The publication productivity of international agricultural research centers

The literature output over one year, 1990, of 22 International Agricultural Research Centers (IARCs), including 16 Consultative Group on International Agricultural Research (CGIAR) centers, was examined. Total output of the IARCs was 1,694 items, of which on average 42% were primary (refereed) literature; 24% were reports and monographs; 18% proceedings papers; 8% book chapters; and 8% semitechnical/popular literature. Total literature production from the IARCs is similar in magnitude to that of FAO. There were 1,230 internationally recruited scientists in the IARCs, with an average annual productivity of 1.38 items per scientist, including 0.58 primary literature articles. There was no correlation between scientific productivity and numbers of scientists in a center. However, there was a significant positive correlation between scientific productivity and center budget, indicating higher efficiency in the larger centers. In view of the nature of IARCs' literature output, we argue that IARCs should reject the trend for scientists to be assessed only by citations in core primary literature; and that IARCs should set up an international standard, perhaps based on the present proportionality of types of their literature output in order to assess IARC individual scientists and the health of their institutional output.     

Architectural layer recovery for software system understanding and evolution

This paper presents an approach to identify software layers for the understanding and evolution of software systems implemented with any object‐oriented programming language. The approach first identifies relations between the classes of a software system and then uses a link analysis algorithm (i.e. the Kleinberg algorithm) to group them into layers. Additionally to assess the approach and the underlying techniques, the paper also presents a prototype of a supporting tool and the results from a case study. Copyright © 2010 John Wiley & Sons, Ltd.     

A recursive algorithm for estimating multiple models continuous transfer function with non-uniform sampling

A multiple model recursive least squares algorithm combined with a first-order low-pass filter transformation method, named λ-transform, is proposed for the simultaneous identification of multiple model orders continuous transfer functions from non-uniformly sampled input–output data. The λ-transformation is shown to be equivalent to a canonical transformation between discrete z-domain and δ-domain using the negative value of the λ-transform filter time-constant instead of the sampling interval parameter. The proposed algorithm deals with oversampling, sampling jitter or non-uniform sample intervals without the need for extra digital anti-aliasing pre-filtering, downsampling or interpolation algorithms, producing multiple models with a cost function that facilitates automatic selection of best-fitted models. Besides, measurement noise is noted as beneficial, bringing up an inherent bias toward low-order models. Simulated examples and a drum-boiler level experimental result exhibiting non-minimum phase behaviour illustrate the application of the proposed method.     

Characterization and distribution of petroleum hydrocarbons and heavy metals in groundwater from three Italian tank farms

The present paper highlights the utility of petroleum chemical fingerprinting in investigating known or suspected tank farm releases. A detailed characterization of groundwater was carried out in three tank farms located in north, central and south Italy. Eighteen parent polycyclic aromatic hydrocarbons (naphthalene through coronene), n-alkanes (n-C(10) through n-C(36)), isoprenoids pristane and phytane, vanadium, nickel and lead were determined. Distribution profiles and diagnostic ratios of specific fuel constituents were studied in order to identify contamination sources. Data analysis shows that in the study sites multiple pollutant sources affecting the tank farms and the surrounding industrial areas are present. Both high concentrations of contaminants coming from fuel releases and noticeable concentrations of biogenic compounds were found. A detailed data analysis suggests the origin and the level of pollution of the three sites. The results demonstrate that threshold concentration approach is not always sufficient and it is necessary to carry out studies of contaminant distribution and their diagnostic ratios in order to perform a successful forensic investigation.     

The “Piano dell’Acqua” sinkholes (San Basile,Northern Calabria,Italy)

The occurrence of sinkholes not directly related to karst has been determined in several areas worldwide in recent years. These phenomena may be particularly dangerous to humans and infrastructure due to their subtle origin and need to be carefully examined. In this work, we describe five sinkholes recently identified in a hilly setting of Southern Italy characterized by Pliocene conglomerate and sand, and variously dislocated by tectonic structures. The sinkholes were examined by different methods (interpretation of multi-temporal aerial photos, geological, geomorphological and geophysical surveys). An historical analysis was performed to collect and critically evaluate information regarding the age of the phenomena. Based on this information, it can be conjectured that two of the five sinkholes developed during the 2000–2001 winter; two of the remaining probably originated during the 70s; the last one opened sometime between February 2001 and November 2007. Based on such chronology, attempts have been performed to identify the likely triggers, through hydrological and seismic analyses. In both cases, no immediate correlation could be found. The origin of the studied phenomena remains uncertain, and may be related to sub-cutaneous erosion, in an area that is renowned to be rich in groundwater. Local changes in the water table, related to climate and/or man-induced activities, may have triggered the development of the cover suffusion-type sinkholes. The present work highlights the potential for this type of phenomena to occur in geological settings without the direct presence of soluble rocks at the surface, a condition quite common in Southern Italy, and the need to carry out further studies in order to better comprehend their mechanisms of origin and successive evolution, and to properly evaluate the related hazard.     

