bluuebunny/crossref_metadata_2025 huggingface dataset:
Membrane topology of conserved components of the type III secretion system from the plant pathogen Xanthomonas campestris pv. vesicatoria
Authors: Berger Carolin , Robin Guillaume P. , Bonas Ulla , Koebnik Ralf
Published: April 2010

Type III secretion (T3S) systems play key roles in the assembly of flagella and the translocation of bacterial effector proteins into eukaryotic host cells. Eleven proteins which are conserved among Gram-negative plant and animal pathogenic bacteria have been proposed to build up the basal structure of the T3S system, which spans both inner and outer bacterial membranes. We studied six conserved proteins, termed Hrc, predicted to reside in the inner membrane of the plant pathogenXanthomonas campestrispv. vesicatoria. The membrane topology of HrcD, HrcR, HrcS, HrcT, HrcU and HrcV was studied by translational fusions to a dual alkaline phosphatase–β-galactosidase reporter protein. Two proteins, HrcU and HrcV, were found to have the same membrane topology as theYersiniahomologues YscU and YscV. For HrcR, the membrane topology differed from the model for the homologue fromYersinia, YscR. For our data on three other protein families, exemplified by HrcD, HrcS and HrcT, we derived the first topology models. Our results provide what is believed to be the first complete model of the inner membrane topology of any bacterial T3S system and will aid in elucidating the architecture of T3S systems by ultrastructural analysis.
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities
Authors: Jolma Arttu , Kivioja Teemu , Toivonen Jarkko , Cheng Lu , Wei Gonghong , Enge Martin , Taipale Mikko , Vaquerizas Juan M. , Yan Jian , Sillanpää Mikko J. , Bonke Martin , Palin Kimmo , Talukder Shaheynoor , Hughes Timothy R. , Luscombe Nicholas M. , Ukkonen Esko , Taipale Jussi
Published: April 2010

The genetic code—the binding specificity of all transfer-RNAs—defines how protein primary structure is determined by DNA sequence. DNA also dictates when and where proteins are expressed, and this information is encoded in a pattern of specific sequence motifs that are recognized by transcription factors. However, the DNA-binding specificity is only known for a small fraction of the ∼1400 human transcription factors (TFs). We describe here a high-throughput method for analyzing transcription factor binding specificity that is based on systematic evolution of ligands by exponential enrichment (SELEX) and massively parallel sequencing. The method is optimized for analysis of large numbers of TFs in parallel through the use of affinity-tagged proteins, barcoded selection oligonucleotides, and multiplexed sequencing. Data are analyzed by a new bioinformatic platform that uses the hundreds of thousands of sequencing reads obtained to control the quality of the experiments and to generate binding motifs for the TFs. The described technology allows higher throughput and identification of much longer binding profiles than current microarray-based methods. In addition, as our method is based on proteins expressed in mammalian cells, it can also be used to characterize DNA-binding preferences of full-length proteins or proteins requiring post-translational modifications. We validate the method by determining binding specificities of 14 different classes of TFs and by confirming the specificities for NFATC1 and RFX3 using ChIP-seq. Our results reveal unexpected dimeric modes of binding for several factors that were thought to preferentially bind DNA as monomers.
A Framework for Evaluating High-Level Design Methodologies for High-Performance Reconfigurable Computers
Authors: El-Araby Esam , Merchant Saumil G. , El-Ghazawi Tarek
Published: April 2010

High-performance reconfigurable computers have potential to provide substantial performance improvements over traditional supercomputers. Their acceptance, however, has been hindered by productivity challenges arising from increased design complexity, a wide array of custom design languages and tools, and often overblown sales literature. This paper presents a review and taxonomy of High-Level Languages (HLLs) and a framework for the comparative analysis of their features. It also introduces new metrics and a model based on computational effort. The proposed concepts are inspired by Netwon's equations of motion and the notion of work and power in an abstract multidimensional space of design specifications. The metrics are devised to highlight two aspects of the design process: the total time-to-solution and the efficient utilization of user and computing resources at discrete time steps along the development path. The study involves analytical and experimental evaluations demonstrating the applicability of the proposed model.
White muscle 20S proteasome activity is negatively correlated to growth rate at low temperature in the spotted wolffish Anarhichas minor
Authors: Lamarre S. G. , Blier P. U. , Driedzic W. R. , Le François N. R.
Published: April 2010

The effect of temperature and mass on specific growth rate (G) was examined in spotted wolffish Anarhichas minor of different size classes (ranging from 60 to 1500 g) acclimated at different temperatures (4, 8 and 12° C). The relationship between G and 20S proteasome activity in heart ventricle, liver and white muscle tissue was then assessed in fish acclimated at 4 and 12° C to determine if protein degradation via the proteasome pathway could be imposing a limitation on somatic growth. Cardiac 20S proteasome activity was not affected by acclimation temperature nor fish mass and had no correlation with G. Hepatic 20S proteasome activity was higher at 12° C but did not show any relationship with G. Partial correlation analysis showed that white muscle 20S proteasome activity was negatively correlated to G (partial Pearson's r = −0·609) but only at cold acclimation temperature (4° C). It is suggested that acclimation to cold temperature involves compensation of the mitochondrial oxidative capacity which would in turn lead to increased production of oxidatively damaged proteins that are degraded by the proteasome pathway and ultimately negatively affects G at cold temperature.
Investment in testes, sperm‐duct glands and lipid reserves differs between male morphs but not between early and late breeding season in Pomatoschistus minutus
Authors: Kvarnemo C. , Svensson O. , Manson W.
Published: April 2010

