Manipulating actions: A selective two-option device for cognitive experiments in wild animals.

Advances in biologging technologies have significantly improved our ability to track individual animals' behaviour in their natural environment. Beyond observations, automation of data collection has revolutionized cognitive experiments in the wild. For example, radio-frequency identification (RFID) antennae embedded in 'puzzle box' devices have allowed for large-scale cognitive experiments where individuals tagged with passive integrated transponder (PIT) tags interact with puzzle boxes to gain a food reward, with devices logging both the identity and solving action of visitors. Here, we extended the scope of wild cognitive experiments by developing a fully automated selective two-option foraging device to specifically control which actions lead to a food reward and which remain unrewarded. Selective devices were based on a sliding-door foraging puzzle, and built using commercially available low-cost electronics. We tested it on two free-ranging PIT-tagged subpopulations of great tits Parus major as a proof of concept. We conducted a diffusion experiment where birds learned from trained demonstrators to get a food reward by sliding the door either to the left or right. We then restricted access of knowledgeable birds to their less preferred side and calculated the latency until birds produced solutions as a measure of behavioural flexibility. A total of 22 of 23 knowledgeable birds produced at least one solution on their less preferred side after being restricted, with higher-frequency solvers being faster at doing so. In addition, 18 of the 23 birds reached their solving rate from prior to the restriction on their less preferred side, with birds with stronger prior side preference taking longer to do so. We therefore introduce and successfully test a new selective two-option puzzle box, providing detailed instructions and freely available software that allows reproducibility. It extends the functionality of existing systems by allowing fine-scale manipulations of individuals' actions and opens a large range of possibilities to study cognitive processes in wild animal populations.

[Development of a program for automatic collection and archiving of clinical data of patients with dysfunction of the temporomandibular joint]. / Razrabotka programmy avtomaticheskogo sbora i arkhivirovaniya klinicheskikh dannykh patsientov s disfunktsiei visochno-nizhnechelyustnogo sustava.

OBJECTIVE: Development of a program for the automatic collection and archiving of clinical patients with TMJ dysfunction. MATERIAL AND METHODS: Based on the clinical examination of 50 patients aged 18 to 30 years with temporomandibular joint dysfunction and the presence of an articular disc dislocation verified by magnetic resonance imaging, 80 signs were identified and terminologically formalized and were divided into 13 groups. RESULTS: This was the basis for the development of a detailed questionnaire for this contingent of patients, which the authors consider as the primary source of systematized data for processing in the program for automatic collection and archiving of clinical data. For graphical (animation) support for patient questioning, a library of "virtual patient" graphic files has been created, which includes static and dynamic animation explanations of the questions. CONCLUSION: An algorithm for optimizing the patient interrogation system based on the principle of excluding irrelevant units has been developed and implemented in the program.

Collecting large datasets of rotational electron diffraction with ParallEM and SerialEM.

A semi-automated protocol has been developed for rotational data collection of electron diffraction patterns by combined use of SerialEM and ParallEM, where SerialEM is used for positioning of sample crystals and ParallEM for rotational data collection. ParallEM calls standard camera control software through an AutoIt script, which adapts to software operational changes and to new GUI programs guiding other cameras. Development included periodic flashing and pausing of data collection during overnight or day-long recording with a cold field-emission beam. The protocol proved to be efficient and accurate in data collection of large-scale rotational series from two JEOL electron microscopes, a general-purpose JEM-2100 and a high-end CRYO ARM 300. Efficiency resulted from simpler steps and task specialization. It is possible to collect 12-20 rotational series from ~-68° to ~68° at a rotation speed of 1°/s in one hour without human supervision.

Focus: The interface between data collection and data processing in cryo-EM.

We present a new software package called Focus that interfaces cryo-transmission electron microscopy (cryo-EM) data collection with computer image processing. Focus creates a user-friendly environment to import and manage data recorded by direct electron detectors and perform elemental image processing tasks in a high-throughput manner while new data is being acquired at the microscope. It provides the functionality required to remotely monitor the progress of data collection and data processing, which is essential now that automation in cryo-EM allows a steady flow of images of single particles, two-dimensional crystals, or electron tomography data to be recorded in overnight sessions. The rapid detection of any errors that may occur greatly increases the productivity of recording sessions at the electron microscope.

Assessing the Validity of Automated Webcrawlers as Data Collection Tools to Investigate Online Child Sexual Exploitation.

