bluuebunny/crossref_metadata_2025 huggingface dataset:
Zeta potential of bacteria cells: Effect of wash buffers
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

Zeta potential, defined as the electric charge at the shear plane, is widely used as a proxy for bacteria cell surface charge. Nonspecific adsorption of ions or polyelectrolytes onto the cell surface, however, alters the value and polarity of the measured zeta potential, leading to erroneous results. Multiple wash and centrifugation steps are commonly used in preparing cells for zeta potential analysis, where various wash buffers (such as 9 g/L NaCl, 0.001M KCl, and 0.1M NaNO3) are routinely used for removing (by charge screening) ions and charged molecules that bind nonspecifically to the cell surface. Preliminary data showed that, for Escherichia coli DH5α (ATCC 53868) grown in LB Lennox (with 2 g/L glucose, or LBG), the zeta potential-pH profile was not significantly different over the pH range from 2 to 12 for deionized water, 9 g/L NaCl, and phosphate buffer saline (PBS) wash buffers. As LBG is a low salt medium without a phosphate buffer, it was likely that the extent of nonspecific adsorption of ions on the cell surface was not substantial, and the different wash buffers would correspondingly not affect measured zeta potential much. For E. coli grown in a semi-defined medium (with a high capacity phosphate buffer system), the zeta potential-pH profile was significantly different over the pH range from 1 to 12 for deionized water, 9 g/L NaCl, 0.1M NaNO3, 0.1M sodium acetate, and 0.1M sodium citrate wash buffers with the extent of difference positively correlated with wash buffer’s ionic strength. Furthermore, the point of zero charge (pHzpc) for E. coli grown in the semi-defined medium varies between 1.5 and 3, in an ionic strength-dependent manner, for the various wash buffers tested. Collectively, this preliminary study suggests that wash buffers' ionic strength strongly affect removal efficiency of nonspecifically absorbed ions on bacteria surfaces, where a threshold exists (0.15M) for charge screening to be effective. At the upper bound, 0.6M ionic strength might result in removal of cations that stabilizes the cell envelope; thus, leading to possible cell surface damage and erroneous measurements.
Investigating readiness to use Internet and mobile services of diabetic patients of a middle-income country
Authors: Jafari Javad Javad , Karimi Moonaghi Hossein , Ahmady Soleiman , Zary Nabil , Masiello Italo
Published: January 2018

Background: Diabetes mellitus is increasing worldwide, especially in developing countries, as a consequence of urbanization. The use of the Internet and mobile service are increasing as well. The independent use of the Internet and mobile technologies by the patients could be a key step towards self-care management of the disease. Methods: A validated questionnaire with two parts was used and was completed by patients who came to two diabetic clinics for routine checkup. The first part consisted of 16 items collecting demographics information. The second part contained 26 items about the specific use of the Internet and mobile services to access information. Results: 407 questionnaires were completed. 108 (26,5 %) had routine access to Internet, of which 95,4 % had routine access to mobile services and 77,8 % were positive to the use of a Persian website for medical information. Yet, 55 % of respondents preferred to get information from TV, radio and educational courses. Conclusions: Data suggest that most diabetic patients who use the Internet in this study were willing to receive educational material by the Internet. However, many still prefer traditional means of information. Our future research is going to focus on early adopters.
Predicting cortical bone adaptation to axial loading in the mouse tibia
Authors: Pereira Andre F , Javaheri Behzad , Pitsillides Andrew , Shefelbine Sandra
Published: January 2018

The development of predictive mathematical models can contribute to a deeper understanding of the specific stages of bone mechanobiology and the process by which bone adapts to mechanical forces. The objective of this work was to predict, with spatial accuracy, cortical bone adaptation to mechanical load, in order to better understand the mechanical cues that might be driving adaptation. The axial tibial loading model was used to trigger cortical bone adaptation in C57BL/6 mice and provide relevant biological and biomechanical information. A method for mapping cortical thickness in the mouse tibia diaphysis was developed, allowing for a thorough spatial description of where bone adaptation occurs. Poroelastic finite-element (FE) models were used to determine the structural response of the tibia upon axial loading and interstitial fluid velocity as the mechanical stimulus. FE models were coupled with mechanobiological governing equations, which accounted for non-static loads and assumed that bone responds instantly to local mechanical cues in an on-off manner.
Development of a semi-defined medium for high cell density cultivation of Escherichia coli in shake flask culture system: Part 1
Authors: Ng Wenfa
Published: January 2018

