bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractAmmonia (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.
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

AbstractHuman 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

AbstractThe 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

AbstractDisclosure 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

AbstractUntil 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&apos;, 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

AbstractMost 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

Abstract
*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

Abstract
*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

AbstractThe 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

AbstractRecent 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

AbstractPhenotypic 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

AbstractThis 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

AbstractThree-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

AbstractThe 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

AbstractPhotosynthesis 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

AbstractA 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

AbstractThe 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.