The distribution of child sexual exploitation (CE) material has been aided by the growth of the Internet. The graphic nature and prevalence of the material has made researching and combating difficult. Although used to study online CE distribution, automated data collection tools (e.g., webcrawlers) have yet to be shown effective at targeting only relevant data. Using CE-related image and keyword criteria, we compare networks starting from CE websites to those from similar non-CE sexuality websites and dissimilar sports websites. Our results provide evidence that (a) webcrawlers have the potential to provide valid CE data, if the appropriate criterion is selected; (b) CE distribution is still heavily image-based suggesting images as an effective criterion; (c) CE-seeded networks are more hub-based and differ from non-CE-seeded networks on several website characteristics. Recommendations for improvements to reliable criteria selection are discussed.

Video-based data acquisition system for use in eye blink classical conditioning procedures in sheep.

Pavlovian eye blink conditioning (EBC) has been extensively studied in humans and laboratory animals, providing one of the best-understood models of learning in neuroscience. EBC has been especially useful in translational studies of cerebellar and hippocampal function. We recently reported a novel extension of EBC procedures for use in sheep, and now describe new advances in a digital video-based system. The system delivers paired presentations of conditioned stimuli (CSs; a tone) and unconditioned stimuli (USs; an air puff to the eye), or CS-alone "unpaired" trials. This system tracks the linear distance between the eyelids to identify blinks occurring as either unconditioned (URs) or conditioned (CRs) responses, to a resolution of 5 ms. A separate software application (Eye Blink Reviewer) is used to review and autoscore the trial CRs and URs, on the basis of a set of predetermined rules, permitting an operator to confirm (or rescore, if needed) the autoscore results, thereby providing quality control for accuracy of scoring. Learning curves may then be quantified in terms of the frequencies of CRs over sessions, both on trials with paired CS-US presentations and on CS-alone trials. The latency to CR onset, latency to CR peak, and occurrence of URs are also obtained. As we demonstrated in two example cases, this video-based system provides efficient automated means to conduct EBC in sheep and can facilitate fully powered studies with multigroup designs that involve paired and unpaired training. This can help extend new studies in sheep, a species well suited for translational studies of neurodevelopmental disorders resulting from gestational exposure to drugs, toxins, or intrauterine distress.

Exploring the influence of washing activities on the transfer and persistence of fibres in forensic science.

In forensic science, a robust and sound interpretation and evaluation of transferred fibre evidence requires an understanding of the principles and mechanisms that underpin fibre transfer, yet existing research lacks consistency and repeatability. This study investigates the impact of washing activities on both the release of fibres into wastewater and the transfer of constituent fibres from donor garments to receiver swatches. Using a low-cost friction tester and automated data collection through photography and ImageJ image processing software, controlled conditions were maintained for repeated experiments. Results indicated significant fibre release during wash cycles, with load size and donor garment history playing crucial roles. The donor garments subjected to repetitive washes exhibit a progressive decrease in the number of fibres transferred, independently of the load size. This study underscores the importance of considering a garment's washing history in forensic science contexts, but also for consistency in the way that data are collected.

A Systems Approach to Study Collagen Type I Self-Assembly: Kinetics and Morphology.

Collagen type I, the main component of the extracellular matrix in vertebrates, is widely used in tissue engineering applications. This is on account that collagen molecules can self-assemble under certain conditions into 3D fibrillar hydrogels. Although there is an extensive body of literature studying collagen self-assembly, there is a lack of systematic understanding on how different experimental factors, such as pH and temperature, and their cumulative effects guide the self-assembly process. In this work, a comprehensive workflow to study the interactive effects of several assembly parameters on the collagen self-assembly process is implemented. This workflow consists of: 1) efficient statistical sampling based on Design of Experiments, 2) high-throughput and automated data collection and 3) automated data analysis. This approach enables to screen several parameters simultaneously and derive a set of mathematical equations that link parameters with the kinetics and morphological aspects of collagen self-assembly, and can be used to design collagen constructs with predefined characteristics.

Perceptions of farming stakeholders towards automating dairy cattle mobility and body condition scoring in farm assurance schemes.

