bluuebunny/crossref_metadata_2025_split huggingface dataset:
Data-driven extraction of relative reasoning rules to limit combinatorial explosion in biodegradation pathway prediction
Authors: Fenner Kathrin , Gao Junfeng , Kramer Stefan , Ellis Lynda , Wackett Larry 
Published: July 2008

AbstractMotivation: The University of Minnesota Pathway Prediction System (UM-PPS) is a rule-based expert system to predict plausible biodegradation pathways for organic compounds. However, iterative application of these rules to generate biodegradation pathways leads to combinatorial explosion. We use data from known biotransformation pathways to rationally determine biotransformation priorities (relative reasoning rules) to limit this explosion.Results: A total of 112 relative reasoning rules were identified and implemented. In one prediction step, i.e. as per one generation predicted, the use of relative reasoning decreases the predicted biotransformations by over 25% for 50 compounds used to generate the rules and by about 15% for an external validation set of 47 xenobiotics, including pesticides, biocides and pharmaceuticals. The percentage of correctly predicted, experimentally known products remains at 75% when relative reasoning is used. The set of relative reasoning rules identified, therefore, effectively reduces the number of predicted transformation products without compromising the quality of the predictions.Availability: The UM-PPS server is freely available on the web to all users at the time of submission of this manuscript and will be available following publication at http://umbbd.msi.umn.edu/predict/.Contact: kathrin.fenner@eawag.chSupplementary information: Supplementary data are available at Bioinformatics online.
Sensitivity of predicted cohort size and catches to errors in estimates of fishing mortality in the terminal year
Authors: Horbowy Jan 
Published: July 2008

Abstract
Horbowy, J. 2008. Sensitivity of predicted cohort size and catches to errors in estimates of fishing mortality in the terminal year. – ICES Journal of Marine Science, 65: 1227–1234. Formulae for the sensitivity of projected cohort size and catches to errors (bias) in estimates of fishing mortality in the terminal year were developed. Assessment models allowing for random errors in the observed catches as well as models in which catches are treated as exact were considered. The formulae were applied to a Gulf of Riga (Baltic Sea) herring assessment to show how well they estimated prediction errors and to evaluate the effect of assessment errors on predictions. The errors propagate quickly with time, and the higher the fishing mortality, the bigger the projection error. The errors in predicted catches are somewhat lower than the errors in predicted cohort sizes. The formulae developed show that with moderate error in estimated fishing mortality (20%), the errors in predicted cohort size can reach 100%, and the errors in predicted catches may be 50% for fishing mortality estimated at 1.0 in the terminal year and the status quo prediction. As the Gulf of Riga herring case demonstrates, the overall error in predicted stock size and catches may be lower when terminal fishing mortality is underestimated at some ages and overestimated at others (cancelling effect).
The Evolution of DNA Regulatory Regions for Proteo-Gamma Bacteria by Interspecies Comparisons
Authors: Rajewsky Nikolaus , Socci Nicholas D. , Zapotocky Martin , Siggia Eric D. 
Published: July 2008

The comparison of homologous noncoding DNA for organisms a suitable evolutionary distance apart is a powerful tool for the identification of cis regulatory elements for transcription and translation and for the study of how they assemble into functional modules. We have fit the three parameters of an affine global probabilistic alignment algorithm to establish the background mutation rate of noncoding seqeunce betweenE. coli and a series of gamma proteobacteria ranging from Salmonella to Vibrio. The lower bound we find to the neutral mutation rate is sufficiently high, even for Salmonella, that most of the conservation of noncoding sequence is indicative of selective pressures rather than of insufficient time to evolve. We then use a local version of the alignment algorithm combined with our inferred background mutation rate to assign a significance to the degree of local sequence conservation between orthologous genes, and thereby deduce a probability profile for the upstream regulatory region of all E. coli protein-coding genes. We recover 75%–85% (depending on significance level) of all regulatory sites from a standard compilation for E. coli, and 66%–85% of sigma sites.We also trace the evolution of known regulatory sites and the groups associated with a given transcription factor. Furthermore, we find that approximately one-third of paralogous gene pairs in E. coli have a significant degree of correlation in their regulatory sequence. Finally, we demonstrate an inverse correlation between the rate of evolution of transcription factors and the number of genes they regulate. Our predictions are available athttp://www.physics.rockefeller.edu/∼siggia. [Online supplemental material available at http://www.genome.org.]
Processed Pseudogenes of Human Endogenous Retroviruses Generated by LINEs: Their Integration, Stability, and Distribution
Authors: Pavlíček Adam , Pačes Jan , Elleder Daniel , Hejnar Jiří 
Published: July 2008

