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Tina Willson,1,2 Scott D Nelson,1,2 Jonathan Newbold,1 Richard E Nelson,2,3 Joanne LaFleur1,2 1University of Utah College of Pharmacy, 2Veterans Affairs Salt Lake City Health Care System, 3University of Utah School of Medicine, Salt Lake City, UT, USAAbstract: Osteoporosis, a musculoskeletal disease characterized by decreased bone mineral density (BMD) and an increased risk of fragility fractures, is now recognized as an important public health problem in men. Osteoporotic fractures, particularly of the hip, result in significant morbidity and mortality in men and lead to considerable societal costs. Many national and international organizations now address screening and treatment for men in their osteoporosis clinical guidelines. However, male osteoporosis remains largely underdiagnosed and undertreated. The objective of this paper is to provide an overview of recent findings in male osteoporosis, including pathophysiology, epidemiology, and incidence and burden of fracture, and discuss current knowledge about the evaluation and treatment of osteoporosis in males. In particular, clinical practice guidelines, fracture risk assessment, and evidence of treatment effectiveness in men are addressed.Keywords: screening, treatment, fracture risk, guidelines, diagnosis

Summary: Interneurons (INs), specifically those in disinhibitory circuits like somatostatin (SST) and vasoactive intestinal peptide (VIP)-INs, are strongly modulated by the behavioral context. Yet, the mechanisms by which these INs are recruited during active states and whether their activity is consistent across sensory cortices remain unclear. We now report that in mice, locomotor activity strongly recruits SST-INs in the primary somatosensory (S1) but not the visual (V1) cortex. This diverse engagement of SST-INs cannot be explained by differences in VIP-IN function but is absent in the presence of visual input, suggesting the involvement of feedforward sensory pathways. Accordingly, inactivating the somatosensory thalamus, but not decreasing VIP-IN activity, significantly reduces the modulation of SST-INs by locomotion. Model simulations suggest that the differences in SST-INs across behavioral states can be explained by varying ratios of VIP- and thalamus-driven activity. By integrating feedforward activity with neuromodulation, SST-INs are anticipated to be crucial for adapting sensory processing to behavioral states.

Cajal-Retzius neurons number drastically decreases during postnatal life. Here, authors show that their programmed death is required for the construction of functional hippocampal circuits and memory with aberrant survival leading to gamma rhythmopathies and susceptibility to seizures.

By modulating the activation state of the Hedgehog pathway, de la Rocha-Muñoz et al demonstrate that Hedgehog signaling controls the expression and transport activity of the neuronal glycine transporter GlyT2. This work begins to reveal a potential link between the Hedgehog signaling pathway and presynaptic glycine availability.

Con el objetivo de evaluar insecticidas químicos, biológicos y botánicos para el manejo del pulgón amarillo del sorgo, se realizó un estudio en la fi nca “El Plantel” en el período comprendido de agosto a octubre del año 2017. Las alternativas evaluadas fueron: Engeo, Imidacloprid, Beauveria bassiana, Metharizium anisopliae y Chile+ajo+jabón en comparación con el Testigo que fue solamente aplicación de agua. Las variables evaluadas fueron: número de ninfas de M. sacchari por planta, de adultos de M. sacchari por planta, de alados de M. sacchari planta, además de algunas variables económicas como el rendimiento en kg ha-1 por tratamiento evaluado, análisis de presupuesto parcial, análisis de dominancia y tasa de retorno marginal. Los resultados obtenidos en el estudio determinan que los tratamientos Engeo e Imidacloprid fueron los que presentaron el mejor control de ninfas, adultos y alados de M. sacchari, los mejores rendimientos comerciales lo obtuvieron los tratamientos Engeo e Imidacloprid, las mejores tasas de retorno marginal fueron obtenidas en el tratamiento Imidacloprid.

The objective of this research was to design indicators for the evaluation of technological innovation (TI) in Puerto López. The methodology used is based on an analysis of the current TI situation and the perspective of the visitors on this issue. The diagnosis reported an incipient technological management by the public institutions and the scarce investment in R+D+i. The results provided 19 indicators to evaluate the TI before, during and after the visit, under the dimensions of product, process, organization and marketing that were identified and validated through experts’ methods. The indicators show the importance to start working on technological intelligence.

Introducción: El síndrome de Burnout es frecuente en el personal sanitario en situaciones de pandemia. Objetivo: Determinar la ocurrencia e intensidad de síndrome de Burnout (SB) en médicos y enfermeros ecuatorianos durante la pandemia de la COVID-19. Método: Se realizó un estudio observacional de corte transversal. Participaron 224 médicos y enfermeros de establecimientos de la red integral de salud ecuatoriana, a quienes se administró el Inventario de Burnout de Maslach. Se analizaron los datos a través de modelos de regresión lineal usando R. Resultados: Más del 90% del personal médico y de enfermería presentó SB de moderado a severo, el que se asoció de manera estadísticamente significativa a función (médico vs. enfermero, edad y género). El personal médico es afectado con mayor frecuencia que el de enfermería, tanto a nivel global como en las subescalas de agotamiento emocional y despersonalización. Conclusiones: Durante la pandemia de la COVID-19 más del 90% del personal médico y de enfermería presentó SB de moderado a severo, siendo el primero, el afectado con más frecuencia. Palabras clave: síndrome de Burnout, personal de salud, COVID-19.

