bluuebunny/crossref_metadata_2025 huggingface dataset:
Enhanced outgrowth of EBV-transformed chronic lymphocytic leukemia B cells mediated by coculture with macrophage feeder cells
Authors: Hwang Kwan-Ki , Chen Xi , Kozink Daniel M. , Gustilo Marietta , Marshall Dawn J. , Whitesides John F. , Liao Hua-Xin , Catera Rosa , Chu Charles C. , Yan Xiao-Jie , Luftig Micah A. , Haynes Barton F. , Chiorazzi Nicholas
Published: December 2011

B-cell chronic lymphocytic leukemia (B-CLL) is characterized by the clonal expansion of CD5-expressing B lymphocytes that produce mAbs often reactive with microbial or autoantigens. Long-term culture of B-CLL clones would permit the collection and characterization of B-CLL mAbs to study antigen specificity and of B-CLL DNA to investigate molecular mechanisms promoting the disease. However, the derivation of long-term cell lines (eg, by EBV), has not been efficient. We have improved the efficiency of EBV B-CLL transformation of CpG oligonucleotide-stimulated cells by incubating patient peripheral blood mononuclear cells in the presence of an irradiated mouse macrophage cell line, J774A.1. Using this approach, peripheral blood mononuclear cells isolated from 13 of 21 B-CLL patients were transformed as documented by IGHV-D-J sequencing. Four clones grew and retained CD5 expression in culture for 2 to 4 months. However, despite documentation of EBV infection by expression of EBNA2 and LMP1, B-CLL cells died after removal of macrophage feeder cells. Nevertheless, using electrofusion technology, we generated 6 stable hetero-hybridoma cell lines from EBV-transformed B-CLL cells, and these hetero-hybridomas produced immunoglobulin. Thus, we have established enhanced methods of B-CLL culture that will enable broader interrogation of B-CLL cells at the genetic and protein levels.
Prognostic factors in transformed mycosis fungoides: a retrospective analysis of 100 cases
Authors: Benner Marchina F. , Jansen Patty M. , Vermeer Maarten H. , Willemze Rein
Published: December 2011

Large cell transformation (LCT) in mycosis fungoides (MF) is generally associated with an aggressive clinical course and poor survival, requiring aggressive therapeutic approach. However, a proportion of cases may follow an indolent clinical course. To identify prognostic factors, we analyzed the prognostic relevance of clinical, histologic, and immunophenotypical features in a large cohort of transformed MF patients, including 75 patients with only skin lesions, 19 patients with LCT in skin and lymph nodes, and 6 patients with LCT in lymph nodes only. Multivariate analysis of the total group showed that CD30 negativity, folliculotropic MF, extent of skin lesions and extracutaneous transformation were associated with reduced disease-specific survival (DSS) and, except for CD30 negativity and folliculotropic MF, also overall survival. In a multivariate analysis of 75 patients with only skin lesions at the time of LCT, CD30 negativity, folliculotropic MF and extent of skin lesions were independent parameters for both DSS and overall survival. Using the most discriminating parameters as a prognostic index, in both study groups differences in DSS between patients with 0-1 unfavorable prognostic factor(s) and ≥ 2 unfavorable prognostic factors were statistically significant (P < .001). This prognostic index may be helpful in predicting prognosis and selecting the most appropriate treatment in patients with transformed MF.
Pathogen-origin horizontally transferred genes contribute to the evolution of Lepidopteran insects
Authors: Li Zi-Wen , Shen Yi-Hong , Xiang Zhong-Huai , Zhang Ze
Published: December 2011

Background

Horizontal gene transfer (HGT), a source of genetic variation, is generally considered to facilitate hosts' adaptability to environments. However, convincing evidence supporting the significant contribution of the transferred genes to the evolution of metazoan recipients is rare.

Results

In this study, based on sequence data accumulated to date, we used a unified method consisting of similarity search and phylogenetic analysis to detect horizontally transferred genes (HTGs) between prokaryotes and five insect species including Drosophila melanogaster, Anopheles gambiae, Bombyx mori, Tribolium castaneum and Apis mellifera. Unexpectedly, the candidate HTGs were not detected in D. melanogaster, An. gambiae and T. castaneum, and 79 genes in Ap. mellifera sieved by the same method were considered as contamination based on other information. Consequently, 14 types of 22 HTGs were detected only in the silkworm. Additionally, 13 types of the detected silkworm HTGs share homologous sequences in species of other Lepidopteran superfamilies, suggesting that the majority of these HTGs were derived from ancient transfer events before the radiation of Ditrysia clade. On the basis of phylogenetic topologies and BLAST search results, donor bacteria of these genes were inferred, respectively. At least half of the predicted donor organisms may be entomopathogenic bacteria. The predicted biochemical functions of these genes include four categories: glycosyl hydrolase family, oxidoreductase family, amino acid metabolism, and others.

Conclusions

The products of HTGs detected in this study may take part in comprehensive physiological metabolism. These genes potentially contributed to functional innovation and adaptability of Lepidopteran hosts in their ancient lineages associated with the diversification of angiosperms. Importantly, our results imply that pathogens may be advantageous to the subsistence and prosperity of hosts through effective HGT events at a large evolutionary scale.
Mining the Gene Wiki for functional genomic knowledge
Authors: Good Benjamin M , Howe Douglas G , Lin Simon M , Kibbe Warren A , Su Andrew I
Published: December 2011

Background

Ontology-based gene annotations are important tools for organizing and analyzing genome-scale biological data. Collecting these annotations is a valuable but costly endeavor. The Gene Wiki makes use of Wikipedia as a low-cost, mass-collaborative platform for assembling text-based gene annotations. The Gene Wiki is comprised of more than 10,000 review articles, each describing one human gene. The goal of this study is to define and assess a computational strategy for translating the text of Gene Wiki articles into ontology-based gene annotations. We specifically explore the generation of structured annotations using the Gene Ontology and the Human Disease Ontology.

