bluuebunny/crossref_metadata_2025 huggingface dataset:
Information visualization on large, high-resolution displays: Issues, challenges, and opportunities
Authors: Andrews Christopher , Endert Alex , Yost Beth , North Chris
Published: August 2011

Larger, higher-resolution displays are becoming accessible to a greater number of users as display technologies decrease in cost and software for the displays improves. The additional pixels are especially useful for information visualization where scalability has typically been limited by the number of pixels available on a display. But how will visualizations for larger displays need to fundamentally differ from visualizations on desktop displays? Are the basic visualization design principles different? With this potentially new design paradigm comes questions such as whether the relative effectiveness of various graphical encodings are different on large displays, which visualizations and datasets benefit the most, and how interaction with visualizations on large, high-resolution displays will need to change. As we explore these possibilities, we shift away from the technical limitations of scalability imposed by traditional displays (e.g. number of pixels) to studying the human abilities that emerge when these limitations are removed. There is much potential for information visualizations to benefit from large, high-resolution displays, but this potential will only be realized through understanding the interaction between visualization design, perception, interaction techniques, and the display technology. In this paper we present critical design issues and outline some of the challenges and future opportunities for designing visualizations for large, high-resolution displays. We hope that these issues, challenges, and opportunities will provide guidance for future research in this area.
Addition–subtraction osteotomy with ligamentoplasty for symptomatic trapezial dysplasia with metacarpal instability
Authors: Goubau J. F. , Ackerman P. , Kerckhove D. , Van Hoonacker P. , Berghs B.
Published: August 2011

Trapeziometacarpal instability with trapezial dysplasia is a disabling condition long before the radiological changes of osteoarthritis appear. In dysplastic joints surgical soft tissue correction fails to prevent the instability, requiring a correction of the bony anatomy. We combined two techniques described in the past, an abduction osteotomy of the first metacarpal and an opening wedge osteotomy of the trapezium, to which we added a ligament reconstruction. The combination of both osteotomy techniques restores the anatomy and centres the forces acting across the joint. We have done this procedure 21 times since 2003 in 18 patients. Seventeen thumbs were reviewed prospectively with a mean follow-up of 39 (range 16–65) months. Mean QuickDASH improved by 33.9 points, the key pinch improved by 1.8 kg and the grip strength improved by 8.7 kg. The visual analogue scale for pain improved from 7.9 preoperatively to 2 postoperatively. This technique preserves the trapeziometacarpal joint, allowing other techniques to be used if painful arthritis should develop in the middle to long term.
Design and development of TT30, a novel C3d-targeted C3/C5 convertase inhibitor for treatment of human complement alternative pathway–mediated diseases
Authors: Fridkis-Hareli Masha , Storek Michael , Mazsaroff Istvan , Risitano Antonio M. , Lundberg Ante S. , Horvath Christopher J. , Holers V. Michael
Published: August 2011

To selectively modulate human complement alternative pathway (CAP) activity implicated in a wide range of acute and chronic inflammatory conditions and to provide local cell surface and tissue-based inhibition of complement-induced damage, we developed TT30, a novel therapeutic fusion protein linking the human complement receptor type 2 (CR2/CD21) C3 fragment (C3frag = iC3b, C3dg, C3d)-binding domain with the CAP inhibitory domain of human factor H (fH). TT30 efficiently blocks ex vivo CAP-dependent C3frag accumulation on activated surfaces, membrane attack complex (MAC) formation and hemolysis of RBCs in a CR2-dependent manner, and with a ∼ 150-fold potency gain over fH, without interference of C3 activation or MAC formation through the classic and lectin pathways. TT30 protects RBCs from hemolysis and remains bound and detectable for at least 24 hours. TT30 selectively inhibits CAP in cynomolgus monkeys and is bioavailable after subcutaneous injection. Using a unique combination of targeting and effector domains, TT30 controls cell surface CAP activation and has substantial potential utility for the treatment of human CAP-mediated diseases.
Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin
Authors: Rodríguez-Moreno Luis , González Víctor M , Benjak Andrej , Martí M Carmen , Puigdomènech Pere , Aranda Miguel A , Garcia-Mas Jordi
Published: August 2011

Background

The melon belongs to the Cucurbitaceae family, whose economic importance among vegetable crops is second only to Solanaceae. The melon has a small genome size (454 Mb), which makes it suitable for molecular and genetic studies. Despite similar nuclear and chloroplast genome sizes, cucurbits show great variation when their mitochondrial genomes are compared. The melon possesses the largest plant mitochondrial genome, as much as eight times larger than that of other cucurbits.

Results

The nucleotide sequences of the melon chloroplast and mitochondrial genomes were determined. The chloroplast genome (156,017 bp) included 132 genes, with 98 single-copy genes dispersed between the small (SSC) and large (LSC) single-copy regions and 17 duplicated genes in the inverted repeat regions (IRa and IRb). A comparison of the cucumber and melon chloroplast genomes showed differences in only approximately 5% of nucleotides, mainly due to short indels and SNPs. Additionally, 2.74 Mb of mitochondrial sequence, accounting for 95% of the estimated mitochondrial genome size, were assembled into five scaffolds and four additional unscaffolded contigs. An 84% of the mitochondrial genome is contained in a single scaffold. The gene-coding region accounted for 1.7% (45,926 bp) of the total sequence, including 51 protein-coding genes, 4 conserved ORFs, 3 rRNA genes and 24 tRNA genes. Despite the differences observed in the mitochondrial genome sizes of cucurbit species, Citrullus lanatus (379 kb), Cucurbita pepo (983 kb) and Cucumis melo (2,740 kb) share 120 kb of sequence, including the predicted protein-coding regions. Nevertheless, melon contained a high number of repetitive sequences and a high content of DNA of nuclear origin, which represented 42% and 47% of the total sequence, respectively.