The Demêni-Mocidade domain (DMD) comprises a large area of granitoid rocks, located on the border between the states of Roraima and Amazonas, Brazil, within the inner part of the Ventuari-Tapajós Province of the Amazonian Craton, where large amounts of granitoid rocks, formed between 2.0-1.8 Ga, are predominant. This study examines six granite samples collected from the Mocidade and Demêni mountains, which are related in time to the Uatumã Silicic Large Igneous Province (SLIP), which, in turn, covers several tectonostratigraphic domains whose evolution is associated with an intercontinental setting, allowing a common association with I- and A-type granitoid rocks formed within the same 1.88 to 1.87 Ga time interval. These rocks are monzogranites and correspond petrographically to holocrystalline anisotropic lithotypes with fine to medium grain sizes. Their textural relationships, including some lithotypes containing phenocrysts with oscillatory zoning and resorbed rims, indicate that crystallization occurred at subvolcanic or hypabyssal depths. Moreover, the association between plutonic and subvolcanic rocks in the same suite shows variations in the crustal development of the magmatic chambers. The granitoids of the DMD share a common geochemical signature with those of the Água Branca Suite, which occurs within the Uatumã and Trombetas-Erepecuru domains of the Guiana Shield, suggesting that their crystallization occurred in similar magmatic chambers. Six U-Pb zircon ages show that most zircon crystals are concordant and the few ones which are discordant are well aligned along Discordia straight lines descending to zero. The calculated Concordia ages, covering the 1884 to 1877 Ma interval, agree within experimental error, indicating a probably similar crystallization age. Such apparent age values, close to 1900 Ma for the DMD, made it possible for the domain of the Uatumã SLIP to spread to the West, and the area of the Ventuari-Tapajós Province could extend towards the Amazonas State of Venezuela. Finally, the coexistence between I- and A-type granitoids in the DMD, with ages within the range 1.88-1.87 Ga, stimulates a discussion, and there are three possibilities: (1) The calc-alkaline magmatism can be associated with late (post-collisional) processes related to subduction. (2) The granitoid rocks are formed in an intracontinental setting under more stable (post-orogenic) tectonic conditions. (3) The granitoid rocks are predominantly formed by A-type and alkaline magmatism in intraplate settings.

Background The healthy user bias is usually overlooked as an explanation in studies in which a strong association is found between poor patient medication adherence and worse disease outcomes. Such studies are increasing in frequency across disease states and influence clinical practice. Adherence to antihypertensive medications was studied to illustrate confounding in such studies. Methods Using data from veterans with hypertension starting antihypertensive treatment, causal models were developed that predicted the risks of hospitalisation, myocardial infarction (MI) and death associated with poor adherence (<80%) while adjusting for patient demographics, baseline disease severity and disease comorbidity. In a second set of otherwise identical models, adjustment was made for time-varying blood pressure (BP), thus controlling for adherence effects that were mediated through the main pharmacological effects of the drugs. It was hypothesised that the second set of models would reveal a positive association between poor adherence and adverse disease outcomes that is largely explained by unmeasured confounders, including health-related behaviours. Results The models that did not adjust for time-varying BP levels showed that patients with poor adherence had statistically significantly increased risks of 3.7% for hospitalisation, 28.1% for MI and 23.3% for death. These estimates exceed the benefits of these drugs demonstrated by clinical trials. When controlling for time-varying BP, the increased risks were similar (3.4% for hospitalisation, 27.7% for MI and 23.4% for death). The findings were consistent across a range of adherence thresholds (50-90%) and when allowing disease status variables to vary. Conclusions The associations between poor adherence and outcomes are largely independent of the pharmacological effects of the drugs on BP control as well as commonly measured patient covariates. This finding suggests that even carefully designed observational adherence studies using rich clinical data are impossibly confounded and probably overestimate the true magnitude of the effect. Clinical practice guidelines based on reported adherence effects should be reconsidered. [ABSTRACT FROM AUTHOR]

O Exame, no contexto brasileiro do encontro entre geografia e educação, de relatos de práticas e de construções teóricas relativas a estas práticas, referenciando a indagação acerca da pertinência em propor que, nesse encontro, podem ser observados indícios de uma reconstrução ontológica.

Immunogenicity of DNA vaccines can be efficiently improved by adding adjuvants into their formulations. In this regard, the application of nano- and microparticles as vaccines adjuvants, or delivery systems, provides a powerful tool in designing modern vaccines. In the present study, we examined the role of “Supramolecular Hacky Sacks” (SHS) particles, made via the hierarchical self-assembly of a guanosine derivative, as a novel immunomodulator for DNA plasmid preparations. These plasmids code for the proteins HIV-1 Gag (pGag), the wild-type vaccinia virus Western Reserve A27 (pA27L), or a codon-optimized version of the latter (pOD1A27Lopt), which is also linked to the sequence of the outer domain-1 (OD1) from HIV-1 gp120 protein. We evaluated the enhancement of the immune responses generated by our DNA plasmid formulations in a murine model through ELISpot and ELISA assays. The SHS particles increased the frequencies of IFN-γ-producing cells in mice independently immunized with pGag and pA27L plasmids. Moreover, the addition of SHS to pGag and pA27L DNA plasmid formulations enhanced the production of IFN-γ (Th1-type) over IL-4 (Th2-type) cellular immune responses. Furthermore, pGag and pA27L plasmids formulated with SHS, triggered the production of antigen-specific IgG in mice, especially the IgG2a isotype. However, no improvement of either of those adaptive immune responses was observed in mice receiving pOD1A27Lopt+SHS. Here, we demonstrated that SHS particles have the ability to improve both arms of adaptive immunity of plasmid coding “wild-type” antigens without additional strategies to boost their immunogenicity. To the best of our knowledge, this is the first report of SHS guanosine-based particles as DNA plasmid adjuvants.

