bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatio-temporal evolutionary analysis of the township enterprises of Beijing suburbs using computational intelligence assisted design framework
Authors: Chen Yi , Song Zhijun , Zhang Guangfeng , Majeed Muhammad Tariq , Li Yun 
Published: March 2018

AbstractTownship and village enterprises (TVEs) are market-oriented public enterprises under the purview of local governments based on townships and villages in the People’s Republic of China. TVEs have become a vibrant part of the Chinese economy following the significant expansion during the 1980s reform period. In the mid-2000s, TVEs became an integrated part of Chinese industry after the property rights transition. In this study, we examined the dynamic behaviours of TVEs in the near-inner-outer suburbs; we simulated these behaviours using computational intelligence aided design framework, which embedded the micro-genetic algorithm with variable populations (VPμGA). Specifically, we assume that conditions follow development, which includes industry scale, industry profit, employees and district development; we then utilise the VPμGA method to simulate the industrial structure and spatio-temporal evolution of the TVEs across seven industrial sectors and closely analyse the consequences of the transition. Our analysis results are consistent with actual observations, and a macro-level analysis showed that TVEs experienced defined scenarios. For Beijing, these scenarios are as follows: rapid development → chaotic development → steady development. The micro-level analysis showed that TVEs and labour have gradually formed a specific industry, a complex trend that evolved in both space and time. We determined the dynamic behaviours of the structures at micro-scales, meso-scales and macro-scales, clarifying the development of TVEs in the Beijing suburbs.
Precision medicine screening using whole-genome sequencing and advanced imaging to identify disease risk in adults
Authors: Perkins Bradley A. , Caskey C. Thomas , Brar Pamila , Dec Eric , Karow David S. , Kahn Andrew M. , Hou Ying-Chen Claire , Shah Naisha , Boeldt Debbie , Coughlin Erin , Hands Gabby , Lavrenko Victor , Yu James , Procko Andrea , Appis Julia , Dale Anders M. , Guo Lining , Jönsson Thomas J. , Wittmann Bryan M. , Bartha Istvan , Ramakrishnan Smriti , Bernal Axel , Brewer James B. , Brewerton Suzanne , Biggs William H. , Turpaz Yaron , Venter J. Craig 
Published: March 2018

Significance
Advances in technology are enabling evaluation for prevention and early detection of age-related chronic diseases associated with premature mortality, such as cancer and cardiovascular diseases. These diseases kill about one-third of men and one-quarter of women between the ages of 50 and 74 years old in the United States. We used whole-genome sequencing, advanced imaging, and other clinical testing to screen 209 active, symptom-free adults. We identified a broad set of complementary age-related chronic disease risks associated with premature mortality.
Directed nucleation and growth by balancing local supersaturation and substrate/nucleus lattice mismatch
Authors: Li L. , Fijneman A. J. , Kaandorp J. A. , Aizenberg J. , Noorduin W. L. 
Published: March 2018

Significance
The energy barrier for a classical heterogeneous crystal nucleation can be controlled by the energy contributions from the substrate/nucleus interface and local supersaturation. Exerting control over crystal growth thus requires modifying either one of these terms. We here introduce a strategy to modulate the contributions of both parameters simultaneously using substrates containing different crystal structures of calcium carbonate. Based on a theoretical analysis, we program both the positioning and growth direction of carbonate salts on preselected polymorphs. These findings may hold relevance for understanding, mimicking, and ultimately expanding upon nature’s mineralization strategies and for developing functional microscale materials.
Flexible egocentric and allocentric representations of heading signals in parietal cortex
Authors: Chen Xiaodong , DeAngelis Gregory C. , Angelaki Dora E. 
Published: March 2018

Significance
Body-centered (egocentric) and world-centered (allocentric) spatial reference frames are both important for spatial navigation. We have previously shown that vestibular heading signals, which are initially coded in a head-centered reference frame, are no longer head-centered in the ventral intraparietal (VIP) area, but instead are represented in either a body- or world-centered frame, as the two frames were not dissociated. Here, we report a flexible switching between egocentric and allocentric reference frames in a subpopulation of VIP neurons, depending on gaze strategy. Other VIP neurons continue to represent heading in a body-centered reference frame despite changes in gaze strategy. These findings suggest that the vestibular representation of heading in VIP is dynamic and may be modulated by task demands.
Ligand channel in pharmacologically stabilized rhodopsin
Authors: Mattle Daniel , Kuhn Bernd , Aebi Johannes , Bedoucha Marc , Kekilli Demet , Grozinger Nathalie , Alker Andre , Rudolph Markus G. , Schmid Georg , Schertler Gebhard F. X. , Hennig Michael , Standfuss Jörg , Dawson Roger J. P. 
Published: March 2018

