bluuebunny/crossref_metadata_2025_split huggingface dataset:
High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies
Authors: Do Hongdo , Krypuy Michael , Mitchell Paul L , Fox Stephen B , Dobrovic Alexander 
Published: May 2008

AbstractBackgroundEpithelial growth factor receptor (EGFR) andKRASmutation status have been reported as predictive markers of tumour response toEGFRinhibitors. High resolution melting (HRM) analysis is an attractive screening method for the detection of both known and unknown mutations as it is rapid to set up and inexpensive to operate. However, up to now it has not been fully validated for clinical samples when formalin-fixed paraffin-embedded (FFPE) sections are the only material available for analysis as is often the case.MethodsWe developed HRM assays, optimised for the analysis of FFPE tissues, to detect somatic mutations inEGFRexons 18 to 21. We performed HRM analysis forEGFRandKRASon DNA isolated from a panel of 200 non-small cell lung cancer (NSCLC) samples derived from FFPE tissues.ResultsAll 73 samples that harbouredEGFRmutations previously identified by sequencing were correctly identified by HRM, giving 100% sensitivity with 90% specificity. Twenty five samples were positive by HRM forKRASexon 2 mutations. Sequencing of these 25 samples confirmed the presence of codon 12 or 13 mutations.EGFRandKRASmutations were mutually exclusive.ConclusionThis is the first extensive validation of HRM on FFPE samples using the detection ofEGFRexons 18 to 21 mutations andKRASexon 2 mutations. Our results demonstrate the utility of HRM analysis for the detection of somaticEGFRandKRASmutations in clinical samples and for screening of samples prior to sequencing. We estimate that by using HRM as a screening method, the number of sequencing reactions needed forEGFRandKRASmutation detection can be reduced by up to 80% and thus result in substantial time and cost savings.
Relationship between risk information on total colonoscopy and patient preferences for colorectal cancer screening options: Analysis using the Analytic Hierarchy Process
Authors: Katsumura Yuichi , Yasunaga Hideo , Imamura Tomoaki , Ohe Kazuhiko , Oyama Hiroshi 
Published: May 2008

Abstract

Background
Although the fecal occult blood test (FOBT) is the preferred program for colorectal cancer screening in Japan, many medical institutions have recently begun to provide total colonoscopy (TCS) as an initial screening program. However, there are a number of severe risks associated with TCS, such as colorectal bleeding and perforation. The justification for performing such a procedure on healthy patients remains unclear. We used the analytic hierarchy process (AHP) to investigate whether risk information on TCS affects patient preferences for colorectal cancer screening.

Methods
We performed a questionnaire survey using an AHP decision-making model, targeting 285 people aged 40–59 years. We randomly assigned the subjects into Groups A (n = 146) and B (n = 139). Both groups were provided with information on the effectiveness, cost and disadvantages of the two screening programs. Group A was provided with additional information regarding the risks of TCS. Individual priorities were calculated with pair-wise comparisons between the two alternatives in each selection criteria. The influence of the risk information was analyzed using a logistic regression analysis.

Results
The aggregated priorities in Group A for 'effectiveness', 'costs', and 'risks' were 0.603, 0.147, and 0.250, respectively, while those in Group B were 0.652, 0.149, and 0.199, respectively. A logistic regression analysis showed that the provision of risk information significantly reduced the subjects' priorities for TCS (p = 0.036).

Conclusion
The lack of risk information was related to the differences in priorities assigned to effectiveness and risks of the two procedures. Patients must be well informed before making decisions concerning their preferred colorectal cancer screening procedure.
A regulatable transgene expression system for cultured Plasmodium falciparum parasites
Authors: Epp Christian , Raskolnikov Dima , Deitsch Kirk W 
Published: May 2008

Abstract

Background
The ability to transfect and create transgenic cultured malaria parasites has transformed the study of Plasmodium falciparum over the last decade. With the completion of the annotated genome sequence, the process of gene discovery now routinely includes gene knockouts, over-expression and complementation analysis. However, while this technology has proven extremely valuable, significant limitations exist. In particular, P. falciparum DNA is often unstable and difficult to clone because of its AT-rich, repetitive nature. As a result, transgene expression constructs can be difficult to assemble due to the need to include two expression cassettes on a single plasmid, one to drive expression of the transgene of interest and a second for expression of the selectable marker. In addition, transgene expression levels are usually not regulatable, making it difficult to assess phenotypes that are sensitive to the amount of protein expressed.

