bluuebunny/crossref_metadata_2025 huggingface dataset:
Mixed-layer illite-smectite in the Kinnekulle K-bentonite, northern Baltic Basin
Authors: Somelar P. , Kirsimäe K. , Środoń J.
Published: February 2010

The composition and particle morphology of diagenetic mixed-layer illite-smectite (I-S) in the shallow buried Ordovician Kinnekulle K-bentonite were studied to understand the process of illitization in the Baltic Basin. The same K-bentonite bed from 12 different locations in the Basin was sampled and analysed by means of X-ray diffraction (XRD), atomic-force microscopy (AFM) and K-Ar dating. Illite-smectite in the samples was identified as a highly illitic R1 type illite-smectite vermiculite (high-charge smectite) mixed-layer mineral with 63–78% illitic layers. Illite-smectite was characterized by log-normally distributed thin particles with an area-weighted mean thickness varying from 1.9 to 3.6 nm and 2.1 to 3.8 nm by XRD-PVP and AFM analysis, respectively. The K-Ar diagenetic ages of the mixed-layer minerals suggest an illitization age of 370 to 420 Ma that agrees with the latest phase of the Caledonian orogeny. Illitization of the Kinnekulle bentonite was probably driven by the intrusion of K-rich fluids.
Acid and alkali treatment of kaolins
Authors: Pentrák M. , Madejová J. , Komadel P.
Published: February 2010

Two kaolins containing kaolinites of different crystallinity, as confirmed by the Aparicio-Galán-Ferrell index, were treated in HCl and KOH solutions at 95º and 80ºC, respectively, for periods up to 36 h. Changes resulting from the treatments have been characterized by several methods. Fe occurs in the octahedral sheets of both kaolinites and dissolves similarly to Al. Lower structural ordering, more structural defects and particles of smaller average size and less regular shape are responsible for faster dissolution of KGa-2 in comparison to well ordered Gold Field (Tanzania) kaolinite. More Si than Al is dissolved in KOH from both kaolins after any dissolution time. An aluminosilicate (feldspathoid) phase is thought to occur in the material prepared from KGa-2 in KOH. Near-IR spectra provide very useful information on changes in the mineral structure upon the treatments, on the solid reaction products and on the adsorbed water molecules.
Donor activating KIR3DS1 is associated with decreased acute GVHD in unrelated allogeneic hematopoietic stem cell transplantation
Authors: Venstrom Jeffrey M. , Gooley Ted A. , Spellman Stephen , Pring James , Malkki Mari , Dupont Bo , Petersdorf Effie , Hsu Katharine C.
Published: February 2010

The natural killer cell receptor KIR3DS1 is associated with improved outcome in malignancies, infections, and autoimmune diseases, but data for the impact of KIR3DS1 in HSCT are inconsistent. Using genomic DNA from the National Marrow Donor Program, we performed donor KIR genotyping for 1087 patients who received an unrelated hematopoietic stem cell transplantation. A total of 33% of donors were KIR3DS1+. Compared with KIR3DS1− donors, donor KIR3DS1 was associated with lower-grade II-IV acute graft-versus-host disease (GVHD; odds ratio = 0.71; 95% confidence interval, 0.55-0.92; P = .009), but not with relapse (hazard ratio = 0.97; 95% confidence interval, 0.73-1.29; P = .82). Furthermore, grade II-IV acute GVHD, overall mortality, and transplantation-related mortality all decreased as the number of copies of donor KIR3DS1 increased (P = .007, P = .03, and P = .02, respectively), with the lowest failure rate occurring among patients homozygous for donor KIR3DS1. Selection of donors with KIR3DS1 may decrease acute GVHD without compromising relapse-free survival, separating the graft-versus-tumor effect from unwanted GVHD.
Identification of novel non-coding RNAs using profiles of short sequence reads from next generation sequencing data
Authors: Jung Chol-Hee , Hansen Martin A , Makunin Igor V , Korbie Darren J , Mattick John S
Published: February 2010

Background

The increasing interest in small non-coding RNAs (ncRNAs) such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs) and recent advances in sequencing technology have yielded large numbers of short (18-32 nt) RNA sequences from different organisms, some of which are derived from small nucleolar RNAs (snoRNAs) and transfer RNAs (tRNAs). We observed that these short ncRNAs frequently cover the entire length of annotated snoRNAs or tRNAs, which suggests that other loci specifying similar ncRNAs can be identified by clusters of short RNA sequences.

Results

We combined publicly available datasets of tens of millions of short RNA sequence tags from Drosophila melanogaster, and mapped them to the Drosophila genome. Approximately 6 million perfectly mapping sequence tags were then assembled into 521,302 tag-contigs (TCs) based on tag overlap. Most transposon-derived sequences, exons and annotated miRNAs, tRNAs and snoRNAs are detected by TCs, which show distinct patterns of length and tag-depth for different categories. The typical length and tag-depth of snoRNA-derived TCs was used to predict 7 previously unrecognized box H/ACA and 26 box C/D snoRNA candidates. We also identified one snRNA candidate and 86 loci with a high number of tags that are yet to be annotated, 7 of which have a particular 18mer motif and are located in introns of genes involved in development. A subset of new snoRNA candidates and putative ncRNA candidates was verified by Northern blot.