Climate change has increased the interannual and seasonal variation in the average temperature and precipitation rate, which determine forage availability globally. Similar patterns of change have occurred in tropical regions, and Ecuador is no exception. This region includes other influencing factors, such as the conversion of tropical forests to extensive pastures. Therefore, this study was carried out to evaluate guinea grass (Panicum maximum) cultivated under silvopastoral systems with different management strategies in both of the seasons of the study region in Ecuador (rainy season and dry season). A randomized complete block design was used for the experiment, with three repetitions and three treatments. Agronomic measures, forage production, chemical composition, animal responses, and soil properties were evaluated. Data were analyzed with the Mixed model of SAS. Differences in all evaluated parameters were observed between treatments, and silvopastoral systems (SPSs) produced better results than conventional grass monoculture. Furthermore, there was a strong seasonal effect on forage production, chemical composition, and soil properties. Therefore, management of Panicum maximum with well-planned grazing can enhance animal responses and help to retain natural resources, lowering the pressure on forests.

A study was conducted at the Escuela Superior Politècnica de Chimborazo, Ecuador, to evaluate the influence of litter size of guinea pigs (Cavia porcellus) on their development and to establish the economic profitability of the production system. Forty-eight animals were used, distributed into litters of two, three, and four rodents per litter, with a balanced diet and green fresh alfalfa for the weaning, growth, and fattening stage, the rodents and litters were randomly selected, applying the statistical model completely randomly and evaluating different variables across 120 days. The litters of three guinea pigs obtained the best productive responses and economic profitability. With respect to sex, the males presented better productive behavior, greater economic increase, and less cost, evidencing that mixed feeding influences the number of guinea pigs per birth in terms of growth and development. The results serve to improve guinea pig meat production for the rural population.

Con base en la regulación colombiana y el estudio de algunas sentencias de la Superintendencia de Industria y Comercio, este texto analiza los requisitos jurídicos para que cierta información pueda considerarse como secreto empresarial. De ahí se argumenta que una cláusula contractual por sí sola no determina la información que puede considerarse como un secreto empresarial, ya que la autonomía de la voluntad no tiene el poder de desconocer la naturaleza jurídica de la información.

Background: A high prevalence of Helicobacter pylori in the esophageal mucosa of dyspeptic Venezuelan patients has been reported. We aimed to assess the genetic composition of the cag genotypes of H. pylori and its relation to histopathological outcomes in the gastroesophageal mucosa. Methods: The presence of cagA, cagE, and virB11 cag pathogenicity island (PAI) genes was detected by PCR in 80 of 150 H. pylori-positive dyspeptic patients in both mucosae. Alterations of the gastroesophageal mucosa were assessed by histological techniques. Results: The frequency of intact, partial, and deleted cag-PAI genes in the stomach of dyspeptic patients was found to be 57.5%, 21.3%, and 21.3%, respectively, whereas in the esophagus, frequencies were 33.8%, 33.8%, and 32.5% respectively. The genetic composition in the stomach was 57.5% cagA-positive, 20.0% cagA-negative, 75.0% cagE, and 77.5% virB11, whereas in the esophagus the distribution was 36.3% cagA-positive, 30.0% cagA-negative, 61.3% cagE, and 63.8% virB11. The gene with the largest difference between the two mucosae was cagA, with 58.8% in the stomach and 37.5% in the esophagus; cagE and virB11 were less variable. The correlation among single and/or mixed cag genotypes with histopathological outcomes in both mucosae from the same patient was higher for intact single cag-PAI genotypes, showing severe alterations. Conclusions: H. pylori may coexist in similar proportions without dominance of one cag genotype, suggesting a heterogeneous distribution in the esophagus. The cagE and virB11 genes can be used as markers of cag-PAI in the esophagus. The single cag-PAI genotype in both mucosae confers an increased risk of developing histological damage.

