bluuebunny/crossref_metadata_2025 huggingface dataset:
A consistency-based consensus algorithm for de novo and reference-guided sequence assembly of short reads
Authors: Rausch Tobias , Koren Sergey , Denisov Gennady , Weese David , Emde Anne-Katrin , Döring Andreas , Reinert Knut
Published: March 2009

Motivation: Novel high-throughput sequencing technologies pose new algorithmic challenges in handling massive amounts of short-read, high-coverage data. A robust and versatile consensus tool is of particular interest for such data since a sound multi-read alignment is a prerequisite for variation analyses, accurate genome assemblies and insert sequencing.

Results: A multi-read alignment algorithm for de novo or reference-guided genome assembly is presented. The program identifies segments shared by multiple reads and then aligns these segments using a consistency-enhanced alignment graph. On real de novo sequencing data obtained from the newly established NCBI Short Read Archive, the program performs similarly in quality to other comparable programs. On more challenging simulated datasets for insert sequencing and variation analyses, our program outperforms the other tools.

Availability: The consensus program can be downloaded from http://www.seqan.de/projects/consensus.html. It can be used stand-alone or in conjunction with the Celera Assembler. Both application scenarios as well as the usage of the tool are described in the documentation.

Contact:  rausch@inf.fu-berlin.de
Changes in the catch composition of artisanal fisheries attributable to dolphin depredation in a Mediterranean marine reserve
Authors: Rocklin Delphine , Santoni Marie-Catherine , Culioli Jean-Michel , Tomasini Jean-Antoine , Pelletier Dominique , Mouillot David
Published: March 2009

Rocklin, D., Santoni, M-C., Culioli, J-M., Tomasini, J-A., Pelletier, D., and Mouillot, D. 2009. Changes in the catch composition of artisanal fisheries attributable to dolphin depredation in a Mediterranean marine reserve. – ICES Journal of Marine Science, 66: 699–707. There is increasing evidence from previous studies, and from fishers’ observations, that coastal dolphins use fishing nets as an easily accessible feeding source, damaging or depredating fish caught in the nets. This study investigates the impact of dolphin depredation on artisanal trammelnets by analysing the catch composition of 614 artisanal fishing operations in the Bonifacio Strait Natural Reserve (France). Common bottlenose dolphins (Tursiops truncatus) attacked, on average, 12.4% of the nets and damaged 8.3% of the catch. However, attacked nets were characterized by statistically significantly higher catch per unit effort than unattacked ones. Catch composition also differed significantly after dolphin attacks; bentho-pelagic fish were more represented and reef-associated fish less represented. Our results suggest that (i) dolphins are attracted by high fish densities in the fishing area and/or nets, and (ii) their attacks induce specific fish-avoidance behaviour, according to the fish position in the water column. Although dolphins depredate a small part of the catch, damage to nets, not yet assessed in this area, could weaken the benefits that reserves can provide to artisanal fisheries.
Darwinian and demographic forces affecting human protein coding genes
Authors: Nielsen Rasmus , Hubisz Melissa J. , Hellmann Ines , Torgerson Dara , Andrés Aida M. , Albrechtsen Anders , Gutenkunst Ryan , Adams Mark D. , Cargill Michele , Boyko Adam , Indap Amit , Bustamante Carlos D. , Clark Andrew G.
Published: March 2009

Past demographic changes can produce distortions in patterns of genetic variation that can mimic the appearance of natural selection unless the demographic effects are explicitly removed. Here we fit a detailed model of human demography that incorporates divergence, migration, admixture, and changes in population size to directly sequenced data from 13,400 protein coding genes from 20 European-American and 19 African-American individuals. Based on this demographic model, we use several new and established statistical methods for identifying genes with extreme patterns of polymorphism likely to be caused by Darwinian selection, providing the first genome-wide analysis of allele frequency distributions in humans based on directly sequenced data. The tests are based on observations of excesses of high frequency–derived alleles, excesses of low frequency–derived alleles, and excesses of differences in allele frequencies between populations. We detect numerous new genes with strong evidence of selection, including a number of genes related to psychiatric and other diseases. We also show that microRNA controlled genes evolve under extremely high constraints and are more likely to undergo negative selection than other genes. Furthermore, we show that genes involved in muscle development have been subject to positive selection during recent human history. In accordance with previous studies, we find evidence for negative selection against mutations in genes associated with Mendelian disease and positive selection acting on genes associated with several complex diseases.
System Analysis of an Arabidopsis Mutant Altered in de Novo Fatty Acid Synthesis Reveals Diverse Changes in Seed Composition and Metabolism
Authors: Chen Mingjie , Mooney Brian P. , Hajduch Martin , Joshi Trupti , Zhou Mingyi , Xu Dong , Thelen Jay J.
Published: March 2009

