bluuebunny/crossref_metadata_2025_split huggingface dataset:
Formation of alteration zones and kaolin genesis, Limnos Island, northeast Aegean Sea, Greece
Authors: Papoulis D. , Tsolis-Katagas P. 
Published: March 2009

AbstractKaolin deposits extending over an area of ~10 km2in the western and southern parts of Limnos Island, northeast Aegean Sea, Greece, were studied. The kaolin deposits are alteration products of volcanic rocks, mainly trachytes, trachyandesites, andesites and dacites. Study of the collected samples was carried out using X-ray powder diffraction (XRPD), scanning electron microscopy (SEM), energy-dispersive scanning electron microscopy (SEM-EDS), Fourier transform Raman spectroscopy (FT-Raman), Fourier transform infrared (FTIR) techniques and inductively-coupled plasma (ICP) bulk rock chemical analyses for major, trace and rare earth elements. The extensive alteration of the parent rocks resulted from the circulation of hydrothermal fluids through faults and fractures. The development of the various assemblages depends not only on the temperature and composition of the hydrothermal fluids but also on the distance of the rock from the fault or the channel of the ascending hydrothermal fluids.Kaolinite, dickite, halloysite, illite, smectite and mixed-layer illite-smectite and jarosite were detected in the altered volcanic rocks forming locally various alteration zones. Smectite-rich zones and illite-rich zones are relatively infrequent. In the halloysite-rich zones, the kaolinization of feldspars is accomplished in four stages. The kaolinizaton of feldspars in the kaolinite-dickite-rich zones follows five discrete stages. In the less altered rocks, thin layers of kaolinite are formed on the surface of feldspars. With increasing kaolinization, kaolinite is developed on the surface of feldspars forming extended parallel booklets of newly formed kaolinite. In the third stage, feldspar crystals are partially altered to kaolinite booklets. As kaolinization advances, kaolinite becomes well formed and, in the most altered rocks, feldspars are partially or completely altered to dickite books, depending on the temperature of the hydrothermal fluids.
Removal of Pb2+ and Ni2 ions from aqueous media by filtration through clay-based beds
Authors: Ribeiro M. J. , Albuquerque C. M. , Labrincha J. A. 
Published: March 2009

AbstractThis work examines possible new applications for common, clay-based formulations. We processed spray-dried grains of a common clay (ZA-4) and collected fines/rejects from the production of lightweight aggregates (LWA), which were used as filtration beds for removal of Pb2+ and Ni2+ from aqueous solutions. Experiments were performed at different contaminant concentrations and by testing several operational conditions. The removal performance of both tested materials is strongly dependent on the particle-size distribution of the batch, being better for beds made of smaller grain size, since packing density and specific contact area for removal are greater. In general, the efficiency for removal of Pb2+ was greater than for Ni2+. When compared with granular activated carbon, clay-based beds performed well. In particular, finer fractions of LWA show stable behaviour, without saturation after consecutive runs. Saturated beds can potentially be reused, in appropriate amounts, for production of new lightweight aggregates or common ceramic items (e.g. bricks), since retained contaminants will be fixed by firing in the clay matrix. Calcination of pressed pellets made of contaminated filter grains created consolidated ceramic components and sorbed metallic species became inert.
FragIdent – Automatic identification and characterisation of cDNA-fragments
Authors: Seelow Dominik , Goehler Heike , Hoffmann Katrin 
Published: March 2009

Abstract

Background
Many genetic studies and functional assays are based on cDNA fragments. After the generation of cDNA fragments from an mRNA sample, their content is at first unknown and must be assigned by sequencing reactions or hybridisation experiments.
Even in characterised libraries, a considerable number of clones are wrongly annotated. Furthermore, mix-ups can happen in the laboratory. It is therefore essential to the relevance of experimental results to confirm or determine the identity of the employed cDNA fragments. However, the manual approach for the characterisation of these fragments using BLAST web interfaces is not suited for larger number of sequences and so far, no user-friendly software is publicly available.