Results

Our system produced 2,983 candidate gene annotations using the Disease Ontology and 11,022 candidate annotations using the Gene Ontology from the text of the Gene Wiki. Based on manual evaluations and comparisons to reference annotation sets, we estimate a precision of 90-93% for the Disease Ontology annotations and 48-64% for the Gene Ontology annotations. We further demonstrate that this data set can systematically improve the results from gene set enrichment analyses.

Conclusions

The Gene Wiki is a rapidly growing corpus of text focused on human gene function. Here, we demonstrate that the Gene Wiki can be a powerful resource for generating ontology-based gene annotations. These annotations can be used immediately to improve workflows for building curated gene annotation databases and knowledge-based statistical analyses.
Molecular detection and speciation of pathogenic Leptospiraspp. in blood from patients with culture-negative leptospirosis
Authors: Boonsilp Siriphan , Thaipadungpanit Janjira , Amornchai Premjit , Wuthiekanun Vanaporn , Chierakul Wirongrong , Limmathurotsakul Direk , Day Nicholas P , Peacock Sharon J
Published: December 2011

Background

Pathogenic Leptospira spp. present in the blood of patients with leptospirosis during the first week of symptoms can be detected using culture or PCR. A proportion of patients who are positive by PCR are negative by culture. Leptospira spp. are fastidious bacteria, and we hypothesized that a false-negative culture result may represent infection with a distinct bacterial subset that fail to grow in standard culture medium.

Methods

We evaluated our hypothesis during a prospective study of 418 consecutive patients presenting to a hospital in northeast Thailand with an acute febrile illness. Admission blood samples were taken for Leptospira culture and PCR. A single tube nested PCR that amplified a region of the rrs gene was developed and applied, amplicons sequenced and a phylogenetic tree reconstructed.

Results

39/418 (9%) patients were culture-positive for Leptospira spp., and 81/418 (19%) patients were culture-negative but rrs PCR-positive. The species associated with culture-positive leptospirosis (37 L. interrogans and 2 L. borgpetersenii) were comparable to those associated with culture-negative, PCR-positive leptospirosis (76 L. interrogans, 4 L. borgpetersenii, 1 unidentified, possibly new species).

Conclusion

Molecular speciation failed to identify a unique bacterial subset in patients with culture-negative, PCR-positive leptospirosis. The rate of false-negative culture was high, and we speculate that antibiotic pre-treatment is the most likely explanation for this.
Circulating levels of insulin-like growth factor-I (IGF-I) correlate with disease status in leprosy
Authors: Rodrigues Luciana Silva , Hacker Mariana Andrea , Illarramendi Ximena , Castelar Pinheiro Maria Fernanda Miguens , da Costa Nery José Augusto , Sarno Euzenir Nunes , Vidal Pessolani Maria Cristina
Published: December 2011

Background

Caused byMycobacterium leprae(ML), leprosy presents a strong immune-inflammatory component, whose status dictates both the clinical form of the disease and the occurrence of reactional episodes. Evidence has shown that, during the immune-inflammatory response to infection, the growth hormone/insulin-like growth factor-I (GH/IGF-I) plays a prominent regulatory role. However, in leprosy, little, if anything, is known about the interaction between the immune and neuroendocrine systems.

Methods

In the present retrospective study, we measured the serum levels of IGF-I and IGBP-3, its major binding protein. These measurements were taken at diagnosis in nonreactional borderline tuberculoid (NR BT), borderline lepromatous (NR BL), and lepromatous (NR LL) leprosy patients in addition to healthy controls (HC). LL and BL patients who developed reaction during the course of the disease were also included in the study. The serum levels of IGF-I, IGFBP-3 and tumor necrosis factor-alpha (TNF-α) were evaluated at diagnosis and during development of reversal (RR) or erythema nodosum leprosum (ENL) reaction by the solid phase, enzyme-labeled, chemiluminescent-immunometric method.

Results

The circulating IGF-I/IGFBP-3 levels showed significant differences according to disease status and occurrence of reactional episodes. At the time of leprosy diagnosis, significantly lower levels of circulating IGF-I/IGFBP-3 were found in NR BL and NR LL patients in contrast to NR BT patients and HCs. However, after treatment, serum IGF-I levels in BL/LL patients returned to normal. Notably, the levels of circulating IGF-I at diagnosis were low in 75% of patients who did not undergo ENL during treatment (NR LL patients) in opposition to the normal levels observed in those who suffered ENL during treatment (R LL patients). Nonetheless, during ENL episodes, the levels observed in RLL sera tended to decrease, attaining similar levels to those found in NR LL patients. Interestingly, IGF-I behaved contrary to what was observed during RR episodes in R BL patients.

Conclusions

Our data revealed important alterations in the IGF system in relation to the status of the host immune-inflammatory response to ML while at the same time pointing to the circulating IGF-I/IGFBP-3 levels as possible predictive biomarkers for ENL in LL patients at diagnosis.
Combining M-FISH and Quantum Dot technology for fast chromosomal assignment of transgenic insertions
Authors: Yusuf Mohammed , Bauer David LV , Lipinski Daniel M , MacLaren Robert E , Wade-Martins Richard , Mir Kalim U , Volpi Emanuela V
Published: December 2011

Background

Physical mapping of transgenic insertions by Fluorescence in situ Hybridization (FISH) is a reliable and cost-effective technique. Chromosomal assignment is commonly achieved either by concurrent G-banding or by a multi-color FISH approach consisting of iteratively co-hybridizing the transgenic sequence of interest with one or more chromosome-specific probes at a time, until the location of the transgenic insertion is identified.