Sufficient quantities of cells of consistent characteristics are needed for studying processes - at the population level and beyond - in many areas of applied microbiology research. Nevertheless, given the relatively low biomass yield of many commercial culture media in shake flasks, producing the requisite biomass by cell culture is generally the rate-limiting step. This work reports the formulation of a semi-defined medium that enabled aerobic high cell density cultivation of Escherichia coli DH5α (ATCC 53868) in shake flasks. The formulated medium (FM) comprises: a buffer system (K2HPO4: 12.54 g/L and KH2PO4: 2.31 g/L); vitamins and trace elements (yeast extract: 12.0 g/L); salts (NaCl: 5.0 g/L and MgSO4: 0.24 g/L); and carbon and nitrogen sources (D-Glucose: 6.0 g/L and NH4Cl: 1.5 g/L). Notable characteristics of this medium are: high buffer capacity (89 mM phosphate), 1:1 molar ratio between D-Glucose and NH4Cl, and yeast extract providing trace elements and a secondary source of carbon and nitrogen. Preliminary data revealed that an OD600nm of 9 was attained after 24 hours of cultivation at 37 oC – most probably fuelled by glucose and NH4Cl. At 48 hours, the OD600nm reached a maximal value of 11 with yeast extract providing the necessary nutrients for cell growth and biomass formation. The broth’s pH varied between 5.5 and 7.8 during cultivation. For comparison, the maximum OD600nm of E. coli grown in three commonly used complex media: Nutrient Broth, LB Lennox, and Tryptic Soy Broth (TSB) were 1.4, 3.2 and 9.2, respectively, under identical culture conditions. Finally, FM maintained the viability of a larger population for three days - compared to a population collapse observed in TSB after one day. Taken together, the present findings suggest that the formulated medium may find use as a high cell density aerobic growth medium for E. coli in shake flask.
Development of a semi-defined medium for high cell density cultivation of Escherichia coli in shake flask culture system: Part 1
Authors: Ng Wenfa
Published: January 2018

Sufficient quantities of cells of consistent characteristics are needed for studying processes - at the population level and beyond - in many areas of applied microbiology research. Nevertheless, given the relatively low biomass yield of many commercial culture media in shake flasks, producing the requisite biomass by cell culture is generally the rate-limiting step. This work reports the formulation of a semi-defined medium that enabled aerobic high cell density cultivation of Escherichia coli DH5α (ATCC 53868) in shake flasks. The formulated medium (FM) comprises: a buffer system (K2HPO4: 12.54 g/L and KH2PO4: 2.31 g/L); vitamins and trace elements (yeast extract: 12.0 g/L); salts (NaCl: 5.0 g/L and MgSO4: 0.24 g/L); and carbon and nitrogen sources (D-Glucose: 6.0 g/L and NH4Cl: 1.5 g/L). Notable characteristics of this medium are: high buffer capacity (89 mM phosphate), 1:1 molar ratio between D-Glucose and NH4Cl, and yeast extract providing trace elements and a secondary source of carbon and nitrogen. Preliminary data revealed that an OD600nm of 9 was attained after 24 hours of cultivation at 37 oC – most probably fuelled by glucose and NH4Cl. At 48 hours, the OD600nm reached a maximal value of 11 with yeast extract providing the necessary nutrients for cell growth and biomass formation. The broth’s pH varied between 5.5 and 7.8 during cultivation. For comparison, the maximum OD600nm of E. coli grown in three commonly used complex media: Nutrient Broth, LB Lennox, and Tryptic Soy Broth (TSB) were 1.4, 3.2 and 9.2, respectively, under identical culture conditions. Finally, FM maintained the viability of a larger population for three days - compared to a population collapse observed in TSB after one day. Taken together, the present findings suggest that the formulated medium may find use as a high cell density aerobic growth medium for E. coli in shake flask. Part 2 of this work describes improvements in medium performance - specifically, higher cell yield as well as a shorter diauxic lag phase and total culture period – achieved through a small reduction in D-Glucose and NH4Cl concentrations in the medium composition. A preprint of the work is available at https://peerj.com/preprints/117v1.
Non-native species in the vascular flora of highlands and mountains of Iceland
Authors: Wasowicz Pawel
Published: January 2018

The highlands and mountains of Iceland (defined here as areas located above 400 m a.s.l) are one of the largest remaining wilderness areas in Europe. The present study provides the first comprehensive and up-to-date data on non-native plant species from these wilderness areas. Overall, 16 non-native vascular plant specieswere detected, including 11 casuals and 5 naturalised taxa (1 invasive). Results showed that the central highlands are most vulnerable to non-native plant colonisation, while other mountain and highland areas in Iceland seem to be far less impacted by non-native plants. Clear hotspots of alien flora are evident, especially in popular tourist areas in the highlands and mountains such as hot springs, geothermal areas, mountain huts and shelters, as well as main roads and tracks. Temporal trends characterizing non-native plant colonization show that the process is still in its initial phase. This research suggests that human-mediated dispersal is the main driving force increasing the risk of invasion in Icelandic highlands and mountain areas.
Development of a semi-defined medium for high cell density cultivation of Escherichia coli in shake flasks: Part 2
Authors: Ng Wenfa , Ting Yen-Peng
Published: January 2018