Conclusions

Whereas the size and gene organisation of chloroplast genomes are similar among the cucurbit species, mitochondrial genomes show a wide variety of sizes, with a non-conserved structure both in gene number and organisation, as well as in the features of the noncoding DNA. The transfer of nuclear DNA to the melon mitochondrial genome and the high proportion of repetitive DNA appear to explain the size of the largest mitochondrial genome reported so far.
Multidrug-resistance proteins are weak tumor associated antigens for colorectal carcinoma
Authors: Mullins Christina S , Eisold Sven , Klar Ernst , Linnebacher Michael
Published: August 2011

Background

Multidrug resistance (MDR) is a clinically, highly relevant phenomenon. Under chemotherapy many tumors show an increasing resistance towards the applied substance(s) and to a certain extent also towards other agents. An important molecular cause of this phenomenon is an increased expression of transporter proteins. The functional relationship between high expression levels and chemotherapy resistance makes these MDR and MRP (MDR related protein) proteins to interesting therapeutic targets. We here wanted to systematically analyze, whether these proteins are tumor specific antigens which could be targeted immunologically.

Results

Using the reverse immunology approach, 30 HLA-A2.1 restricted MDR and MRP derived peptides (MDP) were selected. Stimulated T cell lines grew well and mainly contained activated CD8+ cells. Peptide specificity and HLA-A2.1 restriction were proven in IFN-γ-ELISpot analyses and in cytotoxicity tests against MDP loaded target cells for a total of twelve peptides derived from MDR-1, MDR-3, MRP-1, MRP-2, MRP-3 and MRP-5. Of note, two of these epitopes are shared between MDR-1 and MDR-3 as well as MRP-2 and MRP-3. However, comparably weak cytotoxic activities were additionally observed against HLA-A2.1+ tumor cells even after upregulation of MDR protein expression by in vitro chemotherapy.

Conclusions

Taken together, these data demonstrate that human T cells can be sensitised towards MDPs and hence, there is no absolute immunological tolerance. However, our data also hint towards rather low endogenous tumor cell processing and presentation of MDPs in the context of HLA-A2.1 molecules. Consequently, we conclude that MDR and MRP proteins must be considered as weak tumor specific antigens-at least for colorectal carcinoma. Their direct contribution to therapy-failure implies however, that it is worth to further pursue this approach.
"Glucose and ethanol-dependent transcriptional regulation of the astaxanthin biosynthesis pathway in Xanthophyllomyces dendrorhous"
Authors: Marcoleta Andrés , Niklitschek Mauricio , Wozniak Aniela , Lozano Carla , Alcaíno Jennifer , Baeza Marcelo , Cifuentes Víctor
Published: August 2011

Background

The yeast Xanthophyllomyces dendrorhous is one of the most promising and economically attractive natural sources of astaxanthin. The biosynthesis of this valuable carotenoid is a complex process for which the regulatory mechanisms remain mostly unknown. Several studies have shown a strong correlation between the carbon source present in the medium and the amount of pigments synthesized. Carotenoid production is especially low when high glucose concentrations are used in the medium, while a significant increase is observed with non-fermentable carbon sources. However, the molecular basis of this phenomenon has not been established.

Results

In this work, we showed that glucose caused transcriptional repression of the three genes involved in the synthesis of astaxanthin from geranylgeranyl pyrophosphate in X. dendrorhous, which correlates with a complete inhibition of pigment synthesis. Strikingly, this regulatory response was completely altered in mutant strains that are incapable of synthesizing astaxanthin. However, we found that addition of ethanol caused the induction of crtYB and crtS gene expression and promoted de novo synthesis of carotenoids. The induction of carotenogenesis was noticeable as early as 24 h after ethanol addition.

Conclusion

For the first time, we demonstrated that carbon source-dependent regulation of astaxanthin biosynthesis in X. dendrorhous involves changes at the transcriptional level. Such regulatory mechanism provides an explanation for the strong and early inhibitory effect of glucose on the biosynthesis of this carotenoid.
Purinergic receptor antagonists inhibit odorant-mediated CREB phosphorylation in sustentacular cells of mouse olfactory epithelium
Authors: Dooley Ruth , Mashukova Anastasia , Toetter Bastian , Hatt Hanns , Neuhaus Eva M
Published: August 2011

Background

Extracellular nucleotides have long been known to play neuromodulatory roles and to be involved in intercellular signalling. In the olfactory system, ATP is released by olfactory neurons, and exogenous ATP can evoke an increase in intracellular calcium concentration in sustentacular cells, the nonneuronal supporting cells of the olfactory epithelium. Here we investigate the hypothesis that olfactory neurons communicate with sustentacular cells via extracellular ATP and purinergic receptor activation.

Results

Here we show that exposure of mice to a mixture of odorants induced a significant increase in the levels of the transcription factor CREB phosphorylated at Ser-133 in the nuclei of both olfactory sensory neurons and sustentacular cells. This activation was dependent on adenylyl cyclase III-mediated olfactory signaling and on activation of P2Y purinergic receptors on sustentacular cells. Purinergic receptor antagonists inhibited odorant-dependent CREB phosphorylation specifically in the nuclei of the sustentacular cells.

