Critical mutation rate has an exponential dependence on population size in haploid and diploid populations

Understanding the effect of population size on the key parameters of evolution is particularly important for populations nearing extinction. There are evolutionary pressures to evolve sequences that are both fit and robust. At high mutation rates, individuals with greater mutational robustness can outcompete those with higher fitness. This is survival-of-the-flattest, and has been observed in digital organisms, theoretically, in simulated RNA evolution, and in RNA viruses. We introduce an algorithmic method capable of determining the relationship between population size, the critical mutation rate at which individuals with greater robustness to mutation are favoured over individuals with greater fitness, and the error threshold. Verification for this method is provided against analytical models for the error threshold. We show that the critical mutation rate for increasing haploid population sizes can be approximated by an exponential function, with much lower mutation rates tolerated by small populations. This is in contrast to previous studies which identified that critical mutation rate was independent of population size. The algorithm is extended to diploid populations in a system modelled on the biological process of meiosis. The results confirm that the relationship remains exponential, but show that both the critical mutation rate and error threshold are lower for diploids, rather than higher as might have been expected. Analyzing the transition from critical mutation rate to error threshold provides an improved definition of critical mutation rate. Natural populations with their numbers in decline can be expected to lose genetic material in line with the exponential model, accelerating and potentially irreversibly advancing their decline, and this could potentially affect extinction, recovery and population management strategy. The effect of population size is particularly strong in small populations with 100 individuals or less; the exponential model has significant potential in aiding population management to prevent local (and global) extinction events

Meson-Baryon s-wave Resonances with Strangeness -3

Starting from a consistent SU(6) extension of the Weinberg-Tomozawa (WT) meson-baryon chiral Lagrangian (Phys. Rev. D74 (2006) 034025), we study the s-wave meson-baryon resonances in the strangeness S=-3 and negative parity sector. Those resonances are generated by solving the Bethe-Salpeter equation with the WT interaction used as kernel. The considered mesons are those of the 35-SU(6)-plet, which includes the pseudoscalar (PS) octet of pions and the vector (V) nonet of the rho meson. For baryons we consider the 56-SU(6)-plet, made of the 1/2+ octet of the nucleon and the 3/2+ decuplet of the Delta. Quantum numbers I(J^P)=0(3/2^-) are suggested for the experimental resonances Omega*(2250)- and Omega*(2380)-. Among other, resonances with I=1 are found, with minimal quark content sss\bar{l}l', being s the strange quark and l, l' any of the the light up or down quarks. A clear signal for such a pentaquark would be a baryonic resonance with strangeness -3 and electric charge of -2 or 0, in proton charge units. We suggest looking for K- Xi- resonances with masses around 2100 and 2240 MeV in the sector 1(1/2^-), and for pi Omega- and K- Xi*- resonances with masses around 2260 MeV in the sector 1(3/2^-).Comment: 3 pages, 1 Postscript figure, 7 table

Theory and practice of optimal mutation rate control in Hamming spaces of DNA sequences

We investigate the problem of optimal control of mutation by asexual self-replicating organisms represented by points in a metric space. We introduce the notion of a relatively monotonic fitness landscape and consider a generalisation of Fisher's geometric model of adaptation for such spaces. Using a Hamming space as a prime example, we derive the probability of adaptation as a function of reproduction parameters (e.g. mutation size or rate). Optimal control rules for the parameters are derived explicitly for some relatively monotonic landscapes, and then a general information-based heuristic is introduced. We then evaluate our theoretical control functions against optimal mutation functions evolved from a random population of functions using a meta genetic algorithm. Our experimental results show a close match between theory and experiment. We demonstrate this result both in artificial fitness landscapes, defined by a Hamming distance, and a natural landscape, where fitness is defined by a DNA-protein affinity. We discuss how a control of mutation rate could occur and evolve in natural organisms. We also outline future directions of this work

Monotonicity of fitness landscapes and mutation rate control

A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the performance of evolutionary algorithms. Much biological theory in this area is based on Ronald Fisher's work, who used Euclidean geometry to study the relation between mutation size and expected fitness of the offspring in infinite phenotypic spaces. Here we reconsider this theory based on the alternative geometry of discrete and finite spaces of DNA sequences. First, we consider the geometric case of fitness being isomorphic to distance from an optimum, and show how problems of optimal mutation rate control can be solved exactly or approximately depending on additional constraints of the problem. Then we consider the general case of fitness communicating only partial information about the distance. We define weak monotonicity of fitness landscapes and prove that this property holds in all landscapes that are continuous and open at the optimum. This theoretical result motivates our hypothesis that optimal mutation rate functions in such landscapes will increase when fitness decreases in some neighbourhood of an optimum, resembling the control functions derived in the geometric case. We test this hypothesis experimentally by analysing approximately optimal mutation rate control functions in 115 complete landscapes of binding scores between DNA sequences and transcription factors. Our findings support the hypothesis and find that the increase of mutation rate is more rapid in landscapes that are less monotonic (more rugged). We discuss the relevance of these findings to living organisms

