A novel framework for biomedical entity sense induction.

BACKGROUND: Rapid advancements in biomedical research have accelerated the number of relevant electronic documents published online, ranging from scholarly articles to news, blogs, and user-generated social media content. Nevertheless, the vast amount of this information is poorly organized, making it difficult to navigate. Emerging technologies such as ontologies and knowledge bases (KBs) could help organize and track the information associated with biomedical research developments. A major challenge in the automatic construction of ontologies and KBs is the identification of words with its respective sense(s) from a free-text corpus. Word-sense induction (WSI) is a task to automatically induce the different senses of a target word in the different contexts. In the last two decades, there have been several efforts on WSI. However, few methods are effective in biomedicine and life sciences. METHODS: We developed a framework for biomedical entity sense induction using a mixture of natural language processing, supervised, and unsupervised learning methods with promising results. It is composed of three main steps: (1) a polysemy detection method to determine if a biomedical entity has many possible meanings; (2) a clustering quality index-based approach to predict the number of senses for the biomedical entity; and (3) a method to induce the concept(s) (i.e., senses) of the biomedical entity in a given context. RESULTS: To evaluate our framework, we used the well-known MSH WSD polysemic dataset that contains 203 annotated ambiguous biomedical entities, where each entity is linked to 2-5 concepts. Our polysemy detection method obtained an F-measure of 98%. Second, our approach for predicting the number of senses achieved an F-measure of 93%. Finally, we induced the concepts of the biomedical entities based on a clustering algorithm and then extracted the keywords of reach cluster to represent the concept. CONCLUSIONS: We have developed a framework for biomedical entity sense induction with promising results. Our study results can benefit a number of downstream applications, for example, help to resolve concept ambiguities when building Semantic Web KBs from biomedical text.

Range expansion of the invasive insect Greenidea (Trichosiphon) psidii (Hemiptera: Aphididae) in the Neotropical Region.

Greenidea psidii is an invasive insect from Asia that feeds on a diverse variety of agriculturally and environmentally important plant species. As an essential component of research necessary for development of a better understanding of biodiversity and its conservation, this study documents a major recent expansion in range of G. psidii in the Neotropics to the region of the tropical restinga ecosystem of Brazil, where it was found infesting guava (Psidium guajava) and jabuticaba (Plinia cauliflora). A summary of information on the geographic distribution, host plants, identification, and potential natural enemies of G. psidii that may be useful for integrated management of this pest in the Neotropical Region and other areas where this invasive insect has recently become established and is likely to further spread is also provided.

First Report of Sexual Reproduction of Fusarium solani f. sp. piperis in Bahia, Brazil.