Conclusion

Our results point to a possible role for extracellular nucleotides in mediating intercellular communication between the neurons and sustentacular cells of the olfactory epithelium in response to odorant exposure. Maintenance of extracellular ionic gradients and metabolism of noxious chemicals by sustentacular cells may therefore be regulated in an odorant-dependent manner by olfactory sensory neurons.
[Cost]effectiveness of withdrawal of fall-risk increasing drugs versus conservative treatment in older fallers: design of a multicenter randomized controlled trial (IMPROveFALL-study)
Authors: Hartholt Klaas A , Boyé Nicole DA , Van der Velde Nathalie , Van Lieshout Esther MM , Polinder Suzanne , De Vries Oscar J , Kerver Albert JH , Ziere Gijsbertus , Bruijninckx Milko MM , De Vries Mark R , Mattace-Raso Francesco US , Uitterlinden André G , Van Beeck Ed F , Lips Paul , Patka Peter , Van der Cammen Tischa JM
Published: August 2011

Background

Fall incidents represent an increasing public health problem in aging societies worldwide. A major risk factor for falls is the use of fall-risk increasing drugs. The primary aim of the study is to compare the effect of a structured medication assessment including the withdrawal of fall-risk increasing drugs on the number of new falls versus 'care as usual' in older adults presenting at the Emergency Department after a fall.

Methods/Design

A prospective, multi-center, randomized controlled trial will be conducted in hospitals in the Netherlands. Persons aged ≥65 years who visit the Emergency Department due to a fall are invited to participate in this trial. All patients receive a full geriatric assessment at the research outpatient clinic. Patients are randomized between a structured medication assessment including withdrawal of fall-risk increasing drugs and 'care as usual'. A 3-monthly falls calendar is used for assessing the number of falls, fallers and associated injuries over a one-year follow-up period. Measurements will be at three, six, nine, and twelve months and include functional outcome, healthcare consumption, socio-demographic characteristics, and clinical information. After twelve months a second visit to the research outpatient clinic will be performed, and adherence to the new medication regimen in the intervention group will be measured. The primary outcome will be the incidence of new falls. Secondary outcome measurements are possible health effects of medication withdrawal, health-related quality of life (Short Form-12 and EuroQol-5D), costs, and cost-effectiveness of the intervention. Data will be analyzed using an intention-to-treat analysis.

Discussion

The successful completion of this trial will provide evidence on the effectiveness of withdrawal of fall-risk increasing drugs in older patients as a method for falls reduction.

Trial Registration

The trial is registered in the Netherlands Trial Register (NTR1593)
Collagen induced arthritis increases secondary metastasis in MMTV-PyV MT mouse model of mammary cancer
Authors: Roy Lopamudra Das , Ghosh Sriparna , Pathangey Latha B , Tinder Teresa L , Gruber Helen E , Mukherjee Pinku
Published: August 2011

Background

Several studies have demonstrated that sites of chronic inflammation are often associated with the establishment and growth of various malignancies. A common inflammatory condition in humans is autoimmune arthritis (AA). Although AA and cancer are different diseases, many of the underlying processes that contribute to the disorders of the joints and connective tissue that characterize AA also affect cancer progression and metastasis. Systemically, AA can lead to cellular infiltration and inflammation of the lungs. Several studies have reported statistically significant risk ratios between AA and breast cancer. Despite this knowledge being available, there has been minimal research linking breast cancer, arthritis, and metastasis associated with breast cancer. Notably both diseases are extremely prevalent in older post-menopausal women.

Methods

To establish the novel link between arthritis induced inflammation and secondary metastasis associated with breast cancer, PyV MT mice that spontaneously develop mammary gland carcinoma were injected with Type II collagen (CII) to induce arthritis at 9 and 18 weeks of age for pre-metastatic and metastatic condition. The sites of secondary metastasis and the associated inflammatory microenvironment were evaluated.

Results

A significant increase in breast cancer-associated secondary metastasis to the lungs and bones was observed in the arthritic versus the non-arthritic PyV MT mice along with an increase in primary tumor burden. We report significant increases in the levels of interstitial cellular infiltrates and pro-inflammatory cytokines such as interleukin-17 (IL-17), interleukin-6 (IL-6), Pro- Matrix metallopeptidase 9 (Pro-MMP9), insulin like growth factor-II (GF-II) and macrophage colony stimulating factor (M-CSF) in the arthritic lung and bone milieu as well as in the circulation. These pro-inflammatory cytokines along with the inflammatory microenvironment may be the underlying factors facilitating tumor progression and metastasis in arthritic PyV MT mice. This was further substantiated by treatment with celecoxib, an anti-inflammatory drug + αIL-17 antibody that significantly reduced the secondary metastasis to lung and bone.

Conclusions

The data generated not only reveal the underlying mechanism of high susceptibility to bone and lung metastasis in an arthritic condition but our combination therapies may lead to treatment modalities that will be capable of reducing tumor burden, and preventing relapse and metastasis in arthritic patients with breast cancer.
A randomized, phase III trial of capecitabine plus bevacizumab (Cape-Bev) versus capecitabine plus irinotecan plus bevacizumab (CAPIRI-Bev) in first-line treatment of metastatic colorectal cancer: The AIO KRK 0110 Trial/ML22011 Trial
Authors: Giessen Clemens , von Weikersthal Ludwig Fischer , Hinke Axel , Stintzing Sebastian , Kullmann Frank , Vehling-Kaiser Ursula , Mayerle Julia , Bangerter Markus , Denzlinger Claudio , Sieber Markus , Teschendorf Christian , Freiberg-Richter Jens , Schulz Christoph , Modest Dominik Paul , Moosmann Nicolas , Aubele Philipp , Heinemann Volker
Published: August 2011

Background

Several randomized trials have indicated that combination chemotherapy applied in metastatic colorectal cancer (mCRC) does not significantly improve overall survival when compared to the sequential use of cytotoxic agents (CAIRO, MRC Focus, FFCD 2000-05). The present study investigates the question whether this statement holds true also for bevacizumab-based first-line treatment including escalation- and de-escalation strategies.

