Search

Milagrito, a detector sensitive to gamma-rays at TeV energies, monitored thenorthern sky during the period February 1997 through May 1998. With a largefield of view and high duty cycle, this instrument was used to perform a searchfor TeV counterparts to gamma-ray bursts. Within the Milagrito field of view 54gamma-ray bursts at keV energies were observed by the Burst And TransientSatellite Experiment (BATSE) aboard the Compton Gamma-Ray Observatory. Thispaper describes the results of a preliminary analysis to search for TeVemission correlated with BATSE detected bursts. Milagrito detected an excess ofevents coincident both spatially and temporally with GRB 970417a, with chanceprobability $2.8 \times 10^{-5}$ within the BATSE error radius. No othersignificant correlations were detected. Since 54 bursts were examined thechance probability of observing an excess with this significance in any ofthese bursts is $1.5 \times 10^{-3}$. The statistical aspects and physicalimplications of this result are discussed.

Milagrito, a detector sensitive to gamma-rays at TeV energies, monitored thenorthern sky during the period February 1997 through May 1998. With a largefield of view and high duty cycle, this instrument was used to perform a searchfor TeV counterparts to gamma-ray bursts. Within the Milagrito field of view 54gamma-ray bursts at keV energies were observed by the Burst And TransientSatellite Experiment (BATSE) aboard the Compton Gamma-Ray Observatory. Thispaper describes the results of a preliminary analysis to search for TeVemission correlated with BATSE detected bursts. Milagrito detected an excess ofevents coincident both spatially and temporally with GRB 970417a, with chanceprobability $2.8 \times 10^{-5}$ within the BATSE error radius. No othersignificant correlations were detected. Since 54 bursts were examined thechance probability of observing an excess with this significance in any ofthese bursts is $1.5 \times 10^{-3}$. The statistical aspects and physicalimplications of this result are discussed.

Previous works have shown that water Cherenkov detectors have superiorsensitivity to those of scintillation counters as applied to detectingextensive air showers (EAS). This is in large part due to their much highersensitivity to EAS photons which are more than five times more numerous thanEAS electrons. Large area water Cherenkov detectors can be constructedrelatively cheaply and operated reliably. A sparse detector array has beendesigned which uses these types of detectors to substantially increase the areaover which the Milagro Gamma Ray Observatory collects EAS information.Improvements to the Milagro detector's performance characteristics andsensitivity derived from this array and preliminary results from a prototypearray currently installed near the Milagro detector will be presented.

The Milagro detector is an air shower array which uses the water Cherenkovtechnique and is capable of continuously monitoring the sky at energies near 1TeV. The detector consists of 20000 metric tons of pure water instrumented with723 photo-multiplier tubes (PMTs). The PMTs are arranged in a two-layerstructure on a lattice of 3 m spacing covering 5000 $m^2$ area. The directionof the shower is determined from the relative timing of the PMT signals,necessitating a common time reference and amplitude slewing corrections toimprove the time resolution. The calibration system to provide these consistsof a pulsed laser driving 30 diffusing light sources deployed in the pond toallow cross-calibration of the PMTs. The system is capable of calibrating timesand the pulse-heights from the PMTs using the time-over-threshold technique.The absolute energy scale is provided using single muons passing through thedetector. The description of the calibration system of the Milagro detector andits prototype Milagrito will be presented.

The Milagro Gamma Ray Observatory is the world's first large-area waterCherenkov detector capable of continuously monitoring the sky at TeV energies.Located in northern New Mexico, Milagro will perform an all sky survey of theNorthern Hemisphere at energies between ~250 GeV and 50 TeV. With a high dutycycle, large detector area (~5000 square meters), and a wide field-of-view (~1sr), Milagro is uniquely capable of searching for transient and DC sources ofhigh-energy gamma-ray emission. Milagro has been operating since February,1999. The current status of the Milagro Observatory and initial results will bediscussed.

