bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of null statistics in permutation-based multiple testing for multi-factorial microarray experiments
Authors: Gao Xin 
Published: March 2006

AbstractMotivation: The parametric F-test has been widely used in the analysis of factorial microarray experiments to assess treatment effects. However, the normality assumption is often untenable for microarray experiments with small replications. Therefore, permutation-based methods are called for help to assess the statistical significance. The distribution of the F-statistics across all the genes on the array can be regarded as a mixture distribution with a proportion of statistics generated from the null distribution of no differential gene expression whereas the other proportion of statistics generated from the alternative distribution of genes differentially expressed. This results in the fact that the permutation distribution of the F-statistics may not approximate well to the true null distribution of the F-statistics. Therefore, the construction of a proper null statistic to better approximate the null distribution of F-statistic is of great importance to the permutation-based multiple testing in microarray data analysis.Results: In this paper, we extend the ideas of constructing null statistics based on pairwise differences to neglect the treatment effects from the two-sample comparison problem to the multifactorial balanced or unbalanced microarray experiments. A null statistic based on a subpartition method is proposed and its distribution is employed to approximate the null distribution of the F-statistic. The proposed null statistic is able to accommodate unbalance in the design and is also corrected for the undue correlation between its numerator and denominator. In the simulation studies and real biological data analysis, the number of true positives and the false discovery rate (FDR) of the proposed null statistic are compared with those of the permutated version of the F-statistic. It has been shown that our proposed method has a better control of the FDRs and a higher power than the standard permutation method to detect differentially expressed genes because of the better approximated tail probabilities.Availability: R codes available upon requestContact: xingao@mathstat.yorku.ca
GenRGenS: software for generating random genomic sequences and structures
Authors: Ponty Yann , Termier Michel , Denise Alain 
Published: March 2006

AbstractSummary: GenRGenS is a software tool dedicated to randomly generating genomic sequences and structures. It handles several classes of models useful for sequence analysis, such as Markov chains, hidden Markov models, weighted context-free grammars, regular expressions and PROSITE expressions. GenRGenS is the only program that can handle weighted context-free grammars, thus allowing the user to model and to generate structured objects (such as RNA secondary structures) of any given desired size. GenRGenS also allows the user to combine several of these different models at the same time.Availability: Source and executable files of GenRGenS (in Java) and the complete user's manual are freely available atContact: dev.GenRGenS@lri.fr
Risk and the social construction of ‘Gulf War Syndrome’
Authors: Durodié Bill 
Published: March 2006

Fifteen years since the events that are held by some to have caused it, Gulf War Syndrome continues to exercise the mind and energies of numerous researchers across the world, as well as those who purport to be its victims and their advocates in the media, law and politics.
But it may be that the search for a scientific or medical solution to this issue was misguided in the first place, for Gulf War Syndrome, if there is such an entity, appears to have much in common with other ‘illnesses of modernity’, whose roots are more socially and culturally driven than what doctors would conventionally consider to be diseases.
The reasons for this are complex, but derive from our contemporary proclivity to understand humanity as being frail and vulnerable in an age marked by an exaggerated perception of risk and a growing use of the ‘politics of fear’. It is the breakdown of social solidarities across the twentieth century that has facilitated this process.
Unfortunately, as this paper explores, our inability to understand the social origins of self-hood and illness, combined with a growing cynicism towards all sources of authority, whether political, scientific, medical or corporate, has produced a powerful demand for blame and retribution deriving from a resolute few who continue to oppose all of the evidence raised against them.
Sadly, this analysis suggests that Gulf War Syndrome is likely to prove only one of numerous such instances that are likely to emerge over the coming years.
Cutaneous neuroendocrine adenoma: an uncommon neoplasm
Authors: Mahalingam M. , Kveaton J. F. , Bhawan J. 
Published: March 2006