Embryo-specific overexpression of biotin carboxyl carrier protein 2 (BCCP2) inhibited plastid acetyl-coenzyme A carboxylase (ACCase), resulting in altered oil, protein, and carbohydrate composition in mature Arabidopsis (Arabidopsis thaliana) seed. To characterize gene and protein regulatory consequences of this mutation, global microarray, two-dimensional difference gel electrophoresis, iTRAQ, and quantitative immunoblotting were performed in parallel. These analyses revealed that (1) transgenic overexpression of BCCP2 did not affect the expression of three other ACCase subunits; (2) four subunits to plastid pyruvate dehydrogenase complex were 25% to 70% down-regulated at protein but not transcript levels; (3) key glycolysis and de novo fatty acid/lipid synthesis enzymes were induced; (4) multiple storage proteins, but not cognate transcripts, were up-regulated; and (5) the biotin synthesis pathway was up-regulated at both transcript and protein levels. Biotin production appears closely matched to endogenous BCCP levels, since overexpression of BCCP2 produced mostly apo-BCCP2 and the resulting ACCase-compromised, low-oil phenotype. Differential expression of glycolysis, plastid pyruvate dehydrogenase complex, fatty acid, and lipid synthesis activities indicate multiple, complex regulatory responses including feedback as well as futile “feed-forward” elicitation in the case of fatty acid and lipid biosynthetic enzymes. Induction of storage proteins reveals that oil and protein synthesis share carbon intermediate(s) and that reducing malonyl-coenzyme A flow into fatty acids diverts carbon into amino acid and protein synthesis.
Design of artificial neural networks for slipper analysis of axial piston pumps
Authors: Canbulut Fazil , Koç Erdem , Sinanoğlu Cem
Published: March 2009

Purpose

The purpose of this paper is to experimentally and theoretically investigate slippers, which have an important role on power dissipation in the swash plate axial piston pumps.

Design/methodology/approach

The slipper geometry and working conditions affected on the slipper performance have been analyzed experimentally. The model of the slipper system has been established by original neural network (NN) method.

Findings

First, the effects of the slipper geometry with smooth and conical sliding surfaces on the slipper performance were experimentally analyzed. Smooth sliding surface slippers showed a better performance then the conical surface ones. According to the results, the neural predictor would be used as a predictor for possible experimental applications on modeling this type of system.

Originality/value

This paper discusses a new modeling scheme known as artificial NNs an experimental and a NN approach have been employed for analyzing axial piston pumps. The simulation results suggest that the neural predictor would be used as a predictor for possible experimental applications on modeling bearing system.
The reflective frame
Authors: French Steven
Published: March 2009

Purpose

To implement the concepts developed in this action research (AR) programme in a single company and monitor the results.

Design/methodology/approach

In this paper the ideas canvassed in earlier papers regarding the inductive frame and the deductive frame are applied to a single firm and the response is observed over a period of three years. The CMS concept of a change in management style – from a modernist, traditional hands‐on, hierarchical manager/subordinate style, to a more inclusive, self‐management style is introduced

Findings

The tangible benefits that have been observed in the subject company over a period of three years are described. The strategic thinking process led to a change in company culture, which has resulted in many benefits deriving from significant productivity gains. Financial performance and employee productivity have improved significantly. AR as a philosophy for change and CMS as an epistemological paradigm, which underlies the core philosophies for the business, are now part of the long‐term culture of the firm and it is expected that the AR process will continue indefinitely.

Practical implications

Significant improvements in productivity and profitability have been observed. Sickness and accident leave have also been reduced and a positive culture of self‐responsibility is apparent.

Originality/value

This small business has demonstrated many improvements and it is probable that other businesses would also enjoy the benefits of implementing this strategic process.
Multi‐scale modelling of heterogeneous structures with inelastic constitutive behavior
Authors: Niekamp Rainer , Markovic Damijan , Ibrahimbegovic Adnan , Matthies Hermann G. , Taylor Robert L.
Published: March 2009

Purpose

The purpose of this paper is to consider the computational tools for solving a strongly coupled multi‐scale problem in the context of inelastic structural mechanics.

Design/methodology/approach

In trying to maintain the highest level of generality, the finite element method is employed for representing the microstructure at this fine scale and computing the solution. The main focus of this work is the implementation procedure which crucially relies on a novel software product developed by the first author in terms of component template library (CTL).

Findings

The paper confirms that one can produce very powerful computational tools by software coupling technology described herein, which allows the class of complex problems one can successfully tackle nowadays to be extended significantly.

Originality/value

This paper elaborates upon a new multi‐scale solution strategy suitable for highly non‐linear inelastic problems.
Reinganum's trading strategies revisited
Authors: Yu Susana
Published: March 2009

Purpose

The purpose of this paper is to reexamine the value, momentum and size factors employed in the trading strategy originally proposed by Reinganum. Also to enhance our understanding of the impact of these factors over time; to evaluate the effectiveness of these factors; to develop new strategies through a framework presented by Chan et al.; and to investigate the possibility of limiting the number of filters to allow for a larger universe of eligible stocks without hurting performance for both long and short strategies.

Design/methodology/approach

Using data from 1970 to 1983, Reinganum developed a profitable trading strategy based on four (or nine) variables to select stocks. First this paper shows why it is increasingly difficult to implement his original trading strategy, then tests his strategy on 23 additional years of data through 2006, and compares it to similar strategies that incorporate straightforward modifications to his filters. The analysis is further extended to a long/short trading strategy similar to that of Chan et al.

Findings

Using the Capital Asset Pricing Model, Fama‐French's three‐factor model and Carhart's four‐factor model to evaluate returns following portfolio formation, significant and consistent alphas and portfolio sizes were found.

Research limitations/implications

It is concluded that strategies that mix value, momentum and size filter rules can be developed to produce consistently negative or non‐positive (vs solely positive) alphas.