Conclusions

In this study, we have introduced a new approach to identify new members of known classes of ncRNAs based on the features of TCs corresponding to known ncRNAs. A large number of the identified TCs are yet to be examined experimentally suggesting that many more novel ncRNAs remain to be discovered.
Tracking chromosomal positions of oligomers - a case study with Illumina's BovineSNP50 beadchip
Authors: Schmitt Armin O , Bortfeldt Ralf H , Brockmann Gudrun A
Published: February 2010

Background

High density genotyping arrays have become established as a valuable research tool in human genetics. Currently, more than 300 genome wide association studies were published for human reporting about 1,000 SNPs that are associated with a phenotype. Also in animal sciences high density genotyping arrays are harnessed to analyse genetic variation. To exploit the full potential of this technology single nucleotide polymorphisms (SNPs) on the chips should be well characterized and their chromosomal position should be precisely known. This, however, is a challenge if the genome sequence is still subject to changes.

Results

We have developed a mapping strategy and a suite of software scripts to update the chromosomal positions of oligomer sequences used for SNP genotyping on high density arrays. We describe the mapping procedure in detail so that scientists with moderate bioinformatics skills can reproduce it. We furthermore present a case study in which we re-mapped 54,001 oligomer sequences from Ilumina's BovineSNP50 beadchip to the bovine genome sequence. We found in 992 cases substantial discrepancies between the manufacturer's annotations and our results. The software scripts in the and programming languages are provided as supplements.

Conclusions

The positions of oligomer sequences in the genome are volatile even within one build of the genome. To facilitate the analysis of data from a GWAS or from an expression study, especially with species whose genome assembly is still unstable, it is recommended to update the oligomer positions before data analysis.
MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori
Authors: Liu Shiping , Gao Song , Zhang Danyu , Yin Jiyun , Xiang Zhonghuai , Xia Qingyou
Published: February 2010

Background

MicroRNAs (miRNAs) repress target genes at the post-transcriptional level, and function in the development and cell-lineage pathways of host species. Tissue-specific expression of miRNAs is highly relevant to their physiological roles in the corresponding tissues. However, to date, few miRNAs have been spatially identified in the silkworm.

Results

We establish for the first time the spatial expression patterns of nearly 100 miRNAs in multiple normal tissues (organs) of Bombyx mori females and males using microarray and Northern-blotting analyses. In all, only 10 miRNAs were universally distributed (including bmo-let-7 and bmo-bantam), while the majority were expressed exclusively or preferentially in specific tissue types (e.g., bmo-miR-275 and bmo-miR-1). Additionally, we examined the developmental patterns of miRNA expression during metamorphosis of the body wall, silk glands, midgut and fat body. In total, 63 miRNAs displayed significant alterations in abundance in at least 1 tissue during the developmental transition from larvae to pupae (e.g., bmo-miR-263b and bmo-miR-124). Expression patterns of five miRNAs were significantly increased during metamorphosis in all four tissues (e.g., bmo-miR-275 and bmo-miR-305), and two miRNA pairs, bmo-miR-10b-3p/5p and bmo-miR-281-3p/5p, showed coordinate expression.

Conclusions

In this study, we conducted preliminary spatial measurements of several miRNAs in the silkworm. Periods of rapid morphological change were associated with alterations in miRNA expression patterns in the body wall, silk glands, midgut and fat body during metamorphosis. Accordingly, we propose that corresponding ubiquitous or tissue-specific expression of miRNAs supports their critical roles in tissue specification. These results should facilitate future functional analyses.
Comparative genomic and proteomic analyses of two Mycoplasma agalactiae strains: clues to the macro- and micro-events that are shaping mycoplasma diversity
Authors: Nouvel Laurent X , Sirand-Pugnet Pascal , Marenda Marc S , Sagné Eveline , Barbe Valérie , Mangenot Sophie , Schenowitz Chantal , Jacob Daniel , Barré Aurélien , Claverol Stéphane , Blanchard Alain , Citti Christine
Published: February 2010

Background

While the genomic era is accumulating a tremendous amount of data, the question of how genomics can describe a bacterial species remains to be fully addressed. The recent sequencing of the genome of the Mycoplasma agalactiae type strain has challenged our general view on mycoplasmas by suggesting that these simple bacteria are able to exchange significant amount of genetic material via horizontal gene transfer. Yet, events that are shaping mycoplasma genomes and that are underlining diversity within this species have to be fully evaluated. For this purpose, we compared two strains that are representative of the genetic spectrum encountered in this species: the type strain PG2 which genome is already available and a field strain, 5632, which was fully sequenced and annotated in this study.

Results

The two genomes differ by ca. 130 kbp with that of 5632 being the largest (1006 kbp). The make up of this additional genetic material mainly corresponds (i) to mobile genetic elements and (ii) to expanded repertoire of gene families that encode putative surface proteins and display features of highly-variable systems. More specifically, three entire copies of a previously described integrative conjugative element are found in 5632 that accounts for ca. 80 kbp. Other mobile genetic elements, found in 5632 but not in PG2, are the more classical insertion sequences which are related to those found in two other ruminant pathogens, M. bovis and M. mycoides subsp. mycoides SC. In 5632, repertoires of gene families encoding surface proteins are larger due to gene duplication. Comparative proteomic analyses of the two strains indicate that the additional coding capacity of 5632 affects the overall architecture of the surface and suggests the occurrence of new phase variable systems based on single nucleotide polymorphisms.

Conclusion

Overall, comparative analyses of two M. agalactiae strains revealed a very dynamic genome which structure has been shaped by gene flow among ruminant mycoplasmas and expansion-reduction of gene repertoires encoding surface proteins, the expression of which is driven by localized genetic micro-events.
Serotype- and strain- dependent contribution of the sensor kinase CovS of the CovRS two-component system to Streptococcus pyogenes pathogenesis
Authors: Sugareva Venelina , Arlt Regina , Fiedler Tomas , Riani Catur , Podbielski Andreas , Kreikemeyer Bernd
Published: February 2010

Background

The Streptococcus pyogenes (group A streptococci, GAS) two-component signal transduction system CovRS has been described to be important for pathogenesis of this exclusively human bacterial species. If this system acts uniquely in all serotypes is currently unclear. Presence of serotype- or strain-dependent regulatory circuits and polarity is an emerging scheme in Streptococcus pyogenes pathogenesis. Thus, the contribution of the sensor kinase (CovS) of the global regulatory two-component signal transduction system CovRS on pathogenesis of several M serotypes was investigated.