Black pepper (Piper nigrum L.) is a popular spice native of India, and Brazil is one of its most important producing countries. The main disease of black pepper in Brazil is fusariosis, caused by Fusarium solani f. sp. piperis. Symptoms include leaf chlorosis and defoliation, blight of stems or stem cuttings, and root and foot decay. During surveys conducted in the south of the state of Bahia, municipalities of Taperoá (13°34'S, 39°10'W) and Valencia (13°20'S, 39°14'W), stems of diseased plants covered with red or salmon-colored perithecia were observed, while twigs showed leaf chlorosis, leading to early death of the plants. Ascomata were solitary or in groups, mostly superficial or surrounded by mycelia, globose, subglobose, ovoid, and 122 to 400 µm diameter. Microscopic examination revealed unitunicate, cylindric asci, 60 to 90 × 8.5 to 16 µm, thin-walled, containing eight ascospores arranged obliquely in two rows. Ascospores are hyaline, elliptical to oblong, one-septate, constricted at the central septum, 10 to 16 × 4 to 6.5 µm (means ± S.D.: 13.1 ± 1.4 × 5.1 ± 0.6 µm), length/width (L/W) 1.9 to 3.7. Single-spored cultures were transferred to SNA medium (incubated at 20°C for 7 days with 12-h photoperiod) and on potato dextrose agar (25°C in dark) for characterization. The anamorph is characterized by the presence of chlamydospores, canoe-shaped sporodochial macroconidia with three to four septae, and microconidia formed on long monophialidic conidiophores. Based on morphological markers, isolates were identified as F. solani. The partial fragment of the TEF-1α gene of single-spored isolates (CML 2186, 2187, 2188, 2189, 2190, and 2191) were sequenced. BLAST analysis of the sequence resulted in 94 to 99% identity with a reference strain of F. solani f. sp. piperis (NRRL 22570, CML 1888). For pathogenicity tests, cv. Bragantina was used and two isolates were inoculated as 5-mm diameter mycelial plugs on the stem of four plants each. Four control plants were treated only with sterile culture medium. Plants were maintained in the greenhouse at 25°C and 75 to 85% relative humidity under 70% shade. All inoculated plants showed initial symptoms of stem necrosis in inoculated branches 7 days after inoculation. Symptoms were not observed on stems of control plants. Isolates were successfully reisolated and identified as F. solani f. sp. piperis, fulfilling Koch's postulates. Representative isolates were deposited at the Coleção Micológica de Lavras (CML) at Universidade Federal de Lavras, Brazil. Production of perithecia of the pathogen has been previously reported only in Pará and Espírito Santo States (1,3). It is not yet confirmed if this taxon is homothallic or heterothallic. To our knowledge, this is the first report of the associated teleomorph of F. solani f. sp. piperis infecting and causing black pepper fusariosis in Bahia, Brazil. The results suggest that the spread of ascospores from perithecia is likely to be one of the main inoculum sources of the disease on adjacent vines. There is evidence that this special form of F. solani actually represents a distinct species pathogenic to black pepper (2). References: (1) F. C. Albuquerque and S. Ferraz. Experientiae 22:133, 1976. (2) K. O'Donnell. Mycologia 92:919, 2000. (3) J. A. Ventura et al. Fitopatol. Bras. 11:361, 1986.

First Report of Bacterium and Yeasts Associated with Pineapple Fruit Collapse in Espírito Santo State, Brazil.

In rainy and warm periods of the year, after a dry, hot season (December/March), commercially grown pineapple (Ananas comosus var. comosus) in Espírito Santo State, Brazil has been affected by fruit collapse disease with significant commercial losses (15 to 20%) each year. Symptoms include intense flesh fermentation, spontaneous exudation of liquid and froth, and ripe inner fruit tissue deterioration on plants and postharvest. Isolation of microorganisms of diseased fruits on nutrient agar, potato dextrose agar, and yeast extract peptone dextrose media consistently resulted in the recovery of a bacterium and three different yeasts. Koch's postulates were fulfilled by syringe inoculation of different concentrations of each microorganism (2.0 × 105 to 2.0 × 109 CFU/ml) singly and the organisms in combinations (only bacterium, only the yeasts, one yeast and the bacterium, two yeasts and the bacterium, and three yeasts and the bacterium) into disinfected (0.5% NaOCl) postharvest ripe pineapple fruits (cv. Pérola). Inoculated fruits were kept at 40°C for 5 days. Six fruits were used for each treatment and the experiment was repeated three times. Characteristic symptoms only occurred when all three yeasts and the bacterium were inoculated in combination at all inoculum concentrations. Each microorganism alone could not produce symptoms. Control fruits, inoculated with sterile water, did not develop disease symptoms. Cultures of each isolate were obtained and identified by morphological, physiological, biochemical, and genetic analyses. Molecular characterization by ribosomal sequence analyses of bacterium (16S rDNA) and yeasts (D1/D2 region of 26S rDNA) used universal PCR primers for bacteria (F968 and R1401) and yeast NL1 (5' GCA TAT CAA TAA GCG GAG GAA AAG 3') and NL4 (5' GGT CCG TGT TTC AAG ACG G 3'). Sequences were compared with those in GenBank. On the basis of the results, the bacterium was identified as a Klebsiella sp. and the yeasts as a Candida sp., Saccharomyces sp., and a Kloeckera sp. The bacterium was negative for protease, cellulase, and pectinase activity in the qualitative tests. We concluded that the combination of a Klebsiella sp. with the three yeasts, Candida sp., Saccharomyces sp., and Kloeckera sp., was responsible for the symptoms of pineapple fruit collapse. Symptoms of pineapple fruit collapse are similar to yeasty fermentation reported previously (2,3). These reports did not consider the interaction of yeast and bacteria. No relationship between the pineapple cultivars and the pathogens from specific field sites was found. Disease outbreaks seem related to naturally occurring fruit translucency, a physiological disturbance correlated with calcium, potassium, and nitrogen balance (1,3), which increases fruit cell-wall hydrolases and membrane permeability. This condition releases nutrients from the fruit and favors microbial growth. To our knowledge, this is the first report of a combination of bacterium and yeasts associated with collapse disease of pineapple in Brazil. Information on the pathogens responsible for collapse disease epidemics in Espírito Santo fields will be useful in breeding and disease control strategies. References: (1) R. P. Haff et al. J. Food Process. Preserv. 30:527, 2006. (2) C. Py et al. The Pineapple: Cultivation and Uses. Larose, Paris, 1987. (3) K. G. Rohrbach and M. Johnson. The Pineapple: Botany, Production and Uses. D. P. Bartholomew et al., eds. CABI Publishing, Wallingford, UK, 2003.