Methods/Design

The AIO KRK 0110/ML22011 trial is a two-arm, multicenter, open-label randomized phase III trial comparing the efficacy and safety of capecitabine plus bevacizumab (Cape-Bev) versus capecitabine plus irinotecan plus bevacizumab (CAPIRI-Bev) in the first-line treatment of metastatic colorectal cancer. Patients with unresectable metastatic colorectal cancer, Eastern Cooperative Oncology Group (ECOG) performance status 0-1, will be assigned in a 1:1 ratio to receive either capecitabine 1250 mg/m2 bid for 14d (d1-14) plus bevacizumab 7.5 mg/kg (d1) q3w (Arm A) or capecitabine 800 mg/m2 BID for 14d (d1-14), irinotecan 200 mg/m2 (d1) and bevacizumab 7.5 mg/kg (d1) q3w (Arm B). Patients included into this trial are required to consent to the analysis of tumour tissue and blood for translational investigations. In Arm A, treatment escalation from Cape-Bev to CAPIRI-Bev is recommended in case of progressive disease (PD). In Arm B, de-escalation from CAPIRI-Bev to Cape-Bev is possible after 6 months of treatment or in case of irinotecan-associated toxicity. Re-escalation to CAPIRI-Bev after PD is possible. The primary endpoint is time to failure of strategy (TFS). Secondary endpoints are overall response rate (ORR), overall survival, progression-free survival, safety and quality of life.

Conclusion

The AIO KRK 0110 trial is designed for patients with disseminated, but asymptomatic mCRC who are not potential candidates for surgical resection of metastasis. Two bevacizumab-based strategies are compared: one starting as single-agent chemotherapy (Cape-Bev) allowing escalation to CAPIRI-Bev and another starting with combination chemotherapy (CAPIRI-Bev) and allowing de-escalation to Cape-Bev and subsequent re-escalation if necessary.

Trial Registration

ClinicalTrials.gov Identifier NCT01249638

EudraCT-No.: 2009-013099-38
Enzyme production by filamentous fungi: analysis of the secretome of Trichoderma reesei grown on unconventional carbon source
Authors: Jun He , Kieselbach Thomas , Jönsson Leif J
Published: August 2011

Background

Spent hydrolysates from bioethanolic fermentation processes based on agricultural residues have potential as an abundant and inexpensive source of pentose sugars and acids that could serve as nutrients for industrial enzyme-producing microorganisms, especially filamentous fungi. However, the enzyme mixtures produced in such media are poorly defined. In this study, the secretome of Trichoderma reesei Rut C-30 grown either on a spent hydrolysate model medium (SHMM) or on a lactose-based standard medium (LBSM) was explored using proteomics.

Results

Our results show that both the SHMM and LBSM serve as excellent growth media for T. reesei Rut C-30. In total, 52 protein spots on 2-D gels were identified by using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and electrospray ionization liquid chromatography tandem mass spectrometry (ESI-LC MS/MS). As expected, a considerable number of the identified proteins were related to the degradation of lignocellulosic biomass. The enzyme production profiles in the two media were similar, but β-glucosidase and β-galactosidase were only produced in LBSM. The main cellobiohydrolases (Cel7A/Cel6A) and endoglucanases (Cel7B/Cel5A) were identified in both media and the cellobiohydrolases, i.e. Cel7A and Cel6A, were the most abundant cellulolytic enzymes. Moreover, both media can also serve as a potent inducer of xylanolytic enzymes. Several key enzymes involved in sugar assimilation and regulation of cellulase formation were identified, and were found to be differentially expressed in the two growth media.

Conclusions

This study not only provides a catalogue of the prevalent proteins secreted by T. reesei in the two media, but the results also suggest that production of hydrolytic enzymes using unconventional carbon sources, such as components in spent hydrolysates, deserves further attention in the future.
Effect of iron oxide and gold nanoparticles on bacterial growth leading towards biological application
Authors: Chatterjee Saptarshi , Bandyopadhyay Arghya , Sarkar Keka
Published: August 2011

Background

Nanoparticle-metal oxide and gold represents a new class of important materials that are increasingly being developed for use in research and health related activities. The biological system being extremely critical requires the fundamental understanding on the influence of inorganic nanoparticles on cellular growth and functions. Our study was aimed to find out the effect of iron oxide (Fe3O4), gold (Au) nanoparticles on cellular growth of Escherichia coli (E. coli) and also try to channelize the obtained result by functionalizing the Au nanoparticle for further biological applications.

Result

Fe3O4 and Au nanoparticles were prepared and characterized using Transmission electron microscopy (TEM) and Dynamic Light Scattering (DLS). Preliminary growth analysis data suggest that the nanoparticles of iron oxide have an inhibitory effect on E. coli in a concentration dependant manner, whereas the gold nanoparticle directly showed no such activity. However the phase contrast microscopic study clearly demonstrated that the effect of both Fe3O4 and Au nanoparticle extended up to the level of cell division which was evident as the abrupt increase in bacterial cell length. The incorporation of gold nanoparticle by bacterial cell was also observed during microscopic analysis based on which glutathione functionalized gold nanoparticle was prepared and used as a vector for plasmid DNA transport within bacterial cell.

