The Averted Gaze

The literature of higher education and campus rhetoric convey the impression that academic change is rampant. Organizational gridlock and exceptionally limited change are more apt characterizations of campus life. Ethnographic studies of change in the academy would help to determine the validity of both assertions. The qualitative research community, however, appears to avoid studies of the academy. Reasons for a collective "averted gaze" are here examined.     

Gaze Holding in Healthy Subjects

Eccentric gaze in darkness evokes minor centripetal eye drifts in healthy subjects, as cerebellar control sufficiently compensates for the inherent deficiencies of the brainstem gaze-holding network. This behavior is commonly described using a leaky integrator model, which assumes that eye velocity grows linearly with gaze eccentricity. Results from previous studies in patients and healthy subjects suggest caution when this assumption is applied to eye eccentricities larger than 20 degrees. To obtain a detailed characterization of the centripetal gaze-evoked drift, we recorded horizontal eye position in 20 healthy subjects. With their head fixed, they were asked to fixate a flashing dot (50 ms every 2 s)that was quasi-stationary displacing(0.5 deg/s) between ±40 deg horizontally in otherwise complete darkness. Drift velocity was weak at all angles tested. Linearity was assessed by dividing the range of gaze eccentricity in four bins of 20 deg each, and comparing the slopes of a linear function fitted to the horizontal velocity in each bin. The slopes of single subjects for gaze eccentricities of ±0−20 deg were, in median,0.41 times the slopes obtained for gaze eccentricities of ±20−40 deg. By smoothing the individual subjects'' eye velocity as a function of gaze eccentricity, we derived a population of position-velocity curves. We show that a tangent function provides a better fit to the mean of these curves when large eccentricities are considered. This implies that the quasi-linear behavior within the typical ocular motor range is the result of a tuning procedure, which is optimized in the most commonly used range of gaze. We hypothesize that the observed non-linearity at eccentric gaze results from a saturation of the input that each neuron in the integrating network receives from the others. As a consequence, gaze-holding performance declines more rapidly at large eccentricities.     

Assessing the potential to harness the microbiome through plant genetics

(1) Among all plant traits, functions and pathways that influence microbial communities some will be discoverable in the lab using mutants. (2) From the functions highlighted in lab studies, a subset will overlap with plant traits variable among genotypes and expressed in realistic field conditions. (3) These traits tend to impact microbial communities associated with plants through a subset of important microbes that in turn influence the rest of the community. (4) Microbial communities impacted by host variation, both directly and indirectly, may influence important components of plant performance (5).

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Assessing species misidentification rates through quality assurance of vegetation monitoring

Most studies of observer discrepancies in vegetation recording have beenlimited in the extent to which they can separate different sources of error. Itis straightforward to quantify the degree of disparity between two specieslistsbut not clear how to allocate a particular discrepancy to a specific cause.Misidentification is especially difficult to detect, and is rarely discussed inthe literature. The vegetation monitoring protocol devised by the UnitedKingdomEnvironmental Change Network (ECN) splits each plot to be recorded into cells,within each of which a species list is compiled. This provides an objectivemeasure of the frequency of occurrence of individual species, in place of themore subjective estimation of cover, and allows within-plot variation to bequantified. An added advantage of the ECN methodology is that botanicalexpertise and the use of cells can be combined in quality assurance (QA)studiesto detect instances of consistent misidentification of species, therebyincreasing the repeatability of vegetation recording and enhancing thepossibility of detecting change.This paper reports an analysis of the data obtained from a 1996 ECN QA exerciseand describes the methods used to pinpoint the most likely sources ofdiscrepancies between the original site surveys and the QA survey. Overall itisestimated that 5.9% of specimens were misidentified at species level and 1.9%atgenus level, though it is detectable that sites employing consultant surveyorsachieved slightly better results. Misidentification rates are particularly highfor the lower plants and for woodland plots. The number of unmatched records(the pseudoturnover rate) is high, 24%, but comparable to other studies. Thisdoes not seem to be the result, to any great extent, of seasonal changes oridentification problems, but appears to be largely due to overlooking andpartlya result of relocation problems. The overall percentage agreement betweensurveyors was 57%, also comparable with other studies.     

