bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks
Authors: Oh S June , Joung Je-Gun , Chang Jeong-Ho , Zhang Byoung-Tak 
Published: June 2006

AbstractBackgroundTo infer the tree of life requires knowledge of the common characteristics of each species descended from a common ancestor as the measuring criteria and a method to calculate the distance between the resulting values of each measure. Conventional phylogenetic analysis based on genomic sequences provides information about the genetic relationships between different organisms. In contrast, comparative analysis of metabolic pathways in different organisms can yield insights into their functional relationships under different physiological conditions. However, evaluating the similarities or differences between metabolic networks is a computationally challenging problem, and systematic methods of doing this are desirable. Here we introduce a graph-kernel method for computing the similarity between metabolic networks in polynomial time, and use it to profile metabolic pathways and to construct phylogenetic trees.ResultsTo compare the structures of metabolic networks in organisms, we adopted the exponential graph kernel, which is a kernel-based approach with a labeled graph that includes a label matrix and an adjacency matrix. To construct the phylogenetic trees, we used an unweighted pair-group method with arithmetic mean, i.e., a hierarchical clustering algorithm. We applied the kernel-based network profiling method in a comparative analysis of nine carbohydrate metabolic networks from 81 biological species encompassing Archaea, Eukaryota, and Eubacteria. The resulting phylogenetic hierarchies generally support the tripartite scheme of three domains rather than the two domains of prokaryotes and eukaryotes.ConclusionBy combining the kernel machines with metabolic information, the method infers the context of biosphere development that covers physiological events required for adaptation by genetic reconstruction. The results show that one may obtain a global view of the tree of life by comparing the metabolic pathway structures using meta-level information rather than sequence information. This method may yield further information about biological evolution, such as the history of horizontal transfer of each gene, by studying the detailed structure of the phylogenetic tree constructed by the kernel-based method.
Genomic analysis of Xenopusorganizer function
Authors: Hufton Andrew L , Vinayagam Arunachalam , Suhai Sándor , Baker Julie C 
Published: June 2006

Abstract

Background
Studies of the Xenopus organizer have laid the foundation for our understanding of the conserved signaling pathways that pattern vertebrate embryos during gastrulation. The two primary activities of the organizer, BMP and Wnt inhibition, can regulate a spectrum of genes that pattern essentially all aspects of the embryo during gastrulation. As our knowledge of organizer signaling grows, it is imperative that we begin knitting together our gene-level knowledge into genome-level signaling models. The goal of this paper was to identify complete lists of genes regulated by different aspects of organizer signaling, thereby providing a deeper understanding of the genomic mechanisms that underlie these complex and fundamental signaling events.

Results
To this end, we ectopically overexpress Noggin and Dkk-1, inhibitors of the BMP and Wnt pathways, respectively, within ventral tissues. After isolating embryonic ventral halves at early and late gastrulation, we analyze the transcriptional response to these molecules within the generated ectopic organizers using oligonucleotide microarrays. An efficient statistical analysis scheme, combined with a new Gene Ontology biological process annotation of the Xenopus genome, allows reliable and faithful clustering of molecules based upon their roles during gastrulation. From this data, we identify new organizer-related expression patterns for 19 genes. Moreover, our data sub-divides organizer genes into separate head and trunk organizing groups, which each show distinct responses to Noggin and Dkk-1 activity during gastrulation.

Conclusion
Our data provides a genomic view of the cohorts of genes that respond to Noggin and Dkk-1 activity, allowing us to separate the role of each in organizer function. These patterns demonstrate a model where BMP inhibition plays a largely inductive role during early developmental stages, thereby initiating the suites of genes needed to pattern dorsal tissues. Meanwhile, Wnt inhibition acts later during gastrulation, and is essential for maintenance of organizer gene expression throughout gastrulation, a role which may depend on its ability to block the expression of a host of ventral, posterior, and lateral fate-specifying factors.
Colorectal cancer screening awareness among physicians in Greece
Authors: Xilomenos Apostolos , Mauri Davide , Kamposioras Konstantinos , Gkinosati Athanasia , Zacharias Georgios , Sidiropoulou Varvara , Papadopoulos Panagiotis , Chatzimichalis Georgios , Golfinopoulos Vassilis , Peponi Christina ,   Panhellenic Association for Continual Medical Research (PACMeR)
Published: June 2006

Abstract

Background
Data comparison between SEER and EUROCARE database provided evidence that colorectal cancer survival in USA is higher than in European countries. Since adjustment for stage at diagnosis markedly reduces the survival differences, a screening bias was hypothesized. Considering the important role of primary care in screening activities, the purpose of the study was to investigate the colorectal cancer screening awareness among Hellenic physicians.

