bluuebunny/crossref_metadata_2025 huggingface dataset:
Distinction immune genes of hepatitis-induced heptatocellular carcinoma
Authors: Hu Jinyu , Gao David Zhiwei
Published: October 2012

Motivation: Hepatitis B virus and hepatitis C virus are the two leading causes resulting in hepatocellular carcinoma (HCC). It is observed that hepatitis C virus (HCV) is relatively difficult to induce HCC compared with hepatitis B virus (HBV). This motivates us to reveal the reasons behind this from the viewpoint of immune genes.

Results: To distinguish the immune genes with low-level expression in HBV-induced HCC, but high-level expression in HCV-induced HCC, the concept of distinction immune gene is proposed. A filter is then designed to screen these genes. By using gene positive network with strong correlations between genes, the genes are further filtered to form the set of key distinction immune genes. The 23 key distinction immune genes are screened, which are divided into four clusters, T cells, B cells, immune signalling and major histocompatibility complex. It is evident that the screened genes are important immune genes, which are activated in HCV-induced HCC, but inactivated in HBV-induced HCC. In HCV-induced HCC, the structures of HCV adaptively update, so that they are difficult to be identified by antigens. Therefore, the clinic advice is either to increase the update speed of antigens or reduce the update speed of the viruses during the treatment of HCV-induced HCC. Moreover, it is also advised to add T cells or add the expression levels of T cells to strengthen the ability to kill cancer cells. In contrast, HBV updates slowly, but the immunity system in HBV-induced HCC has been damaged seriously. As a result, the clinic advice is to improve the immune ability of patients subjected to HBV-induced HCC, such as increasing immunoglobulin, T cells and B cells and so forth.

Contact:  zhiwei.gao@northumbria.ac.uk
PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data
Authors: Zhang Lu , Zhang Jing , Yang Jing , Ying Dingge , Lau Yu lung , Yang Wanling
Published: October 2012

Next-generation sequencing has become a valuable tool for detecting mutations involved in Mendelian diseases. However, it is a challenge to identify the small subset of functionally important mutations from tens of thousands of rare variants in a whole exome/genome. Therefore, we developed a toolkit called PriVar, a systematic prioritization pipeline that takes into consideration calling quality of the variants, their predicted functional impact, known connection of the gene to the disease and the number of mutations in a gene, and inference from linkage analysis.

Availability: Executable jar package is available at http://paed.hku.hk/uploadarea/yangwl/html/software.html.

Contact: yangwl@hkucc.hku.hk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Introducing Drugster: a comprehensive and fully integrated drug design, lead and structure optimization toolkit
Authors: Vlachakis Dimitrios , Tsagrasoulis Dimosthenis , Megalooikonomou Vasileios , Kossida Sophia
Published: October 2012

Summary: Drugster is a fully interactive pipeline designed to break the command line barrier and introduce a new user-friendly environment to perform drug design, lead and structure optimization experiments through an efficient combination of the PDB2PQR, Ligbuilder, Gromacs and Dock suites. Our platform features a novel workflow that guides the user through each logical step of the iterative 3D structural optimization setup and drug design process, by providing a seamless interface to all incorporated packages.

Availability: Drugster can be freely downloaded via our dedicated server system at http://www.bioacademy.gr/bioinformatics/drugster/.

Contact:  dvlachakis@bioacademy.gr.
MycPermCheck: the Mycobacterium tuberculosis permeability prediction tool for small molecules
Authors: Merget Benjamin , Zilian David , Müller Tobias , Sotriffer Christoph A.
Published: October 2012

Motivation: With >8 million new cases in 2010, particularly documented in developing countries, tuberculosis (TB) is still a highly present pandemic and often terminal. This is also due to the emergence of antibiotic-resistant strains (MDR-TB and XDR-TB) of the primary causative TB agent Mycobacterium tuberculosis (MTB). Efforts to develop new effective drugs against MTB are restrained by the unique and largely impermeable composition of the mycobacterial cell wall.

Results: Based on a database of antimycobacterial substances (CDD TB), 3815 compounds were classified as active and thus permeable. A data mining approach was conducted to gather the physico-chemical similarities of these substances and delimit them from a generic dataset of drug-like molecules. On the basis of the differences in these datasets, a regression model was generated and implemented into the online tool MycPermCheck to predict the permeability probability of small organic compounds.

Discussion: Given the current lack of precise molecular criteria determining mycobacterial permeability, MycPermCheck represents an unprecedented prediction tool intended to support antimycobacterial drug discovery. It follows a novel knowledge-driven approach to estimate the permeability probability of small organic compounds. As such, MycPermCheck can be used intuitively as an additional selection criterion for potential new inhibitors against MTB. Based on the validation results, its performance is expected to be of high practical value for virtual screening purposes.

Availability: The online tool is freely accessible under the URL http://www.mycpermcheck.aksotriffer.pharmazie.uni-wuerzburg.de

Contact: sotriffer@uni-wuerzburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
13CFLUX2—high-performance software suite for 13C-metabolic flux analysis
Authors: Weitzel Michael , Nöh Katharina , Dalman Tolga , Niedenführ Sebastian , Stute Birgit , Wiechert Wolfgang
Published: October 2012

Summary:  13C-based metabolic flux analysis (13C-MFA) is the state-of-the-art method to quantitatively determine in vivo metabolic reaction rates in microorganisms. 13CFLUX2 contains all tools for composing flexible computational 13C-MFA workflows to design and evaluate carbon labeling experiments. A specially developed XML language, FluxML, highly efficient data structures and simulation algorithms achieve a maximum of performance and effectiveness. Support of multicore CPUs, as well as compute clusters, enables scalable investigations. 13CFLUX2 outperforms existing tools in terms of universality, flexibility and built-in features. Therewith, 13CFLUX2 paves the way for next-generation high-resolution 13C-MFA applications on the large scale.