Animal welfare standards are used within the food industry to demonstrate efforts in reaching higher welfare on farms. To verify compliance with those standards, inspectors conduct regular on-farm animal welfare assessments. Conducting these welfare assessments can, however, be time-consuming and prone to human bias. The emergence of Digital Livestock Technologies (DLTs) offers new ways of monitoring farm animal welfare and can alleviate some of the challenges related to animal welfare assessments by collecting data automatically and more frequently. Whilst automating welfare assessments with DLTs may be promising, little attention has been paid to farmers' perceptions of the challenges that could prevent successful implementation. This study aims to address this gap by focusing on the trial of a DLT (a 3D machinelearning camera) to automate mobility and body condition scoring on 11 dairy cattle farms. Semi-structured, in-depth interviews were conducted with farmers, technology developers and a stakeholder involved in a farm assurance scheme (N14). Findings suggest that stakeholders perceived important benefits to the use of the camera in this context, from building consumer trust by increasing transparency to improved management efficiency. There was also a potential for greater consistency in data collection and thus for enhanced fairness across the UK dairy sector, particularly on the issue of lameness prevalence. However, stakeholders also raised important concerns, such as a lack of clarity around data ownership, reliability, and use, and the possibility of some farmers being penalised (e.g., if the technology failed to work). More clarity should thus be given to farmers in relation to data governance and evidence provided in terms of technical performance and accuracy. The findings of this study highlighted the need for more inclusive approaches to ensure farmers' concerns are adequately identified and addressed. These approaches can help minimise negative consequences to farmers and animal welfare, whilst maximising the potential benefits of automating welfare-related data collection.

Protein-to-structure pipeline for ambient-temperature in situ crystallography at VMXi.

The utility of X-ray crystal structures determined under ambient-temperature conditions is becoming increasingly recognized. Such experiments can allow protein dynamics to be characterized and are particularly well suited to challenging protein targets that may form fragile crystals that are difficult to cryo-cool. Room-temperature data collection also enables time-resolved experiments. In contrast to the high-throughput highly automated pipelines for determination of structures at cryogenic temperatures widely available at synchrotron beamlines, room-temperature methodology is less mature. Here, the current status of the fully automated ambient-temperature beamline VMXi at Diamond Light Source is described, and a highly efficient pipeline from protein sample to final multi-crystal data analysis and structure determination is shown. The capability of the pipeline is illustrated using a range of user case studies representing different challenges, and from high and lower symmetry space groups and varied crystal sizes. It is also demonstrated that very rapid structure determination from crystals in situ within crystallization plates is now routine with minimal user intervention.

Automated Reporting of Patient Outcomes in Hand Surgery: A Pilot Study.

BACKGROUND: Obtaining patient-reported outcomes (PROs) is becoming a standard component of patient care. For nonacademic practices, this can be challenging. From this perspective, we designed a nearly autonomous patient outcomes reporting system. We then conducted a prospective, cohort pilot study to assess the efficacy of the system. METHODS: We created an automated system to gather PROs. All operative patients for 4 surgeons in an upper-extremity private practice were asked to participate. These patients completed the Quick Disabilities of the Arm, Shoulder, and Hand (QuickDASH) questionnaires preoperatively and received follow-up e-mails requesting patients to complete additional QuickDASH questionnaires at 3, 6, and 12 weeks postoperatively and to complete a 13-week postoperative satisfaction survey. Response rates and satisfaction levels are reported with descriptive statistics. RESULTS: Sixty-two percent of participants completed the 3-week assessment, 55% completed the 6-week assessment, and 43% completed the 12-week assessment. Overall, 35% of patients completed all questionnaires, and 73% completed at least 1 postoperative assessment. The collection of follow-up questionnaires required no additional time from the clinical staff, surgeon, or a research associate. CONCLUSIONS: Automated e-mail assessments can collect reliable clinical data, with minimal surgeon or staff intervention required to administer and collect data, minimizing the financial cost. For nonacademic practices, without access to additional research resources, such a system is feasible. Further improvements in communication with patients could increase response rates.

Designing Experiments for Physiological Phenomics.

Phenomics has emerged as the technology of choice for understanding quantitative genetic variation in plant physiology and plant breeding. Phenomics has allowed for unmatched precision in exploring plant life cycles and physiological patterns. As new technologies are developed, it is still vital to follow best practices for designing and planning to be able to fully exploit any experimental results. Here we describe the basic - but sometimes overlooked - considerations of a phenomics experiment to help you maximize the value from the data collected: choosing population and location, accounting for sources of variation, establishing a timeline, and leveraging ground-truth measurements.

SimRFlow: An R-based workflow for automated high-throughput PBPK simulation with the Simcyp® simulator.