Results
A plasmid based system for transgene expression is described that uses a single, bidirectional promoter to drive expression of both the transgene and the selectable marker, thus greatly reducing the size of the construct and enhancing stability. Further, by altering the concentration of drug used for selection, it is possible to modulate the copy number of the concatameric episomes and thereby regulate the expression level of the transgene through a range greater than 10 fold.

Conclusion
The transgene expression system described here should prove useful for both routine protein over-expression and complementation experiments as well as for experiments in which precisely manipulating the expression level of candidate proteins is desirable. This should provide an additional level of precision to the tools used to study the molecular biology of malaria parasites.
The effects of beta2 adrenergic receptor gene polymorphism in lipid profiles
Authors: Kao Wei-Tsung , Yen Yung-Chieh , Lung For-Wey 
Published: May 2008

Abstract

Background
Explore the interaction between apolipoprotein E (Apo E), phospholipase A2 (PLA2) and β2 adrenergic receptor (β2-AR) gene polymorphisms and lipid profiles in an elderly Chinese population.

Methods
Five hundred subjects aged 65 to 74 years were randomly selected from a community in southern Taiwan to assess the relationship between Apo E, PLA2 and β2-AR gene polymorphisms and lipid profiles. Two hundred sixty-seven participants agreed to have venous blood drawn for DNA studies.

Results
Two statistically significant differences were noted in TC and LDL-C in the Gln27Glu of the β2-AR gene polymorphism (P = 0.007, P = 0.022). The low-income group had a higher HDL-C level (p = 0.076). The Gln27Glu polymorphism Glu/Glu or Gln/Glu subjects had lower TC levels compared to the Gln27Glu polymorphism Gln/Gln subjects (p = 0.092). Lower TC levels (p = 0.082) and lower LDL-C levels (p = 0.045) in subjects with the Cys19Arg16Glu27 haplotype. Lower TC levels (p = 0.06) were also noted in subjects with the Cys19Gly 16Glu27 haplotype. On the other hand, higher VLDL-C levels (p = 0.185) and higher triglyceride (TG) levels (p = 0.190) were noted in subjects with the Cys19Gly 16Gln27 haplotype. The ε2 allele combined with low income had a positive effect on HDL-C (p = 0.0011), after adding the income factor in this study.

Conclusion
When the effects of Apo E and PLA2 on lipid profiles were included in this study, β2-AR gene polymorphisms reduced significant effect on lipid profiles. Similarly, low income increased effect on HDL-C. This study appeared that the results of gene-gene and gene-environment interaction, it should be considered in further studies for lipid profiles.
Assessment of Adiponectin and Leptin as Biomarkers of Positive Metabolic Outcomes after Lifestyle Intervention in Overweight and Obese Children
Authors: Cambuli Valentina M. , Musiu M. Cristina , Incani Michela , Paderi Monica , Serpe Roberto , Marras Valeria , Cossu Efisio , Cavallo M. Gisella , Mariotti Stefano , Loche Sandro , Baroni Marco G. 
Published: May 2008

Abstract
Background: A number of metabolic changes are caused by childhood obesity, including insulin resistance, diabetes, and dyslipidemia. To counteract them, lifestyle modification with changes in dietary habits and physical activity is the primary intervention. Anthropometric parameters may not identify all positive changes associated with lifestyle modifications, whereas circulating adipokines may represent an alternative as biomarkers. The aim of this study was to evaluate adiponectin and leptin levels as markers of positive metabolic outcomes in childhood obesity.
Methods: Changes in clinical, anthropometric, and metabolic parameters, including adiponectin and leptin, were assessed in 104 overweight and obese children before and after 1 yr of lifestyle intervention. Obesity and overweight were defined according to the Italian body mass index reference tables for age and sex. Fifty-four normal-weight children were evaluated as controls. Forty-eight of the children (47.5%) returned for follow-up at 1 yr.
Results: Compared with normal-weight children, overweight and obese subjects differed significantly at baseline for glycemia, insulinemia, homeostasis model assessment for insulin resistance, adiponectinemia (5.8 vs. 18.2 μg/ml in controls), low-density lipoprotein-cholesterol, and triglycerides. These parameters were all higher in the overweight/obese children. At follow-up, most parameters improved in overweight/obese children. The most significant changes were observed in adiponectin concentration, which increased by 245% (P &lt; 0.0001), reaching the levels observed in normal-weight children. Leptin levels showed changes unrelated to positive metabolic outcomes, remaining high at 1 yr of follow-up in overweight/obese children. Regardless of changes in weight status, children with lifestyle intervention reported changes in homeostasis model assessment for insulin resistance and in adiponectin that were associated with loss of fat mass.
Conclusions: After lifestyle intervention, adiponectin increased regardless of changes in weight, whereas no consistent changes was observed in serum leptin. Therefore, circulating adiponectin may represent a good biomarker to evaluate the efficacy of lifestyle intervention in overweight/obese children.
Adjunctive Aripiprazole for Bupropion-Resistant Major Depression
Authors: Sokolski Kenneth N 
Published: May 2008

