bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of three microarray probe annotation pipelines: differences in strategies and their effect on downstream analysis
Authors: Neerincx Pieter BT , Casel Pierrot , Prickett Dennis , Nie Haisheng , Watson Michael , Leunissen Jack AM , Groenen Martien AM , Klopp Christophe 
Published: July 2009

Abstract

Background
Reliable annotation linking oligonucleotide probes to target genes is essential for functional biological analysis of microarray experiments. We used the IMAD, OligoRAP and sigReannot pipelines to update the annotation for the ARK-Genomics Chicken 20 K array as part of a joined EADGENE/SABRE workshop. In this manuscript we compare their annotation strategies and results. Furthermore, we analyse the effect of differences in updated annotation on functional analysis for an experiment involving Eimeria infected chickens and finally we propose guidelines for optimal annotation strategies.

Results
IMAD, OligoRAP and sigReannot update both annotation and estimated target specificity. The 3 pipelines can assign oligos to target specificity categories although with varying degrees of resolution. Target specificity is judged based on the amount and type of oligo versus target-gene alignments (hits), which are determined by filter thresholds that users can adjust based on their experimental conditions. Linking oligos to annotation on the other hand is based on rigid rules, which differ between pipelines.
For 52.7% of the oligos from a subset selected for in depth comparison all pipelines linked to one or more Ensembl genes with consensus on 44.0%. In 31.0% of the cases none of the pipelines could assign an Ensembl gene to an oligo and for the remaining 16.3% the coverage differed between pipelines. Differences in updated annotation were mainly due to different thresholds for hybridisation potential filtering of oligo versus target-gene alignments and different policies for expanding annotation using indirect links. The differences in updated annotation packages had a significant effect on GO term enrichment analysis with consensus on only 67.2% of the enriched terms.

Conclusion
In addition to flexible thresholds to determine target specificity, annotation tools should provide metadata describing the relationships between oligos and the annotation assigned to them. These relationships can then be used to judge the varying degrees of reliability allowing users to fine-tune the balance between reliability and coverage. This is important as it can have a significant effect on functional microarray analysis as exemplified by the lack of consensus on almost one third of the terms found with GO term enrichment analysis based on updated IMAD, OligoRAP or sigReannot annotation.
Pathway results from the chicken data set using GOTM, Pathway Studio and Ingenuity softwares
Authors: Bonnet Agnès , Lagarrigue Sandrine , Liaubet Laurence , Robert-Granié Christèle , SanCristobal Magali , Tosser-Klopp Gwenola 
Published: July 2009

Abstract

Background
As presented in the introduction paper, three sets of differentially regulated genes were found after the analysis of the chicken infection data set from EADGENE. Different methods were used to interpret these results.

Results
GOTM, Pathway Studio and Ingenuity softwares were used to investigate the three lists of genes. The three softwares allowed the analysis of the data and highlighted different networks. However, only one set of genes, showing a differential expression between primary and secondary response gave significant biological interpretation.

Conclusion
Combining these databases that were developed independently on different annotation sources supplies a useful tool for a global biological interpretation of microarray data, even if they may contain some imperfections (e.g. gene not or not well annotated).
Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis
Authors: Jiménez-Marín Ángeles , Collado-Romero Melania , Ramirez-Boo María , Arce Cristina , Garrido Juan J 
Published: July 2009

Abstract

Background
Once a list of differentially expressed genes has been identified from a microarray experiment, a subsequent post-analysis task is required in order to find the main biological processes associated to the experimental system. This paper describes two pathways analysis tools, ArrayUnlock and Ingenuity Pathways Analysis (IPA) to deal with the post-analyses of microarray data, in the context of the EADGENE and SABRE post-analysis workshop. Dataset employed in this study proceeded from an experimental chicken infection performed to study the host reactions after a homologous or heterologous secondary challenge with two species of Eimeria.

Results
Analysis of the same microarray data source employing both commercial pathway analysis tools in parallel let to identify several biological and/or molecular functions altered in the chicken Eimeria maxima infection model, including several immune system related pathways. Biological functions differentially altered in the homologous and heterologous second infection were identified. Similarly, the effect of the timing in a homologous second infection was characterized by several biological functions.

