Publications by authors named "Patrick Bennett"

101 Publications

First report of Armillaria cepistipes causing root disease on Populus trichocarpa (black cottonwood) in Oregon, USA.

Plant Dis 2021 Feb 22. Epub 2021 Feb 22.

Oregon State University, Botany and Plant Pathology, North Dakota State University Departmetn of Plant Pathology 306 Walster Hall, Fargo, North Dakota, United States, 58108-6050;

Populus trichocarpa Torr. and Gray (black cottonwood) is an economically and ecologically important tree species native to western North America. It serves as a model tree species in biology and genetics due to its relatively small genome size, rapid growth, and early reproductive maturity (Jansson and Douglas 2007). Black cottonwood is susceptible to root rot caused by at least one species of Armillaria (Raabe 1962), a globally distributed genus that exhibits diverse ecological behaviors (Klopfenstein et al. 2017) and infects numerous woody plant species (Raabe 1962). However, several Armillaria spp. have been isolated from Populus spp. in North America (Mallet 1990), and the most recent report of Armillaria on P. trichocarpa used the now ambiguated name A. mellea (Vahl.) Quel. (see Raabe 1962). In April 2016, mycelial fans and rhizomorphs of an unknown Armillaria species (isolate WV-ARR-3) were collected from P. trichocarpa in a riparian hardwood stand ca. 5.5 km east of Springfield, Oregon, USA (44°3'21.133"N, 122°49'39.935"W). The host was dominant in the canopy, large in diameter (ca. 90-cm dbh) relative to neighboring trees, and exhibited minimal crown dieback (ca. < 5%). A mycelial fan was observed destroying living cambium beneath the inner bark, indicating pathogenicity. The isolate was cultured on malt extract medium (3% malt extract, 3% dextrose, 1% peptone, and 1.5 % agar) and identified as A.cepistipes on the basis of somatic pairing tests and translation elongation factor 1α (tef1) sequences (GenBank Accession No. MK172784). DNA extraction, PCR, and tef1 sequencing followed protocols of Elías-Román et al. (2018). From nine replications of somatic incompatibility tests (18 tester isolates representing six North American Armillaria spp.), the isolate showed high intraspecific compatibility (colorless antagonism) with three A. cepistipes tester isolates (78%), but low compatibility with the other Armillaria spp. (0 - 33%) that occur in the region. Isolate WV-ARR-3 yielded tef1 sequences with a 99% identity to A. cepistipes (GenBank Accession Nos. JF313115 and JF313121). A second isolate (WV-ARR-1; GenBank Accession No. MK172783) with a nearly identical sequence was collected from a maturing P. trichocarpa in a riparian stand ca. 8 km northeast of Monroe, Oregon (44°21'47.57"N, 123°13'14.415"W) along the Willamette River, downstream from the McKenzie river tributary where WV-ARR-3 was collected. Armillaria cepistipes has been reported on Alnus rubra (red alder) in Washington, USA (Banik et al. 1996) and on broad-leaved trees in British Columbia, Canada (Allen et al. 1996). It is generally considered to be a weak pathogen on broad-leaved trees in the Pacific Northwest, but it is also associated with pathogenicity on both coniferous and deciduous trees in Europe (e.g., Lygis et al. 2005). However, a recent phylogenetic study suggested that North American A. cepistipes is phylogenetically distinct from Eurasian A. cepistipes (Klopfenstein et al. 2017), butadditional studies are needed to determine the formal taxonomic status of North American A. cepistipes. To our knowledge, A. cepistipes has not been previously confirmed on P. trichocarpa in the U.S.A. or formally reported as a pathogen of any Populus species in North America. Continued studies are needed to determine the distribution, host range, and ecological role of A. cepistipes in riparian forests of the Pacific Northwest, while monitoring its populations under changing climates.
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http://dx.doi.org/10.1094/PDIS-09-20-1993-PDNDOI Listing
February 2021

Phase integration bias in a motion grouping task.

J Vis 2020 07;20(7):31

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The perception of the direction of global motion depends on our ability to integrate local motion signals over space and time. We examined motion binding using a task requiring integration of relative phase. Observers completed multiple tasks involving clockwise and counter clockwise motion in a stimulus comprising four sets of linearly arranged dots, two moving horizontally and two moving vertically along sinusoidal trajectories differing in phase. Noise jitter was added along the trajectory perpendicular to each dot's motion. The noise acts as a global grouping cue that improves direction discrimination, but surprisingly, the absence of noise causes consistent below-chance performance (Lorenceau, 1996). We explore this phenomenon and subsequently test the hypothesis that observers perceive reverse motion because their representation of the relative phase of the motion components is systematically biased. We employ a number of different objective and subjective measures of motion integration and measure the phenomenon in both younger and older adults. Taken together, the results presented in the current article demonstrate that noise can promote global grouping in the stimulus and that confident, incorrect responses can be observed in the absence of correct global grouping. Generally, the current result raises the possibility that an integration bias could exist in other motion tasks.
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http://dx.doi.org/10.1167/jov.20.7.31DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7424100PMC
July 2020

Perceptual learning of detection of textures in noise.