Results

CovS mutation uniformly repressed capsule expression and hampered keratinocyte adherence in all tested serotypes. However, a serotype- and even strain-dependent contribution on survival in whole human blood and biofilm formation was noted, respectively.

Conclusions

These data provide new information on the action of the CovS sensor kinase and revealed that its activity on capsule expression and keratinocyte adherence is uniform across serotypes, whereas the influence on biofilm formation and blood survival is serotype or even strain dependent. This adds the CovRS system to a growing list of serotype-specific acting regulatory loci in S. pyogenes.
Identification of endogenous control genes for normalisation of real-time quantitative PCR data in colorectal cancer
Authors: Kheirelseid Elrasheid AH , Chang Kah Hoong , Newell John , Kerin Michael J , Miller Nicola
Published: February 2010

Background

Gene expression analysis has many applications in cancer diagnosis, prognosis and therapeutic care. Relative quantification is the most widely adopted approach whereby quantification of gene expression is normalised relative to an endogenously expressed control (EC) gene. Central to the reliable determination of gene expression is the choice of control gene. The purpose of this study was to evaluate a panel of candidate EC genes from which to identify the most stably expressed gene(s) to normalise RQ-PCR data derived from primary colorectal cancer tissue.

Results

The expression of thirteen candidate EC genes: B2M, HPRT, GAPDH, ACTB, PPIA, HCRT, SLC25A23, DTX3, APOC4, RTDR1, KRTAP12-3, CHRNB4 and MRPL19 were analysed in a cohort of 64 colorectal tumours and tumour associated normal specimens. CXCL12, FABP1, MUC2 and PDCD4 genes were chosen as target genes against which a comparison of the effect of each EC gene on gene expression could be determined. Data analysis using descriptive statistics, geNorm, NormFinder and qBasePlus indicated significant difference in variances between candidate EC genes. We determined that two genes were required for optimal normalisation and identified B2M and PPIA as the most stably expressed and reliable EC genes.

Conclusion

This study identified that the combination of two EC genes (B2M and PPIA) more accurately normalised RQ-PCR data in colorectal tissue. Although these control genes might not be optimal for use in other cancer studies, the approach described herein could serve as a template for the identification of valid ECs in other cancer types.
Frequency of Fabry disease in male and female haemodialysis patients in Spain
Authors: Gaspar Paulo , Herrera Julio , Rodrigues Daniel , Cerezo Sebastián , Delgado Rodrigo , Andrade Carlos F , Forascepi Ramón , Macias Juan , del Pino Maria D , Prados Maria D , de Alegria Pilar R , Torres Gerardo , Vidau Pedro , Sá-Miranda Maria C
Published: February 2010

Background

Fabry disease (FD), an X-linked lysosomal storage disorder, is caused by a reduced activity of the lysosomal enzyme α-galactosidase A. The disorder ultimately leads to organ damage (including renal failure) in males and females. However, heterozygous females usually present a milder phenotype with a later onset and a slower progression.

Methods

A combined enzymatic and genetic strategy was used, measuring the activity of α-galactosidase A and genotyping the α-galactosidase A gene (GLA) in dried blood samples (DBS) of 911 patients undergoing haemodialysis in centers across Spain.

Results

GLA alterations were found in seven unrelated patients (4 males and 3 females). Two novel mutations (p.Gly346AlafsX347 and p.Val199GlyfsX203) were identified as well as a previously described mutation, R118C. The R118C mutation was present in 60% of unrelated patients with GLA causal mutations. The D313Y alteration, considered by some authors as a pseudo-deficiency allele, was also found in two out of seven patients.

Conclusions

Excluding the controversial D313Y alteration, FD presents a frequency of one in 182 individuals (0.55%) within this population of males and females undergoing haemodialysis. Moreover, our findings suggest that a number of patients with unexplained and atypical symptoms of renal disease may have FD. Screening programmes for FD in populations of individuals presenting severe kidney dysfunction, cardiac alterations or cerebrovascular disease may lead to the diagnosis of FD in those patients, the study of their families and eventually the implementation of a specific therapy.
Pentastatin-1, a collagen IV derived 20-mer peptide, suppresses tumor growth in a small cell lung cancer xenograft model
Authors: Koskimaki Jacob E , Karagiannis Emmanouil D , Tang Benjamin C , Hammers Hans , Watkins D Neil , Pili Roberto , Popel Aleksander S
Published: February 2010

Background

Angiogenesis is the formation of neovasculature from a pre-existing vascular network. Progression of solid tumors including lung cancer is angiogenesis-dependent. We previously introduced a bioinformatics-based methodology to identify endogenous anti-angiogenic peptide sequences, and validated these predictions in vitro in human umbilical vein endothelial cell (HUVEC) proliferation and migration assays.

Methods

One family of peptides with high activity is derived from the α-fibrils of type IV collagen. Based on the results from the in vitro screening, we have evaluated the ability of a 20 amino acid peptide derived from the α5 fibril of type IV collagen, pentastatin-1, to suppress vessel growth in an angioreactor-based directed in vivo angiogenesis assay (DIVAA). In addition, pentastatin-1 suppressed tumor growth with intraperitoneal peptide administration in a small cell lung cancer (SCLC) xenograft model in nude mice using the NCI-H82 human cancer cell line.