Availability and implementation: 13CFLUX2 is implemented in C++ (ISO/IEC 14882 standard) with Java and Python add-ons to run under Linux/Unix. A demo version and binaries are available at www.13cflux.net.

Contact:  info@13cflux.net or k.noeh@fz-juelich.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
High prevalence of undetected heart failure in long‐term care residents: findings from the Heart Failure in Care Homes (HFinCH) study
Authors: Hancock Helen C. , Close Helen , Mason James M. , Murphy Jerry J. , Fuat Ahmet , Singh Raj , Wood Esther , de Belder Mark , Brennan Gill , Hussain Nehal , Kumar Nitin , Wilson Doug , Hungin A. Pali S.
Published: October 2012

Aims

Diagnosis of heart failure in older people in long‐term care is challenging because of co‐morbidities, cognitive deficit, polypharmacy, immobility, and poor access to services. This study aimed to ascertain heart failure prevalence and clinical management in this population.

Methods and results

A total of 405 residents, aged 65–100 years, in 33 UK care facilities were prospectively enrolled between April 2009 and June 2010. The presence of heart failure was determined using European Society of Cardiology guidelines, modified where necessary for immobility. Evaluation of symptoms and signs, functional capacity, and quality of life, portable on‐site echocardiography, and medical record review were completed in 399 cases. The point prevalence of heart failure was 22.8% [n = 91, 95% confidence interval (CI) 18.8–27.2%]; of these, 62.7% (n = 57, 95% CI 59.6–66.5%) had heart failure with preserved ejection fraction and 37.3% had left ventricular systolic dysfunction (n = 34, 95% CI 34.8–40.5%). A total of 76% (n = 61) of previous diagnoses of heart failure were not confirmed, and up to 90% (n = 82) of study cases were new. No symptoms or signs were reliable predictors of heart failure.

Conclusion

Heart failure was diagnosed in almost a quarter of residents: the prevalence was substantially higher than in other populations. The majority of heart failure cases were undiagnosed, while three‐quarters of previously recorded cases were misdiagnosed. Common symptoms and signs appear to have little clinical utility in this population. Early, accurate differential diagnosis is key to the effective management of heart failure; this may be failing in long‐term care facilities.

Trial registration

ISRCTN19781227
High prevalence of myocarditis in patients with hypertensive heart disease and cardiac deterioration
Authors: Frustaci Andrea , Francone Marco , Petrosillo Nicola , Chimenti Cristina
Published: October 2012

Aims

Structural abnormalities causing cardiac deterioration in hypertensive heart disease (HHD) are poorly understood. The aim of the study was to evaluate left ventricular (LV) myocardial changes in patients with HHD and cardiac failure.

Methods and results

Among 1229 patients undergoing an LV or biventricular endomyocardial biopsy because of unexplained LV dysfunction from 2000 to 2010, 45 had HHD. The HHD population had non‐invasive assessment of cardiac wall thickness, diameters, and function; endomyocardial samples were processed for histology, immunohistochemistry, and polymerase chain reaction (PCR) for cardiotropic viruses. Mean LV end‐diastolic diameter was 63.3 ± 5.9 mm, LV ejection fraction 29.7 ± 7.6%, and maximal wall thickness 12.8 ± 0.9 mm. At histology, hypertrophy with degeneration of cardiomyocytes, increased external/lumen ratio of intramural arterioles, and myocardial fibrosis were observed in 17 patients (38%). In the remaining 28 patients (62%), these histological changes were associated with myocarditis. Myocarditis was present in 40.4% of the cohort without HHD. PCR was negative in HHD without inflammation while it was positive in 10 subjects with myocarditis (enterovirus in 3 cases, adenovirus 4, influenza virus 3). Addition of immunosuppression to supportive therapy in the 18 virus‐negative myocarditis subjects was followed at 6 months by significant recovery of LV function in 15 (83%; ejection fraction from 25.3 ±9.3% to 49.5 ±9.8%) while LV function improved to a minor extent (ejection fraction from 25 ± 5.1% to 36 ± 4.4%) in 12 of 27 patients (44%) on supportive treatment alone.

Conclusion

Myocarditis is a major cause of cardiac deterioration in patients with HHD; its recognition may improve patient treatment and outcome.
Plasma aldosterone levels are elevated in patients with pulmonary arterial hypertension in the absence of left ventricular heart failure: a pilot study
Authors: Maron Bradley A. , Opotowsky Alexander R. , Landzberg Michael J. , Loscalzo Joseph , Waxman Aaron B. , Leopold Jane A.
Published: October 2012

Aims

Elevated levels of the mineralocorticoid hormone aldosterone are recognized as a modifiable contributor to the pathophysiology of select cardiovascular diseases due to left heart failure. In pulmonary arterial hypertension (PAH), pulmonary vascular remodelling induces right ventricular dysfunction and heart failure in the absence of left ventricular (LV) dysfunction. Hyperaldosteronism has emerged as a promoter of pulmonary vascular disease in experimental animal models of PAH; however, the extent to which hyperaldosteronism is associated with PAH in patients is unknown. Thus, the central aim of the current study is to determine if hyperaldosteronism is an unrecognized component of the PAH clinical syndrome.