First Report of Turnip mosaic virus on Watercress in Brazil.

Watercress (Nasturtium officinale L.), a member of the family Brassicaceae, is consumed mainly as salad. Medicinal properties have also been attributed to this species. In Brazil, watercress is grown mainly by very small farmers. The crop is primarily seed propagated and growers can harvest several times per year in an established planting. Very few diseases have been reported in this crop worldwide. In Brazil, watercress infection by Cauliflower mosaic virus (CaMV) (3), Cucumber mosaic virus (CMV) (1), and an unidentified potyvirus (2) were previously reported. In January 2009, 80% of watercress plants, cv. Gigante Redondo, exhibiting severe mosaic, leaf size reduction, and plant stunting were observed in a crop in Marechal Floriano Municipality, State of Espírito Santo, Brazil. Preliminary leaf dip analysis by transmission electron microscopy revealed the presence of potyvirus-like particles. Sap from five infected plants reacted in plate-trapped antigen (PTA)-ELISA with polyclonal antiserum against Turnip mosaic virus (TuMV), but not with antiserum against CMV. Both antisera were produced in the Plant Virology Laboratory, ESALQ/USP. Mechanically inoculated watercress plants developed similar systemic mosaic symptoms. The virus was also transmitted to Nicotiana benthamiana, which exhibited severe mosaic and stunting. The presence of TuMV on these inoculated plants was confirmed by PTA-ELISA and reverse transcription (RT)-PCR. Total RNA extracted from infected and healthy watercress and infected N. benthamiana was analyzed by RT-PCR using specific pairs of primers flanking the coat protein gene of TuMV. Degenerated anti-sense (5'-t/caacccctt/gaacgcca/cagt/ca-3') and sense (5'-gcaggtgaa/gacg/acttgat/ca/gc-3') primers were designed after analysis to an alignment of the nucleotide sequences for five isolates of TuMV available in the GenBank (Accession Nos. NC_002509, D10927, EU680574, AB362513, and D88614). One fragment of 838 bp was amplified from samples in the infected plants, but not in the healthy controls. Two amplicons were purified and directly sequenced in both directions. Comparisons of the 731-bp consensus nucleotide sequence (Accession No. HM008961) to several other isolates of TuMV revealed 94 to 95% identity in the coat protein region. To our knowledge, this is the first report of TuMV in watercress in Brazil. Management of the disease should include propagation by seeds instead of vegetative parts of the plants and rouging of diseased plants to prevent mechanical transmission during successive harvestings. References: (1) A. J. Boari et al. Fitopatol. Bras. 25:438, 2000. (2) A. J. Boari et al. Fitopatol. Bras. 27:S200, 2002. (3) M. L. R. Z. C. Lima et al. Fitopatol. Bras. 9:403, 1984.

Fusarium Wilt Caused by Fusarium oxysporum on Lettuce in Espirito Santo, Brazil.