Conclusion
Functional analysis with ArrayUnlock and IPA provided information related to functional differences with the three comparisons of the chicken infection leading to similar conclusions. ArrayUnlock let an improvement of the annotations of the chicken genome adding InterPro annotations to the data set file. IPA provides two powerful tools to understand the pathway analysis results: the networks and canonical pathways that showed several pathways related to an adaptative immune response.
Microarray data mining using Bioconductor packages
Authors: Nie Haisheng , Neerincx Pieter BT , Poel Jan van der , Ferrari Francesco , Bicciato Silvio , Leunissen Jack AM , Groenen Martien AM 
Published: July 2009

Abstract

Background
This paper describes the results of a Gene Ontology (GO) term enrichment analysis of chicken microarray data using the Bioconductor packages. By checking the enriched GO terms in three contrasts, MM8-PM8, MM8-MA8, and MM8-MM24, of the provided microarray data during this workshop, this analysis aimed to investigate the host reactions in chickens occurring shortly after a secondary challenge with either a homologous or heterologous species of Eimeria. The results of GO enrichment analysis using GO terms annotated to chicken genes and GO terms annotated to chicken-human orthologous genes were also compared. Furthermore, a locally adaptive statistical procedure (LAP) was performed to test differentially expressed chromosomal regions, rather than individual genes, in the chicken genome after Eimeria challenge.

Results
GO enrichment analysis identified significant (raw p-value < 0.05) GO terms for all three contrasts included in the analysis. Some of the GO terms linked to, generally, primary immune responses or secondary immune responses indicating the GO enrichment analysis is a useful approach to analyze microarray data. The comparisons of GO enrichment results using chicken gene information and chicken-human orthologous gene information showed more refined GO terms related to immune responses when using chicken-human orthologous gene information, this suggests that using chicken-human orthologous gene information has higher power to detect significant GO terms with more refined functionality. Furthermore, three chromosome regions were identified to be significantly up-regulated in contrast MM8-PM8 (q-value < 0.01).

Conclusion
Overall, this paper describes a practical approach to analyze microarray data in farm animals where the genome information is still incomplete. For farm animals, such as chicken, with currently limited gene annotation, borrowing gene annotation information from orthologous genes in well-annotated species, such as human, will help improve the pathway analysis results substantially. Furthermore, LAP analysis approach is a relatively new and very useful way to be applied in microarray analysis.
Substance P and beta-endorphin mediate electro-acupuncture induced analgesia in mouse cancer pain model
Authors: Lee Hyo-Jeong , Lee Jae-Ho , Lee Eun-Ok , Lee Hyo-Jung , Kim Kwan-Hyun , Kim Sun-Hyung , Lee Keun-Sung , Jung Hee-Jae , Kim Sung-Hoon 
Published: July 2009

Abstract

Background
Opioid analgesics are generally used to combat the pain associated with cancerous conditions. These agents not only inhibit respiratory function and cause constipation, but also induce other significant side effects such as addiction and tolerance, all of which further contribute to a reduced quality of life for cancer patients. Thus, in the present study, the effects of electro-acupuncture treatment (EA) on mechanical allodynia were examined in a cancer pain mouse model.

Methods
In order to produce a neuropathic cancer pain model, S-180 sarcoma cells were inoculated around the sciatic nerve of left legs of Balb/c mice. Magnetic Resonance Imaging (MRI) scanning confirmed the mass of S-180 cancer cells embedded around the sciatic nerve. Mechanical allodynia was most consistently induced in the mouse sarcoma cell line S-180 (2 × 106sarcoma cells)-treated group compared to all the other groups studied. EA stimulation (2 Hz) was administered daily to ST36 (Zusanli) of S-180 bearing mice for 30 min for 9 days after S-180 inoculation.

Results
EA treatment significantly prolonged paw withdrawal latency from 5 days after inoculation. It also shortened the cumulative lifting duration from 7 days after inoculation, compared to the tumor control. Also, the overexpression of pain peptide substance P in the dorsal horn of the spinal cord was significantly decreased in the EA-treated group compared to the tumor control on Day 9 post inoculation. Furthermore, EA treatment effectively increased the concentration of β-endorphin in blood and brain samples of the mice to a greater extent than that of the tumor control as well as the normal group. The concentration of β-endorphin for EA treatment group increased by 51.457% in the blood and 12.6% in the brain respectively, compared to the tumor control group.