Results
Here we present the development of FragIdent, an application for the automatic identification of open reading frames (ORFs) within cDNA-fragments. The software performs BLAST analyses to identify the genes represented by the sequences and suggests primers to complete the sequencing of the whole insert. Gene-specific information as well as the protein domains encoded by the cDNA fragment are retrieved from Internet-based databases and included in the output. The application features an intuitive graphical interface and is designed for researchers without any bioinformatics skills. It is suited for projects comprising up to several hundred different clones.

Conclusion
We used FragIdent to identify 84 cDNA clones from a yeast two-hybrid experiment. Furthermore, we identified 131 protein domains within our analysed clones. The source code is freely available from our homepage at http://compbio.charite.de/genetik/FragIdent/.
Mapping QTL influencing gastrointestinal nematode burden in Dutch Holstein-Friesian dairy cattle
Authors: Coppieters Wouter , Mes Ted HM , Druet Tom , Farnir Frédéric , Tamma Nico , Schrooten Chris , Cornelissen Albert WCA , Georges Michel , Ploeger Harm W 
Published: March 2009

AbstractBackgroundParasitic gastroenteritis caused by nematodes is only second to mastitis in terms of health costs to dairy farmers in developed countries. Sustainable control strategies complementing anthelmintics are desired, including selective breeding for enhanced resistance.Results and ConclusionTo quantify and characterize the genetic contribution to variation in resistance to gastro-intestinal parasites, we measured the heritability of faecal egg and larval counts in the Dutch Holstein-Friesian dairy cattle population. The heritability of faecal egg counts ranged from 7 to 21% and was generally higher than for larval counts. We performed a whole genome scan in 12 paternal half-daughter groups for a total of 768 cows, corresponding to the ~10% most and least infected daughters within each family (selective genotyping). Two genome-wide significant QTL were identified in an across-family analysis, respectively on chromosomes 9 and 19, coinciding with previous findings in orthologous chromosomal regions in sheep. We identified six more suggestive QTL by within-family analysis. An additional 73 informative SNPs were genotyped on chromosome 19 and the ensuing high density map used in a variance component approach to simultaneously exploit linkage and linkage disequilibrium in an initial inconclusive attempt to refine the QTL map position.
Rapid detection of laboratory cross-contamination with Mycobacterium tuberculosis using multispacer sequence typing
Authors: Djelouadji Zoheira , Orehek Jean , Drancourt Michel 
Published: March 2009

Abstract

Background
The ability to culture Mycobacterium tuberculosis from clinical specimens serves as the gold standard for the diagnosis of tuberculosis. However, a number of false-positive diagnoses may be due to cross-contamination of such specimens. We herein investigate such episode of cross-contamination by using a technique known as multispacer sequence typing (MST). This technique was applied to six M. tuberculosis isolates prepared within the same laboratory over a two-week period of time.

Results
MST analysis indicated a unique and common sequence profile between a strain isolated from a patient with proven pulmonary tuberculosis and a strain isolated from a patient diagnosed with lung carcinoma. Using this approach, we were able to provide a clear demonstration of laboratory cross-contamination within just four working days. Further epidemiological investigations revealed that the two isolates were processed for culture on the same day.

Conclusion
The application of MST has been demonstrated to serve as a rapid and efficient method to investigate cases of possible cross-contamination with M. tuberculosis.
Functional claudication distance: a reliable and valid measurement to assess functional limitation in patients with intermittent claudication
Authors: Kruidenier Lotte M , Nicolaï Saskia PA , Willigendael Edith M , de Bie Rob A , Prins Martin H , Teijink Joep AW 
Published: March 2009

Abstract

Background
Disease severity and functional impairment in patients with intermittent claudication is usually quantified by the measurement of pain-free walking distance (intermittent claudication distance, ICD) and maximal walking distance (absolute claudication distance, ACD). However, the distance at which a patient would prefer to stop because of claudication pain seems a definition that is more correspondent with the actual daily life walking distance. We conducted a study in which the distance a patient prefers to stop was defined as the functional claudication distance (FCD), and estimated the reliability and validity of this measurement.

