Project description:The manner in which the nervous system regulates animal behaviors in natural environments is a fundamental issue in biology. To address this question, C. elegans has been widely used as a model animal for the analysis of various animal behaviors. Previous behavioral assays have been limited to two-dimensional (2-D) environments, confining the worm motion to a planar substrate that does not reflect three-dimensional (3-D) natural environments such as rotting fruits or soil. Here, we develop a 3-D worm tracker (3DWT) for freely moving C. elegans in 3-D environments, based on a stereoscopic configuration. The 3DWT provides us with a quantitative trajectory, including the position and movement direction of the worm in 3-D. The 3DWT is also capable of recording and visualizing postures of the moving worm in 3-D, which are more complex than those in 2-D. Our 3DWT affords new opportunities for understanding the nervous system function that regulates animal behaviors in natural 3-D environments.
Project description:As a cell squeezes its nucleus through adjacent tissue, penetrates a basement membrane, or enters a small blood capillary, chromatin density and nuclear factors could in principle be physically perturbed. Here, in cancer cell migration through rigid micropores and in passive pulling into micropipettes, local compaction of chromatin is observed coincident with depletion of mobile factors. Heterochromatin/euchromatin was previously estimated from molecular mobility measurements to occupy a volume fraction f of roughly two-thirds of the nuclear volume, but based on the relative intensity of DNA and histones in several cancer cell lines drawn into narrow constrictions, f can easily increase locally to nearly 100%. By contrast, mobile proteins in the nucleus, including a dozen that function as DNA repair proteins (e.g., BRCA1, 53BP1) or nucleases (e.g., Cas9, FokI), are depleted within the constriction, approaching 0%. Such losses-compounded by the occasional rupture of the nuclear envelope-can have important functional consequences. Studies of a nuclease that targets a locus in chromosome-1 indeed show that constricted migration delays DNA damage.
Project description:ObjectiveClinical corpora can be deidentified using a combination of machine-learned automated taggers and hiding in plain sight (HIPS) resynthesis. The latter replaces detected personally identifiable information (PII) with random surrogates, allowing leaked PII to blend in or "hide in plain sight." We evaluated the extent to which a malicious attacker could expose leaked PII in such a corpus.Materials and methodsWe modeled a scenario where an institution (the defender) externally shared an 800-note corpus of actual outpatient clinical encounter notes from a large, integrated health care delivery system in Washington State. These notes were deidentified by a machine-learned PII tagger and HIPS resynthesis. A malicious attacker obtained and performed a parrot attack intending to expose leaked PII in this corpus. Specifically, the attacker mimicked the defender's process by manually annotating all PII-like content in half of the released corpus, training a PII tagger on these data, and using the trained model to tag the remaining encounter notes. The attacker hypothesized that untagged identifiers would be leaked PII, discoverable by manual review. We evaluated the attacker's success using measures of leak-detection rate and accuracy.ResultsThe attacker correctly hypothesized that 211 (68%) of 310 actual PII leaks in the corpus were leaks, and wrongly hypothesized that 191 resynthesized PII instances were also leaks. One-third of actual leaks remained undetected.Discussion and conclusionA malicious parrot attack to reveal leaked PII in clinical text deidentified by machine-learned HIPS resynthesis can attenuate but not eliminate the protective effect of HIPS deidentification.
Project description:The amount of artificial light at night is growing worldwide, impacting the behaviour of nocturnal organisms. Yet, we know little about the consequences of these behavioural responses for individual fitness and population viability. We investigated if females of the common glow-worm Lampyris noctiluca-which glow in the night to attract males-mitigate negative effects of artificial light on mate attraction by adjusting the timing and location of glowing to spatial variation in light conditions. We found females do not move away from light when exposed to a gradient of artificial light, but delay or even refrain from glowing. Further, we demonstrate that this response is maladaptive, as our field study showed that staying still when exposed to artificial light from a simulated streetlight decreases mate attraction success, while moving only a short distance from the light source can markedly improve mate attraction. These results indicate that glow-worms are unable to respond to spatial variation in artificial light, which may be a factor in their global decline. Consequently, our results support the hypothesis that animals often lack adaptive behavioural responses to anthropogenic environmental changes and underlines the importance of considering behavioural responses when investigating the effects of human activities on wildlife.
Project description:The stabilization of plummeting hoverflies was filmed and analysed in terms of their wingbeat initiation times as well as the crash and stabilization rates. The flies experienced near-weightlessness for a period of time that depended on their ability to counteract the free fall by triggering their wingbeats. In this paradigm, hoverflies' flight stabilization strategies were investigated here for the first time under two different positions of the light source (overhead and bottom lighting). The crash rates were higher in bottom lighting conditions than with top lighting. In addition, adding a texture to the walls reduced the crash rates only in the overhead lighting condition. The position of the lighting also significantly affected both the stabilization rates and the time taken by the flies to stabilize, which decreased and increased under bottom lighting conditions, respectively, whereas textured walls increased the stabilization rates under both lighting conditions. These results support the idea that flies may mainly base their flight control strategy on visual cues and particularly that the light distribution in the visual field may provide reliable, efficient cues for estimating their orientation with respect to an allocentric reference frame. In addition, the finding that the hoverflies' optic flow-based motion detection ability is affected by the position of the light source in their visual field suggests the occurrence of interactions between movement perception and this visual vertical perception process.