This study of the sand goby Pomatoschistus minutus, a nest‐holding fish with paternal care, focused on gonadal investment among males of different sizes collected early and late in the breeding season. All males caught at the nest had breeding colour, whereas trawl‐caught fish consisted of males both with and without colour. The absence or presence of breeding colour was a good predictor of testes investment. Compared to males with breeding colour, males without colour were smaller in body size but had extraordinarily large testes. In absolute terms, testes mass of males without breeding colour was on average 3·4 times greater than those of males with breeding colour. Since small colourless males are known to reproduce as sneaker males, this heavy investment in testes probably reflects that they are forced to spawn under sperm competition. Contrary to testes size, sperm‐duct glands were largest among males with breeding colour. These glands produce mucins used for making sperm‐containing mucous trails that males place in the nest before and during spawning. Since both sneakers and nest‐holders potentially could benefit from having large glands, this result is intriguing. Yet, high mucus production may be more important for nest‐holders, because it also protects developing embryos from infections. There was no significant effect of season on body size, testes or sperm‐duct glands size, but colourless males tended to be less common late in the season. Possibly this may indicate that individual small colourless males develop into their more colourful counterparts within the breeding season.
Nestin is expressed in HMB‐45 negative melanoma cells in dermal parts of nodular melanoma
Authors: KANOH Maho , AMOH Yasuyuki , TANABE Kenichi , MAEJIMA Hideki , TAKASU Hiroshi , KATSUOKA Kensei
Published: April 2010

Nestin, a marker of neural stem cells, is expressed in the stem cells of the mouse hair follicle. The nestin‐expressing hair follicle stem cells can differentiate into neurons, glia, keratocytes, smooth muscle cells and melanocytes in vitro. These pluripotent nestin‐expressing stem cells are keratin 15 (K15)‐negative, suggesting that they are in a relatively undifferentiated state. Recent studies suggest that the epithelial stem cells are important in tumorigenesis, and nestin expression is thought to be important in tumorigenesis. In the present study, we examined the expression of the hair follicle and neural stem cell marker nestin, as well as S‐100 and HMB‐45, in melanoma. Nestin immunoreactivity was observed in the HMB‐45‐negative melanoma cells in all five cases of amelanotic nodular melanomas. Moreover, nestin immunoreactivity was observed in the dermal parts in seven of 10 cases of melanotic nodular melanomas. Especially, nestin immunoreactivity was observed in the HMB‐45‐negative melanoma cells in the dermal parts of all 10 cases of HMB‐45‐negative amelanotic and melanotic nodular melanomas. On the other hand, nestin expression was negative in 10 of 12 cases of superficial spreading melanoma. These results suggest that nestin is an important marker of HMB‐45‐negative melanoma cells in the dermal parts of patients with nodular melanoma.
Positive treatment effects of ustekinumab in psoriasis: Analysis of lesional and systemic parameters
Authors: REDDY Manjula , TORRES Gisela , McCORMICK Thomas , MARANO Colleen , COOPER Kevin , YEILDING Newman , WANG Yuhua , PENDLEY Charles , PRABHAKAR Uma , WONG Jackson , DAVIS Cuc , XU Stephen , BRODMERKEL Carrie
Published: April 2010

Ustekinumab, a human anti‐interleukin (IL)‐12/IL‐23p40 monoclonal antibody has demonstrated significant efficacy in patients with moderate‐to‐severe psoriasis. Skin lesion biopsies, cell surface markers on peripheral blood lymphocytes, and ex vivo T‐helper (Th)1/Th2 cytokine responses from peripheral blood mononuclear cells (PBMC) from patients receiving ustekinumab 45 or 90 mg, or placebo were evaluated at baseline and week 12. Inflammatory serum protein levels were measured at baseline, week 2 and week 12. At week 12, median epidermal thickness decreased from 312.1 to 132.7 μm, and median levels of cellular proliferation (Ki67) and T‐cell infiltration (CD3) decreased by 84.3% and 70.7%, respectively, in the combined ustekinumab group (all P ≤ 0.002). Serum levels of tumor necrosis factor (TNF)‐α, C‐C motif ligand 27 (CCL27) and other inflammatory cytokines remained unchanged. Minimal variation in the percentage of T cells expressing cutaneous lymphocyte antigen (CLA) was observed following ustekinumab treatment, with no significant variation in the percentage of cells expressing CD45RA, CD45RO, CD25, human leukocyte antigen‐DR (HLA‐DR), and C‐X‐C motif receptor 3 (CXCR3). No apparent effect on the magnitude of Th1/Th2 responses to external stimuli in PBMC was observed following placebo or ustekinumab treatment. Ustekinumab improves histological psoriasis measures, with minimal impact on the systemic immune system.
Role of the subgroups of T, B, natural killer lymphocyte and serum levels of interleukin‐15, interleukin‐21 and immunoglobulin E in the pathogenesis of urticaria
Authors: HUILAN Zhu , RUNXIANG Li , BIHUA Liang , QING Guo
Published: April 2010

