptosis. Immunohistochemistry and Western blot analysis was used to assess antigen expression.

Results
UV-irradiation, either alone or in combination with gamma-irradiation, proved to be extremely effective in controlling the proliferation of melanoma cells. In contrast to gamma-irradiation, UV-irradiation was also capable of inducing significant levels of apoptosis. UV-irradiation, but not gamma-irradiation, was associated with the loss of tyrosinase expression. Neither form of radiation affected the expression of gp100, MART-1/MelanA, or S100.

Conclusion
These results indicate that UV-irradiation may increase the safety of autologous melanoma vaccines, although it may do so at the expense of altering the antigenic profile of the irradiated tumor cells.
P38 MAP kinase inhibitors as potential therapeutics for the treatment of joint degeneration and pain associated with osteoarthritis
Authors: Brown Kimberly K , Heitmeyer Sandra A , Hookfin Erin B , Hsieh Lily , Buchalova Maria , Taiwo Yetunde O , Janusz Michael J 
Published: December 2008

AbstractBackgroundEvaluate the potential role of p38 inhibitors for the treatment of osteoarthritis using an animal model of joint degeneration (iodoacetate-induced arthritis) and a pain model (Hargraeves assay).MethodsP38 kinase activity was evaluated in a kinase assay by measuring the amount of phosphorylated substrate ATF2 using a phosphoATF2 (Thr71) specific primary antibody and an alkaline phosphate coupled secondary antibody and measuring the OD at 405 nm. TNFα and IL-1β secretion from LPS stimulated THP-1 monocytic cells and human peripheral blood mononuclear cells were measured by ELISA. Rats treated with vehicle or p38 inhibitor were injected intra-articularly in one knee with iodoacetate and damage to the tibial plateau was assessed from digitized images captured using an image analyzer. The effect of p38 inhibitors on hyperalgesia was evaluated in rats given an intraplantar injection of carrageenan and 4 h later the paw withdrawal time to a radiant heat source was measured.ResultsSB-203580 and VX-745 are both potent inhibitors of p38 with IC50s of 136 ± 64 nM and 35 ± 14 nM (mean ± S.D.), respectively. Similarly, SB-203580 and VX-745 potently inhibited TNF release from LPS stimulated human THP-1 cells with IC50s of 72 ± 15 nM; and 29 ± 14 nM (mean ± S.D.) respectively. TNF release from LPS stimulated human peripheral blood mononuclear cells was inhibited with IC50s 16 ± 6 nM and 14 ± 8 nM, (mean ± S.D.) for SB-203580 and VX-745 and IL-1 was inhibited with IC50s of 20 ± 8 nM and 15 ± 4 nM (mean ± S.D.), respectively. SB-203580 and VX-745 administered orally at a dose of 50 mg/kg resulted in the significant (p < 0.05) inhibition of joint degeneration in the rat iodoacetate model of 45% and 31%, respectively. SB-203580 demonstrated a dose related inhibition of joint degeneration of 30, 25, 12 and 8% at 50, 25, 10 and 5 mg/kg p.o. b.i.d. in the rat iodoacetate model. Similarly, both p38 inhibitors significantly (p < 0.05) attenuated the pain response (paw withdrawal time) in the Hargraeves hyperalgesia assay when administered orally at 30, 10 and 3 mg/kg.ConclusionSB203580 and VX-745 demonstrated attenuation of both cartilage degeneration and pain in animal models and suggest that p38 inhibitors may be a useful approach for the treatment of osteoarthritis.
The Role of TRPV1 in Different Subtypes of Dorsal Root Ganglion Neurons in Rat Chronic Inflammatory Nociception Induced by Complete Freund's Adjuvant
Authors: Yu Lu , Yang Fei , Luo Hao , Liu Feng-Yu , Han Ji-Sheng , Xing Guo-Gang , Wan You 
Published: December 2008