Background:  Cutaneous neuroendocrine neoplasms are typically malignant. Benign cutaneous neuroendocrine tumors are uncommon.Methods:  We report the case of a 32‐year‐old female who presented with a granular mass in the right external auditory canal.Results:  Microscopic examination of a shave biopsy revealed a poorly circumscribed neoplasm with glandular differentiation. While cytologic atypia and mitotic activity were not evident, pagetoid spread was observed. Immunohistochemistry was indicative of neuroendocrine origin.Conclusions:  This case report of neuroendocrine adenoma indicates that this entity should be entertained in the repertoire of conditions affecting the external ear.
Orotate phosphoribosyltransferase levels measured by a newly established enzyme‐linked immunosorbent assay in gastric carcinoma
Authors: Sakurai Yoichi , Sakamoto Kazuki , Sugimoto Yoshikazu , Yoshida Ikuo , Masui Toshihiko , Tonomura Shuhei , Inaba Kazuki , Shoji Mitsutaka , Nakamura Yasuko , Uyama Ichiro , Komori Yoshiyuki , Ochiai Masahiro , Matsuura Shiro , Tanaka Hideyuki , Oka Toshinori , Fukushima Masakazu 
Published: March 2006

A number of enzymes have been shown to be involved in the process of activation and/or degradation of 5‐fluorouracil (5‐FU), and are potential candidates for predicting chemosensitivity to 5‐FU. Among these, orotate phosphoribosyltransferase (OPRT EC 2.4.2.10) is a key enzyme related to the first‐step activation process of 5‐FU and has been shown to be an important enzyme that helps to predict sensitivity to 5‐FU and its related derivatives. We developed a new enzyme‐linked immunosorbent assay (ELISA) to accurately assess intratumoral activity of OPRT. A new sandwich ELISA was established using anti‐OPRT polyclonal antibodies obtained from the rabbit immunized with the recombinant human peptides of the OPRT molecule. OPRT levels were measured in eight human cancer xenografts and in 75 gastric cancer tissues using both a newly established ELISA and a conventional enzyme assay, using radiolabeled 5‐FU as a substrate. There was a significant correlation between OPRT levels measured by this ELISA and OPRT enzyme activity the in eight human cancer xenografts (r2 = 0.782) and gastric carcinoma tissue (r2 = 0.617). The ELISA system for OPRT requires a minimal amount of carcinoma tissue, making it an easy‐to‐use assay system to predict sensitivity to 5‐FU and its derivatives in gastric carcinoma. There was a significant correlation between tumor growth inhibition rates against the oral administration of oral‐uracil/tegafur (UFT) and OPRT enzyme activity in the human cancer xenografts (r2 = 0.574). These results suggest that this newly developed sandwich ELISA system for the quantification of OPRT levels is technically simple, feasible and a useful tool to predict sensitivity to fluoropyrimidine‐based anticancer chemotherapy in patients with gastric carcinoma and other cancers. (Cancer Sci 2006; 97)
Notes on the distribution and abundance of the caecilian Boulengerula uluguruensis (Amphibia: Gymnophiona: Caeciliidae) in the Uluguru Mountains, Tanzania
Authors: John Measey G. , Mejissa John , Müller Hendrik 
Published: March 2006

AbstractBoulengerula uluguruensis is a terrestrial caeciliid caecilian described from the Uluguru Mountains of Tanzania. We investigated the relative abundance of B. uluguruensis in agricultural and forested habitats at the beginning of the rainy season. This caecilian was found over a wide altitudinal range (450–1175 m a.s.l.), and in many land cover types (including natural forest, plantation forest and small scale agriculture), and different soil textures (including very compact soil). Based on quantitative and semi‐quantitative surveys, B. uluguruensis is more abundant than any other subterranean lower vertebrate in this area, with densities up to 0.4 individuals m−2 in some agricultural plots. The hypothesis proposed, that B. uluguruensis is more abundant in agriculture than their native forest, could not be conclusively tested during this brief visit, although the data that were collected do not indicate to the contrary. Likewise, the size of animals from forest and agricultural populations could not be objectively compared.
Some biological aspects and life history strategies of Nile tilapia Oreochromis niloticus (L.) in Lake Victoria, Kenya
Authors: Njiru M. , Ojuok J. E. , Okeyo‐Owuor J. B. , Muchiri M. , Ntiba M. J. , Cowx I. G. 
Published: March 2006

