bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene expression profiling reveals different pathways related to Abl and other genes that cooperate with c-Myc in a model of plasma cell neoplasia
Authors: Park Eun Sung , Shaughnessy John D , Gupta Shalu , Wang Hongyang , Lee Ju-Seog , Woo Hyun Goo , Zhan Fenghuang , Owens James D , Potter Michael , Janz Siegfried , Mushinski J Frederic 
Published: August 2007

Abstract

Background
To elucidate the genes involved in the neoplastic transformation of B cells, global gene expression profiles were generated using Affymetrix U74Av2 microarrays, containing 12,488 genes, for four different groups of mouse B-cell lymphomas and six subtypes of pristane-induced mouse plasma cell tumors, three of which developed much earlier than the others.

Results
Unsupervised hierarchical cluster analysis exhibited two main sub-clusters of samples: a B-cell lymphoma cluster and a plasma cell tumor cluster with subclusters reflecting mechanism of induction. This report represents the first step in using global gene expression to investigate molecular signatures related to the role of cooperating oncogenes in a model of Myc-induced carcinogenesis. Within a single subgroup, e.g., ABPCs, plasma cell tumors that contained typical T(12;15) chromosomal translocations did not display gene expression patterns distinct from those with variant T(6;15) translocations, in which the breakpoint was in the Pvt-1 locus, 230 kb 3' of c-Myc, suggesting that c-Myc activation was the initiating factor in both. When integrated with previously published Affymetrix array data from human multiple myelomas, the IL-6-transgenic subset of mouse plasma cell tumors clustered more closely with MM1 subsets of human myelomas, slow-appearing plasma cell tumors clustered together with MM2, while plasma cell tumors accelerated by v-Abl clustered with the more aggressive MM3-MM4 myeloma subsets. Slow-appearing plasma cell tumors expressed Socs1 and Socs2 but v-Abl-accelerated plasma cell tumors expressed 4–5 times as much. Both v-Abl-accelerated and non-v-Ab l-associated tumors exhibited phosphorylated STAT 1 and 3, but only v-Abl-accelerated plasma cell tumors lost viability and STAT 1 and 3 phosphorylation when cultured in the presence of the v-Abl kinase inhibitor, STI-571. These data suggest that the Jak/Stat pathway was critical in the transformation acceleration by v-Abl and that v-Abl activity remained essential throughout the life of the tumors, not just in their acceleration. A different pathway appears to predominate in the more slowly arising plasma cell tumors.

Conclusion
Gene expression profiling differentiates not only B-cell lymphomas from plasma cell tumors but also distinguishes slow from accelerated plasma cell tumors. These data and those obtained from the sensitivity of v-Abl-accelerated plasma cell tumors and their phosphorylated STAT proteins indicate that these similar tumors utilize different signaling pathways but share a common initiating genetic lesion, a c-Myc-activating chromosome translocation.
Global analysis of host response to induction of a latent bacteriophage
Authors: Osterhout Robin E , Figueroa Israel A , Keasling Jay D , Arkin Adam P 
Published: August 2007

Abstract

Background
The transition from viral latency to lytic growth involves complex interactions among host and viral factors, and the extent to which host physiology is buffered from the virus during induction of lysis is not known. A reasonable hypothesis is that the virus should be evolutionarily selected to ensure host health throughout induction to minimize its chance of reproductive failure. To address this question, we collected transcriptional profiles of Escherichia coli and bacteriophage lambda throughout lysogenic induction by UV light.

Results
We observed a temporally coordinated program of phage gene expression, with distinct early, middle and late transcriptional classes. Our study confirmed known host-phage interactions of induction of the heat shock regulon, escape replication, and suppression of genes involved in cell division and initiation of replication. We identified 728 E. coli genes responsive to prophage induction, which included pleiotropic stress response pathways, the Arc and Cpx regulons, and global regulators crp and lrp. Several hundred genes involved in central metabolism, energy metabolism, translation and transport were down-regulated late in induction. Though statistically significant, most of the changes in these genes were mild, with only 140 genes showing greater than two-fold change.