Methods and results

Plasma aldosterone levels and invasive cardiopulmonary haemodynamic measurements were obtained for 25 patients referred for evaluation of unexplained dyspnoea or pulmonary hypertension. Compared with controls (n = 5), patients with PAH (n = 18) demonstrated significantly increased plasma aldosterone levels (1200.4 ± 423.9 vs. 5959.1 ± 2817.9 pg/mL, P < 0.02), mean pulmonary artery pressure (21.4 ± 5.0 vs. 45.5 ± 10.4 mmHg, P < 0.002), and pulmonary vascular resistance (PVR) (1.41 ± 0.6 vs. 7.3 ± 3.8 Wood units, P < 0.003) without differences in LV ejection fraction or pulmonary capillary wedge pressure between groups. Among patients not prescribed PAH‐specific pharmacotherapy prior to cardiac catheterization, a subgroup of the cohort with severe pulmonary hypertension, aldosterone levels correlated positively with PVR (r = 0.72, P < 0.02) and transpulmonary gradient (r = 0.69, P < 0.02), but correlated inversely with cardiac output (r = –0.79, P < 0.005).

Conclusions

These data demonstrate a novel cardiopulmonary haemodynamic profile associated with hyperaldosteronism in patients: diminished cardiac output due to pulmonary vascular disease in the absence of LV heart failure.
Collapse of allis shad, Alosa alosa, in the Gironde system (southwest France): environmental change, fishing mortality, or Allee effect?
Authors: Rougier Thibaud , Lambert Patrick , Drouineau Hilaire , Girardin Michel , Castelnaud Gérard , Carry Laurent , Aprahamian Miran , Rivot Etienne , Rochard Eric
Published: October 2012

Rougier, T., Lambert, P., Drouineau, H., Girardin, M., Castelnaud, G., Carry, L., Aprahamian, M., Rivot, E., and Rochard, E. 2012. Collapse of allis shad, Alosa alosa, in the Gironde system (southwest France): environmental change, fishing mortality, or Allee effect? – ICES Journal of Marine Science, 69: 1802–1811. At the end of the 20th century the allis shad population in the Gironde was the largest in Europe. During the first decade of the 21st century, catches declined dramatically by two orders of magnitude, and a fishery moratorium was implemented in 2008. This deterioration in the status of the stock was confirmed by three independent assessments (abundance of juveniles and of potential and effective spawners). Three hypotheses on the cause of the collapse were examined: (i) an environmental change in freshwater and/or in the estuary; (ii) an increase in marine and/or estuarine mortality; and (iii) the presence of an Allee effect. Changes in flow, temperature, and water quality over the period were inconclusive, but remain a possible causative factor. The instantaneous rate of marine (mean: 0.7 year−1, s.e. 0.1 year−1) and estuarine (mean: 2.6 year−1, s.e. 0.1 year−1) mortalities showed no trend between 1991 and 2003. Nevertheless, the past high estuarine (fishing) mortalities combined with a demographic Allee effect in the reproduction dynamics could explain the population collapse and hamper the stock recovery under the moratorium. This conclusion is, however, tentative as it was not possible to prove the presence of the density-dependent mechanism associated with the demographic Allee effect.
Cod catches taken by the German recreational fishery in the western Baltic Sea, 2005–2010: implications for stock assessment and management
Authors: Strehlow Harry V. , Schultz Norbert , Zimmermann Christopher , Hammer Cornelius
Published: October 2012

Strehlow, H. V., Schultz, N., Zimmermann, C., and Hammer, C. 2012. Cod catches taken by the German recreational fishery in the western Baltic Sea, 2005–2010: implications for stock assessment and management. – ICES Journal of Marine Science, 69: 1769–1780. Next to the commercial fishery, the recreational fishery plays an important role in the removal of biomass from fish stocks. In this study, we present estimates of German recreational cod (Gadus morhua) catches in the western Baltic Sea between 2005 and 2010. Fishing effort was estimated using a stratified mail survey and annual sales of fishing licences. Catch per unit effort was estimated by stratified random sampling of access points and interviews about completed trips. Length distributions of cod catches were acquired by sampling recreational cod catches from charter boats and data from community fishing events. Estimates of the total cod biomass removed by the recreational fishery fluctuated between 2159 t in 2009 and 4127 t in 2005. Annual recreational fishery cod harvests accounted for a significant share of the total landings, with a yearly variation from 34 to 70% of the German commercial cod landings from the western Baltic Sea. The majority of recreational fishery cod catches were taken from private boats and charter vessels. Because of the amount and specifically the variability of the recreational catches, they are important for the assessment and management of the resource and, therefore, need to be surveyed annually.
Relationships between North Atlantic salmon, plankton, and hydroclimatic change in the Northeast Atlantic
Authors: Beaugrand Grégory , Reid Philip C.
Published: October 2012

Beaugrand, G. and Reid, P. C. 2012. Relationships between North Atlantic salmon, plankton, and hydroclimatic change in the Northeast Atlantic – ICES Journal of Marine Science, 69: 1549–1562. The abundance of wild salmon (Salmo salar) in the North Atlantic has declined markedly since the late 1980s as a result of increased marine mortality that coincided with a marked rise in sea temperature in oceanic foraging areas. There is substantial evidence to show that temperature governs the growth, survival, and maturation of salmon during their marine migrations through either direct or indirect effects. In an earlier study (2003), long-term changes in three trophic levels (salmon, zooplankton, and phytoplankton) were shown to be correlated significantly with sea surface temperature (SST) and northern hemisphere temperature (NHT). A sequence of trophic changes ending with a stepwise decline in the total nominal catch of North Atlantic salmon (regime shift in ∼1986/1987) was superimposed on a trend to a warmer dynamic regime. Here, the earlier study is updated with catch and abundance data to 2010, confirming earlier results and detecting a new abrupt shift in ∼1996/1997. Although correlations between changes in salmon, plankton, and temperature are reinforced, the significance of the correlations is reduced because the temporal autocorrelation of time-series substantially increased due to a monotonic trend in the time-series, probably related to global warming. This effect may complicate future detection of effects of climate change on natural systems.
Atlantic cod (Gadus morhua) feed during spawning off Newfoundland and Labrador
Authors: Krumsick Kyle J. , Rose George A.
Published: October 2012