Results

Here we report a technical development for fast chromosomal assignment of transgenic insertions at the single cell level in mouse and rat models. This comprises a simplified 'single denaturation mixed hybridization' procedure that combines multi-color karyotyping by Multiplex FISH (M-FISH), for simultaneous and unambiguous identification of all chromosomes at once, and the use of a Quantum Dot (QD) conjugate for the transgene detection.

Conclusions

Although the exploitation of the unique optical properties of QD nanocrystals, such as photo-stability and brightness, to improve FISH performance generally has been previously investigated, to our knowledge this is the first report of a purpose-designed molecular cytogenetic protocol in which the combined use of QDs and standard organic fluorophores is specifically tailored to assist gene transfer technology.
Prescription practices and availability of artemisinin monotherapy in India: where do we stand?
Authors: Mishra Neelima , Anvikar Anupkumar R , Shah Naman K , Kamal Vineet Kumar , Sharma Surya Kant , Srivastava Harish Chandra , Das Manoj Kumar , Pradhan Khageswar , Kumar Hemant , Gupta Yogendra K , Gupta Pooja , Dash Aditya Prasad , Valecha Neena
Published: December 2011

Background

The World Health Organization has urged all member states to deploy artemisinin-based combination therapy and progressively withdraw oral artemisinin monotherapies from the market due to their high recrudescence rates and to reduce the risk of drug resistance. Prescription practices by physicians and the availability of oral artemisinin monotherapies with pharmacists directly affect the pattern of their use. Thus, treatment practices for malaria, with special reference to artemisinin monotherapy prescription, in selected states of India were evaluated.

Methods

Structured, tested questionnaires were used to conduct convenience surveys of physicians and pharmacists in eleven purposively selected districts across six states in 2008. In addition, exit interviews of patients with a diagnosis of uncomplicated malaria or a prescription for an anti-malarial drug were also performed. Logistic regression was used to determine patient clinical care, and institutional factors associated with artemisinin monotherapy prescription.

Results

Five hundred and eleven physicians from 196 health facilities, 530 pharmacists, and 1, 832 patients were interviewed. Artemisinin monotherapy was available in 72.6% of pharmacies and was prescribed by physicians for uncomplicated malaria in all study states. Exit interviews among patients confirmed the high rate of use of artemisinin monotherapy with 14.8% receiving such a prescription. Case management, i.e. method of diagnosis and overall treatment, varied by state and public or private sector. Treatment in the private sector (OR 8.0, 95%CI: 3.8, 17) was the strongest predictor of artemisinin monotherapy prescription when accounting for other factors. Use of the combination therapy recommended by the national drug policy, artesunate + sulphadoxine-pyrimethamine, was minimal (4.9%), with the exception of one state.

Conclusions

Artemisinin monotherapy use was widespread across India in 2008. The accessible sale of oral artemisinin monotherapy in retail market and an inadequate supply of recommended drugs in the public sector health facilities promoted its prescription. This study resulted in notifications to all state drug controllers in India to withdraw the oral artemisinin formulations from the market. In 2010, artesunate + sulphadoxine-pyrimethamine became the universal first-line treatment for confirmed Plasmodium falciparum malaria and was deployed at full scale.
Assessing healthcare providers' knowledge and practices relating to insecticide-treated nets and the prevention of malaria in Ghana, Laos, Senegal and Tanzania
Authors: Hoffman Steven J , Guindon G Emmanuel , Lavis John N , Ndossi Godwin D , Osei Eric JA , Sidibe Mintou Fall , Boupha Boungnong ,   the Research to Policy & Practice Study Team
Published: December 2011

Background

Research evidence is not always being disseminated to healthcare providers who need it to inform their clinical practice. This can result in the provision of ineffective services and an inefficient use of resources, the implications of which might be felt particularly acutely in low- and middle-income countries. Malaria prevention is a particularly compelling domain to study evidence/practice gaps given the proven efficacy, cost-effectiveness and disappointing utilization of insecticide-treated nets (ITNs).

Methods

This study compares what is known about ITNs to the related knowledge and practices of healthcare providers in four low- and middle-income countries. A new questionnaire was developed, pilot tested, translated and administered to 497 healthcare providers in Ghana (140), Laos (136), Senegal (100) and Tanzania (121). Ten questions tested participants' knowledge and clinical practice related to malaria prevention. Additional questions addressed their individual characteristics, working context and research-related activities. Ordinal logistic regressions with knowledge and practices as the dependent variable were conducted in addition to descriptive statistics.

Results

The survey achieved a 75% response rate (372/497) across Ghana (107/140), Laos (136/136), Senegal (51/100) and Tanzania (78/121). Few participating healthcare providers correctly answered all five knowledge questions about ITNs (13%) or self-reported performing all five clinical practices according to established evidence (2%). Statistically significant factors associated with higher knowledge within each country included: 1) training in acquiring systematic reviews through the Cochrane Library (OR 2.48, 95% CI 1.30-4.73); and 2) ability to read and write English well or very well (OR 1.69, 95% CI 1.05-2.70). Statistically significant factors associated with better clinical practices within each country include: 1) reading scientific journals from their own country (OR 1.67, 95% CI 1.10-2.54); 2) working with researchers to improve their clinical practice or quality of working life (OR 1.44, 95% CI 1.04-1.98); 3) training on malaria prevention since their last degree (OR 1.68, 95% CI 1.17-2.39); and 4) easy access to the internet (OR 1.52, 95% CI 1.08-2.14).