J Vis 2020 07;20(7):22

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We examined whether the effects of practice on visual detection are stimulus specific and whether practice alters response bias. Eighty-four subjects performed yes-no detection of band-limited noise patterns (textures) in two levels of external noise, on two consecutive days. On day 2, one-half of the observers switched to novel textures. Texture contrast was varied on signal-present trials using the method of constant stimuli. The signal was present on 50% of the trials. We measured d', detection thresholds, and two measures of response criterion: a global criterion that was based on sensitivity at all signal levels (Jones et al., 2015) and a local criterion computed at a hit rate of 70% or 80% (Wenger & Rasche, 2006). Performance improved for both groups on day 2, indicating that improvement transferred to novel textures. Increases in d' were associated with a decrease in false alarms across days. The global criterion became less liberal and became more optimal (i.e., less biased) with practice; however, this effect was small and was not statistically significant in all conditions. The local criterion measure also became slightly less liberal with practice in most conditions, becoming more or less optimal depending on the hit rate at which it was computed. Overall, the effects of practice on sensitivity in a visual detection task generalized to novel patterns. In addition, we found that practice had relatively small effects on response criterion, and the precise effects on response bias differed between global and local measures of criterion.
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http://dx.doi.org/10.1167/jov.20.7.22DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7424956PMC
July 2020

Evaluation of single molecule array digital immunoassay technology to quantitate neurofilament light chain.

Bioanalysis 2020 Feb 21;12(4):221-229. Epub 2020 Feb 21.

Biomarker Services, Pharmaceutical Product Development (PPD) Laboratories, 2244 Dabney Road, Richmond, VA 23230, USA.

Globally, neurodegeneration accounts for significant morbidity and mortality among the elderly. Millions of people are afflicted with neurodegenerative diseases, with the most notable cases attributed to Alzheimer's, Huntington's, amyotrophic lateral sclerosis and Parkinson's diseases. Sensitive assays that can detect proteopathic anomalies indicative of early neurodegeneration have remained elusive. Therefore, there is an urgent need for sensitive diagnostic and prognostic biomarker assays that can guide the therapeutic regimen in the clinic. Single molecule array digital immunoassay platform has sensitivity about 1000-fold higher than traditional ligand binding assays. Consequently, we are now beginning to implement ultrasensitive techniques in bioanalysis. In the current study, we evaluated single molecule array technology and report specifications to quantitate neurofilament light chain, a bona-fide biomarker for neurodegeneration. Preliminary neurofilament light screening results from 100 human geriatric cerebrospinal fluid samples displayed huge biological variation and warrants further investigation.
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http://dx.doi.org/10.4155/bio-2019-0221DOI Listing
February 2020

Evaluation of sample stability for cellular kinetics and pharmacodynamic flow cytometry methods.

Bioanalysis 2019 Oct;11(20):1881-1884

Biomarker Laboratories, PPD, Richmond, VA 23230, USA.

We evaluated the sample stability for a cellular kinetics and a pharmacodynamic flow cytometry methods. First, the blood collection tubes were compared for the enumeration of chimeric antigen receptor-T cells in human whole blood. Blood samples with chimeric antigen receptor-T cells were stable up to 3 days at room temperature in both conventional EDTA and Cyto-Chex blood collection tubes (Streck Laboratories, NE, USA), but with better consistency in Cyto-Chex-BCT than conventional EDTA tubes. Second, sample storage temperatures were compared for the basophil activation test in human whole blood samples. The samples were stable up to 3 days for basophil activation test when stored at refrigerator temperature, but not stable when stored at room temperature. It is crucial during the development of method to evaluate all the variables which might impact sample integrity.
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http://dx.doi.org/10.4155/bio-2019-0170DOI Listing
October 2019

Sensitivity to curvature deformations along closed contours.

J Vis 2019 11;19(13)

Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ontario, Canada.

Human observers are exquisitely sensitive to curvature deformations along a circular closed contour (Wilkinson, Wilson, & Habak, 1998; Hess, Wang, & Dakin, 1999; Loffler, Wilson, & Wilkinson, 2003). Such remarkable sensitivity has been attributed to the curvature encoding scheme used by V4 neurons, which typically are assumed to be equally sensitive to curvature at all polar angles (Pasupathy & Connor, 2001, 2002; Carlson, Rasquinha, Zhang, & Connor, 2011). To test the assumption that detection thresholds for curvature deformations are invariant across polar angles, we used a novel stimulus class we call Difference of Gaussian (DoG) contours that allowed us to independently manipulate the amplitude, angular frequency, and polar angle of curvature of a closed-contour shape while measuring contour-curvature thresholds. Our results demonstrate that (a) detection thresholds were higher when observers were uncertain about the location of the curvature deformation, but on average, thresholds did not vary significantly across 24 polar angles; (b) the direction and magnitude of the oblique effect varies across individuals; (c) there is a strong association between detecting a contour deformation and identifying its location; (d) curvature detectors may serve as labeled lines.
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http://dx.doi.org/10.1167/19.13.7DOI Listing
November 2019

Environmental variables associated with population structure and Swiss needle cast severity in Western Oregon and Washington.