Originality/value

The paper shows that it is possible to form profitable short‐only and long/short strategies and to increase the number of eligible stocks in the sample despite our modifications to Reinganum's variables. By creating strategies based on mixed filter rules to produce either consistently positive (or negative) risk‐adjusted returns, it can be concluded that slightly different versions of a given filter rule – often much simpler versions – not only enhance return performance but also increase its effectiveness in terms of portfolio size.
A conceptual model of brand‐building for B‐schools: an Indian perspective
Authors: Shahaida P. , Rajashekar H. , Nargundkar R.
Published: March 2009

Purpose

MBA education in India is facing the same challenges as business. Upheaval of technology, changing customer expectations, global competition, online courses and societal responsibility are the major concerns. Failure to adapt to these challenges will question the academic contribution to business practice. Business school (B‐school) branding is crucial to distinguish the services provided by one B‐school from another. Considering the importance and relevance of adapting to the changing market forces, the purpose of this paper is to propose a conceptual model of brand‐building for Indian B‐schools.

Design/methodology/approach

A range of published literature related to the topic is thoroughly searched. The paper examines the viewpoints of various scholars with regard to the role of a student in a B‐school. The services marketing perspective is analyzed and the gaps are identified through a robust literature survey. Based on the literature survey, an original conceptual model for brand‐building for B‐schools is proposed.

Findings

Some B‐schools have adopted certain branding activities, but extant literature review reveals that B‐schools in India do not practice an organized holistic approach to branding activities.

Originality/value

The proposed conceptual model is stage one in the process of understanding what goes into building a B‐school brand. Stage two would empirically test the proposed conceptual model of brand‐building. The proposed model is holistic, considering the role of important stakeholders such as students, faculty and corporate. This conceptual model will help B‐school management to understand the role and importance of branding B‐schools. It will provide an insight into the various parameters on which a B‐school brand has to be built.
The telecommunications policy process in post‐conflict developing countries: the case of Liberia
Authors: Best Michael L. , Thakur Dhanaraj
Published: March 2009

Purpose

The purpose of this paper is to develop an understanding of the telecommunications policy process in immediate post‐conflict countries and how that process differs from traditional settings.

Design/methodology/approach

The authors consider the case of Liberia, a country that recently emerged from a protracted civil war. The authors focus on the Liberian Telecommunications Act of 2007 and the processes through which this act came about by applying a modified research framework. This framework identifies several factors in the literature that are posited to influence the policymaking process in developing countries. The authors also include other factors based on previous studies in post‐conflict countries. The aim is to test the usefulness of this framework using the 2007 act. The authors apply it through the use of interviews with key actors in the government, industry, and international agencies. This was supplemented by secondary data from published reports and other sources.

Findings

From the framework the authors identify the main factors influencing the telecoms policy making process in Liberia such as a weak and nascent institutional environment, intra‐governmental competition, limited human and technical resources, the supportive (especially initially) role of the international actors such as the World Bank, and the dominance of elite groups in decision‐making. The authors then make suggestions on overcoming some of existing challenges to the sector.

Originality/value

This paper looks at the intersection of research in telecommunications policy, policy processes and post‐conflict countries, an area in which there is currently very little work. The results indicate that several dimensions of the framework are germane to the post‐conflict case and that some of these observations are also relevant to the future development of telecommunications in these countries.
Suppression of anti‐Candida activity of macrophages by a quorum‐sensing molecule, farnesol, through induction of oxidative stress
Authors: Abe Shigeru , Tsunashima Rumi , Iijima Ryosuke , Yamada Tsuyoshi , Maruyama Naho , Hisajima Tatsuya , Abe Yoshie , Oshima Haruyuki , Yamazaki Masatoshi
Published: March 2009

Farnesol is well known as a quorum‐sensing molecule of Candida albicans. To assess the pathological function of farnesol, its effects on macrophage viability and functions including growth inhibitory activities against C. albicans were examined in vitro. Murine macrophages, when cultured in the presence of 56–112 μM of farnesol for 1–2 hr, decreased their activity inhibiting the mycelial growth of C. albicans and lost their viability. This suppression of macrophage function by farnesol was neutralized by the coexistence of the anti‐oxidants probucol and trolox. Macrophages cultured in the presence of farnesol for 2 hr displayed morphological change of nuclei and DNA fragmentation, which suggested apoptosis of the cells. Intracellular production of ROS in the farnesol‐treated macrophages was shown by fluorescence of DCFH‐DA and increase of peroxidized materials. These effects of farnesol were blocked by probucol or trolox. These results indicate that farnesol lowered viability of the murine macrophages and suppressed their anti‐Candida activity, perhaps through induction of ROS.
Leukemia‐related transcription factor TEL/ETV6 expands erythroid precursors and stimulates hemoglobin synthesis
Authors: Eguchi‐Ishimae Minenori , Eguchi Mariko , Maki Kazuhiro , Porcher Catherine , Shimizu Ritsuko , Yamamoto Masayuki , Mitani Kinuko
Published: March 2009