Methods
In this clinical validity study we included patients with intermittent claudication, following a supervised exercise therapy program. The first study part consisted of two standardised treadmill tests. During each test ICD, FCD and ACD were determined. Primary endpoint was the reliability as represented by the calculated intra-class correlation coefficients. In the second study part patients performed a standardised treadmill test and filled out the Rand-36 questionnaire. Spearman's rho was calculated to assess validity.

Results
The intra-class correlation coefficients of ICD, FCD and ACD were 0.940, 0.959, and 0.975 respectively. FCD correlated significantly with five out of nine domains, namely physical function (rho = 0.571), physical role (rho = 0.532), vitality (rho = 0.416), pain (rho = 0.416) and health change (rho = 0.414).

Conclusion
FCD is a reliable and valid measurement for determining functional capacity in trained patients with intermittent claudication. Furthermore it seems that FCD better reflects the actual functional impairment. In future studies, FCD could be used alongside ICD and ACD.
Recruitment barriers in a randomized controlled trial from the physicians' perspective – A postal survey
Authors: Spaar Anne , Frey Martin , Turk Alexander , Karrer Werner , Puhan Milo A 
Published: March 2009

Abstract

Background
The feasibility of randomized trials often depends on successful patient recruitment. Although numerous recruitment barriers have been identified it is unclear which of them complicate recruitment most. Also, most surveys have focused on the patients' perspective of recruitment barriers whereas the perspective of recruiting physicians has received less attention. Therefore, our aim was to conduct a postal survey among recruiting physicians of a multi-center trial to weigh barriers according to their impact on recruitment.

Methods
We identified any potential recruitment barriers from the literature and from our own experience with a multi-center trial of respiratory rehabilitation in patients with chronic obstructive pulmonary disease. We developed and pilot-tested a self-administered questionnaire where recruiting physicians were asked to express their agreement with statements about recruitment barriers on a Likert-type scale from 1 (full agreement with statement = very substantial recruitment barrier) to 7 (no agreement with statement = no recruitment barrier).

Results
38 of 55 recruiting physicians returned questionnaires (69% response rate), of which 35 could be analyzed (64% useable response rate). Recruiting physicians reported that "time constraints" (median agreement of 3, interquartile range 2–5) had the most negative impact on recruitment followed by "difficulties including identified eligible patients" (median agreement of 5, IQR 3–6). Other barriers such as "trial design barriers", "lack of access to treatment", "individual barriers of recruiting physicians" or "insufficient training of recruiting physicians" were perceived to have little or no impact on patient recruitment.

Conclusion
Physicians perceived time constraints as the most relevant recruitment barrier in a randomized trial. To overcome recruitment barriers interventions, that are affordable for both industry- and investigator-driven trials, need to be developed and tested in randomized trials.

Trial registration
ISRCTN84612310
The role of PET/CT in detection of gastric cancer recurrence
Authors: Sim Sung Hoon , Kim Yu Jung , Oh Do-Youn , Lee Se-Hoon , Kim Dong-Wan , Kang Won Jun , Im Seock-Ah , Kim Tae-You , Kim Woo Ho , Heo Dae Seog , Bang Yung-Jue 
Published: March 2009

Abstract

Background
In the course of surveillance of gastric cancer recurrence after curative resection, contrast CT scan is used in general. However, new findings from CT scan are not always confirmatory for the recurrence. In this case, we usually use short-term follow up strategy or therapeutic intervention with clinical decision. Recently, the use of fusion Positron Emission Tomography/Computed Tomography (PET/CT) is increasing. The purpose of this study is to evaluate the efficacy and usefulness of PET/CT for detecting recurrence of gastric cancer after curative resection.