The immunological characterization in the pathogenesis of urticaria, mainly regarding cytokine profile, needs more investigation. In this study, subgroups of the T, B and natural killer (NK) lymphocyte from peripheral blood and serum levels of interleukin (IL)‐15, IL‐21 and immunoglobulin (Ig)E were examined in patients with acute urticaria (AU) and chronic urticaria (CU). Moreover, symptom scores and course of the patients were assessed. The percentage of NK cells and the ratio of CD4+/CD8+ increased, however, CD8+ decreased in CU compared to controls (P < 0.01). But no significant changes of T, B and NK lymphocyte were found in AU. IL‐15 and IL‐21 significantly decreased in AU and CU, but IgE increased. CU with a positive autologous serum skin test were more likely to be associated with longer course and higher CD3+, B cells and IL‐21, and lower IgE (P < 0.01). Weak negative correlations were demonstrated between CD3+, CD8+ and scores in CU (r = −0.23, −0.25, P < 0.05). Significant correlations were found between B cells and scores and course in CU (r = 0.49, 0.65, P < 0.01). Moreover, a significant correlation was found between IL‐21 and IgE (r = 0.42, P < 0.01) in CU. But no significant correlations were found in AU. Our findings supported the concept that both humoral immunity and cellular immunity dysregulation in the pathogenesis of urticaria – mainly related to the decrease of the serum levels of IL‐15 and IL‐21 – may induce the increasing expression of IgE produced by B cells.
Molecular typing ofTrichophyton mentagrophytesvar.interdigitaleisolated in a university hospital in Japan based on the non‐transcribed spacer region of the ribosomal RNA gene
Authors: WAKASA Asako , ANZAWA Kazushi , KAWASAKI Masako , MOCHIZUKI Takashi
Published: April 2010

Detecting intraspecies polymorphisms in fungi causing dermatophytoses is important in elucidating routes of infection and determining whetherTinearecurrence is caused by exacerbation or re‐infection. In fungi, the non‐transcribed spacer region (NTS) of the ribosomal RNA gene shows the greatest accumulation of base sequence mutations. We therefore assessed NTS sequences in 64 clinical isolates ofTrichophyton mentagrophytesvar. interdigitale, the second most common species of dermatophytes in Japan. These isolates were among the clinical isolates of dermatophytes in the Department of Dermatology, Kanazawa Medical University Hospital in 2006 and were obtained by morphological and molecular biological identification methods. DNA was extracted from each isolate, as well as from one isolate maintained in our department, to detect length polymorphisms at each of three variable loci, TmiS0, TmiS1 and TmiS2, of the NTS for subtyping. We observed seven patterns for TmiS0, six patterns for TmiS1 and three patterns for TmiS2. The combinations of these patterns enabled us to classify the 65 isolates into 15 types. The most prevalent, constituted 46% (30/65) of all isolates. Eleven types were new combinations, whereas the other four were previously described. These results suggest that this method may be used to determine the molecular epidemiology ofT. mentagrophytesvar.interdigitalein Japan, because it generated results rapidly and in a sensitive manner.
Occupational injuries in children and adolescents in emergency services of Aracaju, Brazil
Authors: De Vasconcelos R. B. A. , Santos J. C. V. , Araujo R. F. , De Souza L. , Dantas R. A. A. , Gurgel R. Q.
Published: April 2010

Background  The incidence of occupational injuries among children and adolescents is not well known in Brazil. This study aims to identify occurrences and characteristics of occupational injuries in children and adolescents at the two major public emergency hospitals in Aracaju, Brazil.

Methods  In a cross sectional study, all children and adolescents (5–17 years) attending the services because of accidents of external cause in October–November 2006 and May–June 2007 were evaluated. The patients and their responsibles were interviewed to obtain information about the injury, family and patient characteristics and relation to work in the last 7 days. Data were analysed in number and percentages using descriptive statistics and chi‐squared and Fisher's exact tests.

Results  There were 917 patients with injuries of external cause in the period studied. Seventy‐one (8%) had worked in the last 7 days and in 40 (4%) the injury was related to work, with 2 (0.21%) deaths. Occupational injuries occurred more frequently in boys (95%); in the 14‐ to 17‐year‐old age group (77%); in agricultural (46%) and commercial activities (18%); to help with family budget (54%); without any safety training (73.5%) and not using personal protective equipment (94%). Main mechanisms of injuries were transportation incidents (42.5%) and contact with tools and equipment (27.5%). Injuries were mostly fractures (37.5%) and lacerations (22.5%). Upper extremities were injured in 49% of cases and the lower extremities in 26.5%. Comparison between the two groups (accident related or not related to labour) shows that there were significant differences for gender, age group, the main mechanism of injury and the part of the body injured, but not for the nature of injury.

Conclusion  Working children and adolescents have been injured during their occupational activities and work‐related injuries represent 4% of injuries of external causes in the emergency departments of Aracaju with 5% lethality.
Use of the Griffiths Mental Development Scales in an agro‐industrial province in the Philippines
Authors: Reyes A. , Pacifico R. , Benitez B. , Villanueva‐Uy E. , Lam H. , Ostrea Jr E. M.
Published: April 2010

Background  There is a need to assess neurobehavioral performance of children in developing countries using standardized developmental tools.

Methods  The Griffiths Mental Development Scales was evaluated in the Philippines by comparing the performance of 742 Filipino children longitudinally at 6, 12 and 24 months old to those of their British counterparts.

Results  The mean general and subquotient scores of Filipino children were all within average for age. Comparison with British children showed that except for performance subscales, Filipino children had significantly higher developmental subquotients at 6 months old. As the Filipino infants grew older, their developmental subquotients in all subscales were significantly lower, except for personal and social skills at 24 months old. The genetic predisposition as evidenced by modest maternal scores on the Wechsler Intelligence Scales and lack of familiarity with test materials are factors that may influence the developmental patterns of Filipino children.