Conclusion

Altogether the study suggests that there is metal nanoparticle-bacteria interaction at the cellular level that can be utilized for beneficial biological application but significantly it also posses potential to produce ecotoxicity, challenging the ecofriendly nature of nanoparticles.
Subtype distribution of lymphomas in Southwest China: Analysis of 6,382 cases using WHO classification in a single institution
Authors: Yang Qun-Pei , Zhang Wen-Yan , Yu Jian-Bo , Zhao Sha , Xu Huan , Wang Wei-Ya , Bi Cheng-Feng , Zuo Zhuo , Wang Xiao-Qing , Huang Juan , Dai Lin , Liu Wei-Ping
Published: August 2011

Background

The subtype distribution of lymphoid neoplasms in Southwest China was analyzed according to WHO classifications. This study aims to analyze subtype distribution of lymphomas in southwest China.

Methods

Lymphoid neoplasms diagnosed within 9 years in a single institution in Southwest China were analyzed according to the WHO classification.

Results

From January 2000 to December 2008, a total number of 6,382 patients with lymphoma were established, of which mature B-cell neoplasms accounted for 56%, mature T- and NK-cell neoplasms occupied 26%, and precursor lymphoid neoplasms and Hodgkin lymphomas were 5% and 13%, respectively. Mixed cellularity (76%) was the major subtype of classical Hodgkin lymphoma; and the bimodal age distribution was not observed. The top six subtypes of non-Hodgkin lymphoma were as follows: diffuse large B-cell lymphoma, extranodal NK/T-cell lymphoma, nasal type, extranodal marginal zone lymphoma of mucosa associated lymphoid tissue, follicular lymphoma, precursor lymphoid neoplasms, and chronic lymphocytic leukemia/small lymphocytic lymphoma. Extranodal lymphomas comprised about half of all cases, and most frequently involved Waldeyer's ring, gastrointestinal tract, sinonasal region and skin.

Conclusions

The lymphoid neoplasms of Southwest China displayed some epidemiologic features similar to those reported in literature from western and Asian countries, as well as other regions of China, whereas some subtypes showed distinct features. The high frequency of mature T/NK cell neoplasms and extranodal lymphomas, especially for extranodal NK/T-cell lymphoma, nasal type, is the most outstanding characteristic of this series.
A glycine zipper motif mediates the formation of toxic β-amyloid oligomers in vitro and in vivo
Authors: Fonte Virginia , Dostal Vishantie , Roberts Christine M , Gonzales Patrick , Lacor Pascale , Magrane Jordi , Dingwell Natalie , Fan Emily Y , Silverman Michael A , Stein Gretchen H , Link Christopher D
Published: August 2011

Background

The β-amyloid peptide (Aβ) contains a Gly-XXX-Gly-XXX-Gly motif in its C-terminal region that has been proposed to form a "glycine zipper" that drives the formation of toxic Aβ oligomers. We have tested this hypothesis by examining the toxicity of Aβ variants containing substitutions in this motif using a neuronal cell line, primary neurons, and a transgenic C. elegans model.

Results

We found that a Gly37Leu substitution dramatically reduced Aβ toxicity in all models tested, as measured by cell dysfunction, cell death, synaptic alteration, or tau phosphorylation. We also demonstrated in multiple models that Aβ Gly37Leu is actually anti-toxic, thereby supporting the hypothesis that interference with glycine zipper formation blocks assembly of toxic Aβ oligomers. To test this model rigorously, we engineered second site substitutions in Aβ predicted by the glycine zipper model to compensate for the Gly37Leu substitution and expressed these in C. elegans. We show that these second site substitutions restore in vivo Aβtoxicity, further supporting the glycine zipper model.

Conclusions

Our structure/function studies support the view that the glycine zipper motif present in the C-terminal portion of Aβ plays an important role in the formation of toxic Aβ oligomers. Compounds designed to interfere specifically with formation of the glycine zipper could have therapeutic potential.
Rare variants in the ATMgene and risk of breast cancer
Authors: Goldgar David E , Healey Sue , Dowty James G , Da Silva Leonard , Chen Xiaoqing , Spurdle Amanda B , Terry Mary Beth , Daly Mary J , Buys Saundra M , Southey Melissa C , Andrulis Irene , John Esther M ,   BCFR,   kConFab, Khanna Kum Kum , Hopper John L , Oefner Peter J , Lakhani Sunil , Chenevix-Trench Georgia
Published: August 2011

Introduction

The ataxia-telangiectasia mutated (ATM) gene (MIM ID 208900) encodes a protein kinase that plays a significant role in the activation of cellular responses to DNA double-strand breaks through subsequent phosphorylation of central players in the DNA damage-response pathway. Recent studies have confirmed that some specific variants in the ATM gene are associated with increased breast cancer (BC) risk. However, the magnitude of risk and the subset of variants that are pathogenic for breast cancer remain unresolved.

Methods

To investigate the role of ATM in BC susceptibility, we studied 76 rare sequence variants in the ATM gene in a case-control family study of 2,570 cases of breast cancer and 1,448 controls. The variants were grouped into three categories based on their likely pathogenicity, as determined by in silico analysis and analyzed by conditional logistic regression. Likely pathogenic sequence variants were genotyped in 129 family members of 27 carrier probands (15 of which carried c.7271T > G), and modified segregation analysis was used to estimate the BC penetrance associated with these rare ATM variants.

Results

In the case-control analysis, we observed an odds ratio of 2.55 and 95% confidence interval (CI, 0.54 to 12.0) for the most likely deleterious variants. In the family-based analyses, the maximum-likelihood estimate of the increased risk associated with these variants was hazard ratio (HR) = 6.88 (95% CI, 2.33 to 20.3; P = 0.00008), corresponding to a 60% cumulative risk of BC by age 80 years. Analysis of loss of heterozygosity (LOH) in 18 breast tumors from women carrying likely pathogenic rare sequence variants revealed no consistent pattern of loss of the ATM variant.

