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arXiv2016

Intriguing symmetry in statistical structures of Siberian larch transcriptome

The paper presents a novel approach to infer a structuredness in a set of symbol sequences such as transcriptome nucleotide sequences. A distribution pattern of triplet frequencies in the Siberian larch (\textit{Larix sibirica}~Ledeb.) transcriptome sequences was investigated in the presented study. It was found that the larch transcriptome demonstrates a number of unexpected symmetries in the statistical and combinatorial properties.

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arXiv2016

Metric dynamics for membrane transformation through regulated cell proliferation

This study develops an equation for describing three-dimensional membrane transformation through proliferation of its component cells regulated by morphogen density distributions on the membrane. The equation is developed in a two-dimensional coordinate system mapped on the membrane, referred to as the membrane coordinates. When the membrane expands, the membrane coordinates expand in the same manner so that the membrane is invariant in the coordinates. In the membrane coordinate system, the transformation of membrane is described with a time-derivative equation for metric tensors. By defining relationships between morphogen density distributions and the direction and rate of cell division, trajectories of membrane transformation are obtained in terms of the morphogen distributions. An example of the membrane transformation is shown numerically.

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arXiv2015

PeppyChains: Simplifying the assembly of 3D-printed generic protein models

Peppytides is a coarse-grained, accurate, physical model of the polypeptide chain. I have shared instructions to make your own polypeptide chain and STL files of Peppytides in MAKE magazine in Jan 2014 issue. However, Peppytides involves a lot of steps and assembly of units. People were asking me, 'Is there any easier way to make these models?'. I have been at several workshops, hands-on sessions, talks and a science events with Peppytides. From the feedback that I got everywhere, most of the makers, teachers and students want something that is 3D-Print-&-Go, or at least easier to make, even at the cost of some features. I have designed a new version of the model, named PeppyChains, in which the backbone chain of the model can be 3d-printed as a single unit. PeppyChains design eliminates the assembling of parts to form the backbone chain, but with the cost of losing the ability to use bias-magnets to favor certain phi/psi angles in the backbone. I have been demonstrating PeppyChains at various talks and workshops along with Peppytides, and I have received requests for making the STL file public. On popular demand, here I am sharing this STL and providing the step-by-step instructions to make PeppyChains. Just add the hydrogen-bond magnets, paint and color-code the atoms, and you are ready to go! No drilling. No time consuming assembly.

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arXiv2016

Contiguity is limited in free recall

Does the "law of contiguity" apply to free recall? I find that conditional response probabilities, often used as evidence for contiguity in free recall, have been displayed insufficiently, limiting the distance from the last item recalled, and only averaged over all items. When fully expanding the x-axis and examining the conditional response probabilities separately for the beginning, middle and end of the presented item list, I show that the law of contiguity applies only locally, even then only sometimes, and breaks down globally.

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arXiv2016

Large individual differences in free recall

Using single factor ANOVA I show that there are large individual differences in free recall (η ranges from 0.09-0.26) including the total recall, the balance between recency and primacy, and the initial recall (subsequent recalls show smaller individual differences). All three memory properties are relatively uncorrelated. The variance in the initial position may be a measure of executive control and is correlated with total recall (the smaller the variation, the larger the recall).

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arXiv2016

Conditional Response Probabilities Confirm Two Stages of Free Recall, Working Memory Very Localized, Second Stage Delocalized, Both with Strong Tendencies to Forward Subsequent Recalls

Recently it was shown that free recall consists of two stages: the first few recalls empty working memory and a second stage concludes the recall (Tarnow, 2015; for a review of the theoretical prediction see Murdock, 1974). Here I investigate conditional response probabilities in Murdock's 40-1 (1962) free recall dataset. I find that the conditional response probabilities confirm the presence of two stages. The first stage is characterized by a large enhancement of the forward subsequent recall (up to 30 times chance) and a large suppression of backward recalls (up to 26 times smaller than chance for recalls between 10 and 40 items away). The second stage forward subsequent recall is enhanced by a factor of 5 and the probability of backward and forward recalls are concentrated at small distances. Thus both stages favor forward subsequent recalls. As in Tarnow (2015), the first stage is much more localized than the second stage. Working memory capacity is estimated in six ways to be about 4.5 word items for the 40-1 word list.