Plants of lettuce cv. Salad Regina that showed symptoms of a wilt disease were observed in commercial fields in the Marechal Floriano and Caxixe production regions in the highlands of Espirito Santo State (ES), Brazil. Wilted plants were first observed during the 2000 cropping season (June to September) when temperatures were between 26 and 34°C. Outbreaks of wilt in the Caxixe Region also occurred in the last 2 years on cultivars of the Lisa type. Symptoms were observed on seedlings and adult plants. Affected plants appeared wilted, showed red-to-brown discoloration of vascular tissues, were stunted, and developed yellow leaves that had brown or black streaks in the vascular system. The vascular streaks in the yellow leaves were continuous from the red-brown vascular discoloration in the crown. A Fusarium sp. was consistently and readily isolated by plating surface-sterilized (with NaOCl) root and crown tissue segments from symptomatic plants onto lactic-acid-amended potato dextrose agar and a Fusarium-selective medium (4). To complete Koch's postulates, a single hyphal tip of the isolated fungi was transferred to carnation leaf agar. Micro- and macroconidia formed abundantly within 8 days and matched the description of Fusarium oxysporum Schlechtend. Fr. Two- to three-week-old lettuce seedlings of each of six cultivars (Monalisa AG-819, Grand Rapids Nacional, Regina, Carolina AG-576, Vitória, and Grandes Lagos), representing the range of lettuce genetic diversity typically planted in Espirito Santo, were inoculated with the isolated fungus by dipping the roots of each plant in a spore suspension (1 × 105 CFU/ml) or planting the seedlings in a steam-sterilized soil infested with the fungus at 1 × 105 conidia/ml potting medium. Ten inoculated seedlings of each cultivar were arranged in a completely randomized design and placed in a greenhouse (26 ± 2°C) to allow development of the infectious agent. Ten noninoculated plants of each cultivar served as control treatments. Wilt symptoms developed on all inoculated plants 20 to 30 days after inoculation, and infected plants showed the same symptoms as observed on the original plants from which the pathogen was isolated. Noninoculated plants remained symptomless. F. oxysporum was consistently reisolated from the inoculated seedlings. The pathogenicity test was conducted twice. A wilt of lettuce attributed to F. oxysporum f. sp. lactucae was previously reported in Japan (3) and later in the United States where the disease was attributed to F. oxysporum f. sp. lactucum (2). In 2002, a lettuce wilt caused by F. oxysporum f. sp. lactucae was reported in Italy (1). Studies are being carried out to determine the formae speciales of these Brazilian lettuce isolates of F. oxysporum. To our knowledge, this is the first report of F. oxysporum on cultivated lettuce in Brazil. References: (1) A. Garibaldi et al. Plant Dis. 86:1052, 2002. (2) J. C. Hubbard and J. S. Gerik. Plant Dis. 77:750, 1993. (3) T. Matuo and S. Motohashi. Trans. Mycol. Soc. Jpn. 8:13,1967. (4) J. A. Ventura. Rev. Ann. Patologia de Plantas 7:271, 1999.

Cost analysis of hospital material management systems.

Integrated healthcare material management begins with manufactures of medical/surgical supplies, uses distributors and ends at the point of use at hospitals. Recent material management philosophies in the healthcare industry, such as just-in-time and stockless systems, are yet to be fully evaluated. In order to evaluate the cost effectiveness of each type of material management technique, a cost model for hospital materials management has been designed. Several case scenarios are analyzed and results are reported.

Ioxilan, a third generation low osmolality nonionic contrast medium. Systemic and renal hemodynamic effects.

The choice between high cost, low toxicity nonionic contrast media (CM) and low cost ionic CM poses a dilemma for radiologists. Ioxilan, a third generation nonionic CM, is obtained by simple conversion from an ionic CM. To examine how this economically promising, low osmolality CM (570 mOsm at 300 mgI/ml) affects canine systemic and renal hemodynamics, IV bolus injections of 350 mgI/ml at 2 ml/kg of Iohexol and Ioxilan were compared. Satisfactory nephrograms and pyelograms were produced by both agents, without significant differences. The effects on systemic and renal hemodynamics were minimal and statistically equal for both CM. The acute systemic and renal responses and radiographic image quality of Ioxilan and Iohexol confirm that the two compounds are biologically equivalent, and that the novel molecular design employed in Ioxilan to achieve very low osmolality also provides good biological tolerance.

Effects of the magnetic resonance contrast medium ferrioxamine methanesulfonate on systemic and renal hemodynamics in the anesthetized dog.

