bluuebunny/crossref_metadata_2025 huggingface dataset:
American Constitutional Faith and the Politics of Hermeneutics
Authors: Lewis Andrew R. , Blake William D. , Mockabee Stephen T. , Friesen Amanda
Published: July 2019

As more debates in American politics become constitutional questions, effective citizens must engage in constitutional interpretation. While most Americans venerate the Constitution as a part of a national, civil religion, levels of constitutional knowledge are also very low. In this paper, we analyze how ordinary Americans approach the task of constitutional interpretation. An analysis of two cross-sectional surveys indicates constitutional hermeneutics are a product of political factors, religious affiliation, and biblical interpretive preferences. We also present the results of a survey experiment where the manipulation of a clergy's interpretation of a biblical passage affects how respondents interpret both scripture and the Constitution, providing a potential causal mechanism for learning how to engage in hermeneutics.
Glyphosate-based herbicide exposure during pregnancy and lactation malprograms the male reproductive morphofunction in F1 offspring
Authors: Teleken Jakeline Liara , Gomes Ellen Carolina Zawoski , Marmentini Carine , Moi Milara Bruna , Ribeiro Rosane Aparecida , Balbo Sandra Lucinei , Amorim Elaine Manoela Porto , Bonfleur Maria Lúcia
Published: July 2019

One of the most consumed pesticides in the world is glyphosate, the active ingredient in the herbicide ROUNDUP®. Studies demonstrate that glyphosate can act as an endocrine disruptor and that exposure to this substance at critical periods in the developmental period may program the fetus to induce reproductive damage in adulthood. Our hypothesis is that maternal exposure to glyphosate during pregnancy and lactation in mice will affect the development of male reproductive organs, impairing male fertility during adult life. Female mice consumed 0.5% glyphosate-ROUNDUP® in their drinking water [glyphosate-based herbicide (GBH) group] or filtered water [control (CTRL) group] from the fourth day of pregnancy until the end of the lactation period. Male F1 offspring were designated, according to their mother’s treatment, as CTRL-F1 and GBH-F1. Female mice that drank glyphosate displayed reduced body weight (BW) gain during gestation, but no alterations in litter size. Although GBH male F1 offspring did not exhibit modifications in BW, they demonstrated delayed testicular descent. Furthermore, at PND150, GBH-F1 mice presented a lower number of spermatozoa in the cauda epididymis and reduced epithelial height of the seminiferous epithelium. Notably, intratesticular testosterone concentrations were enhanced in GBH-F1 mice; we show that it is an effect associated with increased plasma and pituitary concentrations of luteinizing hormone. Therefore, data indicate that maternal exposure to glyphosate-ROUNDUP® during pregnancy and lactation may lead to decreased spermatogenesis and disruptions in hypothalamus–pituitary–testicular axis regulation in F1 offspring.
A Practical Method to Compensate for the Effect of Echo Spacing on the Shale NMRT2Spectrum
Authors: Ge Xinmin , Zhao Jier , Zhang Fengsheng , Fan Yiren , Liu Jianyu , Cai Jianchao , Nie Shengdong , Wang Changjiang
Published: July 2019

The low field nuclear magnetic resonance (NMR) technique is considered as one of the most effective methods to characterize the pore size and fluid distribution in geophysical prospecting. The signal of NMR is noninvasive and lithology independent, while the effect of NMR responses influenced by the echo spacing (TE) is significant when applied to unconventional reservoirs which are featured with ultralow porosity and pore radius.TEis expected to be as low as possible to ensure most of the hydrogen signals are accounted for, but it is hard to achieve in downhole NMR measurement. We develop a practical method to compensate for the influence ofTEon the transversal relaxation time (T2) spectrum of shale. Based on the experiments with differentTE, the relationship between the NMR calibrated porosity and theTEis established to recover the signal amplitude. The effect ofTEon the peak position is investigated, and then an empirical equation is constructed to move the peak position to its original state. By the above two‐step correction algorithm, theT2spectrums of shale at largeTEare compensated precisely. The proposed method provides an effective way to obtain the realT2spectrum and achieves good results in the downhole NMR data processing of shale reservoir.
Formation of Arctic Stratocumuli Through Atmospheric Radiative Cooling
Authors: Simpfendoerfer Lucien F. , Verlinde Johannes , Harrington Jerry Y. , Shupe Matthew D. , Chen Yao‐Sheng , Clothiaux Eugene E. , Golaz Jean‐Christophe
Published: July 2019

Stratocumulus clouds are important to the Arctic climate because they are prevalent and exert a strong radiative forcing on the surface. However, relatively little is known about how stratocumulus clouds form in the Arctic. In this study, radiative transfer calculations are used to show that the timescale over which stably stratified Arctic temperature and water vapor profiles cool to saturation is less than typical residence times for individual air parcels in the Arctic. This result is consistent with previous studies in suggesting that elevated stratocumulus can form naturally through clear‐sky radiative cooling during all seasons, without assistance from frontal lifting or other atmospheric forcing. Single column model simulations of the cloud formation process, after radiative cooling has resulted in saturation in a stably stratified profile, suggest that stratocumulus cloud properties are sensitive to the characteristics of the environment in which the formation process takes place. For example, sensitivity tests suggest that clouds may attain liquid water paths of over 50 g/m2 if they form in moist environments but may become locked in a low‐liquid water path quasi steady state or dissipate within hours if they form in dry environments. A potential consequence of these sensitivities is that when an Arctic stratocumulus layer forms by radiative cooling, it is more likely to become optically thick, optically thin, or dissipate than it is to obtain an intermediate optical thickness. This could help explain why the cloudy and radiatively clear atmospheric states are so prevalent across the Arctic.
Reply to Comment by Swtizer and Teodoro on “U.S. Urban Water Prices: Cheaper When Drier”
Authors: Luby Ian H. , Polasky Stephen , Swackhamer Deborah L.
Published: July 2019