Conclusions

Improving healthcare providers' knowledge and practices is an untapped opportunity for expanding ITN utilization and preventing malaria. This study points to several strategies that may help bridge the gap between what is known from research evidence and the knowledge and practices of healthcare providers. Training on acquiring systematic reviews and facilitating internet access may be particularly helpful.
Expression of circadian clock gene human Period2 (hPer2) in human colorectal carcinoma
Authors: Wang Yaping , Hua Luchun , Lu Chao , Chen Zongyou
Published: December 2011

Background

Recent studies have shown that disruption of circadian rhythms is one of the tumor promoting factors which contribute to mammalian cancer development and progression, but very little is known about the molecular changes of circadian genes in colorectal carcinoma (CRC). Thus, in this study, changes in the expression of human Period2 (hPer2), one of the key circadian clock regulators, in CRC and its correlation with prognosis were investigated.

Methods

Immunohistochemical (IHC) staining and real-time PCR for hPer2 were performed for 38 CRC cases.

Results

IHC analysis detected positive staining for hPer2 in 81.6% (31/38) of CRC tissues and 97.4% (37/38) of surrounding non-cancerous tissues (P < 0.05). Most colorectal cells in non-cancerous tissues were homogeneously stained. In contrast, in the paired cancerous tissues, a heterogeneous pattern was found with a significant portion of cancer cells displaying negative or weak hPer2 staining. In over 60% cases (24/38), the staining for hPer2 was much stronger in non-cancerous cells than in the paired cancerous cells. Well-differentiated cancer cells are more likely to maintain hPer2 expression than poorly-differentiated ones. Furthermore, associations of decreased hPer2 levels with patients' age, histological grade, TNM stage and expression of nucleus proliferation related antigen: Ki67 were also detected (P < 0.05). Expression of hPer2 did not correlate with that of either p53 or C-erB-2. Similar to hPer2 protein expression, quantitative RT-PCR for hPer2 also showed decreased mRNA expression in CRC.

Conclusion

These results suggest a role for hPer2 in normal colorectal cell function and the potential deregulation of hPer2 expression in the development, invasion, and metastasis of CRC.
Structural evolution of GeMn/Ge superlattices grown by molecular beam epitaxy under different growth conditions
Authors: Wang Ya , Liao Zhiming , Xu Hongyi , Xiu Faxian , Kou Xufeng , Wang Yong , Wang Kang L , Drennan John , Zou Jin
Published: December 2011

GeMn/Ge epitaxial 'superlattices' grown by molecular beam epitaxy with different growth conditions have been systematically investigated by transmission electron microscopy. It is revealed that periodic arrays of GeMn nanodots can be formed on Ge and GaAs substrates at low temperature (approximately 70°C) due to the matched lattice constants of Ge (5.656 Å) and GaAs (5.653 Å), while a periodic Ge/GeMn superlattice grown on Si showed disordered GeMn nanodots with a large amount of stacking faults, which can be explained by the fact that Ge and Si have a large lattice mismatch. Moreover, by varying growth conditions, the GeMn/Ge superlattices can be manipulated from having disordered GeMn nanodots to ordered coherent nanodots and then to ordered nanocolumns.

PACS: 75.50.Pp; 61.72.-y; 66.30.Pa; 68.37.L.
Selection of recombinant MVA by rescue of the essential D4R gene
Authors: Ricci Patricia S , Schäfer Birgit , Kreil Thomas R , Falkner Falko G , Holzer Georg W
Published: December 2011

Modified vaccinia virus Ankara (MVA) has become a promising vaccine vector due to its immunogenicity and its proven safety in humans. As a general approach for stringent and rapid selection of recombinant MVA, we assessed marker rescue of the essential viral D4R gene in an engineered deletion mutant that is fully replication defective in wild-type cells. Recombinant, replicating virus was obtained by re-introduction of the deleted viral gene as a dominant selection marker into the deletion mutant.
Construction and characterization of an infectious clone of coxsackievirus A16
Authors: Liu Fei , Liu Qingwei , Cai Yicun , Leng Qibin , Huang Zhong
Published: December 2011

Background

Coxsackievirus A16 (CVA16) is a member of theEnterovirusgenus of thePicornaviridaefamily and it is a major etiological agent of hand, foot, and mouth disease (HFMD), which is a common illness affecting children. CVA16 possesses a single-stranded positive-sense RNA genome containing approximately 7410 bases. Current understanding of the replication, structure and virulence determinants of CVA16 is very limited, partly due to difficulties in directly manipulating its RNA genome.

Results

Two overlapping cDNA fragments were amplified by RT-PCR from the genome of the shzh05-1 strain of CVA16, encompassing the nucleotide regions 1-4392 and 4381-7410, respectively. These two fragments were then joinedviaa nativeXbaI site to yield a full-length cDNA. A T7 promoter and poly(A) tail were added to the 5' and 3' ends, respectively, forming a full CVA16 cDNA clone. Transfection of RD cellsin vitrowith RNA transcribed directly from the cDNA clone allowed the recovery of infectious virus in culture. The CVA16 virus recovered from these cultures was functionally and genetically identical to its parent strain.

