New tool use by wild Sumatran orangutans (Pongo pygmaeus abelii)

Two forms of tool use by wild Sumatran orangutans are reported from the Agusan Monitoring Station, a new research site in Indonesia. One form, a branch "hook" used in locomotion, has not been reported previously in wild orangutans. The second form, a leaf "pad" used to protect the hands and feet from thorns while feeding, shares similarities in form and function with a tool type used by orangutans at Ketambe, a nearby research site. Both instances of tool use occurred in areas of disturbance, and appear to be spontaneous inventions under novel conditions, although habitual use of the tool in other ecological contexts is plausible. A summary of the distribution of tool use types in wild orangutans is presented.     

Modeling of a Developing Planar Network of Cortical Neurons for Studying the Effects of Pharmacologically Modified Synaptic Connectivity on Cell Rhythmogenesis

A software tool for studying neural networks grown on planar substrates is described. The tool provides: (i) modeling the neuritic fields of individual neurons and their dynamic connectivity, (ii) creation of templates, cloning and connecting multiple instances of the neurons, (iii) computing the cellular electrical activity and Ca²⁺ dynamics, and (iv) estimating synchronization of the networked cells. Examples are shown of employing this tool for the study of synchronization of burst discharges in a network of the cortical neurons, whose connectivity is modified by neuropsin.     

SENSE tool: easy-to-use web-based tool to calculate food product environmental impact

Purpose

The purpose of the European SENSE project was to define an integral system to assess and communicate the environmental impacts of food products and to develop a web-based tool for Small and Medium size Enterprises (SMEs). The tool has been tested in salmon, beef-and-dairy, and fruit juice production sectors.

Methods

The SENSE project has evaluated several existing methodologies for environmental impact assessment over the life cycle including also social aspects, in order to deliver a new integral system for the environmental and social assessment of agricultural and aquaculture food products.

Results and discussion

The system includes a standardization of a data gathering system, a selection of relevant key environmental performance indicators for food supply chains and a common methodology to perform simplified life cycle impact assessment. The results are based on collected information on the use of resources and emissions generated along the supply chain of food or drink products. The main result is a web-based software tool that is based on a summation of the partial impacts of the different steps in food supply chains. In this software, different actors in the supply chain can enter their own data and link them to the data of other companies. The results obtained in the tool could be used for at least six different approaches: (i) environmental impact assessment of the product, (ii) food chain hot spot identification, (iii) comparison of hypothetical or real improvement scenarios, (iv) assessment of the environmental impact development over the years, (v) benchmarking opportunity for the companies, and (vi) a business to business communication strategy. The scientific robustness of the tool has been tested comparing the obtained results with the same analysis with commercial software.

Conclusions

The SENSE tool is a simplified tool designed for food and drink SMEs to assess their sustainability on their own. This cannot be fully compared to a complete LCA study. The testing with SMEs showed that they need additional support for filling in the questionnaires correctly and interpret the results. The simplified evaluation of environmental impacts based on a life cycle approach could lead to benefits to SMEs within the food industry. The future application and development of the tool will be focused on adapting the tool to the Product Environmental Footprint initiative requirements and self-assessment opportunities.

     

Invention and modification of a new tool use behavior: ant-fishing in trees by a wild chimpanzee (Pan troglodytes verus) at Bossou, Guinea

Wild chimpanzees are known to have a different repertoire of tool use unique to each community. For example, "ant-dipping" is a tool use behavior known in several chimpanzee communities across Africa targeted at driver ants (Dorylus spp.) on the ground, whereas "ant-fishing," which is aimed at carpenter ants (Camponotus spp.) in trees, has primarily been observed among the chimpanzees of Mahale in Tanzania. Although the evidence for differences between field sites is accumulating, we have little knowledge on how these tool use behaviors appear at each site and on how these are modified over time. This study reports two"ant-fishing" sessions which occurred 2 years apart by a young male chimpanzee at Bossou, Guinea. Ant-fishing had never been observed before in this community over the past 27 years. During the first session, at the age of 5, he employed wands of similar length when ant-fishing in trees to those used for ant-dipping on the ground, which is a customary tool use behavior of this community. Two years later, at the age of 7, his tools for ant-fishing were shorter and more suitable for capturing carpenter ants. This observation is a rare example of innovation in the wild and does provide insights into problem-solving and learning processes in chimpanzees.     