The characteristics of the culture vessel determine, to a large extent, the type of growth medium suitable for use. For example, most growth media for high cell density cultivation are designed for expensive bioreactors operating either in continuous or fed-batch mode, where provision of additional nutrients and/or removal of metabolic waste products from the basal medium – comprising salts, buffer components and small amount of carbon and nitrogen sources - help increase biomass yield by maintaining culture conditions within the range conducive for growth. The inexpensive and ubiquitous shake flask, in contrast, is usually operated in batch mode and contains, at the outset, a comprehensive medium with all necessary nutrients for conversion into biomass, and also serves as a repository for secreted metabolites - some of which are detrimental for cell growth. Thus, designing medium for high cell density cultivation in shake flask is an optimization process with the aim to increase biomass formation while reducing toxic metabolite secretion. This preprint reports improvements to a previously reported semi-defined medium for high cell density aerobic cultivation of Escherichia coli DH5α (ATCC 53868) in shake flasks. Specifically, by reducing the concentrations of glucose (from 6.0 to 4.0 g/L) and ammonium chloride (from 1.5 to 1.0 g/L), the following improvements were obtained: a shorter diauxic lag phase (3 versus 5 hours); a higher maximal optical density (12.0 versus 11.0) in a shorter total culture period (27 versus 48 hours), and smaller pH variation during cultivation (6.0 to 7.6 versus 5.5 to 7.8). Similar to the earlier study, glucose and yeast extract served as principal carbon sources in separate growth phases for E. coli in the improved formulated medium (FMimproved). Specifically, an OD600nm of 6.6 was attained after 9 hours of growth on glucose at 37 oC. Following a lag phase of 3 hours, growth resumed on yeast extract and the OD600nm reached 12.0 after 27 hours. The broth’s pH decreased from 7.1 to 6.0 during the first growth phase, whereupon it gradually rose to 7.6 at the end of culture. A smaller pH decrease along with higher biomass yield in the first growth phase suggested that the lower glucose concentration in FMimproved might have prevented overflow metabolism - and associated negative effects on growth - thus, resulting in a shorter diauxic lag phase and total culture period. Collectively, increase in cell yield, as well as decrease in total culture time and a shorter diauxic lag phase arise from a small reduction in glucose concentration - which suggested that an optimum exist, beyond which occurrence of overflow metabolism would reduce cell yield and biomass formation.
A test of ecological and ethnolinguistic determinants of maize diversity in southern Mexico
Authors: Orozco-Ramírez Quetzalcóatl , Santacruz-Varela Amalio , Ross-Ibarra Jeffrey , Brush Stephen B
Published: January 2018

While prevailing theories of crop evolution suggest that crop diversity and cultural diversity should be linked, empirical evidence for such a link remains inconclusive. In particular, few studies have investigated such patterns on a local scale. Here, we address this issue by examining the determinants of maize diversity in a local region of high cultural and biological richness in Southern Mexico. We collected maize samples from Mixtec and Chatino villages at low and mid elevations. Although morphological traits show few patterns of population structure, we see clear genetic differentiation among villages, with ethnicity explaining a larger proportion of the differentiation than altitude. Consistent with an important role of ethnicity in patterning seed exchange, metapopulation model-based estimates of differentiation match the genetic data within village and ethnic group, but dramatically underestimate differentiation when all four villages are taken together. Our research provides insights about the importance of social origin in structuring maize diversity at the local scale.
Aggressiveness, reliable signaling and survival in a wild songbird
Authors: Akçay Çağlar , Campbell S. Elizabeth , Beecher Michael D.
Published: January 2018

The evolution and maintenance of honest or reliable signaling has been a major question in evolutionary biology. The question is especially puzzling for a particular class of signals used in aggressive interactions: threat signals. Here we report a study on song sparrows (Melospiza melodia) in which we assayed males with playbacks in their territories to quantify their aggressiveness (flights, and close proximity) and aggressive signaling levels (rates of soft song, a close range signal reliably predicting attack) and asked whether these traits affect individuals’ survival on territory. We found that the effect of aggressive signaling via soft song interacted with aggressive behaviors such that there was a negative correlational selection: among males with low aggression, those males that signaled at higher levels (over-signalers) had higher survival whereas among males with high aggression those that signaled at low levels (under-signalers) survived longer. In other words, males who deviate from reliable signaling have a survival advantage. These results, along with previous research that suggested most of the deviation from reliable signaling in this system is in the form of under-signaling (high aggression males signaling at low levels) pose a puzzle for future research on how this reliable signaling system is maintained.
Does contemporary premature feather loss among common tern chicks in Lake Ontario reflect persistent pollutants, enigmatic diseases or novel pathogens?
Authors: Arnold Jennifer M , Tyerman Donald J , Oswald Stephen
Published: January 2018