SimRFlow is a high-throughput physiologically based pharmacokinetic (PBPK) modelling tool which uses Certara's Simcyp® simulator. The workflow is comprised of three main modules: 1) a Data Collection module for automated curation of physicochemical (from ChEMBL and the Norman Suspect List databases) and experimental data (i.e.: clearance, plasma-protein binding, and blood-to-plasma ratio, from httk-R package databases), 2) a Simulation module which activates the Simcyp® simulator and runs Monte Carlo simulations on virtual subjects using the curated data, and 3) a Data Visualisation module for understanding the simulated compound-specific profiles and predictions. SimRFlow has three administration routes (oral, intravenous, dermal) and allows users to change some simulation parameters including the number of subjects, simulation duration, and dosing. Users are only expected to provide a file of the compounds they wish to simulate, and in return the workflow provides summary statistics, concentration-time profiles of various tissue types, and a database file (containing in-depth results) for each simulated compound. This is presented within a guided and easy-to-use R Shiny interface which provides many plotting options for the visualisation of concentration-time profiles, parameter distributions, trends between the different parameters, as well as comparison of predicted parameters across all batch-simulated compounds. The in-built R functions can be assembled in user-customised scripts which allows for the modification of the workflow for different purposes. SimRFlow proves to be a time-efficient tool for simulating a large number of compounds without any manual curation of physicochemical or experimental data necessary to run Simcyp® simulations.

Detecting child sexual abuse images: Traits of child sexual exploitation hosting and displaying websites.

BACKGROUND: Automated detection of child sexual abuse images (CSAI) often relies on image attributes, such as hash values. However, electronic service providers and others without access to hash value databases are limited in their ability to detect CSAI. Additionally, the increasing amount of CSA content being distributed means that a large percentage of images are not yet cataloged in hash value databases. Therefore, additional detection criteria need to be determined to improve identification of non-hashed CSAI. OBJECTIVE: We aim to identify patterns in the locations and folder/file naming practices of websites hosting and displaying CSAI, to use as additional detection criteria for non-hashed CSAI. METHODS: Using a custom-designed web crawler and snowball sampling, we analyzed the locations and naming practices of 103 Surface Web websites hosting and/or displaying 8108 known CSAI hash values. RESULTS: Websites specialize in either hosting or displaying CSAI with only 20% doing both. Neither hosting nor displaying websites fear repercussions. Over 27% of CSAI were displayed in the home directory (i.e., main page) with only 6% located in at least 4th-level sub-folder. Websites focused more on organizing images than hiding them with 68% of hosted and 54% of displayed CSAI being found in folders formatted year/month. Qualitatively, hosting websites were likely to use alphanumeric or disguised folder and file names to conceal images, while displaying websites were more explicit. CONCLUSION: File and folder naming patterns can be combined with existing criteria to improve automated detection of websites and website locations likely hosting and/or displaying CSAI.

Computer-controlled liquid-nitrogen drizzling device for removing frost from cryopreserved crystals.

Cryocrystallography is a technique that is used more often than room-temperature data collection in macromolecular crystallography. One of its advantages is the significant reduction in radiation damage, which is especially useful in synchrotron experiments. Another advantage is that cryopreservation provides simple storage of crystals and easy transportation to a synchrotron. However, this technique sometimes results in the undesirable adhesion of frost to mounted crystals. The frost produces noisy diffraction images and reduces the optical visibility of crystals, which is crucial for aligning the crystal position with the incident X-ray position. To resolve these issues, a computer-controlled device has been developed that drizzles liquid nitrogen over a crystal to remove frost. It was confirmed that the device works properly, reduces noise from ice rings in diffraction images and enables the centering of crystals with low visibility owing to frost adhesion.

Low-dose in situ prelocation of protein microcrystals by 2D X-ray phase-contrast imaging for serial crystallography.

Serial protein crystallography has emerged as a powerful method of data collection on small crystals from challenging targets, such as membrane proteins. Multiple microcrystals need to be located on large and often flat mounts while exposing them to an X-ray dose that is as low as possible. A crystal-prelocation method is demonstrated here using low-dose 2D full-field propagation-based X-ray phase-contrast imaging at the X-ray imaging beamline TOMCAT at the Swiss Light Source (SLS). This imaging step provides microcrystal coordinates for automated serial data collection at a microfocus macromolecular crystallography beamline on samples with an essentially flat geometry. This prelocation method was applied to microcrystals of a soluble protein and a membrane protein, grown in a commonly used double-sandwich in situ crystallization plate. The inner sandwiches of thin plastic film enclosing the microcrystals in lipid cubic phase were flash cooled and imaged at TOMCAT. Based on the obtained crystal coordinates, both still and rotation wedge serial data were collected automatically at the SLS PXI beamline, yielding in both cases a high indexing rate. This workflow can be easily implemented at many synchrotron facilities using existing equipment, or potentially integrated as an online technique in the next-generation macromolecular crystallography beamline, and thus benefit a number of dose-sensitive challenging protein targets.