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arXiv2016

First direct evidence of two stages in free recall and three corresponding estimates of working memory capacity

I find that exactly two stages can be seen directly in sequential free recall distributions. These distributions show that the first three recalls come from the emptying of working memory, recalls 6 and above come from a second stage and the 4th and 5th recalls are mixtures of the two. A discontinuity, a rounded step function, is shown to exist in the fitted linear slope of the recall distributions as the recall shifts from the emptying of working memory (positive slope) to the second stage (negative slope). The discontinuity leads to a first estimate of the capacity of working memory at 4-4.5 items. Working memory accounts for the recency effect. The primacy effect comes from the second stage with a contribution also from working memory for short lists (the first item). The different slopes of the working memory and secondary stages, and that the two have different functional forms, accounts for the u-shaped serial position curve. The total recall is shown to be a linear combination of the content of working memory and items recalled in the second stage with 3.0-3.9 items coming from working memory, a second estimate of the capacity of working memory. A third, separate upper limit on the capacity of working memory is found (3.06 items), corresponding to the requirement that the content of working memory cannot exceed the total recall, item by item. This third limit presumably corresponds to the least chunked item. This is the best limit on the capacity of unchunked working memory.

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arXiv2016

Free Recall Shows Similar Reactivation Behavior as Recognition & Cued Recall

I find that the total retrieval time in word free recall increases linearly with the total number of items recalled. Measured slopes, the time to retrieve an additional item, vary from 1.4-4.5 seconds per item depending upon presentation rate, subject age and whether there is a delay after list presentation or not. These times to retrieve an additional item obey a second linear relationship as a function of the recall probability averaged over the experiment, explicitly independent of subject age, presentation rate and whether there is a delay after the list presentation or not. This second linear relationship mimics the relationships in recognition and cued recall (Tarnow, 2008) which suggests that free recall retrieval uses the same reactivation mechanism as recognition or cued recall. Extrapolation limits the time to retrieve an additional item to a maximum of 7.2 seconds per item if the probability of recall is near 0%. Earlier upper limits for recognition and cued recall varied with the item type between 0.2 and 1.8 seconds per item (Tarnow, 2008). Implications include that there are only two types of short term memory: working memory and reactivation.

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arXiv2016

Direct Evidence Delay with A Task Decreases Working Memory Content in Free Recall

Recently it was shown that free recall consists of two stages: the first few recalls empty the working memory and a second stage concludes the recall (Tarnow, 2015; for a review of the theoretical prediction see Murdock, 1974). It is commonly believed that a delay with a task before the recall starts removes the content of working memory (Glanzer & Cunitz, 1966). Here is presented the first direct evidence that this is indeed the case.

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arXiv2016

A Precise Measure of Working Memory Reveals Subjects Difficulties Managing Limited Capacity

Free recall consists of two separate stages: the emptying of working memory and reactivation [1]. The Tarnow Unchunkable Test (TUT, [2]) uses double integer items to separate out only the first stage by making it difficult to reactivate items due to the lack of intra-item relationships. 193 Russian college students were tested via the internet version of the TUT. The average number of items remembered in the 3 item test was 2.54 items. In the 4 item test, the average number of items decreased to 2.38. This, and a number of other qualitative distribution differences between the 3 and 4 item tests, indicates that the average capacity limit of working memory has been reached at 3 items. This provides the first direct measurement of the unchunkable capacity limit of language based items. That the average number of items remembered decreased as the number of items increased from 3 to 4 indicates that most subjects were unable to manage their working memories as the number of items increased just beyond the average capacity. Further evidence for the difficulty in managing the capacity limit is that 25% of subjects could not remember any items correctly at least in one of three 4 item tests and that the Pearson correlation between the 3 item and 4 item subject recalls was a relatively small 38%. This failure of managing a basic memory resource should have important consequences for pedagogy including instruction, text book design and test design. Because working memory scores are important for academic achievement, it also suggests that an individual can gain academically by learning how to manage her or his capacity limit.