Milagrito, a prototype for the Milagro detector, operated for 15 months in1997-8 and collected 8.9 billion events. It was the first extensive air shower(EAS) array sensitive to showers intiated by primaries with energy below 1 TeV.The shadows of the sun and moon observed with cosmic rays can be used to studysystematic pointing shifts and measure the angular resolution of EAS arrays.Below a few TeV, the paths of cosmic rays coming toward the earth are bent bythe helio- and geo-magnetic fields. This is expected to distort and displacethe shadows of the sun and the moon. The moon shadow, offset from the nominal(undeflected) position, has been observed with high statistical significance inMilagrito. This can be used to establish energy calibrations, as well as tosearch for the anti-matter content of the VHE cosmic ray flux. The shadow ofthe sun has also been observed with high significance.

The Milagrito water Cherenkov telescope operated for over a year. The mostprobable gamma-ray energy was ~1 TeV and the trigger rate was as high as 400Hz. We have developed an efficient technique for searching the entire sky forshort duration bursts of TeV photons. Such bursts may result from "traditional"gamma-ray bursts that were not in the field-of-view of any other instruments,the evaporation of primordial black holes, or some as yet undiscoveredphenomenon. We have begun to search the Milagrito data set for bursts ofduration 10 seconds. Here we will present the technique and the expectedresults. Final results will be presented at the conference.

Solar Energetic Particles from the 6 November 1997 solar flare/CME(coronalmass ejection) with energies exceeding 10 GeV have been detected by Milagrito,a prototype of the Milagro Gamma Ray Observatory. While particle accelerationbeyond 1 GeV at the Sun is well established, few data exist for protons or ionsbeyond 10 GeV. The Milagro observatory, a ground based water Cherenkov detectordesigned for observing very high energy gamma ray sources, can also be used tostudy the Sun. Milagrito, which operated for approximately one year in 1997/98,was sensitive to solar proton and neutron fluxes above ~5- 10 GeV. Milagritooperated in a scaler mode, which was primarily sensitive to muons, low energyphotons, and electrons, and the detector operated in a mode sensitive toshowers and high zenith angle muons. In its scaler mode, Milagrito registered arate increase coincident with the 6 November 1997 ground level event observedby Climax and other neutron monitors. A preliminary analysis suggests thepresence of >10 GeV particles.

The Milagro water Cherenkov detector near Los Alamos, New Mexico, has beenoperated as a sky monitor at energies of a few TeV between February 1997 andApril 1998. Serving as a test run for the full Milagro detector, Milagrito hastaken data during the strong and long-lasting 1997 flare of Mrk 501. We presentresults from the analysis of Mrk 501 and compare the excess and backgroundrates with expectations from the detector simulations.

Observing gamma ray bursts (GRBs) in the TeV energy range can be extremelyvaluable in providing insight to GRB radiation mechanisms and in constrainingsource distances. The Milagrito detector was an air shower array which used thewater Cherenkov technique to search for TeV sources. Data from this detectorwas analyzed to look for a TeV component of GRBs coincident with low energy-rays detected by the BATSE instrument on the Compton Gamma Ray Observatory. Asample of 54 BATSE GRBs which were in the field of view of the Milagritodetector during its lifetime (February 1997 to May 1998) was used.

The Milagrito water Cherenkov detector in the Jemez Mountains near LosAlamos, New Mexico took data from February 1997 to April 1998. Milagrito servedas a prototype for the larger Milagro detector, which has just begunoperations. Milagrito was the first large-aperture gamma-ray detector withsensitivity to gamma rays below 1 TeV. We report here on a search for steadyemission from point sources over most of the northern sky using data fromMilagrito.

Abstract We have studied the recombination rate behaviour of a set of 140 genes which were investigated for their potential importance in inflammatory disease. Each gene was extensively sequenced in 24 individuals of African descent and 23 individuals of European descent, and the recombination process was studied separately in the two population samples. The results obtained from the two populations were highly correlated, suggesting that demographic bias does not affect our population genetic estimation procedure. We found evidence that levels of recombination correlate with levels of nucleotide diversity. High marker density allowed us to study recombination rate variation on a very fine spatial scale. We found that about 40 per cent of genes showed evidence of uniform recombination, while approximately 12 per cent of genes carried distinct signatures of recombination hotspots. On studying the locations of these hotspots, we found that they are not always confined to introns but can also stretch across exons. An investigation of the protein products of these genes suggested that recombination hotspots can sometimes separate exons belonging to different protein domains; however, this occurs much less frequently than might be expected based on evolutionary studies into the origins of recombination. This suggests that evolutionary analysis of the recombination process is greatly aided by considering nucleotide sequences and protein products jointly.