Conclusion
Overall, we observe that prophage induction has a surprisingly low impact on host physiology. This study provides the first global dynamic picture of how host processes respond to lambda phage induction.
High resolution melting for mutation scanning of TP53exons 5–8
Authors: Krypuy Michael , Ahmed Ahmed Ashour , Etemadmoghadam Dariush , Hyland Sarah J ,   Australian Ovarian Cancer Study Group, deFazio Anna , Fox Stephen B , Brenton James D , Bowtell David D , Dobrovic Alexander 
Published: August 2007

Abstract

Background
p53 is commonly inactivated by mutations in the DNA-binding domain in a wide range of cancers. As mutant p53 often influences response to therapy, effective and rapid methods to scan for mutations in TP53 are likely to be of clinical value. We therefore evaluated the use of high resolution melting (HRM) as a rapid mutation scanning tool for TP53 in tumour samples.

Methods
We designed PCR amplicons for HRM mutation scanning of TP53 exons 5 to 8 and tested them with DNA from cell lines hemizygous or homozygous for known mutations. We assessed the sensitivity of each PCR amplicon using dilutions of cell line DNA in normal wild-type DNA. We then performed a blinded assessment on ovarian tumour DNA samples that had been previously sequenced for mutations in TP53 to assess the sensitivity and positive predictive value of the HRM technique. We also performed HRM analysis on breast tumour DNA samples with unknown TP53 mutation status.

Results
One cell line mutation was not readily observed when exon 5 was amplified. As exon 5 contained multiple melting domains, we divided the exon into two amplicons for further screening. Sequence changes were also introduced into some of the primers to improve the melting characteristics of the amplicon. Aberrant HRM curves indicative of TP53 mutations were observed for each of the samples in the ovarian tumour DNA panel. Comparison of the HRM results with the sequencing results revealed that each mutation was detected by HRM in the correct exon. For the breast tumour panel, we detected seven aberrant melt profiles by HRM and subsequent sequencing confirmed the presence of these and no other mutations in the predicted exons.

Conclusion
HRM is an effective technique for simple and rapid scanning of TP53 mutations that can markedly reduce the amount of sequencing required in mutational studies of TP53.
Outcome related to impact on daily living: preliminary validation of the ORIDL instrument
Authors: Reilly David , Mercer Stewart W , Bikker Annemieke P , Harrison Tansy 
Published: September 2007

AbstractBackgroundThe challenge of finding practical, patient-rated outcome measures is a key issue in the evaluation of health care systems and interventions. The ORIDL (Outcome in Relation to Impact on Daily Living) instrument (formerly referred to as the Glasgow Homoeopathic Hospital Outcomes Scale or GHHOS) has been developed to measure patient's views of the outcome of their care by asking about change, and relating this to impact on daily life. The aim of the present paper is to describe the background and potential uses of the ORIDL, and to report on its preliminary validation in a series of three studies in secondary and primary care.MethodsIn the first study, 105 patients attending the Glasgow Homoeopathic Hospital (GHH) were followed-up at 12 months and changes in health status were measured by the EuroQol (EQOL) and the ORIDL. In the second study, 187 new patients at the GHH were followed-up at 3, 12, and 33 months, using the ORIDL, the Short Form 12 (SF-12), and the Measure Yourself Medical Outcome Profile (MYMOP). In study three, 323 patients in primary care were followed for 1 month post-consultation using the ORIDL and MYMOP. In all 3 studies the Patient Enablement Instrument (PEI) was also used as an outcome measure.ResultsStudy 1 showed substantial improvements in main complaint and well-being over 12 months using the ORIDL, with two-thirds of patients reporting improvements in daily living. These improvements were not significantly correlated with changes in serial measures of the EQOL between baseline and 12 months, but were correlated with the EQOL transitions measure. Study 2 showed step-wise improvements in ORIDL scores between 3 and 33 months, which were only weakly associated with similar changes in SF-12 scores. However, MYMOP change scores correlated well with ORIDL scores at all time points. Study 3 showed similar high correlations between ORIDL scores and MYMOP scores. In all 3 studies, ORIDL scores were also significantly correlated with PEI-outcome scores.ConclusionThere is significant agreement between patient outcomes assessed by the ORIDL and the EQOL transition scale, the MYMOP, and the PEI-outcome instrument, suggesting that the ORIDL may be a valid and sensitive tool for measuring change in relation to impact on life.
The impact of generational change and retirement on psychiatry to 2025
Authors: Fletcher Susan L , Schofield Deborah J 
Published: September 2007