Conclusion  Although the performance of the Filipino children in the Griffiths test were within average with age, their performance on developmental subquotients at later ages of 12 and 24 months were significantly lower than British children and may have been influenced by differences in ethnicity, cultural traditions and limited environmental resources.
Child sexual abuse in Lebanon during war and peace
Authors: Usta J. , Farver J.
Published: April 2010

Purpose Child sexual abuse (CSA) is rarely addressed in the Arab world. This study examined the prevalence, risk factors and consequences associated with CSA in Lebanese children before, during and after the 2006 Hezbollah‐Israeli war.

Method A total of 1028 Lebanese children (556 boys; 472 girls) were administered an interview questionnaire that included the International Child Abuse Screening Tool, the Trauma Symptom Checklist and the Family Functioning in Adolescence Questionnaire.

Results In total, 249 (24%) children reported at least one incident of CSA; 110 (11%) occurred before the war, 90 (8%) took place in the 1‐year period after the war to the time of the data collection and 49 (5%) occurred during the 33‐day war. There were no gender differences in CSA reports before or after the war, but boys reported more incidents during the war than did girls. Girls who reported CSA had higher trauma‐related symptoms for sleep disturbance, somatization, Post Traumatic Stress Disorder (PTSD) and anxiety than did boys. There were geographic differences in the reports of abuse that may be associated with poverty and living standards. Logistic regression analyses correctly classified 89.9% of the cases and indicated that children's age, family size, fathers' education level and family functioning significantly predicted CSA during the period following the war.

Conclusions The prevalence of CSA in the current study is within the reported international range. Given the increase in the incidents of CSA during the war and the significant findings for family‐related risk factors, there is an urgent need to provide multi‐component culturally appropriate interventions that target the child and the family system in times of peace and conflict.
Prevalence of overweight and obesity among preadolescent schoolchildren in Galicia, Spain
Authors: Vázquez F. L. , Díaz O. , Pomar C.
Published: April 2010

Background  Childhood obesity is rising rapidly in many countries. Preadolescents appear to be at particularly high risk. This study estimated the prevalence of overweight and obesity in preadolescent schoolchildren in Galicia, Spain.

Methods  The heights and weights of a random sample of 2305 Galician schoolchildren aged 10–12 years were measured using calibrated standardized scales and measures. Overweight and obesity were identified using the criteria of the International Obesity Task Force.

Results  The prevalences of obesity and overweight were respectively 9.2% and 31.0% among boys, 8.6% and 28.8% among girls and 8.9% and 29.9% overall. Taking boys and girls together, the combined prevalence of overweight and obesity fell significantly with increasing age. Overweight was more prevalent in rural than urban areas (30.7% vs. 28.4%), as also was obesity (9.8% vs. 7.2%).

Conclusions  Our study evidences the emergence of the obesity epidemic among preadolescents in Galicia, especially in rural areas. Both overweight and obesity in this age group are more prevalent in Galicia than in other areas of Spain or most other Western nations.
The prevalence of carriage of meticillin‐resistant staphylococci by veterinary dermatology practice staff and their respective pets
Authors: Morris Daniel O. , Boston Raymond C. , O’Shea Kathleen , Rankin Shelley C.
Published: April 2010

It has been shown that people and pets can harbour identical strains of meticillin‐resistant (MR) staphylococci when they share an environment. Veterinary dermatology practitioners are a professional group with a high incidence of exposure to animals infected by Staphylococcus spp. The objective of this study was to assess the prevalence of carriage of MR Staphylococcus aureus (MRSA), MR S. pseudintermedius (MRSP) and MR S. schleiferi (MRSS) by veterinary dermatology practice staff and their personal pets. A swab technique and selective media were used to screen 171 veterinary dermatology practice staff and their respective pets (258 dogs and 160 cats). Samples were shipped by over‐night carrier. Human subjects completed a 22‐question survey of demographic and epidemiologic data relevant to staphylococcal transmission. The 171 human‐source samples yielded six MRSA (3.5%), nine MRSP (5.3%) and four MRSS (2.3%) isolates, while 418 animal‐source samples yielded eight MRSA (1.9%) 21 MRSP (5%), and two MRSS (0.5%) isolates. Concordant strains (genetically identical by pulsed‐field gel electrophoresis) were isolated from human subjects and their respective pets in four of 171 (2.9%) households: MRSA from one person/two pets and MRSP from three people/three pets. In seven additional households (4.1%), concordant strains were isolated from only the pets: MRSA in two households and MRSP in five households. There were no demographic or epidemiologic factors statistically associated with either human or animal carriage of MR staphylococci, or with concordant carriage by person–pet or pet–pet pairs. Lack of statistical associations may reflect an underpowered study.
A marker associated with increased risk for severe liver disease in cystic fibrosis
Authors: De Haan W
Published: April 2010

Genetic modifiers of liver disease in cystic fibrosis Bartlett et al. (2009)

The Journal of the American Medical Association 302: 1076–1083
A folate receptor defect that causes treatable neurological disorder in children
Authors: De Haan W
Published: April 2010

Folate receptor alpha defect causes cerebral folate transport deficiency: a treatable neurodegenerative disorder associated with disturbed myelin metabolism

Steinfeld et al. (2009)

The American Journal of Human Genetics 85: 354–363
Lipodystrophy and muscular dystrophy caused by PTRF mutations
Authors: De Haan W
Published: April 2010

Human PTRF mutations cause secondary deficiency of caveolins resulting in muscular dystrophy with generalized lipodystrophy

Hayashi et al. (2009)

The Journal of Clinical Investigation 119: 2623–2633
The pancreas allograft donor: current status, controversies, and challenges for the future
Authors: Fridell Jonathan A. , Rogers Jeffrey , Stratta Robert J.
Published: April 2010

Fridell JA, Rogers J, Stratta RJ. The pancreas allograft donor: current status, controversies, and challenges for the future. Clin Transplant 2010: 24: 433–449. © 2010 John Wiley & Sons A/S.