Ecol Evol 2019 Oct 12;9(19):11379-11394. Epub 2019 Sep 12.

Department of Botany and Plant Pathology Oregon State University Corvallis OR USA.

The environment has a strong influence on the abundance and distribution of plant pathogenic organisms and plays a major role in plant disease. Climatological factors may also alter the dynamics of the interactions between plant pathogens and their hosts. (=) , the causal agent of Swiss needle cast (SNC) of Douglas-fir, is endemic to western North America where it exists as two sympatric, reproductively isolated lineages. The abundance of this fungus and the severity of SNC are strongly influenced by climate. We used statistical and population genetic analyses to examine relationships between environment, pathogen population structure, and SNC severity. Although Lineage 2 in western Oregon and Washington was most abundant where SNC symptoms were most severe, we did not detect a significant relationship between Lineage 2 and disease severity. Warmer winter temperatures were inversely correlated with foliage retention () and positively correlated with the relative abundance of Lineage 2 (). However when distance inland, which was strongly correlated with both and , was included in the model, there was no significant relationship between Lineage 2 and . Spring/early summer dew point temperatures also were positively associated with total abundance (colonization index ()) and inversely correlated with . Warmer summer mean temperatures were associated with lower and higher . Our results suggest that the two lineages have overlapping environmental optima, but slightly different tolerance ranges. Lineage 2 was absent from more inland sites where winters are colder and summers are warm and dry, while Lineage 1 occurred at most sites across an environmental gradient suggesting broader environmental tolerance. These relationships suggest that climate influences the abundance and distribution of this ecologically important plant pathogen and may have played a role in the evolutionary divergence of these two cryptic fungal lineages.
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http://dx.doi.org/10.1002/ece3.5639DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6802072PMC
October 2019

Importance of probe design for bioanalysis of oligonucleotides using hybridization-based LC-fluorescence assays.

Bioanalysis 2019 Nov 22;11(21):1917-1925. Epub 2019 Oct 22.

Chongqing Denali Medpharma, Chongqing, PR China.

The importance of the length and/or structure of fluorescently labeled PNA (peptide nucleic acid) probes for quantitative determination of oligodeoxynucleotides (ODNs) is demonstrated in human plasma using hybridization-based LC-fluorescence assays. The length of the PNA probes impacts the peak shape and chromatographic separation of the resulting PNA/ODN hybridization complexes and affects assay sensitivity, dynamic range and carryover. For quantitative determination of an 18-mer phosphodiester ODN (DNL1818) in human plasma, an assay utilizing an Atto dye-labeled 12-mer PNA probe provided a linear quantitation range of 0.1-50 ng/ml with excellent accuracy and precision (within -5.3-7.73%). This method provides a convenient method for sensitive and specific quantification of ODNs in biological matrix with limited sample volume and no special extraction.
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http://dx.doi.org/10.4155/bio-2019-0154DOI Listing
November 2019

12th GCC Closed Forum: critical reagents; oligonucleotides; CoA; method transfer; HRMS; flow cytometry; regulatory findings; stability and immunogenicity.

Bioanalysis 2019 Jun 19;11(12):1129-1138. Epub 2019 Jul 19.

WuXi Apptec, Plainsboro, NJ 08536, USA.

The 12th GCC Closed Forum was held in Philadelphia, PA, USA, on 9 April 2018. Representatives from international bioanalytical Contract Research Organizations were in attendance in order to discuss scientific and regulatory issues specific to bioanalysis. The issues discussed at the meeting included: critical reagents; oligonucleotides; certificates of analysis; method transfer; high resolution mass spectrometry; flow cytometry; recent regulatory findings and case studies involving stability and nonclinical immunogenicity. Conclusions and consensus from discussions of these topics are included in this article.
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http://dx.doi.org/10.4155/bio-2019-0131DOI Listing
June 2019

Evaluating spatiotemporal interactions between shapes.

J Vis 2019 04;19(4):30

Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ontario, Canada.