Methods
211 primary care physicians were surveyed by mean of a self-reported prescription-habits questionnaire. Both physicians' colorectal cancer screening behaviors and colorectal cancer screening recommendations during usual check-up visits were analyzed.

Results
Only 50% of physicians were found to recommend screening for colorectal cancer during usual check-up visits, and only 25% prescribed cost-effective procedures. The percentage of physicians recommending stool occult blood test and sigmoidoscopy was 24% and 4% respectively. Only 48% and 23% of physicians recognized a cancer screening value for stool occult blood test and sigmoidoscopy. Colorectal screening recommendations were statistically lower among physicians aged 30 or less (p = 0.012). No differences were found when gender, level and type of specialization were analyzed, even though specialists in general practice showed a trend for better prescription (p = 0.054).

Conclusion
Contemporary recommendations for colorectal cancer screening are not followed by implementation in primary care setting. Education on presymptomatic control and screening practice monitoring are required if primary care is to make a major impact on colorectal cancer mortality.
Health seeking behaviour, health system experience and tuberculosis case finding in Gambians with cough
Authors: Kasse Yaya , Jasseh Momodou , Corrah Tumani , Donkor Simon A , Antonnio Martin , Jallow Adama , Adegbola Richard A , Hill Philip C 
Published: June 2006

Abstract

Background
Studies in Africa investigating health-seeking behaviour by interviewing tuberculosis patients have revealed patient knowledge issues and significant delays to diagnosis. We aimed to study health-seeking behaviour and experience of those with cough in The Gambia and to identify whether they had tuberculosis.

Methods
During a round of a population under 3-monthly demographic surveillance, we identified people >10 years old who had been coughing ≥ 3 weeks. A questionnaire was administered concerning demographic data, cough, knowledge, health seeking, and experience at health facilities. Case finding utilised sputum smear and chest X-ray.

Results
122/29,871 coughing individuals were identified. Of 115 interviewed, 93 (81%) had sought treatment; 76 (81.7%) from the health system. Those that visited an alternative health provider first were significantly older than those who visited the health system first (p = 0.03). The median time to seek treatment was 2 weeks (range 0 – 106). 54 (58.1%) made their choice of provider because they believed it was right. Of those who left the health system to an alternative provider (n = 13): 7 believed it was the best place, 3 cited cost and 2 failure to improve. 3 cases were identified by sputum analysis, 11 more by X-ray; all had visited the health system first. Total 'excess' cough time was 1079 person weeks.

Conclusion
The majority of people with cough in this population seek appropriate help early. Improved case detection might be achieved through the use of chest X-ray in addition to sputum smear.
Why do adult women in Vietnam take iron tablets?
Authors: Aikawa Ritsuko , Jimba Masamine , Nguen Khan C , Zhao Yun , Binns Colin W , Lee Mi Kyung 
Published: June 2006

Abstract

Background
Conducting iron supplementation programs has been a major strategy to reduce iron deficiency anemia in pregnancy. However, only a few countries have reported improvements in the anemia rate at a national level. The strategies used for control of nutrition problems need regular review to maintain and improve their effectiveness. The objective of this study was to analyze the factors in compliance with taking iron tablets, where daily doses of iron (60 mg) and folic acid (400 μg) were distributed in rural Vietnamese communes.

Methods
A cross sectional survey was conducted in Nghe An province, Vietnam in January, 2003. The study population was adult women aged less than 35 years who delivered babies between August 1st 2001 and December 1st 2002 (n = 205), of which 159 took part in the study. Data for the study were collected from a series of workshops with community leaders, focus group discussions with community members and a questionnaire survey.