A Functional Variomics Tool for Discovering Drug-Resistance Genes and Drug Targets

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Highlights? A functional variomics tool for drug-target identification is described ? This tool compares favorably with other target-identification tools ? This tool will greatly facilitate the linking of phenotypes to point mutations ? This work discovered Pmp3 as a target of amphotericin B     

New tools suggest local variation in tool use by a montane community of the rare Nigeria–Cameroon chimpanzee, <Emphasis Type="Italic">Pan troglodytes ellioti</Emphasis>, in Nigeria

Regional variations in tool use among chimpanzee subspecies and between populations within the same subspecies can often be explained by ecological constraints, although cultural variation also occurs. In this study we provide data on tool use by a small, recently isolated population of the endangered Nigeria–Cameroon chimpanzee Pan troglodytes ellioti, thus demonstrating regional variation in tool use in this rarely studied subspecies. We found that the Ngel Nyaki chimpanzee community has its own unique tool kit consisting of five different tool types. We describe a tool type that has rarely been observed (ant-digging stick) and a tool type that has never been recorded for this chimpanzee subspecies or in West Central Africa (food pound/grate stone). Our results suggest that there is fine- scale variation in tool use among geographically close communities of P. t. ellioti, and that these variations likely reflect both ecological constraints and cultural variation.     

Hook tool manufacture in New Caledonian crows: behavioural variation and the influence of raw materials

Background

New Caledonian crows use a range of foraging tools, and are the only non-human species known to craft hooks. Based on a small number of observations, their manufacture of hooked stick tools has previously been described as a complex, multi-stage process. Tool behaviour is shaped by genetic predispositions, individual and social learning, and/or ecological influences, but disentangling the relative contributions of these factors remains a major research challenge. The properties of raw materials are an obvious, but largely overlooked, source of variation in tool-manufacture behaviour. We conducted experiments with wild-caught New Caledonian crows, to assess variation in their hooked stick tool making, and to investigate how raw-material properties affect the manufacture process.

Results

In Experiment 1, we showed that New Caledonian crows’ manufacture of hooked stick tools can be much more variable than previously thought (85 tools by 18 subjects), and can involve two newly-discovered behaviours: ‘pulling’ for detaching stems and bending of the tool shaft. Crows’ tool manufactures varied significantly: in the number of different action types employed; in the time spent processing the hook and bending the tool shaft; and in the structure of processing sequences. In Experiment 2, we examined the interaction of crows with raw materials of different properties, using a novel paradigm that enabled us to determine subjects’ rank-ordered preferences (42 tools by 7 subjects). Plant properties influenced: the order in which crows selected stems; whether a hooked tool was manufactured; the time required to release a basic tool; and, possibly, the release technique, the number of behavioural actions, and aspects of processing behaviour. Results from Experiment 2 suggested that at least part of the natural behavioural variation observed in Experiment 1 is due to the effect of raw-material properties.

Conclusions

Our discovery of novel manufacture behaviours indicates a plausible scenario for the evolutionary origins, and gradual refinement, of New Caledonian crows’ hooked stick tool making. Furthermore, our experimental demonstration of a link between raw-material properties and aspects of tool manufacture provides an alternative hypothesis for explaining regional differences in tool behaviours observed in New Caledonian crows, and some primate species.

     

PMS: A Panoptic Motif Search Tool

Background

Identification of DNA/Protein motifs is a crucial problem for biologists. Computational techniques could be of great help in this identification. In this direction, many computational models for motifs have been proposed in the literature.

Methods

One such important model is the motif model. In this paper we describe a motif search web tool that predominantly employs this motif model. This web tool exploits the state-of-the art algorithms for solving the motif search problem.

Results

The online tool has been helping scientists identify many unknown motifs. Many of our predictions have been successfully verified as well. We hope that this paper will expose this crucial tool to many more scientists.

Availability and requirements

Project name: PMS - Panoptic Motif Search Tool. Project home page: http://pms.engr.uconn.edu or http://motifsearch.com. Licence: PMS tools will be readily available to any scientist wishing to use it for non-commercial purposes, without restrictions. The online tool is freely available without login.     

The role of terrestriality in promoting primate technology

"Complex technology" has often been considered a hallmark of human evolution. However, recent findings show that wild monkeys are also capable of habitual tool use. Here we suggest that terrestriality may have been of crucial importance for the innovation, acquisition, and maintenance of "complex" technological skills in primates. Here we define complex technological skills as tool-use variants that include at least two tool elements (for example, hammer and anvil), flexibility in manufacture or use (that is, tool properties are adjusted to the task at hand), and that skills are acquired in part by social learning. Four lines of evidence provide support for the terrestriality effect. First, the only monkey populations exhibiting habitual tool use seem to be particularly terrestrial. Second, semi-terrestrial chimpanzees have more complex tool variants in their repertoire than does their arboreal Asian relative, the orangutan. Third, tool variants of chimpanzees used in a terrestrial setting tend to be more complex than those used exclusively in arboreal contexts. Fourth, the higher frequency in tool use among captive versus wild primates of the same species may be attributed in part to a terrestriality effect. We conclude that whereas extractive foraging, intelligence, and social tolerance are necessary for the emergence of habitual tool use, terrestriality seems to be crucial for acquiring and maintaining complex tool variants, particularly expressions of cumulative technology, within a population. Hence, comparative evidence among primates supports the hypothesis that the terrestriality premium may have been a major pacemaker of hominin technological evolution.     

