bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum
Authors: Hass-Jacobus Barbara L , Futrell-Griggs Montona , Abernathy Brian , Westerman Rick , Goicoechea Jose-Luis , Stein Joshua , Klein Patricia , Hurwitz Bonnie , Zhou Bin , Rakhshan Fariborz , Sanyal Abhijit , Gill Navdeep , Lin Jer-Young , Walling Jason G , Luo Mei Zhong , Ammiraju Jetty Siva S , Kudrna Dave , Kim Hye Ran , Ware Doreen , Wing Rod A , Miguel Phillip San , Jackson Scott A 
Published: August 2006

Abstract

Background
With the completion of the genome sequence for rice (Oryza sativa L.), the focus of rice genomics research has shifted to the comparison of the rice genome with genomes of other species for gene cloning, breeding, and evolutionary studies. The genus Oryza includes 23 species that shared a common ancestor 8–10 million years ago making this an ideal model for investigations into the processes underlying domestication, as many of the Oryza species are still undergoing domestication. This study integrates high-throughput, hybridization-based markers with BAC end sequence and fingerprint data to construct physical maps of rice chromosome 1 orthologues in two wild Oryza species. Similar studies were undertaken in Sorghum bicolor, a species which diverged from cultivated rice 40–50 million years ago.

Results
Overgo markers, in conjunction with fingerprint and BAC end sequence data, were used to build sequence-ready BAC contigs for two wild Oryza species. The markers drove contig merges to construct physical maps syntenic to rice chromosome 1 in the wild species and provided evidence for at least one rearrangement on chromosome 1 of the O. sativa versus Oryza officinalis comparative map. When rice overgos were aligned to available S. bicolor sequence, 29% of the overgos aligned with three or fewer mismatches; of these, 41% gave positive hybridization signals. Overgo hybridization patterns supported colinearity of loci in regions of sorghum chromosome 3 and rice chromosome 1 and suggested that a possible genomic inversion occurred in this syntenic region in one of the two genomes after the divergence of S. bicolor and O. sativa.

Conclusion
The results of this study emphasize the importance of identifying conserved sequences in the reference sequence when designing overgo probes in order for those probes to hybridize successfully in distantly related species. As interspecific markers, overgos can be used successfully to construct physical maps in species which diverged less than 8 million years ago, and can be used in a more limited fashion to examine colinearity among species which diverged as much as 40 million years ago. Additionally, overgos are able to provide evidence of genomic rearrangements in comparative physical mapping studies.
Bloodstream infection following 217 consecutive systemic-enteric drained pancreas transplants
Authors: Berger Natalie , Guggenbichler Sigmund , Steurer Wolfgang , Margreiter Christian , Mayer Gert , Kafka Reinhold , Mark Walter , Rosenkranz Alexander R , Margreiter Raimund , Bonatti Hugo 
Published: August 2006

Abstract

Background
Combined kidney pancreas transplantation (PTx) evolved as excellent treatment for diabetic nephropathy. Infections remain common and serious complications.

Methods
217 consecutive enteric drained PTxs performed from 1997 to 2004 were retrospectively analyzed with regard to bloodstream infection. Immunosuppression consisted of antithymocyteglobuline induction, tacrolimus, mycophenolic acid and steroids for the majority of cases. Standard perioperative antimicrobial prophylaxis consisted of pipercillin/tazobactam in combination with ciprofloxacin and fluconazole.

Results
One year patient, pancreas and kidney graft survival were 96.4%, 88.5% and 94.8%, surgical complication rate was 35%, rejection rate 30% and rate of infection 59%. In total 46 sepsis episodes were diagnosed in 35 patients (16%) with a median onset on day 12 (range 1–45) post transplant. Sepsis source was intraabdominal infection (IAI) (n = 21), a contaminated central venous line (n = 10), wound infection (n = 5), urinary tract infection (n = 2) and graft transmitted (n = 2). Nine patients (4%) experienced multiple episodes of sepsis. Overall 65 pathogens (IAI sepsis 39, line sepsis 15, others 11) were isolated from blood. Gram positive cocci accounted for 50 isolates (77%): Coagulase negative staphylococci (n = 28, i.e. 43%) (nine multi-resistant), Staphylococcus aureus (n = 11, i.e. 17%) (four multi-resistant), enterococci (n = 9, i.e. 14%) (one E. faecium). Gram negative rods were cultured in twelve cases (18%). Patients with blood borne infection had a two year pancreas graft survival of 76.5% versus 89.4% for those without sepsis (p = 0.036), patient survival was not affected.