Krumsick, K. J., and Rose, G. A. 2012. Atlantic cod (Gadus morhua) feed during spawning off Newfoundland and Labrador. – ICES Journal of Marine Science, 69: 1701–1709. We test a current assumption that Atlantic cod (Gadus morhua) off Newfoundland and Labrador, Canada, do not feed during the protracted spawning season (March–September). Stomach contents were analysed from 10 473 cod from four Northwest Atlantic Fisheries Organization regions (2J, 3K, 3L, and 3Ps) over 9 years from which gonads were also analysed to determine sex and maturity status. Adult cod in spawning condition did feed in all regions, usually at rates equivalent to or even greater than non-spawning fish and juveniles. Both sexes fed during spawning, though females consumed lesser amounts. Regional differences were evident. The total fullness index was greater in the northern (2J) than the southern (3Ps) region, with no consistent differences between spawners and non-spawners. The most southerly region (3Ps) exhibited the greatest prey diversity, the northern region (2J) the least. Shrimp was the major diet item in the northern regions. Capelin, zooplankton, crab, and other fish increased in importance to the south. Differences in prey items between non-spawning and spawning individuals of both sexes were possibly related to spawning behaviour. Models using consumption rates should not assume that cod do not feed during the protracted spawning season in these waters.
Indicators of fishing pressure and seafloor integrity
Authors: Piet G. J. , Hintzen N. T.
Published: October 2012

Piet, G. J., and Hintzen, N. T. 2012. Indicators of fishing pressure and seafloor integrity. – ICES Journal of Marine Science, 69: 1850–1858. This study calculates a suite of indicators reflecting the spatial extent of fishing and its impact on the seafloor and discusses the usefulness of these indicators to inform future management and the issues to consider. It explores several methods to calculate the indicators and shows that they can be informative to report on both fishing pressure and the status of the seafloor. However, although observed overall trends were robust against the specific method of calculation, the absolute values vary greatly with the calculation method. As both aspects are important from a policy perspective, agreement on the methodology to calculate the indicators is required. This study based on the Dutch Exclusive Economic Zone (EEZ) shows that it is possible to calculate indicators required to inform decision-makers on the pressure of fishing as well as the status of the seafloor pending a decision on the following issues: (i) choice of an appropriate grid cell resolution, (ii) use of interpolated VMS tracks instead of VMS position registrations, (iii) choice of an “intensity threshold” dependent on the benthic community recovery capacity, and (iv) the level of confidence required when assessing if an area is not impacted.
Effects of Varying CDS Levels and Drying and Cooling Temperatures on Flowability Properties of DDGS
Authors: Bhadra Rumela , Muthukumarappan Kasiviswanathan , Rosentrater Kurt A.
Published: October 2012

Demand for alternative fuels and the need to reduce dependence on fossil fuels have triggered the growth of corn‐based ethanol production, which is expected to rise in future years. Transportation of the coproduct distillers dried grains with solubles (DDGS) from this industry occurs under various environmental conditions. Transporting DDGS is often problematic, because caking between the particles can lead to flow problems. In this study, we have prepared DDGS by combining condensed distillers solubles (CDS) with distillers wet grains and then drying. We investigated the effects of CDS level (10, 15, and 20%, wb), drying temperature (100, 200, and 300°C), and cooling temperature (–12, 25, and 35°C) on the flowability of the resulting DDGS. Statistical analyses of the resulting data found significant differences among the cooling temperature levels for angle of repose, total flow and flood indices, dispersibility, water activity, and protein dispersibility index. Additionally, significant interaction effects between CDS, drying temperature, and cooling temperature levels for angle of repose, total flow and flood indices, dispersibility, and protein dispersibility index were observed. Response surface regression on selected dimensionless flowability parameters was also applied. However, multivariate PLS regression yielded better results (R2 > 0.8) than response surface plots. Understanding the effects of drying and cooling temperatures as well as CDS levels can be used to help improve the industrial processing of DDGS and improve storage and transportation.
Amount and Size Distribution of Monomeric and Polymeric Proteins in the Grain of Organically Produced Wheat
Authors: Hussain Abrar , Larsson Hans , Kuktaite Ramune , Prieto‐Linde Maria Luisa , Johansson Eva
Published: October 2012

In the present study, we evaluated 444 organically grown wheat genotypes for the amount and size distribution of polymeric proteins by size‐exclusion HPLC. The investigated genotypes were divided into six genotype groups—selection, spelt, old cultivar, primitive, landrace, and cultivar—and these were grown in four different locations, namely, Alnarp, Bohuslän, Gotland, and Uppsala in Sweden. The results showed that the percentage of unextractable polymeric proteins in total polymeric proteins (%UPP) and percentage of large unextractable polymeric proteins in total polymeric proteins were higher in the cultivar group as compared with the rest of the investigated genotype groups. The amounts of total extractable polymeric proteins (TOTE) and total unextractable polymeric proteins were low in cultivars and selections, respectively. Spring wheat grain was found to have a significantly higher amount of all protein fractions as compared with winter wheat. The genotype Kenya was found to belong to both groups of the 20 genotypes with the highest TOTE and %UPP. Thus, the genotype Kenya might be of relevance for consumption and future breeding to improve the breadmaking quality of organically produced wheat.
First Report of Pilidium concavum causing Leaf Necrosis on Fallopia japonica in the United States
Authors: Bruckart W. L. , Eskandari F. M. , Coombs E. M. , Rossman A. Y. , Palm M. E.
Published: October 2012