TEL/ETV6 located at chromosome 12p13 encodes a member of the E26 transformation‐specific family of transcription factors. TEL is known to be rearranged in a variety of leukemias and solid tumors resulting in the formation of oncogenic chimeric protein. Tel is essential for maintaining hematopoietic stem cells in the bone marrow. To understand the role of TEL in erythropoiesis, we generated transgenic mice expressing human TEL under the control of Gata1 promoter that is activated during the course of the erythroid‐lineage differentiation (GATA1‐TEL transgenic mice). Although GATA1‐TEL transgenic mice appeared healthy up to 18 months of age, the level of hemoglobin was higher in transgenic mice compared to non‐transgenic littermates. In addition, CD71+/TER119+ and c‐kit+/CD41+ populations proliferated with a higher frequency in transgenic mice when bone marrow cells were cultured in the presence of erythropoietin and thrombopoietin, respectively. In transgenic mice, enhanced expression of Alas‐e and β‐major globin genes was observed in erythroid‐committed cells. When embryonic stem cells expressing human TEL under the same Gata1 promoter were differentiated into hematopoietic cells, immature erythroid precursor increased better compared to controls as judged from the numbers of burst‐forming unit of erythrocytes. Our findings suggest some roles of TEL in expanding erythroid precursors and accumulating hemoglobin. (Cancer Sci 2009; 100: 689–697)
Breast cancer resistance protein/ABCG2 is differentially regulated downstream of extracellular signal‐regulated kinase
Authors: Imai Yasuo , Ohmori Kyoko , Yasuda Shin’ichi , Wada Mariko , Suzuki Tsukasa , Fukuda Kazunori , Ueda Yoshihiko
Published: March 2009

Breast cancer resistance protein (BCRP)/ABCG2 is a drug efflux pump responsible for multidrug resistance in cancer cells. We report that dephosphorylation of extracellular signal‐regulated kinase (ERK) by treatment with mitogen‐activated protein kinase/ERK kinase (MEK) inhibitors causes two opposing effects, transcriptional upregulation and prompted protein degradation of endogenous BCRP in breast cancer MCF‐7 cells. Endogenous BCRP was eventually found to be upregulated. Conversely, treatment with epidermal growth factor was associated with its downregulation in the cells. MEK inhibitors also caused prompted degradation of exogenous BCRP in MCF‐7 and gastric cancer NCI‐N87 cells that express exogenous BCRP without affecting its transcriptional levels, and potentiated anticancer agents in the cells. A lysosomal inhibitor abolished this prompted degradation of exogenous BCRP, but a proteasome inhibitor did not. Inhibition of p90 ribosomal protein S6 kinase (RSK), one of the downstream effectors of ERK, resulted in transcriptional upregulation of endogenous BCRP but did not affect the protein degradation of exogenous BCRP. The data suggest that BCRP expression is differentially regulated downstream of the MEK‐ERK pathway, transcriptionally upregulated through the inhibition of the MEK‐ERK‐RSK pathway, and post‐transcriptionally downregulated through the inhibition of the MEK‐ERK‐non‐RSK pathway. Although the immediate downstream effector of ERK remains to be elucidated, the data provide new insights into regulatory mechanisms of BCRP activity and may assist the development of BCRP‐specific expression modulators. (Cancer Sci 2009; 100: 1118–1127)
Synergistic interactions between the synthetic retinoid tamibarotene and glucocorticoids in human myeloma cells
Authors: Fukui Tomoya , Kodera Yasuo , Nishio Kazuto , Masuda Noriyuki , Tamura Tomohide , Koizumi Fumiaki
Published: March 2009

Tamibarotene (TM411) is a synthetic retinoic acid receptor‐α/‐β selective retinoid that is chemically more stable than all‐trans retinoic acid. This study was designed to evaluate the activity of TM411 in multiple myeloma (MM) and the effects of TM411 combined with a glucocorticoid (GC). In vitro, five human myeloma cells were treated with TM411 alone, GC alone, or TM411 + GC. Cell survival was analyzed by the tetrazolium dye assay and the Hoechst 33342/propidium iodide double‐staining method. The effect of TM411 + GC was assessed by the isobologram method. In vivo, the growth‐inhibitory effects of the drugs on RPMI‐8226 cell xenografts established in SCID mice were examined. The effects of the agents on IL‐6‐mediated signaling pathways were also analyzed by Western blotting. TM411 was 2‐ to 10‐fold more potent, in terms of its growth‐inhibitory effect, than all‐trans retinoic acid. The combination of TM411 and GC was found to show a markedly synergistic interaction. While increased expressions of the IL‐6 receptor, phosphorylated MAPK, and Akt were observed after exposure to GC, TM411 attenuated this increase in the expressions, suggesting that such modification of the effect of GC by TM411 might be the possible mechanism underlying the synergistic interaction. Furthermore, TM411 + GC showed a supra‐additive inhibitory effect in a xenograft model as compared with TM411 or GC alone. These results imply that the combination of TM411 + GC might be highly effective against MM, and suggest the need for clinical evaluation of TM411 + GC for the treatment of MM. (Cancer Sci 2009; 100: 1137–1143)
The influence of introduced trout on the benthic communities of paired headwater streams in the Sierra Nevada of California
Authors: HERBST DAVID B. , SILLDORFF ERIK L. , COOPER SCOTT D.
Published: March 2009

1. Non‐native trout have been stocked in streams and lakes worldwide largely without knowledge of the consequences for native ecosystems. Although trout have been introduced widely throughout the Sierra Nevada of California, U.S.A., fishless streams and their communities of native invertebrates persist in some high elevation areas, providing an opportunity to study the effects of trout introductions on natural fishless stream communities.

2. We compared algal biomass and cover, organic matter levels and invertebrate assemblages in 21 natural fishless headwater streams with 21 paired nearby streams containing stocked trout in Yosemite National Park.

3. Although environmental conditions and particulate organic matter levels did not differ between the fishless and trout streams, algal biomass (as chlorophyllaconcentration) and macroalgal cover were, on average, approximately two times and five times higher, respectively, in streams containing trout.

4. There were no differences in the overall densities of invertebrates in fishless versus paired trout streams; however, invertebrate richness (after rarefaction), evenness, and Simpson and Shannon diversities were 10–20% higher in fishless than in trout streams.