This work determines the thermo hydraulics behavior of smooth configuration surface for a compact heat exchanger by means of numerical simulation. The objective is to use the results as baseline for research in the enhancement of heat transfer and drag reduction, directed to reduce the energy consumption and diminish the environmental impact. The fin tube heat exchanger models described.The constraints used in the implementation of the equation solver are announced. The average heat transfer coefficient and pressure drop obtained from numerical simulation are compare to experimental results presented in literature for models with the same dimensions and configuration. A good agreement between numerical and experimental results is reached. Local mechanisms responsible for the heat transfer and pressure drop are detailed. The study is conducted inside thelaminar regime for frontal velocities ranging between 0.5 and 6 m/s.Key words: compact heat exchanger, heat transfer coefficient, numerical simulation, pressure drop.______________________________________________________________________________ResumenEste trabajo determina el comportamiento termo hidráulico de una superficie perteneciente a un intercambiador de calor compacto en configuración lisa utilizando un método de simulación numérica. El objetivo es caracterizar la superficie para poder utilizarla como una referencia en las comparaciones con superficies de intercambio de calor intensificadas. Los datos obtenidos seutilizaran en la determinación de los valores relativos de intensificación de la transferencia de calor y el arrastre intentando reducir el consumo energético y su impacto ambiental. Se describe el modelo de intercambiador de calor con tubos aletados. Los resultados numéricos obtenidos presentan unbuen ajuste con los valores experimentales. Los resultados del coeficiente de transferencia de calor global y la caída de presión son explicados a partir de las particularidades locales del campo de velocidad y temperatura. El estudio es conducido en régimen laminar con velocidades a la entrada del modelo entre 0.5 and 6 m/s.Palabras claves: intercambiadores de calor compactos, coeficiente de transferencia de calor, simulación numérica, caída de presión.

Non-H. pylori helicobacters (NHPH) have been demonstrated as gastric spiral-shaped bacteria in specimens obtained from dogs; however, their roles in the pathogenesis of upper gastrointestinal disease have not yet been clearly established. The purpose of this study was to evaluate the prevalence of NHPH DNA in the gastric mucosa of dogs and its association with histopathology. Helicobacter was detected through histopathological techniques, PCR, and FISH analysis from fundic biopsies of twenty dogs with or without signs of gastrointestinal disease. PCR and FISH were based on partial 16S rRNA gene sequences. Nineteen dogs showed mild to marked gastritis in the fundus, and only one dog had a healthy gastric mucosa. NHPH DNA was detected in 18 dogs with gastritis and one with normal gastric mucosa. However, there was no significant correlation between the presence of NHPH DNA and the degree of gastritis. These results show a high prevalence of NHPH DNA in the gastric mucosa of dogs from Venezuela. Further studies are necessary to determine a possible association between a specific NHPH species and the degree of gastritis.

Se estudió el indumento y la morfología de los tricomas del envés de las hojas y del endocarpo de 9 especies del género Mortoniodendron (Tiliaceae). Se establece el tipo de indumento y de tricomas según la forma, simetría, tamaño y densidad, mediante microscopía electrónica de barrido y óptica. En las hojas y endocarpo se definen 2 categorías para el tipo de indumento. Para las hojas, el axilar se presenta en 7 especies y glabrescente en 9 y para el endocarpo glabrescente en 5 especies y el resto glabras. Con relación a la forma, simetría y tamaño se reconocen 4 tipos de tricomas: simples de un brazo, fasciculados de 2 a 5 brazos, estrellados de 3 a 18 brazos y capitados uni y multicelulares. Los tricomas simples y fasciculados predominan en M. costaricense, M. hirsutum y M. vestitum. Los estrellados están presentes en todas las especies y se distinguen 4 categorías según el tamaño y número de brazos. Sólo en M. palaciosii y M. ruizii se encuentran tricomas capitados. En el endocarpo predominan los tricomas estrellados, excepto en M. vestitum con tricomas fasciculados largos. Se discute la importancia taxonómica de los resultados y se elabora una clave para identificar las especies.The indument and trichome morphology in leaves and endocarp for 9 species of Mortoniodendron (Tiliaceae) were studied. The distribution and the type of trichomes were established according to their form, symmetry, size, and density using scanning electron and optical microscopy. Two categories for the distribution of trichomes were defined in the leaves and the endocarp. In the case of the leaves, 7 species have axillar indument and it is glabrescent in 9, while in the endocarp 5 species show glabrescent and others glabrous. Four types of trichomes were recognized: acicular with a single arm, fasciculate with 2-5 arms, stellate with 3-18 arms, and uni or multicellular capitate. Acicular and fasciculate trichomes prevail in M. costaricense, M. hirsutum and M. vestitum. Stellate trichomes are present in all the species, but 4 categories are distinguished according to size and number of arms. Only M. palaciosii and M. ruizii possess capitate trichomes. In the endocarp stellate trichomes prevail, except for M. vestitum with long fasciculate trichomes. The taxonomic usefulness of the results is discussed and a key to identify the species is provided.