Significance
A substantial number of known genetic disorders have their origin in mutations that cause misfolding or dysfunction of G protein-coupled receptors (GPCRs). Pharmacological chaperones can rescue such mutant receptors from the endoplasmic reticulum by stabilizing protein conformations that support trafficking into the target membrane. Rhodopsin-mediated retinitis pigmentosa is a misfolding disease that might be targeted by PCs. Here we present a structure-based drug design approach to identify nonretinal compounds that bind and stabilize the receptor. Surprisingly, selected hits induce a previously unknown conformation of the seven-transmembrane helix bundle. Our study thus provides a remarkable example for compound class discovery and for the adaptability of GPCRs to chemically diverse ligands.
Expansions, diversification, and interindividual copy number variations of AID/APOBEC family cytidine deaminase genes in lampreys
Authors: Holland Stephen J. , Berghuis Lesley M. , King Justin J. , Iyer Lakshminarayan M. , Sikora Katarzyna , Fifield Heather , Peter Sarah , Quinlan Emma M. , Sugahara Fumiaki , Shingate Prashant , Trancoso Inês , Iwanami Norimasa , Temereva Elena , Strohmeier Christine , Kuratani Shigeru , Venkatesh Byrappa , Evanno Guillaume , Aravind L. , Schorpp Michael , Larijani Mani , Boehm Thomas 
Published: March 2018

SignificanceCytidine deaminases of the AID/APOBEC family mutate the genetic material of pathogens or contribute to the generation and diversification of antibody repertoires in jawed vertebrates. In the extant jawless vertebrate, the lamprey, two members of the AID/APOBEC family are implicated in the somatic diversification of variable lymphocyte receptor (VLR) repertoires. We discovered an unexpected diversity of cytidine deaminase genes within and among lamprey species. The cytidine deaminases with features comparable to jawed vertebrate AID are always present, suggesting that they are involved in essential processes, such as VLR assembly. In contrast, other genes show a remarkable copy number variation, like the APOBEC3 genes in mammals. This suggests an unexpected similarity in functional deployment of AID/APOBEC cytidine deaminases across all vertebrates.
Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity
Authors: Krishnan Arunkumar , Iyer Lakshminarayan M. , Holland Stephen J. , Boehm Thomas , Aravind L. 
Published: March 2018

Significance
Mutagenic AID/APOBEC deaminases (AADs) are central to processes such as generation of antibody diversity and antiviral defense in vertebrates. Their presence and role outside vertebrates are poorly characterized. We report the discovery of several AADs, including some that are secreted, across diverse metazoan, dictyosteliid, and algal lineages. They appear to have emerged from an early transfer of an AAD from bacterial toxin systems, followed by extensive diversification into multiple eukaryotic clades, showing dramatic structural innovation, rapid divergence, gene loss, polymorphism, and lineage-specific expansions. We uncover evidence for their divergence in arms-race scenarios with viruses and genomic retroelements and show that AAD-based nucleic acid mutagenesis as a basis of immune defense is widespread across metazoa, slime molds, and algae.
The role of consolidation in learning context-dependent phonotactic patterns in speech and digital sequence production
Authors: Anderson Nathaniel D. , Dell Gary S. 
Published: March 2018

Significance
Language is among the most important things humans learn. It has long been debated about the extent to which language learning employs mechanisms that may not apply in nonlinguistic domains. The current work uses a metaanalysis to document an important property of how speakers learn novel simple and complex rules about how consonants and vowels form syllables: The simple rules are learned quickly, but the complex ones require a consolidation period before they influence behavior. It is then demonstrated that similar results are seen in the learning of sequential patterns of responses made with fingers and thumbs. Thus, an important property of language learning was demonstrated in a nonlinguistic domain, suggesting that some relevant learning mechanisms are domain-general.
Glucagon contributes to liver zonation
Authors: Cheng Xiping , Kim Sun Y. , Okamoto Haruka , Xin Yurong , Yancopoulos George D. , Murphy Andrew J. , Gromada Jesper 
Published: March 2018