We observed premature feather loss (PFL) among common terns Sterna hirundo at a small colony in northern Lake Ontario, Canada in July 2014. This condition is characterized by affected chicks losing all their wing, tail, head and body feathers several weeks after hatching. Rarely observed in wild birds, to our knowledge PFL in terns has not been recorded since 1974 (despite the banding of tens of thousands of tern chicks across North America since then). In July 2014, we observed PFL in chicks at between 2 and 4 weeks of age. The extent of feather loss was more extreme than in previous reports but was not accompanied by other aberrant developmental or physical deformities. Complete feather loss occurred over a period of a few days but all affected chicks quickly began to grow replacement feathers and all but one most likely fledged 10-20 days after normal fledging age. Feather samples, both shed feathers and re-growing live feathers, were collected from both affected chicks and normal individuals. One subsequently dead PFL chick was collected. Samples are awaiting further analysis. There was striking temporal association between the onset of PFL and persistent strong southwesterly winds that caused extensive mixing of near-shore, surface water with cool, deep lake waters. To our current knowledge it seems most probable that the PFL we observed in 2014 was caused by pathogens (viruses, bacteria, algal toxins) welling up from these deep waters along the shoreline but a direct link has not yet been made. The re-emergence of PFL in common terns may indicate acute health risks for birds and other wildlife in the Lake Ontario region and may also have potential for human health risks.
Global drivers of species variation in mobilized point-occurrence information
Authors: Meyer Carsten , Jetz Walter , Guralnick Robert P , Fritz Susanne A , Kreft Holger
Published: January 2018

Despite the central role of species distributions in ecology and conservation, occurrence information remains geographically and taxonomically incomplete and biased. Numerous socio-economic and ecological drivers of uneven record collection and mobilization among species have been suggested, but the generality of their effects remains untested. We develop scale-independent metrics of range coverage and geographical record bias, and apply them to 2.8M point-occurrence records of 3,625 mammal species to evaluate 13 putative drivers of species-level variation in data availability. We find that data limitations are mainly linked to range size and shape, and the geography of socio-economic conditions. Surprisingly, species attributes related to detection and collection probabilities, such as body size or diurnality, are much weaker predictors of the amount and range coverage of available records. Our results highlight the need to prioritize range-restricted species and to address the key socio-economic drivers of data bias in data mobilization efforts and distribution modeling.
Astrocyte activation in the anterior cingulate cortex and altered glutamatergic gene expression during paclitaxel-induced neuropathic pain in mice
Authors: Masocha Willias
Published: January 2018

Spinal astrocyte activation contributes to the pathogenesis of paclitaxel-induced neuropathic pain (PINP) in animal models. We examined gene expression of glial fibrillary acidic protein (GFAP; an astrocyte marker), glutamate transporters and receptor subunits in the anterior cingulate cortex (ACC) by real time PCR at 7 days post first administration of paclitaxel, a time point when mice had developed thermal hyperalgesia. Changes in the ACC, an area in the brain involved in pain perception and modulation, might contribute to the pathophysiology of PINP. GFAP transcripts levels were elevated by more than fivefold in the ACC of paclitaxel-treated mice. The 6 glutamate transporters (GLAST, GLT-1 EAAC1, EAAT4, VGLUT-1 and VGLUT-2) quantified were not significantly altered by paclitaxel treatment. Of the 12 ionotropic glutamate receptor subunits transcripts analysed 6 (GLuA1, GLuA3, GLuK2, GLuK3, GLuK5 and GLuN1) were significantly up-regulated, whereas GLuA2, GLuK1, GLuK4, GLuN2A and GLuN2B were not significantly altered and GLuA4 was lowly expressed. Amongst the 8 metabotropic receptor subunits analysed only mGLuR 8 was significantly elevated. In conclusion, during PINP there is astrocyte activation, no change in glutamate transporter expression and differential up-regulation of glutamate receptor subunits in the ACC. Thus, targeting astrocyte activation and the glutamatergic system might be another therapeutic avenue for management of PINP.
Modulatory Interactions between the Default Mode Network and Task Positive Networks in Resting-State
Authors: Di Xin , Biswal Bharat B.
Published: January 2018

Communications between different brain systems are critical to support complex brain functions. Unlike generally high functional connectivity between brain regions from same system, functional connectivity between regions from different systems are more variable. In the present study, we examined whether the connectivity between different brain networks were modulated by other regions by using physiophysiological interaction (PPI) on resting-state functional magnetic resonance imaging data. Spatial independent component analysis was first conducted to identify the default mode network (DMN) and several task positive networks, including the salience, dorsal attention, left and right executive networks. PPI analysis was conducted between pairs of these networks to identify networks or regions that showed modulatory interactions with the two networks. Network-wise analysis revealed reciprocal modulatory interactions between the DMN, salience, and executive networks. Together with the anatomical properties of the salience network regions, the results suggest that the salience network may modulate the relationship between the DMN and executive networks. In addition, voxel-wise analysis demonstrated that the basal ganglia and thalamus positively interacted with the salience network and the dorsal attention network, and negatively interacted with the salience network and the DMN. The results demonstrated complex relationships among brain networks in resting-state, and suggested that between network communications of these networks may be modulated by some critical brain structures such as the salience network, basal ganglia, and thalamus.
Persistent and extreme outliers in causes of death by state, 1999-2013
Authors: Boscoe Francis P
Published: January 2018