INTRODUCTION: Disinfection of dentin surfaces is desirable so long as it does not interfere with subsequent bonding of adhesive resins. OBJECTIVE: To test the null hypothesis that bond strengths to dentin are not affected by previous application of an iodine disinfecting solution. MATERIALS AND METHODS: Twenty-four extracted non-carious molars were selected. Occlusal enamel was removed producing a flat dentin substrate. Test teeth were all treated with 2% Iodine disclosing/disinfecting solution (I2DDS) for 20 sec and rinsed for 20 sec followed by the application of self- or total- etching bonding systems, generating five adhesive groups (n=3): Single Bond; ; Prime & Bond NT; Clearfil SE Bond; Opti-Bond Plus. The control groups (n=3 per adhesive) had no disclosing/disinfectant application prior to adhesive application. A 4-mm thick resin restoration was built up on each tooth for microtensile testing. Statistical analyses between experimental and control groups were performed by student's t-test (alpha= 0.05). RESULTS: In general, experimental groups (previously treated with I2DDS) showed significantly lower bond strength values when compared with their respective controls (p0.05). CONCLUSION: Acetone-base adhesive systems seem not to be affected by the application of I2DDS prior to etching and bonding procedures.INTRODUÇÃO: A desinfecção das superfícies de dentina é desejada desde que não haja interferência na adesão dos agentes adesivos. OBJETIVO: Testar a hipótese nula de que a resistência adesiva não é afetada pela aplicação prévia de uma solução desinfetante de iodo. MATERIAL AND MÉTODO: Vinte e quatro molares hígidos foram selecionados. O esmalte oclusal destes dentes foi removido, e sobre as superfícies planas de dentina expostas foi aplicada da solução desinfetante de Iodo a 2% (I2DDS), que permaneceu sobre a superfície por 20 s e foi lavada por 20 s com água deionizada. Sobre as superfícies desinfetadas foram aplicados um dos seguintes sistemas adesivos (n=3): Single Bond; Prime & Bond NT; Clearfil SE Bond; Opti-Bond Plus. Os grupos controle (n=3) não tiveram a supeficie de dentina tratada com I2DDS antes dos precedimentos adesivos. Em todos os grupos, após hibridização da dentina, foi construída uma "restauração" de resina composta com cerca de 4 mm de espessura. Após 7 dias de armazenagem em água destilada, os dentes foram secionados de modo a originarem espécimes a serem submetidos ao teste de microtração (palitos). Análise estatística para comparação dos dados foi realizada pelo teste t de student (alfa=0,05). RESULTADOS: De forma geral, os grupos experimentais (tratados com I2DDS) apresentraram resistência adesiva significativamente menor do que os respectivos grupos controle (p0.05). Assim, a hipótese nula deve ser rejeitada para os adesivos a base de etanol e/ou a base de água, mas aceita para o adesivo a base de acetona. CONCLUSÃO: O uso da solução experimental de iodo previamente à realização dos procedimentos adesivos afetou a efetividade da união à dentina apenas quando do emprego de sistemas adesivos a base de etanol e/ou água.

In the neocortex, the coexistence of temporally locked excitation and inhibition governs complex network activity underlying cognitive functions, and is believed to be altered in several brain diseases. Here we show that this equilibrium can be unlocked by increased activity of layer 5 pyramidal neurons of the mouse neocortex. Somatic depolarization or short bursts of action potentials of layer 5 pyramidal neurons induced a selective long-term potentiation of GABAergic synapses (LTPi) without affecting glutamatergic inputs. Remarkably, LTPi was selective for perisomatic inhibition from parvalbumin basket cells, leaving dendritic inhibition intact. It relied on retrograde signaling of nitric oxide, which persistently altered presynaptic GABA release and diffused to inhibitory synapses impinging on adjacent pyramidal neurons. LTPi reduced the time window of synaptic summation and increased the temporal precision of spike generation. Thus, increases in single cortical pyramidal neuron activity can induce an interneuron-selective GABAergic plasticity effectively altering the computation of temporally coded information.

Argopecten purpuratus es uno de los recursos marinos de mayor importancia comercial en Chile. Una de las etapas críticas en el cultivo de esta especie, es el traspaso de las post-larvas al medio natural, ya que durante este período se produce un significativo descenso en el número de post-larvas. Los factores que provocan estas bajas sobrevivencias pueden ser diversos, pero aún son desconocidos. En el presente estudio se evaluó la incidencia en la sobrevivencia y crecimiento de las variables origen de las larvas, distribución de los colectores en diferentes estaciones de Bahía Inglesa, III región (27° 03' 24" S, 70° 51' 30" O) y los cambios en la bacterioflora asociadas a las post-larvas. Los organismos utilizados en el estudio fueron obtenidas desde los "hatcheries" de Cultivos Marinos Internacionales (III región) y Cultivos Guayacán (IV región). Los resultados del estudio indican claramente que la ubicación y origen de las post-larvas en la bahía incide en la sobrevivencia de éstas. Sin embargo, el crecimiento no es afectado por las variables estudiadas (P < 0,05). Desde un punto de vista microbiológico se observa que Vibrio spp. llega a ser un componente predominante en la microflora de ambas poblaciones larvales alcanzando porcentajes de 53,36 %. El análisis de componentes principales revela que no hay diferencias entre los Vibrio spp. cultivables de ambos cultivos. No obstante, la microflora residente de las larvas de Guayacánes más estable a los incrementos de bacterias del medio circundanteArgopecten purpuratus is one of the most commercially important marine resources in Chile. One of the most critical steps in the massive culture of this species is the transference of postlarvae from hatchery production to the sea where significant mortality regularly occurs. The factors behind this low survival rate are probably diverse, and are as yet unknown. In the present study, postlarval survival and growth was observed as a function of origin of postlarvae, distribution of postlarvae in the bay, and microbial loading of the postlarvae. Survival rates were measured for different sites in Bahia Inglesa, Chile (27° 03' 24" S, 70° 51' 30" W) as well as changes in the bacterioflora of the postlarvae. Postlarvae utilized in the study were obtained from Cultivos Marinos Internacionales (III Región) and Cultivos Guayacan (IV Región). Results of the study clearly indicated that survival in culture of the postlarvae was related to their location in the bay and the origin of the postlarvae. However, the growth of the post-larvae is not affected (P < 0.05). Microbiologically, it was observed that Vibrio spp. were the bacterial component most represented among strains isolated from the postlarvae (53.36 %) from both populations studied. Principal component analysis revealed no differences between cultivable vibrios from both cultures. However, microflora from the Guayacan group were less susceptible to increases in bacteria originating in their surrounding environment