AbstractThe life history characteristics of introduced Nile tilapia (Oreochromis niloticus L.) in Lake Victoria, including, sex ratio, fecundity, reproduction, weight‐length relationship and body condition were studied and compared with those of other populations. Samples were collected by trawling and seining in the Kenyan sector of Lake Victoria between June 1998 and December 2000. Males predominated over females (sex ratio 1.42 : 1 : 00). O. niloticus spawned throughout the year but with a peak between December and June. Length at first maturity was (mean ± SD) 30.81 ± 0.09 for females and 34.5 ± 6 0.48 for males. There was little seasonal variation in relative condition, which ranged from 0.92 to 1.05 in males and 0.94 to 1.07 in females. Gonadosomatic index (GSI) was low during the postspawning period (July to October) and high during the protracted breeding period (December and June). Fecundity ranged from 905 to 7619 oocytes for fish of 28 to 51 cm total length (TL) respectively. The relationships between fecundity (F) and total length (L), weight (W) and ovary weight (OW) were: F = 8.159L1.53, F = 96.269W0.4504, F = 1806 + 39.4OW. The slope b of the weight‐length relationship was 3.08–3.32 for males and 3.07–3.22 for females. Growth was allometric in both cases and was significantly different from the expected value of 3. The life history strategy of O. niloticus is discussed in context of environmental changes occurring in the lake.
Patterns of den occupation by the spotted hyaena (Crocuta crocuta)
Authors: Boydston Erin E. , Kapheim Karen M. , Holekamp Kay E. 
Published: March 2006

AbstractSpotted hyaenas utilize isolated natal dens (NDs) and communal dens (CDs) for rearing their cubs. Here we describe patterns of natal and CD occupation by hyaenas belonging to one well‐studied clan in the Maasai Mara National Reserve during a 10‐year period. Locations of 98 den sites that were used as natal or CDs by hyaenas in the study clan were digitized in a Geographic Information System, and the duration of use of each den site, frequency of re‐use, and distances involved in den moves were quantified. Hyaenas moved their CD monthly on average. Most CD sites were occupied only once during the study, but several sites were used repeatedly. On rare occasions, the movement of hyaenas to a new den site could be attributed to a disturbance event at the CD, but factors regularly prompting hyaenas to move to new CD sites were unclear. High‐ranking female hyaenas were more likely to rear their cubs from birth in a CD than low‐ranking females. Low‐ranking females almost always utilized isolated NDs for the first few weeks of a litter's development, and low‐ranking females transferred their cubs over longer distances than did high‐ranking females.
A possible role for CCL27/CTACK‐CCR10 interaction in recruiting CD4+ T cells to skin in human graft‐versus‐host disease
Authors: Faaij Claudia M. J. M. , Lankester Arjan C. , Spierings Eric , Hoogeboom Manja , Bowman Edward P. , Bierings Marc , Révész Tom , Egeler R. Maarten , Van Tol Maarten J. D. , Annels Nicola E. 
Published: March 2006

SummaryGraft‐versus‐host disease (GvHD) is a serious complication of allogeneic stem cell transplantation (SCT) affecting the skin, gut and liver. The involvement of distinct organs suggests a role for tissue‐specific chemokines and their receptors in directing activated donor T cells to these sites. In this study the potential involvement of the skin‐specific CCL27/CTACK‐CCR10 interaction was investigated in 15 paediatric SCT patients with skin GvHD. During the course of skin GvHD, peripheral blood T cells from these patients contained a high proportion of CD4+ CCR10+ T cells that disappeared after the GvHD was resolved. These cells were CD45RO+, expressed additional skin homing markers (cutaneous lymphocyte‐associated antigen and CCR4), and produced the T‐cell helper type 1‐cytokines tumour necrosis factor‐alpha and interleukin‐2. The increase in CD4+ CCR10+ T cells was absent in SCT patients without GvHD. Immunohistochemical investigations showed CD4+ CCR10+ T cells in the GvHD skin biopsies of the same patients, but not in the gut biopsies of patients also suffering from gut GvHD. The infiltration of CD4+ CCR10+ T cells in the GvHD‐affected skin correlated with an enhanced epidermal expression of CCL27/CTACK, the ligand for CCR10. These findings support the involvement of CCL27/CTACK‐CCR10 interaction in recruiting CD4+ T cells to the skin, thus contributing to the pathogenesis of acute GvHD.
Somatic hypermutation and VH gene usage in hairy cell leukaemia
Authors: Arons Evgeny , Sunshine Joel , Suntum Tara , Kreitman Robert J. 
Published: March 2006