In the United States, state-specific mortality rates that are high relative to national rates can result from legitimate reasons or from variability in coding practices. This paper identifies instances of state-specific mortality rates that were at least twice the national rate in each of three consecutive five-year periods (termed persistent outliers), along with rates that were at least five times the national rate in at least one five-year period (termed extreme outliers). The resulting set of 71 outliers, 12 of which appeared on both lists, illuminates mortality variations within the country, including some that are amenable to improvement either because they represent preventable causes of death or highlight weaknesses in coding techniques. Because the approach used here is based on relative rather than absolute mortality, it is not dominated by the most common causes of death such as heart disease and cancer.
Cancer as a script and possible implications on workings of genome
Authors: Khan Muhummadh
Published: January 2018

There is a need for an genomic theoretical framework which would allow for phenomena observed in cell and also explain evolution of cellular life. The search for a genomic explanation to cancer lead to the concept of the genomic script which extends its influence over the workings of genome of a normal cell too. This framework explains multiple phenomenon like the development of an embryo, differentiation of cells, and genomic workings of cancer. It also explains the evolution of unicellular and multicellular organisms. Yet it remains a simple construct; a perennial loop with adaptor loops constituting the genomic script.
The glow in trilobite eyes
Authors: Schoenemann Brigitte , Clarkson Euan N.K.
Published: January 2018

Trilobites are extinct marine arthropods that dominated the faunas of the Palaeozoic. They were equipped with highly differentiated compound eyes. By contrast with all other arthropods, the lenses of these compound eyes were of pure calcite. Calcite shows photoluminescence under short-waved light. Here we show the phenomenon that in trilobite eyes the lenses glow under black-light illumination (UVA 365nm). Any inhomogenous distribution of light patterns across the lattice of facets in their compound eye, which is caused by an non homogenous UV-pattern inside the environment, would give orientational information to the trilobite. While many modern arthropods developed specialised UV-photoreceptor cells, the blue greenish light of the UV-induced fluorescence in the optical systems of the trilobites works without such modifications. We propose a new specialised optical system, ~400 million years old which is unique in the animal realm, and may be a role model for present technical applications.
Collecting reliable clades using the Greedy Strict Consensus Merger
Authors: Fleischauer Markus , Böcker Sebastian
Published: January 2018

Supertree methods combine a set of phylogenetic trees into a single supertree. Similar to supermatrix methods, these methods provide a way to reconstruct larger parts of the Tree of Life, potentially evading the computational complexity of phylogenetic inference methods such as maximum likelihood. The supertree problem can be formalized in different ways, to cope with contradictory information in the input. Many supertree methods have been developed. Some of them solve NP-hard optimization problems like the well known Matrix Representation with Parsimony, others have polynomial worst-case running time but work in a greedy fashion (FlipCut). Both can profit from a set of clades that are already known to be part of the supertree. The Superfine approach shows how the Greedy Strict Consensus Merger (GSCM) can be used as preprocessing to find these clades. We introduce different scoring functions for the GSCM, a randomization, as well as a combination thereof to improve the GSCM to find more clades. This helps, in turn, to improve the resolution of the final supertree. We find this modifications to increase the number of true positive clades by 16% while decreasing the number of false positive clades by 3% compared to the currently used Overlap scoring.
Discrete time-cost tradeoff model for optimizing multi-mode construction project resource allocation
Authors: Nie Shuangshuang , Gao Jihong
Published: January 2018

The resource-constrained project scheduling problem has received broad attentions and was evolved into various sub-problems such as resource-constrained discrete time-cost tradeoff problem. The resource leveling problem was proposed to reduce the resource fluctuation and was always studied independently with RCPSP. This research proposed a new model which integrates the resource leveling problem and resource-constrained time-cost tradeoff problem. The evolutionary multi-objective optimization technique, strength Pareto evolutionary approach II (SPEA II) was applied to calculate the Pareto front of time and cost. The resource leveling measured by the metric, resource release/re-hiring, was converted to resource cost. The analysis of the time complexity of the model showed that the runtime of the algorithm was polynomial times of the number of activities. The results of case testing showed that the model was reasonably accurate in comparison with a proposed baseline model.
Screening level mixture risk assessment of pharmaceuticals in STP effluents
Authors: Backhaus Thomas , Karlsson Maja
Published: January 2018