Ferrioxamine methanesulfonate (S-FDF) is a new magnetic resonance (MR) contrast agent developed to improve magnetic resonance imaging of the abdomen and pelvis. This stable complex of deferoxamine methanesulfonate and iron is excreted in the urine by glomerular filtration modified by active renal tubular resorption. This study examines the acute systemic and renal hemodynamic responses to this agent after intravenous administration either as an infusion of 25 mg/kg over 5 minutes or as a rapid bolus at a dose of 50 mg/kg. In eight anesthetized dogs, renal plasma flow (RPF) was measured with an electromagnetic flowmeter, and GFR was determined by the renal extraction of technetium-99m-DTPA. Mean arterial pressure (MAP), pulse rate, and a lead II ECG were assessed. At a dose of 25 mg/kg over 5 minutes, MAP decreased significantly (control 146.0 +/- 6.5 mm Hg vs. 107 +/- 18 mm Hg at 2 minutes; P less than .05). In two of the eight animals, the MAP dropped below 60 mm Hg. Significant decreases in GFR and RPF also were noted. All four of the animals receiving the rapid injection of S-FDF experienced profound hypotension (MAP less than 50 mm Hg). The drop in heart rate from 152 +/- 11.6 bpm to 121 +/- 4.9 bpm was associated with a marked depression of the ST wave in the lead II ECG. Further animal studies are needed to assess the mechanism of toxicity and a potential synergism of action with pentobarbital anesthesia.

Role of angiotensin II in renal hemodynamic functions during the initial stages of acute ureteral obstruction.

This investigation examines the role of Angiotensin II in renal hemodynamic functions during acute unilateral ureteral obstruction (UUO) in a dog model. An electro magnetic flow probe was utilized to assess renal blood flow while the arteriovenous extraction technique of technetium 99m DTPA was utilized for the assessment of changes in filtration fraction and glomerular filtration rate. The effects of Angiotensin II receptor blockade on renal hemodynamic functions during acute UUO was evaluated in six dogs and compared to acute ureteral obstruction without receptor blockade in seven dogs. Angiotensin II blockade with (Sar1, Thr8)-Angiotensin II during UUO led to a striking increase in renal blood flow that was significantly different in comparison to normalized values from UUO alone (+delta 63 +/- 17 vs. +delta 22 +/- 6% at 30 min; p less than 0.05). There were, however, no significant differences in the magnitude of the decrease in filtration fraction and glomerular filtration rate in comparison to UUO alone. This investigation demonstrates that Angiotensin II has an inhibitory effect on the initial increase in renal blood flow with acute UUO. The possibility of successful pharmacologic intervention in the setting of UUO can be examined using animal models similar to the one described here. Pharmacologic treatment in the setting of acute UUO in patients might permit better preservation of renal function.

A comparison of clearance and arteriovenous extraction techniques for measurements of renal hemodynamic functions.

No previous studies have directly compared timed urine collections (UV/P) vs. arteriovenous (A-V) extraction methods for determination of renal function in whole kidney preparations. We examined different markers and techniques for assessing renal plasma flow (RPF), filtration fraction (FF), and glomerular filtration rate (GFR) in both steady-state and rapidly changing conditions following 2 ml/kg bolus intravenous injections of either Renografin 76% (meglumine/sodium diatrizoate-76%) or hypertonic mannitol 25%. During steady-state conditions, excellent correlations were obtained when comparing markers and techniques. Thus, timed urinary clearances of inulin vs. 99m-technetium DTPA (Tc) had a correlation coefficient (R) of .96 (P less than .01; n = 16), and the A-V extraction technique of inulin vs. Tc as determinants of GFR showed a correlation of R = .98 (P less than .01; n = 15). The timed urinary clearance of inulin vs. the A-V extraction of inulin for glomerular filtration gave a correlation of R = .93 (P less than .01; n = 15). The clearance of para-aminohippurate (PAH) divided by the extraction of PAH vs. flow determinations using the electromagnetic flowmeter gave a correlation of R = .92 (P less than .01; n = 16). The anticipated decrease in GFR following contrast medium and hypertonic mannitol was observed using the A-V extraction technique, whereas an artifactual, exaggerated increase in GFR was observed using the timed urine collection technique. Similarly, we noted an exaggerated increase in RPF using CPAH/EPAH as the methodology. We conclude that rapid changes in renal hemodynamics may be measured accurately using the A-V extraction technique but not with clearance techniques requiring timed urine collections.

Acute systemic and renal hemodynamic effects of meglumine/sodium diatrizoate 76% and iopamidol in euvolemic and dehydrated dogs.