Spatiotemporal interactions between stimuli can alter the perceived curvature along the outline of a shape (Habak, Wilkinson, Zakher, & Wilson, 2004; Habak, Wilkinson, & Wilson, 2006). To better understand these interactions, we used a forward and backward masking paradigm with radial frequency (RF) contours while measuring RF detection thresholds. In Experiment 1, we presented a mask alongside a target contour and altered the stimulus onset asynchrony between this target-mask pair and a temporal mask. We found that a temporal mask increased thresholds when it preceded the target-mask stimulus by 130-180 ms but decreased thresholds when it followed the target-stimulus mask by 180 ms. Furthermore, Experiment 2 demonstrated that the effects of temporal and spatial masks are approximately additive. We discuss these findings in relation to theories of transient and sustained channels in vision.
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http://dx.doi.org/10.1167/19.4.30DOI Listing
April 2019

Recommendations for classification of commercial LBA kits for biomarkers in drug development from the GCC for bioanalysis.

Bioanalysis 2019 Apr 17;11(7):645-653. Epub 2019 Apr 17.

WuXi Apptec, Plainsboro, NJ, USA.

Over the last decade, the use of biomarker data has become integral to drug development. Biomarkers are not only utilized for internal decision-making by sponsors; they are increasingly utilized to make critical decisions for drug safety and efficacy. As the regulatory agencies are routinely making decisions based on biomarker data, there has been significant scrutiny on the validation of biomarker methods. Contract research organizations regularly use commercially available immunoassay kits to validate biomarker methods. However, adaptation of such kits in a regulated environment presents significant challenges and was one of the key topics discussed during the 12th Global Contract Research Organization Council for Bioanalysis (GCC) meeting. This White Paper reports the GCC members' opinion on the challenges facing the industry and the GCC recommendations on the classification of commercial kits that can be a win-win for commercial kit vendors and end users.
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http://dx.doi.org/10.4155/bio-2019-0072DOI Listing
April 2019

Phase-selective masking with radial frequency contours.

Vision Res 2019 01 9;154:1-13. Epub 2018 Nov 9.

Department of Psychology, Neuroscience and Behaviour, McMaster University, Hamilton, Ontario, Canada. Electronic address:

Sensitivity to changes in the shape of a closed-contour figure is affected by surrounding figures (Vision Research 44 (2004) 2815-2823). We examined how between-contour masking depends on radial frequency. Experiment 1 replicated previous studies that found that masking between adjacent radial frequency (RF) patterns was greatest when the two shapes were phase aligned, and that the magnitude of masking declined approximately linearly with increasing phase offsets. In addition, we found that the effect of phase offset on masking was very similar for RFs ranging from 3 to 8, a result that suggests that sensitivity to phase decreases with increasing radial frequency. Experiment 2 tested this idea and found that phase discrimination threshold for single cycles of curvature was approximately proportional to radial frequency. Experiment 3 showed that both curvature maxima and minima contribute to phase dependent masking between RF contours. Together, Experiments 1-3 demonstrate that the strength of phase-dependent masking does not depend on RF, but is related to sensitivity for phase shifts in isolated contours, and is affected by both positive and negative curvature extrema. We discuss these results in relation to properties of curvature sensitive neurons.
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http://dx.doi.org/10.1016/j.visres.2018.10.013DOI Listing
January 2019

Flow cytometry in cell-based pharmacokinetics or cellular kinetics in adoptive cell therapy.

Bioanalysis 2018 09 14;10(18):1457-1459. Epub 2018 Sep 14.

PPD Laboratories, 2244 Dabney Road, Richmond, VA 23230, USA.

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http://dx.doi.org/10.4155/bio-2018-0203DOI Listing
September 2018

Classification images characterize age-related deficits in face discrimination.

Vision Res 2019 04 1;157:97-104. Epub 2018 Aug 1.

Rotman Research Institute, Baycrest Health Sciences, Toronto, Ontario M6A 2E1, Canada; Department of Psychology, University of Toronto, Toronto, Ontario M5S 3G3, Canada; Department of Psychology, Neuroscience, and Behaviour, McMaster University, Hamilton, Ontario L8S 4K1, Canada. Electronic address:

Face perception is impaired in older adults, but the cause of this decline is not well understood. We examined this issue by measuring Classification Images (CIs) in a face discrimination task in younger and older adults. Faces were presented in static, white visual noise, and face contrast was varied with a staircase to maintain an accuracy rate of ≈71%. The noise fields were used to construct a CI using the method described by Nagai et al. (2013) and each observer's CI was cross-correlated with the visual template of a linear ideal discriminator to obtain an estimate of the absolute efficiency of visual processing. Face discrimination thresholds were lower in younger than older adults. Like Sekuler, Gaspar, Gold, and Bennett (2004), we found that CIs from younger adults contained structure near the eyes and brows, suggesting that those observers consistently relied on information conveyed by pixels in those regions of the stimulus. CIs obtained from older adults were noticeably different: CIs from only two older adults exhibited structure near the eye/brow regions, and CIs from the remaining older observers showed no obvious structure. Nevertheless, face discrimination thresholds in both groups were strongly and similarly correlated with the cross-correlation between the CI and the ideal template, suggesting that despite older observers' lack of consistent structure, the CI method is sensitive to between-subject differences in older observers' perceptual strategy.
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http://dx.doi.org/10.1016/j.visres.2018.07.002DOI Listing
April 2019

Singlicate analysis: should this be the default for biomarker measurements using ligand-binding assays?