DPPrimer – A Degenerate PCR Primer Design Tool

Designed degenerate primers unlike conventional primers are superior in matching and amplification of large number of genes, from related gene families. DPPrimer tool was designed to predict primers for PCR amplification of homologous gene from related or diverse plant species. The key features of this tool include platform independence and user friendliness in primer design. Embedded features such as search for functional domains, similarity score selection and phylogebetic tree further enhance the user friendliness of DPPrimer tool. Performance of DPPrimer tool was evaluated by successful PCR amplification of ADP-glucose phosphorylase genes from wheat, barley and rice.

Availability

DPPrimer is freely accessible at http://202.141.12.147/DGEN_tool/index.html     

Lessons learned developing a diagnostic tool for HIV-associated dementia feasible to implement in resource-limited settings: pilot testing in Kenya

Objective

To conduct a preliminary evaluation of the utility and reliability of a diagnostic tool for HIV-associated dementia (HAD) for use by primary health care workers (HCW) which would be feasible to implement in resource-limited settings.

Background

In resource-limited settings, HAD is an indication for anti-retroviral therapy regardless of CD4 T-cell count. Anti-retroviral therapy, the treatment for HAD, is now increasingly available in resource-limited settings. Nonetheless, HAD remains under-diagnosed likely because of limited clinical expertise and availability of diagnostic tests. Thus, a simple diagnostic tool which is practical to implement in resource-limited settings is an urgent need.

Methods

A convenience sample of 30 HIV-infected outpatients was enrolled in Western Kenya. We assessed the sensitivity and specificity of a diagnostic tool for HAD as administered by a primary HCW. This was compared to an expert clinical assessment which included examination by a physician, neuropsychological testing, and in selected cases, brain imaging. Agreement between HCW and an expert examiner on certain tool components was measured using Kappa statistic.

Results

The sample was 57% male, mean age was 38.6 years, mean CD4 T-cell count was 323 cells/µL, and 54% had less than a secondary school education. Six (20%) of the subjects were diagnosed with HAD by expert clinical assessment. The diagnostic tool was 63% sensitive and 67% specific for HAD. Agreement between HCW and expert examiners was poor for many individual items of the diagnostic tool (K = .03–.65). This diagnostic tool had moderate sensitivity and specificity for HAD. However, reliability was poor, suggesting that substantial training and formal evaluations of training adequacy will be critical to enable HCW to reliably administer a brief diagnostic tool for HAD.     

sandflyDST: a dynamic web‐based decision support tool for the morphological identification of sandflies present in Anatolia and mainland Europe,and user study

Species identification of sandflies is mainly performed according to morphological characters using classical written identification keys. This study introduces a new web‐based decision support tool (sandflyDST) for guiding the morphological identification of sandfly species present in Anatolia and mainland Europe and classified in the Phlebotomus and Sergentomyia genera (both: Diptera: Psychodidae). The current version of the tool consists of 111 questions and 36 drawings obtained from classical written keys, and 107 photographs for the quick and easy identification of 26 species of the genus Phlebotomus and four species of the genus Sergentomyia. The tool guides users through a decision tree using yes/no questions about the morphological characters of the specimen. The tool was applied by 30 individuals, who then completed study questionnaires. The results of subsequent analyses indicated that the usability () and users' level of appreciation (86.6%) of the tool were quite high; almost all of the participants considered recommending the tool to others. The tool may also be useful in training new entomologists and maintaining their level of expertise. This is a dynamic tool and can be improved or upgraded according to feedback. The tool is now available online at http://parasitology.ege.edu.tr/sandflyDST/index.php .     