Birds use their visual systems for important tasks, such as foraging and predator detection, that require them to resolve an image. However, visual acuity (the ability to perceive spatial detail) varies by two orders of magnitude across birds. Prior studies indicate that eye size and aspects of a species' ecology may drive variation in acuity, but these studies have been restricted to small numbers of species. We used a literature review to gather data on acuity measured either behaviorally or anatomically for 94 species from 38 families. We then examined how acuity varies in relation to (1) eye size, (2) habitat spatial complexity, (3) habitat light level, (4) diet composition, (5) prey mobility and (6) foraging mode. A phylogenetically controlled model including all of the above factors as predictors indicated that eye size and foraging mode are significant predictors of acuity. Examining each ecological variable in turn revealed that acuity is higher in species whose diet comprises vertebrates or scavenged food and whose foraging modes require resolving prey from farther away. Additionally, species that live in spatially complex, vegetative habitats have lower acuity than expected for their eye sizes. Together, our results suggest that the need to detect important objects from far away - such as predators for species that live in open habitats, and food items for species that forage on vertebrate and scavenged prey - has likely been a key driver of higher acuity in some species, helping us to elucidate how visual capabilities may be adapted to an animal's visual needs., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2024. Published by The Company of Biologists Ltd.)

Bullough et al. introduce Weber's Law and proportional processing during perception., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Many animals use shading to infer the three-dimensional (3D) shape of objects, and mimicking natural shading patterns can produce the illusion of 3D form on a flat surface. Over 150 years ago, Charles Darwin noted that the ocelli (eyespots) on the feathers of the great argus Argusianus argus , when held vertically during courtship displays to females, were perfectly shaded to resemble 3D hemispheres to human viewers. We tested whether these ocelli appear 3D to birds by training chickens Gallus gallus domesticus to select images of either convex or concave shapes using shading cues, and then presenting them with images of great argus ocelli. Chickens successfully learned how to discriminate between convex and concave shapes, and treated the great argus pheasant ocelli in the same way as convex training stimuli. Our findings are consistent with previous studies that birds can perceive 3D shape from shading cues in a similar manner to humans. The perception of great argus ocelli as consistent with 3D shape by avian viewers suggests that shape illusions can play a role in male courtship.

Camouflage is a fundamental way for animals to avoid detection and recognition. While depth information is critical for object detection and recognition, little is known about how camouflage patterns might interfere with the mechanisms of depth perception. We reveal how many common camouflage strategies could exploit 3D visual processing mechanisms., Competing Interests: Declaration of interests The authors have no interests to declare., (Crown Copyright © 2022. Published by Elsevier Ltd. All rights reserved.)

Wild animals encounter humans on a regular basis, but humans vary widely in their behaviour: whereas many people ignore wild animals, some people present a threat, while others encourage animals' presence through feeding. Humans thus send mixed messages to which animals must respond appropriately to be successful. Some species appear to circumvent this problem by discriminating among and/or socially learning about humans, but it is not clear whether such learning strategies are actually beneficial in most cases. Using an individual-based model, we consider how learning rate, individual recognition (IR) of humans, and social learning (SL) affect wild animals' ability to reach an optimal avoidance strategy when foraging in areas frequented by humans. We show that 'true' IR of humans could be costly. We also find that a fast learning rate, while useful when human populations are homogeneous or highly dangerous, can cause unwarranted avoidance in other scenarios if animals generalize. SL reduces this problem by allowing conspecifics to observe benign interactions with humans. SL and a fast learning rate also improve the viability of IR. These results provide an insight into how wild animals may be affected by, and how they may cope with, contrasting human behaviour., Competing Interests: The authors have no competing interests., (© 2022 The Authors.)