Results

Pentastatin-1 decreased the invasion of vessels into angioreactors in vivo in a dose dependent manner. The peptide also decreased the rate of tumor growth and microvascular density in vivo in a small cell lung cancer xenograft model.

Conclusions

The peptide treatment significantly decreased the invasion of microvessels in angioreactors and the rate of tumor growth in the xenograft model, indicating potential treatment for angiogenesis-dependent disease, and for translational development as a therapeutic agent for lung cancer.
A new approach to dual-color two-photon microscopy with fluorescent proteins
Authors: Tillo Shane E , Hughes Thomas E , Makarov Nikolay S , Rebane Aleks , Drobizhev Mikhail
Published: February 2010

Background

Two-photon dual-color imaging of tissues and cells labeled with fluorescent proteins (FPs) is challenging because most two-photon microscopes only provide one laser excitation wavelength at a time. At present, methods for two-photon dual-color imaging are limited due to the requirement of large differences in Stokes shifts between the FPs used and their low two-photon absorption (2PA) efficiency.

Results

Here we present a new method of dual-color two-photon microscopy that uses the simultaneous excitation of the lowest-energy electronic transition of a blue fluorescent protein and a higher-energy electronic transition of a red fluorescent protein.

Conclusion

Our method does not require large differences in Stokes shifts and can be extended to a variety of FP pairs with larger 2PA efficiency and more optimal imaging properties.
Hypothyroidism among military infants born in countries of varied iodine nutrition status
Authors: Cranston Marcus M , Ryan Margaret AK , Smith Tyler C , Sevick Carter J , Brodine Stephanie K
Published: February 2010

Background

Iodine deficiency is a global problem representing the most common preventable cause of mental retardation. Recently, the impact of subtle deficiencies in iodine intake on children and pregnant women has been questioned. This study was designed to compare hypothyroidism among infants born to US military families in countries of varied iodine nutrition status.

Methods

A cohort design was used to analyze data from the Department of Defense Birth and Infant Health Registry for infants born in 2000-04 (n = 447,691). Hypothyroidism was defined using ICD-9-CM codes from the first year of life (n = 698). The impact of birth location on hypothyroidism was assessed by comparing rates in Germany, Japan, and US territories with the United States, while controlling for infant gender, plurality, gestational age, maternal age, maternal military status, and military parent's race/ethnicity.

Results

Hypothyroidism did not vary by birth location with adjusted odds ratios (OR) as follows: Germany (OR 0.82, [95% CI 0.50, 1.35]), Japan (OR 0.67, [95% CI 0.37, 1.22]), and US territories (OR 1.29, [95% CI 0.57, 2.89]). Hypothyroidism was strongly associated with preterm birth (OR 5.44, [95% CI 4.60, 6.42]). Hypothyroidism was also increased among infants with civilian mothers (OR 1.24, [95% CI 1.00, 1.54]), and older mothers, especially ages 40 years and older (OR 2.09, [95% CI 1.33, 3.30]).

Conclusions

In this study, hypothyroidism in military-dependent infants did not vary by birth location, but was associated with other risk factors, including preterm birth, civilian maternal status, and advanced maternal age.
Effect of a peer-educational intervention on provider knowledge and reported performance in family planning services: a cluster randomized trial
Authors: Mohammad-Alizadeh Charandabi Sakineh , Vahidi Rezagoli , Marions Lena , Wahlström Rolf
Published: February 2010

Background

Peer education is an interactive method of teaching or learning which is widely used for educating school and college students, in a variety of different forms. However, there are few studies on its effectiveness for in-service education. The aim of this study was to evaluate the effect of an educational programme including peer discussions, based on a needs assessment, on the providers' knowledge and reported performance in family planning services.

Methods

An educational programme was designed and applied in a random selection of half of in-charges of the 74 family health units (intervention group) in Tabriz at a regular monthly meeting. The other half constituted the control group. The programme included eight pages of written material and a two-hour, face-to-face discussion session with emphasis on the weak areas identified through a needs assessment questionnaire. The educated in-charges were requested to carry out a similar kind of programme with all peers at their health facilities within one month. All in-charges received one self-administered questionnaire containing knowledge questions one month after the in-charge education (follow-up I: 61 responses), and another one containing knowledge and self-reported performance questions 26 months later (follow-up II: 61 responses). Also, such tests were done for the peers facilitated by the in-charges one (105 responses) and 27 months (114 responses) after the peer discussions. Multiple linear regression was used for comparing mean total scores, and Chi square for comparing proportions between control and intervention groups, after defining facility as the unit of randomization.

Results

The mean total percentage scores of knowledge (percent of maximal possible score) in the intervention group were significantly higher than in the control group, both at follow-up I (63%) and at follow-up II (57%); with a difference of 16 (95% CI: 11, 22) and 5 (95% CI: 0.4, 11) percentage units, respectively. Only two of the nine reported performance items were significantly different among the non in-charges in the intervention group at follow-up II.

Conclusions

The educational programme including peer discussions using existing opportunities with no need for additional absence from the workplace might be a useful complement to formal large group education for the providers.
Differential roles of cyclin D1 and D3 in pancreatic ductal adenocarcinoma
Authors: Radulovich Nikolina , Pham Nhu-An , Strumpf Dan , Leung Lisa , Xie Wing , Jurisica Igor , Tsao Ming-Sound
Published: February 2010

Background

The cyclin D1 (CCND1) and cyclin D3 (CCND3) are frequently co-overexpressed in pancreatic ductal adenocarcinoma (PDAC). Here we examine their differential roles in PDAC.