SummaryTo examine the usage and mutational status of VH genes in hairy cell leukaemia (HCL), we analysed 24 immunoglobulin heavy chain (IgH) sequences expressed in 23 patients. None had premature stop codons. VH3‐23 was the most common gene and a VH6 gene was observed for the first time in HCL. Although the mean mutation frequency was 6·1%, slightly higher than in previous HCL series, four patients had 99·6–100% homology to germline sequences, three of whom had high tumour burdens and poor outcomes. Despite the high mutation frequency, only two of 24 rearrangements had clear statistical evidence of antigen‐dependent somatic mutation. Our results increase the database of reported functional HCL rearrangements to 94 in 92 patients. Overall, both gene usage and mutation frequency are very similar to mucosa‐associated lymphoid tissue‐type marginal zone lymphoma. The data are consistent with HCL originating from post‐germinal centre marginal zone B cells, although the heterogeneity observed suggests that HCL may originate differently in some patients, and this could have implications for prognosis and treatment.
Distinguishing between type 2B and pseudo‐von Willebrand disease and its clinical importance
Authors: Enayat Mohammad S. , Guilliatt Andrea M. , Lester William , Wilde Jonathan T. , Williams Michael D. , Hill Frank G.H. 
Published: March 2006

SummaryPseudo‐von Willebrand disease (p‐VWD) and type 2B von Willebrand disease (VWD) have similar phenotypic parameters and clinical symptoms, but different aetiologies. Fourteen individuals from five families with a historical diagnosis of type 2B VWD but with no mutation in the von Willebrand factor gene were re‐investigated for the possibility of p‐VWD, using platelet aggregation in the presence of cryoprecipitate. p‐VWD was confirmed by targeted DNA sequencing of the glycoprotein Ibα gene, identifying a heterozygous Glycine 233 Valine substitution. This study suggests that p‐VWD may be under diagnosed, and that platelet aggregation in the presence of cryoprecipitate is useful in differentiating this disorder from type 2B VWD.
Toll‐like receptor ligands as adjuvants in allergen‐specific immunotherapy
Authors: Johansen P. , Senti G. , Martinez Gomez J. M. , Storni T. , von Beust B. R. , Wüthrich B. , Bot A. , Kündig T. M. 
Published: March 2006

SummaryBackground
Allergen‐specific immunotherapy (SIT) leads to long‐term amelioration of T‐helper type 2 (Th2)‐mediated allergic symptoms and is therefore recommended as a first line therapy for allergies. The major disadvantage of SIT is its low efficiency, requiring treatment over years.Objective
In this study, we evaluated the potential of Toll‐like receptor (TLR) ligands to facilitate Th1‐type immune responses.Methods
The immunogenicity and therapeutic potential of the major bee venom allergen phospholipase A2 (PLA2) combined with various TLR ligands were tested in mice and compared with immune responses induced by conventional aluminium‐based preparations.Results
Regarding total IgG against PLA2, TLR2/4‐binding lipopolysaccharide and TLR3‐binding polyriboinosinic polyribocytidylic (PolyI:C) were the superior adjuvants for prophylactic vaccination. However, TLR9‐binding phosphorothioate‐modified cytosine–guanosine‐rich oligonucleotide (CpG), TLR‐3‐binding PolyI:C, and TLR2/6‐binding peptidoglycan skewed the immune responses more towards IgG2a isotype and Th1 cytokines. Furthermore, in a therapeutic approach, CpG, PolyI:C and TLR7/8‐binding 3M003 had immune modulating properties as they suppressed established IgE titres.Conclusion
The potential of TLR ligands to adjuvate the immunogenicity of bee venom PLA2 and to skew the Th1–Th2 balance proved very heterogeneous. With respect to SIT, CpG, PolyI:C, and 3M003 were very promising. Hence, TLR ligands should be considered as adjuvants or immune modulators in SIT in human as to improve its efficiency regarding the Th1–Th2 balance of the immune response with a likely effect on therapy duration.
ADAM33 polymorphisms are associated with asthma susceptibility in a Japanese population
Authors: Noguchi E. , Ohtsuki Y. , Tokunaga K. , Yamaoka‐Sageshima M. , Ichikawa K. , Aoki T. , Shibasaki M. , Arinami T. 
Published: March 2006