We report here the presence of numerous processed pseudogenes derived from the W family of endogenous retroviruses in the human genome. These pseudogenes are structurally colinear with the retroviral mRNA followed by a poly(A) tail. Our analysis of insertion sites of HERV-W processed pseudogenes shows a strong preference for the insertion motif of long interspersed nuclear element (LINE) retrotransposons. The genomic distribution, stability during evolution, and frequent truncations at the 5′ end resemble those of the pseudogenes generated by LINEs. We therefore suggest that HERV-W processed pseudogenes arose by multiple and independent LINE-mediated retrotransposition of retroviral mRNA. These data document that the majority of HERV-W copies are actually nontranscribed promoterless pseudogenes. The current search for HERV-Ws associated with several human diseases should concentrate on a small subset of transcriptionally competent elements.[Online supplementary material available at http://www.genome.org]
A Genome-Wide Screen for Normally Methylated Human CpG Islands That Can Identify Novel Imprinted Genes
Authors: Strichman-Almashanu Liora Z. , Lee Richard S. , Onyango Patrick O. , Perlman Elizabeth , Flam Folke , Frieman Matthew B. , Feinberg Andrew P. 
Published: July 2008

DNA methylation is a covalent modification of the nucleotide cytosine that is stably inherited at the dinucleotide CpG by somatic cells, and 70% of CpG dinucleotides in the genome are methylated. The exception to this pattern of methylation are CpG islands, CpG-rich sequences that are protected from methylation, and generally are thought to be methylated only on the inactive X-chromosome and in tumors, as well as differentially methylated regions (DMRs) in the vicinity of imprinted genes. To identify chromosomal regions that might harbor imprinted genes, we devised a strategy for isolating a library of normally methylated CpG islands. Most of the methylated CpG islands represented high copy number dispersed repeats. However, 62 unique clones in the library were characterized, all of which were methylated and GC-rich, with a GC content >50%. Of these, 43 clones also showed a CpGobs/CpGexp >0.6, of which 30 were studied in detail. These unique methylated CpG islands mapped to 23 chromosomal regions, and 12 were differentially methylated regions in uniparental tissues of germline origin, i.e., hydatidiform moles (paternal origin) and complete ovarian teratomas (maternal origin), even though many apparently were methylated in somatic tissues. We term these sequences gDMRs, for germline differentially methylated regions. At least two gDMRs mapped near imprinted genes, HYMA1 and a novel homolog of Elongin A and Elongin A2, which we termElongin A3. Surprisingly, 18 of the methylated CpG islands were methylated in germline tissues of both parental origins, representing a previously uncharacterized class of normally methylated CpG islands in the genome, and which we term similarly methylated regions (SMRs). These SMRs, in contrast to the gDMRs, were significantly associated with telomeric band locations (P = .0008), suggesting a potential role for SMRs in chromosome organization. At least 10 of the methylated CpG islands were on average 85% conserved between mouse and human. These sequences will provide a valuable resource in the search for novel imprinted genes, for defining the molecular substrates of the normal methylome, and for identifying novel targets for mammalian chromatin formation.[The sequence data described in this paper have been submitted to the GenBank data library under accession nos.AF484557–AF484583.]
Evaluation of Electrostatically Endothelial Cell Seeded Expanded Polytetrafluoroethylene Grafts in a Canine Femoral Artery Model
Authors: Fields Charles , Cassano Anthony , Makhoul Raymond G. , Allen Cynthia , Sims Rick , Bulgrin Jeffrey , Meyer Andrew , Bowlin Gary L. , Rittgers Stanley E. 
Published: July 2008