5. The densities of invertebrates belonging to the scraper‐algivore and predator functional feeding guilds were higher, and those for the collector‐gatherer guild lower, in fishless than trout streams, but there was considerable variation in the effects of trout on specific taxa within functional feeding groups.

6. We found that the densities of 10 of 50 common native invertebrate taxa (found in more than half of the stream pairs) were reduced in trout compared to fishless streams. A similar number of rarer taxa also were absent or less abundant in the presence of trout. Many of the taxa that declined with trout were conspicuous forms (by size and behaviour) whose native habitats are primarily high elevation montane streams above the original range of trout.

7. Only a few taxa increased in the presence of trout, possibly benefiting from reductions in their competitors and predators by trout predation.

8. These field studies provide catchment‐scale evidence showing the selective influence of introduced trout on stream invertebrate and algal communities. Removal of trout from targeted headwater streams may promote the recovery of native taxa, community structure and trophic organisation.
Discordant antibody response in monozygotic twins with severe haemophilia A caused by intensive treatment
Authors: GOUW S. C. , TER AVEST P. C. , VAN HELDEN P. M. , VOORBERG J. , Van Den BERG H. M.
Published: March 2009

Summary. Both genetic factors and environmental factors are suggested to play a role in the aetiology of inhibitor development in patients with severe haemophilia A. Monozygotic twins are ideal candidates to study the influence of environmental factors. We describe a pair of 3‐year‐old monozygotic twin brothers with severe haemophilia A. Prenatal diagnosis confirmed the presence of an intron 22 inversion. Other patient‐related factors such as birth weight, vaccinations and the duration of breastfeeding were similar. At the age of 7 months, one boy suffered from a spontaneous subdural haematoma, which needed complete correction of haemostasis with continuous infusion of a third‐generation recombinant factor VIII. A persistent high‐titre inhibitor with severe clinical symptoms developed, that could only be eradicated with high‐dose immune tolerance induction (ITI) for 36 months in combination with rituximab therapy. His twin brother first received treatment at 9 months of age with the same FVIII product. After treatment on nine exposure days, he developed a low‐titre inhibitor at the age of 14.5 months. Unlike his brother, he was tolerized without difficulties with low‐dose ITI within 2 months. The discordant antibody responses were underlined by dissimilar IgG1 and IgG4 levels in their plasma. The discordant immune response to FVIII in this pair of monozygotic twin brothers seemed to be related to intensity of treatment and severity of bleeds. This confirms that these environmental factors play an additional role in the development of inhibitors.
Myxobolus erythrophthalmi sp. n. and Myxobolus shaharomae sp. n. (Myxozoa: Myxobolidae) from the internal organs of rudd, Scardinius erythrophthalmus (L.), and bleak, Alburnus alburnus (L.)
Authors: Molnár K , Eszterbauer E , Marton Sz , Cech G , Székely Cs
Published: March 2009

During a survey of myxosporean parasites of cyprinid fish in Hungary, infections caused by unknown Myxobolus spp. were found in the internal organs of rudd, Scardinius erythrophthalmus, and bleak, Alburnus alburnus. Small plasmodia developed in blood vessels of the kidney, liver, testes and intestinal wall. The parasites were studied on the basis of spore morphology and by histological and molecular methods. In most cases, plasmodia were surrounded by host tissue without a host reaction; however, in advanced cases, a connective tissue capsule was seen around plasmodia. Spores collected from the two fish species differed from each other and from the known Myxobolus spp. both in their morphology and 18S rDNA sequences. The two species, described as M. erythrophthalmi sp. n. from rudd and M. shaharomae sp. n. from bleak, are characterized by a specific histotropism to blood vessels, while the organ specificity involves the kidney and for the latter species, most internal organs.
Clinical value of 12 occlusal features for the prediction of disc displacement with reduction (RDC/TMD Axis I group IIa)
Authors: CHIAPPE G. , FANTONI F. , LANDI N. , BIONDI K. , BOSCO M.
Published: March 2009

Summary  The purpose of this study is to quantify the clinical value of 12 occlusal variables for the prediction of disc displacement with reduction diagnosed according to research diagnostic criteria (RDC)/temporomandibular disorder (TMD). Twelve occlusal features were clinically assessed by the same three operators. The sample consisted of 165 TMD patients (65 males, 100 females; mean age: 32·55 ± 11·685years) with only disc displacement with reduction (RDC/TMD Axis I group IIa) and a control sample of 145 healthy subjects (65 males, 80 females; mean age: 31·24 ± 12·436 years) diagnosed with RDC/TMD Axis I group 0. A stepwise multiple logistic regression model was used to identify the significant correlation between occlusal features and disease. The odds ratio for disc displacement was 2·84 for absence of canine guidance, 2·14 for mediotrusive interference and 1·75 for retruded contact position (RCP)/maximum intercuspation (MI) slide ≥2 mm. Other occlusal variables did not reveal to be statistically significant. The percentage of the total log likelihood for disc displacement explained by the significant occlusal factors was acceptable with a Nagelkerke’s R2 = 0·124. The final model including the significant occlusal features revealed an optimal discriminant capacity to predict patients with disc displacement with a sensitivity of 63·6% or with a specificity of 64·8% for healthy subjects and an accuracy of 64·2%. Occlusal features showed a low predictive value for detecting disc displacement. Multifactorial complex pathologies such as TMD should be investigated using a multivariate statistical analysis; moreover, the future of aetiopathogenic research in this matter requires a multifactorial approach.
Historical divergence of mechanical isolation agents in the ground beetle Carabus arrowianus as revealed by phylogeographical analyses
Authors: NAGATA NOBUAKI , KUBOTA KOHEI , TAKAMI YASUOKI , SOTA TEIJI
Published: March 2009

