bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multidrug resistance gene (MDR1) polymorphisms are associated with major molecular responses to standard-dose imatinib in chronic myeloid leukemia
Authors: Dulucq Stéphanie , Bouchet Stéphane , Turcq Béatrice , Lippert Eric , Etienne Gabriel , Reiffers Josy , Molimard Mathieu , Krajinovic Maja , Mahon François-Xavier 
Published: June 2008

Abstract
Despite the excellent efficacy of imatinib in chronic myeloid leukemia (CML), the response in patients is heterogeneous, which may in part be caused by pharmacogenetic variability. Imatinib has been reported to be a substrate of the P-glycoprotein pump. In the current study, we focused on the ABCB1 (MDR1) genotype. We analyzed the 3 most relevant single nucleotide polymorphisms of MDR1 in 90 CML patients treated with imatinib. Among the patients homozygous for allele 1236T, 85% achieved a major molecular response versus 47.7% for the other genotypes (P = .003). For the 2677G>T/A polymorphism, the presence of G allele was associated with worse response (77.8%, TT/TA; vs 47.1%, GG/GA/GT; P = .018). Patients with 1236TT genotype had higher imatinib concentrations. One of the haplotypes (1236C-2677G-3435C) was statistically linked to less frequent major molecular response (70% vs 44.6%; P = .021). Hence, we demonstrated the usefulness of these single nucleotide polymorphisms in the identification of CML who may or may not respond optimally to imatinib.
AFLP analysis reveals a lack of phylogenetic structure within Solanum section Petota
Authors: Jacobs Mirjam MJ , van den Berg Ronald G , Vleeshouwers Vivianne GAA , Visser Marcel , Mank Rolf , Sengers Mariëlle , Hoekstra Roel , Vosman Ben 
Published: June 2008

Abstract

Background
The secondary genepool of our modern cultivated potato (Solanum tuberosum L.) consists of a large number of tuber-bearing wild Solanum species under Solanum section Petota. One of the major taxonomic problems in section Petota is that the series classification (as put forward by Hawkes) is problematic and the boundaries of some series are unclear. In addition, the classification has received only partial cladistic support in all molecular studies carried out to date.
The aim of the present study is to describe the structure present in section Petota. When possible, at least 5 accessions from each available species and 5 individual plants per accession (totally approx. 5000 plants) were genotyped using over 200 AFLP markers. This resulted in the largest dataset ever constructed for Solanum section Petota. The data obtained are used to evaluate the 21 series hypothesis put forward by Hawkes and the 4 clade hypothesis of Spooner and co-workers.

Results
We constructed a NJ tree for 4929 genotypes. For the other analyses, due to practical reasons, a condensed dataset was created consisting of one representative genotype from each available accession. We show a NJ jackknife and a MP jackknife tree. A large part of both trees consists of a polytomy. Some structure is still visible in both trees, supported by jackknife values above 69. We use these branches with >69 jackknife support in the NJ jackknife tree as a basis for informal species groups. The informal species groups recognized are: Mexican diploids, Acaulia, Iopetala, Longipedicellata, polyploid Conicibaccata, diploid Conicibaccata, Circaeifolia, diploid Piurana and tetraploid Piurana.

Conclusion
Most of the series that Hawkes and his predecessors designated can not be accepted as natural groups, based on our study. Neither do we find proof for the 4 clades proposed by Spooner and co-workers. A few species groups have high support and their inner structure displays also supported subdivisions, while a large part of the species cannot be structured at all. We believe that the lack of structure is not due to any methodological problem but represents the real biological situation within section Petota.
Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences
Authors: Su Wan-Lin , Modrek Barmak , GuhaThakurta Debraj , Edwards Stephen , Shah Jyoti K , Kulkarni Amit V , Russell Archie , Schadt Eric E , Johnson Jason M , Castle John C 
Published: June 2008

Abstract

Background
Studies have shown that genetic and sex differences strongly influence gene expression in mice. Given the diversity and complexity of transcripts produced by alternative splicing, we sought to use microarrays to establish the extent of variation found in mouse strains and genders. Here, we surveyed the effect of strain and sex on liver gene and exon expression using male and female mice from three different inbred strains.