Results

CCND1 and CCND3 expression were selectively suppressed by shRNA in PDAC cell lines with expression levels of equal CCND1 and CCND3 (BxPC3), enhanced CCND1 (HPAC) or enhanced CCND3 (PANC1). Suppression of cell proliferation was greater with CCND3 than CCND1 downregulation. CCND3 suppression led to a reduced level of phosphorylated retinoblastoma protein (Ser795p-Rb/p110) and resulted in decreased levels of cyclin A mRNA and protein. A global gene expression analysis identified deregulated genes in D1- or D3-cyclin siRNA-treated PANC1 cells. The downregulated gene targets in CCND3 suppressed cells were significantly enriched in cell cycle associated processes (p < 0.005). In contrast, focal adhesion/actin cytoskeleton, MAPK and NF B signaling appeared to characterize the target genes and their interacting proteins in CCND1 suppressed PANC1 cells.

Conclusions

Our results suggest that CCND3 is the primary driver of the cell cycle, in cooperation with CCND1 that integrates extracellular mitogenic signaling. We also present evidence that CCND1 plays a role in tumor cell migration. The results provide novel insights for common and differential targets of CCND1 and CCND3 overexpression during pancreatic duct cell carcinogenesis.
Dextran sulfate sodium and 2,4,6-trinitrobenzene sulfonic acid induce lipid peroxidation by the proliferation of intestinal gram-negative bacteria in mice
Authors: Lee In-Ah , Bae Eun-Ah , Hyun Yang-Jin , Kim Dong-Hyun
Published: February 2010

Abstrect

Background

To understand whether TLR-4-linked NF-kB activation negatively correlates with lipid peroxidation in colitic animal models, we caused colitis by the treatment with dextran sulfate sodium (DSS) or 2,4,6-trinitrobenzenesulfonic acid (TNBS) to C3H/HeJ (TLR-4-defective) and C3H/HeN (wild type) mice, investigated inflammatory markers, lipid peroxidation, proinflammatory cytokines and TLR-4-linked NF-κB activation, in colon and intestinal bacterial composition in vivo.

Methods

Orally administered DSS and intrarectally injected TNBS all caused severe inflammation, manifested by shortened colons in both mice. These agents increased intestinal myeloperoxidase activity and the expression of the proinflammatory cytokines, IL-1β, TNF-α and IL-6, in the colon.

Results

DSS and TNBS induced the protein expression of TLR-4 and activated transcription factor NF-κB. However, these colitic agents did not express TLR-4 in C3H/HeJ mice. Of proinflammatory cytokines, IL-1β was most potently expressed in C3H/HeN mice. IL-1β potently induced NF-κB activation in CaCo-2 cells, but did not induce TLR-4 expression. DSS and TNBS increased lipid peroxide (malondialdehyde) and 4-hydroxy-2-nonenal content in the colon, but reduced glutathione content and superoxide dismutase and catalase activities. These colitic inducers increased the number of Enterobacteriaceae grown in DHL agar plates in both mice, although the number of anaerobes and bifidobacteria grown in GAM and BL agar plates was reduced.E. coli, K. pneumoniaeandProteus mirabilisisolated in DHL agar plates increased lipid peroxidation in liposomes prepared by L-α-phosphatidylcholine, butB. animalisandB. choleriumisolated from BL agar plates inhibited it.

Discussion

These findings suggest that DSS and TNBS may cause colitis by inducing lipid peroxidation and enterobacterial proliferation, which may deteriorate the colitis by regulating proinflammatory cytokines via TLR-4-linked NF-κB activation pathway.
High Erk activity suppresses expression of the cell cycle inhibitor p27Kip1 in colorectal cancer cells
Authors: Kress Theresia R , Raabe Thomas , Feller Stephan M
Published: February 2010

The molecular heterogeneity of human cancer cells at the level of signaling protein activities remains poorly understood. Using a panel of 64 colorectal (CRC) cancer cell lines the activity status of the MAP kinases Erk1 and Erk2 was investigated. Erk1/2 activity varied greatly within the CRC cell line panel and was not detectably associated with the speed of cell growth in 10 CRC lines analyzed. As expected, mutations in K-Ras or B-Raf were often, albeit not always, linked to high Erk1/2 activity. The phosphorylation of several known Erk1/2 targets investigated did not generally reflect Erk1/2 activity in the 10 CRC lines analyzed. However, the reduction of Erk1/2 activity with MEK inhibitors generally abolished cell growth but only led to an increase of cellular p27Kip1 levels in CRC cells with high Erk1/2 activity levels. The results indicate that high Erk1/2 activation is utilized by some CRC lines to override the cell cycle brake p27Kip1, while others presumably rely on different mechanisms in order to inactivate this important cell cycle brake. Such detailed knowledge of the molecular diversity of cancer cell signaling mechanisms may eventually help to develop molecularly targeted, patient-specific therapeutic strategies and treatments.
The STRIPES Trial - Support to Rural India's Public Education System
Authors: Eble Alex , Mann Vera , Bhakta Preetha , Lakshminarayana Rashmi , Frost Chris , Elbourne Diana , Boone Peter
Published: February 2010

Background

Performance of primary school students in India lags far below government expectations, and major disparity exists between rural and urban areas. The Naandi Foundation has designed and implemented a programme using community members to deliver after-school academic support for children in over 1,100 schools in five Indian states. Assessments to date suggest that it might have a substantial effect. This trial aims to evaluate the impact of this programme in villages of rural Andhra Pradesh and will compare test scores for children in three arms: a control and two intervention arms. In both intervention arms additional after-school instruction and learning materials will be offered to all eligible children and in one arm girls will also receive an additional 'kit' with a uniform and clothes.