Key Points

The Palmer Drought Severity Index (PDSI) is not an appropriate measure of water scarcity

Using our preferred metric, we find that water rates, both in terms of total bills and marginal prices, are cheaper where water is scarcer

Switzer and Teodoro have misinterpreted our Key Point 3; average prices can decline while marginal prices increase with greater water use
Evaluation of a Microwave Emissivity Module for Desert Regions With CMEM
Authors: Lange M. , de Rosnay P.
Published: July 2019

To overcome deficiencies of current state‐of‐the‐art L‐band microwave emission models a microwave emissivity parameterization for desert regions, as derived by Grody and Weng (2008) using dense media theory, has been implemented in European Centre for Medium‐Range Weather Forecasts' Community Microwave Emission Modeling platform (CMEM). Simulations of L‐Band brightness temperatures were conducted over Africa for 2013 using the default CMEM parameterization of the soil dielectric constant from Wang and Schmugge, and using the desert emissivity parameterization from Grody and Weng. Results are evaluated against Soil Moisture and Ocean Salinity mission data. The Grody and Weng parameterization shows clear improvements over dry soil in arid areas with reduced bias and root‐mean‐square deviations at both polarizations. However deficiencies for semi‐arid areas, where the bare soil model of Wang and Schmugge shows best results in rainy conditions, suggest that hybrid implementation combining soil dielectric and desert emissivity models should be investigated for global scale applications.
Characterizing Variations in Concentration Data Measured From Unknown Releases
Authors: Singh Sarvesh Kumar , Turbelin Grégory , Issartel Jean‐Pierre
Published: July 2019

The statistics of concentration data, measured during unknown atmospheric dispersion events, are not fully understood although they are required in modeling, assessment, uncertainty analysis, and information fusion. The concentrations measured over a field of monitoring network is regarded as a vector which contains both magnitude and direction. Traditional statistics (mean, standard deviations, etc.) based on magnitude of concentration data summarize data properties but are limited in characterizing variations in data and their modeling quality. Comparatively, directions are efficient in providing valuable information to address these issues. Here we propose a statistical framework which transforms concentration measurements into directions projected on a hypersphere and analyzes their orientation and distribution. The directional data measured in identical conditions are expected to be rotationally symmetric around its principal axis and follow Watson distribution. The clustering parameter of Watson distribution measures tightness of directional data and, thus, can measure indirectly variations in observed data. It is shown that the clustering parameter is able to summarize an overall variation in data and modeling quality of data in a dispersion trial. The study analyzes real data taken from continuous release experiments, called “Fusion Field Trials,” conducted at Dugway Proving Ground, Utah, United States.
An Integrated History of the Australian-Antarctic Basin
Authors: Cook Terri
Published: July 2019

The first basin-wide compilation of seismic and geologic data shows that both margins experienced similar sedimentation patterns prior to the onset of Antarctic glaciation.
Places to Celebrate Apollo 11’s Fiftieth Anniversary
Authors: Cartier Kimberly
Published: July 2019

Apollo 11’s golden anniversary is this weekend, but the celebration lasts all year long.
An Index to Better Estimate Tropical Cyclone Intensity Change in the Western North Pacific
Authors: Lee Woojeong , Kim Sung‐Hun , Chu Pao‐Shin , Moon Il‐Ju , Soloviev Alexander V.
Published: July 2019

A revised predictor called the net energy gain rate (NGR) is suggested by considering wind‐dependent drag coefficient based on the existing maximum potential intensity theory. A series of wind speed‐dependent NGR, known as NGR‐w, is calculated based on pretropical cyclone (TC) averaged ocean temperatures from the surface down to 120 m (at 10‐m intervals) to include the TC‐induced vertical mixing for 13 years (2004–2016) in the western North Pacific. It turns out that NGR50‐w (NGR‐w based on temperature averaged over top 50 m) has the highest correlation with 24‐hr TC intensity change compared with the commonly used sea surface temperature‐based intensification potential (POT), depth‐averaged temperature‐based POT (POTDAT), and constant drag coefficient in the NGR. To demonstrate the effectiveness of NGR50‐w, we designed and conducted experiments for training (2004–2014) and testing (2015–2016). The model with NGR50‐w shows greater skill than does the model with POTDAT or POT by reducing prediction errors by about 16%.
Vegetation Pattern and Terrestrial Carbon Variation in Past Warm and Cold Climates
Authors: Lu Zhengyao , Miller Paul A. , Zhang Qiong , Wårlind David , Nieradzik Lars , Sjolte Jesper , Li Qiang , Smith Benjamin
Published: July 2019