Assessing the distribution of sedimentary C40 carotenoids through time

A comprehensive marine biomarker record of green and purple sulfur bacteria (GSB and PSB, respectively) is required to test whether anoxygenic photosynthesis represented a greater fraction of marine primary productivity during the Precambrian than the Phanerozoic, as current models of ocean redox evolution suggest. For this purpose, we analyzed marine rock extracts and oils from the Proterozoic to the Paleogene for C₄₀ diagenetic products of carotenoid pigments using new analytical methods. Gas chromatography coupled with tandem mass spectrometry provides a new perspective on the temporal distributions of carotenoid biomarkers for phototrophic sulfur bacteria, specifically okenane, chlorobactane, and paleorenieratane. According to conventional paleoredox interpretations, this revised stratigraphic distribution of the GSB and PSB biomarkers implies that the shallow sunlit surface ocean (<24 m) became sulfidic more frequently in the geologic past than was previously thought. We reexamine whether there is evidence supporting a planktonic source of GSB and PSB pigments in marine systems or whether additional factors are required to explain the marine phototrophic sulfur bacteria record. To date, planktonic GSB and PSB and their pigments have been identified in restricted basins and lakes, but they have yet to be detected in the unrestricted, transiently sulfidic, marine systems. Based on modern observations, additional environmental factors, including basin restriction, microbial mats, or sediment transport, may be required to fully explain GSB and PSB carotenoids in the geologic record.     

Assessing ecological risk through automated drainage extraction and watershed delineation

Decision makers are frequently involved in projects requiring ecological risk definition, which are inherent to biological conservation process. It is important to recognize these risks in order to invest wisely in the management and protection of biological resources. In this matter, Geographic Information System tools and remote sensing data have been used frequently as important components in planning and management of conservation units, Rabus et al. (2003), Valeriano et al. (2009) and Valeriano et al. (2010) stressed the advantages of using data that were gathered during the Shuttle Radar Topographic Mission (SRTM) for biological and geomorphologic purposes. For Brazil's national territory, the SRTM data were refined (Valeriano, 2008) and offered as free access on the TOPODATA Project website (http://www.dsr.inpe.br/topodata) where geomorphometric information (including elevation data) at a resolution of 30 m are provided. The aim of this paper is to demonstrate an example of how TOPODATA products have been applied in order to determine the ecological risk of the border of a Conservation Unit, located in the State of São Paulo—Brazil, in the Brazilian Atlantic Forest, using automated drainage network and watershed extraction. A comparison between SRTM, TOPODATA, and ASTER DEM was carried out, showing an advantage of TOPODATA drainage network product. The vectors generated using this data are more similar to the official drainage network vectors than the drainage network extracted using ASTER-DEM or SRTM. The network product generated using ASTER-DEM produced many commission errors and the one generated using SRTM produced a poor network, with generalized vectors, less detailed than the others. The results showed that using the TOPODATA Project‘s Digital Elevation Model (DEM) can provide important data for ecological analysis and significant additional information for decision making, regarding drainage networks and watershed features. The produced map for border ecological risk showed to fit perfectly to the field work analyses, produced in other works. Furthermore, the extracted watershed polygons might furnish important information unrevealing best conservation unit boundaries, which means more efficient management and best biological conservation results.     

Assessing monoclonal antibody product quality attribute criticality through clinical studies

Recombinant therapeutic proteins, including antibodies, contain a variety of chemical and physical modifications. Great effort is expended during process and formulation development in controlling and minimizing this heterogeneity, which may not affect safety or efficacy and, therefore, may not need to be controlled. Many of the chemical conversions also occur in vivo and knowledge about the alterations can be applied to assessment of the potential impact on characteristics and the biological activity of therapeutic proteins. Other attributes may affect the drug clearance and thereby alter drug efficacy. In this review article, we describe attribute studies conducted using clinical samples and how information gleaned from them is applied to attribute criticality assessment. In general, how fast attributes change in vivo compared to the rate of mAb elimination is the key parameter used in these evaluations. An attribute with more rapidly changing levels may have greater potential to affect safety or efficacy and thereby reach the status of a Critical Quality Attribute (CQA) that should be controlled during production and storage, but the effect will depend on whether compositional changes are due to chemical conversion or differential clearance.Key words: quality by design, critical quality attributes, pharmacokinetics, biotransformations, microheterogeneity     

Assessing monoclonal antibody product quality attribute criticality through clinical studies

Recombinant therapeutic proteins, including antibodies, contain a variety of chemical and physical modifications. Great effort is expended during process and formulation development in controlling and minimizing this heterogeneity, which may not affect safety or efficacy, and, therefore, may not need to be controlled. Many of the chemical conversions also occur in vivo, and knowledge about the alterations can be applied to assessment of the potential impact on characteristics and the biological activity of therapeutic proteins. Other attributes may affect the drug clearance and thereby alter drug efficacy. In this review article, we describe attribute studies conducted using clinical samples and how information gleaned from them is applied to attribute criticality assessment. In general, how fast attributes change in vivo compared to the rate of mAb elimination is the key parameter used in these evaluations. An attribute with more rapidly changing levels may have greater potential to affect safety or efficacy and thereby reach the status of a Critical Quality Attribute (CQA) that should be controlled during production and storage, but the effect will depend on whether compositional changes are due to chemical conversion or differential clearance.     