Results
Improvements in the rate of anemia was not given a high priority as one of the commune's needs, but the participants still made efforts to continue taking iron tablets. Two major factors motivated the participants to continue taking iron tablets; their experience of fewer spells of dizziness (50%), and their concern for the health of their newborn baby (54%). When examining the reasons for taking iron tablets for at least 5–9 months, the most important factor was identified as 'a frequent supply of iron tablets' (OR = 11.93, 95% CI: 4.33–32.85).

Conclusion
The study found that multiple poor environmental risk factors discouraged women from taking iron tablets continuously. The availability (frequent supply) of iron tablets was the most effective way to help adult women to continue taking iron tablets.
Optimal search strategies for detecting cost and economic studies in EMBASE
Authors: McKinlay R James , Wilczynski Nancy L , Haynes R Brian ,   the Hedges Team
Published: June 2006

Abstract
Background
Economic evaluations in the medical literature compare competing diagnosis or treatment methods for their use of resources and their expected outcomes. The best evidence currently available from research regarding both cost and economic comparisons will continue to expand as this type of information becomes more important in today's clinical practice. Researchers and clinicians need quick, reliable ways to access this information. A key source of this type of information is large bibliographic databases such as EMBASE. The objective of this study was to develop search strategies that optimize the retrieval of health costs and economics studies from EMBASE.

Methods
We conducted an analytic survey, comparing hand searches of journals with retrievals from EMBASE for candidate search terms and combinations. 6 research assistants read all issues of 55 journals indexed by EMBASE for the publishing year 2000. We rated all articles using purpose and quality indicators and categorized them into clinically relevant original studies, review articles, general papers, or case reports. The original and review articles were then categorized for purpose (i.e., cost and economics and other clinical topics) and depending on the purpose as 'pass' or 'fail' for methodologic rigor. Candidate search strategies were developed for economic and cost studies, then run in the 55 EMBASE journals, the retrievals being compared with the hand search data. The sensitivity, specificity, precision, and accuracy of the search strategies were calculated.

Results
Combinations of search terms for detecting both cost and economic studies attained levels of 100% sensitivity with specificity levels of 92.9% and 92.3% respectively. When maximizing for both sensitivity and specificity, the combination of terms for detecting cost studies (sensitivity) increased 2.2% over the single term but at a slight decrease in specificity of 0.9%. The maximized combination of terms for economic studies saw no change in sensitivity from the single term and only a 0.1% increase in specificity.

Conclusion
Selected terms have excellent performance in the retrieval of studies of health costs and economics from EMBASE.
Quality of life in patients with psoriasis
Authors: Bhosle Monali J , Kulkarni Amit , Feldman Steven R , Balkrishnan Rajesh 
Published: June 2006

Abstract
Psoriasis is one of the prevalent skin conditions in the United States. This chronic condition has a significant negative impact on patients' quality of life. Psoriasis has been linked to the depression and suicidal tendencies in the patients. The costs associated with decrements in quality of life, lost productivity, and work absenteeism may be enormous, increasing overall costs associated with the disease management. This review attempts to outline different quality of life measures available for psoriasis and describes their use in studies examining patient reported outcomes associated with pharmacological interventions for psoriasis. Factors associated with quality of life in psoriasis patients are described. It further describes physician's role in the psoriasis management to improve patients' overall well-being.
Xanthogranulomatous prostatitis: a mimic of carcinoma of prostate
Authors: Rafique Muhammad , Yaqoob Nausheen 
Published: June 2006

Abstract

Background
Xanthogranulomatous prostatitis is an unusual benign inflammatory process of prostate. Clinically it mimics prostatic carcinoma, requiring pathological examination for diagnosis.

Case presentation
A 60-year-old patient presented with 6 months history of increasing difficulty in micturition. On digital rectal examination prostate was hard and nodular and estimated weight was 50-gram. His serum prostate specific antigen (PSA) was 150 ng/ml. Clinically a locally advanced carcinoma of prostate was suspected. In view of severe obstructive urinary symptoms and significant post-micturition residual urine, transurethral resection of prostate was carried out. Histopathological examination of resected prostatic tissue revealed xanthogranulomatous prostatitis with no evidence of malignancy. Patient remains symptom free at 16 months follow-up and serum PSA has decreased to 6 ng/ml.