In the carabid genus Carabus subgenus Ohomopterus, diverged body size and genital morphology serve as mechanical reproductive barriers. To elucidate the diverging process of body and genital sizes in Carabus arrowianus, which exhibits marked morphological diversity among geographical populations and may represent an early stage of speciation, we analysed a mitochondrial gene sequence for 1051 individuals from 63 populations and male morphology for 359 individuals from 47 populations. Two discrete morphological groups segregated by geographical barriers were distinguished, one of which possessed smaller bodies and shorter genitalia (S group) than the other (L group), which exhibited larger bodies and exaggerated genitalia. Genetic divergence between the two groups was significant but not large. Phylogeographical and population genetic analyses indicated that the L group was derived from the S group, and a coalescent simulation revealed that the two groups diverged during the latest middle Pleistocene (0.13 million years ago), with a much larger effective population size in the L group than the S group. Because the body size divergence could not be explained by adaptation to climatic conditions and genital morphology is considered to be subject to sexual selection, we postulated that a population division and colonization in favourable habitats caused by the Pleistocene climatic and geographical change might facilitate natural and sexual selection for enlarged body and genital sizes in the L group.
Evolution of tracheal aspiration in severe traumatic brain injury‐related oropharyngeal dysphagia: 1‐year longitudinal follow‐up study
Authors: Terré R. , Mearin F.
Published: March 2009

Abstract  The aims of the article were to ascertain the clinical evolution and prognostic factors of aspiration recovery and feeding outcome in patients with severe traumatic brain injury (TBI) and a videofluoroscopic (VFS) diagnosis of tracheal aspiration. Twenty‐six patients with severe TBI and VFS diagnosis of tracheal aspiration were prospectively evaluated. Clinical evaluation of oropharyngeal dysphagia and VFS examination were performed at admission and repeated at 1, 3, 6 and 12 months of follow‐up. At admission, all patients had VFS aspiration. During follow‐up, an improvement was observed in both oral and pharyngeal function, with the number of patients with aspiration decreasing progressively. The most significant change occurred in the examination made at 3 months. At 1 year, only 23% of patients had aspiration. No patient had clinically significant respiratory infections during the follow‐up period. Persistent aspiration at 1 year of follow‐up correlated with baseline variables: Rancho Los Amigos Level Cognitive Function Scale score, Disability Rating Scale score, tongue control alteration, velopharyngeal reflex abolition and delay in triggering swallowing reflex. Swallowing physiology in severe TBI greatly improved during follow‐up and the number of aspirations decreased progressively, with the most significant reduction at between 3 and 6 months of evolution. This study revealed several prognostic factors for persisting aspiration: neurological involvement (evaluated with the Rancho Los Amigos Level Cognitive Function Scale and Disability Rating Scale), tongue control alteration, oropharyngeal reflex abolition and delay in triggering swallowing reflex at baseline.
The early IL‐6 and IL‐10 response in trauma is correlated with injury severity and mortality
Authors: STENSBALLE J. , CHRISTIANSEN M. , TØNNESEN E. , ESPERSEN K. , LIPPERT F. K. , RASMUSSEN L. S.
Published: March 2009

Background: Trauma has previously been shown to influence interleukin (IL)‐6 and IL‐10 levels, but the association of injury severity and mortality with IL‐6 and IL‐10 responses in the early phase of accidental trauma remains to be investigated. We wished to describe serum levels of IL‐6 and IL‐10 in the first 24 h after trauma and to assess the relationship with severity of injury and mortality.

Methods: Prospective, descriptive cohort study in a Level 1 trauma centre, Copenhagen, Denmark. We included 265 consecutive adult trauma patients admitted directly from the accident scene during an 18‐month period. Serum levels of IL‐6 and IL‐10 were measured upon arrival and at 6, 12, and 24 h after admittance using an enzyme‐linked immunosorbent assay. Correlation analysis was used to assess the relationship between Injury Severity Score (ISS) and levels of IL‐6 and IL‐10. Analysis of variance was used to describe the IL‐6 and IL‐10 concentrations in relation to 30‐day mortality in a mixed‐effect model repeated measures analysis.

Results: Mortality was 10.9% (29/265) at 30 days. A significant increase of both IL‐6 and IL‐10 concentrations was found over time, and a significant correlation was found between ISS and the levels of both IL‐6 and IL‐10 at all sampling points. Serum concentrations of IL‐6 and IL‐10 were significantly higher in patients not surviving 30 days (P<0.0001).

Conclusion: The early systemic inflammatory response measured as IL‐6 and IL‐10 in serum is correlated with injury severity and 30‐day mortality following trauma.
Continuous lumbar epidural infusion of levobupivacaine: effects of small‐or large‐volume regimen of infusion
Authors: DANELLI G. , VENUTI F. S. , ZASA M. , SINARDI D. , FANELLI A. , GHISI D. , FANELLI G.
Published: March 2009

Background: The question of whether the dose, concentration or volume of a local anesthetic solution is the relevant determinant of the spread and quality of post‐operative epidural analgesia is still open. In this prospective, randomized, double‐blind study, we compared the effects of a large volume–low concentration with a small‐volume–high‐concentration lumbar epidural infusion of levobupivacaine.