Abstract:  The pancreas allograft is a scarce resource that is currently underutilized. The selection of appropriate deceased donors for pancreas procurement is of paramount importance for minimizing technical failure and optimizing long‐term outcomes in pancreas transplantation. Despite the increasing demand for pancreas transplantation, increases in overall organ donation rates and the evolution of criteria that constitute an “acceptable” pancreas donor, the number of deceased donor pancreas transplants being performed in the United States has actually declined in recent years. Although there are many factors that must be considered during evaluation of the potential pancreas allograft donor to minimize morbidity and graft loss, it is evident that there are transplantable organs that are not used. In this review, deceased donor pancreas identification, management, selection, allocation, assessment, preservation, and the problem of pancreas underutilization will be discussed.
Nitric oxide for post‐liver‐transplantation hypoxemia in pediatric hepatopulmonary syndrome: Case report and review
Authors: Schiller Ofer , Avitzur Yaron , Kadmon Gili , Nahum Elchanan , Steinberg Ran M. , Nachmias Vered , Schonfeld Tommy
Published: April 2010

Schiller O, Avitzur Y, Kadmon G, Nahum E, Steinberg RM, Nachmias V, Schonfeld T. Nitric oxide for post‐liver‐transplantation hypoxemia in pediatric hepatopulmonary syndrome: Case report and review. Pediatr Transplantation 2011: 15: E130–E134. © 2010 John Wiley & Sons A/S.

Abstract:  HPS is rare in the pediatric population. Liver transplantation is the ultimate treatment for severe HPS. There are only a few case reports and one series of children in whom HPS was the main indication for liver transplantation. Outcome was good in most of them, with full regression of the pulmonary process. However, hypoxemia in the early post‐operative course can have severe consequences, and effective treatment modalities are needed. There are rare instances of the use of iNO for the treatment of post‐operative hypoxemia. We describe a 10.5‐yr‐old boy with severe HPS owing to chronic liver disease after bone marrow transplantation. Liver transplantation from a living related donor (the same sister who donated the bone marrow) was complicated by severe hypoxemia on POD 2. iNO was administered via the ventilator circuit and, after extubation, through nasal prongs. It was slowly tapered down and stopped on POD 10. The child had an otherwise uneventful course and was discharged home on POD 21 with normal oxygen saturation. Liver transplantation should be offered to children with severe HPS. iNO can reverse the hypoxemia that may occur after the operation.
Detection of telomerase activity in cultured cells and tumor tissue of lung carcinoma by modified telomeric repeat amplification protocol
Authors: Liu Yan , Wu Bing‐quan , Zhong Hao‐hao , Xu Mei‐lin , Fang Wei‐gang
Published: April 2010

Telomerase activity is found in various cell types including stem cells, neoplastic cells, and immortalized cells, suggesting a close association with their proliferation capacity. The telomeric repeat amplification protocol (TRAP) has been traditionally used to detect semi‐quantitatively the telomerase activity by polyacrylamide gel electrophoresis (PAGE), which is difficult to apply for large scale analysis because of laborious post‐PCR manipulation and potential carryover contamination. In the present study, a specific reverse primer was designed and the TRAP protocol was adapted to either PAGE or real‐time PCR assay. Using cultured cell lines, the real‐time TRAP showed a dramatic improvement in the reliability and accuracy of quantitation of telomerase activity and was able to discriminate the A549 cells from hundreds‐fold human embryonic lung cells. Using clinical samples of 60 lung cancers and 8 inflammatory lesions, the real‐time TRAP was also superior in quantitation, high‐throughput capability and standardization. Our modified real‐time TRAP should be applicable for the detection of telomerase activity for the initial screening and progression monitoring of lung cancer patients. Our approach is particularly useful when only limited clinical specimen is available, such as fine needle aspiration or other cytological specimens that may contain only a small number of tumor cells.
Lipopolysaccharide induced connective tissue growth factor gene expression in human bronchial epithelial cells
Authors: NISHIOKA Michiyoshi , OGAWA Emiko , KINOSE Daisuke , HARUNA Akane , OHARA Tadashi , ITO Isao , HOSHINO Yuma , ITO Yutaka , MATSUMOTO Hisako , NIIMI Akio , MIO Tadashi , CHIN Kazuo , HIRAI Toyohiro , MURO Shigeo , MISHIMA Michiaki
Published: April 2010

Background and objective:  Connective tissue growth factor (CTGF) is up‐regulated in the lungs of patients with chronic obstructive pulmonary disease (COPD). Cigarette smoke and repeated bacterial infections, both of which are rich sources of LPS, are major causes of COPD. The high levels of LPS in lung epithelial lining fluid also suggest that it may have a considerable impact on the airway epithelium, in terms of cytokine and growth factor production. The aim of this study was to clarify the mechanism of LPS‐induced CTGF expression in bronchial epithelial cells.

Methods:  The expression and transcriptional regulation of the CTGF gene were assessed using the cultured human bronchial epithelial cell line, BEAS‐2B.