Results
71 liver RNA samples from three mouse strains – DBA/2J, C57BL/6J and C3H/HeJ – were profiled using a custom-designed microarray monitoring exon and exon-junction expression of 1,020 genes representing 9,406 exons. Gene expression was calculated via two different methods, using the 3'-most exon probe ("3' gene expression profiling") and using all probes associated with the gene ("whole-transcript gene expression profiling"), while exon expression was determined using exon probes and flanking junction probes that spanned across the neighboring exons ("exon expression profiling"). Widespread strain and sex influences were detected using a two-way Analysis of Variance (ANOVA) regardless of the profiling method used. However, over 90% of the genes identified in 3' gene expression profiling or whole transcript profiling were identified in exon profiling, along with 75% and 38% more genes, respectively, showing evidence of differential isoform expression. Overall, 55% and 32% of genes, respectively, exhibited strain- and sex-bias differential gene or exon expression.

Conclusion
Exon expression profiling identifies significantly more variation than both 3' gene expression profiling and whole-transcript gene expression profiling. A large percentage of genes that are not differentially expressed at the gene level demonstrate exon expression variation suggesting an influence of strain and sex on alternative splicing and a need to profile expression changes at sub-gene resolution.
Comparing factors affecting commencement and cessation of betel quid chewing behavior in Taiwanese adults
Authors: Yap Shue-Fang , Ho Pei-Shan , Kuo Hsiao-Ching , Yang Yi-Hsin 
Published: June 2008

Abstract

Background
Betel quid is the fourth most common used substance in the world after tobacco, alcohol and caffeine. Although factors related to betel quid chewing or cessation of behaviors were reported previously, few studies simultaneously compared both behaviors in the same population. In addition, it is essential to consider time-to-event concept, since the chance of developing or stopping habit may vary over time. The purpose of this study was to compare the risk factors for commencement and cessation of betel quid chewing behaviors in a time-to-event setting.

Methods
A stratified multi-stage cluster sampling with selection probabilities proportional to size (PPS) was designed for Taiwanese adults with aged 18 years old and above. Kaplan-Meier estimates and Cox proportional hazard regression models were used to compare and calculate the hazard rate ratios for related factors to commencement or cessation of chewing habits.

Results
In Taiwan, men had a higher betel quid chewing rate (M: 20.9%, W: 1.2%), but woman chewers had a lower cessation rate (M: 27.5%, W: 12.7%). The hazard rate ratio (HRR) of having chewing habit changed from 4.22 (men vs women) univariately to 1.38 multivariablely, which indicated gender differences were confounded by other factors. In multivariable analysis, the risk factors of gender, education and ethnicity were significantly associated with both starting and cessation of betel quid chewing behavior. The factors of occupation, cigarette smoking and alcohol drinking were only associated with starting habit.

Conclusion
Commencement or cessation of chewing behavior involves a scenario of time, hence it is preferable to use a time-to-event approach for the comparison. The cessation rates of betel quid chewing were decreasingly associated with the daily consumption of betel quid. Hence, reducing of daily amount in betel quid cessation program may be associated with future stopping habit.
Protein profiling of the dimorphic, pathogenic fungus, Penicillium marneffei
Authors: Chandler Julie M , Treece Erin R , Trenary Heather R , Brenneman Jessica L , Flickner Tressa J , Frommelt Jonathan L , Oo Zaw M , Patterson Megan M , Rundle William T , Valle Olga V , Kim Thomas D , Walker Gary R , Cooper Chester R 
Published: June 2008

Abstract

Background

Penicillium marneffei is a pathogenic fungus that afflicts immunocompromised individuals having lived or traveled in Southeast Asia. This species is unique in that it is the only dimorphic member of the genus. Dimorphism results from a process, termed phase transition, which is regulated by temperature of incubation. At room temperature, the fungus grows filamentously (mould phase), but at body temperature (37°C), a uninucleate yeast form develops that reproduces by fission. Formation of the yeast phase appears to be a requisite for pathogenicity. To date, no genes have been identified in P. marneffei that strictly induce mould-to-yeast phase conversion. In an effort to help identify potential gene products associated with morphogenesis, protein profiles were generated from the yeast and mould phases of P. marneffei.