Joint Attention without Gaze Following: Human Infants and Their Parents Coordinate Visual Attention to Objects through Eye-Hand Coordination

The coordination of visual attention among social partners is central to many components of human behavior and human development. Previous research has focused on one pathway to the coordination of looking behavior by social partners, gaze following. The extant evidence shows that even very young infants follow the direction of another''s gaze but they do so only in highly constrained spatial contexts because gaze direction is not a spatially precise cue as to the visual target and not easily used in spatially complex social interactions. Our findings, derived from the moment-to-moment tracking of eye gaze of one-year-olds and their parents as they actively played with toys, provide evidence for an alternative pathway, through the coordination of hands and eyes in goal-directed action. In goal-directed actions, the hands and eyes of the actor are tightly coordinated both temporally and spatially, and thus, in contexts including manual engagement with objects, hand movements and eye movements provide redundant information about where the eyes are looking. Our findings show that one-year-olds rarely look to the parent''s face and eyes in these contexts but rather infants and parents coordinate looking behavior without gaze following by attending to objects held by the self or the social partner. This pathway, through eye-hand coupling, leads to coordinated joint switches in visual attention and to an overall high rate of looking at the same object at the same time, and may be the dominant pathway through which physically active toddlers align their looking behavior with a social partner.     

Assessing the reliability of sequence similarities detected through hydrophobic cluster analysis

Hydrophobic cluster analysis (HCA) has long been used as a tool to detect distant homologies between protein sequences, and to classify them into different folds. However, it relies on expert human intervention, and is sensitive to subjective interpretations of pattern similarities. In this study, we describe a novel algorithm to assess the similarity of hydrophobic amino acid distributions between two sequences. Our algorithm correctly identifies as misattributions several HCA-based proposals of structural similarity between unrelated proteins present in the literature. We have also used this method to identify the proper fold of a large variety of sequences, and to automatically select the most appropriate structure for homology modeling of several proteins with low sequence identity to any other member of the protein data bank. Automatic modeling of the target proteins based on these templates yielded structures with TM-scores (vs. experimental structures) above 0.60, even without further refinement. Besides enabling a reliable identification of the correct fold of an unknown sequence and the choice of suitable templates, our algorithm also shows that whereas most structural classes of proteins are very homogeneous in hydrophobic cluster composition, a tenth of the described families are compatible with a large variety of hydrophobic patterns. We have built a browsable database of every major representative hydrophobic cluster pattern present in each structural class of proteins, freely available at http://www2.ufp.pt/ pedros/HCA_db/index.htm.     

Assessing conservation biology priorities through the development of biodiversity indicators.

Biodiversity erosion is now a recognized phenomenon within the scientific community, and it is understood that there is an urgent need for action to relieve this loss. However, no consensus exists on how to go about achieving this goal. This is due to two kinds of problems: namely, that there are many different reasons which can motivate conservation attempts and hence they can lead to different priorities, sometimes in direct contrast with one another; and that of the complexity of the natural world which we have to operate in. Regarding the latter, several authors have lamented a severe lack of theoretical support for many conservation decisions. We briefly review some of the criteria that are commonly adopted in conservation, and indicate some of their problems; we then introduce a new theoretical framework based on the use of a series of biological indicators, many of which have already been proposed in the past but never fully explained and/or adopted. In addition, we propose two indices for one of these potential indicators, i.e. evolutionary potential. We conclude with an appeal for a greater collaboration between conservation scientists and evolutionary biologists, in order to encompass evolutionary evidence in the decision-making process. In doing so, we hope to increase the chances of successful conservation efforts.     

Assessing metacommunity processes through signatures in spatiotemporal turnover of community composition

Although metacommunity ecology has been a major field of research in the last decades, with both conceptual and empirical outputs, the analysis of the temporal dynamics of metacommunities has only emerged recently and consists mostly of repeated static analyses. Here we propose a novel analytical framework to assess metacommunity processes using path analyses of spatial and temporal diversity turnovers. We detail the principles and practical aspects of this framework and apply it to simulated datasets to illustrate its ability to decipher the respective contributions of entangled drivers of metacommunity dynamics. We then apply it to four empirical datasets. Empirical results support the view that metacommunity dynamics may be generally shaped by multiple ecological processes acting in concert, with environmental filtering being variable across both space and time. These results reinforce our call to go beyond static analyses of metacommunities that are blind to the temporal part of environmental variability.