Bioanalysis 2018 06 20;10(12):909-912. Epub 2018 Jun 20.

Biomarker Services, PPD Laboratories, 2244 Dabney Road, Richmond, VA 23230, USA.

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http://dx.doi.org/10.4155/bio-2018-0067DOI Listing
June 2018

Report on the 18th Annual Land O'Lakes Bioanalytical Conference.

Bioanalysis 2018 Apr 10;10(7):445-449. Epub 2018 Apr 10.

Bristol-Myers Squibb, Princeton, NJ 08540, USA.

The 18th Annual Land O'Lakes Bioanalytical Conference, titled 'Cutting-Edge Bioanalytical Technologies and Concepts - Issues, Solutions and Practical Considerations for Applications in Novel and Emerging Modalities', was held 10-13 July 2017 in Madison, WI, USA. This Land O'Lakes Conference is presented each year by the Division of Pharmacy Professional Development within the School of Pharmacy at the University of Wisconsin-Madison (USA). The purpose of this conference is to provide an educational forum to discuss issues and applications associated with the analysis of xenobiotics, metabolites, biologics and biomarkers in biological matrices. The conference is designed to include and encourage an open exchange of scientific and methodological applications for bioanalysis. This report summarized the presentations at the 18th Annual Conference.
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http://dx.doi.org/10.4155/bio-2018-4000DOI Listing
April 2018

The effect of training with inverted faces on the selective use of horizontal structure.

Vision Res 2019 04 27;157:24-35. Epub 2018 Apr 27.

Department of Psychology, Neuroscience & Behaviour, McMaster University, Hamilton, ON, Canada; Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada; Department of Psychology, University of Toronto, Toronto, ON, Canada. Electronic address:

A growing body of evidence demonstrates that selective processing of structure conveyed by horizontally oriented spatial frequency components is associated with upright face discrimination accuracy and the magnitude of the face inversion effect. In this study, we examined whether the increase in discrimination accuracy for inverted faces that is known to result from practice would coincide with more selective processing of horizontal structure in inverted faces. To assess this hypothesis, our observers practiced discrimination of inverted faces for three training sessions and we measured accuracy, efficiency relative to an ideal observer, and horizontal selectivity before and after training. As hypothesized, we observed more efficient discrimination and more selective processing of horizontal structure after training. However, the effects of training did not generalize reliably to novel face exemplars.
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http://dx.doi.org/10.1016/j.visres.2018.04.003DOI Listing
April 2019

The role of horizontal facial structure on the N170 and N250.

Vision Res 2019 04 23;157:12-23. Epub 2018 Mar 23.

Department of Psychology, Neuroscience & Behaviour, McMaster University, Hamilton, ON, Canada; Rotman Research Institute, Baycrest Health Sciences, Toronto, ON, Canada; Department of Psychology, University of Toronto, Toronto, ON, Canada. Electronic address:

Recent studies have shown that horizontal facial structure is important for face identification (Dakin and Watt, 2009; Goffaux and Dakin, 2010). Also, sensitivity to horizontal structure is associated with the size of the face inversion effect (Pachai et al., 2013). However, it is unclear how the N170 and N250, two components of visual event-related potentials ERPs that have been implicated in face perception, are modulated by oriented facial structure in an upright face identification task. Here, we recorded ERPs and behavioural accuracy from adult observers performing a 1-of-6 face identification task in conditions that parametrically manipulated the orientation structure of upright faces. Faces were filtered with ideal orientation filters centred on either 0 (horizontal) or 90 deg (vertical). Filter bandwidth was varied across conditions from ±45 to ±90 deg in steps of ±9 deg. As has been reported previously, response accuracy was significantly higher for faces that contained horizontal structure than vertical structure, and the horizontal-vertical difference was correlated with accuracy for unfiltered faces. In addition, the N170 and N250 were affected by the manipulation of horizontal facial structure. Furthermore, for the N250, but not the N170, the relative sensitivity to horizontal compared to vertical facial structure was significantly correlated with identification accuracy for unfiltered faces. We suggest that in a face identification task, the N250 but not the N170 is modulated by the amount of diagnostic information conveyed by horizontal structure.
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http://dx.doi.org/10.1016/j.visres.2018.02.006DOI Listing
April 2019

The Bandwidth of Diagnostic Horizontal Structure for Face Identification.

Perception 2018 Apr 19;47(4):397-413. Epub 2018 Jan 19.

Department of Psychology, Neuroscience & Behaviour, McMaster University, Hamilton, ON, Canada.