Among fishes in the family Poeciliidae, signals such as colour patterns, ornaments and courtship displays play important roles in mate choice and male-male competition. Despite this, visual capabilities in poeciliids are understudied, in particular, visual acuity, the ability to resolve detail. We used three methods to quantify visual acuity in male and female green swordtails (Xiphophorus helleri), a species in which body size and the length of the male's extended caudal fin ('sword') serve as assessment signals during mate choice and agonistic encounters. Topographic distribution of retinal ganglion cells (RGCs) was similar in all individuals and was characterized by areas of high cell densities located centro-temporally and nasally, as well as a weak horizontal streak. Based on the peak density of RGCs in the centro-temporal area, anatomical acuity was estimated to be approximately 3 cycles per degree (cpd) in both sexes. However, a behavioural optomotor assay found significantly lower mean acuity in males (0.8 cpd) than females (3.0 cpd), which was not explained by differences in eye size between males and females. An additional behavioural assay, in which we trained individuals to discriminate striped gratings from grey stimuli of the same mean luminance, also showed lower acuity in males (1-2 cpd) than females (2-3 cpd). Thus, although retinal anatomy predicts identical acuity in males and females, two behavioural assays found higher acuity in females than males, a sexual dimorphism that is rare outside of invertebrates. Overall, our results have implications for understanding how poeciliids perceive visual signals during mate choice and agonistic encounters., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2021. Published by The Company of Biologists Ltd.)

The motion dazzle hypothesis posits that high contrast geometric patterns can cause difficulties in tracking a moving target and has been argued to explain the patterning of animals such as zebras. Research to date has only tested a small number of patterns, offering equivocal support for the hypothesis. Here, we take a genetic programming approach to allow patterns to evolve based on their fitness (time taken to capture) and thus find the optimal strategy for providing protection when moving. Our 'Dazzle Bug' citizen science game tested over 1.5 million targets in a touch screen game at a popular visitor attraction. Surprisingly, we found that targets lost pattern elements during evolution and became closely background matching. Modelling results suggested that targets with lower motion energy were harder to catch. Our results indicate that low contrast, featureless targets offer the greatest protection against capture when in motion, challenging the motion dazzle hypothesis.

Humans have a profound effect on the planet's ecosystems, and unprecedented rates of human population growth and urbanization have brought wild animals into increasing contact with people. For many species, appropriate responses toward humans are likely to be critical to survival and reproductive success. Although numerous studies have investigated the impacts of human activity on biodiversity and species distributions, relatively few have examined the effects of humans on the behavioral responses of animals during human-wildlife encounters, and the cognitive processes underpinning those responses. Furthermore, while humans often present a significant threat to animals, the presence or behavior of people may be also associated with benefits, such as food rewards. In scenarios where humans vary in their behavior, wild animals would be expected to benefit from the ability to discriminate between dangerous, neutral and rewarding people. Additionally, individual differences in cognitive and behavioral phenotypes and past experiences with humans may affect animals' ability to exploit human-dominated environments and respond appropriately to human cues. In this review, we examine the cues that wild animals use to modulate their behavioral responses toward humans, such as human facial features and gaze direction. We discuss when wild animals are expected to attend to certain cues, how information is used, and the cognitive mechanisms involved. We consider how the cognitive abilities of wild animals are likely to be under selection by humans and therefore influence population and community composition. We conclude by highlighting the need for long-term studies on free-living, wild animals to fully understand the causes and ecological consequences of variation in responses to human cues. The effects of humans on wildlife behavior are likely to be substantial, and a detailed understanding of these effects is key to implementing effective conservation strategies and managing human-wildlife conflict., (Copyright © 2020 Goumas, Lee, Boogert, Kelley and Thornton.)