(1) Purpose: The purpose of this study was to evaluate the extent (luminal coverage) of the endothelial cell (EC) lining/neointimal development and the thromboresistance of electrostatically EC seeded small diameter e-PTFE vascular grafts. (2) Methods: This evaluation consisted of harvesting autologous, canine jugular vein ECs, electrostatically EC seeding the e-PTFE grafts (4 mm GORE-TEX,® Length = 6 cm), implanting the grafts in a canine femoral artery model for six weeks, and excising the graft for histological and scanning electron microscopy evaluations. (3) Results: The results of the histological evaluation (mid-graft region only) indicated that the electrostatic EC seeding significantly affected neointimal development (p<0.01) and the degree of thrombus formation (p<0.001) within the EC seeded grafts versus the untreated control grafts. Scanning electron microscopy examination demonstrated a mature, confluent endothelium with a “cobblestone” appearance on the EC seeded graft luminal surface. The control grafts demonstrated an equal distribution of SMCs through the graft wall while the electrostatically EC seeded graft sections exhibited an uneven SMC cellular distribution which was skewed toward the graft luminal surface. (4) Conclusions: The presence of electrostatic EC seeding significantly (p<0.01) enhanced the development of a neointima and reduced the incidence of thrombosis in e-PTFE grafts implanted in a canine femoral artery model. Results of the mid-graft SMC migration measurements indicate that the electrostatic EC seeding had a significant (p<0.001) impact on the acute healing of the standard wall e-PTFE vascular graft specimens.
Bridging the Modulus Gap between LLDPE and HDPE
Authors: Williams Kelly L. 
Published: July 2008

Developing blown film resins for the production of films that exhibit the toughness properties of linear low density polyethylene (LLDPE) with the stiffness and tensile characteristics of high density polyethylene (HDPE) has historically been difficult to achieve for both resin producers and film converters. Resin producers have attempted to push the density higher for LLDPE film resins and lower for HDPE film resins. Separately, film producers are continuously searching for the same hybrid film through blending low (LDPE), linear low (LLDPE), medium (MDPE) and high-density (HDPE) polyethylenes. Producing successful film blends for heavy-duty applications with densities over 0.918 g/cm3 usually results in a high performance LLDPE film resin being blended with low levels of a MDPE or HDPE. As the level of MDPE or HDPE increases, loss of critical toughness properties such as machine direction tear (MD tear) and dart impact strength is observed. There now exists a novel method of producing films that possess a full density range between 0.918 g/cm3 and 0.938 g/cm3. This approach is based on the utilization of a new family of high molecular weight medium density polyethylene (HMW-MDPE) film resins. By blending an HMW-MDPE with a resin density of 0.938 g/cm3 with high performance LLDPE film resins, films can be fabricated over a wide range of densities without the loss of tear and impact properties. These blends can be produced at thin or thick gauges on either high stalk or conventional blown film equipment.
Haem‐regulated eIF2α kinase is necessary for adaptive gene expression in erythroid precursors under the stress of iron deficiency
Authors: Liu Sijin , Bhattacharya Sanchita , Han Anping , Suragani Rajasekhar N. V. S. , Zhao Wanting , Fry Rebecca C. , Chen Jane‐Jane 
Published: July 2008

SummaryHaem‐regulated eIF2α kinase (HRI) is essential for the regulation of globin gene translation and the survival of erythroid precursors in iron/haem deficiency. This study found that that in iron deficiency, fetal definitive erythropoiesis is inhibited at the basophilic erythroblast stage with increased proliferation and elevated apoptosis. This hallmark of ineffective erythropoiesis is more severe in HRI deficiency. Microarray gene profiling analysis showed that HRI was required for adaptive gene expression in erythroid precursors during chronic iron deficiency. The number of genes with expression affected more than twofold increased, from 213 in iron deficiency and 73 in HRI deficiency, to 3135 in combined iron and HRI deficiencies. Many of these genes are regulated by Gata1 and Fog1. We demonstrate for the first time that Gata1 expression in developing erythroid precursors is decreased in iron deficiency, and is decreased further in combined iron and HRI deficiencies. Additionally, Fog1 expression is decreased in combined deficiencies, but not in iron or HRI deficiency alone. Our results indicate that HRI confers adaptive gene expression in developing erythroblasts during iron deficiency through maintaining Gata1/Fog1 expression.
A population‐specific Mini‐Nutritional Assessment can effectively grade the nutritional status of stroke rehabilitation patients in Taiwan
Authors: Tsai Alan C , Shih Chi‐Ling 
Published: July 2008