Results:  LPS significantly up‐regulated CTGF mRNA expression in a dose‐dependent fashion, with 100 µg/mL LPS causing a twofold increase after 2 h. CTGF protein expression was also up‐regulated by LPS after 8 h. Transforming growth factor‐β1 mRNA expression was not changed by LPS treatment. A pharmacological inhibitor of nuclear factor (NF)‐κB, MG132, inhibited LPS‐induced CTGF mRNA expression. Furthermore, luciferase assays demonstrated that deletion of base pairs −253 to −53 from the CTGF promoter, where the Smad and proximal NF‐κB binding sites are located, decreased the induction of CTGF by LPS. After stimulation with LPS, the p65 subunit of NF‐κB was shown to be bound to the CTGF promoter in vitro and in situ.

Conclusions:  LPS directly induced CTGF expression in bronchial epithelial cells, independently of transforming growth factor‐β1, suggesting a possible mechanism for airway remodelling in COPD that is induced by smoking and repeated bacterial infections.
Peak power estimated from 6‐minute walk distance in Asian patients with idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease
Authors: KOZU Ryo , JENKINS Sue , SENJYU Hideaki , MUKAE Hiroshi , SAKAMOTO Noriho , KOHNO Shigeru
Published: April 2010

Background and objective:  Pulmonary rehabilitation guidelines recommend cycle ergometry training at an intensity that exceeds 60% of peak power (Ppeak) with the aim of achieving a physiologic response. However, many clinicians do not have access to an incremental cycle ergometry test (ICET) to allow prescription of training intensity. No studies have investigated whether the 6MWT can be used to estimate the Ppeak achieved during an ICET in subjects with IPF or in Asian subjects with COPD.

Methods:  A total of 90 Japanese subjects (IPF n = 45, COPD n = 45) undertook a 6MWT and a symptom‐limited ICET in random order. Anthropometry, quadriceps strength and lung function were measured.

Results:  Exercise tests were prematurely terminated in 10 subjects with IPF due to profound oxygen desaturation (SpO2 < 80%). The ICET elicited higher peak heart rates, dyspnea and leg fatigue in both subject cohorts (all P < 0.01). The magnitude of oxygen desaturation was greater during the 6MWT (P < 0.01). 6MWD was strongly associated with Ppeak (r = 0.80, P < 0.01) in both subject cohorts. In subjects with IPF, the predictive equation that accounted for the greatest proportion of variance in Ppeak included 6MWD and FVC %pred (R2 = 0.70). In the COPD subjects, 6MWD alone accounted for 64% of the variance in Ppeak and the inclusion of other variables did not increase R2.

Conclusions:  Ppeak can be estimated from the 6MWT in Japanese subjects with IPF and COPD. This may allow individualized prescription of the intensity for cycle‐based training based on the 6MWT.
Primary pulmonary coccidioidomycosis in China
Authors: LAN Fen , TONG Yao‐Zhi , HUANG Hong , XIONG Wei‐Ning , XU Yong‐Jian , XIONG Sheng‐Dao
Published: April 2010

Coccidioidomycosis is a fungal infection endemic to south‐west USA, north Mexico and parts of Central and South America. We report here a case of primary pulmonary coccidioidomycosis in a previously healthy 14‐year‐old boy in China, which is considered a non‐endemic country. The patient had non‐specific symptoms of pulmonary infection, including fever, non‐productive cough and night sweats. Both spherules and endospores of Coccidioides immitis were seen histologically following transbronchial biopsy of a cavitary lesion. The patient was treated with amphotericin B and fluconazole. Follow up 6 months post discharge found that the patient made a good recovery.
The use of non‐invasive ventilation for life‐threatening asthma attacks: Changes in the need for intubation
Authors: MURASE Kimihiko , TOMII Keisuke , CHIN Kazuo , TSUBOI Tomomasa , SAKURAI Ayako , TACHIKAWA Ryo , HARADA Yuka , TAKESHIMA Yoshimi , HAYASHI Michio , ISHIHARA Kyosuke
Published: April 2010

Background and objective:  Although non‐invasive ventilation (NIV) has been shown to be effective in a wide variety of respiratory diseases, its role in severe asthma attacks remains uncertain. The aim of this study was to clarify the effectiveness of NIV in patients experiencing severe attacks of asthma.

Methods:  A retrospective cohort study was performed, comparing the periods November 1999–October 2003 (pre‐introduction of NIV) and November 2004–October 2008 (post‐introduction of NIV). The data and clinical outcomes for patients who experienced severe attacks of asthma, and who fulfilled the inclusion criteria, were retrieved and compared.

Results:  Fifty events (48 patients) from the pre‐NIV period and 57 events (54 patients) from the post‐NIV period, which required hospitalization, were included in the analysis. Nine of the 50 pre‐NIV events (mean PaO2/fraction of inspired O2 (FiO2) 241 ± 161; PaCO2 79 ± 40) were treated primarily by endotracheal intubation (ETI), while 17 of the 57 post‐NIV events (PaO2/FiO2 197 ± 132, P = 0.39; PaCO2 77 ± 30, P = 0.95) were treated primarily by NIV. The rate of ETI decreased in the post‐NIV period (2/57 (3.5%) vs 9/50 (18%), P = 0.01). NIV was started earlier than mechanical ventilation (MV) with ETI (mean time interval between arrival and start of MV 171.7 ± 217.9 min vs 38.5 ± 113.8 min for NIV, P < 0.05). In the post‐NIV cohort, there was a trend towards a reduction in the duration of MV with ETI or NIV (36.9 ± 38.4 h vs 20.3 ± 35.8 h, P = 0.09), and hospital stay was shortened (12.6 ± 4.2 vs 8.4 ± 2.8 days, P < 0.01). No deaths occurred during this period as a consequence of asthma attacks.