Substantial progress has been made in the past 15 years regarding how prey use a variety of visual camouflage types to exploit both predator visual processing and cognition, including background matching, disruptive coloration, countershading and masquerade. By contrast, much less attention has been paid to how predators might overcome these defences. Such strategies include the evolution of more acute senses, the co-opting of other senses not targeted by camouflage, changes in cognition such as forming search images, and using behaviours that change the relationship between the cryptic individual and the environment or disturb prey and cause movement. Here, we evaluate the methods through which visual camouflage prevents detection and recognition, and discuss if and how predators might evolve, develop or learn counter-adaptations to overcome these. This article is part of the theme issue 'Signal detection theory in recognition systems: from evolving models to experimental tests'.

While many animals are negatively affected by urbanization, some species appear to thrive in urban environments. Herring gulls ( Larus argentatus ) are commonly found in urban areas and often scavenge food discarded by humans. Despite increasing interactions between humans and gulls, little is known about the cognitive underpinnings of urban gull behaviour and to what extent they use human behavioural cues when making foraging decisions. We investigated whether gulls are more attracted to anthropogenic items when they have been handled by a human. We first presented free-living gulls with two identical food objects, one of which was handled, and found that gulls preferentially pecked at the handled food object. We then tested whether gulls' attraction to human-handled objects generalizes to non-food items by presenting a new sample of gulls with two non-food objects, where, again, only one was handled. While similar numbers of gulls approached food and non-food objects in both experiments, they did not peck at handled non-food objects above chance levels. These results suggest that urban gulls generally show low levels of neophobia, but that they use human handling as a cue specifically in the context of food. These behaviours may contribute to gulls' successful exploitation of urban environments., Competing Interests: We declare that we have no competing interests., (© 2020 The Authors.)

Genome3D (https://www.genome3d.eu) is a freely available resource that provides consensus structural annotations for representative protein sequences taken from a selection of model organisms. Since the last NAR update in 2015, the method of data submission has been overhauled, with annotations now being 'pushed' to the database via an API. As a result, contributing groups are now able to manage their own structural annotations, making the resource more flexible and maintainable. The new submission protocol brings a number of additional benefits including: providing instant validation of data and avoiding the requirement to synchronise releases between resources. It also makes it possible to implement the submission of these structural annotations as an automated part of existing internal workflows. In turn, these improvements facilitate Genome3D being opened up to new prediction algorithms and groups. For the latest release of Genome3D (v2.1), the underlying dataset of sequences used as prediction targets has been updated using the latest reference proteomes available in UniProtKB. A number of new reference proteomes have also been added of particular interest to the wider scientific community: cow, pig, wheat and mycobacterium tuberculosis. These additions, along with improvements to the underlying predictions from contributing resources, has ensured that the number of annotations in Genome3D has nearly doubled since the last NAR update article. The new API has also been used to facilitate the dissemination of Genome3D data into InterPro, thereby widening the visibility of both the annotation data and annotation algorithms., (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Instructor Talk-noncontent language used by instructors in classrooms-is a recently defined and promising variable for better understanding classroom dynamics. Having previously characterized the Instructor Talk framework within the context of a single course, we present here our results surrounding the applicability of the Instructor Talk framework to noncontent language used by instructors in novel course contexts. We analyzed Instructor Talk in eight additional biology courses in their entirety and in 61 biology courses using an emergent sampling strategy. We observed widespread use of Instructor Talk with variation in the amount and category type used. The vast majority of Instructor Talk could be characterized using the originally published Instructor Talk framework, suggesting the robustness of this framework. Additionally, a new form of Instructor Talk-Negatively Phrased Instructor Talk, language that may discourage students or distract from the learning process-was detected in these novel course contexts. Finally, the emergent sampling strategy described here may allow investigation of Instructor Talk in even larger numbers of courses across institutions and disciplines. Given its widespread use, potential influence on students in learning environments, and ability to be sampled, Instructor Talk may be a key variable to consider in future research on teaching and learning in higher education.