Fallopia japonica (Houtt.) Ronse Decr. (= Polygonum cuspidatum Siebold & Zucc.; Japanese knotweed, JKW) is an invasive perennial forb in the Polygonaceae. It has been identified as a target for biological control in many parts of the world, including the United States. Several potted JKW plants in an outdoor study at the Oregon Department of Agriculture, Salem (44.93° N, 122.99° W) developed leaf spots. Samples collected on August 20, 2007, were sent to the FDWSRU for identification of the disease. The necrotic leaf spots were brown and large, 1 to 3 cm in diameter, and in some cases occupying 30% of the leaf area. Both hemispherical and discoid conidiomata with gloeoid spore masses (3) developed in necrotic areas of all leaves placed in moist chambers. Discoid conidiomata had dark, pedicellate bases subtending a fimbriate disc on which pale brown to brown gloeoid conidial masses were produced. Hemispherical conidiomata were black, circular, sessile, and somewhat flattened, within which similar, gloeoid conidial masses were produced. Conidia from each type of conidioma were unicellular, cylindrical to fusiform, hyaline, and 4.5 to 7.2 × 0.9 to 1.8 μm (mean 5.7 × 1.33). Artificial inoculation of 15 plants was made on two occasions with a suspension of 106 conidia per ml, followed by two 16-hr dew periods at 25°C that were separated by an 8-hr “day;” a similar set of 15 non-inoculated plants served as controls each time. Symptoms similar to those in the original sample developed within 2 months after inoculation. The fungus was easily reisolated, and conidia from each type of conidioma produced similar growth on artificial media and similar disease after inoculation. The characteristics of conidial size and distinctly different conidiomata are diagnostic of Pilidium concavum (Desm.) Höhn (3,4). A sequence of the ITS1-5.8S-ITS2 region DNA, extracted using a DNeasy Plant Mini Kit (QIAGEN), was found identical to that of P. concavum from Rosa sp. (BPI 1107275; GenBank Accession No. AY487094), using BLAST. This isolate, FDWSRU 07-116, has been deposited in the US National Fungus Collection (BPI 883546) and at the Centraalbureau voor Schimmelcultures (CBS 132725). Sequence data have been deposited in GenBank (JQ790789). To our knowledge, this is the first report of P. concavum causing disease on a member of the Polygonaceae in North America (1), a disease clearly different from a Japanese Mycosphaerella sp. under consideration for biological control of JKW in the United Kingdom (2).

References: (1) D. F. Farr, and A. Y. Rossman. Fungal Databases, Systematic Mycology and Microbiology Laboratory, ARS, USDA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , May 15, 2012. (2) D. Kurose et al. MycoSci. 50:179, 2009. (3) M. E. Palm, Mycologia 83:787, 1991. (4) A. Y. Rossman, et al. Mycol. Progr. 3:275, 2004.
First Report of Bhendi yellow vein mosaic virus Associated with Yellow Vein Mosaic of Okra (Abelmoschus esculentus) in Thailand
Authors: Tsai W. S. , Shih S. L. , Lee L. M. , Wang J. T. , Duangsong U. , Kenyon L.
Published: October 2012

A disease of okra (Abelmoschus esculentus) causing yellowing veins and mosaic on leaves and fruit has emerged in Thailand. Incidences of 50 to 100% diseased plants were observed in fields in Kanchanaburi and Nakhon Pathom provinces in 2009 and 2010, respectively. Leaf samples were collected from three and four diseased plants in Kanchanaburi and Nakhon Pathom, respectively. All seven samples tested positive for begomovirus by PCR using universal primer pair PAL1v1978B/PAR1c715H (3). One sample from Kanchanaburi also tested positive by ELISA using Okra mosaic virus (Genus Tymovirus) antiserum (DSMZ, Braunschweig, Germany). When the nucleotide sequences of the 1.5 kb begomovirus PCR products were compared they were found to share 99.1 to 99.5% identity with each other, and 97.5 to 97.7% identity to Bhendi yellow vein mosaic virus Okra isolate from India (GenBank Accession No. GU112057; BYVMV-[IN: Kai:OY: 06]). The complete DNA-A sequence for a Kanchanaburi isolate (JX678967) was obtained using abutting primers WTHOK6FL-V/-C (WTHOK6FL-V: 5′-GCGAAGCTTAGATAACGCTCCTT-3′; WTHOK6FL-C: 5′-TCCAAGCTTTGAGTCTGCAACGT-3′), while that of a Nakhon Pathom isolate (JX678966) was obtained with primers WTHOK6FLV/WTHOK2FL-C (WTHOK2FL-C: 5′-TCCAAGCTTTGAGTCTGCATCGT-3′). The DNA-A sequences of both isolates are 2,740 nucleotides in length and share 99.6% identity. Each has the geminivirus conserved sequence (TAATATTAC), two open reading frames (ORFs) in the virus sense (V1 and V2) and four in the complementary sense (C1 to C4). Based on BLASTn searching GenBank and sequence analysis using MegAlign (DNASTAR), both DNA-A sequences have greatest nucleotide identity (96.2 to 96.4%) with BYVMV-[IN: Kai:OY: 06] from India. Also, BYVMV-associated betasatellite DNA (1.4 kb) was detected in all begomovirus-positive samples, except one sample from Nakhon Pathom (1). However, no virus DNA-B was detected in any of the samples using either general detection primer pair DNABLC1/DNABLV2 or DNABLC2/DNABLV2 (2). Okra infected with BYVMV has been reported in South Asia in Bangladesh, India, and Pakistan. To the best of our knowledge, this is the first report of BYVMV associated with Okra Yellow Vein Mosaic Disease in Southeast Asia. Since fruits with symptoms are regarded as low quality and have little market value, even low incidence of the disease is likely to cause significant reductions in marketable yield. Strategies for managing BYVMV in okra in South and Southeast Asia should be sought, including the breeding and selecting of resistant varieties.