Methods
Fifty two patients who received curative resection of gastric cancer and had undergone PET/CT and contrast CT for surveillance of recurrence until Dec 2006 in Seoul National University Hospital were analyzed retrospectively. Recurrence of gastric cancer was validated by histologic confirmation (n = 17) or serial contrast CT follow up with at least 5 month interval (n = 35). McNemar's test and Fisher's exact test were used to evaluate sensitivity and specificity of PET/CT and contrast CT.

Results
Of 52 patients, 38 patients were confirmed as recurrence. The sensitivity was 68.4% (26/38) for PET/CT and 89.4% (34/38) for contrast CT (p = 0.057). The specificity was 71.4% (10/14) and 64.2% (9/14), respectively (p = 1.0). In terms of the recurred sites, the sensitivity and specificity of PET/CT were similar to those of contrast CT in all sites except peritoneum. Contrast CT was more sensitive than PET/CT (p = 0.039) for detecting peritoneal seeding. Additional PET/CT on contrast CT showed no further increase of positive predictive value regardless of sites. Among 13 patients whose image findings between two methods were discordant and tissue confirmation was difficult, the treatment decision was made in 7 patients based on PET/CT, showing the final diagnostic accuracy of 42.8% (3/7).

Conclusion
PET/CT was as sensitive and specific as contrast CT in detection of recurred gastric cancer except peritoneal seeding. However, additional PET/CT on contrast CT did not increase diagnostic accuracy in detection of recurred gastric cancer. Further studies are warranted to validate the role of PET/CT in detection of gastric cancer recurrence.
Intrinsic anticarcinogenic effects of Piper sarmentosum ethanolic extract on a human hepatoma cell line
Authors: Zainal Ariffin Shahrul Hisham , Wan Omar Wan Haifa Haryani , Zainal Ariffin Zaidah , Safian Muhd Fauzi , Senafi Sahidan , Megat Abdul Wahab Rohaya 
Published: March 2009

AbstractBackgroundPiper sarmentosum, locally known as kaduk is belonging to the family of Piperaceae. It is our interest to evaluate their effect on human hepatoma cell line (HepG2) for the potential of anticarcinogenic activity.ResultsThe anticarcinogenic activity of an ethanolic extract fromPiper sarmentosumin HepG2 and non-malignant Chang's liver cell lines has been previously determined using (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyl-tetrazolium bromide) (MTT) assays, where the IC50value was used as a parameter for cytotoxicity. The ethanolic extract that showed anticarcinogenic properties in HepG2 cells had an IC50of 12.5 μg mL-1, while IC50values in the non-malignant Chang's liver cell line were greater than 30 μg mL-1. Apoptotic morphological changes in HepG2 cells were observed using an inverted microscope and showed chromatin condensation, cell shrinkage and apoptotic bodies following May-Grunwald-Giemsa's staining. The percentage of apoptotic cells in the overall population (apoptotic index) showed a continuously significant increase (p < 0.05) in 12.5 μg mL-1ethanolic extract-treated cells at 24, 48 and 72 hours compared to controls (untreated cells). Following acridine orange and ethidium bromide staining, treatment with 10, 12 and 14 μg mL-1of ethanolic extracts caused typical apoptotic morphological changes in HepG2 cells. Molecular analysis of DNA fragmentation was used to examine intrinsic apoptosis induced by the ethanolic extracts. These results showed a typical intrinsic apoptotic characterisation, which included fragmentation of nuclear DNA in ethanolic extract-treated HepG2 cells. However, the non-malignant Chang's liver cell line produced no DNA fragmentation. In addition, the DNA genome was similarly intact for both the untreated non-malignant Chang's liver and HepG2 cell lines.ConclusionTherefore, our results suggest that the ethanolic extract fromP. sarmentosuminduced anticarcinogenic activity through an intrinsic apoptosis pathway in HepG2 cellsin vitro.
IGOB131, a novel seed extract of the West African plant Irvingia gabonensis, significantly reduces body weight and improves metabolic parameters in overweight humans in a randomized double-blind placebo controlled investigation
Authors: Ngondi Judith L , Etoundi Blanche C , Nyangono Christine B , Mbofung Carl MF , Oben Julius E 
Published: March 2009

Abstract

Background
A recent in vitro study indicates that IGOB131, a novel seed extract of the traditional West African food plant Irvingia gabonensis, favorably impacts adipogenesis through a variety of critical metabolic pathways including PPAR gamma, leptin, adiponectin, and glycerol-3 phosphate dehydrogenase. This study was therefore aimed at evaluating the effects of IGOB131, an extract of Irvingia gabonensis, on body weight and associated metabolic parameters in overweight human volunteers.