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Abstract Background Data that directly associate utilization of novel systemic therapies with survival trends in metastatic breast cancer (MBC) are limited. In the setting of de novo MBC, large registry analyses cite positive temporal trends in survival, but the extent to which advances in systemic therapy have contributed to these gains is not clear. Methods The City of Hope Cancer Registry was used to identify a consecutive series of patients with de novo MBC who received their first line of therapy between 1985 and 2004. Comprehensive clinicopathologic and treatment-related data were collected for each patient. Univariate analyses were conducted via Cox regression to identify factors associated with improved survival. Multivariate analysis was also conducted via Cox regression and the stepwise procedure was used to identify independent predictors of survival. Results A total of 324 patients with de novo MBC were identified. After application of exclusion criteria, including the sole presence of supraclavicular node metastasis, 274 patients were retained in the analysis. The treatment-related characteristics associated with improved survival included: use of endocrine therapy (hazard ratio [HR] 0.60, 95%CI 0.47-0.77; P Conclusions The overall survival of women with de novo metastatic breast cancer has improved over the past 20 years. However, the contribution of conventional cytotoxic agents to this improvement is minimal.

Abstract Background Next generation sequencing is transforming our understanding of transcriptomes. It can determine the expression level of transcripts with a dynamic range of over six orders of magnitude from multiple tissues, developmental stages or conditions. Patterns of gene expression provide insight into functions of genes with unknown annotation. Results The RNA Seq-Atlas presented here provides a record of high-resolution gene expression in a set of fourteen diverse tissues. Hierarchical clustering of transcriptional profiles for these tissues suggests three clades with similar profiles: aerial, underground and seed tissues. We also investigate the relationship between gene structure and gene expression and find a correlation between gene length and expression. Additionally, we find dramatic tissue-specific gene expression of both the most highly-expressed genes and the genes specific to legumes in seed development and nodule tissues. Analysis of the gene expression profiles of over 2,000 genes with preferential gene expression in seed suggests there are more than 177 genes with functional roles that are involved in the economically important seed filling process. Finally, the Seq-atlas also provides a means of evaluating existing gene model annotations for the Glycine max genome. Conclusions This RNA-Seq atlas extends the analyses of previous gene expression atlases performed using Affymetrix GeneChip technology and provides an example of new methods to accommodate the increase in transcriptome data obtained from next generation sequencing. Data contained within this RNA-Seq atlas of Glycine max can be explored at http://www.soybase.org/soyseq.

Abstract Background Studies on host-pathogen interactions in a range of pathosystems have revealed an array of mechanisms by which plants reduce the efficiency of pathogenesis. While R-gene mediated resistance confers highly effective defense responses against pathogen invasion, quantitative resistance is associated with intermediate levels of resistance that reduces disease progress. To test the hypothesis that specific loci affect distinct stages of fungal pathogenesis, a set of maize introgression lines was used for mapping and characterization of quantitative trait loci (QTL) conditioning resistance to Setosphaeria turcica, the causal agent of northern leaf blight (NLB). To better understand the nature of quantitative resistance, the identified QTL were further tested for three secondary hypotheses: (1) that disease QTL differ by host developmental stage; (2) that their performance changes across environments; and (3) that they condition broad-spectrum resistance. Results Among a set of 82 introgression lines, seven lines were confirmed as more resistant or susceptible than B73. Two NLB QTL were validated in BC4F2 segregating populations and advanced introgression lines. These loci, designated qNLB1.02 and qNLB1.06, were investigated in detail by comparing the introgression lines with B73 for a series of macroscopic and microscopic disease components targeting different stages of NLB development. Repeated greenhouse and field trials revealed that qNLB1.06Tx303 (the Tx303 allele at bin 1.06) reduces the efficiency of fungal penetration, while qNLB1.02B73 (the B73 allele at bin 1.02) enhances the accumulation of callose and phenolics surrounding infection sites, reduces hyphal growth into the vascular bundle and impairs the subsequent necrotrophic colonization in the leaves. The QTL were equally effective in both juvenile and adult plants; qNLB1.06Tx303 showed greater effectiveness in the field than in the greenhouse. In addition to NLB resistance, qNLB1.02B73 was associated with resistance to Stewart's wilt and common rust, while qNLB1.06Tx303 conferred resistance to Stewart's wilt. The non-specific resistance may be attributed to pleiotropy or linkage. Conclusions Our research has led to successful identification of two reliably-expressed QTL that can potentially be utilized to protect maize from S. turcica in different environments. This approach to identifying and dissecting quantitative resistance in plants will facilitate the application of quantitative resistance in crop protection.