Conclusions

We report the first construction and characterization of an infectious cDNA clone of CVA16. The availability of this infectious clone will greatly enhance future virological investigations and vaccine development for CVA16.
Efficacy of vinblastine in central nervous system Langerhans cell histiocytosis: a nationwide retrospective study
Authors: Ng Wing Tin Sophie , Martin-Duverneuil Nadine , Idbaih Ahmed , Garel Catherine , Ribeiro Maria , Parker Judith Landman , Defachelles Anne-Sophie , Lambilliotte Anne , Barkaoui Mohamed , Munzer Martine , Gardembas Martine , Sibilia Jean , Lutz Patrick , Fior Renato , Polak Michel , Robert Alain , Aumaitre Olivier , Plantaz Dominique , Armari-Alla Corinne , Genereau Thierry , Berard Perrine Marec , Talom Ghislain Nokam , Pennaforte Jean-Loup , Le Pointe Hubert Ducou , Barthez Marie-Anne , Couillault Gérard , Haroche Julien , Mokhtari Karima , Donadieu Jean , Hoang-Xuan Khê ,   the French LCH study group
Published: December 2011

Background

Vinblastine (VBL) is the standard treatment for systemic Langerhans cell histiocytosis (LCH), but little is known about its efficacy in central nervous system (CNS) mass lesions.

Methods

A retrospective chart review was conducted. Twenty patients from the French LCH Study Group register met the inclusion criteria. In brief, they had CNS mass lesions, had been treated with VBL, and were evaluable for radiologic response.

Results

The median age at diagnosis of LCH was 11.5 years (range: 1-50). Intravenous VBL 6 mg/m2 was given in a 6-week induction treatment, followed by a maintenance treatment. The median total duration was 12 months (range: 3-30). Eleven patients received steroids concomitantly. Fifteen patients achieved an objective response; five had a complete response (CR: 25%), ten had a partial response (PR: 50%), four had stable disease (SD: 20%) and one patient progressed (PD: 5%). Of interest, four out of the six patients who received VBL without concomitant steroids achieved an objective response. With a median follow-up of 6.8 years, the 5-year event-free and overall survival was 61% and 84%, respectively. VBL was well-tolerated and there were no patient withdrawals due to adverse events.

Conclusion

VBL, with or without steroids, could potentially be a useful therapeutic option in LCH with CNS mass lesions, especially for those with inoperable lesions or multiple lesions. Prospective clinical trials are warranted for the evaluation of VBL in this indication.
Analysis of hypermethylation and expression profiles of APC and ATM genes in patients with oral squamous cell carcinoma
Authors: Rigi-Ladiz Mohammad Ayub , Kordi-Tamandani Dor Mohammad , Torkamanzehi Adam
Published: December 2011

Background

Adenomatous polyposis coli (APC) and Ataxia-telangiectasia-mutated (ATM) gene products have an important role in cell cycle control and maintenance of genomic stability. Our aim was to analyze ATM and APC methylation and its relationship with oral squamous cell carcinoma (OSCC).

Materials and methods

Eighty-four OSCC tissues that have been fixed in paraffin along with 57 control oral samples have been used for analyzing promoter methylation of ATM and APC genes by Methylation Specific Polymerase Chain Reaction (MS-PCR). In addition, 10 cases of OSCC and the same of matched controls were examined for estimating expression of the above mentioned genes using Real-Time Reverse-Transcription PCR.

Results

Observed promoter methylations were 71.42% and 87.71% for the APC gene and 88.09% and 77.19% for the ATM gene in cases and controls, respectively. Analysis of these data showed that promoter methylation at APC was significantly different in cases compared to healthy controls (p = 0.01), but no difference was detected for the ATM gene. Furthermore, the mRNA expression levels did not differ statistically between cases and controls for both ATM (cases = 9, controls = 10) and APC (cases = 11, controls = 10) genes.

Conclusions

Our results, for the first time, provide methylation profiles of ATM and APC genes in a sample of patients with OSCC in a southeast Iranian population. The present data support related evidence of APC methylation effect on OSCC development.
Immortalized pathological human myoblasts: towards a universal tool for the study of neuromuscular disorders
Authors: Mamchaoui Kamel , Trollet Capucine , Bigot Anne , Negroni Elisa , Chaouch Soraya , Wolff Annie , Kandalla Prashanth K , Marie Solenne , Di Santo James , St Guily Jean Lacau , Muntoni Francesco , Kim Jihee , Philippi Susanne , Spuler Simone , Levy Nicolas , Blumen Sergiu C , Voit Thomas , Wright Woodring E , Aamiri Ahmed , Butler-Browne Gillian , Mouly Vincent
Published: December 2011

Background

Investigations into both the pathophysiology and therapeutic targets in muscle dystrophies have been hampered by the limited proliferative capacity of human myoblasts. Isolation of reliable and stable immortalized cell lines from patient biopsies is a powerful tool for investigating pathological mechanisms, including those associated with muscle aging, and for developing innovative gene-based, cell-based or pharmacological biotherapies.

Methods

Using transduction with both telomerase-expressing and cyclin-dependent kinase 4-expressing vectors, we were able to generate a battery of immortalized human muscle stem-cell lines from patients with various neuromuscular disorders.

Results

The immortalized human cell lines from patients with Duchenne muscular dystrophy, facioscapulohumeral muscular dystrophy, oculopharyngeal muscular dystrophy, congenital muscular dystrophy, and limb-girdle muscular dystrophy type 2B had greatly increased proliferative capacity, and maintained their potential to differentiate both in vitro and in vivo after transplantation into regenerating muscle of immunodeficient mice.