Understanding the transition of biosphere‐atmosphere carbon exchange between glacial and interglacial climates can constrain uncertainties in its future projections. Using an individual‐based dynamic vegetation model, we simulate vegetation distribution and terrestrial carbon cycling in past cold and warm climates and elucidate the forcing effects of temperature, precipitation, atmospheric CO2 concentration (pCO2), and landmass. Results are consistent with proxy reconstructions and reveal that the vegetation extent is mainly determined by temperature anomalies, especially in a cold climate, while precipitation forcing effects on global‐scale vegetation patterns are marginal. The pCO2 change controls the global carbon balance with the fertilization effect of higher pCO2 linking to higher vegetation coverage, an enhanced terrestrial carbon sink, and increased terrestrial carbon storage. Our results indicate carbon transfer from ocean and permafrost/peat to the biosphere and atmosphere and highlight the importance of forest expansion as a driver of terrestrial ecosystem carbon stock from cold to warm climates.
Currents Associated With Saturn's Intra‐D Ring Azimuthal Field Perturbations
Authors: Hunt G.J. , Cowley S.W.H. , Provan G. , Cao H. , Bunce E.J. , Dougherty M.K. , Southwood D.J.
Published: July 2019

During the final 22 full revolutions of the Cassini mission in 2017, the spacecraft passed at periapsis near the noon meridian through the gap between the inner edge of Saturn's D ring and the denser layers of the planet's atmosphere, revealing the presence of an unanticipated low‐latitude current system via the associated azimuthal perturbation field peaking typically at ~10–30 nT. Assuming approximate axisymmetry, here we use the field data to calculate the associated horizontal meridional currents flowing in the ionosphere at the feet of the field lines traversed, together with the exterior field‐aligned currents required by current continuity. We show that the ionospheric currents are typically~0.5–1.5 MA per radian of azimuth, similar to auroral region currents, while the field‐aligned current densities above the ionosphere are typically ~5–10 nA/m2, more than an order less than auroral values. The principal factor involved in this difference is the ionospheric areas into which the currents map. While around a third of passes exhibit unidirectional currents flowing northward in the ionosphere closing southward along exterior field lines, many passes also display layers of reversed northward field‐aligned current of comparable or larger magnitude in the region interior to the D ring, which may reverse sign again on the innermost field lines traversed. Overall, however, the currents generally show a high degree of north‐south conjugacy indicative of an interhemispheric system, certainly on the larger overall spatial scales involved, if less so for the smaller‐scale structures, possibly due to rapid temporal or local time variations.
Properties of Electron Phase Space Holes in the Lunar Plasma Environment
Authors: Malaspina David M. , Hutchinson Ian H.
Published: July 2019

The spatial distribution and amplitudes of electron phase space holes observed in the plasma environment near Earth's Moon are presented. When the Moon is in the solar wind, the overwhelming majority of holes in its vicinity occur in its wake, and we attribute them to an instability caused by distortion of the electron distribution by the wake, as predicted by theory. Approximately 30% of these wake holes are statistically correlated with observed magnetic discontinuities nearby, which implies that external effects can influence and trigger these wake instabilities, yet the wake is the determining factor. When the Moon is deep in the Earth's magnetotail, and no detectable lunar wake is present, the hole occurrence is greatly reduced and is distributed approximately homogeneously about the Moon, implicating a different production mechanism. Near the boundary of the magnetotail, homogeneously occurring holes are more frequent, showing that other instabilities associated with the magnetopause region are also active. These results demonstrate ways in which the Earth's Moon is a unique plasma physics laboratory where plasma wake physics and electron instabilities can be studied in detail.
Ambient Ammonia Concentrations Across New York State
Authors: Zhou Chuanlong , Zhou Hao , Holsen Thomas M. , Hopke Philip K. , Edgerton Eric S. , Schwab James J.
Published: July 2019

Ammonia (NH3) was monitored at four locations (two urban and two rural) across New York State from April 2016 to October 2017 using active and passive systems. The two rural sites were Pinnacle State Park (PIN) and the Village of Potsdam, and the two urban sites were the City of Rochester and Queens College in New York City. Active and passive concentrations were well correlated across all sites (r2 = 0.866), but the active systems measured 6.2% higher NH3 concentrations. The mean (±SD) NH3 concentrations measured using active systems in Queens College, City of Rochester, Village of Potsdam, and PIN were 3.22 ± 2.23, 2.84 ± 1.91, 1.29 ± 1.12, and 0.82 ± 0.64 ppb, respectively. Ambient NH3 concentrations varied with diel vehicular and seasonal agricultural activities. NH3 concentrations at the urban sites had lower seasonal variability than the rural sites. NH3 concentrations were generally related to regional and in‐state NH3 emissions although less regional influence was observed at the urban sites. Local NH3 source directions were identified using conditional bivariate probability function. The urban sites were affected by local NH3 sources such as vehicular emissions and urban population centers. Likely distant NH3 source locations affecting the four sites were identified using simplified quantitative transport bias analysis model. Rural sites were more highly affected by transported NH3. Midwestern and Atlantic were major NH3 source areas. NH3 emissions from the south of PIN were probably due to the use of diesel trucks and other diesel engines in the hydraulic fracturing industry in Pennsylvania near the New York State border.
A Thin Film Viscoplastic Theory for Calving Glaciers: Toward a Bound on the Calving Rate of Glaciers
Authors: Bassis J. N. , Ultee L.
Published: July 2019