Abstract
Background
Australia is currently experiencing widespread shortages of psychiatrists. The changing nature of the workforce and increasing demand mean that these shortages are unlikely to ease. This study aims to identify demographic change and retirement patterns of the Australian psychiatry workforce from 1995 to 2003, and the implications of those changes for future workforce planning.

Methods
Data from the Australian Institute of Health and Welfare (AIHW) Medical Labour Force Survey from 1995 to 2003 is used to examine ageing of the psychiatry workforce and attrition of psychiatrists aged 50 years and over. Future attrition from the workforce is projected to 2025.

Results
Sixty two percent of psychiatrists practicing in the year 2000 are predicted to have retired by 2025. Most psychiatrists continue to work until late in life, with only 18 per cent retiring before age 65. The psychiatry workforce aged significantly between 1995 and 2003 (p < 0.001), with men older than women in both years. A reduction in hours worked by psychiatrists reflects both the increasing proportion of females and the older members of the profession reducing their hours in preparation for retirement.

Conclusion
The impact of ageing of the workforce may be more immediate for psychiatry than for some other health professions. With the growing proportion of females and their typically lower workforce participation, more than one younger psychiatrist will be required to replace each of the mostly male retirees.
The SCI Exercise Self-Efficacy Scale (ESES): development and psychometric properties
Authors: Kroll Thilo , Kehn Matthew , Ho Pei-Shu , Groah Suzanne 
Published: August 2007

Abstract

Background
Rising prevalence of secondary conditions among persons with spinal cord injury (SCI) has focused recent attention to potential health promotion programs designed to reduce such adverse health conditions. A healthy lifestyle for people with SCI, including and specifically, the adoption of a vigorous exercise routine, has been shown to produce an array of health benefits, prompting many providers to recommend the implementation of such activity to those with SCI. Successfully adopting such an exercise regimen however, requires confidence in one's ability to engage in exercise or exercise self-efficacy. Exercise self-efficacy has not been assessed adequately for people with SCI due to a lack of validated and reliable scales, despite self efficacy's status as one of the most widely researched concepts and despite its broad application in health promotion studies. Exercise self efficacy supporting interventions for people with SCI are only meaningful if appropriate measurement tools exist. The objective of our study was to develop a psychometrically sound exercise self-efficacy self-report measure for people with SCI.

Methods
Based on literature reviews, expert comments and cognitive testing, 10 items were included and made up the 4-point Likert SCI Exercise Self-Efficacy Scale (ESES) in its current form. The ESES was administered as part of the first wave of a nationwide survey (n = 368) on exercise behavior and was also tested separately for validity in four groups of individuals with SCI. Reliability and validity testing was performed using SPSS 12.0.

Results
Cronbach's alpha was .9269 for the ESES. High internal consistency was confirmed in split-half (EQ Length Spearman Brown = .8836). Construct validity was determined using principal component factor analysis by correlating the aggregated ESES items with the Generalised Self Efficacy Scale (GSE). We found that all items loaded on one factor only and that there was a statistically significant correlation between Exercise Self-Efficacy Scale (ESES) and Generalised Self Efficacy Scale (GSE) (Spearman RHO = .316; p < .05; n = 53, 2-sided).

Conclusion
Preliminary findings indicate that the ESES is a reliable instrument with high internal consistency and scale integrity. Content validity both in terms of face and construct validity is satisfactory.
Multiple organ failure after trauma affects even long-term survival and functional status
Authors: Ulvik Atle , Kvåle Reidar , Wentzel-Larsen Tore , Flaatten Hans 
Published: September 2007

Abstract
Background
The aim of this study was to assess the incidence of organ failure in trauma patients treated in an intensive care unit (ICU), and to study the relationship between organ failure and long-term survival and functional status.