We modeled the ecotoxicological risks of the pharmaceutical mixtures emitted into the environment from STP effluents. The classic mixture toxicity concept of Concentration Addition was used to calculate the total expect risk of the analytically determined mixtures, compare the expected impact of seven effluent streams and pinpoint the most sensitive group of species. Single substance-based assessments underestimate the actual risks from pharmaceutical mixtures often by more than a factor of 1 000 in several of the surveyed effluent streams, clearly indicating the need to take the joint presence of pharmaceuticals into consideration in order to provide an environmentally realistic assessment for a given water body. The mixture risk quotients regularly exceed 1, indicating a potential risk for the environment, depending on the specific environmental conditions, in particular the dilution in the recipient stream. The top 10 mixture components explain more than 95% of the mixture risk in all cases. A mixture toxicity assessment cannot go beyond the underlying single substance data. The lack of data on the chronic toxicity of most pharmaceuticals as well as the very few data available for in vivo fish toxicity has to be regarded as a major knowledge gap in this context. On the other hand, ignoring Independent Action or even using the sum of individual risk quotients as a rough approximation of Concentration Addition does not have a major impact on the final risk estimate.
Selection and sex-biased dispersal: the influence of philopatry on adaptive variation
Authors: Portnoy David S , Puritz Jonathan B , Hollenbeck Christopher M , Gelsleichter James , Chapman Demian , Gold John R
Published: January 2018

Sex-biased dispersal is expected to homogenize nuclear genetic variation relative to variation in genetic material inherited through the philopatric sex. When site fidelity occurs across a heterogeneous environment, local selective regimes may alter this pattern. We assessed spatial patterns of variation in nuclear-encoded, single nucleotide polymorphisms (SNPs) and sequences of the mitochondrial control region in bonnethead sharks (Sphyrna tiburo) collected, a species thought to exhibit female philopatry, from summer habitat used for gestation. Geographic patterns of mtDNA haplotypes and putatively neutral SNPs confirmed female philopatry and male-mediated gene flow along the northeastern coast of the Gulf of Mexico. A total of 30 outlier SNP loci were identified; alleles at over half of these loci exhibited signatures of latitude-associated selection. Our results indicate that in species with sex-biased dispersal, philopatry can facilitate sorting of locally adaptive variation, with the dispersing sex facilitating movement of potentially adaptive variation among locations and environments.
ProCS15: A DFT-based chemical shift predictor for backbone and C β atoms in proteins
Authors: Larsen Anders S , Bratholm Lars A , Christensen Anders S , Channir Maher Jan , Jensen Jan H.
Published: January 2018

We present ProCS15: A program that computes the isotropic chemical shielding values of backbone and C β atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural models of hydrogen-bonding. The ProCS15-predicted chemical shielding values are compared to experimentally measured chemical shifts for Ubiquitin and the third IgG-binding domain of Protein G through linear regression and yield RMSD values of up to 2.2, 0.7, and 4.8 ppm for carbon, hydrogen, and nitrogen atoms. These RMSD values are very similar to corresponding RMSD values computed using OPBE/6-31G(d,p) for the entire structure for each proteins. These maximum RMSD values can be reduced by using NMR-derived structural ensembles of Ubiquitin. For example, for the largest ensemble the largest RMSD values are 1.7, 0.5, and 3.5 ppm for carbon, hydrogen, and nitrogen. The corresponding RMSD values predicted by several empirical chemical shift predictors range between 0.7 - 1.1, 0.2 - 0.4, and 1.8 - 2.8 ppm for carbon, hydrogen, and nitrogen atoms, respectively.
A unifying theory to describe transmembrane transport derived from thermodynamic principles
Authors: Herrera-Valdez Marco A
Published: January 2018

Cells communicate with their environments using transmembrane molecular transport that is, in turn, mediated by proteins that facilitate diffusion (channels), or alternatively, translocate ions against the electrochemical gradient (pumps). Transmembrane transport has been modelled in many studies using many functional forms that were not always derived from the same assumptions. A generic formulation that describes transmembrane fluxes regard- less of whether they are mediated by pumps or open channels is presented here. The functional form of the flux was obtained from thermodynamic first principles. Further, taking a slightly different approach, the same generic formulation mentioned above can be obtained from the Nernst-Planck equation for the case of channel-mediated electrodiffusion. The generic formula can be regarded as the product of an amplitude term and a driving force term. The former captures the characteristics of the membrane-spanning protein mediating the transport and the latter is a non-linear function of the transmembrane concentrations of the ions. The generic formulation explicitly shows that the basal rate at which ions cross the membrane is the main difference between currents mediated by pumps and channels. Electrogenic transmembrane fluxes can be converted to currents to construct models of membrane excitability in which all the transmembrane currents have the same functional form. The applicability of the generic derivations presented here is illustrated with models of excitability for neurones and pacemaker cardiocytes.
A unifying theory to describe transmembrane transport derived from thermodynamic principles
Authors: Herrera-Valdez Marco A
Published: January 2018