Conclusions

Dystrophic cellular models are required as a supplement to animal models to assess cellular mechanisms, such as signaling defects, or to perform high-throughput screening for therapeutic molecules. These investigations have been conducted for many years on cells derived from animals, and would greatly benefit from having human cell models with prolonged proliferative capacity. Furthermore, the possibility to assess in vivo the regenerative capacity of these cells extends their potential use. The innovative cellular tools derived from several different neuromuscular diseases as described in this report will allow investigation of the pathophysiology of these disorders and assessment of new therapeutic strategies.
Searching for mechanisms that matter in early septic acute kidney injury: an experimental study
Authors: Benes Jan , Chvojka Jiri , Sykora Roman , Radej Jaroslav , Krouzecky Ales , Novak Ivan , Matejovic Martin
Published: December 2011

Introduction

In almost half of all sepsis patients, acute kidney injury (AKI) develops. However, the pathobiologic differences between sepsis patients with and without AKI are only poorly understood. We used a unique opportunity to examine dynamic inflammatory, renal hemodynamic, and microvascular changes in two clinically relevant large-animal models of sepsis. Our aim was to assess variability in renal responses to sepsis and to identify both hemodynamic and nonhemodynamic mechanisms discriminating individuals with AKI from those in whom AKI did not develop.

Methods

Thirty-six pigs were anesthetized, mechanically ventilated, and instrumented. After a recovery period, progressive sepsis was induced either by peritonitis (n = 13) or by continuous intravenous infusion of live Pseudomonas aeruginosa (n = 15). Eight sham operated-on animals served as time-matched controls. All animals received standard intensive care unit (ICU) care, including goal-directed hemodynamic management. Before, and at 12, 18, and 22 hours of sepsis, systemic and renal (ultrasound flow probe) hemodynamics, renal cortex microcirculation (laser Doppler), inflammation (interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), oxidative stress (thiobarbituric acid reactive species (TBARS), nitrite/nitrate concentrations (NOx), and renal oxygen kinetics and energy metabolism were measured.

Results

In 14 (50%) pigs, AKI developed (62% in peritonitis, 40% in bacteria infusion model). Fecal peritonitis resulted in hyperdynamic circulation, whereas continuous bacteria infusion was associated with normodynamic hemodynamics. Despite insults of equal magnitude, comparable systemic hemodynamic response, and uniform supportive treatment, only those pigs with AKI exhibited a progressive increase in renal vascular resistance. This intrarenal vasoconstriction occurred predominantly in the live-bacteria infusion model. In contrast to AKI-free animals, the development of septic AKI was preceded by early and remarkable inflammatory response (TNF-α, IL-6) and oxidative stress (TBARS).

Conclusions

The observed variability in susceptibility to septic AKI in our models replicates that of human disease. Early abnormal host response accompanied by subsequent uncoupling between systemic and renal vascular resistance appear to be major determinants in the early phase of porcine septic AKI. Nonuniform and model-related renal hemodynamic responses that are unpredictable from systemic changes should be taken into consideration when evaluating hemodynamic therapeutic interventions in septic AKI.
Induced pluripotent stem cells from GMP-grade hematopoietic progenitor cells and mononuclear myeloid cells
Authors: Ohmine Seiga , Dietz Allan B , Deeds Michael C , Hartjes Katherine A , Miller David R , Thatava Tayaramma , Sakuma Toshie , Kudva Yogish C , Ikeda Yasuhiro
Published: December 2011

Introduction

The induced pluripotent stem cell (iPSC) technology allows generation of patient-specific pluripotent stem cells, thereby providing a novel cell-therapy platform for severe degenerative diseases. One of the key issues for clinical-grade iPSC derivation is the accessibility of donor cells used for reprogramming.

Methods

We examined the feasibility of reprogramming mobilized GMP-grade hematopoietic progenitor cells (HPCs) and peripheral blood mononuclear cells (PBMCs) and tested the pluripotency of derived iPS clones.

Results

Ectopic expression of OCT4, SOX2, KLF4, and c-MYC in HPCs and PBMCs resulted in rapid iPSC derivation. Long-term time-lapse imaging revealed efficient iPSC growth under serum- and feeder-free conditions with frequent mitotic events. HPC- and PBMC-derived iPS cells expressed pluripotency-associated markers, including SSEA-4, TRA-1-60, and NANOG. The global gene-expression profiles demonstrated the induction of endogenous pluripotent genes, such as LIN28, TERT, DPPA4, and PODXL, in derived iPSCs. iPSC clones from blood and other cell sources showed similar ultrastructural morphologies and genome-wide gene-expression profiles. On spontaneous and guided differentiation, HPC- and PBMC-derived iPSCs were differentiated into cells of three germ layers, including insulin-producing cells through endodermal lineage, verifying the pluripotency of the blood-derived iPSC clones.

Conclusions

Because the use of blood cells allows minimally invasive tissue procurement under GMP conditions and rapid cellular reprogramming, mobilized HPCs and unmobilized PBMCs would be ideal somatic cell sources for clinical-grade iPSC derivation, especially from diabetes patients complicated by slow-healing wounds.
Consistency in the Analysis and Reporting of Primary End Points in Oncology Randomized Controlled Trials From Registration to Publication: A Systematic Review
Authors: You Benoit , Gan Hui K. , Pond Gregory , Chen Eric X.
Published: December 2011

Purpose

To improve the quality of reporting of randomized clinical trials (RCTs), international registries for RCTs and guidelines for primary end point (PEP) analysis were established. The objectives of this systematic review were to evaluate concordance of PEP between publication and the corresponding registry and to assess intrapublication consistency in PEP reporting.

Methods

All adult oncology RCTs in solid tumors published in 10 journals between 2005 and 2009 were reviewed. Registration information was extracted from international trial registries.