References: (1) R. W. Briddon et al. Mol. Biotechnol. 20:315, 2002. (2) S. K. Green et al. Plant Dis. 85:1286, 2001. (3) W. S. Tsai et al. Plant Pathol. 60:787, 2011.
Harsh childhood environmental characteristics predict exploitation and retaliation in humans
Authors: McCullough Michael E. , Pedersen Eric J. , Schroder Jaclyn M. , Tabak Benjamin A. , Carver Charles S.
Published: October 2012

Across and within societies, people vary in their propensities towards exploitative and retaliatory defection in potentially cooperative interaction. We hypothesized that this variation reflects adaptive responses to variation in cues during childhood that life will be harsh, unstable and short—cues that probabilistically indicate that it is in one's fitness interests to exploit co-operators and to retaliate quickly against defectors. Here, we show that childhood exposure to family neglect, conflict and violence, and to neighbourhood crime, were positively associated for men (but not women) with exploitation of an interaction partner and retaliatory defection after that partner began to defect. The associations between childhood environment and both forms of defection for men appeared to be mediated by participants' endorsement of a ‘code of honour’. These results suggest that individual differences in mutual benefit cooperation are not merely due to genetic noise, random developmental variation or the operation of domain-general cultural learning mechanisms, but rather, might reflect the adaptive calibration of social strategies to local social–ecological conditions.
Xiangella phaseoli gen. nov., sp. nov., a member of the family

Micromonosporaceae
Authors: Wang Xiangjing , Jia Feiyu , Liu Chongxi , Zhao Junwei , Wang Liang , Shen Yue , Wang Jidong , Zhang Ji , Li Chuang , Xiang Wensheng
Published: October 2012

A novel endophytic actinomycete, designated strain NEAU-J5T was isolated from roots of snap bean (Phaseolus vulgaris L.). Comparative analysis of the 16S rRNA gene sequence indicated that NEAU-J5T is phylogenetically related to members of the family

Micromonosporaceae

. The whole-cell sugars were galactose, mannose and glucose. The predominant menaquinones were MK-9(H4) and MK-9(H6). The major fatty acids were C16 : 0, C18 : 0, C17 : 1ω7c, iso-C15 : 0 and C17 : 0. The phospholipids were phosphatidylmethylethanolamine, phosphatidylethanolamine, phosphatidylcholine, phosphatidylinositol and phosphatidylinositol mannoside. The DNA G+C content was 72.2 mol%. On the basis of the morphological and chemotaxonomic characteristics, phylogenetic analysis and characteristic patterns of 16S rRNA gene signature nucleotides, strain NEAU-J5T represents a novel species of a new genus within the family

Micromonosporaceae

, for which the name Xiangella phaseoli gen. nov., sp. nov. is proposed. The type strain of Xiangella phaseoli is strain NEAU-J5T ( = CGMCC 4.7038T = DSM 45730T).
Fasting Blood Glucose and Lipid Profile Alterations following Twelve-Month Androgen Deprivation Therapy in Men with Prostate Cancer
Authors: Sağlam Hasan S. , Köse Osman , Kumsar Şükrü , Budak Salih , Adsan Öztuğ
Published: October 2012

Purpose.In this retrospective study, we aimed to investigate the effects of androgen deprivation therapy (ADT) on blood glucose and blood cholesterol levels over a 12-month period.Materials and Methods.Between January 2010 and June 2012, the data of 44 patients with prostate cancer who were receiving ADT were collected from a hospital database. Patients with additional malignancy or diabetes and those who had been prescribed and were currently taking cholesterol-lowering medication were excluded from the study. Data (including fasting blood glucose levels and a cholesterol profile) were collected and analysed statistically. A value <0.05 was considered statistically significant.Results.Twelve months after the initiation of ADT, fasting blood glucose (FBG), total cholesterol (TC), low-density lipoprotein (LDL) cholesterol, high-density lipoprotein (HDL) cholesterol, and triglyceride (TG) levels changed. FBG, TC, LDL cholesterol, and TG increased significantly (, 0.000, 0.000, and 0.000, resp.), while HDL cholesterol decreased ().Conclusion.ADT may increase FBG, TC, LDL cholesterol, and TG but decrease HDL cholesterol by the end of a year of treatment. Therefore, close followup may be needed as a consequence of one-year ADT regarding metabolic alterations.
G9a/GLP-dependent histone H3K9me2 patterning during human hematopoietic stem cell lineage commitment
Authors: Chen Xiaoji , Skutt-Kakaria Kyobi , Davison Jerry , Ou Yang-Li , Choi Edward , Malik Punam , Loeb Keith , Wood Brent , Georges George , Torok-Storb Beverly , Paddison Patrick J.
Published: October 2012