Human-wildlife conflict is one of the greatest threats to species populations worldwide. One species facing national declines in the UK is the herring gull (Larus argentatus), despite an increase in numbers in urban areas. Gulls in urban areas are often considered a nuisance owing to behaviours such as food-snatching. Whether urban gull feeding behaviour is influenced by human behavioural cues, such as gaze direction, remains unknown. We therefore measured the approach times of herring gulls to a food source placed in close proximity to an experimenter who either looked directly at the gull or looked away. We found that only 26% of targeted gulls would touch the food, suggesting that food-snatching is likely to be conducted by a minority of individuals. When gulls did touch the food, they took significantly longer to approach when the experimenter's gaze was directed towards them compared with directed away. However, inter-individual behaviour varied greatly, with some gulls approaching similarly quickly in both treatments, while others approached much more slowly when the experimenter was looking at them. These results indicate that reducing human-herring gull conflict may be possible through small changes in human behaviour, but will require consideration of behavioural differences between individual gulls.

PhyreRisk is an open-access, publicly accessible web application for interactively bridging genomic, proteomic and structural data facilitating the mapping of human variants onto protein structures. A major advance over other tools for sequence-structure variant mapping is that PhyreRisk provides information on 20,214 human canonical proteins and an additional 22,271 alternative protein sequences (isoforms). Specifically, PhyreRisk provides structural coverage (partial or complete) for 70% (14,035 of 20,214 canonical proteins) of the human proteome, by storing 18,874 experimental structures and 84,818 pre-built models of canonical proteins and their isoforms generated using our in house Phyre2. PhyreRisk reports 55,732 experimentally, multi-validated protein interactions from IntAct and 24,260 experimental structures of protein complexes. Another major feature of PhyreRisk is that, rather than presenting a limited set of precomputed variant-structure mapping of known genetic variants, it allows the user to explore novel variants using, as input, genomic coordinates formats (Ensembl, VCF, reference SNP ID and HGVS notations) and Human Build GRCh37 and GRCh38. PhyreRisk also supports mapping variants using amino acid coordinates and searching for genes or proteins of interest. PhyreRisk is designed to empower researchers to translate genetic data into protein structural information, thereby providing a more comprehensive appreciation of the functional impact of variants. PhyreRisk is freely available at http://phyrerisk.bc.ic.ac.uk., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Many efforts to improve science teaching in higher education focus on a few faculty members at an institution at a time, with limited published evidence on attempts to engage faculty across entire departments. We created a long-term, department-wide collaborative professional development program, Biology Faculty Explorations in Scientific Teaching (Biology FEST). Across 3 years of Biology FEST, 89% of the department's faculty completed a weeklong scientific teaching institute, and 83% of eligible instructors participated in additional semester-long follow-up programs. A semester after institute completion, the majority of Biology FEST alumni reported adding active learning to their courses. These instructor self-reports were corroborated by audio analysis of classroom noise and surveys of students in biology courses on the frequency of active-learning techniques used in classes taught by Biology FEST alumni and nonalumni. Three years after Biology FEST launched, faculty participants overwhelmingly reported that their teaching was positively affected. Unexpectedly, most respondents also believed that they had improved relationships with departmental colleagues and felt a greater sense of belonging to the department. Overall, our results indicate that biology department-wide collaborative efforts to develop scientific teaching skills can indeed attract large numbers of faculty, spark widespread change in teaching practices, and improve departmental relations., (© 2018 M. T. Owens et al. CBE—Life Sciences Education © 2018 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).)