Horizontally oriented spatial frequency components are a diagnostic source of face identity information, and sensitivity to this information predicts upright identification accuracy and the magnitude of the face-inversion effect. However, the bandwidth at which this information is conveyed, and the extent to which human tuning matches this distribution of information, has yet to be characterized. We designed a 10-alternative forced choice face identification task in which upright or inverted faces were filtered to retain horizontal or vertical structure. We systematically varied the bandwidth of these filters in 10° steps and replaced the orientation components that were removed from the target face with components from the average of all possible faces. This manipulation created patterns that looked like faces but contained diagnostic information in orientation bands unknown to the observer on any given trial. Further, we quantified human performance relative to the actual information content of our face stimuli using an ideal observer with perfect knowledge of the diagnostic band. We found that the most diagnostic information for face identification is conveyed by a narrow band of orientations along the horizontal meridian, whereas human observers use information from a wide range of orientations.
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http://dx.doi.org/10.1177/0301006618754479DOI Listing
April 2018

Parallelism experiments to evaluate matrix effects, selectivity and sensitivity in ligand-binding assay method development: pros and cons.

Bioanalysis 2017 Jul 24;9(14):1107-1122. Epub 2017 Jul 24.

Biomarker Services, PPD Laboratories, 2244 Dabney Road, Richmond, VA 23230, USA.

Parallelism is an essential experiment characterizing relative accuracy for a ligand-binding assay (LBA). By assessing the effects of dilution on the quantitation of endogenous analyte(s) in matrix, selectivity, matrix effects, minimum required dilution, endogenous levels of healthy and diseased populations and the LLOQ are assessed in a single experiment. This review compares and discusses all available approaches that can be used to assess key assay parameters for pharmacokinetic and biomarker LBAs, as well as the advantages and disadvantages of each approach. This review also summarizes a systematic approach that can apply to guide endogenous LBA method development and optimization with a suggested way to interpret parallelism data.
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http://dx.doi.org/10.4155/bio-2017-0084DOI Listing
July 2017

Implicit Valuation of the Near-Miss is Dependent on Outcome Context.

J Gambl Stud 2018 Mar;34(1):181-197

Department of Neuroscience, University of Lethbridge, EP 1219, 4401 University Drive W, Lethbridge, AB, T1K 6T5, Canada.

Gambling studies have described a "near-miss effect" wherein the experience of almost winning increases gambling persistence. The near-miss has been proposed to inflate the value of preceding actions through its perceptual similarity to wins. We demonstrate here, however, that it acts as a conditioned stimulus to positively or negatively influence valuation, dependent on reward expectation and cognitive engagement. When subjects are asked to choose between two simulated slot machines, near-misses increase valuation of machines with a low payout rate, whereas they decrease valuation of high payout machines. This contextual effect impairs decisions and persists regardless of manipulations to outcome feedback or financial incentive provided for good performance. It is consistent with proposals that near-misses cause frustration when wins are expected, and we propose that it increases choice stochasticity and overrides avoidance of low-valued options. Intriguingly, the near-miss effect disappears when subjects are required to explicitly value machines by placing bets, rather than choosing between them. We propose that this task increases cognitive engagement and recruits participation of brain regions involved in cognitive processing, causing inhibition of otherwise dominant systems of decision-making. Our results reveal that only implicit, rather than explicit strategies of decision-making are affected by near-misses, and that the brain can fluidly shift between these strategies according to task demands.
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http://dx.doi.org/10.1007/s10899-017-9705-3DOI Listing
March 2018

Personal familiarity enhances sensitivity to horizontal structure during processing of face identity.

J Vis 2017 06;17(6)

Department of Psychology, Visual and Social Neuroscience, University of Fribourg, Fribourg,

What makes identification of familiar faces seemingly effortless? Recent studies using unfamiliar face stimuli suggest that selective processing of information conveyed by horizontally oriented spatial frequency components supports accurate performance in a variety of tasks involving matching of facial identity. Here, we studied upright and inverted face discrimination using stimuli with which observers were either unfamiliar or personally familiar (i.e., friends and colleagues). Our results reveal increased sensitivity to horizontal spatial frequency structure in personally familiar faces, further implicating the selective processing of this information in the face processing expertise exhibited by human observers throughout their daily lives.
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http://dx.doi.org/10.1167/17.6.5DOI Listing
June 2017

Online Modulation of Selective Attention is not Impaired in Healthy Aging.

Exp Aging Res 2017 May-Jun;43(3):217-232

b Department of Psychology, Neuroscience Behaviour , McMaster University , Hamilton , Ontario , Canada.

Background/Study Context: Reduced processing speed pervades a great many aspects of human aging and cognition. However, little is known about one aspect of cognitive aging in which speed is of the essence, namely, the speed with which older adults can deploy attention in response to a cue.