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arXiv2016

Velvet Worms (Onychophora) in Folklore and Art: Geographic Pattern, Types of Cultural Reference and Public Perception

Aims: To document and preserve folkloric beliefs and art inspired by velvet worms (Onychophora), rare invertebrates that are considered "living fossils", have full placental organs and capture prey with a rough "net" built in a fraction of a second. Study Design: This study is a combination of field interviews, online surveys and automatic database search. Methods: We asked open-ended questions to farmers who know the worms, consulted experts and searched the Internet to document folkloric and artistic instances using all the names that these animals receive in English, Spanish and Portuguese (languages of the countries where they occur) as well as other languages, and automatic image search, in Web of Science, CrossRef, Google Scholar and Google. Results: We found more than 80 cases of direct references to velvet worms in folklore and art, mostly from the USA, Australia, Brazil, Costa Rica and New Zealand. Per capita the countries with more cases are New Zealand (24 cases per million inhabitants), Costa Rica (16 cases per million inhabitants) and Australia (3 cases per million inhabitants). The most frequent expressions are cartoons, followed by tourism agencies using velvet worms in their ads, products with velvet worm representations, folkloric beliefs, and music bands or songs named after them. In almost all cases the animals are seen in a favorable light, inspiring folklore and art that highlight their extraordinary nature. Conclusion: The unique prey capture mechanism of velvet worms seems to have inspired an unexpected number of artistic and folkloric expressions, preserved for the future in the present article, which starts a totally new line of research: the effect of "living fossils" on human culture.

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arXiv2015

Study of human accessibility: physical tests versus numerical simulation

Consideration of physical dimensions of the user population is essential to design adapted environment. This variability in body dimensions (called "anthropometry") is involved in design tools commonly used today to assess user's accommodation (physical mock-ups, population models, database, boundary manikins, hybrid methods or digital human modeling). Databases are created from campaigns of measurement. Besides the fact that such measures are costly in time and money, they give more "static" measures of man. They do not take into account possible stretching limbs that could allow increased accessibility. This paper presents a methodology for human body modeling, in a dynamic way, not static. The methodology allows to highlight influences of design and human behaviour on reach skills, directly induced by the interaction with real prototypes and not just considered by human physical dimensions. The first part of the method is to create a database of measurements (arms length, hip breadth, etc.). From these data, a model of accessibility is proposed. The accessibility field is determined purely numerically. In parallel, an experiment is set up to measure the extension of the accessibility field, with the same people. A comparison of the results is then performed and a new model of the human body is proposed.

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arXiv2016

Modelling Early Transitions Toward Autonomous Protocells

This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the conceptual perspective developed. The central subject matter addressed is the emergence and maintenance of compartmentalised chemistries as precursors of more complex systems with a proper cellular organization. Whereas an evolutionary conception of life dominates prebiotic chemistry research and overflows into the protocells field, this thesis defends that the 'autonomous systems perspective' of living phenomena is a suitable - arguably the most suitable - conceptual framework to serve as a backdrop for protocell research. The autonomy approach allows a careful and thorough reformulation of the origins of cellular life problem as the problem of how integrated autopoietic chemical organisation, present in all full-fledged cells, originated and developed from more simple far-from-equilibrium chemical aggregate systems.

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arXiv2016

The "Hard Problem" of Life

Chalmer's famously identified pinpointing an explanation for our subjective experience as the "hard problem of consciousness". He argued that subjective experience constitutes a "hard problem" in the sense that its explanation will ultimately require new physical laws or principles. Here, we propose a corresponding "hard problem of life" as the problem of how `information' can affect the world. In this essay we motivate both why the problem of information as a causal agent is central to explaining life, and why it is hard - that is, why we suspect that a full resolution of the hard problem of life will, similar to as has been proposed for the hard problem of consciousness, ultimately not be reducible to known physical principles.