Results

A total 366 RCTs were identified. Trial registration was found for 215 trials, and the rate increased from 43% in 2005 to 82% in 2009 (P < .001). There were 134 RCTs with clearly defined PEPs in registry, with the rate increasing from 15% to 67% (P < .001). PEP differed between registration and final publication in 14% trials with clearly defined PEPs. Reporting issues in methodology were found in 15% of RCTs, mainly because of inadequate reporting of PEP or sample size calculation. Problems with the interpretation of trial results were found in 22% publications, mostly resulting from negative superiority studies being interpreted as showing equivalence.

Conclusion

The rates of trial registration and of trials with clearly defined PEPs have improved over time; however, 14% of these trials reported a different PEP in the final publication. Intrapublication inconsistencies in PEP reporting are frequent. Our findings highlight the need for investigators, peer reviewers, and readers to exercise increased awareness and scrutiny of reporting outcomes of oncology RCTs.
The Consequences of Radical Reform: The French Revolution
Authors: Acemoglu Daron , Cantoni Davide , Johnson Simon , Robinson James A
Published: December 2011

The French Revolution had a momentous impact on neighboring countries. It removed the legal and economic barriers protecting oligarchies, established the principle of equality before the law, and prepared economies for the new industrial opportunities of the second half of the 19th century. We present within-Germany evidence on the long-run implications of these institutional reforms. Occupied areas appear to have experienced more rapid urbanization growth, especially after 1850. A two-stage least squares strategy provides evidence consistent with the hypothesis that the reforms instigated by the French had a positive impact on growth. JEL: N13, N43, O47
US International Equity Investment and Past and Prospective Returns
Authors: Curcuru Stephanie E , Thomas Charles P , Warnock Francis E , Wongswan Jon
Published: December 2011

Counter to extant stylized facts, using newly available data on country allocations in US investors' foreign equity portfolios we find that (i) US investors do not exhibit returns-chasing behavior, but, consistent with partial portfolio rebalancing, tend to sell past winners; and (ii) US investors increase portfolio weights on a country's equity market just prior to its strong performance, behavior inconsistent with an informational disadvantage. Over the past two decades, US investors' foreign equity portfolios outperformed a value-weighted foreign benchmark by 160 basis points per year. JEL: C58, G11, G15
Structural Workshop Paper—Descriptive, Structural, and Experimental Empirical Methods in Marketing Research
Authors: Reiss Peter C.
Published: December 2011

What can be learned about marketing phenomena from descriptive, structural, and experimental empirical models? Is structure implicit in a descriptive empirical model? What is a “reduced-form model?” What is a natural experiment, and what can one infer from a study that uses experimental data? Having clear answers to these questions can improve empirical dialog. This paper defines descriptive, structural, and experimental empirical work, provides examples, discusses their similarities and differences, and comments on their strengths and weaknesses. An important theme is that the marketing question and the data available should determine the methods used, and not the other way around. Most of the examples discussed reference linear models that are widely employed in the marketing literature. Many of the points, however, extend to the development and interpretation of cutting-edge nonlinear, dynamic, or nonparametric models used in marketing.
Cloud-Computing-Anwendungen in Bibliotheken
Authors: Tang Jingnan , Shen Guoqin
Published: December 2011

In diesem Beitrag wird zunächst ein kurzer Überblick über Cloud Computing und seine Anwendungen in Bibliotheken vorgestellt. Es wird gezeigt, dass Cloud Computing die Auslagerung von Anwendungen, Daten und Rechenvorgängen in das Internet bedeutet. Mit der Cloud-Computing-Technologie kann man im Internet Cloud-Computing-Bibliotheken errichten. Anschließend werden Auswirkungen des Cloud Computings auf die Bibliotheken aufgeführt. Es wird darauf hingewiesen, dass Cloud-Computing-Anwendungen in den Bibliotheken viele Veränderungen und zugleich viele dringend zu lösende Probleme auslösen können. Weiterhin wird der Entwicklungsstand des Cloud Computings dargestellt. Im letzten Abschnitt werden zudem zwei Punkte erwähnt, die man bei der Anwendung des Cloud-Computing-Bibliotheksmodells berücksichtigen soll, und ein Ausblick auf die zukünftige Situation der Cloud-Computing-Anwendungen in Bibliotheken geboten.
A novel role for reciprocal CD30-CD30L signaling in the cross-talk between natural killer and dendritic cells
Authors: Simhadri Vijaya Lakshmi , Hansen Hinrich P. , Simhadri Venkateswara R. , Reiners Katrin S. , Bessler Martina , Engert Andreas , von Strandmann Elke Pogge
Published: December 2011

The interplay between dendritic cells (DCs) and natural killer (NK) cells directs adaptive immune responses. The molecular basis of the cross-talk is largely undefined. Here, we provide evidence for a contribution of CD30 (TNFRSF8) and its ligand CD30L (TNFSF8) expressed on NK cells and DCs, respectively. We demonstrate that CD30-mediated engagement of CD30L induced cytokine secretion from immature DCs via the mitogen-activated protein kinase pathway. Moreover, CD30L engagement promoted differentiation to mature DCs. On the contrary, the engagement of CD30 on NK cells resulted in an NF-κB-dependent release of TNF-α/IFN-γ. These data uncover a novel and unexpected role for CD30/CD30L that contributes to proinflammatory immune responses.
From head to toe of the norovirus 3C-like protease
Authors: Someya Yuichi
Published: December 2011