Conclusion
Sepsis remains a serious complication after PTx with significantly reduced pancreas graft, but not patient survival. The most common source is IAI.
Mutations in PIK3CAare infrequent in neuroblastoma
Authors: Dam Vincent , Morgan Brian T , Mazanek Pavel , Hogarty Michael D 
Published: August 2006

Abstract

Background
Neuroblastoma is a frequently lethal pediatric cancer in which MYCN genomic amplification is highly correlated with aggressive disease. Deregulated MYC genes require co-operative lesions to foster tumourigenesis and both direct and indirect evidence support activated Ras signaling for this purpose in many cancers. Yet Ras genes and Braf, while often activated in cancer cells, are infrequent targets for activation in neuroblastoma. Recently, the Ras effector PIK3CA was shown to be activated in diverse human cancers. We therefore assessed PIK3CA for mutation in human neuroblastomas, as well as in neuroblastomas arising in transgenic mice with MYCN overexpressed in neural-crest tissues. In this murine model we additionally surveyed for Ras family and Braf mutations as these have not been previously reported.

Methods
Sixty-nine human neuroblastomas (42 primary tumors and 27 cell lines) were sequenced for PIK3CA activating mutations within the C2, helical and kinase domain "hot spots" where 80% of mutations cluster. Constitutional DNA was sequenced in cases with confirmed alterations to assess for germline or somatic acquisition. Additionally, Ras family members (Hras1, Kras2 and Nras) and the downstream effectors Pik3ca and Braf, were sequenced from twenty-five neuroblastomas arising in neuroblastoma-prone transgenic mice.

Results
We identified mutations in the PIK3CA gene in 2 of 69 human neuroblastomas (2.9%). Neither mutation (R524M and E982D) has been studied to date for effects on lipid kinase activity. Though both occurred in tumors with MYCN amplification the overall rate of PIK3CA mutations in MYCN amplified and single-copy tumors did not differ appreciably (2 of 31 versus 0 of 38, respectively). Further, no activating mutations were identified in a survey of Ras signal transduction genes (including Hras1, Kras2, Nras, Pik3ca, or Braf genes) in twenty-five neuroblastic tumors arising in the MYCN-initiated transgenic mouse model.

Conclusion
These data suggest that activating mutations in the Ras/Raf-MAPK/PI3K signaling cascades occur infrequently in neuroblastoma. Further, despite compelling evidence for MYC and RAS cooperation in vitro and in vivo to promote tumourigenesis, activation of RAS signal transduction does not constitute a preferred secondary pathway in neuroblastomas with MYCN deregulation in either human tumors or murine models.
Development and testing of innovative patient resources for the management of coronary heart disease (CHD): a descriptive study
Authors: Redfern Julie , Ellis Elizabeth , Briffa Tom , Freedman Saul B 
Published: August 2006

Abstract
Background
Although heart disease is a major cause of morbidity and mortality the majority of patients do not access existing rehabilitation programs and patient resources are not designed to facilitate patient choice and decision-making. The objective of this study was to develop and test a series of risk factor modules and corresponding patient information leaflets for secondary prevention of CHD.

Methods
In phase one, a series of risk factor modules and management options were developed following analysis of literature and interviews with health professionals. In phase two, module information leaflets were developed using published guidelines and interviews of people with CHD. In phase three, the leaflets were tested for quality (DISCERN), readability (Flesch) and suitability (SAM) and were compared to the existing cardiac rehabilitation (CR) information leaflet. Finally, the patients assessed the leaflets for content and relevance.