Abstract Background Scientific data integration and computational service discovery are challenges for the bioinformatic community. This process is made more difficult by the separate and independent construction of biological databases, which makes the exchange of data between information resources difficult and labor intensive. A recently described semantic web protocol, the Simple Semantic Web Architecture and Protocol (SSWAP; pronounced "swap") offers the ability to describe data and services in a semantically meaningful way. We report how three major information resources (Gramene, SoyBase and the Legume Information System [LIS]) used SSWAP to semantically describe selected data and web services. Methods We selected high-priority Quantitative Trait Locus (QTL), genomic mapping, trait, phenotypic, and sequence data and associated services such as BLAST for publication, data retrieval, and service invocation via semantic web services. Data and services were mapped to concepts and categories as implemented in legacy and de novo community ontologies. We used SSWAP to express these offerings in OWL Web Ontology Language (OWL), Resource Description Framework (RDF) and eXtensible Markup Language (XML) documents, which are appropriate for their semantic discovery and retrieval. We implemented SSWAP services to respond to web queries and return data. These services are registered with the SSWAP Discovery Server and are available for semantic discovery at http://sswap.info. Results A total of ten services delivering QTL information from Gramene were created. From SoyBase, we created six services delivering information about soybean QTLs, and seven services delivering genetic locus information. For LIS we constructed three services, two of which allow the retrieval of DNA and RNA FASTA sequences with the third service providing nucleic acid sequence comparison capability (BLAST). Conclusions The need for semantic integration technologies has preceded available solutions. We report the feasibility of mapping high priority data from local, independent, idiosyncratic data schemas to common shared concepts as implemented in web-accessible ontologies. These mappings are then amenable for use in semantic web services. Our implementation of approximately two dozen services means that biological data at three large information resources (Gramene, SoyBase, and LIS) is available for programmatic access, semantic searching, and enhanced interaction between the separate missions of these resources.

Abstract Background Transposable elements are the most abundant components of all characterized genomes of higher eukaryotes. It has been documented that these elements not only contribute to the shaping and reshaping of their host genomes, but also play significant roles in regulating gene expression, altering gene function, and creating new genes. Thus, complete identification of transposable elements in sequenced genomes and construction of comprehensive transposable element databases are essential for accurate annotation of genes and other genomic components, for investigation of potential functional interaction between transposable elements and genes, and for study of genome evolution. The recent availability of the soybean genome sequence has provided an unprecedented opportunity for discovery, and structural and functional characterization of transposable elements in this economically important legume crop. Description Using a combination of structure-based and homology-based approaches, a total of 32,552 retrotransposons (Class I) and 6,029 DNA transposons (Class II) with clear boundaries and insertion sites were structurally annotated and clearly categorized, and a soybean transposable element database, SoyTEdb, was established. These transposable elements have been anchored in and integrated with the soybean physical map and genetic map, and are browsable and visualizable at any scale along the 20 soybean chromosomes, along with predicted genes and other sequence annotations. BLAST search and other infrastracture tools were implemented to facilitate annotation of transposable elements or fragments from soybean and other related legume species. The majority (> 95%) of these elements (particularly a few hundred low-copy-number families) are first described in this study. Conclusion SoyTEdb provides resources and information related to transposable elements in the soybean genome, representing the most comprehensive and the largest manually curated transposable element database for any individual plant genome completely sequenced to date. Transposable elements previously identified in legumes, the third largest family of flowering plants, are relatively scarce. Thus this database will facilitate structural, evolutionary, functional, and epigenetic analyses of transposable elements in soybean and other legume species.

Abstract Background SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on the web. SSWAP was developed as a hybrid semantic web services technology to overcome limitations found in both pure web service technologies and pure semantic web technologies. Results There are currently over 2400 resources published in SSWAP. Approximately two dozen are custom-written services for QTL (Quantitative Trait Loci) and mapping data for legumes and grasses (grains). The remaining are wrappers to Nucleic Acids Research Database and Web Server entries. As an architecture, SSWAP establishes how clients (users of data, services, and ontologies), providers (suppliers of data, services, and ontologies), and discovery servers (semantic search engines) interact to allow for the description, querying, discovery, invocation, and response of semantic web services. As a protocol, SSWAP provides the vocabulary and semantics to allow clients, providers, and discovery servers to engage in semantic web services. The protocol is based on the W3C-sanctioned first-order description logic language OWL DL. As an open source platform, a discovery server running at http://sswap.info (as in to "swap info") uses the description logic reasoner Pellet to integrate semantic resources. The platform hosts an interactive guide to the protocol at http://sswap.info/protocol.jsp, developer tools at http://sswap.info/developer.jsp, and a portal to third-party ontologies at http://sswapmeet.sswap.info (a "swap meet"). Conclusion SSWAP addresses the three basic requirements of a semantic web services architecture (i.e., a common syntax, shared semantic, and semantic discovery) while addressing three technology limitations common in distributed service systems: i.e., i) the fatal mutability of traditional interfaces, ii) the rigidity and fragility of static subsumption hierarchies, and iii) the confounding of content, structure, and presentation. SSWAP is novel by establishing the concept of a canonical yet mutable OWL DL graph that allows data and service providers to describe their resources, to allow discovery servers to offer semantically rich search engines, to allow clients to discover and invoke those resources, and to allow providers to respond with semantically tagged data. SSWAP allows for a mix-and-match of terms from both new and legacy third-party ontologies in these graphs.