The study of tool use as the way for general estimation of cognitive abilities in animals

Investigation of tool use is an effective way to determine cognitive abilities of animals. This approach raises hypotheses, which delineate limits of animal's competence in understanding of objects properties and interrelations and the influence of individual and social experience on their behaviour. On the basis of brief review of different models of manipulation with objects and tools manufacturing (detaching, subtracting and reshaping) by various animals (from elephants to ants) in natural conditions the experimental data concerning tool usage was considered. Tool behaviour of anumals could be observed rarely and its distribution among different taxons is rather odd. Recent studies have revealed that some species (for instance, bonobos and tamarins) which didn't manipulate tools in wild life appears to be an advanced tool users and even manufacturers in laboratory. Experimental studies of animals tool use include investigation of their ability to use objects physical properties, to categorize objects involved in tool activity by its functional properties, to take forces affecting objects into account, as well as their capacity of planning their actions. The crucial question is whether animals can abstract general principles of relations between objects regardless of the exact circumstances, or they develop specific associations between concerete things and situations. Effectiveness of laboratory methods is estimated in the review basing on comparative studies of tool behaviour, such as "support problem", "stick problem", "tube- and tube-trap problem", and "reserve tube problem". Levels of social learning, the role of imprinting, and species-specific predisposition to formation of specific domains are discussed. Experimental investigation of tool use allows estimation of the individuals' intelligence in populations. A hypothesis suggesting that strong predisposition to formation of specific associations can serve as a driving force and at the same time as obstacle to animals' activity is discussed. In several "technically gifted" species (such as woodpecker finches, New Caledonian crows, and chimpanzees) tool use seems to be guided by a rapid process of trial and error learning. Individuals that are predisposed to learn specific connections do this too quickly and thus become enslaved by stereotypic solutions of raising problems.     

Family fingerprints: a global approach to structural classification

Protein domain classification is a useful tool to deduce functional properties of proteins. Many software to classify domains according to available databases have been proposed so far. This paper introduces the notion of "fingerprint" as an easy and readable digest of the similarities between a protein fragment and an entire set of sequences. This concept offers us a rationale for building an automatic SCOP classifier which assigns a query sequence to the most likely family. Fingerprint-based analysis has been implemented in a software tool and we report some experimental validations for it.     

DECOMP: A PDB decomposition tool on the web

The protein databank (PDB) contains high quality structural data for computational structural biology investigations. We have earlier described a fast tool (the decomp_pdb tool) for identifying and marking missing atoms and residues in PDB files. The tool also automatically decomposes PDB entries into separate files describing ligands and polypeptide chains. Here, we describe a web interface named DECOMP for the tool. Our program correctly identifies multi­monomer ligands, and the server also offers the preprocessed ligand­protein decomposition of the complete PDB for downloading (up to size: 5GB)

Availability

http://decomp.pitgroup.org     

The MERG Suite: Tools for discovering competencies and associated learning resources

Background

As the demands for competency-based education grow, the need for standards-based tools to allow for publishing and discovery of competency-based learning content is more pressing. This project focused on developing federated discovery services for competency-based medical e-learning content.

Methods

We built a tool suite for authoring and discovery of medical e-learning metadata. The end-user usability of the tool suite was evaluated through a web-based survey.

Results

The suite, implemented as an open-source system, was evaluated to identify areas for improvement.

Conclusion

The MERG suite is a starting point for organizations implementing competency-based e-learning resources.     

Automated image processing as an analytical tool in cell cryopreservation for bioprocess development

The continuous availability of cells with defined cell characteristics represents a crucial issue in the biopharmaceutical and cell therapy industry. Here, development of cell banks with a long-term stability is essential and ensured by a cryopreservation strategy. The strategy needs to be optimized for each cell application individually and usually comprises controlled freezing, storage at ultra-low temperature, and fast thawing of cells. This approach is implemented by the development of master and working cell banks. Currently, empirical cryopreservation strategy development is standard, but a knowledge-based approach would be highly advantageous. In this article, we report the development of a video-based tool for the characterisation of freezing and thawing behaviour in cryopreservation process to enable a more knowledge-based cryopreservation process development. A successful tool validation was performed with a model cryopreservation process for the β-cell line INS-1E. Performance was evaluated for two working volumes (1.0 mL and 2.0 mL), based on freezing-thawing rates (20 °C to − 80 °C) and cell recovery and increase of biomass, to determine tool flexibility and practicality. Evaluation confirmed flexibility by correctly identifying a delay in freezing and thawing for the larger working volume. Further more, a decrease in cell recovery from 0.94 (± 0.14) % using 1.0 mL working volume to 0.61 (± 0.05) % using a 2.0 mL working volume displays tool practicality. The video-based tool proposed in this study presents a powerful tool for cell-specific optimisation of cryopreservation protocols. This can facilitate faster and more knowledge-based cryopreservation process development

Graphical abstract

In this study, a video-based analytical tool was developed for the characterisation of freezing and thawing behaviour in cryopreservation process development. Evaluation of the practicality and flexibility of the developed tool was done based on a scale-up case study with the cell line INS-1E. Here, the influence of sample working volume on process performance was investigated. Increasing the volume from 1to 2 mL led to a delay in freezing and thawing behaviour which caused cell recovery loss. We believe that the developed tool will facilitate more directed and systematic cryopreservation process development.