Conclusion
The findings of this study suggest that a S-180 cancer pain model is useful as a consistent and short time animal model. It also indicated that EA treatment could be used as an alternative therapeutic method for cancer pain due to a consequent decrease in substance P and increase in β-endorphin levels.
Results from the national sepsis practice survey: predictions about mortality and morbidity and recommendations for limitation of care orders
Authors: O'Brien James M , Aberegg Scott K , Ali Naeem A , Diette Gregory B , Lemeshow Stanley 
Published: July 2009

Abstract
Introduction
Critically ill patients and families rely upon physicians to provide estimates of prognosis and recommendations for care. Little is known about patient and clinician factors which influence these predictions. The association between these predictions and recommendations for continued aggressive care is also understudied.

Methods
We administered a mail-based survey with simulated clinical vignettes to a random sample of the Critical Care Assembly of the American Thoracic Society. Vignettes represented a patient with septic shock with multi-organ failure with identical APACHE II scores and sepsis-associated organ failures. Vignettes varied by age (50 or 70 years old), body mass index (BMI) (normal or obese) and co-morbidities (none or recently diagnosed stage IIA lung cancer). All subjects received the vignettes with the highest and lowest mortality predictions from pilot testing and two additional, randomly selected vignettes. Respondents estimated outcomes and selected care for each hypothetical patient.

Results
Despite identical severity of illness, the range of estimates for hospital mortality (5th to 95th percentile range, 17% to 78%) and for problems with self-care (5th to 95th percentile range, 2% to 74%) was wide. Similar variation was observed when clinical factors (age, BMI, and co-morbidities) were identical. Estimates of hospital mortality and problems with self-care among survivors were significantly higher in vignettes with obese BMIs (4.3% and 5.3% higher, respectively), older age (8.2% and 11.6% higher, respectively), and cancer diagnosis (5.9% and 6.9% higher, respectively). Higher estimates of mortality (adjusted odds ratio 1.29 per 10% increase in predicted mortality), perceived problems with self-care (adjusted odds ratio 1.26 per 10% increase in predicted problems with self-care), and early-stage lung cancer (adjusted odds ratio 5.82) were independently associated with recommendations to limit care.

Conclusions
The studied clinical factors were consistently associated with poorer outcome predictions but did not explain the variation in prognoses offered by experienced physicians. These observations raise concern that provided information and the resulting decisions about continued aggressive care may be influenced by individual physician perception. To provide more reliable and accurate estimates of outcomes, tools are needed which incorporate patient characteristics and preferences with physician predictions and practices.
Determinants of weaning success in patients with prolonged mechanical ventilation
Authors: Carlucci Annalisa , Ceriana Piero , Prinianakis Georgios , Fanfulla Francesco , Colombo Roberto , Nava Stefano 
Published: July 2009

Abstract
Introduction
Physiological determinants of weaning success and failure are usually studied in ventilator-supported patients, comparing those who failed a trial of spontaneous breathing with those who tolerated such a trial and were successfully extubated. A major limitation of these studies was that the two groups may be not comparable concerning the severity of the underlying disease and the presence of comorbidities. In this physiological study, we assessed the determinants of weaning success in patients acting as their own control, once they are eventually liberated from the ventilator.

Methods
In 30 stable tracheotomised ventilator-dependent patients admitted to a weaning center inside a respiratory intensive care unit, we recorded the breathing pattern, respiratory mechanics, inspiratory muscle function, and tension-time index of diaphragm (TTdi = Pdisw/Pdimax [that is, tidal transdiaphragmatic pressure over maximum transdiaphragmatic pressure] × Ti/Ttot [that is, the inspiratory time over the total breath duration]) at the time of weaning failure (T0). The measurements were repeated in all the patients (T1) either during a successful weaning trial (successful weaning [SW] group, n = 16) or 5 weeks later, in the case of repeated weaning failure (failed weaning [FW] group, n = 14).

Results
Compared to T0, in the FW group at T1, significant differences were observed only for a reduction in spontaneous breathing frequency and in TTdi (0.21 ± 0.122 versus 0.14 ± 0.054, P = 0.008). SW patients showed a significant increase in Pdimax (34.9 ± 18.9 cm H2O versus 43.0 ± 20.0, P = 0.02) and decrease in Pdisw/Pdimax (36.0% ± 15.8% versus 23.1% ± 7.9%, P = 0.004).