Methods/Design

The trial is a cluster-randomised controlled trial conducted in conjunction with the CHAMPION trial. In the CHAMPION trial 464 villages were randomised so that half receive health interventions aiming to reduce neonatal mortality. STRIPES will be introduced in those CHAMPION villages which have a public primary school attended by at least 15 students at the time of a baseline test in 2008. 214 villages of the 464 were found to fulfil above criteria, 107 belonging to the control and 107 to the intervention arm of the CHAMPION trial. These latter 107 villages will serve as control villages in the STRIPES trial. A further randomisation will be carried out within the 107 STRIPES intervention villages allocating half to receive an additional kit for girls on the top of the instruction and learning materials. The primary outcome of the trial is a composite maths and language test score.

Discussion

The study is designed to measure (i) whether the educational intervention affects the exam score of children compared to the control arm, (ii) if the exam scores of girls who receive the additional kit are different from those of girls living in the other STRIPES intervention arm. One of the goals of the STRIPES trial is to provide benefit to the controls of the CHAMPION trial. We will also conduct a cost-benefit analysis in which we calculate the programme cost for 0.1 standard deviation improvement for both intervention arms.

Trial Registration

Current controlled trials ISRCTN69951502
Neoadjuvant radiotherapy of primary irresectable unicentric Castleman's disease: a case report and review of the literature
Authors: de Vries Iris AC , van Acht Marjolein MS , Demeyere Thomas BJ , Lybeert Marnix LM , de Zoete Jean-Paul , Nieuwenhuijzen Grard AP
Published: February 2010

Background

Castleman disease (CD) is a rare benign disorder characterised by hyperplasia of lymphoid tissue that may develop at a single site or throughout the body. The etiology of this disorder is unclear, although the histopathological presentation can be differentiated into a hyaline vascular variant, a plasma cell variant and a mixed variant. Clinically, it has been recorded that 3 manifestations of CD are characterized: a localized unicentric type, a generalized multicentric type and a mixed form. Surgery remains the main treatment for resectable unicentric CD, since removal of the large node is possible without further complications. No consensus has been reached concerning the most adequate treatment for irresectable unicentric CD.

Methods

Case report of a 67 year old woman.

Results

This report, describes the case of a 67-year-old woman with unicentric Castleman disease located in the right lower abdomen. The patient had symptoms of fatigue, dyspnoea and pain in the right lower abdomen. Computed tomography (CT)- examination revealed a tumour, which had grown to form a close relationship with the common iliac vessels and the sacral bone. A Laparotomy procedure revealed that the tumour was an irresectable mass. Neo-adjuvant radiotherapy (40 Gy) was administered in order to downsize the tumour. Six weeks later a new CT-scan revealed a major reduction of the tumour, which enabled a successful radical resection of the tumour to be performed. Histopathological analysis of the tumour showed the hyaline vascular type of CD.

Conclusions

Neo-adjuvant radiotherapy should be considered in case of an irresectable unicentric CD.
A distinctive gene expression fingerprint in mentally retarded male patients reflects disease-causing defects in the histone demethylase KDM5C
Authors: Jensen Lars R , Bartenschlager Heinz , Rujirabanjerd Sinitdhorn , Tzschach Andreas , Nümann Astrid , Janecke Andreas R , Spörle Ralf , Stricker Sigmar , Raynaud Martine , Nelson John , Hackett Anna , Fryns Jean-Pierre , Chelly Jamel , de Brouwer Arjan PM , Hamel Ben , Gecz Jozef , Ropers Hans-Hilger , Kuss Andreas W
Published: February 2010

Background

Mental retardation is a genetically heterogeneous disorder, as more than 90 genes for this disorder has been found on the X chromosome alone. In addition the majority of patients are non-syndromic in that they do not present with clinically recognisable features. This makes it difficult to determine the molecular cause of this disorder on the basis of the phenotype alone. Mutations in KDM5C (previously named SMCX or JARID1C), a gene that encodes a transcriptional regulator with histone demethylase activity specific for dimethylated and trimethylated H3K4, are a comparatively frequent cause of non-syndromic X-linked mental retardation (NS-XLMR). Specific transcriptional targets of KDM5C, however, are still unknown and the effects of KDM5C deficiency on gene expression have not yet been investigated.

Results

By whole-mount in situ hybridisation we showed that the mouse homologue of KDM5C is expressed in multiple tissues during mouse development.

We present the results of gene expression profiling performed on lymphoblastoid cell lines as well as blood from patients with mutations in KDM5C. Using whole genome expression arrays and quantitative reverse transcriptase polymerase chain reaction (QRT-PCR) experiments, we identified several genes, including CMKOR1, KDM5B and KIAA0469 that were consistently deregulated in both tissues.

Conclusions

Our findings shed light on the pathological mechanisms underlying mental retardation and have implications for future diagnostics of this heterogeneous disorder.
Intranodal palisaded myofibroblastoma: a case report
Authors: Karvouni Helen , Yiallourou Anneza I , Kyriazi Maria , Stafyla Vaia , Smyrniotis Vassilis , Kondi-Pafiti Agathi
Published: February 2010

Intranodal palisaded myofibroblastoma is a rare benign soft tissue tumor, almost always arising from inguinal lymph nodes. It usually presents as a painless, slow-growing inguinal mass. We report herein a case of an intranodal palisaded myofibroblastoma occurring in a 36-year-old man. The salient clinicopathologic features of this unusual tumor are presented and the literature is briefly reviewed.
Autophagy induction and CHOP under-expression promotes survival of fibroblasts from rheumatoid arthritis patients under endoplasmic reticulum stress
Authors: Shin Yong-Joo , Han Song-Hee , Kim Do-Sung , Lee Geum-Hwa , Yoo Wan-Hee , Kang Yong-Mo , Choi Je-Yong , Lee Yong Chul , Park Seoung Ju , Jeong Seul-Ki , Kim Hyung-Tae , Chae Soo-Wan , Jeong Hyun-Ja , Kim Hyung-Ryong , Chae Han-Jung
Published: February 2010

Introduction

Synovial fibroblasts from rheumatoid arthritis show resistance to apoptotic stimuli, indicating they may be difficult to treat. To clearly understand these mechanisms of resistance, rheumatoid and osteoarthritis synovial fibroblasts (RASF and OASF) were exposed to endoplasmic reticulum (ER) stress such as thapsigargin, Ca2+-ATPase inhibitor.