Conclusion
Xanthogranulomatous prostatitis is a benign inflammatory disorder of prostate that can clinically and even biochemically mimic prostatic carcinoma. A high degree of suspecion and close co-operation with pathologist is necessary for the diagnosis of xanthogranulomatous prostatitis.
Three rounds (1R/2R/3R) of genome duplications and the evolution of the glycolytic pathway in vertebrates
Authors: Steinke Dirk , Hoegg Simone , Brinkmann Henner , Meyer Axel 
Published: June 2006

Abstract

Background

Evolution of the deuterostome lineage was accompanied by an increase in systematic complexity especially with regard to highly specialized tissues and organs. Based on the observation of an increased number of paralogous genes in vertebrates compared with invertebrates, two entire genome duplications (2R) were proposed during the early evolution of vertebrates. Most glycolytic enzymes occur as several copies in vertebrate genomes, which are specifically expressed in certain tissues. Therefore, the glycolytic pathway is particularly suitable for testing theories of the involvement of gene/genome duplications in enzyme evolution.

Results

We assembled datasets from genomic databases of at least nine vertebrate species and at least three outgroups (one deuterostome and two protostomes), and used maximum likelihood and Bayesian methods to construct phylogenies of the 10 enzymes of the glycolytic pathway. Through this approach, we intended to gain insights into the vertebrate specific evolution of enzymes of the glycolytic pathway. Many of the obtained gene trees generally reflect the history of two rounds of duplication during vertebrate evolution, and were in agreement with the hypothesis of an additional duplication event within the lineage of teleost fish. The retention of paralogs differed greatly between genes, and no direct link to the multimeric structure of the active enzyme was found.

Conclusion

The glycolytic pathway has subsequently evolved by gene duplication and divergence of each constituent enzyme with taxon-specific individual gene losses or lineage-specific duplications. The tissue-specific expression might have led to an increased retention for some genes since paralogs can subdivide the ancestral expression domain or find new functions, which are not necessarily related to the original function.
Boosting with intranasal dendrimeric Aβ1–15 but not Aβ1–15 peptide leads to an effective immune response following a single injection of Aβ1–40/42 in APP-tg mice
Authors: Seabrook Timothy J , Jiang Liying , Thomas Katelyn , Lemere Cynthia A 
Published: June 2006

Abstract

Background
Immunotherapy for Alzheimer's disease (AD) is emerging as a potential treatment. However, a clinical trial (AN1792) was halted after adverse effects occurred in a small subset of subjects, which may have been caused by a T cell-mediated immunological response. In general, aging limits the humoral immune response, therefore, immunogens and vaccination regimes are required that induce a strong antibody response with less potential for an adverse immune response.

Method
In the current study, we immunized both wildtype and J20 APP-tg mice with a priming injection of Aβ1–40/42, followed by multiple intranasal boosts with the novel immunogen dAβ1–15 (16 copies of Aβ1–15 on a lysine tree), Aβ1–15 peptide or Aβ1–40/42 full length peptide.

Results
J20 APP-tg mice primed with Aβ1–40/42 subcutaneously and subsequently boosted intranasally with Aβ1–15 peptide did not generate a cellular or humoral immune response. In contrast, J20 APP-tg mice boosted intranasally with dAβ1–15 or full length Aβ1–40/42 produced high levels of anti-Aβ antibodies. Splenocyte proliferation was minimal in mice immunized with dAβ1–15. Wildtype littermates of the J20 APP-tg mice produced higher amounts of anti-Aβ antibodies compared to APP-tg mice but also had low T cell proliferation. The anti-Aβ antibodies were mainly composed of IgG2b and directed to an epitope within the Aβ1–7 region, regardless of the immunogen. Examination of the brain showed a significant reduction in Aβ plaque burden in the J20 APP-tg mice producing antibodies compared to controls. Biochemically, Aβ40 or Aβ42 were also reduced in brain homogenates and elevated in plasma but the changes did not reach significance.