Conclusions

The risk estimates from this study suggest that women carrying the pathogenic variant, ATM c.7271T > G, or truncating mutations demonstrate a significantly increased risk of breast cancer with a penetrance that appears similar to that conferred by germline mutations in BRCA2.
Cistrome: an integrative platform for transcriptional regulation studies
Authors: Liu Tao , Ortiz Jorge A , Taing Len , Meyer Clifford A , Lee Bernett , Zhang Yong , Shin Hyunjin , Wong Swee S , Ma Jian , Lei Ying , Pape Utz J , Poidinger Michael , Chen Yiwen , Yeung Kevin , Brown Myles , Turpaz Yaron , Liu X Shirley
Published: August 2011

The increasing volume of ChIP-chip and ChIP-seq data being generated creates a challenge for standard, integrative and reproducible bioinformatics data analysis platforms. We developed a web-based application called Cistrome, based on the Galaxy open source framework. In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip- and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome feature association, gene expression analyses, and motif discovery. Cistrome is available at http://cistrome.org/ap/.
Elevated Bone Turnover Predicts for Bone Metastasis in Postmenopausal Breast Cancer: Results of NCIC CTG MA.14
Authors: Lipton Allan , Chapman Judy-Anne W. , Demers Laurence , Shepherd Lois E. , Han Lei , Wilson Carolyn F. , Pritchard Kathleen I. , Leitzel Kim E. , Ali Suhail M. , Pollak Michael
Published: August 2011

Purpose

We investigated the association of bone-only relapse with a pretreatment marker of bone resorption: serum beta C-terminal telopeptide (B-CTx) of type I collagen.

Methods

Pretreatment serum B-CTx concentrations were determined from 621 of 667 patients with primary breast cancer enrolled onto the NCIC CTG MA.14 phase III adjuvant trial of tamoxifen with or without octreotide. Recurrence-free survival (RFS) was a secondary end point; the focus here was bone-only relapse. We analyzed continuous or categorical (.71 ng/mL cut point) serum B-CTx in stepwise forward multivariate Cox regression, adjusted for trial stratification factors. We also examined B-CTx and bone relapse by pretrial chemotherapy status.

Results

At median 7.9 years follow-up, 123 of 621 patients experienced recurrence; 19 (3.1%) of 621 had bone-only recurrence, and 47 (7.5%) of 621 had bone plus other sites of recurrence. Larger pathologic tumor size (P = .001) and elevated continuous and categorical serum B-CTx were associated with shorter bone-only RFS (both P = .02) when added to a model with factors significant in the main trial analyses (hazard ratio [HR], 3.43 and 3.50, respectively; 95% CI, 1.20 to 9.77 and 1.26 to 9.75, respectively). The univariate HR for B-CTx was 2.80 (95% CI, 1.05 to 7.48; P = .03). Elevated serum B-CTx was also associated with shorter bone-only RFS (P = .02) when added to a model with factors significant in the main trial analyses. Serum B-CTx level was not associated with any other type of recurrence. Serum B-CTx was not significantly different for patients who underwent pretrial chemotherapy, compared with those who did not (P = .27), nor did pretrial chemotherapy affect bone relapse (P = .48 for bone only; P = .76 for bone with other relapse).

Conclusion

Higher pretreatment serum B-CTx was a significant predictor of shorter RFS for bone-only metastasis. Increased bone resorption creates an environment that promotes growth of breast cancer cells.
Randomized Phase II Placebo-Controlled Trial of Maintenance Therapy Using the Oral Triple Angiokinase Inhibitor BIBF 1120 After Chemotherapy for Relapsed Ovarian Cancer
Authors: Ledermann Jonathan A. , Hackshaw Allan , Kaye Stan , Jayson Gordon , Gabra Hani , McNeish Iain , Earl Helena , Perren Tim , Gore Martin , Persic Mojca , Adams Malcolm , James Lindsay , Temple Graham , Merger Michael , Rustin Gordon
Published: August 2011

Purpose

Inhibiting angiogenesis is one of the most promising avenues for new therapies for ovarian cancer. We investigated the efficacy and safety of a novel agent, BIBF 1120, a triple angiokinase inhibitor, after chemotherapy for relapsed disease.

Patients and Methods

We conducted a randomized, double-blind, controlled phase II trial in 83 patients who had just completed chemotherapy for relapsed ovarian cancer, with evidence of response, but at high risk of further early recurrence. The patients were randomly assigned to receive maintenance therapy using BIBF 1120 250 mg or placebo, twice per day, continuously for 36 weeks. End points were progression-free survival (PFS), toxicity, and overall survival.

Results

Thirty-six–week PFS rates were 16.3% and 5.0% in the BIBF 1120 and placebo groups, respectively (hazard ratio, 0.65; 95% CI, 0.42 to 1.02; P = .06). Four patients continued on BIBF 1120, including two patients for another year or more. The proportion of patients with any grade 3 or 4 adverse events was similar between the groups (34.9% for BIBF 1120 v 27.5% for placebo; P = .49; mostly grade 3). However, more patients on BIBF 1120 experienced diarrhea, nausea, or vomiting (mainly grade 1 or 2 and no grade 4). There was a higher rate of grade 3 or 4 hepatotoxicity in patients on BIBF 1120 (51.2%) compared with patients on placebo (7.5%; P < .001), but this was rarely of clinical significance, and patients continued with the trial treatment. A single-level dose reduction to 150 mg was made in 15 patients, all on active drug.