We examined the acute systemic and renal hemodynamic effects of intravenous meglumine/sodium diatrizoate-76% and iopamidol in euvolemic and dehydrated dogs. The physiologic responses were compared with acute changes in the level of an endogenous heparin-like material (EHM). One of eight dehydrated dogs receiving diatrizoate (2 ml/kg) had an immediate vomiting reflex associated with a very significant decline in all measured renal hemodynamic parameters; none of eight dehydrated dogs receiving iopamidol experienced a similar reaction. EHM levels did not correspond to the magnitude of the physiologic responses following either iopamidol or diatrizoate. Significant differences between iopamidol and diatrizoate were noted when comparing the magnitude of the decrease in systemic pressure (- delta 3.8 +/- 3.02, iopamidol, n = 8; vs. - delta 19.4 +/- 7.3 mm Hg, diatrizoate, n = 8; P less than .03), increased renal plasma flow (+ delta 6.2 +/- 4.9, iopamidol, n = 8; vs. + delta 33.7 +/- 8.0 ml/min, diatrizoate, n = 8; P less than .05), and decreased filtration fraction (- delta 0.09 +/- 0.01, iopamidol, n = 8; vs. - delta 0.14 +/- 0.02, diatrizoate, n = 8; P less than .03). There was no significant difference in the decrease in glomerular filtration rate (- delta 7.4 +/- 1.0, iopamidol, n = 8; vs. - delta 9.3 +/- 1.3, diatrizoate, n = 8; P greater than .05), since the marked drop in filtration fraction occurring with diatrizoate was counterbalanced by the marked increase in renal plasma flow. Acute systemic and renal hemodynamic effects are significantly lessened when comparing iopamidol with diatrizoate.

Effects of contrast media on renal function and subcellular morphology in the dog.

The effects of intravenous contrast media (CM) on renal excretory function and subcellular morphology are examined in this animal investigation. A decrease in GFR (12.0 +/- 1.6 vs. control 30.2 +/- 2.5 ml/min) was observed when renal function was evaluated by means of the artero-venous extraction method with Tc99m DTPA and the anticipated inverse relationship to urinary flow (Vml/min) noted. An artifactual increase in GFR (43.5 +/- 10.0 vs. control 39.1 +/- 3.8 ml/min) was observed using the timed urinary clearance of inulin. V(ml/min) increased four-fold (0.6 +/- 0.16 control vs. 2.7 +/- 0.7 ml/min; P less than .05) over the first five minutes after injection of CM. Urine osmolality initially approached isotonicity and then returned toward preinjection values. Osmolal clearance (Cosm) rose 2.5 times (1.4 +/- 0.3 control vs. 3.7 +/- 1.0 ml/min; P less than .05). The fractional excretion of both Na+ (FENa+) and K+ (FEK+) increased. A comparison of urinary osmolality vs. time after injection of CM confirms a nonspecific osmotic effect on tubular (and hence total urine) flow. The hemodynamic effects of CM on the kidney via the i.v. route reflect a predominant and nonspecific osmotically mediated vasodilation. No significant light or electron microscopic changes were observed. These findings suggest that the major renal physiologic actions of hypertonic CM are a nonspecific response to agent osmolality.

Glomerular filtration response to acute ureteral obstruction in the dog.

In order to assess the glomerular filtration responses to acute ureteral obstruction in the dog we employed an established method that does not require timed urine collections. Our results show a 57 per cent increase in renal blood flow (baseline: 203.8 +/- 50.9 vs. 319 +/- 69.4 ml./min. at 105 minutes; no. = 7) that was associated with a monophasic decrease in filtration fraction to -70 per cent at 120 minutes (0.26 +/- 0.025 vs. 0.08 +/- 0.007) and an increase in ureteral pressure to 63.1 +/- 6.1 mm. Hg at 120 minutes. A biphasic GFR response was noted with an initial small increase (baseline: 32.5 +/- 7.5 vs. 36.3 +/- 11.0 ml./min. at 2 minutes) followed by a continual decline to -55 per cent at 120 minutes (to 14.5 +/- 2.6 ml./min.). This investigation has confirmed the results of micropuncture studies showing maintenance of GFR early after complete ureteral ligation.