Projections of the growth and demise of ice sheets and glaciers require physical models of the processes governing flow and fracture of ice. The flow of glacier ice has been treated using increasingly sophisticated models. By contrast, fracture, the process ultimately responsible for half of the mass lost from ice sheets through iceberg calving, is often included using ad hoc parameterizations. In this study we seek to bridge this gap by introducing a model where ice obeys a power law rheology appropriate for intact ice below a yield strength. Above the yield strength, we introduce a separate rheology appropriate for the flow of heavily fractured ice, where ice deformation occurs more readily along faults and fractures. We show that, provided the motion of fractured ice is sufficiently rapid compared to that of intact ice, the behavior of glaciers depends solely on the rheology of intact ice and the yield strength of ice and is insensitive to the precise rheology of fractured ice. Moreover, assuming that glacier ice is unyielded allows us to bound the long‐term average rate of terminus advance, providing a first principles estimate of rates of retreat associated with the marine ice cliff instability. We illustrate model behavior using idealized geometries and climate forcing and show that the model not only exhibits realistic patterns of advance and retreat but also has the potential to exhibit hysteresis. This hysteresis could provide an explanation for the sudden onset of rapid retreat observed in marine‐terminating glaciers.
Modelling Hepatic Endoderm Development: Highly Efficient Differentiation of Human Embryonic Stem Cells to Functional Hepatic Endoderm Requires ActivinA and Wnt3a Signalling.
Authors: Hay David , Fletcher Judy , Payne Catherine , Terrace John , Gallagher Ronald , Snoeys Jan , Black Jim , Wojtacha Davina , Samuel Kay , Hannoun Zara , Pryde Anne , Filippi Celine , Currie Ian , Forbes Stuart , Ross James , Newsome Philip , Iredale John
Published: July 2019

Human embryonic stem cells (hESCs) are a valuable source of pluripotential primary cells. However, their homogeneous cellular differentiation to specific cell types in vitro has proven difficult thus far. Wnt signalling has been shown to play important roles in coordinating development and we demonstrate that Wnt3a is differentially expressed at critical stages of human liver development in vivo. The essential role of Wnt3a in hepatocyte differentiation from hESCs is paralleled by our in vitro model, demonstrating the importance of a physiological approach to cellular differentiation. Our studies provide compelling evidence that Wnt3a signaling is important for coordinated hepato-cellular function in vitro and in vivo. In addition, we demonstrate Wnt3a facilitates clonal plating of hESCs capable of hepatic endoderm differentiation. These studies represent an important step forward toward the use of hESC-derived hepatocytes in biomedical applications and has opened the door to high through-put metabolic analysis of human liver function.
Interoperability With Moby 1.0 - It's Better Than Sharing Your Toothbrush!
Authors: Wilkinson Mark
Published: July 2019

The BioMoby project was initiated in 2001 from within the model organism database community. It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach. Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry API, and supporting Perl and Java code-bases. Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow. Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been instrumental to its deployment and use by a wide community of bioinformatics service providers. The standard, client software, and supporting code libraries are all freely available at http://www.biomoby.org/
Hypothetical Allotropes of Carbon Built from 1,4-Cyclohexadiene Rings
Authors: Bucknum Michael
Published: July 2019

Disclosure Document 337,466 filed with the U.S. Patent & Trademark Office on August 23, 1993 describes, for the first time in the published literature, certain hypothetical constructions known as 3-,4-connected networks built from 1,4-cyclohexadiene rings, as allotropes of carbon and binaries. These hypothetical structures include an allotrope of carbon of tetragonal symmetry (space group P4(2)/mmc) built entirely from 1,4-cyclohexadiene rings and called glitter, and an allotrope of carbon of orthorhombic symmetry (space group Pmmm) built entirely from 1,4-cyclohexadiene rings, as well, and given another name.
A novel class of endogenous shRNAs in human cells
Authors: Gu Tongjun , Yin James , Xu Yanwei , Dai ZhengHua , Qiu Zhengge , Feng Shenzhong , Yi Xiang , Jiang Ling , Zhang Hongjie
Published: July 2019

Until now it is still not clear how many types and amounts of small RNAs (sRNAs) exist in humans. Here we report the identification of 1258 distinct sRNAs derived from intronic regions of protein-coding genes in human with a new approach. These endogenous short hairpin RNAs (shRNAs) appear to be similar to exogenous shRNAs in structure, have a broad distribution in the stem length, and function as microRNAs (miRNAs), small interfering RNAs (siRNA) and/or piwi-interacting RNAs (piRNAs). Except for a few shRNAs, the majority of shRNAs are not phylogenetically conserved. They are differentially expressed in different cells and at diverse developmental stages. Overall, their expression levels are lower than miRNAs', but can be detected by quantitative real-time PCR and microarrays, implying that like other known sRNAs, this type of shRNAs should have important functions in modulating gene expression, and that they may exist in other genomic regions and many species.
The spread of antimalarial drug resistance: A mathematical model with practical implications for ACT drug policies
Authors: Pongtavornpinyo Wirichada , Yeung Shunmay , Hastings Ian , Dondorp Arjen , Day Nicholas , White Nicholas
Published: July 2019