Methods: Seventy patients scheduled for total hip replacement were enrolled. After surgery, patients were randomly allocated to receive a continuous epidural infusion of levobupivacaine (10.5 mg/h) using either 0.125% levobupivacaine infused at 8.4 ml/h (low concentration group, n=35) or 0.75% levobupivacaine infused at 1.4 ml/h (high concentration group, n=35). We blindly recorded the degree of pain relief at rest and during movement every 8 h for the first two post‐operative days, as well as hip flexion, motor block, rescue analgesic consumption and adverse events.

Results: No difference in pain relief was observed between groups as estimated with the areas under the curve of the verbal Numerical Rating Scale for pain over time, both at rest and during movement. Similarly, there was no difference between groups in hip flexion degree, motor blockade and hemodynamic stability.

Conclusions: Continuous lumbar epidural infusion of 0.75% levobupivacaine was as effective as continuous lumbar epidural infusion of 0.125% levobupivacaine, when administered at the same hourly dose of 10.5 mg, in achieving adequate analgesia both at rest and during movement, without differences in the incidence of hypotension and motor blockade.
Hypertrophied hearts: what of sevoflurane cardioprotection?
Authors: LARSEN J. R. , SMERUP M. , HASENKAM J. M. , CHRISTENSEN S. D. , SIVESGAARD K. , TORP P. , SLOTH E.
Published: March 2009

Background: Recent studies have demonstrated that inhalation anaesthetics, like sevoflurane, confer cardioprotection both experimentally and clinically. However, coexisting cardiac disease might diminish anaesthetic cardioprotection and could partly explain why the clinical results of cardioprotection with anaesthetics remain controversial – in contrast to solid experimental evidence. Concomitant left ventricular hypertrophy is found in some cardiac surgery patients and could change cardioprotection efficacy. Hypertrophy could potentially render the heart less susceptible to sevoflurane cardioprotection and more susceptible to ischaemic injury. We investigated whether hypertrophy blocks sevoflurane cardioprotection, and whether tolerance to ischaemia is altered by left ventricular hypertrophy, in an established experimental animal model of ischaemia–reperfusion.

Methods: Anaesthetized juvenile pigs (n=7–12/group) were subjected to 45 min distal coronary artery balloon occlusion, followed by 120 min of reperfusion. Controls were given pentobarbital, while sevoflurane cardioprotection was achieved by 3.2% inhalation throughout the experiment. Chronic banding of the ascending aorta resulted in left ventricular hypertrophy development in two further groups and these animals underwent identical ischaemia–reperfusion protocols, with or without sevoflurane cardioprotection. Myocardial infarct sizes were compared post‐mortem.

Results: The mean myocardial infarct size (% of area‐at‐risk) was reduced from mean 55.0 (13.6%) (±SD) in controls to 17.5 (13.2%) by sevoflurane (P=0.001). Sevoflurane reduced the infarct size in hypertrophied hearts to 14.6 (10.4%) (P=0.001); however, in hypertrophic controls, infarcts were reduced to 34.2 (10.2%) (P=0.001).

Conclusion: Sevoflurane abrogated ischaemic injury to similar levels in both normal and left ventricular hypertrophied hearts.
Dose‐dependent effect of S(+) ketamine on post‐ischemic endogenous neurogenesis in rats
Authors: WINKELHEIDE U. , LASARZIK I. , KAEPPEL B. , WINKLER J. , WERNER C. , KOCHS E. , ENGELHARD K.
Published: March 2009

Background: Ketamine is a non‐competitive antagonist at N‐methyl‐d‐aspartate (NMDA) receptors and reduces neuronal injury after cerebral ischemia by blocking the excitotoxic effects of glutamate. However, cerebral regeneration by means of endogenous neurogenesis may be impaired with blockade of NMDA receptors. The effects of S(+) ketamine on post‐ischemic neurogenesis are unknown and investigated in this study.

Methods: Thirty‐two male Sprague–Dawley rats were randomly assigned to the following treatment groups with intravenous S(+) ketamine anesthesia: S(+) ketamine 0.75 mg/kg/min with or without cerebral ischemia and S(+) ketamine 1.0 mg/kg/min with or without cerebral ischemia. Eight non‐anesthetized, non‐ischemic animals were investigated as naïve controls. Forebrain ischemia was induced by bilateral common carotid artery occlusion in combination with hemorrhagic hypotension. 5‐bromo‐2‐deoxyuridine (BrdU) was injected intraperitoneally for seven consecutive post‐operative days. BrdU‐positive neurons in the dentate gyrus and histopathological damage of the hippocampus were analyzed after 28 days.

Results: The number of new neurons was not affected by S(+) ketamine in the absence of cerebral ischemia. The ischemia‐induced increase in neurogenesis was reduced by high‐dose S(+) ketamine. Cell death of ischemic animals did not vary between low‐ and high‐dose S(+) ketamine.