Methods

Fibroblasts were assessed microscopically for cell viability by trypan blue exclusion and for autophagic cells by LC-3II formation. Caspase-3 activity was measured as aminomethyl-coumarin (AMC) liberated from AC-DEVD-AMC. Immunoblotting was performed to compare protein expression in OASF and RASF.

Results

ER stress caused cell death in OASF but not in RASF. Thapsigargin, a Ca2+-ATPase inhibitor, did not change the expression of GRP78, an ER chaperone in OASF and RASF, but induced another ER stress protein, CCAAT/enhancer binding protein (C/EBP) homologous protein (CHOP) differently, showing high levels in OASF and low levels in RASF. Thapsigargin increased the autophagy response in RASF, with autophagosome formation, beclin expression, and LC3-II conversion. Transfection with beclin siRNA inhibited autophagy and increased the susceptibility to ER stress-induced cell death. On the other hand, CHOP siRNA increased autophagy and improved cell survival, especially in RASF, indicating that CHOP is involved in regulation of autophagy and cell death, but that low expression of CHOP protects RASF from apoptosis.

Conclusions

Autophagy induction and CHOP under-expression increases cell resistance against ER stress-induced cell death in fibroblasts from rheumatoid arthritis patients.
Open-Label, Phase II, Multicenter, Randomized Study of the Efficacy and Safety of Two Dose Levels of Pertuzumab, a Human Epidermal Growth Factor Receptor 2 Dimerization Inhibitor, in Patients With Human Epidermal Growth Factor Receptor 2–Negative Metastatic Breast Cancer
Authors: Gianni Luca , Lladó Anna , Bianchi Giulia , Cortes Javier , Kellokumpu-Lehtinen Pirkko-Liisa , Cameron David A. , Miles David , Salvagni Stefania , Wardley Andrew , Goeminne Jean-Charles , Hersberger Veronica , Baselga José
Published: February 2010

Purpose

Pertuzumab is a humanized monoclonal antibody inhibiting human epidermal growth factor receptor 2 (HER2) dimerization. The aim of this phase II trial was to assess the antitumor activity and safety profile of pertuzumab monotherapy in patients with HER2-negative metastatic breast cancer. The utility of biomarkers detected in paraffin-embedded tissue as predictors of response was also explored.

Patients and Methods

This was an international, multicenter, open-label, randomized phase II study. Patients (n = 79) with centrally confirmed HER2-negative metastatic breast cancer were randomly assigned to receive pertuzumab once every 3 weeks with a loading dose of 840 mg followed thereafter by either 420 mg (arm A) or 1,050 mg (arm B). Patients were stratified by country and prior taxane therapy.

Results

Of 79 patients who were randomly assigned, 78 were included in the intent-to-treat population. In arm A (n = 41), two patients had partial responses, and 18 patients (44%) experienced stable disease (SD) lasting ≥ 12 weeks. In arm B (n = 37), SD was observed in 14 patients (38%). Overall, six of 78 patients responded or had SD ≥ 6 months. Pertuzumab was generally well tolerated, and most adverse events were mild to moderate. Decline in left ventricular ejection fraction of ≥ 10% and/or to less than 50% was observed in eight patients, with one case of congestive heart failure in arm A. Pharmacokinetic data supported a fixed dose of pertuzumab once every 3 weeks.

Conclusion

The limited efficacy observed in this study, generally SD of relatively short duration, suggested little benefit of further investigation of single-agent pertuzumab in unselected patients with HER2-negative disease.
Positron Emission Tomography With [18F]Fluorodeoxyglucose Improves Staging and Patient Management in Patients With Head and Neck Squamous Cell Carcinoma: A Multicenter Prospective Study
Authors: Lonneux Max , Hamoir Marc , Reychler Hervé , Maingon Philippe , Duvillard Christian , Calais Gilles , Bridji Boumédiène , Digue Laurence , Toubeau Michel , Grégoire Vincent
Published: February 2010

Purpose

To address the impact of positron emission tomography with [18F]fluorodeoxyglucose (PET-FDG) on the initial staging and management of patients with head and neck squamous cell carcinoma (HNSCC).

Patients and Methods

This multicenter, prospective study included 233 patients with newly diagnosed and untreated HNSCC. TNM stage and therapeutic decision were first determined based on the conventional work-up (including physical examination, computed tomography [CT]/magnetic resonance imaging of the head and neck region, and thoracic CT) and sealed in envelope 1. Whole-body PET-FDG was then performed, and subsequent TNM stage and therapeutic decision were written in envelope 2. Changes in TNM stages and in patient management as a result of PET-FDG imaging were recorded. Clinical outcome and histopathology were used as gold standards to validate the TNM stage. Conventional and PET stages were compared using the McNemar test.