Methods: The authors compared rapid temporal modulation of cued visual attention in younger (M = 22.3 years) and older (M = 68.9 years) adults. On each trial of a short-term memory task, a cue identified which of two briefly presented stimuli was task relevant and which one should be ignored. After a short delay, subjects demonstrated recall by reproducing from memory the task-relevant stimulus. This produced estimates of (i) accuracy with which the task-relevant stimulus was recalled, (ii) the influence of stimuli encountered on previous trials (a prototype effect), and (iii) the influence of the trial's task-irrelevant stimulus.

Results: For both groups, errors in recall were considerably smaller when selective attention was cued before rather than after presentation of the stimuli. Both groups showed serial position effects to the same degree, and both seemed equally adept at exploiting the stimuli encountered on previous trials as a means of supplementing recall accuracy on the current trial.

Conclusion: Younger and older subjects may not differ reliably in capacity for cue-directed temporal modulation of selective attention, or in ability to draw on previously seen stimuli as memory support.
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http://dx.doi.org/10.1080/0361073X.2017.1298954DOI Listing
November 2017

The 10th GCC Closed Forum: rejected data, GCP in bioanalysis, extract stability, BAV, processed batch acceptance, matrix stability, critical reagents, ELN and data integrity and counteracting fraud.

Bioanalysis 2017 Apr 24;9(7):505-516. Epub 2017 Mar 24.

WuXi Apptec, Plainsboro, NJ, USA.

The 10th Global CRO Council (GCC) Closed Forum was held in Orlando, FL, USA on 18 April 2016. In attendance were decision makers from international CRO member companies offering bioanalytical services. The objective of this meeting was for GCC members to meet and discuss scientific and regulatory issues specific to bioanalysis. The issues discussed at this closed forum included reporting data from failed method validation runs, GCP for clinical sample bioanalysis, extracted sample stability, biomarker assay validation, processed batch acceptance criteria, electronic laboratory notebooks and data integrity, Health Canada's Notice regarding replicates in matrix stability evaluations, critical reagents and regulatory approaches to counteract fraud. In order to obtain the pharma perspectives on some of these topics, the first joint CRO-Pharma Scientific Interchange Meeting was held on 12 November 2016, in Denver, Colorado, USA. The five topics discussed at this Interchange meeting were reporting data from failed method validation runs, GCP for clinical sample bioanalysis, extracted sample stability, processed batch acceptance criteria and electronic laboratory notebooks and data integrity. The conclusions from the discussions of these topics at both meetings are included in this report.
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http://dx.doi.org/10.4155/bio-2017-5000DOI Listing
April 2017

Effects of aging on figure-ground perception: Convexity context effects and competition resolution.

J Vis 2017 02;17(2):15

McMaster University, Hamilton, Ontario,

We examined age-related differences in figure-ground perception by exploring the effect of age on Convexity Context Effects (CCE; Peterson & Salvagio, 2008). Experiment 1, using Peterson and Salvagio's procedure and black and white stimuli consisting of 2 to 8 alternating concave and convex regions, established that older adults exhibited reduced CCEs compared to younger adults. Experiments 2 and 3 demonstrated that this age difference was found at various stimulus durations and sizes. Experiment 4 compared CCEs obtained with achromatic stimuli, in which the alternating convex and concave regions were each all black or all white, and chromatic stimuli in which the concave regions were homogeneous in color but the convex regions varied in color. We found that the difference between CCEs measured with achromatic and colored stimuli was larger in older than in younger adults. Our results are consistent with the hypothesis that the senescent visual system is less able to resolve the competition among various perceptual interpretations of the figure-ground relations among stimulus regions.
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http://dx.doi.org/10.1167/17.2.15DOI Listing
February 2017

Characterizing Population EEG Dynamics throughout Adulthood.

eNeuro 2016 Nov-Dec;3(6). Epub 2016 Dec 12.

Department of Psychology, Neuroscience, and Behaviour, McMaster University , Hamilton, Ontario, L8S 4K1, Canada.

For decades, electroencephalography (EEG) has been a useful tool for investigating the neural mechanisms underlying human psychological processes. However, the amount of time needed to gather EEG data means that most laboratory studies use relatively small sample sizes. Using the Muse, a portable and wireless four-channel EEG headband, we obtained EEG recordings from 6029 subjects 18-88 years in age while they completed a category exemplar task followed by a meditation exercise. Here, we report age-related changes in EEG power at a fine chronological scale for δ, θ, α, and β bands, as well as peak α frequency and α asymmetry measures for both frontal and temporoparietal sites. We found that EEG power changed as a function of age, and that the age-related changes depended on sex and frequency band. We found an overall age-related shift in band power from lower to higher frequencies, especially for females. We also found a gradual, year-by-year slowing of the peak α frequency with increasing age. Finally, our analysis of α asymmetry revealed greater relative right frontal activity. Our results replicate several previous age- and sex-related findings and show how some previously observed changes during childhood extend throughout the lifespan. Unlike previous age-related EEG studies that were limited by sample size and restricted age ranges, our work highlights the advantage of using large, representative samples to address questions about developmental brain changes. We discuss our findings in terms of their relevance to attentional processes and brain-based models of emotional well-being and aging.
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http://dx.doi.org/10.1523/ENEURO.0275-16.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5150228PMC
October 2017

Biomarkers: more of a challenge for bioanalysis than expected.