Methods
This is a cohort study of all adult ICU trauma patients admitted to a university hospital during 1998 to 2003. Organ failure was quantified by the Sequential Organ Failure Assessment (SOFA) score. A telephone interview was conducted in 2005 (2 to 7 years after trauma) using the Karnofsky Index to measure functional status, and the Glasgow Outcome Score to measure recovery.

Results
Of the 322 patients included, 47% had multiple organ failure (MOF), and 28% had single organ failure. In a Cox regression, MOF increased the overall risk of death 6.0 times. At follow-up, 242 patients (75%) were still alive. Patients with MOF had 3.9 times greater odds for requiring personal assistance in activities of daily living compared to patients without organ failure. Long-term survival and functional status were the same for patients suffering single organ failure and no organ failure. Complete recovery occurred in 52% of survivors, and 87% were able to look after themselves.

Conclusion
Almost half of the ICU trauma patients had MOF. While single organ failure had no impact on long-term outcomes, the presence of MOF greatly increased mortality and the risk of impaired functional status. MOF expressed by SOFA score may be used to define trauma patients at particular risk for poor long-term outcomes.
Clinical risk conditions for acute lung injury in the intensive care unit and hospital ward: a prospective observational study
Authors: Ferguson Niall D , Frutos-Vivar Fernando , Esteban Andrés , Gordo Federico , Honrubia Teresa , Peñuelas Oscar , Algora Alejandro , García Gema , Bustos Alejandra , Rodríguez Inmaculada 
Published: September 2007

Abstract
Background
Little is known about the development of acute lung injury outside the intensive care unit. We set out to document the following: the association between predefined clinical conditions and the development of acute lung injury by using the American–European consensus definition; the frequency of lung injury development outside the intensive care unit; and the temporal relationship between antecedent clinical risk conditions, intensive care admission, and diagnosis of lung injury.

Methods
We conducted a 4-month prospective observational study in three Spanish teaching hospitals, enrolling consecutive patients who developed clinical conditions previously linked to lung injury, both inside and outside the intensive care unit. Patients were followed prospectively for outcomes, including the diagnosis of acute lung injury or acute respiratory distress syndrome.

Results
A total 815 patients were identified with at least one clinical insult; the most common were sepsis, pneumonia, and pancreatitis. Pulmonary risk conditions were observed in 30% of cases. Fifty-three patients (6.5%) developed acute lung injury; 33 of these (4.0%) met criteria for acute respiratory distress syndrome. Lung injury occurred most commonly in the setting of sepsis (46/53; 86.7%), but shock (21/59; 36%) and pneumonia (20/211; 9.5%) portended the highest proportional risk; this risk was higher in patients with increasing numbers of clinical risk conditions (2.2%, 14%, and 21% (P < 0.001) in patients with one, two, and three conditions, respectively). Median days (interquartile range) from risk condition to diagnosis of lung injury was shorter with pulmonary (0 (0 to 2)) versus extrapulmonary (3 (1 to 5)) (P = 0.029) risk conditions. Admission to the intensive care unit was provided to 9/20 (45%) patients with acute lung injury and to 29/33 (88%) of those with acute respiratory distress syndrome. Lung injury patients had higher mortality than others (acute lung injury 25.0%; acute respiratory distress syndrome 45.5%; others 10.3%; P < 0.001).

Conclusion
The time course from clinical insult to diagnosis of lung injury was rapid, but may be longer for extrapulmonary cases. Some patients with lung injury receive care and die outside the intensive care unit; this observation needs further study.
Functional constraint and small insertions and deletions in the ENCODE regions of the human genome
Authors: Clark Taane G , Andrew Toby , Cooper Gregory M , Margulies Elliott H , Mullikin James C , Balding David J 
Published: September 2007

Abstract
Background
We describe the distribution of indels in the 44 Encyclopedia of DNA Elements (ENCODE) regions (about 1% of the human genome) and evaluate the potential contributions of small insertion and deletion polymorphisms (indels) to human genetic variation. We relate indels to known genomic annotation features and measures of evolutionary constraint.