Conclusion
Our results demonstrate that priming with full length Aβ40/42 followed by boosting with dAβ1–15 but not Aβ1–15 peptide led to a robust humoral immune response with a minimal T cell response in J20 APP-tg mice. In addition, Aβ plaque burden was reduced in mice producing anti-Aβ antibodies. Interestingly, wildtype mice produced higher levels of anti-Aβ antibodies, indicating that immune tolerance may be present in J20 APP-tg mice. Together, these data suggest that dAβ1–15 but not Aβ1–15 peptide may be useful as a boosting immunogen in an AD vaccination regime.
The Dapsone Hypersensitivity Syndrome revisited: a potentially fatal multisystem disorder with prominent hepatopulmonary manifestations
Authors: Kosseifi Semaan G , Guha Bhuvana , Nassour Dima N , Chi David S , Krishnaswamy Guha 
Published: June 2006

Abstract
4,4'-Diaminodiphenylsulphone (Dapsone) is widely used for a variety of infectious, immune and hypersensitivity disorders, with indications ranging from Hansen's disease, inflammatory disease and insect bites, all of which may be seen as manifestations in certain occupational diseases. However, the use of dapsone may be associated with a plethora of adverse effects, some of which may involve the pulmonary parenchyma. Methemoglobinemia with resultant cyanosis, bone marrow aplasia and/or hemolytic anemia, peripheral neuropathy and the potentially fatal dapsone hypersensitivity syndrome (DHS), the focus of this review, may all occur individually or in combination. DHS typically presents with a triad of fever, skin eruption, and internal organ (lung, liver, neurological and other systems) involvement, occurring several weeks to as late as 6 months after the initial administration of the drug. In this sense, it may resemble a DRESS syndrome (Drug Rash with Eosinophilia and Systemic Symptoms). DHS must be promptly identified, as untreated, the disorder could be fatal. Moreover, the pulmonary/systemic manifestations may be mistaken for other disorders. Eosinophilic infiltrates, pneumonitis, pleural effusions and interstitial lung disease may be seen. This syndrome is best approached with the immediate discontinuation of the offending drug and prompt administration of oral or intravenous glucocorticoids. An immunological-inflammatory basis of the syndrome can be envisaged, based on the pathological picture and excellent response to antiinflammatory therapy. Since dapsone is used for various indications, physicians from all specialties may encounter DHS and need to familiarize themselves with the salient features about the syndrome and its management.
Effects of cyanobacterial extracellular products and gibberellic acid on salinity tolerance in Oryza sativaL
Authors: Rodríguez AA , Stella AM , Storni MM , Zulpa G , Zaccaro MC 
Published: June 2006

Abstract
Salt stress is one of the most serious factors limiting the productivity of rice, the staple diet in many countries. Gibberellic acid has been reported to reduce NaCl-induced growth inhibition in some plants including rice. Most paddy soils have a natural population of Cyanobacteria, prokaryotic photosynthethic microorganisms, which synthesize and liberate plant growth regulators such as gibberellins that could exert a natural beneficial effect on salt stressed rice plants. The aim of this work was to evaluate the effect of the cyanobacterium Scytonema hofmanni extracellular products on the growth of rice seedlings inhibited by NaCl and to compare it with the effect of the gibberellic acid in the same stress condition. Growth (length and weight of the seedlings) and biochemical parameters (5-aminolevulinate dehydratase activity, total free porphyrin and pigments content) were evaluated.
Salt exposure negatively affected all parameters measured, with the exception of chlorophyll. Chlrorophyll concentrations nearly doubled upon exposure to high salt. Gibberellic acid counteracted the effect of salt on the length and dry weight of the shoot, and on carotenoid and chlorophyll b contents. Extracellular products nullified the salt effect on shoot dry weight and carotenoid content; partially counteracted the effect on shoot length (from 54% to 38% decrease), root dry weight (from 59% to 41% decrease) and total free porphyrin (from 31 to 13% decrease); reduced by 35% the salt increase of chlorophyll a; had no effect on root length and chlorophyll b. Gibberellic acid and extracellular products increased 5-aminolevulinate dehydratase activity over the control without salt. When coincident with high salinity, exposure to either EP or GA3, resulted in a reversal of shoot-related responses to salt stress. We propose that Scytonema hofmanni extracellular products may counteract altered hormone homeostasis of rice seedlings under salt stress by producing gibberellin-like plant growth regulators.