Results
Whole cell proteins from the early stages of mould and yeast development in P. marneffei were resolved by two-dimensional gel electrophoresis. Selected proteins were recovered and sequenced by capillary-liquid chromatography-nanospray tandem mass spectrometry. Putative identifications were derived by searching available databases for homologous fungal sequences. Proteins found common to both mould and yeast phases included the signal transduction proteins cyclophilin and a RACK1-like ortholog, as well as those related to general metabolism, energy production, and protection from oxygen radicals. Many of the mould-specific proteins identified possessed similar functions. By comparison, proteins exhibiting increased expression during development of the parasitic yeast phase comprised those involved in heat-shock responses, general metabolism, and cell-wall biosynthesis, as well as a small GTPase that regulates nuclear membrane transport and mitotic processes in fungi. The cognate gene encoding the latter protein, designated RanA, was subsequently cloned and characterized. The P. marneffei RanA protein sequence, which contained the signature motif of Ran-GTPases, exhibited 90% homology to homologous Aspergillus proteins.

Conclusion
This study clearly demonstrates the utility of proteomic approaches to studying dimorphism in P. marneffei. Moreover, this strategy complements and extends current genetic methodologies directed towards understanding the molecular mechanisms of phase transition. Finally, the documented increased levels of RanA expression suggest that cellular development in this fungus involves additional signaling mechanisms than have been previously described in P. marneffei.
Coefficient of Consolidation by the Slope Method
Authors: Al-Zoubi Mohammed Shukri 
Published: June 2008

Abstract
The slope method explicitly relates the coefficient of consolidation cv to the slope of the initial linear segment of the observed δt-t curve and to the end of primary settlement δp. The slope method utilizes the same graphical construction as the Taylor method but eliminates the use of the factor 1.15 that usually leads to lower δp and higher cv as compared to the Casagrande method and pore water pressure measurements. Instead, the point at which the δt-t curve deviates from the linear portion (at U of about 50 %) is considered for estimating δp. Oedometer test results on four soils show that the cv values of the slope and Casagrande methods are comparable but lower than those of the Taylor method.
Repeated Scaling Versus Surgery in Young Adults With Generalized Advanced Periodontitis
Authors: König Jörgen , Schwahn Christian , Fanghänel Jutta , Plötz Jutta , Hoffmann Thomas , Kocher Thomas 
Published: June 2008

Background: Residual probing depth (PD) after subgingival scaling can be treated with repeated scaling or periodontal surgery. Ambiguous results about the additional clinical benefit of a second scaling procedure exist. Therefore, we performed a prospective study comparing the clinical results of repeated subgingival scaling versus periodontal surgery in 30‐ to 40‐year‐old subjects with generalized advanced periodontitis.Methods: Twenty‐six subjects (mean age, 37 ± 3 years) were treated after an initial examination (t1), initial subgingival scaling, and baseline examination (t2) with a randomly assigned second subgingival scaling (test) and periodontal surgery (control) in a split‐mouth design. The final examination (t3) took place 6 months postoperatively. Intraindividual comparisons of mean PD and clinical attachment level (CAL) were analyzed.Results: PD was reduced from 4.1 ± 0.2 mm initially (t1) to 3.1 ± 0.1 mm at baseline (t2), and to 2.9 ± 0.1 mm at the end of the study (t3) for the test sites; and from 4.5 ± 0.2 mm (t1) to 3.5 ± 0.1 mm (t2), and 3.1 ± 0.1 mm (t3) for the control sites. The total PD decrease from t1 to t3 was significant (P <0.001) for both therapies. PD reduction from t2 to t3 was only significant (P <0.001) for control sites, resulting in a significant (P = 0.010) difference between test and control at the final examination. CAL increased 0.2 ± 0.1 mm (t2) plus 0.3 ± 0.1 mm (t3) for the test sites and 0.2 ± 0.1 mm (t2) plus 0.2 ± 0.1 mm (t3) for the control sites. Total CAL gain was statistically significant for the test and control sites. CAL gain from t2 to t3 was only significant (P = 0.022) for the test sites.Conclusions: Both treatments reduced PD and increased CAL. A second subgingival scaling resulted in significant additional CAL gain and reduced the need for surgery.
Root Coverage Using Acellular Dermal Matrix and Comparing a Coronally Positioned Tunnel to a Coronally Positioned Flap Approach
Authors: Papageorgakopoulos Georgios , Greenwell Henry , Hill Margaret , Vidal Ricardo , Scheetz James P. 
Published: June 2008