Results
Four key risk factors identified were cholesterol, blood pressure, smoking and physical inactivity. Choice management options were selected for each risk factor and included medical consultation, intensive health professional led program, home program and self direction. Patient information needs were then identified and leaflets were developed. DISCERN quality scores were high for cholesterol (62/80), blood pressure (59/80), smoking (62/80) and physical activity (62/80), all scoring 4/5 for overall rating. The mean Flesch readability score was 75, representing "fairly easy to read", all leaflets scored in the superior category for suitability and were reported to be easy to understand, useful and motivating by persons with CHD risk factors. The developed leaflets scored higher on each assessment than the existing CR leaflets.

Conclusion
Using a progressive three phase approach, a series of risk factor modules and information leaflets were successfully developed and tested. The leaflets will contribute to shared-decision making and empowerment for persons with CHD.
Exposure of hairdressing apprentices to airborne hazardous substances
Authors: Mounier-Geyssant Estelle , Oury Véronique , Mouchot Lory , Paris Christophe , Zmirou-Navier Denis 
Published: August 2006

Abstract

Background
Few studies have investigated exposure of hairdressing apprentices to airborne irritants. This study describes exposure levels of apprentices to chemical products used in hairdressing salons in relation with their activity.

Methods
Following a two stages study design, a group of 300 students completed a questionnaire on their work activities and environment. Among these, a group of 28 subjects volunteered to undergo personal exposure and workplace concentrations measurements over a work shift, during a cold and a hot season, with the agreement of the salon owners. Three chemical substances were studied (ammonia, hydrogen peroxide and persulfates) because they are respiratory tract irritants and because their concentrations could be quantified within a 5 to 8 hour shift period.

Results
Personal exposure values for H2O2and NH3 (averages [standard deviations] are 0.05 [0.04] and 0.90 [0.76] mg.m-3, respectively) were greater than workplace ambient air concentrations (corresponding values of 0.04 [0.03] and 0.68 [0.42] mg.m-3) for H2O2 and NH3, with no significant seasonal variation. By contrast, workplace concentrations of persulfates (0.019 [0.018] mg.m-3) were greater than personal exposure (0.016 [0.021] mg.m-3, a finding that is consistent with the fact that bleaching is more often undertaken by senior hairdressers. However, all exposure values were lower than the current TLV TWA values. This study also shows that over half of technical spaces where chemical substances used for dying, permanenting or bleaching are manipulated, have no ventilation system, and not even a door or a window opening outside.

Conclusion
The study hairdressing salons, on average, were small, the most probable reason why occupational hygiene measures such as appropriate ventilation were too seldom implemented. As a consequence, young apprentices and senior hairdressers experience substantial exposure to known airways irritants.
Evaluation of the sensitization rates and identification of IgE-binding components in wild and genetically modified potatoes in patients with allergic disorders
Authors: Lee Soo-Keol , Ye Young-Min , Yoon Sung-Ho , Lee Bou-Oung , Kim Seung-Hyun , Park Hae-Sim 
Published: August 2006

Abstract

Background
The potato is one of the most common types of genetically modified (GM) food. However, there are no published data evaluating the impact of genetic manipulations on the allergenicity of GM potatoes. To compare the allergenicity of GM potatoes with that of wild-type potatoes using in vivo and in vitro methods in adult allergy patients sensitized to potatoes.

Methods
A total of 1886 patients with various allergic diseases and 38 healthy controls participated in the study. Skin-prick testing and IgE-ELISA were carried out with extracts prepared from wild-type and GM potatoes. An ELISA inhibition test was used to confirm the binding specificity. IgE-binding components in extracts from the two types of potato were identified by SDS-PAGE and IgE-immunoblotting. The effects of digestive enzymes and heat on the allergenicity of the extracts was evaluated by preincubating the potatoes with or without simulated gastric and intestinal fluids in the absence or presence of heat.