Objective: To examine the effects of adjunctive aripiprazole in patients with major depression refractory to adequate therapy with bupropion. Case Summary: Four consecutive patients diagnosed with major depression (hat was not responsive to a minimum of 2 months of therapy with bupropion 150-450 mg/day were given adjunctive aripiprazole 2.5–10 mg/day and followed for at least 4 months. Chart notes were used to record patient responses. All patients reported rapid improvement in depressive symptoms following the addition of low-dose aripiprazole. Antidepressant effects were sustained for at least 4 months in all patients; however, the mood disturbance subsequently returned in 2 patients. Adjunctive aripiprazole was well tolerated, with one patient developing akathisia that responded to lowering the aripiprazole dose and another exhibiting worsening of preexisting insomnia. Weight and metabolic parameters were not monitored during the observation period. Discussion: Transitory Improvements in depressive symptoms that occurred in some of the 4 patients may have been due to compensatory mechanisms in dopaminergic systems. Adjunctive use of the atypical antipsychotic aripiprazole has been demonstrated to benefit depressed patients who are resistant to selective serotonin-reuptake Inhibitors. The response to aripiprazole in patients refractory to bupropion has not been previously reported. Conclusions: Adjunctive aripiprazole given in low doses resulted in rapid improvements in depressed patients who were refractory to adequate therapy with bupropion. Additional studies are required to determine whether these results can be generalized to other depressed individuals who are refractory to bupropion treatment.
Role of Gabapentin in the Treatment of Uremic Pruritus
Authors: Vila Tania , Gommer Jennifer , Scates Ann C 
Published: May 2008

Objective: To evaluate the efficacy of gabapentin for the treatment of uremic pruritus (UP). Data Sources: Literature retrieval was accessed through MEDLINE (1950–March week 3. 2006; In-Process & Other Non-Indexed Citations, April 1, 2008} and International Pharmaceutical Abstracts (1970–March 2008) using the terms gabapentin, pruritus, itch, urem$ (truncated), dialysis, and kidney disease. The Google Scholar search engine was used to identify articles that MEDLINE did not capture with the described search terms. Additionally, reference citations from publications identified were reviewed. Study Selection and Data Extraction: Alt articles in English and studies conducted in humans were identified and evaluated. Data Synthesis: UP is an unpleasant Itching sensation that affects approximately 30% of patients on hemodialysis (HD). The current mainstays of therapy include antihistamines and topical therapies, although many patients remain symptomatic despite these treatments. Alternative therapeutic approaches, Including topical, oral, and intravenous drugs; dialysis modifications; homeopathic therapies; and physical treatments have been used, but few evidence-based studies exist to support their utility. Gabapentin has been evaluated for the treatment of UP in 2 small, randomized, placebo-controlled studies, 1 pilot evaluation, and 1 index case. Gabapentin has demonstrated efficacy in the treatment of multiple types of itch and shows promise in treating patients with UP who are unresponsive to standard therapies. Ail of the controlled studies consisted of 4 weeks of active treatment, and no patients discontinued gabapentin due to adverse events. The most common adverse events noted in these trials were consistent with gabapentin's safety profile (dizziness, somnolence, fatigue, nausea). Conclusions: Available data support the use of gabapentin as a welt-tolerated and effective treatment option for patients with UP who are unresponsive to traditional therapies. Further well-designed trials are warranted to establish the most appropriate dosing regimen in patients on HD.
Microstructure of organo-bentonites in water and the effect of steric hindrance on the uptake of organic compounds
Authors: Zhu Jianxi , Zhu Lizhong , Zhu Runliang , Chen Baoliang 
Published: May 2008