Background: The primary aim of this randomized, controlled, masked clinical trial was to compare the percentage of root coverage obtained with a coronally positioned flap plus acellular dermal matrix (ADM) allograft to that of a tunnel technique plus ADM 4 months post‐surgically.Methods: Twenty‐four subjects with one site with ≥3 mm Miller Class I or II recession were treated and followed for 4 months. Twelve patients received a coronally positioned flap plus ADM and were considered the positive control group (CPF). The test group consisted of 12 subjects treated with a coronally positioned tunnel technique plus ADM (TUN). Subjects were randomly selected by a coin toss to receive the test or control treatment.Results: The mean facial recession defect at the initial examination for the TUN group was 3.1 ± 0.3 mm; this was reduced to 0.7 ± 0.9 mm at the 4‐month examination for a gain of 2.4 ± 1.0 mm or 78% defect coverage (P <0.05). The mean facial recession defect at the initial examination for the CPF group was 3.4 ± 0.8 mm; it was reduced to 0.2 ± 0.3 mm at the 4‐month examination for a gain of 3.2 ± 0.9 mm or 95% defect coverage (P <0.05). There was no statistically significant difference between groups (P >0.05).Conclusions: The coronally positioned flap plus ADM produced a defect coverage of 95%, whereas the tunnel technique plus ADM produced only 78% coverage. This difference was considered clinically significant but was not statistically significant.
INTUITIONISM'S BURDEN: THOMAS REID ON THE PROBLEM OF MORAL MOTIVATION
Authors: CUNEO TERENCE 
Published: June 2008

Hume bequeathed to rational intuitionists a problem concerning moral judgment and the will – a problem of sufficient severity that it is still cited as one of the major reasons why intuitionism is untenable.1Stated in general terms, the problem concerns how an intuitionist moral theory can account for the intimate connection between moral judgment and moral motivation. One reason that this is still considered to be a problem for intuitionists is that it is widely assumed that the early intuitionists made little progress towards solving it. In this essay, I wish to challenge this assumption by examining one of the more subtle intuitionist responses to Hume, viz., that offered by Thomas Reid. For reasons that remain unclear to me, Reid's response to Hume on this issue has been almost entirely neglected. I shall argue that it is nonetheless one that merits our attention, for at least two reasons.In the first place, Reid's response to Hume's challenge to rational intuitionism bears a close affinity to the type of response that he offers to Hume's broadly skeptical challenge to realist views regarding our perception of the external world. Since Reid's strategy in the latter case is widely regarded as exhibiting significant promise, it is natural to wonder whether, when applied to the moral domain, this type of strategy displays similar promise.2I will suggest that it does. That is, I will suggest that since Reid's broadly nativist position in perception is one well worth considering, then so also is his broadly nativist account of moral motivation. Second, Reid's position regarding moral motivation represents an intriguing attempt to blend a broadly intuitionist view with important insights from the sentimentalist tradition. In this respect, Reid's view is a genuine hybrid position unlike that offered by other intuitionists such as Richard Price. The synthetic character of Reid's position, I claim, gives it a unique type of theoretical richness, since it incorporates some very attractive features of both rational intuitionism and sentimentalism.
Photopatternable Conductive PDMS Materials for Microfabrication
Authors: Cong Hailin , Pan Tingrui 
Published: June 2008

AbstractConductive photodefinable polydimethylsiloxane (PDMS) composites that provide both high electrical conductivity and photopatternability have been developed. The photosensitive composite materials, which consist of a photosensitive component, a conductive filler, and a PDMS pre‐polymer, can be used as a negative photoresist or a positive photoresist with an additional curing agent. A standard photolithographic approach has been used to fabricate conductive elastomeric microstructures. Feature sizes of 60 µm in the positive photoresist and 10 µm in the negative photoresist have been successfully achieved. Moreover, as the conductive filler, silver powders significantly improve the electrical conductivity of the PDMS polymer, but also provide enhanced mechanical and thermal properties as well as interesting biological properties. The combined electrical, mechanical, thermal, and biological properties along with photopatternability make the PDMS‐Ag composite an excellent processable and structural material for various microfabrication applications.
Successful use of the anti‐CD25 antibody daclizumab in an adult patient with hemophagocytic lymphohistiocytosis
Authors: Olin Rebecca L. , Nichols Kim E. , Naghashpour Mojdeh , Wasik Mariusz , Shelly Brenda , Stadtmauer Edward A. , Vogl Dan T. 
Published: June 2008