Conclusion: While low concentrations of S(+) ketamine allow an ischemia‐induced increase in the number of new neurons, high S(+) ketamine concentrations block the post‐ischemic increase in newly generated neurons. This effect is irrespective of the extent of other histopathological damage and in line with studies showing that NMDA receptor antagonists like MK‐801 inhibit neurogenesis after cerebral ischemia.
Investigation of the phenotypic and genetic properties of Brenneria nigrifluens strains, the causal agent of walnut bark canker in Kurdistan province, Iran
Authors: Roshangar R. , Harighi B.
Published: March 2009

Phenotypic and genetic properties of Brenneria nigrifluens, the causal agent of walnut bark canker disease were studied using a combination of key biochemical tests, analysis of whole‐cell protein extracts and genetic fingerprints based on DNA primers corresponding to conserved motifs in bacterial repetitive (repetitive extragenic palindromic, enterobacterial repetitive intergenic consensus and BOX) elements and to the 16s rRNA gene. Phenotypic properties indicated that 11 strains showed a high degree of similarity and <5% of isolates showed different properties such as utilization of dulcitol and inositol. A majority of isolates produced rep‐PCR profiles similar (>80%) to a B. nigrifluens reference strain. This study showed that the majority of strains had 0–3 plasmids with estimated sizes ranging 9–32 Kb. Strains were clustered into two and three groups by whole‐cell protein analysis and rep‐PCR, respectively.
Inhibitions of urinary oxidative stress and renal calcium level by an extract of Quercus salicina Blume/Quercus stenophylla Makino in a rat calcium oxalate urolithiasis model
Authors: Moriyama Manabu T , Suga Koudai , Miyazawa Katsuhito , Tanaka Tatsuro , Higashioka Masaya , Noda Kumiko , Oka Michiko , Tanaka Mitsushi , Suzuki Koji
Published: March 2009

Objectives:  To clarify the mechanism of Urocalun, an extract of Quercus salicina Blume/Quercus stenophylla Makino (QS), in the treatment of urolithiasis.

Methods:  Rat calcium oxalate urolithiasis was induced by oral administration of ethylene glycol and the vitamin D3 analog alfa‐calcidol for 14 days. QS extract was repeatedly given to rats. After the last administration, biochemistries in urine and plasma, renal calcium, and urinary malondialdehyde (an oxidative stress marker) were measured.

Results:  Ethylene glycol and alfa‐calcidol treatment increased urinary malondialdehyde and renal calcium levels. This increase was significantly suppressed by the administration of QS extract, suggesting that the inhibition of renal calcium accumulation by QS extract is due to its antioxidative activity.

Conclusions:  These findings suggest that the antioxidative activity of QS extract plays a role in the prevention of stone formation and recurrence in urolithiasis.
SUPERFICIALLY ELEVATED‐TYPE SERRATED HYPERPLASTIC LESION OF THE STOMACH WITH MINUTE ADENOCARCINOMA
Authors: Hasuo Tadateru , Semba Shuho , Satake Shinya , Shirasaka Daisuke , Aoyama Nobuo , Yokozaki Hiroshi
Published: March 2009

We report a case of gastric serrated hyperplastic lesion with minute adenocarcinoma. A 65‐year‐old Japanese man underwent endoscopic submucosal dissection to the superficially elevated‐type (0‐IIa) lesion located at the lesser curvature of the gastric angle. Histological observation revealed hyperplastic change of foveolar epithelium with serrated glandular structure as well as a minute tubular adenocarcinoma component. Immunohistochemically, the lesion demonstrated gastrointestinal, predominantly gastric, phenotype (MUC5AC++, MUC6+, MUC2+, CD10−). Positive p53 immunoreactivity was detected in the carcinoma component of the lesion with a point mutation (G877T; R209I) of the gene and microsatellite instability of the BAT‐RII locus; however, immunoreactivity of the mismatch repair gene product hMLH1 was well preserved in the cancer as well as in the hyperplastic lesion. The hyperplastic lesion with serrated glandular pattern would be a precancerous lesion of adenocarcinoma of the stomach.
EFFICACY OF LAPAROSCOPIC RADIOFREQUENCY ABLATION FOR HEPATOCELLULAR CARCINOMA COMPARED TO PERCUTANEOUS RADIOFREQUENCY ABLATION WITH ARTIFICIAL ASCITES
Authors: Hirooka Masashi , Kisaka Yoshiyasu , Uehara Takahide , Ishida Kiyotaka , Kumagi Teru , Watanabe Yuji , Abe Masanori , Matsuura Bunzo , Hiasa Yoichi , Onji Morikazu
Published: March 2009

Aim:  Hepatocellular carcinoma (HCC) nodules close to the liver surface exhibit high recurrence compared to those in distal parts of the liver. Moreover, when nodules remain adjacent to the gastrointestinal tract or gallbladder, severe complications such as perforation of those organs may occur due to invasive therapy. Percutaneous radiofrequency ablation (PRFA) with artificial ascites or laparoscopic radiofrequency ablation (LRFA) are used to treat these patients to avoid complications. The purpose of the present study was to assess the efficacy and safety of these two methods.

Methods:  Subjects comprised 74 patients (48 men, 26 women; mean age, 68.5 ± 8.0 years; range, 46–89 years) with 86 HCC nodules. PRFA with artificial ascites was carried out for 37 patients (44 nodules) and LRFA was used for 37 patients (42 nodules). Clinical profiles were compared between groups.

Results:  No significant differences in clinical profiles were found between patients treated by PRFA or LRFA. Mean number of treatments was significantly lower for LRFA (1.0 ± 0.0) than for PRFA (2.1 ± 1.0, P < 0.001). Mean number of PRFA treatments was 2.2 ± 1.0 in patients with HCC nodules >2 cm in diameter, whereas all tumors were completely ablated with only one session of LRFA. The safety margin was significantly wider for LRFA than for PRFA.

Conclusion:  LRFA is a better treatment option for ablation of HCC nodules >2.0 cm in diameter.