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arXiv2016

Natural calcium carbonate for biomedical applications

Sea shells are found to be a very rich natural resource for calcium carbonate. Sea shells are made up of CaCO3 mainly in the aragonite form, which are columnar or fibrous or microsphere structured crystals. The bioactivity of nanoparticles of sea shell has been studied in this work. The sea shells collected were thoroughly washed, dried and pulverized. The powder was sieved and particles in the range of 45 to 63 microns were collected. The powdered sea shells were characterized using X-Ray Diffraction and Field Emission Scanning Electron Microscopy. The XRD data showed that the particles were mainly microspheres. Traces of calcite and vaterite were also present. Experiments were conducted to study the aspirin and strontium ranelate drug loading into the sea shell powder using soak and dry method. Different concentrations of drug solution was made in ethanol and water. The shell powder was soaked in drug solutions and was kept soaking for 48 hrs with intermittent ultrasonication. The mixture was gently dried in a vacuum oven. The in vitro drug release studies were done using Phosphate Buffered Saline. The FESEM images displayed a distribution of differently sized and shaped particles. The sea shells due to its natural porosity and crystallinity are expected to be useful for drug delivery. About 50% drug entrapment efficiency for aspirin and 39% for strontium ranelate was seen. A burst release of the drug (80 percent) was observed within two hours for both the drugs studied. Rest of the drug was released slowly in 19 hrs. Further modification of the sea shell with non toxic polymers is also planned as a part of this work. Sea shell powder has become a potential candidate for drug delivery due to all the aforementioned advantages.

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arXiv2016

Stem Cell Networks

We present a general computational theory of stem cell networks and their developmental dynamics. Stem cell networks are special cases of developmental control networks. Our theory generates a natural classification of all possible stem cell networks based on their network architecture. Each stem cell network has a unique topology and semantics and developmental dynamics that result in distinct phenotypes. We show that the ideal growth dynamics of multicellular systems generated by stem cell networks have mathematical properties related to the coefficients of Pascal's Triangle. The relationship to cancer stem cells and their control networks is indicated. The theory lays the foundation for a new research paradigm for understanding and investigating stem cells. The theory of stem cell networks implies that new methods for generating and controlling stem cells will become possible.

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arXiv2016

Can Bioinformatics Be Considered as an Experimental Biological Science?

The objective of this short report is to reconsider the subject of bioinformatics as just being a tool of experimental biological science. To do that, we introduce three examples to show how bioinformatics could be considered as an experimental science. These examples show how the development of theoretical biological models generates experimentally verifiable computer hypotheses, which necessarily must be validated by experiments in vitro or in vivo.

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arXiv2017

Permutation, Multiscale and Modified Multiscale Entropies a Natural Complexity for Low-High Infection Level Intracellular Viral Reaction Kinetics

Viral infectious diseases, such as HIV virus growth, cause an important health concern. Study of intracellular viral processes can provide us to develop drug and understanding the drug dose to decrease the HIV virus in during growth. Kinetics Monte Carlo simulation has been done for solving Master equation about dynamics of intracellular viral reaction kinetics. Scaling relationship between equilibrium time and initial population of template has been found as power low, , where N , are the number of initial population of template species , equilibrium time, a = 163.1 , b = -0.1429 respectively. Stochastic dynamics shows that increasing initial population of template decreases the time of equilibrium. Entropy generation has been considered in low, intermediate and high infection level of intracellular viral kinetics reaction in during dynamical process. Permutation, multi scaling and modified multiscaling entropies have been calculated for three kinds of species in intracellular reaction dynamics, genome, structural protein, and template. Our result shows that presence of noise in dynamical process of intracellular reaction will change order of permutation entropy for the mentioned of three species. In addition to multiscaling entropy is computed for mentioned model and it has the following order: template > structural protein> genome. Dependency of permutation entropy result to permutation order becomes small in high infection level in intracellular viral kinetics dynamics. At short time scale in intracellular reaction dynamics, convergency of permutation entropy occurs with medium permutation order value. In the big time scale of intracellular dynamics, permutation entropy scale with permutation order n as a scaling relation .

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