Conclusions
The recovery of an inadequate inspiratory muscle force could be the major determinant of 'late' weaning success, since this allows the patients to breathe far below the diaphragm fatigue threshold.
A transcriptional network associated with natural variation in Drosophilaaggressive behavior
Authors: Edwards Alexis C , Ayroles Julien F , Stone Eric A , Carbone Mary Anna , Lyman Richard F , Mackay Trudy FC 
Published: July 2009

Abstract
Background
Aggressive behavior is an important component of fitness in most animals. Aggressive behavior is genetically complex, with natural variation attributable to multiple segregating loci with allelic effects that are sensitive to the physical and social environment. However, we know little about the genes and genetic networks affecting natural variation in aggressive behavior. Populations of Drosophila melanogaster harbor quantitative genetic variation in aggressive behavior, providing an excellent model system for dissecting the genetic basis of naturally occurring variation in aggression.

Results
Correlating variation in transcript abundance with variation in complex trait phenotypes is a rapid method for identifying candidate genes. We quantified aggressive behavior in 40 wild-derived inbred lines of D. melanogaster and performed a genome-wide association screen for quantitative trait transcripts and single feature polymorphisms affecting aggression. We identified 266 novel candidate genes associated with aggressive behavior, many of which have pleiotropic effects on metabolism, development, and/or other behavioral traits. We performed behavioral tests of mutations in 12 of these candidate genes, and show that nine indeed affected aggressive behavior. We used the genetic correlations among the quantitative trait transcripts to derive a transcriptional genetic network associated with natural variation in aggressive behavior. The network consists of nine modules of correlated transcripts that are enriched for genes affecting common functions, tissue-specific expression patterns, and/or DNA sequence motifs.

Conclusions
Correlations among genetically variable transcripts that are associated with genetic variation in organismal behavior establish a foundation for understanding natural variation for complex behaviors in terms of networks of interacting genes.
Probe-level estimation improves the detection of differential splicing in Affymetrix exon array studies
Authors: Laajala Essi , Aittokallio Tero , Lahesmaa Riitta , Elo Laura L 
Published: July 2009

AbstractThe recent advent of exon microarrays has made it possible to reveal differences in alternative splicing events on a global scale. We introduce a novel statistical procedure that takes full advantage of the probe-level information on Affymetrix exon arrays when detecting differential splicing between sample groups. In comparison to existing ranking methods, the procedure shows superior reproducibility and accuracy in distinguishing true biological findings from background noise in high agreement with experimental validations.
An arrestin-dependent multi-kinase signaling complex mediates MIP-1β/CCL4 signaling and chemotaxis of primary human macrophages
Authors: Cheung Ricky , Malik Mobeen , Ravyn Vipa , Tomkowicz Brian , Ptasznik Andrzej , Collman Ronald G 
Published: July 2009

Abstract
CCR5-triggered chemotaxis in primary human macrophages depends on both Giα-dependent pathways and a novel Giα-independent mechanism.
MIP-1β/CCL4 is a principal regulator of macrophage migration and signals through CCR5. Several protein kinases are linked to CCR5 in macrophages including the src kinase Lyn, PI3K, focal adhesion related kinase Pyk2, and members of the MAPK family, but whether and how these kinases regulate macrophage chemotaxis are not known. To define the role of these signaling molecules, we examined the functions and interactions of endogenous proteins in primary human macrophages. Using siRNA gene silencing and pharmacologic inhibition, we show that chemotaxis in response to CCR5 stimulation by MIP-1β requires activation of Pyk2, PI3K p85, and Lyn, as well as MAPK ERK. MIP-1β activation of CCR5 triggered translocation of Pyk2 and PI3K p85 from the cytoplasm to colocalize with Lyn at the plasma membrane with formation of a multimolecular complex. We show further that arrestins were recruited into the complex, and arrestin down-regulation impaired complex formation and macrophage chemotaxis toward MIP-1β. Together, these results identify a novel mechanism of chemokine receptor regulation of chemotaxis and suggest that arrestins may serve as scaffolding proteins linking CCR5 to multiple downstream signaling molecules in a biologically important primary human cell type.
Radiation Dose and Breast Cancer Risk in the Childhood Cancer Survivor Study
Authors: Inskip Peter D. , Robison Leslie L. , Stovall Marilyn , Smith Susan A. , Hammond Sue , Mertens Ann C. , Whitton John A. , Diller Lisa , Kenney Lisa , Donaldson Sarah S. , Meadows Anna T. , Neglia Joseph P. 
Published: July 2009