Results

Conventional and PET stage were discordant in 100 (43%) of 233 patients. PET proved to be accurate in 47 patients and inaccurate in 13 patients. TNM status was left unconfirmed in 40 patients because no therapeutic change was expected from the stage difference. Conventional + PET TNM classification (envelope 2) was significantly more accurate than conventional classification (envelope 1; P < .0001, McNemar test). PET-FDG altered the therapeutic plan in 32 (13.7%) of 233 patients.

Conclusion

Adding whole-body PET-FDG to the pretherapeutic conventional staging of HNSCC improved the TNM classification of the disease and altered the management of 13.7% of patients. These findings support the implementation of PET-FDG in the routine imaging work-up of HNSCC.
Cytokine Working Group Study of Lymphodepleting Chemotherapy, Interleukin-2, and Granulocyte-Macrophage Colony-Stimulating Factor in Patients With Metastatic Melanoma: Clinical Outcomes and Peripheral-Blood Cell Recovery
Authors: Gunturu Krishna S. , Meehan Kenneth R. , Mackenzie Todd A. , Crocenzi Todd S. , McDermott David , Usherwood Edward J. , Margolin Kim A. , Crosby Nancy A. , Atkins Michael B. , Turk Mary Jo , Ahonen Cory , Fuse Shinichiro , Clark Joseph I. , Fisher Jan L. , Noelle Randolph J. , Ernstoff Marc S.
Published: February 2010

Purpose

Recovery of lymphocyte populations after lymphocyte depletion is implicated in therapeutic immune pathways in animal models and in patients with cancer. We sought to evaluate the effects of chemotherapy-induced lymphodepletion followed by granulocyte-macrophage colony-stimulating factor (GM-CSF) and high-dose interleukin-2 (IL-2) therapy on clinical response and the recovery of lymphocyte subcompartments in patients with metastatic melanoma.

Patients and Methods

This was a two-stage phase II trial design. Patients with measurable metastatic melanoma were treated with intravenous cyclophosphamide (60 mg/kg, days 1 and 2) and fludarabine (25 mg/m2, day 3 through 7) followed by two 5-day courses of intravenous high-dose bolus IL-2 (600,000 U/kg; days 8 through 12 and 21 through 25). GM-CSF (250 μg/m2/d beginning day 8) was given until granulocyte recovery. Lymphocyte recovery profiles were determined by flow cytometric phenotyping at regular intervals, and clinical outcome was assessed by Response Evaluation Criteria in Solid Tumors (RECIST).

Results

The trial was stopped at the end of stage 1 with four of 18 objective responses noted. Twelve patients had detailed lymphocyte subcompartments evaluated. After lymphodepletion, we observed an induction of regulatory cells (CD4+ T regulatory cells; CD8+ T suppressor cells) and of T memory cells (CD8+ T central memory cells; T effector memory RA+ cells). Expansion of circulating melanoma-specific CD8+ cells was observed in one of four HLA-A2-positive patients.

Conclusion

Chemotherapy-induced lymphodepletion modulates the homeostatic repopulation of the lymphocyte compartment and influences recovering lymphocyte subpopulations. Clinical activity seems similar to standard high-dose aldesleukin alone.
Significant Effect of Polymorphisms inCYP2D6andABCC2on Clinical Outcomes of Adjuvant Tamoxifen Therapy for Breast Cancer Patients
Authors: Kiyotani Kazuma , Mushiroda Taisei , Imamura Chiyo K. , Hosono Naoya , Tsunoda Tatsuhiko , Kubo Michiaki , Tanigawara Yusuke , Flockhart David A. , Desta Zeruesenay , Skaar Todd C. , Aki Fuminori , Hirata Koichi , Takatsuka Yuichi , Okazaki Minoru , Ohsumi Shozo , Yamakawa Takashi , Sasa Mitsunori , Nakamura Yusuke , Zembutsu Hitoshi
Published: February 2010

Purpose

The clinical efficacy of tamoxifen is suspected to be influenced by the activity of drug-metabolizing enzymes and transporters involved in the formation, metabolism, and elimination of its active forms. We investigated relationships of polymorphisms in transporter genes and CYP2D6 to clinical outcome of patients receiving tamoxifen.

Patients and Methods

We studied 282 patients with hormone receptor–positive, invasive breast cancer receiving tamoxifen monotherapy, including 67 patients who have been previously reported. We investigated the effects of allelic variants of CYP2D6 and haplotype-tagging single nucleotide polymorphisms (tag-SNPs) of ABCB1, ABCC2, and ABCG2 on recurrence-free survival using the Kaplan-Meier method and Cox regression analysis. Plasma concentrations of tamoxifen metabolites were measured in 98 patients receiving tamoxifen 20 mg/d.

Results

CYP2D6 variants were significantly associated with shorter recurrence-free survival (P = .000036; hazard ratio [HR] = 9.52; 95% CI, 2.79 to 32.45 in patients with two variant alleles v patients without variant alleles). Among 51 tag-SNPs in transporter genes, a significant association was found at rs3740065 in ABCC2 (P = .00017; HR = 10.64; 95% CI, 1.44 to 78.88 in patients with AA v GG genotypes). The number of risk alleles of CYP2D6 and ABCC2 showed cumulative effects on recurrence-free survival (P = .000000055). Patients carrying four risk alleles had 45.25-fold higher risk compared with patients with ≤ one risk allele. CYP2D6 variants were associated with lower plasma levels of endoxifen and 4-hydroxytamoxifen (P = .0000043 and .00052), whereas no significant difference was found among ABCC2 genotype groups.

Conclusion

Our results suggest that polymorphisms in CYP2D6 and ABCC2 are important predictors for the prognosis of patients with breast cancer treated with tamoxifen.