Most malaria-endemic countries are implementing a change in antimalarial drug policy to artemisinin combination therapy (ACT). The impact of different drug choices and implementation strategies is uncertain. A comprehensive model was constructed incorporating important epidemiological and biological factors and used to illustrate the spread of resistance in low and high transmission settings. The model predicts robustly that in low transmission settings drug resistance spreads faster than in high transmission settings, and that in low transmission areas ACTs slows the spread of drug resistance to a partner drug, especially at high coverage rates. This effect decreases exponentially with increasing delay in deploying the ACT and decreasing rates of coverage. A major obstacle to achieving the benefits of high coverage is the current cost of the drugs. This argues strongly for a global subsidy to make ACTs generally available and affordable in endemic areas.
Motif analysis of amphioxus, lamprey and invertebrate estrogen receptors and amphioxus and human estrogen-related receptors: Towards a better understanding of estrogen receptor evolution
Authors: Baker Michael , Chandsawangbhuwana Charlie
Published: July 2019

*Background.*

The origins of steroid-dependent regulation of the vertebrate estrogen receptor (ER) are poorly understood. Genes with statistically significant sequence similarity to vertebrate ERs have been found in lamprey, a basal vertebrate, and amphioxus, a basal chordate. Motif analysis of these sequences provides an opportunity to investigate early events in the evolution of the ER.

*Results.*

We used artificial intelligence-based software to construct twelve motifs specific to the estrogen-binding domain of ER[alpha] and ER[beta] in land vertebrates and teleosts. We mapped these ER-specific motifs onto the sequences of lamprey, amphioxus, invertebrate and selected vertebrate ERs and amphioxus and human estrogen-related receptor (ERR). We find that lamprey ER contains eleven motifs common to ERs in the training set. In contrast, amphioxus ER contains only six motifs. Various invertebrate ERs contain either seven or eight motifs. Unexpectedly, human and amphioxus ERRs contain nine of the twelve motifs, despite extensive sequence divergence during the descent of chordate ERs and ERRs from a common ancestor. We mapped the twelve motifs onto a multiple alignment of human, lamprey and amphioxus ERs, which depicted residues in human ER[alpha] that are known to bind estradiol. There is excellent conservation of these key residues in lamprey ER and poor conservation in amphioxus ER. Out of seventeen residues on human ER[alpha] that bind estradiol, sixteen and six are identical in lamprey and amphioxus ER, respectively. A phylogenetic tree of ERs and ERRs reveals a long branch for amphioxus ER, which is in agreement with the low sequence and motif similarity between amphioxus ER and other ERs.

*Conclusions.*

There are significant differences between B. floridae ER and vertebrate ERs in the steroid-binding domain as measured by motif analysis and percent of amino acids that are known to stabilize estradiol in human ER[alpha]. This suggests that novel steroids regulate transcriptional activity of B. floridae ER. The absence in lamprey ER of motif 10, which maps to the c-terminus half of [alpha]-helix 9, may be important in recognition of novel estrogens, such as 15[alpha]-hydroxy-estradiol.
Motif analysis of amphioxus, lamprey and invertebrate estrogen receptors and amphioxus and human estrogen-related receptors: Towards a better understanding of estrogen receptor evolution
Authors: Baker Michael , Chandsawangbhuwana Charlie
Published: July 2019

*Background.*

The origins of steroid-dependent regulation of the vertebrate estrogen receptor (ER) are poorly understood. Genes with statistically significant sequence similarity to vertebrate ERs have been found in lamprey, a basal vertebrate, and amphioxus, a basal chordate. Motif analysis of these sequences provides an opportunity to investigate early events in the evolution of the ER.

*Results.*

We used artificial intelligence-based software to construct twelve motifs specific to the estrogen-binding domain of ER[alpha] and ER[beta] in land vertebrates and teleosts. We mapped these ER-specific motifs onto the sequences of lamprey, amphioxus, invertebrate and selected vertebrate ERs and amphioxus, Ciona and human estrogen-related receptor (ERR). We find that lamprey ER contains eleven motifs common to ERs in the training set. In contrast, amphioxus ER contains only six motifs. Various invertebrate ERs contain either six or seven motifs. Unexpectedly, human and amphioxus ERRs contain nine of the twelve motifs, despite extensive sequence divergence during the descent of chordate ERs and ERRs from a common ancestor. We mapped the twelve motifs onto a multiple alignment of human, lamprey and amphioxus ERs, which depicted residues in human ER[alpha] that are known to bind estradiol. There is excellent conservation of these key residues in lamprey ER and poor conservation in amphioxus ER. Out of seventeen residues on human ER[alpha] that bind estradiol, sixteen and six are identical in lamprey and amphioxus ER, respectively. A phylogenetic tree of ERs and ERRs reveals a long branch for amphioxus ER, which is in agreement with the low sequence and motif similarity between amphioxus ER and other ERs.