A unifying theory of physiological transmembrane transport. Cellular homeostasis involves transmembrane molecular transport along, or against the (electro) chemical gradient of the molecules being transported. Such transport is typically mediated by membrane-spanning proteins that either carry the molecules across the membrane, or facilitate their (electro)diffusion. Transmembrane transport has been modelled in many studies using many functional forms that were not always derived from the same assump- tions. A generic formulation that describes transmembrane fluxes, mediated either by carrier proteins or by open channels, is presented here. The functional form of the flux was obtained from basic thermodynamic principles. The same generic formulation mentioned above can also be obtained from the Nernst-Planck equation for the case of channel-mediated electrodiffusion. The generic formulation can be regarded as the product of an amplitude term and a driving force term, both nonlinear functions of the transmembrane concentrations of the molecules being transported, and possibly the transmembrane potential. The former captures the characteristics of the membrane- spanning protein mediating the transport and the latter is a non-linear function of the transmembrane concentrations of the ions. The generic formulation explicitly shows that the basal rate at which ions cross the membrane is the main difference between currents mediated by pumps and channels. Electrogenic transmembrane fluxes can be converted to currents to construct models of membrane excitability in which all the transmembrane currents have the same functional form. The applicability of the generic derivations presented here is illustrated with models of excitability for neurones and pacemaker cardiocytes.
Generation of high order geometry representations in octree meshes
Authors: Klimach Harald G , Zudrop Jens , Roller Sabine P
Published: January 2018

A robust method to obtain high order approximations of material distributions from arbitrary surface descriptions is presented. The method is used in the context of mesh generation with an octree structure and the resulting mesh and material distribution is intended to be used in a discontinuous Galerkin solver. The method is described in detail, its properties are discussed and some results from applying it to various geometries is shown. Its implementation is available in our open-source mesh generator Seeder.
Modelling lake trophic state: A random forest approach
Authors: Hollister Jeffrey W , Milstead W. Bryan , Kreakie Betty J.
Published: January 2018

Productivity of lentic ecosystems is well studied and it is widely accepted that as nutrient inputs increase, productivity increases and lakes transition from lower trophic state (e.g. oligotrophic) to higher trophic states (e.g. eutrophic). These broad trophic state classifications are good predictors of ecosystem condition, services, and disservices (e.g. recreation, aesthetics, and harmful algal blooms). While the relationship between nutrients and trophic state provides reliable predictions, it requires in situ water quality data in order to parameterize the model. This limits the application of these models to lakes with existing and, more importantly, available water quality data. To address this, we take advantage of the availability of a large national lakes water quality database (i.e. the National Lakes Assessment), land use/land cover data, lake morphometry data, other universally available data, and apply data mining approaches to predict trophic state. Using this data and random forests, we first model chlorophyll a, then classify the resultant predictions into trophic states. The full model estimates chlorophyll a with both in situ and universally available data. The mean squared error and adjusted R2 of this model was 0.09 and 0.8, respectively. The second model uses universally available GIS data only. The mean squared error was 0.22 and the adjusted R2 was 0.48. The accuracy of the trophic state classifications derived from the chlorophyll a predictions were 69% for the full model and 49% for the “GIS only” model. Random forests extend the usefulness of the class predictions by providing prediction probabilities for each lake. This allows us to make trophic state predictions and also indicate the level of uncertainity around those predictions. For the full model, these predicted class probabilites ranged from 0.42 to 1. For the GIS only model, they ranged from 0.33 to 0.96. It is our conclusion that in situ data are required for better predictions, yet GIS and universally available data provide trophic state predictions, with estimated uncertainty, that still have the potential for a broad array of applications. The source code and data for this manuscript are available from https://github.com/USEPA/LakeTrophicModelling.
Aortic aneurysm in diabetic mice with renovascular hypertension
Authors: Kashyap Sonu , Engel Sean , Al-Saiegh Yousif , Wongjarupong Asarn , Grande Joseph P
Published: January 2018

Purpose. Type 2 diabetes is the leading cause of end stage renal disease in the United States. Atherosclerotic renal artery stenosis is commonly observed in diabetic patients and impacts the rate of renal and cardiovascular disease progression. We hypothesized that renal artery stenosis contributes to bilateral renal disease in diabetics. In our original study, we found that leptin-deficient diabetic (db/db) mice subjected to RAS developed severe and bilateral renal disease, with the contralateral (uncuffed) kidney showing features reminiscent of progressive diabetic nephropathy. In non-diabetic mice (WT), the cuffed kidney developed progressive atrophy, but the contralateral kidney showed minimal histopathologic alterations. In doing these studies, we observed increased sudden death in db/db mice with RAS, but not in WT mice with RAS. The objective of this study was to characterize the aortic and cardiac phenotype of db/db mice subjected to RAS. Methods. We developed a murine model of renal artery stenosis by placement of a polytetrafluoroethylene cuff on the right renal artery in db/db mice. We studied 109 WT and 95 db/db mice subjected to Renal artery stenosis (RAS) or sham surgery. Results. The mortality rate of db/db RAS mice was about 23.5%, whereas only 1.5% deaths were observed in WT RAS mice. Interestingly, 60% of mortality in the db/db mice occurred in the first two weeks following RAS surgery. Necropsy showed massive intrathoracic hemorrhage associated with aortic dissection. Aortas from db/db RAS mice showed more smooth muscle dropout, medial disruption, and hemorrhage than aortas from WT mice with RAS. Cardiac tissue from db/db RAS mice had more fibrosis than did cardiac tissue from WT RAS mice. Conclusions. Db/db mice subjected to RAS are prone to develop fatal aortic dissection, which is not observed in WT mice with RAS. The db/db RAS model provides the basis for future studies directed towards defining basic mechanisms underlying the interaction of hypertension and diabetes on the development of aortic lesions.
Multidimensional biases, gaps and uncertainties in global plant occurrence information
Authors: Meyer Carsten , Kreft Holger , Weigelt Patrick
Published: January 2018

