Visual Perception: Larger Is Faster

A recent study has shown that neurons in the inferior temporal cortex of the macaque monkey brain show earlier selectivity to global and large shapes than to local and small ones, which may underlie the faster behavioral responses to global aspects of a scene.     

Finding and Mapping New Genes Faster than Ever: Revisited

This article recounts some of the early days of the Human Genome Project, covering the important and sometimes controversial role that complementary DNA-based approaches played in the discovery and mapping of the majority of human genes. It also describes my involvement in this effort and my lab''s development of methods for rapid sequence identification and mapping of human genes.     

Bird communication: two voices are better than one

How do emperor penguins find their mates on a featureless ice flow, packed at densities of ten animals per square meter? A recent study has revealed how use of their 'two-voice' calls enables emperor penguins to locate their mates and chicks under some of nature's most extreme conditions.     

Visual perception: more than meets the eye

A recent study shows that objects changing in colour, luminance, size or shape appear to stop changing when they move. These and other compelling illusions provide tantalizing clues about the mechanisms and limitations of object analysis.     

The Impact of Accelerating Faster than Exponential Population Growth on Genetic Variation

Current human sequencing projects observe an abundance of extremely rare genetic variation, suggesting recent acceleration of population growth. To better understand the impact of such accelerating growth on the quantity and nature of genetic variation, we present a new class of models capable of incorporating faster than exponential growth in a coalescent framework. Our work shows that such accelerated growth affects only the population size in the recent past and thus large samples are required to detect the models’ effects on patterns of variation. When we compare models with fixed initial growth rate, models with accelerating growth achieve very large current population sizes and large samples from these populations contain more variation than samples from populations with constant growth. This increase is driven almost entirely by an increase in singleton variation. Moreover, linkage disequilibrium decays faster in populations with accelerating growth. When we instead condition on current population size, models with accelerating growth result in less overall variation and slower linkage disequilibrium decay compared to models with exponential growth. We also find that pairwise linkage disequilibrium of very rare variants contains information about growth rates in the recent past. Finally, we demonstrate that models of accelerating growth may substantially change estimates of present-day effective population sizes and growth times.     

Messages Do Diffuse Faster than Messengers: Reconciling Disparate Estimates of the Morphogen Bicoid Diffusion Coefficient

The gradient of Bicoid (Bcd) is key for the establishment of the anterior-posterior axis in Drosophila embryos. The gradient properties are compatible with the SDD model in which Bcd is synthesized at the anterior pole and then diffuses into the embryo and is degraded with a characteristic time. Within this model, the Bcd diffusion coefficient is critical to set the timescale of gradient formation. This coefficient has been measured using two optical techniques, Fluorescence Recovery After Photobleaching (FRAP) and Fluorescence Correlation Spectroscopy (FCS), obtaining estimates in which the FCS value is an order of magnitude larger than the FRAP one. This discrepancy raises the following questions: which estimate is "correct''''; what is the reason for the disparity; and can the SDD model explain Bcd gradient formation within the experimentally observed times? In this paper, we use a simple biophysical model in which Bcd diffuses and interacts with binding sites to show that both the FRAP and the FCS estimates may be correct and compatible with the observed timescale of gradient formation. The discrepancy arises from the fact that FCS and FRAP report on different effective (concentration dependent) diffusion coefficients, one of which describes the spreading rate of the individual Bcd molecules (the messengers) and the other one that of their concentration (the message). The latter is the one that is more relevant for the gradient establishment and is compatible with its formation within the experimentally observed times.     

Faster onset of action with topical levocabastine than with oral cetirizine

This international multicentre, open-label, parallel-group trial was undertaken to compare the therapeutic efficacy and tolerability of topical levocabastine and oral cetirizine in patients with perennial allergic rhinoconjunctivitis, with particular reference to the comparative onset of action of the two drugs. A total of 207 patients were randomized to receive either levocabastine nasal spray (0.5 mg/ml, two sprays in each nostril twice daily) plus levocabastine eye drops as required (0.5 mg/ml, one drop in each eye twice daily p.r.n.) or cetirizine orally (10 mg once daily) with a treatment duration of 2 weeks. Onset of action was found to be significantly more rapid with levocabastine than with cetirizine for both nasal and ocular symptoms (p < 0.001). Within 15 min of study drug administration, 36% of levocabastine-treated patients reported relief from nasal symptoms and 32% relief from ocular symptoms compared with 10% and 17% of patients on cetirizine, respectively. At 1 h, the percentages of patients reporting relief were 76% and 38% for nasal symptoms, and 81% and 48% for ocular symptoms in the levocabastine and cetirizine treatment groups, respectively. At 8 h there were no differences between the two treatments. Overall therapeutic efficacy was found to be comparable in the two treatment groups over the 2-week study period with no significant intergroup differences in symptom severity or global therapeutic efficacy. Both drugs were well tolerated with no significant differences in the incidence or type of adverse reactions between the two groups. In conclusion, levocabastine eye drops and nasal spray are as effective and well tolerated as oral cetirizine for the treatment of perennial allergic rhinoconjunctivitis with the advantage of a significantly faster onset of action for both nasal and ocular symptoms.     