*Conclusions.*

There are significant differences between B. floridae ER and vertebrate ERs in the steroid-binding domain as measured by motif analysis and percent of amino acids that are known to stabilize estradiol in human ER[alpha]. The absence in lamprey ER of motif 10, which maps to the C-terminus half of [alpha]-helix 9, may be important in recognition of novel estrogens, such as 15[alpha]-hydroxy-estradiol.
Speciation of chilean Rhinocryptidae (Avian) based on their behaviour
Authors: Correa Rueda Alejandro , Mpodozis Jorge
Published: July 2019

The current classification of the chilean representatives of the passerine family Rhinocryptidae includes eight species. Three of them contain subspecies that don't exhibit clear differences. Moreover, differences among two lineages of Scytalopus genera and two species of Pteroptochos are cryptic. We propose a new methodology based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds. According to our results, we postulate that there is not a cut criteria to establish differences among three sister lineages of current classification. This way the methodology developed by us does not allow to establish divergence for a given common ancestor. Our methodology allows to establish comparison among previously determined phylogenetic lineages. Our results show how when integrating behaviour and ecological terms as biological traits next to morphological characters of the plumage, it allows us to conclude that there is decrease of the distances among sister lineages in the cluster tree.
Altered cholesterol ester cycle in ex vivo skin fibroblasts from Alzheimer patients
Authors: Pani Alessandra , Dessi Sandra , Diaz Giacomo , Abete Claudia , Mulas Claudia , Norfo Claudia , Putzolu Marirosa , Cannas Maria Dolores , Orru Christina Doriana , Mocali Alessandra , Cocco Pier Luigi , La Colla Paolo , Paoletti Francesco
Published: July 2019

Recent studies in both animal and cell models of Alzheimer's disease (AD) indicated that sub-cellular cholesterol distribution seems to regulate amyloid-beta (A[beta]) generation in the brain. In particular, cholesterol-esters (CE), rather than total cholesterol levels, appear directly correlated with A[beta] production. Here we observed that, similarly to brain cells, skin fibroblasts obtained from AD patients produce and accumulate more CE than skin fibroblasts from age-matched healthy controls do. AD fibroblasts also exhibited a 2 fold increase in the expression of ACAT1, in addition to lower levels of SREBP2, nCEH, Caveolin-1 and ABCA1 mRNA levels, all of which are involved in the CE cycle. HMGCoA-reductase and LDL-receptor mRNAs levels did not show statistically significant changes in AD, compared to non-AD, cells. Furthermore, although APP mRNA did not significantly vary, neprilysin (NEP), the most important enzyme in the proteolysis of A[beta], was expressed at very low levels in skin fibroblasts of sporadic AD patients. Our results contribute to the concept that AD may be the consequence of a basic and systemic defect in the CE cycle. Moreover, our results identify new possible targets for the diagnosis, prevention, and cure or, at least, amelioration of the symptoms of AD.
Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes
Authors: Choi Jung Kyoon , Hwang Sohyun , Kim Young-Joon
Published: July 2019

Phenotypic diversity and fidelity can be balanced by controlling stochastic molecular mechanisms. Epigenetic silencing is one that has a critical role in stress response. Here we show that in yeast, incomplete silencing increases stochastic noise in gene expression, probably owing to unstable chromatin structure. Telomere position effect is suggested as one mechanism. Expression diversity in a population achieved in this way may render a subset of cells to readily respond to various acute stresses. By contrast, strong silencing tends to suppress noisy expression of genes, in particular those involved in life cycle control. In this regime, chromatin may act as a noise filter for precisely regulated responses to environmental signals that induce huge phenotypic changes such as a cell fate transition. These results propose modulation of chromatin stability as an important determinant of environmental adaptation and cellular differentiation.
How could a natural catastrophe impact the ecology of a species? The Nicobar megapode and tsunami
Authors: Kuppusamy Sivakumar
Published: July 2019

This study on the impact of the 2004 tsunami on the Nicobar megapode Megapodius nicobariensis, endemic coastal living bird species in the Nicobar group of islands showed a significant decline (nearly 70%) in the number of individuals when compared to before tsunami populations (Paired sample test, t=2.061, df=14, p<0.05). The tsunami has also adversely influenced the nest-site selection of the megapodes. The post tsunami impact on this species is also expected to be severe, pushing the species into the category of "critically endangered".
3D computer modeling in micropalaeontology – Late Paleozoic conodonts and foraminifers as example
Authors: Zhuravlev Andrey , Vevel Yadviga
Published: July 2019

Three-dimension modeling of fossils is one of the branches of computer using in palaeontology. The branch has wide perspectives but it is hardly developed, especially in micropalaeontology. Proposed method of 3D modelling of microfossils demands no unique and expansive equipment and can be realized practically in any palaeontological laboratory. Lower accuracy of the models developed is not critical for most the fields of their utilization: for teaching purposes, construction of illustrated databases and virtual atlases, and for the display of microfossils to a general audience.
Covalently bound substrate at the regulatory site triggers allosteric enzyme activation
Authors: Kutter Steffen , Weiss Manfred , Wille Georg , Golbik Ralph , Spinka Michael , König Stephan
Published: July 2019