Project description:Behavioural phenotyping of model organisms is widely used to investigate fundamental aspects of organism biology, from the functioning of the nervous system to the effects of genetic mutations, as well as for screening new drug compounds. However, our capacity to observe and quantify the full range and complexity of behavioural responses is limited by the inability of conventional microscopy techniques to capture volumetric image information at sufficient speed. In this article we describe how combining light field microscopy with computational depth estimation provides a new method for fast, quantitative assessment of 3D posture and movement of the model organism Caenorhabditis elegans (C. elegans). We apply this technique to compare the behaviour of cuticle collagen mutants, finding significant differences in 3D posture and locomotion. We demonstrate the ability of quantitative light field microscopy to provide new fundamental insights into C. elegans locomotion by analysing the 3D postural modes of a freely swimming worm. Finally, we consider relative merits of the method and its broader application for phenotypic imaging of other organisms and for other volumetric bioimaging applications.
Project description:PurposeStrabisPIX is a smartphone application that allows clinicians to prescribe a series of self-obtained images of head position and eye alignment in nine positions of gaze that are uploaded onto a secure platform for clinician review. This study evaluates the clinical utility of this application.MethodsIn this prospective, nonmasked, cross-sectional study, 30 strabismus patients aged ≥2 years were evaluated. Participants received standardized instructions, used StrabisPIX to obtain images as prompted, and completed a satisfaction survey. During the same visit, an orthoptist obtained standard clinical images with a professional camera. All 60 image sets were evaluated by three observers.ResultsStrabisPIX image quality was similar to that of clinic photographs. Clinic photographs had significantly higher acceptability for horizontal versions (81% vs. 67%), vertical versions (76% vs. 60%), and head posture (93% vs. 81%). Abnormalities were detected at a similar rate for versions, head posture, eyelid position, and pupil size. StrabisPIX had significantly higher detection of alignment abnormalities (89% vs. 77% for clinical photos). Interrater/intrarater agreements were moderate to high (κ = 0.44-1.00) for all parameters except pupil abnormality, which had poor to fair agreement. Most patients reported that StrabisPIX was easy to learn and use.ConclusionsOverall, StrabisPIX images had similar quality and were as useful as images obtained in the clinic in detecting abnormalities.Translational relevanceThe StrabisPIX application will enhance the use of telemedicine by allowing physicians to prescribe self-obtained images documenting strabismus.
Project description:Recent breakthroughs in machine learning and big data analysis are allowing our online activities to be scrutinized at an unprecedented scale, and our private information to be inferred without our consent or knowledge. Here, we focus on algorithms designed to infer the opinions of Twitter users toward a growing number of topics, and consider the possibility of modifying the profiles of these users in the hope of hiding their opinions from such algorithms. We ran a survey to understand the extent of this privacy threat, and found evidence suggesting that a significant proportion of Twitter users wish to avoid revealing at least some of their opinions about social, political, and religious issues. Moreover, our participants were unable to reliably identify the Twitter activities that reveal one's opinion to such algorithms. Given these findings, we consider the possibility of fighting AI with AI, i.e., instead of relying on human intuition, people may have a better chance at hiding their opinion if they modify their Twitter profiles following advice from an automated assistant. We propose a heuristic that identifies which Twitter accounts the users should follow or mention in their tweets, and show that such a heuristic can effectively hide the user's opinions. Altogether, our study highlights the risk associated with developing machine learning algorithms that analyze people's profiles, and demonstrates the potential to develop countermeasures that preserve the basic right of choosing which of our opinions to share with the world.
Project description:We produced a miniaturized, multicode, multiband, and programmable light-emitting diode (LED) stimulator for wireless control of optogenetic experiments. The LED stimulator is capable of driving three independent LEDs upon reception of an infrared (IR) signal generated by a custom-made IR transmitter. Individual LED photopulse patterns are assigned to different codes of the IR signals (up to 256 codes). The photopulse patterns can be programmed in the on-board microcontroller by specifying the parameters of duration ([Formula: see text]), frequency ([Formula: see text]), and pulse width ([Formula: see text]). The IR signals were modulated at multiple carrier frequencies to establish multiband IR transmission. Using these devices, we could remotely control the moving direction of a Thy1-ChR2-YFP transgenic mouse by transcranially illuminating the corresponding hemisphere of the primary motor cortex. IR transmitter and LED stimulator will be particularly useful in experiments where free movement or patterned concurrent stimulation is desired, such as testing social communication of rodents.
Project description:The blue glow of the mucus from Chaetopterus involves a photoprotein, iron and flavins. Identity and respective role of these components remain, however, largely unresolved today, likely because of viscosity issues and inhibition of this system by oxidizers conventionally used to track bioluminescence activity. Here, we used gentle centrifugation to obtain a mucus supernatant showing no inhibition to oxidizers, allowing for further analysis. We applied conventional chromatographic techniques to isolate major proteins associated with light emission. Luminescence ability of elutriate fractions was tested with hydrogen peroxide to track photoprotein and/or protein-bound chromophore. Fractions producing light contained few major proteins, one with similarity to ferritin. Addition to the mucus of elements with inhibitory/potentiary effect on ferritin ferroxidase activity induced corresponding changes in light production, emphasizing the possible role of ferritin in the worm bioluminescence. DNA of the protein was cloned, sequenced, and expressed, confirming its identity to a Chaetopterus Ferritin (ChF). Both ferric and ferrous iron were found in the mucus, indicating the occurrence of both oxidase and reductase activity. Biochemical analysis showed ChF has strong ferroxidase activity, which could be a source of biological iron and catalytic energy for the worm bioluminescence when coupled to a reduction process with flavins.