InsteaDMatic: towards cross-platform automated continuous rotation electron diffraction.

A DigitalMicrograph script, InsteaDMatic, has been developed to facilitate rapid automated 3D electron diffraction/microcrystal electron diffraction data acquisition by continuous rotation of a crystal with a constant speed, denoted as continuous rotation electron diffraction. The script coordinates microscope functions, such as stage rotation, and camera functions relevant for data collection, and stores the experiment metadata. The script is compatible with any microscope that can be controlled by DigitalMicrograph and has been tested on both JEOL and Thermo Fisher Scientific microscopes. A proof of concept has been performed through employing InsteaDMatic for data collection and structure determination of a ZSM-5 zeolite. The influence of illumination settings and electron dose rate on the quality of diffraction data, unit-cell determination and structure solution has been investigated in order to optimize the data acquisition procedure.

ZOO: an automatic data-collection system for high-throughput structure analysis in protein microcrystallography.

Owing to the development of brilliant microfocus beamlines, rapid-readout detectors and sample changers, protein microcrystallography is rapidly becoming a popular technique for accessing structural information from complex biological samples. However, the method is time-consuming and labor-intensive and requires technical expertise to obtain high-resolution protein crystal structures. At SPring-8, an automated data-collection system named ZOO has been developed. This system enables faster data collection, facilitates advanced data-collection and data-processing techniques, and permits the collection of higher quality data. In this paper, the key features of the functionality put in place on the SPring-8 microbeam beamline BL32XU are described and the major advantages of this system are outlined. The ZOO system will be a major driving force in the evolution of the macromolecular crystallography beamlines at SPring-8.

Automated serial rotation electron diffraction combined with cluster analysis: an efficient multi-crystal workflow for structure determination.

Serial rotation electron diffraction (SerialRED) has been developed as a fully automated technique for three-dimensional electron diffraction data collection that can run autonomously without human intervention. It builds on the previously established serial electron diffraction technique, in which submicrometre-sized crystals are detected using image processing algorithms. Continuous rotation electron diffraction (cRED) data are collected on each crystal while dynamically tracking the movement of the crystal during rotation using defocused diffraction patterns and applying a set of deflector changes. A typical data collection screens up to 500 crystals per hour, and cRED data are collected from suitable crystals. A data processing pipeline is developed to process the SerialRED data sets. Hierarchical cluster analysis is implemented to group and identify the different phases present in the sample and to find the best matching data sets to be merged for subsequent structure analysis. This method has been successfully applied to a series of zeolites and a beam-sensitive metal-organic framework sample to study its capability for structure determination and refinement. Two multi-phase samples were tested to show that the individual crystal phases can be identified and their structures determined. The results show that refined structures obtained using automatically collected SerialRED data are indistinguishable from those collected manually using the cRED technique. At the same time, SerialRED has lower requirements of expertise in transmission electron microscopy and is less labor intensive, making it a promising high-throughput crystal screening and structure analysis tool.

Programmable Automated System for Songbird Ecobehavioral Research (PASSER): Using flexible computer-integrated feeders to conduct high resolution studies of environment-behavior dynamics in songbirds.

Field studies seeking to identify interactions between the environment and behaviors of wild songbirds are often restricted by time, labor, and accessibility of the site; hampering the collection of long-term, high-resolution data. Here, we describe the development, utilization, and initial results of a long-term field study of wild songbird feeding patterns using data collected through an inexpensive microcomputer-controlled automated feeder. Our studies indicate the "smart feeder" is capable of reliable and accurate data collection on feeding and behavioral metrics over long durations with relation to a wide range of environmental conditions. This enables detailed analysis of songbird's environment-behavior interactions. Our results have identified trends in environment-behavior interactions, microhabitat variations, species-specific feeding profiles, and differences in the frequency and involvement of displacement events. Computerized feeders enabled us to address environment-behavior interactions, resulting in more detailed data than traditional observational methods. This reinforces conclusions from previous work regarding the potential for automated data collection to be adapted for a wide variety of research studies across the field of ethology.