Noroviruses are major causative agents of viral gastroenteritis in humans. Currently, there are no therapeutic medications to treat noroviral infections, nor are there effective vaccines against these pathogens. The viral 3C-like protease is solely responsible for the maturation of viral protein components. The crystal structures of the proteases were resolved at high atomic resolution. The protease was also explored by means of mutagenesis. These studies revealed the active-site amino acid residues and factors determining and affecting substrate specificity as well as the principle of architecting the protease molecule. The possible mechanism of proteolysis was also suggested. Consideration of the data accumulated thus far will be useful for development of therapeutic drugs targeting the viral protease.
Regenerating proteins and their expression, regulation, and signaling
Authors: Parikh Abhirath , Stephan Anne-Fleur , Tzanakakis Emmanuel S.
Published: December 2011

The regenerating (Reg) protein family comprises C-type lectin-like proteins discovered independently during pancreatitis and pancreatic islet regeneration. However, an increasing number of studies provide evidence of participation of Reg proteins in the proliferation and differentiation of diverse cell types. Moreover, Reg family members are associated with various pathologies, including diabetes and forms of gastrointestinal cancer. These findings have led to the emergence of key roles for Reg proteins as anti-inflammatory, antiapoptotic, and mitogenic agents in multiple physiologic and disease contexts. Yet, there are significant gaps in our knowledge regarding the regulation of expression of different Reg genes. In addition, the pathways relaying Reg-triggered signals, their targets, and potential cross-talk with other cascades are still largely unknown. In this review, the expression patterns of different Reg members in the pancreas and extrapancreatic tissues are described. Moreover, factors known to modulate Reg levels in different cell types are discussed. Several signaling pathways, which have been implicated in conferring the effects of Reg ligands to date, are also delineated. Further efforts are necessary for elucidating the biological processes underlying the action of Reg proteins and their involvement in various maladies. Better understanding of the function of Reg genes and proteins will be beneficial in the design and development of therapies utilizing or targeting this protein group.
Life history ofChaetomorpha valida(Cladophoraceae, Chlorophyta) in culture
Authors: Deng Yunyan , Tang Xiaorong , Huang Bingxin , Ding Lanping
Published: December 2011

The marine green algaChaetomorpha valida(Cladophoraceae, Cladophorales) has been found for several years fouling aquaculture ponds along coasts of the cities Dalian and Rongcheng, P.R. China. Using unialgal culture and microscopic observation, we completed the life history ofC. validaand discovered fragment regeneration for the first time. The life history comprised an isomorphic alternation between gametophytes and sporophytes typical of most other members of the Cladophorales. Male and female gametes fused into zygotes then developed into sporophytes. Quadriflagellate zoospores produced by mature sprophytes gave rise to new gametophytes that yielded biflagellate gametes. Germination of zygotes and zoospores was of the bipolar erect type, as observed in some other species ofChaetomorpha. Fragment regeneration occurred in both gametophytes and sporophytes via production of polar algal fragments, which directly developed into entire filaments to give a self-replicating gene­ration. The results improved understanding of the seasonal abundances ofC. validain spring and summer.
Serum mesothelin and megakaryocyte potentiating factor in pancreatic and biliary cancers
Authors: Sharon Elad , Zhang Jingli , Hollevoet Kevin , Steinberg Seth M. , Pastan Ira , Onda Masanori , Gaedcke Jochen , Ghadimi B. Michael , Ried Thomas , Hassan Raffit
Published: December 2011

Tumor mesothelin overexpression is present in different malignancies, including the majority of patients with pancreatic or biliary cancers. The objective of this study was to evaluate the use of shed serum mesothelin and megakaryocyte potentiating factor (MPF) concentrations as biomarkers for these cancers.

A total of 151 individuals, divided into five groups, were retrospectively analyzed: healthy donors (n=15), patients with benign non-pancreatic conditions (n=52), benign pancreatic conditions (n=33), biliary carcinoma (n=9), and pancreatic ductal adenocarcinoma (n=42). Mesothelin and MPF concentrations were measured in serum with the Mesomark™ and Human MPF ELISA, respectively.

Mesothelin and MPF concentrations did not significantly differ among the five individual participant groups (p=0.34, p=0.33, respectively), nor did any other combination and pair-wise comparison of the participant groups demonstrated a significant difference in biomarker concentrations. In patients with pancreatic cancer, mesothelin or MPF concentrations were not associated with tumor stage (p=0.87, p=0.48, respectively) or differentiation grade (p=0.73, p=0.52, respectively).

Serum mesothelin and MPF concentrations, measured with standard available ELISAs, were not specific for benign or pancreatic disease. Both biomarkers were not elevated in patients with pancreatic or biliary cancers, and consequently do not appear to be useful biomarkers for these malignancies.
One-pot three-component solvent-free synthesis of 1-[(1,3-thiazol-2-ylamino)methyl]-2-naphthols
Authors: Li Zheng , Mao Xuerong
Published: December 2011

A series of 1-[(1,3-thiazol-2-ylamino)methyl]-2-naphthols were synthesized via one-pot three-component Mannich reaction of 2-aminothiazoles, aldehydes and 2-naphthol under solvent-free conditions. This protocol has advantages of no use of volatile organic solvents and hazardous catalysts. Work-up procedure is simple and yields are high.
Synthesis of novel chromeno[4′,3′-b]pyrano[6,5-b]quinoline derivatives
Authors: Motamedi Radineh
Published: December 2011

New coumarin heteroanalogs were synthesized by condensation of 2-amino-4-aryl-3-cyano-5-oxo-4H,5H-pyrano-[3,2-c]chromenes and 1,3-cyclohexanedione in 35–78% yield.