HNE Michael adducts to histidine and histidine-containing peptides as biomarkers of lipid-derived carbonyl stress in urines: LC-MS/MS profiling in Zucker obese rats

A new liquid chromatography-tandem mass spectrometric (LC-MS/MS) approach, based on the precursor ion scanning technique using a triple-stage quadrupole, has been developed to detect free and protein-bound histidine (His) residues modified by reactive carbonyl species (RCS) generated by lipid peroxidation. This approach has been applied to urines from Zucker obese rats, a nondiabetic animal model characterized by obesity and hyperlipidemia, where RCS formation plays a key role in the development of renal and cardiac dysfunction. The immonium ion of His at m/z 110 was used as a specific product ion of His-containing peptides to generate precursor ion spectra, followed by MS2 acquisitions of each precursor ion of interest for structural characterization. By this approach, three novel adducts, which are excreted in free form only, have been identified, two of them originating from the conjugation of 4-hydroxy-trans-2-nonenal (HNE) to His, followed by reduction/oxidation of the aldehyde: His-1,4-dihydroxynonane (His-DHN), His-4-hydroxynonanoic acid (His-HNA), and carnosine-HNE, this last recognized in previous in vitro studies as a new potential biomarker of carbonyl stress. No free His-HNE was found in urines, which was detected only in protein hydrolysates. The same LC-MS/MS method, working in multiple reaction monitoring (MRM) mode, has been developed, validated, and applied to quantitatively profile in Zucker urines both conventional (1,4-dihydroxynonane mercapturic acid, DHN-MA) and the newly identified adducts, except His-HNA. The analytes were separated on a C12 reversed-phase column by gradient elution from 100% A (water containing 5 mM nonafluoropentanoic acid) to 80% B (acetonitrile) in 24 min at a flow rate of 0.2 mL/min and analyzed for quantification in MRM mode by applying the following precursor-to-product ion transitions m/z 322.2 --> 164.1 + 130.1 (DHN-MA), m/z 314.7 --> 268.2 + 110.1 (His-DHN), m/z 312.2 --> 110.1 + 156.0 (His-HNE), m/z 383.1 --> 266.2 + 110.1 (CAR-HNE), m/z 319.2 --> 301.6 + 156.5 (H-Tyr-His-OH, internal standard). Precision and accuracy data, as well as the lower limits of quantification in urine, were highly satisfactory (from 0.01 nmol/mL for CAR-HNE, His-DHN, His-HNE, to 0.075 nmol/mL for DHN-MA). The method, applied to evaluate for the first time the advanced lipoxidation end products profile in urine from obese Zucker rats, an animal model for the metabolic syndrome, has proved to be suitable and sensitive enough for testing in vivo the carbonyl quenching ability of newly developed RCS sequestering agents.     

The Gas family of proteins of Saccharomyces cerevisiae: characterization and evolutionary analysis

The GAS multigene family of Saccharomyces cerevisiae is constituted by five genes (GAS1-GAS5), but GAS1 was the only one to have been characterized to date. Gas1 is a glycosylphosphatidylinositol-anchored protein predominantly localized in the plasma membrane and is also a representative of family GH72 of glycosidase/transglycosidases, a wide group of yeast and fungal enzymes involved in cell wall assembly. Gas1-Gas5 proteins share a common N-terminal domain but exhibit different C-terminal extensions, in which a domain named Cys-Box is located. This domain is similar to the carbohydrate binding module 43 and is present only in Gas1p and Gas2p. Here we report the expression in P. pastoris of soluble forms of Gas proteins. Gas1, 2, 4 and 5 proteins were secreted with a yield of about 30-40 mg/l of medium, whereas the yield for Gas3p was about three times lower. Gas proteins proved to be N-glycosylated. Purified Gas proteins were tested for enzymatic activity. Gas2, Gas4 and Gas5p showed a beta-(1,3)-glucanosyltransferase activity similar to Gas1p. A phylogenetic tree of the N-terminal regions of family GH72 members was constructed. Two subfamilies of N-terminal regions were distinguished: one subfamily, GH72(+), contains proteins that possess a Cys-box in the C-terminal region, whereas family GH72(-) comprises proteins that lack a Cys-box. On the basis of this net distinction, we speculate that the type of C-tail region imposed constraints to the evolution of the N-terminal portion.     

Persistent organic pollutants in edible marine species from the Gulf of Naples, Southern Italy

Edible tissues from 10 marine species, collected from the Gulf of Naples in the Southern Tyrrhenian Sea (Italy) between February and July 2003, were analysed for the presence of organochlorine pesticides hexachlorobenzene (HCB) and DDTs (p,p'-DDT, p,p'-DDE, and p,p'-DDD), and 20 polychlorinated biphenyls (PCBs). The PCB levels (calculated as the sum of all the determined congeners) were found to be the highest (from 56.8 to 47909.5 ng/g on lipid basis), followed by the DDTs (sum of p,p'-DDT and its metabolites; 相似文献   

16S rRNA of Mucosal Colon Microbiome and CCL2 Circulating Levels Are Potential Biomarkers in Colorectal Cancer

Colorectal cancer (CRC) is one of the most common malignancies in the Western world and intestinal dysbiosis might contribute to its pathogenesis. The mucosal colon microbiome and C-C motif chemokine 2 (CCL2) were investigated in 20 healthy controls (HC) and 20 CRC patients using 16S rRNA sequencing and immunoluminescent assay, respectively. A total of 10 HC subjects were classified as overweight/obese (OW/OB_HC) and 10 subjects were normal weight (NW_HC); 15 CRC patients were classified as OW/OB_CRC and 5 patients were NW_CRC. Results: Fusobacterium nucleatum and Escherichia coli were more abundant in OW/OB_HC than in NW_HC microbiomes. Globally, Streptococcus intermedius, Gemella haemolysans, Fusobacterium nucleatum, Bacteroides fragilis and Escherichia coli were significantly increased in CRC patient tumor/lesioned tissue (CRC_LT) and CRC patient unlesioned tissue (CRC_ULT) microbiomes compared to HC microbiomes. CCL2 circulating levels were associated with tumor presence and with the abundance of Fusobacterium nucleatum, Bacteroides fragilis and Gemella haemolysans. Our data suggest that mucosal colon dysbiosis might contribute to CRC pathogenesis by inducing inflammation. Notably, Fusobacterium nucleatum, which was more abundant in the OW/OB_HC than in the NW_HC microbiomes, might represent a putative link between obesity and increased CRC risk.