Conclusions:  The need for ETI in patients with severe attacks of asthma was decreased after introduction of NIV. The ready availability of NIV enabled the rapid commencement of MV and may decrease the need for ETI. NIV is an acceptable and useful method of stabilizing patients experiencing severe attacks of asthma.
Endocannabinoid regulation of spinal nociceptive processing in a model of neuropathic pain
Authors: Sagar Devi Rani , Jhaveri Maulik D. , Richardson Denise , Gray Roy A. , De Lago Eva , Fernández‐Ruiz Javier , Barrett David A. , Kendall David A. , Chapman Victoria
Published: April 2010

Models of neuropathic pain are associated with elevated spinal levels of endocannabinoids (ECs) and altered expression of cannabinoid receptors on primary sensory afferents and post‐synaptic cells in the spinal cord. We investigated the impact of these changes on the spinal processing of sensory inputs in a model of neuropathic pain. Extracellular single‐unit recordings of spinal neurones were made in anaesthetized neuropathic and sham‐operated rats. The effects of spinal administration of the cannabinoid CB1receptor antagonistN‐(piperidin‐1‐yl)‐5‐(4‐iodophenyl)‐1‐(2,4‐dichlorophenyl)‐4‐methyl‐1H‐pyrazole‐3‐carboxamide (AM251) and the cannabinoid receptor type 2 (CB2) receptor antagonistN‐[(1S)‐endo‐1,3,3‐trimethylbicycloheptan‐2‐yl]‐5‐(4‐chloro‐3‐methylphenyl)‐1‐(4‐methylbenzyl)‐pyrazole‐3‐carboxamide (SR144528) on mechanically‐evoked responses of spinal neurones were determined. The effects of spinal administration of (5Z,8Z11Z,14Z)‐N‐(3‐furanylmethyl)‐5,8,11,14‐eicosatetraenamide (UCM707), which binds to CB2receptors and alters transport of ECs, on evoked responses of spinal neurones and spinal levels of ECs were also determined. The cannabinoid CB1receptor antagonist AM251, but not the CB2receptor antagonist, significantly facilitated 10‐g‐evoked responses of spinal neurones in neuropathic, but not sham‐operated, rats. Spinal administration of UCM707 did not alter spinal levels of ECs but did significantly inhibit mechanically‐evoked responses of neurones in neuropathic, but not sham‐operated, rats. Pharmacological studies indicated that the selective inhibitory effects of spinal UCM707 in neuropathic rats were mediated by activation of spinal CB2receptors, as well as a contribution from transient receptor potential vanilloid 1 (TRPV1) channels. This work demonstrates that changes in the EC receptor system in the spinal cord of neuropathic rats influence the processing of sensory inputs, in particular low‐weight inputs that drive allodynia, and indicates novel effects of drugs acting via multiple elements of this receptor system.
Risk‐preference differentiates orbitofrontal cortex responses to freely chosen reward outcomes
Authors: Roitman Jamie D. , Roitman Mitchell F.
Published: April 2010

To successfully evaluate potential courses of action and choose the most favorable, we must consider the outcomes that may result. Many choices involve risk, our assessment of which may lead us to success or failure in matters financial, legal or health‐related. The orbitofrontal cortex (OFC) has been implicated as critical for evaluating choices based on risk. To measure how outcomes of risky decisions are represented in the OFC, we recorded the electrophysiological activity of single neurons while rats made behavioral responses to obtain rewards under conditions of either certainty or risk. Rats exhibited different risk‐preferences when given the opportunity to choose. In risk‐preferring rats, OFC responses were enhanced following the delivery of large rewards obtained under risk compared with smaller, certain rewards and reward omission. However, in risk‐neutral rats, neurons showed similarly enhanced responses to both large rewards obtained under risk and smaller, certain rewards compared with reward omission. Thus, the responses of OFC neurons reflected the subjective evaluation of outcomes in individuals with different risk‐preferences. Such enhanced neural responding to risky rewards may serve to bias individuals towards risk‐preference in decision‐making.
Expression of cell fate determinants and plastic changes after neurotoxic lesion of adult mice spinal cord by cholera toxin‐B saporin
Authors: Gulino Rosario , Perciavalle Vincenzo , Gulisano Massimo
Published: April 2010

Recent studies have attempted to repair the damaged spinal cord (SC) by stimulating neurogenesis or neuroplasticity. Sonic hedgehog (Shh), Notch‐1 and Numb are involved in the stem cell functioning. Additionally, Notch‐1 has a role as modulator of synaptic plasticity. However, little is known about the role of these proteins in the adult SC after removal of motoneurons. In this study, we have injected cholera toxin‐B saporin into the gastrocnemius muscle to induce a depletion of motoneurons within the lumbar SC of adult mice, and analysed the expression of choline acetyltransferase (ChAT), Synapsin‐I, Shh, Notch‐1 and Numb proteins. The functional outcome of the lesion was monitored by grid walk and rotarod tasks. The neurotoxin lesion determined a motoneuron depletion and a transient decrease of ChAT, Synapsin‐I, Shh and Numb levels in the lumbar SC. ChAT was associated with Synapsin‐I expression and motor performance at 1 week but not 1 month after lesion, suggesting that the recovery of locomotion could depend on synaptic plasticity, at least in an early phase. Shh and Notch‐1 were associated with Synapsin‐I levels, suggesting a role in modulating synaptic plasticity. Numb expression also appeared reduced after lesion and linked to motor performance. Moreover, unlike other lesion models, we observed glial reaction but no evidence of cell proliferation within the depleted SC. Given the mentioned roles of Shh, Notch‐1 and Numb, we believe that an in vivo manipulation of their signalling after lesion could represent a suitable way to improve functional recovery by modulating synaptic plasticity and/or neurogenesis.
Caffeine prevents sleep loss‐induced deficits in long‐term potentiation and related signaling molecules in the dentate gyrus
Authors: Alhaider Ibrahim A. , Aleisa Abdulaziz M. , Tran Trinh T. , Alkadhi Karim A.
Published: April 2010