PurposeThe purpose of this study was to quantify the risk of breast cancer in relation to radiation dose and chemotherapy among survivors of childhood cancer.MethodsWe conducted a case-control study of breast cancer in a cohort of 6,647 women who were 5-year survivors of childhood cancer and who were treated during 1970 through 1986. One hundred twenty patients with histologically confirmed breast cancer were identified and were individually matched to four selected controls on age at initial cancer and time since initial cancer. Medical physicists estimated radiation dose to the breast tumor site and ovaries on the basis of medical records.ResultsThe odds ratio for breast cancer increased linearly with radiation dose, and it reached 11-fold for local breast doses of approximately 40 Gy relative to no radiation (P for trend < .0001). Risk associated with breast irradiation was sharply reduced among women who received 5 Gy or more to the ovaries (P = .002). The excess odds ratio per Gy was 0.36 for those who received ovarian doses less than 5 Gy and was 0.06 for those who received higher doses. Radiation-related risk did not vary significantly by age at exposure. Borderline significantly elevated risks were seen for doxorubicin, dactinomycin, dacarbazine, and carmustine.ConclusionResults confirm the radiation sensitivity of the breast in girls age 10 to 20 years but do not demonstrate a strong effect of age at exposure within this range. Irradiation of the ovaries at doses greater than 5 Gy seems to lessen the carcinogenic effects of breast irradiation, most likely by reducing exposure of radiation-damaged breast cells to stimulating effects of ovarian hormones.
Brief Report: Natural History of Individuals With Clinically Recognized Monoclonal B-Cell Lymphocytosis Compared With Patients With Rai 0 Chronic Lymphocytic Leukemia
Authors: Shanafelt Tait D. , Kay Neil E. , Rabe Kari G. , Call Timothy G. , Zent Clive S. , Maddocks Kami , Jenkins Greg , Jelinek Diane F. , Morice William G. , Boysen Justin , Schwager Susan , Bowen Deborah , Slager Susan L. , Hanson Curtis A. 
Published: July 2009

Purpose The diagnosis of monoclonal B-cell lymphocytosis (MBL) is used to characterize patients with a circulating population of clonal B cells, a total B-cell count of less than 5 × 109/L, and no other features of a B-cell lymphoproliferative disorder including lymphadenopathy/organomegaly. The natural history of clinically identified MBL is unclear. The goal of this study was to explore the outcome of patients with MBL relative to that of individuals with Rai stage 0 chronic lymphocytic leukemia (CLL). Patients and Methods We used hematopathology records to identify a cohort of 631 patients with newly diagnosed MBL or Rai stage 0 CLL. Within this cohort, 302 patients had MBL (B-cell counts of 0.02 to 4.99 × 109/L); 94 patients had Rai stage 0 CLL with an absolute lymphocyte count (ALC) ≤ 10 × 109/L; and 219 patients had Rai stage 0 CLL with an ALC more than 10 × 109/L. Data on clinical outcome were abstracted from medical records. Results The percentage of MBL patients free of treatment at 1, 2, and 5 years was 99%, 98%, and 93%, respectively. B-cell count as a continuous variable (hazard ratio [HR] = 2.9, P = .04) and CD38 status (HR = 10.8, P = .006) predicted time to treatment (TTT) among MBL patients. The likelihood of treatment for MBL patients was lower (HR = 0.32, P = .04) than that of both Rai stage 0 CLL patients with an ALC less than 10 × 109/L (n = 94) and Rai stage 0 CLL patients with an ALC more than 10 × 109/L (n = 219; P = .0003). Conclusion Individuals with MBL identified in clinical practice have a low risk for progression at 5 years. Because B-cell count seems to relate to TTT as a continuous variable, additional studies are needed to determine what B-cell count should be used to distinguish between MBL and CLL.