Background:The present study aims to investigate the role of transient receptor potential vanilloid 1 (TRPV1) in dorsal root ganglion (DRG) neurons in chronic pain including thermal hyperalgesia and mechanical allodynia. Chronic inflammatory nociception of rats was produced by intraplantar injection of complete Freund's adjuvant (CFA) and data was collected until day 28 following injection.Results:Thermal hyperalgesia was evident from day 1 to day 28 with peak at day 7, while mechanical allodynia persisted from day 1 to day 14 and was greatest at day 7. Intrathecal administration of AMG 9810 at day 7, a selective TRPV1 antagonist, significantly reduced thermal hyperalgesia and mechanical allodynia. TRPV1 expression in DRG detected by Western blotting was increased relative to baseline throughout the observation period. Double labeling of TRPV1 with neuronal marker neurofilament 200 (NF200), calcitonin gene-related peptide (CGRP) or isolectin B4 (IB4) was used to distinguish different subtypes of DRG neurons. TRPV1 expression was increased in the medium-sized myelinated A fiber (NF200 positive) neurons and in small non-peptidergic (IB4 positive) neurons from day 1 to day 14 and was increased in small peptidergic (CGRP positive) neurons from day 1 to day 28.Conclusion:TRPV1 expression increases in all three types of DRG neurons after CFA injection and plays a role in CFA-induced chronic inflammatory pain including thermal hyperalgesia and mechanical allodynia.
Short scales to assess cannabis-related problems: a review of psychometric properties
Authors: Piontek Daniela , Kraus Ludwig , Klempova Danica 
Published: December 2008

Abstract

Aims
The purpose of this paper is to summarize the psychometric properties of four short screening scales to assess problematic forms of cannabis use: Severity of Dependence Scale (SDS), Cannabis Use Disorders Identification Test (CUDIT), Cannabis Abuse Screening Test (CAST) and Problematic Use of Marijuana (PUM).

Methods
A systematic computer-based literature search was conducted within the databases of PubMed, PsychINFO and Addiction Abstracts. A total of 12 publications reporting measures of reliability or validity were identified: 8 concerning SDS, 2 concerning CUDIT and one concerning CAST and PUM. Studies spanned adult and adolescent samples from general and specific user populations in a number of countries worldwide.

Results
All screening scales tended to have moderate to high internal consistency (Cronbach's α ranging from .72 to .92). Test-retest reliability and item total correlation have been reported for SDS with acceptable results. Results of validation studies varied depending on study population and standards used for validity assessment, but generally sensitivity, specificity and predictive power are satisfactory. Standard diagnostic cut-off points that can be generalized to different populations do not exist for any scale.

Conclusion
Short screening scales to assess dependence and other problems related to the use of cannabis seem to be a time and cost saving opportunity to estimate overall prevalences of cannabis-related negative consequences and to identify at-risk persons prior to using more extensive diagnostic instruments. Nevertheless, further research is needed to assess the performance of the tests in different populations and in comparison to broader criteria of cannabis-related problems other than dependence.
Possible immunotherapeutic potentiation with D-Fraction in prostate cancer cells
Authors: Pyo Paul , Louie Brandon , Rajamahanty Srinivas , Choudhury Muhammad , Konno Sensuke 
Published: December 2008

Abstract

Background
Prostate cancer remains the most common malignancy among elderly men and the second leading cause of cancer death in the United States. Although several conventional therapies are currently available, they have a low efficacy and the more effective treatment modalities need to be established. Interferons (IFNs) are one of such options known as immunotherapy and demonstrated their antitumor effects on certain cancer types. Yet such antitumor activity should be improved or potentiated to have the satisfactory outcomes. In fact, combination therapy has been proposed as an alternative approach and is being underway in human and animal studies. Accordingly, we studied whether the combination of IFN-α and D-fraction (PDF), a bioactive mushroom extract, might potentiate anticancer activity of IFN-α in prostate cancer PC-3 cells in vitro.