Abstract Background Soybeans grown in the upper Midwestern United States often suffer from iron deficiency chlorosis, which results in yield loss at the end of the season. To better understand the effect of iron availability on soybean yield, we identified genes in two near isogenic lines with changes in expression patterns when plants were grown in iron sufficient and iron deficient conditions. Results Transcriptional profiles of soybean (Glycine max, L. Merr) near isogenic lines Clark (PI548553, iron efficient) and IsoClark (PI547430, iron inefficient) grown under Fe-sufficient and Fe-limited conditions were analyzed and compared using the Affymetrix® GeneChip® Soybean Genome Array. There were 835 candidate genes in the Clark (PI548553) genotype and 200 candidate genes in the IsoClark (PI547430) genotype putatively involved in soybean's iron stress response. Of these candidate genes, fifty-eight genes in the Clark genotype were identified with a genetic location within known iron efficiency QTL and 21 in the IsoClark genotype. The arrays also identified 170 single feature polymorphisms (SFPs) specific to either Clark or IsoClark. A sliding window analysis of the microarray data and the 7X genome assembly coupled with an iterative model of the data showed the candidate genes are clustered in the genome. An analysis of 5' untranslated regions in the promoter of candidate genes identified 11 conserved motifs in 248 differentially expressed genes, all from the Clark genotype, representing 129 clusters identified earlier, confirming the cluster analysis results. Conclusion These analyses have identified the first genes with expression patterns that are affected by iron stress and are located within QTL specific to iron deficiency stress. The genetic location and promoter motif analysis results support the hypothesis that the differentially expressed genes are co-regulated. The combined results of all analyses lead us to postulate iron inefficiency in soybean is a result of a mutation in a transcription factor(s), which controls the expression of genes required in inducing an iron stress response.

Abstract Background Soybean, Glycine max (L.) Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Department of Energy Joint Genome Institute and United States Department of Agriculture jointly announced the sequencing of the soybean genome. One of the initial concerns is to what extent sequence identity in homeologous regions would have on whole genome shotgun sequence assembly. Results Seventeen BACs representing ~2.03 Mb were sequenced as representative potential homeologous regions from the soybean genome. Genetic mapping of each BAC shows that 11 of the 20 chromosomes are represented. Sequence comparisons between homeologous BACs shows that the soybean genome is a mosaic of retained paleopolyploid regions. Some regions appear to be highly conserved while other regions have diverged significantly. Large-scale "batch" reassembly of all 17 BACs combined showed that even the most homeologous BACs with upwards of 95% sequence identity resolve into their respective homeologous sequences. Potential assembly errors were generated by tandemly duplicated pentatricopeptide repeat containing genes and long simple sequence repeats. Analysis of a whole-genome shotgun assembly of 80,000 randomly chosen JGI-DOE sequence traces reveals some new soybean-specific repeat sequences. Conclusion This analysis investigated both the structure of the paleopolyploid soybean genome and the potential effects retained homeology will have on assembling the whole genome shotgun sequence. Based upon these results, homeologous regions similar to those characterized here will not cause major assembly issues.

Abstract Background Large scale gene analysis of most organisms is hampered by incomplete genomic sequences. In many organisms, such as soybean, the best source of sequence information is the existence of expressed sequence tag (EST) libraries. Soybean has a large (1115 Mbp) genome that has yet to be fully sequenced. However it does have the 6th largest EST collection comprised of ESTs from a variety of soybean genotypes. Many EST libraries were constructed from RNA extracted from various genetic backgrounds, thus gene identification from these sources is complicated by the existence of both gene and allele sequence differences. We used the ESTminer suite of programs to identify potential soybean gene transcripts from a single genetic background allowing us to observe functional classifications between gene families as well as structural differences between genes and gene paralogs within families. The identification of potential gene sequences (pHaps) from soybean allows us to begin to get a picture of the genomic history of the organism as well as begin to observe the evolutionary fates of gene copies in this highly duplicated genome. Results We identified approximately 45,000 potential gene sequences (pHaps) from EST sequences of Williams/Williams82, an inbred genotype of soybean (Glycine max L. Merr.) using a redundancy criterion to identify reproducible sequence differences between related genes within gene families. Analysis of these sequences revealed single base substitutions and single base indels are the most frequently observed form of sequence variation between genes within families in the dataset. Genomic sequencing of selected loci indicate that intron-like intervening sequences are numerous and are approximately 220 bp in length. Functional annotation of gene sequences indicate functional classifications are not randomly distributed among gene families containing few or many genes. Conclusion The predominance of single nucleotide insertion/deletions and substitution events between genes within families (individual genes and gene paralogs) is consistent with a model of gene amplification followed by single base random mutational events expected under the classical model of duplicated gene evolution. Molecular functions of small and large gene families appear to be non-randomly distributed possibly indicating a difference in retention of duplicates or local expansion.

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