Plants are a hyperdiverse clade that plays a key role in maintaining ecological and evolutionary processes as well as human livelihoods. Glaring biases, gaps, and uncertainties in plant occurrence information remain a central problem in ecology and conservation, but these limitations have never been assessed globally. In this synthesis, we propose a conceptual framework for analyzing information biases, gaps and uncertainties along taxonomic, geographical, and temporal dimensions and apply it to all c. 370,000 species of land plants. To this end, we integrated 120 million point-occurrence records with independent databases on plant taxonomy, distributions, and conservation status. We find that different data limitations are prevalent in each dimension. Different information metrics are largely uncorrelated, and filtering out specific limitations would usually lead to extreme trade-offs for other information metrics. In light of these multidimensional data limitations, we critically discuss prospects for global plant ecological and biogeographical research, monitoring and conservation, and outline critical next steps towards more effective information usage and mobilization. We provide an empirical baseline for evaluating and improving global floristic knowledge and our conceptual framework can be applied to the study of other hyperdiverse clades.
Emotion detection from Natural walking
Authors: Cui Liqing , Li Shun , Zhu Tingshao
Published: January 2018

Emotion identification aims to automatically determine person's affective state, which has immense potential value in action tendency, health care, psychological detection and human-computer(robot) interaction. In this paper, we propose a novel method of identifying emotion from natural walking. After obtaining the three-axis acceleration data of wrist and ankle recorded by smartphone, we run a sliding average filter with different window size w, then cut actual data into slices. We extract 114 features including time-domain, frequency domain, power and distribution features from each slice, then use principal component analysis (PCA) for feature selection. We train SVM, Decision Tree, Multilayerperception, Random Tree and Random Forest classification models, and compare the accuracy on datasets of wrist and ankle with respect to different w. The performance of emotion identification on acceleration data of ankle is better than wrist. Among them, SVM yields the best accuracy of 90.31% for anger vs.neutral, 89.76% for happy vs.neutral, and 87.10% for anger vs.happy. The model for identifying anger/neutral/happy yields the best accuracy of 85%- 78%-78%. The results show that it is capable of identifying personal emotional states through the gait of walking.
Analyzing Machupo virus-receptor binding by molecular dynamics simulations
Authors: Meyer Austin G , Sawyer Sara L , Ellington Andrew D , Wilke Claus O
Published: January 2018

In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein-­protein interactions. However, many commonly used methods to predict these effects perform poorly in important test cases. In particular, the effects of multiple mutations, non­alanine substitutions, and flexible loops are difficult to predict with available tools and protocols. We present here an existing method applied in a novel way to a new test case; we interrogate affinity differences resulting from mutations in a host-­virus protein-­protein interface. We use steered molecular dynamics (SMD) to computationally pull the machupo virus (MACV) spike glycoprotein (GP1) away from the human transferrin receptor (hTfR1). We then approximate affinity using the maximum applied force of separation and the area under the force-­versus-­distance curve. We find, even without the rigor and planning required for free energy calculations, that these quantities can provide novel biophysical insight into the GP1/hTfR1 interaction. First, with no prior knowledge of the system we can differentiate among wild type and mutant complexes. Moreover, we show that this simple SMD scheme correlates well with relative free energy differences computed via free energy perturbation. Second, although the static co-­crystal structure shows two large hydrogen-­bonding networks in the GP1/hTfR1 interface, our simulations indicate that one of them may not be important for tight binding. Third, one viral site known to be critical for infection may mark an important evolutionary suppressor site for infection-­resistant hTfR1 mutants. Finally, our approach provides a framework to compare the effects of multiple mutations, individually and jointly, on protein­ protein interactions.
Outline for an information theoretic search engine
Authors: Vanderwilt Koos
Published: January 2018

It is proposed an information theoretic search engine is like RADAR. The query words are the emitted signals and the document database is the object to be detected. Various echoes come off the database, and analogous with echo cancelation, the signal with the lowest entropy is selected. Commensurate with Shannon's theory, low entropy documents are signal, higher entropy documents are noise. Thus, my proposal separates signal from noise. As many relevant documents can be tined to be signal as desired.