Results
Potential effects of recombinant IFN-α2b (0–100,000 IU/ml), PDF (0–1,000 μg/ml), or their combinations were assessed on the growth of PC-3 cells at 72 h. Cell cycle analysis using a flow cytometer and Western blot analysis were performed to explore antiproliferative mechanism of these agents. The dose-dependent study showed that IFN-α2b up to 20,000 (20 K) IU/ml had no significant effects, but >60% growth reduction was attained ≤50 K IU/ml. Similarly, PDF showed no effects up to 250 μg/ml but ~65% growth reduction was seen at 1,000 μg/ml. When IFN-α2b and PDF were combined, a relatively low concentration (10 K IU/ml) of IFN-α2b and PDF (250 μg/ml) resulted in a ~65% growth reduction. This was accompanied by a G1 cell cycle arrest, indicated by cell cycle analysis. Western blots also revealed that the G1-specific cell cycle regulators, CDK2, CDK4, CDK6, cyclin D1, and cyclin E, had been significantly (>60%) down-regulated in IFN/PDF-treated cells.

Conclusion
The combination of IFN-α2b (10 K IU/ml) and PDF (250 μg/ml) is capable of inducing a ~65% reduction in PC-3 cell growth. This appears to be due to a synergistic potentiation of two agents, leading to a G1 cell cycle arrest. Thus, it is conceivable that PDF may potentiate IFN-α2b activity, improving immunotherapy for prostate cancer.
Evidence for common short natural transsense-antisense pairing between transcripts from protein coding genes
Authors: Wang Ping , Yin Shanye , Zhang Zhenguo , Xin Dedong , Hu Landian , Kong Xiangyin , Hurst Laurence D 
Published: December 2008

Abstract
Background
There is increasing realization that regulation of genes is done partly at the RNA level by sense-antisense binding. Studies typically concentrate on the role of non-coding RNAs in regulating coding RNA. But the majority of transcripts in a cell are likely to be coding. Is it possible that coding RNA might regulate other coding RNA by short perfect sense-antisense binding? Here we compare all well-described human protein coding mRNAs against all others to identify sites 15-25 bp long that could potentially perfectly match sense-antisense.

Results
From 24,968 protein coding mRNA RefSeq sequences, none failed to find at least one match in the transcriptome. By randomizations generating artificial transcripts matched for G+C content and length, we found that there are more such trans short sense-antisense pairs than expected. Several further features are consistent with functionality of some of the putative matches. First, transcripts with more potential partners have lower expression levels, and the pair density of tissue specific genes is significantly higher than that of housekeeping genes. Further, the single nucleotide polymorphism density is lower in short pairing regions than it is in flanking regions. We found no evidence that the sense-antisense pairing regions are associated with small RNAs derived from the protein coding genes.

Conclusions
Our results are consistent with the possibility of common short perfect sense-antisense pairing between transcripts of protein coding genes.
Fauzi Al-Qawuqji and the Arab Liberation Army in the 1948 War toward the Attainment of King `Abdallah's Political Ambitions in Palestine
Authors: Yitzhak Ronen 
Published: December 2008

King `Abdallah's political ambitions in Palestine—the annexation of Palestine to Transjordan under his rule—and his wish to send his army (the Arab Legion) to realize these ambitions, worried leaders of Arab countries. In an attempt to prevent King `Abdallah from realizing this goal, the Arab League decided in December 1947 to establish an Arab volunteer army, known as the Arab Liberation Army, under the command of Fauzi al-Qawuqji. The aim of this irregular army was to fight the Jews and to prevent the Arabs from sending their regular armies (including the Arab Legion) to Palestine.
Al-Qawuqji and King `Abdallah, however, had been very close since 1936, when with the king's help al-Qawuqji escaped from the British to Transjordan. Al-Qawuji was opposed to the former mufti of Jerusalem, Hajj Amin al-Huseini, and therefore al-Qawuji and King `Abdallah were on one side against the mufti and opposed to his political ambition to establish an independent Palestinian state. This political closeness between the two leaders formed the basis of King `Abdallah's aid to al-Qawuqji and to the Arab Liberation Army's entrance into Palestine from Transjordan, in return for Palestine's staying in the Arab territories—the territories King `Abdallah wanted to annex to Transjordan. The Arab Liberation Army soldiers deployed in these territories clashed with the mufti's supporters and diminished the mufti's influence in Palestine, helping King `Abdallah finally to conquer the territories and to annex them to Transjordan.
Soil Water Measurements Relevant to Agronomic and Environmental Functions of Chemically Treated Soil
Authors: Sojka R. E. , Lehrsch G. A. , Kostka S. J. , Reed J. L. , Koehn A. C. , Foerster J. A. 
Published: December 2008