AbstractTo further elucidate adsorption-to-partition transitional mechanisms which have been proposed previously for organo-bentonites with different surfactant loadings, the structural characteristics of interlayer surfactant aggregates on organo-bentonite with different surfactant cetyltrimethylammonium bromide loading levels (0.20–2.56 times cation exchange capacity, CEC) have been investigated by in situ X-ray diffraction (XRD) and Fourier TransformInfrared (FTIR) spectroscopy. The sorption properties and the structure of the clay interlayers changed according to the type of surfactant, the surfactant loading level, and the state of hydration in the clays. Based on the sorption of nitrobenzene, phenol, and aniline to organobentonites, the contaminant sorption coefficients (Ksf), normalized with the organic carbon content, show a remarkable dependence on surfactant loading levels. The Ksf values first increased with surfactant loading until reaching a maximum at 1.0 to 1.2 times the CEC, and then decreased. According to the theoretical calculation of the volume fractions relating to the interlamellar space, the interlamellar microenvironment became a more hydrophobic medium, contributing to the dissolution of organic contaminants, as the surfactant loading increased from 0.20 to 2.56 times the CEC. However, the increase in packing density (ρ) for the intercalates, and induced steric hindrances both affect the result in terms of a reduction in the accessible free space where the organic contaminants can be located, which might be a negative factor in the sorption capacity.
Diffusion of Na and Cs in montmorillonite
Authors: Kosakowski Georg , Churakov Sergey V. , Thoenen Tres 
Published: May 2008

AbstractThe state and dynamics of water and cations in pure and mixed Na-Cs-montmorillonite as a function of the interlayer water content were investigated in the present study, using Monte Carlo and classical, molecular-dynamics methods. While highly idealized, the simulations showed that the swelling behavior of hetero-ionic Na-Cs-montmorillonite is comparable to the swelling of a homo-ionic Na- or Cs-montmorillonite. The mixed Na-Cs-montmorillonite is characterized by intermediate interlayer distances compared to homo-ionic Na- and Cs-montmorillonites. Dry, hetero-ionic Na-Cs-montmorillonite is characterized by a symmetric sheet configuration, as is homo-ionic Cs-montmorillonite.We found that at low degrees of hydration the absolute diffusion coefficient of Cs+ is less than for Na+, whereas at greater hydration states the diffusion coefficient of Cs+ is greaterthan for Na+. An analysis of the relative diffusion coefficients (the ratio between the diffusion coefficient of an ion in the interlayer and its diffusion coefficient in bulk water) revealed that water and Na+ are always less retarded than Cs+. With large interlayer water contents, tetralayer or more, Na+ ions preferentially form outer-sphere complexes. The mobility perpendicular to the clay surface is limited and the diffusion is equivalent to two-dimensional diffusion in bulk water. In contrast, Cs+ ions preferentially form ‘inner-sphere complexes’ at all hydration states and their two-dimensional diffusion coefficient is less than in bulk water.The question remains unanswered as to why experimentally derived relative diffusion coefficients of Cs+ in the interlayer of clays are about 20 times less than those we obtained by classical molecular dynamics studies.
The occurrence and genesis of clay minerals associated with Quaternary caliches in the Mersin area, southern Turkey
Authors: Kadir Selahattin , Eren Muhsin 
Published: May 2008

AbstractCaliche in various forms, namely powdery, nodule, tube, fracture-infill, laminar crust, hard laminated crust (hardpan), and pisolitic crust, is widespread in the Mersin area in southern Turkey. It generally occurs within and/or over the reddish-brown mudstone of the Kuzgun Formation (Tortonian, Miocene) and alluvial red soils of the Quaternary. The mineralogical distribution along representative caliche profiles was examined by X-ray diffraction, scanning electron microscopy, differential thermal analysis-thermal gravimetry, and chemical techniques. Calcite is the most abundant mineral associated with minor amounts of palygorskite in caliche samples, whereas smectite is prevalent mainly in the reddish-brown mudstone and alluvial red soils of the caliche parent materials and is associated with appreciable amounts of palygorskite. These minerals are also accompanied by trace amount of illite, quartz, feldspar, and a poorly crystalline phase. Palygorskite fibers and fiber bundles were developed authigenically on euhedral or subhedral calcite crystals of the caliche units and at the edges of smectite flakes in the caliche host-rocks or sediments. Intense, continuous evaporation of subsurface soil-water resulted in an increase in pH and the dissolution of detrital smectite within the red mudstones and alluvial red soils that enclose the isolated caliche forms, and caused an increase in the Al+Fe and Mg/Ca ratio, favoring the formation of palygorskite under alkaline conditions. The calcium required for caliche formation may have originated from eolian dust, detrital carbonate minerals, and/or other caliche materials, which are dissolved by carbonic acid.
Planar compact sets whose intersections are starshaped via orthogonally convex paths
Authors: Breen Marilyn 
Published: May 2008