Authors:
Patrick Bennett

Bioanalysis 2016 Nov 5;8(22):2295-2298. Epub 2016 Oct 5.

Biomarker Laboratories, PPD Inc., Richmond, VA 23230, USA.

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http://dx.doi.org/10.4155/bio-2016-4991DOI Listing
November 2016

9th GCC closed forum: CAPA in regulated bioanalysis; method robustness, biosimilars, preclinical method validation, endogenous biomarkers, whole blood stability, regulatory audit experiences and electronic laboratory notebooks.

Bioanalysis 2016 Mar 26;8(6):487-95. Epub 2016 Feb 26.

WuXi/XBL, 107 Morgan Lane, Plainsboro, NJ, USA.

The 9th GCCClosed Forum was held just prior to the 2015 Workshop on Recent Issues in Bioanalysis (WRIB) in Miami, FL, USA on 13 April 2015. In attendance were 58 senior-level participants, from eight countries, representing 38 CRO companies offering bioanalytical services. The objective of this meeting was for CRO bioanalytical representatives to meet and discuss scientific and regulatory issues specific to bioanalysis. The issues selected at this year's closed forum include CAPA, biosimilars, preclinical method validation, endogenous biomarkers, whole blood stability, and ELNs. A summary of the industry's best practices and the conclusions from the discussion of these topics is included in this meeting report.
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http://dx.doi.org/10.4155/bio.16.16DOI Listing
March 2016

Effects of aging on identifying emotions conveyed by point-light walkers.

Psychol Aging 2016 Feb 14;31(1):126-38. Epub 2016 Jan 14.

School of Psychology, University of Aberdeen.

The visual system is able to recognize human motion simply from point lights attached to the major joints of an actor. Moreover, it has been shown that younger adults are able to recognize emotions from such dynamic point-light displays. Previous research has suggested that the ability to perceive emotional stimuli changes with age. For example, it has been shown that older adults are impaired in recognizing emotional expressions from static faces. In addition, it has been shown that older adults have difficulties perceiving visual motion, which might be helpful to recognize emotions from point-light displays. In the current study, 4 experiments were completed in which older and younger adults were asked to identify 3 emotions (happy, sad, and angry) displayed by 4 types of point-light walkers: upright and inverted normal walkers, which contained both local motion and global form information; upright scrambled walkers, which contained only local motion information; and upright random-position walkers, which contained only global form information. Overall, emotion discrimination accuracy was lower in older participants compared with younger participants, specifically when identifying sad and angry point-light walkers. In addition, observers in both age groups were able to recognize emotions from all types of point-light walkers, suggesting that both older and younger adults are able to recognize emotions from point-light walkers on the basis of local motion or global form.
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http://dx.doi.org/10.1037/a0040009DOI Listing
February 2016

A robust and representative lower bound on object processing speed in humans.

Eur J Neurosci 2016 07 14;44(2):1804-14. Epub 2015 Nov 14.

Institute of Neuroscience and Psychology, College of Medical, Veterinary and Life Sciences, University of Glasgow, 58 Hillhead Street, Glasgow, G12 8QB, UK.

How early does the brain decode object categories? Addressing this question is critical to constrain the type of neuronal architecture supporting object categorization. In this context, much effort has been devoted to estimating face processing speed. With onsets estimated from 50 to 150 ms, the timing of the first face-sensitive responses in humans remains controversial. This controversy is due partially to the susceptibility of dynamic brain measurements to filtering distortions and analysis issues. Here, using distributions of single-trial event-related potentials (ERPs), causal filtering, statistical analyses at all electrodes and time points, and effective correction for multiple comparisons, we present evidence that the earliest categorical differences start around 90 ms following stimulus presentation. These results were obtained from a representative group of 120 participants, aged 18-81, who categorized images of faces and noise textures. The results were reliable across testing days, as determined by test-retest assessment in 74 of the participants. Furthermore, a control experiment showed similar ERP onsets for contrasts involving images of houses or white noise. Face onsets did not change with age, suggesting that face sensitivity occurs within 100 ms across the adult lifespan. Finally, the simplicity of the face-texture contrast, and the dominant midline distribution of the effects, suggest the face responses were evoked by relatively simple image properties and are not face specific. Our results provide a new lower benchmark for the earliest neuronal responses to complex objects in the human visual system.
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http://dx.doi.org/10.1111/ejn.13100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4982026PMC
July 2016