G9a and GLP are conserved protein methyltransferases that play key roles during mammalian development through mono- and dimethylation of histone H3 Lys 9 (H3K9me1/2), modifications associated with transcriptional repression. During embryogenesis, large H3K9me2 chromatin territories arise that have been proposed to reinforce lineage choice by affecting high-order chromatin structure. Here we report that in adult human hematopoietic stem and progenitor cells (HSPCs), H3K9me2 chromatin territories are absent in primitive cells and are formed de novo during lineage commitment. In committed HSPCs, G9a/GLP activity nucleates H3K9me2 marks at CpG islands and other genomic sites within genic regions, which then spread across most genic regions during differentiation. Immunofluorescence assays revealed the emergence of H3K9me2 nuclear speckles in committed HSPCs, consistent with progressive marking. Moreover, gene expression analysis indicated that G9a/GLP activity suppresses promiscuous transcription of lineage-affiliated genes and certain gene clusters, suggestive of regulation of HSPC chromatin structure. Remarkably, HSPCs continuously treated with UNC0638, a G9a/GLP small molecular inhibitor, better retain stem cell-like phenotypes and function during in vitro expansion. These results suggest that G9a/GLP activity promotes progressive H3K9me2 patterning during HSPC lineage specification and that its inhibition delays HSPC lineage commitment. They also inform clinical manipulation of donor-derived HSPCs.
Deciphering Systemic Wound Responses of the Pumpkin Extrafascicular Phloem by Metabolomics and Stable Isotope-Coded Protein Labeling
Authors: Gaupels Frank , Sarioglu Hakan , Beckmann Manfred , Hause Bettina , Spannagl Manuel , Draper John , Lindermayr Christian , Durner Jörg
Published: October 2012

In cucurbits, phloem latex exudes from cut sieve tubes of the extrafascicular phloem (EFP), serving in defense against herbivores. We analyzed inducible defense mechanisms in the EFP of pumpkin (Cucurbita maxima) after leaf damage. As an early systemic response, wounding elicited transient accumulation of jasmonates and a decrease in exudation probably due to partial sieve tube occlusion by callose. The energy status of the EFP was enhanced as indicated by increased levels of ATP, phosphate, and intermediates of the citric acid cycle. Gas chromatography coupled to mass spectrometry also revealed that sucrose transport, gluconeogenesis/glycolysis, and amino acid metabolism were up-regulated after wounding. Combining ProteoMiner technology for the enrichment of low-abundance proteins with stable isotope-coded protein labeling, we identified 51 wound-regulated phloem proteins. Two Sucrose-Nonfermenting1-related protein kinases and a 32-kD 14-3-3 protein are candidate central regulators of stress metabolism in the EFP. Other proteins, such as the Silverleaf Whitefly-Induced Protein1, Mitogen Activated Protein Kinase6, and Heat Shock Protein81, have known defensive functions. Isotope-coded protein labeling and western-blot analyses indicated that Cyclophilin18 is a reliable marker for stress responses of the EFP. As a hint toward the induction of redox signaling, we have observed delayed oxidation-triggered polymerization of the major Phloem Protein1 (PP1) and PP2, which correlated with a decline in carbonylation of PP2. In sum, wounding triggered transient sieve tube occlusion, enhanced energy metabolism, and accumulation of defense-related proteins in the pumpkin EFP. The systemic wound response was mediated by jasmonate and redox signaling.
Magnetic resonance imaging findings and outcome of neuro‐Behçet's disease: the predictive factors
Authors: Farahangiz Siamak , Sarhadi Sirous , Safari Anahid , Borhani‐Haghighi Afshin
Published: October 2012

Aim

To investigate MRI findings that may predict unfavorable outcomes in the patients with neuro‐Behçet's disease.

Subjects and Methods

All consecutive patients referred from 2002 to 2009 to the Behçet Clinic at Nemazee Hospital, Shiraz, Iran, who fulfilled International Study Group criteria for Behçet's disease and diagnosed as having neuro‐Behçet's disease, were enrolled into this study. Characteristics of initial brain MRI were studied in patients with different courses of neuro‐Behçet's disease.

Results

Initial MRIs of 58 patients (31 women) with a mean ± SD age of 38.9 ± 9.7 years were reviewed. Forty‐nine (84%) patients had parenchymal and nine (16%) had non‐parenchymal neuro‐Behçet's disease. Of those patients with parenchymal neuro‐Behçet's disease, 15 (31%) had monophasic, 13 (27%) polyphasic and 10 (20%) progressive courses; 11 (22%) had only headache attributed to Behçet's disease. The most common sites of involvement in patients with parenchymal neuro‐Behçet's disease were periventricular and superficial cerebral white matter, midbrain and pons, respectively. Of those with parenchymal involvement, 12 (24%) had extension of lesions, seven (14%) had contrast enhancement, 12 (24%) had black holes and five (10%) had brainstem atrophy. Patients with a progressive course had a significantly (P = 0.017; OR = 18, 95% CI: 1.7–19.1) higher rate of brainstem atrophy than those with a non‐progressive course (monophasic or polyphasic).