Strong Decays of Strange Quarkonia

In this paper we evaluate strong decay amplitudes and partial widths of strange mesons (strangeonia and kaonia) in the 3P0 decay model. We give numerical results for all energetically allowed open-flavor two-body decay modes of all nsbar and ssbar strange mesons in the 1S, 2S, 3S, 1P, 2P, 1D and 1F multiplets, comprising strong decays of a total of 43 resonances into 525 two-body modes, with 891 numerically evaluated amplitudes. This set of resonances includes all strange qqbar states with allowed strong decays expected in the quark model up to ca. 2.2 GeV. We use standard nonrelativistic quark model SHO wavefunctions to evaluate these amplitudes, and quote numerical results for all amplitudes present in each decay mode. We also discuss the status of the associated experimental candidates, and note which states and decay modes would be especially interesting for future experimental study at hadronic, e+e- and photoproduction facilities. These results should also be useful in distinguishing conventional quark model mesons from exotica such as glueballs and hybrids through their strong decays.Comment: 69 pages, 5 figures, 39 table

Discovery of palladium, antimony, tellurium, iodine, and xenon isotopes

Currently, thirty-eight palladium, thirty-eight antimony, thirty-nine tellurium, thirty-eight iodine, and forty xenon isotopes have been observed and the discovery of these isotopes is discussed here. For each isotope a brief synopsis of the first refereed publication, including the production and identification method, is presented.Comment: to be published in At. Data Nucl. Data Table

Preliminary development of proxy-rated quality-of-life scales for children and adults with Niemann-Pick type C

OBJECTIVES: Niemann-Pick disease type C (NPC) is a rare life-limiting disease for which there is no cure. No scales currently exist to measure the impact of medication, physical therapy or clinical trials. The aim of this study was to develop age-appropriate Quality-of-Life (QoL) scales to measure the impact of NPC on children and adults. DESIGN: Scale development study using a phenomenological approach to data generation and analysis. METHODS: Fourteen interviews were conducted with people living with NPC and/or their parents/carers. Themes were generated and examined against an existential-phenomenological theory of wellbeing. A matrix was constructed to represent the phenomenological insight gained on participants' subjective experiences and a bank of items that were related to their QoL was developed. RESULTS: NPC quality-of-life questionnaires for children (NPCQLQ-C) and adults (NPCQLQ-A) proxy prototype scales were produced and completed by 23 parents/carers of children (child age mean = 8.61 years) and 20 parents/carers of adults (adult age = 33.4 years). Reliability analysis resulted in a 15-item NPCQLQ-C and a 30-item NPCQLQ-A, which showed excellent internal consistency, Cronbach's α = 0.925 and 0.947, respectively. CONCLUSION: The NPCQLQ-C and NPCQLQ-A are the first disease-specific QoL scales to be developed for people living with NPC. This novel approach to scale development values the experiential, real life impact of living with NPC and focused on the lived-experiences and impact on QoL. The scales will enable healthcare professionals and researchers to have a better understanding and quantifiable measurement of the impact of living with NPC on a patient's daily life

Simple and Effective Curriculum Pointer-Generator Networks for Reading Comprehension over Long Narratives

This paper tackles the problem of reading comprehension over long narratives where documents easily span over thousands of tokens. We propose a curriculum learning (CL) based Pointer-Generator framework for reading/sampling over large documents, enabling diverse training of the neural model based on the notion of alternating contextual difficulty. This can be interpreted as a form of domain randomization and/or generative pretraining during training. To this end, the usage of the Pointer-Generator softens the requirement of having the answer within the context, enabling us to construct diverse training samples for learning. Additionally, we propose a new Introspective Alignment Layer (IAL), which reasons over decomposed alignments using block-based self-attention. We evaluate our proposed method on the NarrativeQA reading comprehension benchmark, achieving state-of-the-art performance, improving existing baselines by $51\%$ relative improvement on BLEU-4 and $17\%$ relative improvement on Rouge-L. Extensive ablations confirm the effectiveness of our proposed IAL and CL components.Comment: Accepted to ACL 201

Lifestyle Choices That Help Prevent Women from Reincarceration

There is immense research about recidivism rates in different populations such as African Americans, men, and other population groups. During our preliminary research and literature reviews, we saw a need for more research about recidivism rates in women. This research proposal hopes to examine the different lifestyle choices that would be most conducive to helping women stay out of prison after being released. Fifty women will undergo individual, in-depth interviews through a fixed purposive sample panel that will be confidential and anonymous. These fifty women will be found by posting flyers at social service agencies, prisons, AA meetings, NA meetings, and other places deemed appropriate in the state of Ohio. Interviews will include questions concerning lifestyle factors from their past, present, and future. The semi-structured interviews will provide a more in-depth look into personal stories. Overall, this research proposal hopes to find the different factors that participants might have in common that can help researchers better understand how past, present, and future life circumstances impact recidivism rates. We expect to find that healthier lifestyle choices will decrease recidivism rates for women. This research proposal is an exploratory study and calls for more research and data from other researchers