Transgenic Animal Technology: Everything You Always Wanted to Know about Transgenics

Transgenic Research -     

The Effect of Shortening on the Time-Course of Active State Decay

The active state describes the force developed in a muscle when the contractile elements are neither lengthening nor shortening. Recently it was suggested that perturbations used to measure the active state also alter the time-course of the active state. The present research was undertaken to assess quantitatively the effect of two such perturbations, isotonic shortening and quick release, on the active state in frog sartorius muscle. Methods were developed which allowed the determination of active state points following periods of controlled isotonic shortening or quick release early in the contraction cycle. All experiments were carried out within the plateau region of the length-tension curve. Both isotonic shortening and quick release altered the active state decay. The active state force decreased as the extent of shortening or release was increased. For each 0.1 mm of isotonic shortening there was a 2% decrease in active state force. Quick release produced a larger decrement. From this data we conclude that the time-course of active state can be measured only in relative terms because it is altered by the motion which takes place in the contractile machine while the active state is being measured. This finding helps to resolve paradoxes in the literature relating to the time-course of the active state, calculated and experimentally determined isometric tetanic myograms, and the heat of shortening.     

Perspectives: The Looking Time Experimental Paradigm in Studies of Animal Visual Perception and Cognition

Experiments are the foundation of empirical science, and experimental paradigms that are broadly applicable across settings and species are particularly useful for comparative research. Originally developed to address questions related to perception and cognition of pre‐verbal human infants, the looking time experimental paradigm has been increasingly used to study animal behavior and cognition, particularly in non‐human primates. Looking time experiments are based on the assumption that animals direct eye gaze toward objects or scenes based on their degree of interest, and use looking behavior to infer perceptual or cognitive characteristics of subjects. This paradigm can be used in a variety of contexts and is not based on species‐typical behaviors, allowing for intra‐ and interspecific comparisons. Here, we describe the history of use of looking time measures, provide an overview of the problems and controversies related to this method, and offer recommendations on how to implement looking time tasks, focusing on the preparation of stimuli, experimental procedures, and data analysis. Our overview focuses on non‐human primates, where most work has been carried out, but the issues discussed should be applicable to a wide range of species. We conclude that despite pertinent criticism, looking time tasks are practical when executed and interpreted properly. The further implementation of these methods in studies of animal behavior and cognition is likely to be fruitful.     

Faster heme loss from hemoglobin E than HbS,in acidic pH: Effect of aminophospholipids

We report studies on loss of heme at or below pH 3.0 from two clinically important hemoglobin variants, HbE and HbS, in the presence and absence of phopholipid membranes. The kinetics of heme loss has been studied at pH 3.0 to simulate the same at a faster rate than at physiological pH, for spectroscopic investigation. Results obtained from the study clearly establish the probable fate of the lost heme to partition into the phospholipid bilayer independent of the pH range. This is also of particular importance to membranes containing the aminophospholipid and cholesterol which are predominantly localized in the inner leaflet of erythrocytes. Absorption measurements indicated such loss of heme when the Soret peak at 415 nm blue-shifted to 380 nm at pH 3.0. The extent of this blue shift decreased from 35 nm to ~15 nm in the presence of small unilammelar vesicles of both dimyristoyl- and dioleoyl-based phosphatidylcholine and phosphatidylethanolamine, indicating partitioning of the released heme in the membrane bilayer. The kinetics of heme loss was faster from HbE than HbA and HbS, obeying first-order reaction kinetics. Released heme could be involved in the premature destruction of erythrocytes in hemoglobin disorders.     