Autotransporters (ATs) belong to a family of modular proteins secreted by the Type V, subtype a, secretion system (T5aSS) and considered as an important source of virulence factors in lipopolysaccharidic diderm bacteria (archetypical Gram-negative bacteria). While exported by the Sec pathway, the ATs are further secreted across the outer membrane via their own C-terminal translocator forming a β-barrel, through which the rest of the protein, namely the passenger, can pass. In several ATs, an autochaperone domain (AC) present at the C-terminal region of the passenger and upstream of the translocator was demonstrated as strictly required for proper secretion and folding. However, considering it was functionally characterised and identified only in a handful of ATs, wariness recently fells on the commonality and conservation of this structural element in the T5aSS. To circumvent the issue of sequence divergence and taking advantage of the resolved three-dimensional structure of some ACs, identification of this domain was performed following structural alignment among all AT passengers experimentally resolved by crystallography before searching in a dataset of 1523 ATs. While demonstrating that the AC is indeed a conserved structure found in numerous ATs, phylogenetic analysis further revealed a distribution into deeply rooted branches, from which emerge 20 main clusters. Sequence analysis revealed that an AC could be identified in the large majority of SAATs (self-associating ATs) but not in any LEATs (lipase/esterase ATs) nor in some PATs (protease autotransporters) and PHATs (phosphatase/hydrolase ATs). Structural analysis indicated that an AC was present in passengers exhibiting single-stranded right-handed parallel β-helix, whatever the type of β-solenoid, but not with α-helical globular fold. From this investigation, the AC of type 1 appears as a prevalent and conserved structural element exclusively associated to β-helical AT passenger and should promote further studies about the protein secretion and folding via the T5aSS, especially toward α-helical AT passengers.

A big challenge in current systems biology research arises when different types of data must be accessed from separate sources and visualized using separate tools. The high cognitive load required to navigate such a workflow is detrimental to hypothesis generation. Accordingly, there is a need for a robust research platform that incorporates all data and provides integrated search, analysis, and visualization features through a single portal. Here, we present ePlant (http://bar.utoronto.ca/eplant), a visual analytic tool for exploring multiple levels of Arabidopsis thaliana data through a zoomable user interface. ePlant connects to several publicly available web services to download genome, proteome, interactome, transcriptome, and 3D molecular structure data for one or more genes or gene products of interest. Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type. We describe the development of ePlant in this article and present several examples illustrating its integrative features for hypothesis generation. We also describe the process of deploying ePlant as an "app" on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research., (© 2017 American Society of Plant Biologists. All rights reserved.)

Some animals hide food to consume later; however, these caches are susceptible to theft by conspecifics and heterospecifics. Caching animals can use protective strategies to minimize sensory cues available to potential pilferers, such as caching in shaded areas and in quiet substrate. Background matching (where object patterning matches the visual background) is commonly seen in prey animals to reduce conspicuousness, and caching animals may also use this tactic to hide caches, for example, by hiding coloured food in a similar coloured substrate. We tested whether California scrub-jays ( Aphelocoma californica ) camouflage their food in this way by offering them caching substrates that either matched or did not match the colour of food available for caching. We also determined whether this caching behaviour was sensitive to social context by allowing the birds to cache when a conspecific potential pilferer could be both heard and seen (acoustic and visual cues present), or unseen (acoustic cues only). When caching events could be both heard and seen by a potential pilferer, birds cached randomly in matching and non-matching substrates. However, they preferentially hid food in the substrate that matched the food colour when only acoustic cues were present. This is a novel cache protection strategy that also appears to be sensitive to social context. We conclude that studies of cache protection strategies should consider the perceptual capabilities of the cacher and potential pilferers., (© 2017 The Author(s).)

Active-learning pedagogies have been repeatedly demonstrated to produce superior learning gains with large effect sizes compared with lecture-based pedagogies. Shifting large numbers of college science, technology, engineering, and mathematics (STEM) faculty to include any active learning in their teaching may retain and more effectively educate far more students than having a few faculty completely transform their teaching, but the extent to which STEM faculty are changing their teaching methods is unclear. Here, we describe the development and application of the machine-learning-derived algorithm Decibel Analysis for Research in Teaching (DART), which can analyze thousands of hours of STEM course audio recordings quickly, with minimal costs, and without need for human observers. DART analyzes the volume and variance of classroom recordings to predict the quantity of time spent on single voice (e.g., lecture), multiple voice (e.g., pair discussion), and no voice (e.g., clicker question thinking) activities. Applying DART to 1,486 recordings of class sessions from 67 courses, a total of 1,720 h of audio, revealed varied patterns of lecture (single voice) and nonlecture activity (multiple and no voice) use. We also found that there was significantly more use of multiple and no voice strategies in courses for STEM majors compared with courses for non-STEM majors, indicating that DART can be used to compare teaching strategies in different types of courses. Therefore, DART has the potential to systematically inventory the presence of active learning with ∼90% accuracy across thousands of courses in diverse settings with minimal effort.