Conclusion

BIBF 1120 is well tolerated and associated with a potential improvement in PFS. The observed treatment effect is sufficient to justify further study within a large phase III trial.
Emerging Therapies to Prevent Skeletal Morbidity in Men With Prostate Cancer
Authors: Saylor Philip J. , Lee Richard J. , Smith Matthew R.
Published: August 2011

Skeletal morbidity is a prominent burden to men with advanced prostate cancer throughout the natural history of the disease. Bone metastases can cause pain and greatly elevate the risk for fractures and other structural complications. Distinct from the problem of metastases, treatment-related osteoporosis and associated fragility fractures are potential complications of androgen-deprivation therapy. Bone-targeted therapies for prostate cancer have therefore been the focus of considerable research and drug development efforts. The osteoclast is a validated therapeutic target in the management of prostate cancer. Osteoclast inhibition with zoledronic acid (a bisphosphonate) or with denosumab (a monoclonal antibody to RANK ligand) reduces risk for skeletal events in men with castration-resistant prostate cancer metastatic to bone. Osteoclast inhibition with any of several bisphosphonates improves bone mineral density, a surrogate for osteoporotic fracture risk. Denosumab and toremifene (a selective estrogen receptor modulator) have each been shown to reduce osteoporotic fracture risk among men receiving androgen-deprivation therapy. Beta-emitting radiopharmaceuticals reduce pain due to metastatic disease. Investigations involving alpha-emitting radium-223, endothelin-A receptor antagonists atrasentan and zibotentan, proto-oncogene tyrosine-protein kinase (SRC) inhibitor dasatinib, and tyrosine kinase inhibitor cabozantinib (XL184) are ongoing in clinical trials and are also discussed.
Knockdown of embryonic myosin heavy chain reveals an essential role in the morphology and function of the developing heart
Authors: Rutland Catrin Sian , Polo-Parada Luis , Ehler Elisabeth , Alibhai Aziza , Thorpe Aaran , Suren Suganthi , Emes Richard D. , Patel Bhakti , Loughna Siobhan
Published: August 2011

The expression and function of embryonic myosin heavy chain (eMYH) has not been investigated within the early developing heart. This is despite the knowledge that other structural proteins, such as alpha and beta myosin heavy chains and cardiac alpha actin, play crucial roles in atrial septal development and cardiac function. Most cases of atrial septal defects and cardiomyopathy are not associated with a known causative gene, suggesting that further analysis into candidate genes is required. Expression studies localised eMYH in the developing chick heart. eMYH knockdown was achieved using morpholinos in a temporal manner and functional studies were carried out using electrical and calcium signalling methodologies. Knockdown in the early embryo led to abnormal atrial septal development and heart enlargement. Intriguingly, action potentials of the eMYH knockdown hearts were abnormal in comparison with the alpha and beta myosin heavy chain knockdowns and controls. Although myofibrillogenesis appeared normal, in knockdown hearts the tissue integrity was affected owing to apparent focal points of myocyte loss and an increase in cell death. An expression profile of human skeletal myosin heavy chain genes suggests that human myosin heavy chain 3 is the functional homologue of the chick eMYH gene. These data provide compelling evidence that eMYH plays a crucial role in important processes in the early developing heart and, hence, is a candidate causative gene for atrial septal defects and cardiomyopathy.
Differentiated skeletal cells contribute to blastema formation during zebrafish fin regeneration
Authors: Sousa Sara , Afonso Nuno , Bensimon-Brito Anabela , Fonseca Mariana , Simões Mariana , Leon Joaquín , Roehl Henry , Cancela Maria Leonor , Jacinto António
Published: August 2011

The origin of cells that generate the blastema following appendage amputation has been a long-standing question in epimorphic regeneration studies. The blastema is thought to originate from either stem (or progenitor) cells or differentiated cells of various tissues that undergo dedifferentiation. Here, we investigate the origin of cells that contribute to the regeneration of zebrafish caudal fin skeletal elements. We provide evidence that the process of lepidotrichia (bony rays) regeneration is initiated as early as 24 hours post-amputation and that differentiated scleroblasts acquire a proliferative state, detach from the lepidotrichia surface, migrate distally, integrate into the blastema and dedifferentiate. These findings provide novel insights into the origin of cells in epimorphic appendage regeneration in zebrafish and suggest conservation of regeneration mechanisms between fish and amphibians.
Loss of MAP3K1 enhances proliferation and apoptosis during retinal development
Authors: Mongan Maureen , Wang Jingcai , Liu Hongshan , Fan Yunxia , Jin Chang , Kao Winston Y.-W. , Xia Ying
Published: August 2011

Precise coordination of progenitor cell proliferation and differentiation is essential for proper organ morphogenesis and function during mammalian development. The mitogen-activated protein kinase kinase kinase 1 (MAP3K1) has a well-established role in anterior eyelid development, as Map3k1-knockout mice have defective embryonic eyelid closure and an `eye-open at birth' (EOB) phenotype. Here, we show that MAP3K1 is highly expressed in the posterior of the developing eye and is required for retina development. The MAP3K1-deficient mice exhibit increased proliferation and apoptosis, and Müller glial cell overproduction in the developing retinas. Consequently, the retinas of these mice show localized rosette-like arrangements in the outer nuclear layer, and develop abnormal vascularization, broken down retinal pigment epithelium, photoreceptor loss and early onset of retinal degeneration. Although the retinal defect is associated with increased cyclin D1 and CDK4/6 expression, and RB phosphorylation and E2F-target gene upregulation, it is independent of the EOB phenotype and of JNK. The retinal developmental defect still occurs in knockout mice that have undergone tarsorrhaphy, but is absent in compound mutant Map3k1+/ΔKDJnk1–/– and Map3k1+/ΔKDJnk+/–Jnk2+/– mice that have EOB and reduced JNK signaling. Our results unveil a novel role for MAP3K1 in which it crosstalks with the cell cycle regulatory pathways in the prevention of retina malformation and degeneration.
MAB-10/NAB acts with LIN-29/EGR to regulate terminal differentiation and the transition from larva to adult in C. elegans
Authors: Harris David T. , Horvitz H. Robert
Published: August 2011