Own-Race Faces Capture Attention Faster than Other-Race Faces: Evidence from Response Time and the N2pc

Studies have shown that people are better at recognizing human faces from their own-race than from other-races, an effect often termed the Own-Race Advantage. The current study investigates whether there is an Own-Race Advantage in attention and its neural correlates. Participants were asked to search for a human face among animal faces. Experiment 1 showed a classic Own-Race Advantage in response time both for Chinese and Black South African participants. Using event-related potentials (ERPs), Experiment 2 showed a similar Own-Race Advantage in response time for both upright faces and inverted faces. Moreover, the latency of N2pc for own-race faces was earlier than that for other-race faces. These results suggested that own-race faces capture attention more efficiently than other-race faces.     

The Time-Course of Hatching Enzyme Secretion in the Sea Urchin Strongylocentrotus purpuratus

By two independent methods, we have determined approximately the time-course of hatching enzyme secretion in the sea urchin Strongylocentrotus purpuratus . A quick-kill method indicates that a significant fraction of the enzyme is secreted between 90% and 97% of the fertilization-hatching interval. A direct assay method indicates that the remainder of the enzyme is secreted on either side of the 90–97%"window". The entire period of secretion spans from 75% to 100% or more of the fertilization-hatching interval. For embryos raised at 15°C this translates to an interval of 4.8 or more hr.     

Faster intrinsic rate of torque development in elbow flexors than knee extensors: Effect of muscle architecture?

We studied the effect of pennate vs. fusiform muscle architecture on the rate of torque development (RTD) by examining the predominately fusiform elbow flexors (EF) and highly-pennate knee extensors (KE). Seventeen male volunteers (28.4 ± 6.2 years) performed explosive isometric EF and KE contractions (MVCs). Biceps brachii and vastus lateralis fascicle angles were measured to confirm their architecture, and both the rate of voluntary muscle activation (root-mean-square EMG in the 50 ms before contraction onset; EMG_-50) and electromechanical delay (EMD; depicting muscle-tendon series elasticity) were assessed as control variables to account for their influence on RTD. MVC torque, early (RTD₅₀) and late (RTD₂₀₀) RTDs were calculated and expressed as absolute and normalized values. Absolute MVC torque (+412%), RTD₅₀ (+215%), and RTD₂₀₀ (+427%) were significantly (p < 0.001) higher in KE than EF. However, EF RTD₅₀ was faster (+178%) than KE after normalization (p = 0.02). EMG_-50 and EMD did not differ between muscle groups. The results suggest that the faster absolute RTD in KE is largely associated with its higher maximal torque capacity, however in the absence of differences in rates of muscle activation, fiber type, and EMD the fusiform architecture of EF may be considered a factor allowing its faster early RTD relative to strength capacity.     

The Multiplicity of the Mitotic Centers and the Time-Course of Their Duplication and Separation

In this study, the reproduction of the mitotic centers in the eggs of a sea urchin, Strongylocentrotus purpuratus and a sand dollar Dendraster excentricus has been studied by means of experimental designs that do not depend on the actual visualization of centrioles. The centers are defined in operational terms as potential poles. Blockage of mitosis by mercaptoethanol, it was found, inhibits the duplication of the centers, but does not inhibit the splitting and separation of centers that have already duplicated and thus potential poles could be realized as actual poles in multipolar divisions. At all times, the center is at least a duplex structure; that is, it contains two potential poles. The actual duplication process is the earliest event in a given mitotic cycle, taking place at very early interphase or in late telophase of the previous division. The splitting of the centers following duplication is a distinct process, dissociable from the duplication as such. Duplication and splitting normally occur at about the same time in the mitotic cycle, with a precession of the former. That is, as the two members of a pair of "old" centers split, each one gives rise to a new one, which remains associated with it until the next phase of splitting and duplication occurs. The results are consistent with what is termed a "generative" model of the self-reproduction of an intracellular body. According to this, the body does not immediately produce a full-fledged copy of itself, with simultaneous fission, but the primary duplication event involves only a part of the parent structure. This gives rise to a "germ" or "seed" which then grows to be equivalent to the parent body, and finally splits from it.     

Faster mass spectrometry-based protein inference: junction trees are more efficient than sampling and marginalization by enumeration

The problem of identifying the proteins in a complex mixture using tandem mass spectrometry can be framed as an inference problem on a graph that connects peptides to proteins. Several existing protein identification methods make use of statistical inference methods for graphical models, including expectation maximization, Markov chain Monte Carlo, and full marginalization coupled with approximation heuristics. We show that, for this problem, the majority of the cost of inference usually comes from a few highly connected subgraphs. Furthermore, we evaluate three different statistical inference methods using a common graphical model, and we demonstrate that junction tree inference substantially improves rates of convergence compared to existing methods. The python code used for this paper is available at http://noble.gs.washington.edu/proj/fido.