Abstract
Modern agricultural, turf, and landscape management routinely apply and depend upon chemical applications to optimize system function for specific outcomes. The effectiveness of these applied chemicals to achieve desired outcomes usually depends upon their interaction with and transport by water. To fully and accurately assess the role of water as a chemical delivery and activation system requires a good understanding of how the applied chemicals, soil, and water interact, the scale at which a phenomenon is important, the nature of soil variability, and which of the three dominant soil water properties (content, movement, or potential energy) is most suited to assessing water’s role. The science of this assessment process is extensive and its literature is voluminous. For the uninitiated, however, it is worth being aware at least of the basics of soil water assessment and where some of the pitfalls lie. This presentation describes soil as a three-phase system (solids, liquid, and gases) and highlights some of the key measurements and measurement considerations necessary to appropriately characterize treatment efficacy for specific, and especially, non-intuitive effects. The presentation cannot be comprehensive or substitute for requisite university-level courses in soil physics and soil chemistry, but can, perhaps, alert applicators to situations and considerations that demand more than mere cursory assessment for proper evaluation and interpretation.
Development of Fatigue Loading Spectra
Authors: Potter JM , Watanabe RT 
Published: December 2008

Description
Documents the state of the art in characterizing and standardizing cyclic loads experienced by structures in service. From characterizing measured data, to development of standard test spectra. Papers include: Development of Jet Transport Airframe Fatigue Test Spectra, Variable Amplitude Load Models for Fatigue Damage and Crack Growth, and Compilation of Procedures for Fatigue Crack Propagation Testing Under Complex Load Sequences.
Effect of Rheological Properties of Asphalts on Pavement Cracking
Authors: Kandhal PS , Koehler WC 
Published: December 2008

Both load and nonload-associated cracking of asphalt pavements are prevalent in Canada and the northern United States. It is essential to identify the rheological properties of the asphalt binder responsible for this type of distress. An asphalt durability research project began with the construction of six test pavements in Pennsylvania in September 1976 using AC-20 asphalt cements from different sources.
For seven years (1976 to 1984), periodical pavement performance evaluations were carried out, and climatological data were gathered. The rheological properties of original and aging asphalt binders were evaluated from periodic core samples.
The stiffness moduli of original and aged asphalt binders and asphaltic concrete were determined by two indirect methods (Heukelom and McLeod) at −23°C (−10°F) to evaluate low-temperature nonload-associated transverse cracking. Diametral creep measurements were made on pavement cores after seven years in service. Creep moduli were determined over a convenient range of loading times up to 1000 s and in the 4 to −20°C (39.2 to −20°F) temperature range. The creep data for each asphalt were reduced to a master curve using the superposition method so that the stiffness modulus of the viscoelastic asphaltic concrete can be obtained at a desired temperature and time of loading. Both indirect methods and direct measurements indicate that the stiffness modulus of the asphaltic concrete is a better indicator of the potential low temperature nonload-associated cracking.
Asphalt ductility values, determined at 15.6°C (60°F) after six years in service, seem to be consistent with the pavement performance. Higher ductility values are associated with lower incidence of load-associated longitudinal cracking.
Recommendations have been made to optimize the rheological properties of asphalt binders and asphaltic concrete to minimize the incidence of both load and nonload-associated cracking of asphalt pavements.