We have previously reported that caffeine prevented sleep deprivation‐induced impairment of long‐term potentiation (LTP) of area CA1 as well as hippocampus‐dependent learning and memory performance in the radial arm water maze. In this report we examined the impact of long‐term (4‐week) caffeine consumption (0.3 g/L in drinking water) on synaptic plasticity (Alhaider et al., 2010) deficit in the dentate gyrus (DG) area of acutely sleep‐deprived rats. The sleep deprivation and caffeine/sleep deprivation groups were sleep‐deprived for 24 h by using the columns‐in‐water technique. We tested the effect of caffeine and/or sleep deprivation on LTP and measured the basal levels as well as stimulated levels of LTP‐related molecules in the DG. The results showed that chronic caffeine administration prevented the impairment of early‐phase LTP (E‐LTP) in the DG of sleep‐deprived rats. Additionally, chronic caffeine treatment prevented the sleep deprivation‐associated decreases in the basal levels of the phosphorylated calcium/calmodulin‐dependent protein kinase II (P‐CaMKII) and brain derived neurotrophic factor (BDNF) as well as in the stimulated levels of P‐CaMKII in the DG area. The results suggest that chronic use of caffeine prevented anomalous changes in the basal levels of P‐CaMKII and BDNF associated with sleep deprivation and as a result contributes to the revival of LTP in the DG region.
Distribution and diversity of carbon monoxide‐oxidizing bacteria and bulk bacterial communities across a succession gradient on a Hawaiian volcanic deposit
Authors: Weber C. F. , King G. M.
Published: April 2010

Relatively little is known about the distribution and diversity of CO‐oxidizing bacteria during succession on volcanic deposits even though they are among the primary colonists. We surveyed CO‐oxidizing communities across a vegetation gradient on a 1959 cinder deposit using coxL (large subunit gene of carbon monoxide dehydrogenase) sequences. Sequences most closely related to a coxL sequence from Ktedonobacter racemifer, dominated unvegetated cinders, while Proteobacteria‐like sequences dominated vegetated sites. The number of coxL operational taxonomic units (OTUs) increased threefold with increased vegetation, and correlated most strongly with the increased β‐Proteobacteria richness (r = 0.987). These compositional shifts were also reflected in overall bacterial community compositions as determined by 16S rRNA gene analysis. Notably, coxL OTU:16S rRNA OTU ratios increased with increased vegetation, indicating that CO oxidizers became a larger fraction of total bacterial richness during succession. Results from most probable number estimates and maximum potential CO uptake activity assays indicate that increased richness is paralleled by increased CO oxidizer abundance, which likely results from increased vegetation and organic carbon content. Collectively, results suggest that in contrast to patterns observed for plant succession, a versatile bacterial functional group that is important during early colonization and succession can remain important in later stages of succession, irrespective of dramatic environmental changes.
Spectral Mesh Processing
Authors: Zhang H. , Van Kaick O. , Dyer R.
Published: April 2010

Spectral methods for mesh processing and analysis rely on the eigenvalues, eigenvectors, or eigenspace projections derived from appropriately defined mesh operators to carry out desired tasks. Early work in this area can be traced back to the seminal paper by Taubin in 1995, where spectral analysis of mesh geometry based on a combinatorial Laplacian aids our understanding of the low‐pass filtering approach to mesh smoothing. Over the past 15 years, the list of applications in the area of geometry processing which utilize the eigenstructures of a variety of mesh operators in different manners have been growing steadily. Many works presented so far draw parallels from developments in fields such as graph theory, computer vision, machine learning, graph drawing, numerical linear algebra, and high‐performance computing. This paper aims to provide a comprehensive survey on the spectral approach, focusing on its power and versatility in solving geometry processing problems and attempting to bridge the gap between relevant research in computer graphics and other fields. Necessary theoretical background is provided. Existing works covered are classified according to different criteria: the operators or eigenstructures employed, application domains, or the dimensionality of the spectral embeddings used. Despite much empirical success, there still remain many open questions pertaining to the spectral approach. These are discussed as we conclude the survey and provide our perspective on possible future research.
Optical Image Processing Using Light Modulation Displays
Authors: Wetzstein Gordon , Heidrich Wolfgang , Luebke David
Published: April 2010

We propose to enhance the capabilities of the human visual system by performing optical image processing directly on an observed scene. Unlike previous work which additively superimposes imagery on a scene, or completely replaces scene imagery with a manipulated version, we perform all manipulation through the use of a light modulation display to spatially filter incoming light. We demonstrate a number of perceptually motivated algorithms including contrast enhancement and reduction, object highlighting for preattentive emphasis, colour saturation, de‐saturation and de‐metamerization, as well as visual enhancement for the colour blind. A camera observing the scene guides the algorithms for on‐the‐fly processing, enabling dynamic application scenarios such as monocular scopes, eyeglasses and windshields.