Aims and objectives.  To determine whether a modified version of the Mini‐Nutritional Assessment without body mass index could effectively assess the nutritional risk status of stroke rehabilitation patients in Taiwan.Background.  The Mini‐Nutritional Assessment was developed on the basis of clinical data of Western populations. Although widely used, its application to assess stroke rehabilitation patients has been limited. Further, to get best results, population‐specific modifications to address anthropometric and lifestyle differences have been suggested, especially for non‐Caucasian populations.Design.  The study assessed the nutritional status of stroke rehabilitation patients who enrolled in the Long‐term Care Service of Taipei. Strokes who were >40 years old, in the program for >1 month and cognitively able to answer the questions were recruited to participate in the study.Methods.  An on‐site in‐person interview with structured questionnaire elicited information on personal data, disease history and healthcare use and answers to the Mini‐Mental State Examination, the Activities of Daily Living and the Mini‐Nutritional Assessment. Patient’s nutritional status was assessed with the Mini‐Nutritional Assessment in three versions: the original, population‐specific (MNA‐TI) and population‐specific, without body mass index (MNA‐TII).Results.  The original Mini‐Nutritional Assessment rated 24% of patients malnourished and 57% at risk of malnutrition. Similar results, 14 and 64%, respectively, for MNA‐TI; and 19 and 57%, respectively, for MNA‐TII were observed.Conclusion.  Both the original and the modified versions of the Mini‐Nutritional Assessment can effectively rate the nutritional risk status of stroke rehabilitation patients in Taiwan. Version MNA‐TII that adopted population‐specific anthropometric cut‐values but without body mass index can effectively predict the nutritional status of stroke patients.Relevance to clinical practice.  The modified scale (MNA‐TII) can enhance the application of the tool and timely detection and intervention of undernutrition among stroke rehabilitation patients. It can also help to improve job efficiency of the primary care professionals.
Histopathology of mast cells and cytokines during healing of human mucosal leishmaniasis
Authors: AMATO V. S. , TUON F. F. , NICODEMO A. C. , DUARTE M. I. S. 
Published: July 2008

SUMMARY Mast cells (MCs) are associated with chronic inflammatory diseases. However, there is no study evaluating the importance of MCs in the mucosal leishmaniasis (ML). The aim of this study was to quantify the most important cytokines associated with mucosal leishmaniasis, before and after disease treatment, correlating with the healing. A cohort of 12 patients with ML was evaluated, and biopsies were taken before and after the treatment. A quantitative estimation of MCs and some cytokines was analysed by density of the labelled cells through immunohistochemistry. The MCs count in the tissue from patients with ML before treatment showed a mean of 29·3 ± 37·9 cells/mm2. The MCs count in patients with ML after healing decreased to 14·8 ± 23·9 cells/mm2. There was an inverse relation of MCs with IFN‐γ and IL‐4 expression (r2 = 29·4 and r2 = 22·3 with P < 0·05). The expression of IL‐10 and TNF‐α was not related with MCs count. MCs decrease after treatment associated with decrease of IL‐4 and IFN‐γ. The explanations of cytokine correlation are discussed in the article.
A quantitative and morphometric study of mast cells in cutaneous leishmaniasis
Authors: TUON F. F. , DUARTE M. I. S. , AMATO V. S. 
Published: July 2008