In Caenorhabditis elegans, a well-defined pathway of heterochronic genes ensures the proper timing of stage-specific developmental events. During the final larval stage, an upregulation of the let-7 microRNA indirectly activates the terminal differentiation factor and central regulator of the larval-to-adult transition, LIN-29, via the downregulation of the let-7 target genes lin-41 and hbl-1. Here, we identify a new heterochronic gene, mab-10, and show that mab-10 encodes a NAB (NGFI-A-binding protein) transcriptional co-factor. MAB-10 acts with LIN-29 to control the expression of genes required to regulate a subset of differentiation events during the larval-to-adult transition, and we show that the NAB-interaction domain of LIN-29 is conserved in Kruppel-family EGR (early growth response) proteins. In mammals, EGR proteins control the differentiation of multiple cell lineages, and EGR-1 acts with NAB proteins to initiate menarche by regulating the transcription of the luteinizing hormone β subunit. Genome-wide association studies of humans and various studies of mouse recently have implicated the mammalian homologs of the C. elegans heterochronic gene lin-28 in regulating cellular differentiation and the timing of menarche. Our work suggests that human homologs of multiple C. elegans heterochronic genes might act in an evolutionarily conserved pathway to promote cellular differentiation and the onset of puberty.
Molecular Aggregation State and Electrical Properties of Terthiophenes/Imogolite Nanohybrids
Authors: Yah Weng On , Irie Atsushi , Jiravanichanun Nattha , Otsuka Hideyuki , Takahara Atsushi
Published: August 2011

Organic/inorganic nanohybrid materials composed of terthiophenes and imogolite were prepared by means of specific surface interaction between a phosphonic acid group in terthiophene derivatives and aluminol groups on the surface of imogolite. The new materials were investigated by FTIR, UV–vis absorption, fluorescence spectroscopy, TEM observation, nitrogen adsorption–desorption, and I–V measurement. Addition of terthiophene of phosphonic acid derivatives into imogolite brought some changes in absorption and photoluminescence spectra, suggesting the formation of H-type aggregate on imogolite surface. The analysis of UV–vis spectra and nitrogen adsorption–desorption data provided insight into the effect of molecular structure of terthiophenes on the adsorption and aggregation behaviors on the imogolite surface. In addition, a significant enhanced current flow was observed through imogolite film when imogolite was chemisorbed by electron-withdrawing terthiophenes. In contrast, current flow decreased as the electron-donating terthiophene was chemisorbed on imogolite. A possible mechanism for such phenomena is discussed.
Effect of the Crystal Packing and LIESST Effect of a Two-Dimensional Iron(II) Spin-Crossover Complex: [FeII(HLH,Me)2](CF3SO3)2 (HLH,Me: 8-(Imidazol-4-ylmethylideneamino)-2-methylquinoline)
Authors: Hagiwara Hiroaki , Sakaguchi Osamu , Nishi Koshiro , Hashimoto Shingo , Matsumoto Naohide
Published: August 2011

A 2D iron(II) spin-crossover (SCO) complex, [FeII(HLH,Me)2](CF3SO3)2, was synthesized, where HLH,Me: 8-(imidazol-4-ylmethylideneamino)-2-methylquinoline, and its structures and magnetic properties were investigated. The complex [FeII(HLH,Me)2](CF3SO3)2 has no crystal solvent and has structure isomorphous to the complex [FeII(HLH,Me)2](ClO4)2·1.5MeCN, and shows a gradual and reversible one-step SCO between the HS (S = 2) and LS (S = 0) states at T1/2 = 215 K without hysteresis. The T1/2 value is higher than that of corresponding desolvated ClO4− compound, [FeII(HLH,Me)2](ClO4)2, about 35 K, although the spin transition is more gradual than that of ClO4− compound and the hysteresis is absent, which is observed in ClO4− compound. The crystal structures were determined at 296 (HS state) and 100 K (LS state), where the crystal system and space group showed no change between these temperatures. The structures at both temperatures have the same 2D layered structure, which is constructed of both the bifurcated NH···O− hydrogen bonds between two CF3SO3− ions and two neighboring imidazole NH groups of the [FeII(HLH,Me)2]2+ cations and the π–π interactions between the two quinolyl rings of the two adjacent cations. This network structure is the same as that of ClO4− compound. 600 nm light irradiation at 10 K induced the LIESST effect.
Complex Formation of Cyclodextrins with a Dumbbell Molecule Bearing Two Ferrocene Moieties at the Ends
Authors: Yamamoto Takaya , Oi Wataru , Hashidzume Akihito , Harada Akira
Published: August 2011

The complexation behavior of cyclodextrins (CDs) with a dumbbell molecule possessing ferrocene (Fc) moieties at both the ends (FcC10Fc) was investigated by 1H NMR, two-dimensional rotating frame Overhauser spectroscopy, circular dichroism spectroscopy, and cyclic voltammetry. α-CD includes the cyclopentadienyl rings of the Fc moiety shallowly from the wider side but not the decamethylene (C10) moiety, whereas β-CD and γ-CD include not only the Fc moiety but also the C10 moiety. These observations indicate that the Fc moiety can pass through β-CD and γ-CD cavities but not the α-CD cavity.