Results
Positive responses (ratio of the wheal size induced by the allergen to that induced by histamine (A/H) ≥ 2+) to wild-type or GM potato extracts, as demonstrated by the skin-prick test, were observed in 108 patients (5.7%). Serum-specific IgE was detected in 0–88% of subjects who tested positively. ELISA inhibition tests indicated significant inhibition when extract from each type of potato was added. IgE-immunoblot analysis demonstrated the presence of 14 IgE-binding components within the wild-type potato and 9 within the GM potato. Furthermore, a common 45-kDa binding component that yielded similar IgE-binding patterns was noted in more than 80% of the reactions using sera from patients sensitized to wild-type or GM potato. Exposure to simulated gastric fluid and heat treatment similarly inhibited IgE binding by extracts from wild-type and GM potatoes, whereas minimal changes were obtained following exposure of the extracts to simulated intestinal fluid.

Conclusion
Our results strongly suggest that genetic manipulation of potatoes does not increase their allergenic risk. The sensitization rate of adult allergy patients to both types of extract was 5.7%, and a common major allergen (45 kDa) was identified.
Validation of an English version of the Child-OIDP index, an oral health-related quality of life measure for children
Authors: Yusuf Huda , Gherunpong Sudaduang , Sheiham Aubrey , Tsakos Georgios 
Published: August 2006

Abstract

Background
To evaluate the psychometric properties of the Child-OIDP for use among children in the UK and report on the prevalence of oral impacts in a sample of schoolchildren in Westminster.

Methods
Children aged 10–11 years in the final year of primary school (year 6) were selected from seven schools where annual screenings are carried out. A total of 228 children participated (99% response rate). A clinical examination was conducted followed by a questionnaire designed to measure oral health-related quality of life in children, namely the Child-OIDP. The psychometric properties of the Child-OIDP were evaluated in terms of face, content and concurrent validity in addition to internal and test-retest reliability.

Results
The Child-OIDP revealed excellent validity and good reliability. Weighted Kappa was 0.82. Cronbach's alpha coefficient was 0.58. The index showed significant associations with perceived oral treatment needs and perceived satisfaction with mouth and oral health status (p < 0.001).

Conclusion
This study has demonstrated that the Child-OIDP is a valid and reliable index to be used among 10–11 year old schoolchildren in the UK.
Burden of premature mortality in rural Vietnam from 1999 – 2003: analyses from a Demographic Surveillance Site
Authors: Huong Dao Lan , Minh Hoang Van , Vos Theo , Janlert Urban , Van Do Duc , Byass Peter 
Published: August 2006

Abstract

Background
Assessing the burden of disease contributes towards evidence-based allocation of limited health resources. However, such measures are not yet commonly available in Vietnam. Taking advantage of the FilaBavi Demographic Surveillance Site (FilaBavi DSS) in Vietnam, this study aimed to establish the feasibility of applying the Years of Life Lost (YLL) technique in the context of a defined DSS, and to estimate the importance of the principal causes of premature mortality in a rural area of Vietnam between 1999 and 2003.

Methods
Global Burden of Disease methods were applied. Causes of death were ascertained by verbal autopsy.

Results
In five years, 1,240 deaths occurred and for 1,220 cases cause of death information from verbal autopsy was available. Life expectancy at birth was 71.0 (95% confidence interval 69.9–72.1) in males and 80.9 (79.9–81.9) in females. The discounted, but not age weighted YLL per 1,000 population was 85 and 55 for males and females, respectively. The leading causes of YLL and death counts were cardiovascular diseases, malignant neoplasms, unintentional injuries, and neonatal causes. Males contributed 54% of total deaths and 59% of YLL. Males experienced higher YLL than women across all causes. Filabavi mortality estimates are considerably lower than 2002 WHO country estimates for Vietnam. Also the FilaBavi cause distribution varies considerably from the WHO result.