SignificanceThe lobules are the functional units of the liver. They consist of 15–25 layers of hepatocytes with specialized metabolic functions and gene expression patterns relative to their position along the lobule, a phenomenon referred to as metabolic zonation. The Wnt/β-catenin pathway regulates hepatocyte function but how the zonation is controlled to meet the metabolic demands of the liver is unclear. Glucagon regulates hepatic function. We now demonstrate that glucagon contributes to liver zonation by interacting and opposing the actions of the Wnt/β-catenin pathway.
Identification of a queen and king recognition pheromone in the subterranean termite
Reticulitermes flavipes
Authors: Funaro Colin F. , Böröczky Katalin , Vargo Edward L. , Schal Coby 
Published: March 2018

Significance
Understanding the mechanisms that social insects use to communicate their individual status within the colony is vital to understanding the evolution of sociality. This study accomplishes this goal by identifying a royal-recognition pheromone in termites, as well as a king pheromone. Our behavioral assay defines royal-specific responses for one species of termites, which will foster future studies of termite behavior. This study also dates cuticular hydrocarbons as royal pheromones to the rise of termites ∼150 million years ago, suggesting that termites and social Hymenoptera convergently evolved the use of these ubiquitous compounds for communication. In conclusion, we have expanded our understanding of chemically mediated royal recognition in termites and helped to understand the evolution of insect societies.
Local growth rules can maintain metabolically efficient spatial structure throughout growth
Authors: Guo Yipei , Tikhonov Mikhail , Brenner Michael P. 
Published: March 2018

SignificanceIn many biological systems, efficient implementation of a multistep chemical reaction is achieved by an ordered spatial arrangement of individual reaction units. How can independently acting agents assemble into such a structure, and how much communication between them is required? We consider a model of a metabolically coupled multispecies bacterial colony and show that surprisingly simple threshold-based responses to local environment are sufficient to assemble a wide variety of structures. We also predict when additional signaling mechanisms between cells may be required.
Synthesis of reference compounds related to Chemical Weapons Convention for verification and drug development purposes – a Brazilian endeavour
Authors: Cavalcante S F A , de Paula R L , Kitagawa D A S , Barcellos M C , Simas A B C , Granjeiro J M 
Published: March 2018

Abstract
This paper deals with challenges that Brazilian Army Organic Synthesis Laboratory has been going through to access reference compounds related to the Chemical Weapons Convention in order to support verification analysis and for research of novel antidotes. Some synthetic procedures to produce the chemicals, as well as Quality Assurance issues and a brief introduction of international agreements banning chemical weapons are also presented.
Schistosomiasis Presenting as Recurring Sigmoid Volvulus in a Danish Man With an Inconspicuous Travel History—A Case Report
Authors: Krog Asger D , Axelsson Johanna M , Bondgaard Anna-Louise R , Kurtzhals Jørgen A 
Published: March 2018

Abstract
A healthy 72-year-old Danish male presenting with recurring sigmoid volvulus was found to be infested with Schistosoma mansoni. No other explanation for recurring volvulus was found. A travel history 12 years ago, which included bathing in the Botswana Okavango delta for 10 minutes, revealed the likely time and place of infection. To our knowledge, this is the first reported case of recurrent sigmoid volvulus and chronic intestinal schistosomiasis in a patient from a nonendemic area.
Evidence for sex microchromosomes in a species with temperature-influenced sex determination (Crotaphytus collaris)
Authors: Wiggins Jodie M. , Santoyo-Brito Enrique , Scales Jon B. , Fox Stanley F. 
Published: March 2018

AbstractThe characteristics of a species’ evolution can be powerfully influenced by its mode of sex determination and, indeed, sex determination mechanisms vary widely among eukaryotes. In non-avian reptiles, sex was long thought to be determined bimodally, either by temperature or genetics. Here we add to the growing evidence that sex determining mechanisms in reptiles fall along a continuum rather than existing as a mutually exclusive dichotomy. Using qPCR, we demonstrate that the lizard Crotaphytus collaris possesses sex-based gene dosage consistent with the presence of sex michrochromosomes, despite that extreme incubation temperatures can influence hatchling sex ratio. Our results suggest a temperature override that switches genotypic females to phenotypic males at high and low temperatures.
Multisensory expectations shape olfactory input to the brain
Authors: Czarnecki Lindsey A. , Moberly Andrew H. , Fast Cynthia D. , Turkel Daniel J. , McGann John P. 
Published: March 2018