Methods
The study participants comprised of 102 healthy, overweight and/or obese volunteers (defined as BMI > 25 kg/m2) randomly divided into two groups. The groups received on a daily basis, either 150 mg of IGOB131 or matching placebo in a double blinded fashion, 30–60 minutes before lunch and dinner. At baseline, 4, 8 and 10 weeks of the study, subjects were evaluated for changes in anthropometrics and metabolic parameters to include fasting lipids, blood glucose, C-reactive protein, adiponectin, and leptin.

Results
Significant improvements in body weight, body fat, and waist circumference as well as plasma total cholesterol, LDL cholesterol, blood glucose, C-reactive protein, adiponectin and leptin levels were observed in the IGOB131 group compared with the placebo group.

Conclusion

Irvingia gabonensis administered 150 mg twice daily before meals to overweight and/or obese human volunteers favorably impacts body weight and a variety of parameters characteristic of the metabolic syndrome. This is the first double blind randomized placebo controlled clinical trial regarding the anti-obesity and lipid profile modulating effects of an Irvingia gabonensis extract. The positive clinical results, together with our previously published mechanisms of gene expression modulation related to key metabolic pathways in lipid metabolism, provide impetus for much larger clinical studies. Irvingia gabonensis extract may prove to be a useful tool in dealing with the emerging global epidemics of obesity, hyperlipidemia, insulin resistance, and their co-morbid conditions.

Trial registration
ClinicalTrials.gov NCT00645775
Early-cleavage is a reliable predictor for embryo implantation in the GnRH agonist protocols but not in the GnRH antagonist protocols
Authors: Yang Wen-Jui , Hwu Yuh-Ming , Lee Robert Kuo-kuang , Li Sheng-Hsiang , Fleming Steven 
Published: March 2009

Abstract

Background
To test if early-cleavage was a strong predictor of pregnancy in patients receiving either a GnRH agonist long protocol or a GnRH antagonist protocol for in-vitro fertilization treatment (IVF) and intracytoplasmic sperm injection (ICSI).

Methods
This retrospective study included 534 patients undergoing a fresh cycle of oocyte retrieval and the day-3 embryo transfer (from 22 to 46 years old). Of the 534 patients treated, 331 received a GnRH agonist long stimulation protocol (GnRH agonist group) for ovarian stimulation and 203 patients received a GnRH antagonist protocol (GnRH antagonist group). In each group, patients who had at least one early-cleavage embryo transferred were designated as the 'early-cleavage' subgroup. Patients who had no early-cleavage embryos transferred were designated as the 'late-cleavage' subgroup.

Results
The early cleavage rate was significantly lower in the GnRH antagonist group compared with that in the GnRH agonist group (IVF cycles: 34% versus 20%; ICSI cycles: 50% versus 37.8%, respectively, P < 0.0001). In the GnRH agonist group, the pregnancy rates were significantly higher in the early-cleavage subgroup than those in the late-cleavage subgroup (53.7% vs 33.9%, P < 0.0001). In the GnRH antagonist group, the pregnancy rates were not significantly different between the early-cleavage and late-cleavage subgroups (45.9% vs 43.8%, P > 0.05).

Conclusion
Early cleavage of zygote is not a reliable predictor for embryo implantation potential in using the GnRH antagonist protocol. Furthermore, the implantation rates between the GnRH agonist and GnRH antagonist groups were comparable.