Relationship between Bacterial Community Composition and Bottom-Up versus Top-Down Variables in Four Eutrophic Shallow Lakes

Bacterial community composition was monitored in four shallow eutrophic lakes during one year using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified prokaryotic rDNA genes. Of the four lakes investigated, two were of the clearwater type and had dense stands of submerged macrophytes while two others were of the turbid type characterized by the occurrence of phytoplankton blooms. One turbid and one clearwater lake had high nutrient levels (total phosphorus, >100 μg liter⁻¹) while the other lakes had relatively low nutrient levels (total phosphorus, <100 μg liter⁻¹). For each lake, seasonal changes in the bacterial community were related to bottom-up (resources) and top-down (grazers) variables by using canonical correspondence analysis (CCA). Using an artificial model dataset to which potential sources of error associated with the use of relative band intensities in DGGE analysis were added, we found that preferential amplification of certain rDNA genes over others does not obscure the relationship between bacterial community composition and explanatory variables. Besides, using this artificial dataset as well as our own data, we found a better correlation between bacterial community composition and explanatory variables by using relative band intensities compared to using presence/absence data. While bacterial community composition was related to phytoplankton biomass in the high-nutrient lakes no such relation was found in the low-nutrient lakes, where the bacterial community is probably dependent on other organic matter sources. We used variation partitioning to evaluate top-down regulation of bacterial community composition after bottom-up regulation has been accounted for. Using this approach, we found no evidence for top-down regulation of bacterial community composition in the turbid lakes, while grazing by ciliates and daphnids (Daphnia and Ceriodaphnia) was significantly related to changes in the bacterial community in the clearwater lakes. Our results suggest that in eutrophic shallow lakes, seasonality of bacterial community structure is dependent on the dominant substrate source as well as on the food web structure.     

Lifespan and Aggregate Size Variables in Specifications of Mortality or Survivorship

A specification of mortality or survivorship provides respective explicit details about mortality''s or survivorship''s relationships with one or more other variables (e.g., age, sex, etc.). Previous studies have discovered and analyzed diverse specifications of mortality or survivorship; these discoveries and analyses suggest that additional specifications of mortality or survivorship have yet to be discovered and analyzed. In consistency with previous research, multivariable limited powered polynomials regression analyses of mortality and survivorship of selected humans (Swedes, 1760–2008) and selected insects (caged medflies) show age-specific, historical-time-specific, environmental-context-specific, and sex-specific mortality and survivorship. These analyses also present discoveries of hitherto unknown lifespan-specific, contemporary-aggregate-size-specific, and lifespan-aggregate-size-specific mortality and survivorship. The results of this investigation and results of previous research help identify variables for inclusion in regression models of mortality or survivorship. Moreover, these results and results of previous research strengthen the suggestion that additional specifications of mortality or survivorship have yet to be discovered and analyzed, and they also suggest that specifications of mortality and survivorship indicate corresponding specifications of frailty and vitality. Furthermore, the present analyses reveal the usefulness of a multivariable limited powered polynomials regression model-building approach. This article shows that much has yet to be learned about specifications of mortality or survivorship of diverse kinds of individuals in diverse times and places.     

Integrating Top-Down and Bottom-Up Sensory Processing by Somato-Dendritic Interactions

The classical view of cortical information processing is that of a bottom-up process in a feedforward hierarchy. However, psychophysical, anatomical, and physiological evidence suggests that top-down effects play a crucial role in the processing of input stimuli. Not much is known about the neural mechanisms underlying these effects. Here we investigate a physiologically inspired model of two reciprocally connected cortical areas. Each area receives bottom-up as well as top-down information. This information is integrated by a mechanism that exploits recent findings on somato-dendritic interactions. (1) This results in a burst signal that is robust in the context of noise in bottom-up signals. (2) Investigating the influence of additional top-down information, priming-like effects on the processing of bottom-up input can be demonstrated. (3) In accordance with recent physiological findings, interareal coupling in low-frequency ranges is characteristically enhanced by top-down mechanisms. The proposed scheme combines a qualitative influence of top-down directed signals on the temporal dynamics of neuronal activity with a limited effect on the mean firing rate of the targeted neurons. As it gives an account of the system properties on the cellular level, it is possible to derive several experimentally testable predictions.     

Marine plant harvest in Portugal

This work brings together the scattered information on marine plant harvests and the colloid extraction industry in Portugal, as an initial contribution to the improvement of resource management. The first phase of exploitation of marine plant resources started prior to the 14th century, with the gathering and sale of storm-tossed seaweeds for fertilizer. The harvest of seagrasses and algae at Ria de Aveiro was of great economic importance. The second phase of resource exploitation began with the wider scale harvest of agarophyte species for colloid extraction. Portugal is at present the third largest harvester of the agarophytes Gelidium and Pterocladia (2500 t annually), and it is the fifth largest agar producer (350 t annually). Other colloid-producing species, including Chondrus crispus and Mastocarpus stellatus, are also harvested for export. The total agarophyte landings, agar production and income from agar exports is far below the maximum levels attained in the early 1970s. The status of stocks in each different harvest zone on the continental coast and the Azores is examined. Although there is an effective management structure for the Portuguese marine plant resource, research is needed to provide a sound biological basis for management. author for correspondence     

Hepatozoonosis in foxes from Portugal

Hepatozoon, sp. is described for the first time in foxes (Vulpes vulpes silacea) in Portugal. Of 301 foxes examined, 143 (48%) were infected. The gametocyte was the predominant stage of the life cycle and was found in every organ except the bone marrow, where schizonts were the most abundant stage. The morphological similarity of this parasite's gametocytes to Hepatozoon canis is emphasized.     