SummaryBackground
Asthma is the most common chronic disorder in childhood, and asthma exacerbation is an important cause of childhood morbidity and hospitalization. Asthma is believed to be a complex disorder involving genetic and environmental factors, and several asthma susceptibility loci have been identified through genome‐wide screening. A disintegrin and metalloprotease 33 (ADAM33) was the first asthma susceptibility gene to be discovered by positional cloning in 2002.Objective
The aim of the present study was to investigate whether single‐nucleotide polymorphisms (SNPs) in ADAM33 are associated with childhood asthma in the Japanese population.Methods
Twenty‐three ADAM33 SNPs were genotyped by fluorescence correlation spectroscopy with the use of DNA from 155 families (538 members) identified through children with atopic asthma. The transmission disequilibrium test (TDT) was performed for family‐based association study.Results
TDT revealed that minor alleles of S+1, ST+4, and T2 SNPs were over‐transmitted to asthma‐affected offspring (P<0.05). According to the haplotype TDT, no haplotype of ADAM33 was transmitted preferentially to asthmatic offspring.Conclusion
Our results confirm the involvement of ADAM33 in the development of childhood asthma among the Japanese.
Abundance and primary production of filamentous green algae Zygogonium ericetorum in an extremely acid (pH 2.9) mining lake and its impact on alkalinity generation
Authors: KLEEBERG ANDREAS , SCHUBERT HENDRIK , KOSCHORRECK MATTHIAS , NIXDORF BRIGITTE 
Published: March 2006

Summary1. In extremely acid mining lakes, benthic filamentous green algae (Zygnemataceae, Chlorophyta) thrive as effective competitors for limited carbon (C). These algae could supply C for microbial‐mediated benthic alkalinity generation. However, biomass, productivity and impact of the acidobiontic filamentous green algae at pH ≤3 have not previously been determined.2. Periphytic filamentous green algae was mapped by harvesting their biomass from 85 1 × 1 m quadrats in mining lake Grünewalder Lauch. Zygogonium ericetorum colonised water depths between 1.6 and 10.5 m covering 88% of total area. Biomass peaked at 5–6 m depth. Total Zygogonium biomass amounted to 72.2 t dry weight for the whole lake (0.94 km2), which corresponds to 16.1 t C and the accumulation of primary production from 2.2 years.3. Growth of Zygogonium is moderately N, C and extremely P deficient, and seriously stressed by high rates of Fe deposition during summer. Consequently, net primary production (NPP) of Zygogonium, calculated from measured photosynthesis versus irradiance characteristics and calculated underwater irradiance (0.13 g C m−2 year−1) and in situ oxygen measurements (7.8 g C m−2 year−1), corresponds to only 0.3% and 18.1% of pelagic NPP.4. Neither pelagic nor benthic Zygogonium primary production can supply enough C for efficient acidity removal. However, at rates of benthic NPP in summer of 21.4 mg C m−2 day−1, Zygogonium contributed 26% of the C equivalents to remove acidity associated with ferric iron, contributing at least seasonally to efficient alkalinity generation.
Analysis of expressed sequence tags from Rhynchosciara americana salivary glands
Authors: Siviero F. , Rezende‐Teixeira P. , Andrade A. , Machado‐Santelli G. M. , Santelli R. V. 
Published: March 2006

AbstractThe diptera Rhynchosciara americana (sciaridae) is an important model organism in polyteny and gene amplification research, but up to now a limited amount of data regarding DNA sequences and molecular aspects of this species is available. Considering the importance of going further on the DNA puffs biological meaning, we proposed to generate EST sequences from a DNA library constructed from salivary glands. After their categorization in gene ontology terms, they were used to construct an ‘electronic Northern’ that represents a general view of the salivary gland metabolic status in an important phase of larval development: the spinning of communal cocoon. In this phase occurs the last polytene DNA replication cycle concomitantly with the specific loci amplification related to protein secretion.
Immulectin‐4 from the tobacco hornworm Manduca sexta binds to lipopolysaccharide and lipoteichoic acid
Authors: Yu X.‐Q. , Ling E. , Tracy M. E. , Zhu Y. 
Published: March 2006

AbstractInsect C‐type lectins function as pattern recognition receptors in innate immunity. In the tobacco hornworm Manduca sexta, we have previously isolated three C‐type lectins named immulectins, which are involved in innate immune responses. Here, we report a new member of the immulectin family, immulectin‐4 (IML‐4). IML‐4 mRNA was detected in the fat body of control larvae and was induced in the fat body when larvae were injected with bacteria. Recombinant IML‐4 bound to bacterial lipopolysaccharide (LPS) and lipoteichoic acid (LTA), and the binding activity was not affected by addition of calcium or EGTA. IML‐4 agglutinated bacteria and yeast, and agglutination of Escherichia coli by IML‐4 was concentration‐ and calcium‐dependent. IML‐4 also enhanced haemocyte encapsulation and melanization.