The mechanism by which the enzyme pyruvate decarboxylase from yeast is activated allosterically has been elucidated. A total of seven three-dimensional structures of the enzyme, of enzyme variants or of enzyme complexes form two yeast species (three of them reported here for the first time) provide detailed atomic resolution snapshots along the activation coordinate. The prime event is the covalent binding of the substrate pyruvate to the side chain of cysteine 221, thus forming a thiohemiketal. This reaction causes the shift of a neighbouring amino acid, which eventually leads to the rigidification of two otherwise flexible loops, where one of the loops provides two histidine residues necessary to complete the enzymatically competent active site architecture. The structural data are complemented and supported by kinetic investigations and binding studies and provide a consistent picture of the structural changes, which occur upon enzyme activation.
Incident light orientation lets C4 monocotyledonous leaves make light work differently
Authors: Soares Ana , Driscoll Simon , Pellny Till , Olmos Enrique , Arrabaça Maria , Foyer Christine
Published: July 2019

Photosynthesis is an important driver of ecosystem sustainability in the face of climate change. Monocotyledonous crop species with C4 photosynthesis such as maize (Zea mays L; corn) and sugar cane are crucial for future food security and biofuel crop requirements, while C4 pasture grasses such as Paspalum are central to natural ecosystems. The global demand for corn will exceed that for wheat and rice by 2020, making it the world's most important crop. Light-driven photosynthesis supports plant biomass production, but plants have also evolved safety valve mechanisms that attenuate the absorption of potentially lethal levels of excess light. The array of survival responses that enables leaves to evade photoinhibition is complex and involves chloroplast and leaf movement as well as the molecular rearrangements that facilitate thermal energy dissipation. Here we report a novel morphological mechanism that allows C4 monocotyledonous leaves to regulate photosynthesis independently on each surface with respect to incident light allowing better adaptation to water deficits and light stress. We show that under abaxial illumination as occurs when monocotyledonous leaves curl in response to water stress the stomata close and photosynthetic metabolism shuts down on the adaxial surface of C4 leaves but these parameters increase in function to the abaxial surface. We discuss how this regulation confers a survival advantage to the C4 relative to C3 leaves which are unable to regulate their dorso-ventral functions in relation to light.
Systemic similarity analysis of compatibility drug-induced multiple pathway patterns in vivo
Authors: Wang Zhong , Zhang Zhan-jun , Wang Yi , Cheng Yiyu , Tong Weida , Wang Yongyan
Published: July 2019

A major challenge in post-genomic research is to understand how physiological and pathological phenotypes arise from the networks of expressed genes and to develop powerful tools for translating the information exchanged between gene and the organ system networks. Although different expression modules may contribute independently to different phenotypes, it is difficult to interpret microarray experimental results at the level of single gene associations. The global effects and response pathways of small molecules in cells have been investigated, but the quantitative details of the activation mechanisms of multiple pathways in vivo are not well understood. Similar response networks indicate similar modes of action, and gene networks may appear to be similar despite differences in the behaviour of individual gene groups. Here we establish the method for assessing global effect spectra of the complex signaling forms using Global Similarity Index (GSI) in cosines vector included angle. Our approach provides quantitative multidimensional measures of genes expression profile based on drug-dependent phenotypic alteration in vivo. These results make a starting point for identifying relationships between GSI at the molecular level and a step toward phenotypic outcomes at a system level to predict action of unknown compounds and any combination therapy.
Less is more: rarity trumps quality in luxury markets
Authors: Gault Agnes , Meinard Yves , Courchamp Franck
Published: July 2019

The international market for luxury goods has almost doubled since 1990, with a worldwide increase of 10% annually. This trade is fuelled by a great deal of legally and illegally exploited wildlife species, putting enormous pressure on many of them, with potentially irreversible consequences. The dramatic decline of sturgeon populations exploited for their caviar, is a good example: all 27 species are threatened and the most coveted are on the verge of extinction. We aim to identify the mechanism responsible for the continued overexploitation of sturgeon species, despite caviar's ever-increasing price and the imminent loss of these species. Here, we demonstrate consumer preference for rarity over intrinsic quality: customers tasting two caviar samples more often chose the one they thought was rare, although both were identical. In a game theory model, we demonstrate that the most rational behaviour is to rush to consume rare species, even though this precipitates their extinction. We conclude that the human predisposition to place exaggerated value on rarity probably drives the entire market for luxury goods from reptile skins to exotic woods. Our findings suggest that allowing low levels of legal trade will exacerbate the arbitrary value of rare species and thereby stimulate demand. Only a total ban on trade from the wild (with very strict controls) combined with strong support for farmed equivalents will protect rare species.
Icebergs boost phytoplankton growth in the Southern Ocean
Authors: Schwarz Jill , Schodlok Michael
Published: July 2019

Icebergs which calve from the Antarctic ice shelves and drift in the Southern Ocean deliver fresh water, dust and minerogenic particles to the surface ocean along the iceberg's path. Each of these components may have an effect on growth conditions for phytoplankton, as might the mechanical effects of the iceberg keel disturbing the water. Although anecdotal evidence and small-scale surveys suggest that drifting icebergs increase local primary production, no large-scale studies have reported on this possibility in detail. A combination of satellite and automated iceberg tracking data presented here shows that the probability of increased surface phytoplankton biomass was two-fold higher in the wake of a tracked iceberg compared to background biomass fluctuations. Only during the month of February were the effects of icebergs on surface biomass likely to be negative. These results confirm icebergs as a factor affecting phytoplankton in the Southern Ocean and highlight the need for detailed process studies so that responses to future changes in the Antarctic ice sheets may be predicted.
Preincision Processing of Cyclobutane Pyrimidine Dimers in Escherichia coli
Authors: Paul Sunirmal , Hashimoto Mitsumasa , Bhanot Opinder , Kow Yoke , Tang Moon-shong
Published: July 2019