Abstract
A Helly-type theorem previously established for a finite family of simply connected orthogonal polygons may be extended to a family of planar compact sets having connected complements: If every three (not necessarily distinct) members of have a nonempty intersection that is starshaped via orthogonally convex paths, then all members of have such an intersection. When is finite, an analogous result holds with orthogonally convex paths replaced by staircase paths. The number three is best possible in each case. Moreover, the results fail without the requirement that the sets have connected complements.
Defect and Hodge numbers of hypersurfaces
Authors: Rams Sławomir 
Published: May 2008

Abstract
We define defect for hypersurfaces with A-D-E singularities in complex projective normal Cohen–Macaulay fourfolds having some vanishing properties of Bott-type and prove formulae for Hodge numbers of big resolutions of such hypersurfaces. We compute Hodge numbers of Calabi–Yau manifolds obtained as small resolutions of cuspidal triple sextics and double octics with higher A
j
singularities.
Diplopsalopsis kisselevii sp. nov. (Dinophyceae) from the northwestern Sea of Japan
Authors: Selina Marina S. , Konovalova Galina V. , Begun Andrey A. , Morozova Tatiana V. 
Published: May 2008

Abstract
A new species of the genus Diplopsalopsis, D. kisselevii sp. nov., was found in Amursky Bay off the northwestern coast of the Sea of Japan. This species combines the Diplopsalopsis plate pattern with a protoperidinoid shape. The plate tabulation is Po, X, 3′, 2a, 7″, 4c, 4s, 5′″, 2″″. Cells are oval or almost rounded, slightly longer than wide and slightly flattened dorso-ventrally, 34–48 μm long and 34–46 μm wide. The length/width ratio is 1.0–1.05. The epitheca is slightly shorter than the hypotheca. The cingular list is very narrow, smooth and without ribs. The left sulcal list is narrow and short. The apical sunken depression of the theca contains the comma-like pore complex. Two intercalary plates are present. The narrow, long and hexagonal 1a contacts the 2′, 1″, 2″, 3″, 4″, and 2a plates. The large pentagonal 2a is positioned on the dorsal side of the epitheca with no contact to the Po plate. Diplopsalopsis kisselevii sp. nov. is similar to D. latipeltata in cell shape, and possesses reduced cingular and left sulcal lists and a long intercalary plate. However, D. kisselevii can be differentiated from D. latipeltata by the structure of the theca, the tabulation formula of the epitheca, and the shape, size and position of the anterior intercalary 1a plate.
Growth and reproductive phenology of Pterocladiella capillacea (Rhodophyta: Gelidiales) from the southern Adriatic Sea
Authors: Bottalico Antonella , Delle Foglie Costanza Ilaria , Fanelli Margherita 
Published: May 2008

Abstract
Growth, external morphology and reproductive phenology of a southern Adriatic population of Pterocladiella capillacea from a marine cave were investigated. Production of new uprights from creeping axes was limited to late autumn–winter; upright growth in length and branching order increase reached their maxima in late summer. Tetrasporic fronds were dominant from June to September, with a peak in July, while cystocarpic uprights were rather rare and recorded in August only. Two stable, distinct morphotypes occurred in this population at two sampling sites exposed to different daily photon irradiances. Uprights from the more illuminated site were regularly pinnate, with numerous closely packed lateral branches, representing the best-known phenotype of the species; in contrast, uprights from the more shaded inner site had very long and narrow axes, greater intervals between first-order branches and lower branching order. Statistical analysis demonstrated that upright growth in length and branching was significantly different at the two sites; upright biomass in the more illuminated site was generally higher because of the higher orders of branching.