AbstractHemophagocytic lymphohistiocytosis (HLH) is a rare and severe inflammatory disorder marked by abnormal cytotoxic T and natural killer cell activity, resulting in impaired clearance of pathogen, excessive cytokine production, and continued immune system activation. Soluble IL‐2 receptor (sIL‐2R or sCD25) is typically elevated in HLH and can serve as a marker of disease activity, although its role in the pathophysiology of the disease is unclear. Here we present a case of an adult patient with steroid‐dependent HLH who was treated successfully with daclizumab, a monoclonal anti‐CD25 antibody, allowing successful withdrawal of steroid therapy without an increase in symptoms. Am. J. Hematol., 2008. © 2008 Wiley‐Liss, Inc.
Rethinking isolated cleft palate: Evidence of occult lip defects in a subset of cases
Authors: Weinberg Seth M. , Brandon Carla A. , McHenry Toby H. , Neiswanger Katherine , Deleyiannis Frederic W.B. , de Salamanca Javier E. , Castilla Eduardo E. , Czeizel Andrew E. , Vieira Alexandre R. , Marazita Mary L. 
Published: June 2008

AbstractEmerging research suggests that subepithelial defects of the upper lip musculature are part of the phenotypic spectrum of cleft lip and/or palate (CL/P) and may represent an occult, subclinical manifestation of the anomaly. The present study investigates whether similar occult lip defects are present in individuals affected with isolated cleft palate (CP). To this end, upper lip ultrasounds of 33 CP cases (12 males, 21 females) were evaluated retrospectively for the presence of discontinuities (i.e., breaks) within theorbicularis orismuscle (OOM). In four CP cases (2 males, 2 females), distinct discontinuities of the OOM were identified. Of the remaining CP individuals, 23 demonstrated normal lip morphology on ultrasound (7 males, 16 females), while, in 6 cases (3 males, 3 females), a definitive evaluation was not possible. As CP and CL/P are traditionally thought to be etiologically distinct, these findings raise the possibility that some CP cases may be misclassified. Such diagnostic errors could have important implications for recurrence risk estimation and studies aimed at discovering etiology. © 2008 Wiley‐Liss, Inc.
The role of geomorphology in substratum patch selection by freshwater mussels in the Hawkesbury–Nepean River (New South Wales) Australia
Authors: Brainwood M. , Burgin Shelley , Byrne M. 
Published: June 2008

AbstractMicrohabitat preferences of freshwater mussels and associated substrate characteristics were investigated across a range of geomorphic reaches in the Hawkesbury–Nepean River, Australia.The structure of substratum patches available was strongly influenced by geomorphic reach type. In each reach type, mussel distribution was most frequently correlated with coarse sand and a roughness element characteristic for that reach. Roughness elements such as boulders and cobbles create a flow refuge and were linked with mussel size.Small mussels tended to be associated with boulder‐stabilized habitats and medium sized mussels with cobble habitats. Large mussels rarely co‐occurred with any particular roughness element. Individual species were strongly linked to geomorphic reach type. This association may be due to species' differences in ability to colonize available microhabitat types.The highly tolerantVelesunio ambiguusdominated shale reaches, characterized by fine sediments and human impacts. In contrast,Hyridella depressadominated in gorges, utilizing small flow refuges among boulders, whileH. australiswere present in low densities across a range of substrate conditions.The persistence of multispecies assemblages in mussel beds throughout the Hawkesbury–Nepean River implies similar niche utilization among species. Partitioning of habitats across species on the basis of size suggests some degree of habitat selection, or differential survival. At the local scale, microhabitat characteristics influenced the size distribution and densities of mussel assemblages. Continuing declines in mussel densities are likely to result from ongoing channel modification and increased siltation resulting from changes to riparian vegetation.Copyright © 2008 John Wiley & Sons, Ltd.