In both prokaryotes and eukaryotes cyclobutane pyrimidine dimers (CPD) formed by UV-irradiation are repaired mainly by the nucleotide excision repair (NER) pathway. Evidence has been presented that CPDs are repaired more rapidly and efficiently in vivo than when using purified NER components in vitro, and raises the possibility that CPD can be processed at the preincision stage before being removed by NER pathway. We investigated this hypothesis in E. coli cells and found that the phosphodiester bonds in CPDs are indeed incised (for the sake of simplicity we term this result as CPD*) in a time-dependent fashion in NER-proficient cells. This CPD preincision processing also occurs in NER-deficient uvrB- and uvrC-, but not in uvrA-mutant cells, and in endonuclease V (nfi) mutant cells. Introduction of the nfi mutation into wild type or uvrB-mutant cells results in disablement of CPD to CPD* conversion and enhances UV sensitization to the level of uvrA-mutant cells. We found that in a reconstituted in vitro system, that purified UvrA and Nfi are necessary but not sufficient to convert CPD to CPD*. A UvrC homologous protein, Cho, is also needed for this conversion. In addition, we found that Nfi does not bind to UV-irradiated DNA, suggesting that UvrA and Cho proteins may function as matchmakers for Nfi-CPD binding, which consequently results in the conversion of CPD to CPD*. We further demonstrated that CPD*, but not CPD, can allow efficient translesion bypass synthesis with accuracy. We thus have elucidated a new CPD preincision processing mechanism and genes involved in this process. The biological significance of these findings is discussed elsewhere (another manuscript in preparation).
Minimum Information about a Neuroscience Investigation (MINI) Electrophysiology
Authors: Gibson Frank , Overton Paul , Smulders Tom , Schultz Simon , Eglen Stephen , Ingram Colin , Panzeri Stefano , Bream Phil , Sernagor Evelyne , Cunningham Mark , Adams Christopher , Echtermeyer Christoph , Simonotto Jennifer , Kaiser Marcus , Swan Daniel , Fletcher Marty , Lord Phillip
Published: July 2019

This module represents the formalized opinion of the authors and the CARMEN consortium, which identifies the minimum information required to report the use of electrophysiology in a neuroscience study, for submission to the CARMEN system (www.carmen.org.uk).
Pancreas islets in metabolic signaling - focus on the β-cell
Authors: Suckale Jakob , Solimena Michele
Published: July 2019

Taken together the Islets of Langerhans form a nutrient sensing network spread throughout the pancreas. They are tightly connected to the source organ - the intestine - and the target organs - liver, muscle, and fat cells. The expression of a unique set of proteins enables [beta] cells, the most frequent islet cell type, to detect elevated blood glucose levels and secrete insulin accordingly. Neighbouring [beta]-cells achieve tighter regulation of glucose-induced insulin secretion by coordination through cell surface proteins. They also adjust their secretory pathway capacity and flow to avoid being damaged. The immediate reaction of the [beta] cell to nutrients is regulated by translational mechanisms, while longer term adaptations involve changes in transcription. Glucose increases protein synthesis in the [beta] cell overall and especially that of some secretory proteins including insulin. This effect may be mediated through recognition of RNA motifs in the untranslated regions of those messengers. Failure of essential molecular components of the nutrient sensing system due to mutation or weakness paired with cellular stress can lead to dysfunctions, which on a larger scale manifest as diseases like diabetes mellitus.
Requirement of RIZ1 for cancer prevention by methyl-balanced diet
Authors: Zhou Wenyun , Alonso Sergio , Takai Daisaku , Lu Shelly , Yamamoto Fumiichiro , Perucho Manuel , Huang Shi
Published: July 2019

The typical Western diet is not balanced in methyl nutrients that regulate the level of the methyl donor S-adenosylmethionine (SAM) and its derivative metabolite S-adenosylhomocysteine (SAH), which in turn may control the activity of certain methyltransferases. Feeding rodents with amino acid defined and methyl-imbalanced diet decreases hepatic SAM and causes liver cancers. RIZ1 (PRDM2 or KMT8) is a tumor suppressor and functions in transcriptional repression by methylating histone H3 lysine 9. Here we show that a methyl-balanced diet conferred additional survival benefits compared to a tumor-inducing methyl-imbalanced diet only in mice with wild type RIZ1 but not in mice deficient in RIZ1. While absence of RIZ1 was tumorigenic in mice fed the balanced diet, its presence did not prevent tumor formation in mice fed the imbalanced diet. Unlike most of its related enzymes, RIZ1 was upregulated by methyl-balanced diet. Methyl-balanced diet did not fully repress oncogenes such as c-Jun in the absence of RIZ1. The data identify RIZ1 as a critical target of methyl-balanced diet in cancer prevention. The molecular understanding of dietary carcinogenesis may help people make informed choices on diet, which may greatly reduce the incidence of cancer.