Extracellular Matrix Stiffness and Architecture Govern Intracellular Rheology in Cancer

Little is known about the complex interplay between the extracellular mechanical environment and the mechanical properties that characterize the dynamic intracellular environment. To elucidate this relationship in cancer, we probe the intracellular environment using particle-tracking microrheology. In three-dimensional (3D) matrices, intracellular effective creep compliance of prostate cancer cells is shown to increase with increasing extracellular matrix (ECM) stiffness, whereas modulating ECM stiffness does not significantly affect the intracellular mechanical state when cells are attached to two-dimensional (2D) matrices. Switching from 2D to 3D matrices induces an order-of-magnitude shift in intracellular effective creep compliance and apparent elastic modulus. However, for a given matrix stiffness, partial blocking of β1 integrins mitigates the shift in intracellular mechanical state that is invoked by switching from a 2D to 3D matrix architecture. This finding suggests that the increased cell-matrix engagement inherent to a 3D matrix architecture may contribute to differences observed in viscoelastic properties between cells attached to 2D matrices and cells embedded within 3D matrices. In total, our observations show that ECM stiffness and architecture can strongly influence the intracellular mechanical state of cancer cells.     

Two Interlinked Bistable Switches Govern Mitotic Control in Mammalian Cells

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Top-Down but Not Bottom-Up Visual Scanning is Affected in Hereditary Pure Cerebellar Ataxia

The aim of this study was to clarify the nature of visual processing deficits caused by cerebellar disorders. We studied the performance of two types of visual search (top-down visual scanning and bottom-up visual scanning) in 18 patients with pure cerebellar types of spinocerebellar degeneration (SCA6: 11; SCA31: 7). The gaze fixation position was recorded with an eye-tracking device while the subjects performed two visual search tasks in which they looked for a target Landolt figure among distractors. In the serial search task, the target was similar to the distractors and the subject had to search for the target by processing each item with top-down visual scanning. In the pop-out search task, the target and distractor were clearly discernible and the visual salience of the target allowed the subjects to detect it by bottom-up visual scanning. The saliency maps clearly showed that the serial search task required top-down visual attention and the pop-out search task required bottom-up visual attention. In the serial search task, the search time to detect the target was significantly longer in SCA patients than in normal subjects, whereas the search time in the pop-out search task was comparable between the two groups. These findings suggested that SCA patients cannot efficiently scan a target using a top-down attentional process, whereas scanning with a bottom-up attentional process is not affected. In the serial search task, the amplitude of saccades was significantly smaller in SCA patients than in normal subjects. The variability of saccade amplitude (saccadic dysmetria), number of re-fixations, and unstable fixation (nystagmus) were larger in SCA patients than in normal subjects, accounting for a substantial proportion of scattered fixations around the items. Saccadic dysmetria, re-fixation, and nystagmus may play important roles in the impaired top-down visual scanning in SCA, hampering precise visual processing of individual items.     

Infraslow State Fluctuations Govern Spontaneous fMRI Network Dynamics

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Discriminant Variables

Several fundamental properties of discriminant variables are developed. In addition, the proportionality of the discriminant variables, canonical variables and RAO principal components is demonstrated.     

Identifying Prognostic Features by Bottom-Up Approach and Correlating to Drug Repositioning

Background

Traditionally top-down method was used to identify prognostic features in cancer research. That is to say, differentially expressed genes usually in cancer versus normal were identified to see if they possess survival prediction power. The problem is that prognostic features identified from one set of patient samples can rarely be transferred to other datasets. We apply bottom-up approach in this study: survival correlated or clinical stage correlated genes were selected first and prioritized by their network topology additionally, then a small set of features can be used as a prognostic signature.

Methods

Gene expression profiles of a cohort of 221 hepatocellular carcinoma (HCC) patients were used as a training set, ‘bottom-up’ approach was applied to discover gene-expression signatures associated with survival in both tumor and adjacent non-tumor tissues, and compared with ‘top-down’ approach. The results were validated in a second cohort of 82 patients which was used as a testing set.

Results

Two sets of gene signatures separately identified in tumor and adjacent non-tumor tissues by bottom-up approach were developed in the training cohort. These two signatures were associated with overall survival times of HCC patients and the robustness of each was validated in the testing set, and each predictive performance was better than gene expression signatures reported previously. Moreover, genes in these two prognosis signature gave some indications for drug-repositioning on HCC. Some approved drugs targeting these markers have the alternative indications on hepatocellular carcinoma.

Conclusion

Using the bottom-up approach, we have developed two prognostic gene signatures with a limited number of genes that associated with overall survival times of patients with HCC. Furthermore, prognostic markers in these two signatures have the potential to be therapeutic targets.