Results
Indel rates are observed to be reduced approximately 20-fold to 60-fold in exonic regions, 5-fold to 10-fold in sequence that exhibits high evolutionary constraint in mammals, and up to 2-fold in some classes of regulatory elements (for instance, formaldehyde assisted isolation of regulatory elements [FAIRE] and hypersensitive sites). In addition, some noncoding transcription and other chromatin mediated regulatory sites also have reduced indel rates. Overall indel rates for these data are estimated to be smaller than single nucleotide polymorphism (SNP) rates by a factor of approximately 2, with both rates measured as base pairs per 100 kilobases to facilitate comparison.

Conclusion
Indel rates exhibit a broadly similar distribution across genomic features compared with SNP density rates, with a reduction in rates in coding transcription and evolutionarily constrained sequence. However, unlike indels, SNP rates do not appear to be reduced in some noncoding functional sequences, such as pseudo-exons, and FAIRE and hypersensitive sites. We conclude that indel rates are greatly reduced in transcribed and evolutionarily constrained DNA, and discuss why indel (but not SNP) rates appear to be constrained at some regulatory sites.
Dynamic cumulative activity of transcription factors as a mechanism of quantitative gene regulation
Authors: He Feng , Buer Jan , Zeng An-Ping , Balling Rudi 
Published: September 2007

Abstract
Background
The regulation of genes in multicellular organisms is generally achieved through the combinatorial activity of different transcription factors. However, the quantitative mechanisms of how a combination of transcription factors controls the expression of their target genes remain unknown.

Results
By using the information on the yeast transcription network and high-resolution time-series data, the combinatorial expression profiles of regulators that best correlate with the expression of their target genes are identified. We demonstrate that a number of factors, particularly time-shifts among the different regulators as well as conversion efficiencies of transcription factor mRNAs into functional binding regulators, play a key role in the quantification of target gene expression. By quantifying and integrating these factors, we have found a highly significant correlation between the combinatorial time-series expression profile of regulators and their target gene expression in 67.1% of the 161 known yeast three-regulator motifs and in 32.9% of 544 two-regulator motifs. For network motifs involved in the cell cycle, these percentages are much higher. Furthermore, the results have been verified with a high consistency in a second independent set of time-series data. Additional support comes from the finding that a high percentage of motifs again show a significant correlation in time-series data from stress-response studies.

Conclusion
Our data strongly support the concept that dynamic cumulative regulation is a major principle of quantitative transcriptional control. The proposed concept might also apply to other organisms and could be relevant for a wide range of biotechnological applications in which quantitative gene regulation plays a role.
Metabolic peculiarities of Aspergillus niger disclosed by comparative metabolic genomics
Authors: Sun Jibin , Lu Xin , Rinas Ursula , Zeng An Ping 
Published: September 2007

Abstract
Background
Aspergillus niger is an important industrial microorganism for the production of both metabolites, such as citric acid, and proteins, such as fungal enzymes or heterologous proteins. Despite its extensive industrial applications, the genetic inventory of this fungus is only partially understood. The recently released genome sequence opens a new horizon for both scientific studies and biotechnological applications.

Results
Here, we present the first genome-scale metabolic network for A. niger and an in-depth genomic comparison of this species to seven other fungi to disclose its metabolic peculiarities. The raw genomic sequences of A. niger ATCC 9029 were first annotated. The reconstructed metabolic network is based on the annotation of two A. niger genomes, CBS 513.88 and ATCC 9029, including enzymes with 988 unique EC numbers, 2,443 reactions and 2,349 metabolites. More than 1,100 enzyme-coding genes are unique to A. niger in comparison to the other seven fungi. For example, we identified additional copies of genes such as those encoding alternative mitochondrial oxidoreductase and citrate synthase in A. niger, which might contribute to the high citric acid production efficiency of this species. Moreover, nine genes were identified as encoding enzymes with EC numbers exclusively found in A. niger, mostly involved in the biosynthesis of complex secondary metabolites and degradation of aromatic compounds.

Conclusion
The genome-level reconstruction of the metabolic network and genome-based metabolic comparison disclose peculiarities of A. niger highly relevant to its biotechnological applications and should contribute to future rational metabolic design and systems biology studies of this black mold and related species.