Many animals build structures to provide shelter, avoid predation, attract mates or house offspring, but the behaviour and potential cognitive processes involved during building are poorly understood. Great bowerbird ( Ptilinorhynchus nuchalis ) males build and maintain display courts by placing tens to hundreds of objects in a positive size-distance gradient. The visual angles created by the gradient create a forced perspective illusion that females can use to choose a mate. Although the quality of illusion is consistent within males, it varies among males, which may reflect differences in how individuals reconstruct their courts. We moved all objects off display courts to determine how males reconstructed the visual illusion. We found that all individuals rapidly created the positive size-distance gradient required for forced perspective within the first 10 objects placed. Males began court reconstruction by placing objects in the centre of the court and then placing objects further out, a technique commonly used when humans lay mosaics. The number of objects present after 72 h was not related to mating success or the quality of the illusion, indicating that male skill at arranging objects rather than absolute number of objects appears to be important. We conclude that differences arise in the quality of forced perspective illusions despite males using the same technique to reconstruct their courts.

The identification of structurally similar proteins can provide a range of biological insights, and accordingly, the alignment of a query protein to a database of experimentally determined protein structures is a technique commonly used in the fields of structural and evolutionary biology. The PhyreStorm Web server has been designed to provide comprehensive, up-to-date and rapid structural comparisons against the Protein Data Bank (PDB) combined with a rich and intuitive user interface. It is intended that this facility will enable biologists inexpert in bioinformatics access to a powerful tool for exploring protein structure relationships beyond what can be achieved by sequence analysis alone. By partitioning the PDB into similar structures, PhyreStorm is able to quickly discard the majority of structures that cannot possibly align well to a query protein, reducing the number of alignments required by an order of magnitude. PhyreStorm is capable of finding 93±2% of all highly similar (TM-score>0.7) structures in the PDB for each query structure, usually in less than 60s. PhyreStorm is available at http://www.sbg.bio.ic.ac.uk/phyrestorm/., (Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Phyre2 is a suite of tools available on the web to predict and analyze protein structure, function and mutations. The focus of Phyre2 is to provide biologists with a simple and intuitive interface to state-of-the-art protein bioinformatics tools. Phyre2 replaces Phyre, the original version of the server for which we previously published a paper in Nature Protocols. In this updated protocol, we describe Phyre2, which uses advanced remote homology detection methods to build 3D models, predict ligand binding sites and analyze the effect of amino acid variants (e.g., nonsynonymous SNPs (nsSNPs)) for a user's protein sequence. Users are guided through results by a simple interface at a level of detail they determine. This protocol will guide users from submitting a protein sequence to interpreting the secondary and tertiary structure of their models, their domain composition and model quality. A range of additional available tools is described to find a protein structure in a genome, to submit large number of sequences at once and to automatically run weekly searches for proteins that are difficult to model. The server is available at http://www.sbg.bio.ic.ac.uk/phyre2. A typical structure prediction will be returned between 30 min and 2 h after submission., Competing Interests: MJES is a Director and shareholder in Equinox Pharma Ltd which uses bioinformatics and chemoinformatics in drug discovery research and services.

Protein domains are generally thought to correspond to units of evolution. New research raises questions about how such domains are defined with bioinformatics tools and sheds light on how evolution has enabled partial domains to be viable.

Genome3D (http://www.genome3d.eu) is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the resource. We have annotated representatives from Pfam families to improve coverage of diverse sequences and added a fast sequence search to the website to allow users to find Genome3D-annotated sequences similar to their own. We have improved and extended the Genome3D data, enlarging the source data set from three model organisms to 10, and adding VIVACE, a resource new to Genome3D. We have analysed and updated Genome3D's SCOP/CATH mapping. Finally, we have improved the superposition tools, which now give users a more powerful interface for investigating similarities and differences between structural models., (© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.)