Conclusion

Presence of brainstem atrophy in the initial MRIs may predict a progressive course in patients with neuro‐Behçet's disease.
Omega‐3 fatty acids deficiency aggravates glutamatergic synapse and astroglial aging in the rat hippocampal CA1
Authors: Latour Alizée , Grintal Barbara , Champeil‐Potokar Gaelle , Hennebelle Marie , Lavialle Monique , Dutar Patrick , Potier Brigitte , Billard Jean‐Marie , Vancassel Sylvie , Denis Isabelle
Published: October 2012

Epidemiological data suggest that a poor ω3 status favoured by the low ω3/ω6 polyunsaturated fatty acids ratio in western diets contributes to cognitive decline in the elderly, but mechanistic evidence is lacking. We therefore explored the impact of ω3 deficiency on the evolution of glutamatergic transmission in the CA1 of the hippocampus during aging by comparing 4 groups of rats aged 6–22 months fed ω3‐deficient or ω3/ω6‐balanced diets from conception to sacrifice: Young ω3 Balanced (YB) or Deficient (YD), Old ω3 Balanced (OB) or Deficient (OD) rats. ω3 Deficiency induced a 65% decrease in the amount of docosahexaenoic acid (DHA, the main ω3 in cell membranes) in brain phospholipids, but had no impact on glutamatergic transmission and astroglial function in young rats. Aging induced a 10% decrease in brain DHA, a 35% reduction of synaptic efficacy (fEPSP/PFV) due to decreased presynaptic glutamate release and a 30% decrease in the astroglial glutamate uptake associated with a marked astrogliosis (+100% GFAP). The ω3 deficiency further decreased these hallmarks of aging (OD vs. OB rats: −35% fEPSP/PFV P < 0.05, −15% astroglial glutamate uptake P < 0.001, +30% GFAP P < 0.01). This cannot be attributed to aggravation of the brain DHA deficit because the brains of OD rats had more DHA than those of YD rats. Thus, ω3 deficiency worsens the age‐induced degradation of glutamatergic transmission and its associated astroglial regulation in the hippocampus.
Next‐generation peptide vaccines for advanced cancer
Authors: Yamada Akira , Sasada Tetsuro , Noguchi Masanori , Itoh Kyogo
Published: October 2012

Many clinical trials of peptide vaccines have been carried out since the first clinical trial of a melanoma antigen gene‐1‐derived peptide‐based vaccine was reported in 1995. The earlier generations of peptide vaccines were composed of one to several human leukocyte antigen class I‐restricted CTL‐epitope peptides of a single human leukocyte antigen type. Currently, various types of next‐generation peptide vaccines are under development. In this review, we focus on the clinical trials of the following categories of peptide vaccines mainly published from 2008 to 2012: (i) multivalent long peptide vaccines; (ii) multi‐peptide vaccines consisting of CTL‐ and helper‐epitopes; (iii) peptide cocktail vaccines; (iv) hybrid peptide vaccines; (v) personalized peptide vaccines; and (vi) peptide‐pulsed dendritic cell vaccines. (Cancer Sci 2013; 104: 15–21)
Diagnostic and prognostic value of plasma and tissue ubiquitin‐like, containing PHD and RING finger domains 1 in breast cancer patients
Authors: Geng Yao , Gao Yanfang , Ju Huangxian , Yan Feng
Published: October 2012

Ubiquitin‐like, containing PHD and RING finger domains 1 (UHRF1) has been reported to play an important role in breast carcinogenesis. This work investigated the correlation of UHRF1 DNA level in plasma with clinical characteristics of breast cancer and its clinical significance in breast cancer diagnosis. The expression of UHRF1 in primary breast cancer tissue was examined by Western blot. The UHRF1 DNA levels in plasma and UHRF1 mRNA expression in tissues were determined by accurate real‐time quantitative PCR. The associations of UHRF1 levels with clinical variables were evaluated using standard statistical methods. The UHRF1 DNA in plasma of 229 breast cancer patients showed higher expression than healthy controls, which showed high specificity up to 76.2% at a sensitivity of 79.2%, and was significantly associated with c‐erbB2 positive status, cancer stage and lymph node metastasis. High UHRF1 DNA level in plasma was significantly associated with short progression‐free survival. The UHRF1 DNA level in plasma is highly correlative with breast cancer and its status and stage, and may be a potential independent diagnostic and prognostic factor for both breast cancer and the survival of breast cancer patients.
Intraperitoneal delivery of a small interfering RNA targeting NEDD1 prolongs the survival of scirrhous gastric cancer model mice
Authors: Fujita Takeshi , Yanagihara Kazuyoshi , Takeshita Fumitaka , Aoyagi Kazuhiko , Nishimura Takao , Takigahira Misato , Chiwaki Fumiko , Fukagawa Takeo , Katai Hitoshi , Ochiya Takahiro , Sakamoto Hiromi , Konno Hiroyuki , Yoshida Teruhiko , Sasaki Hiroki
Published: October 2012

The prognosis of patients with advanced diffuse‐type gastric cancer (GC), especially scirrhous gastric cancer (SGC) remains extremely poor. Peritoneal carcinomatosis is a frequent form of metastasis of SGC. With survival rates of patients with peritoneal metastasis at 3 and 5 years being only 9.8% and 0%, respectively, development of a new treatment is urgently crucial. For such development, the establishment of a therapeutic mouse model is required. Among the 11 GC cell lines we examined, HSC‐60 showed the most well‐preserved expression profiles of the Hedgehog and epithelial‐mesenchymal transition pathways found in primary SGCs. After six cycles of harvest of ascitic tumor cells and their orthotopic inoculation in scid mice, a highly metastatic subclone of HSC‐60, 60As6 was obtained, by means of which we successfully developed peritoneal metastasis model mice. The mice treated with small interfering (si) RNA targeting NEDD1, which encodes a gamma‐tubulin ring complex‐binding protein, by the atelocollagen‐mediated delivery system showed a significantly prolonged survival. Our mouse model could thus be useful for the development of a new therapeutic modality. Intraperitoneal administration of siRNAs of targeted genes such as NEDD1 could provide a new opportunity in the treatment of the peritoneal metastasis of SGC.