SUMMARY Background
Mast cells (MCs) are related with healing process in chronic inflammatory diseases, although in cutaneous leishmaniasis (CL) its importance is unknown. The aim of this study was to determine the correlation of MC with clinical findings in patients with the localized form of CL. Methods
A cohort of 85 patients with CL was evaluated. MCs count was performed in pre‐treatment biopsies and correlation with clinical findings and Leishmania species determined by PCR were performed. Results
The MCs count in patients with CL caused by Leishmania (V.) braziliensis was 14·3 ± 9·8 cells/mm2, and 7·0 ± 6·5 cells/mm2 in patients with L. (L.) amazonensis (P < 0·05). The linear regression of MCs count with the age showed a tendency of cell number decreasing, according to ageing of the patient (r2 = 0·05; P < 0·05). The association of disease's duration and MCs count was positive (r2 = 0·11; P < 0·05). There was not any association of MCs count with number of lesions neither with Leishmania antigen expression. The MCs count was higher in patients with earlier healing after treatment (P < 0·05). Conclusion
MC can be important in CL and related with healing lesion.
Being ‘fat’ in today’s world: a qualitative study of the lived experiences of people with obesity in Australia
Authors: Thomas Samantha L. , Hyde Jim , Karunaratne Asuntha , Herbert Dilinie , Komesaroff Paul A. 
Published: July 2008

AbstractObjective  To develop an in‐depth picture of both lived experience of obesity and the impact of socio‐cultural factors on people living with obesity.Design  Qualitative methodology, utilizing in‐depth semi‐structured interviews with a community sample of obese adults (body mass index ≥30). Community sampling methods were supplemented with purposive sampling techniques to ensure a diverse range of individuals were included.Results  Seventy‐six individuals (aged 16–72) were interviewed. Most had struggled with their weight for most of their lives (n = 45). Almost all had experienced stigma and discrimination in childhood (n = 36), as adolescents (n = 41) or as adults (n = 72). About half stated that they had been humiliated by health professionals because of their weight. Participants felt an individual responsibility to lose weight, and many tried extreme forms of dieting to do so. Participants described an increasing culture of ‘blame’ against people living with obesity perpetuated by media and public health messages. Eighty percent said that they hated or disliked the word obesity and would rather be called fat or overweight.Discussion and Conclusion  There are four key conclusions: (i) the experiences of obesity are diverse, but there are common themes, (ii) people living with obesity have heard the messages but find it difficult to act upon them, (iii) interventions should be tailored to address both individual and community needs and (iv) we need to rethink how to approach obesity interventions to ensure that avoid recapitulating damaging social stereotypes and exacerbating social inequalities.
Comparative Immunolocalization of Heat Shock Proteins (Hsp)‐60, ‐70, ‐90 in Boar, Stallion, Dog and Cat Spermatozoa
Authors: Volpe S , Galeati G , Bernardini C , Tamanini C , Mari G , Zambelli D , Seren E , Spinaci M 
Published: July 2008

ContentsHeat shock proteins (Hsp)‐60, ‐70 and ‐90 are important testis chaperones that fulfil several functions during sperm cell maturation. In post‐meiotic cells, their expression may change or may be undetectable and in some species it may be evident in mature spermatozoa. The aims of this study were to verify whether Hsp60, ‐70 and ‐90 are present in the sperm, and to compare their localization in boar, stallion, cat and dog spermatozoa by immunofluorescence. Hsp‐60 immunoreactivity was detected in sperm midpiece in all the species examined. In stallion sperm, Hsp70 signal was localized in the sub‐equatorial band, whereas immunoreactivity was evident on the neck of dog spermatozoa and on both neck and sub‐equatorial region of cat spermatozoa. In agreement with our previous observations, a triangular fluorescent signal in the equatorial segment of fresh boar sperm was detected. Hsp90 immunoreactivity was present in different portions of sperm tail: in the midpiece of both boar and cat spermatozoa and in the neck and throughout the tail in dog and stallion spermatozoa, respectively. When capacitation and acrosome reaction were induced in boar, stallion and dog spermatozoa, no changes in both Hsp60 and ‐90 were recorded by either Western blot or immunofluorescence. After induction of acrosome reaction, a Hsp70 redistribution in boar spermatozoa and an increased percentage of stallion spermatozoa showing the post‐acrosomal signal were observed although no changes were recorded by Western blot; in dog spermatozoa, no changes in Hsp70 were found by Western blot and immunofluorescence after capacitation and acrosome reaction.