Conclusion
The combination of localised demographic surveillance, verbal autopsy and the application of YLL methods enable new insights into the magnitude and importance of significant public health issues in settings where evidence for planning is otherwise scarce. Local mortality data vary considerably from the WHO model-based estimates.
Papillary microcarcinomas of the thyroid gland and immunohistochemical analysis of expression of p53 protein in papillary microcarcinomas
Authors: Corapcioglu Demet , Sak Serpil D , Delibasi Tuncay , Tonyukuk Vedia , Kamel Nuri , Uysal Ali R , Kocak Savas , Aydintug Semih , Erdogan Gurbuz 
Published: August 2006

Abstract

Background
Thyroid papillary microcarcinoma (TPM) is defined according to WHO criteria as a thyroid tumor smaller than 1–1.5 cm. TPMs are encountered in 0.5–35.6 % of autopsies or surgical specimens where carcinoma had been unsuspected. The purpose of the present study was to evaluate patients who had TPMs in terms of clinical findings, histopathological features and immunohistochemical evidence of expression of the tumor suppressor gene p53.

Methods
A total of 44 patients with TPMs less than 1.0 cm in diameter were included in the study. The patients were evaluated clinically and the tumors were evaluated in terms of their histopathological and immunohistochemical features, including expression of p53.

Results
The female/male ratio was 2.8/1, and the median age at time of diagnosis was 49 years (range 20–71 years). The maximum diameter of the smallest focus was 0.1 mm, and that of the largest was 10 mm microscopically. The mean diameter of all tumors was 5.7 mm. There was no correlation between tumor size and age or gender. Of the TPMs, 72 % were found in the right lobe, 24 % in the left lobe and 4 % in the isthmus. Fine-needle aspiration biopsy provided the diagnosis of TPM in only 43.2 % of the patients. All patients were treated with surgery, with 20 undergoing conservative surgery, i.e. lobectomy or isthmusectomy, and 24 undergoing total thyroidectomy. Frozen section provided the diagnosis of TPM in only 56.8 % of the patients. We found lymphocytic thyroiditis in 13.6% of patients, follicular variants in 11.9%, capsular invasion in 26.8%, lymph node involvement in 11.9%, soft tissue metastases in the neck in 12.1% and multifocality in 31.7 %, and none of these were related to age or gender (p > 0.05). No distant metastases were observed during approximately 10 years of follow up. We found p53 positivity in 34.5 % of TPM tumors. However, p53 expression was not statistically related to age or gender.

Conclusion
Our findings imply that TPMs may not be entirely innocent since they are associated with signs of poor prognosis such as capsular invasion, multifocal presentation, lymph node involvement and p53 positivity. Therefore, TPMs should be evaluated and followed like classical papillary cancers.
Astrogliosis is delayed in type 1 interleukin-1 receptor-null mice following a penetrating brain injury
Authors: Lin Hsiao-Wen , Basu Anirban , Druckman Charles , Cicchese Michael , Krady J Kyle , Levison Steven W 
Published: August 2006

AbstractThe cytokines IL-1α and IL-1β are induced rapidly after insults to the CNS, and their subsequent signaling through the type 1 IL-1 receptor (IL-1R1) has been regarded as essential for a normal astroglial and microglial/macrophage response. To determine whether abrogating signaling through the IL-1R1 will alter the cardinal astrocytic responses to injury, we analyzed molecules characteristic of activated astrocytes in response to a penetrating stab wound in wild type mice and mice with a targeted deletion of IL-1R1. Here we show that after a stab wound injury, glial fibrillary acidic protein (GFAP) induction on a per cell basis is delayed in the IL-1R1-null mice compared to wild type counterparts. However, the induction of chondroitin sulfate proteoglycans, tenascin, S-100B as well as glutamate transporter proteins, GLAST and GLT-1, and glutamine synthetase are independent of IL-1RI signaling. Cumulatively, our studies on gliosis in the IL-1R1-null mice indicate that abrogating IL-1R1 signaling delays some responses of astroglial activation; however, many of the important neuroprotective adaptations of astrocytes to brain trauma are preserved. These data recommend the continued development of therapeutics to abrogate IL-1R1 signaling to treat traumatic brain injuries. However, astroglial scar related proteins were induced irrespective of blocking IL-1R1 signaling and thus, other therapeutic strategies will be required to inhibit glial scarring.