SummaryThe mammalian brain interprets sensory input based on prior multisensory knowledge of the external world, but it is unknown how this knowledge influences neural processing in individual sensory modalities. We found that GABAergic periglomerular interneuron populations in the olfactory bulb endogenously respond not only to odors but also to visual, auditory, and somatosensory stimuli in waking (but not anesthetized) mice. When these stimuli predict future odors, they evoke enhanced interneuron activity during the time odor normally occurs. When expectations are violated by omitting an expected “warning tone” before an odor, odor presentation evokes a burst of interneuron activity. The resulting GABA release presynaptically suppresses neurotransmitter release from the axon terminals of olfactory sensory neurons, the cells that transduce odor in the nasal epithelium and communicate this information to the brain. Expectations, even those evoked by cues in other sensory modalities, can thus affect the very first neurons in the olfactory system.
Diverse RNA interference strategies in early-branching metazoans
Authors: Calcino Andrew D. , Fernandez-Valverde Selene L. , Taft Ryan J. , Degnan Bernard M. 
Published: March 2018

ABSTRACTBackgroundMicro RNAs (miRNAs) and piwi interacting RNAs (piRNAs), along with the more ancient eukaryotic endogenous small interfering RNAs (endo-siRNAs) constitute the principal components of the RNA interference (RNAi) repertoire of most animals. RNAi in non-bilaterians – sponges, ctenophores, placozoans and cnidarians - appears to be more diverse than that of bilaterians, and includes structurally variable miR-NAs in sponges, an enormous number of piRNAs in cnidarians and the absence of miRNAs in ctenophores and placozoans.ResultsHere we identify thousands of endo-siRNAs and piRNAs from the sponge Amphimedon queens-landica, the ctenophore Mnemiopsis leidyi and the cnidarian Nematostella vectensis using a computational approach that clusters mapped small RNA sequences and annotates each cluster based on the read length and relative abundance of the constituent reads. This approach was validated on 11 small RNA libraries in Drosophila melanogaster, demonstrating the successful annotation of RNAi associated loci with properties consistent with previous reports. In the non-bilaterians we uncover seven new miRNAs from Amphimedon and four from Nematostella as well as sub-populations of candidate cis-natural antisense transcript (cis-NAT) endo-siRNAs. In the ctenophore, the absence of miRNAs is confirmed and an abundance of endo-siRNAs is revealed. Analysis of putative piRNA structure suggests that conserved localised secondary structures in primary transcripts may be important for the production of mature piRNAs in Amphimedon and Nematostella, as is also the case for endo-siRNAs.ConclusionTogether, these findings suggest that the last common ancestor of animals did not have the entrained RNAi system that typifies bilaterians. Instead it appears that bilaterians, cnidarians, ctenophores and sponges express unique repertoires and combinations of miRNAs, piRNAs and endo-siRNAs.
Reproducible inference of transcription factor footprints in ATAC-seq and DNase-seq datasets via protocol-specific bias modeling
Authors: Karabacak Calviello Aslihan , Hirsekorn Antje , Wurmus Ricardo , Yusuf Dilmurat , Ohler Uwe 
Published: March 2018

ABSTRACTDNase-seq and ATAC-seq are broadly used methods to assay open chromatin regions genome-wide. The single nucleotide resolution of DNase-seq has been further exploited to infer transcription factor binding sites (TFBS) in regulatory regions via footprinting. Recent studies have demonstrated the sequence bias of DNase I and its adverse effects on footprinting efficiency. However, footprinting and the impact of sequence bias have not been extensively studied for ATAC-seq. Here, we undertake a systematic comparison of the two methods and show that a modification to the ATAC-seq protocol increases its yield and its agreement with DNase-seq data from the same cell line. We demonstrate that the two methods have distinct sequence biases and correct for these protocol-specific biases when performing footprinting. Despite differences in footprint shapes, the locations of the inferred footprints in ATAC-seq and DNase-seq are largely concordant. However, the protocol-specific sequence biases in conjunction with the sequence content of TFBSs impacts the discrimination of footprint from background, which leads to one method outperforming the other for some TFs. Finally, we address the depth required for reproducible identification of open chromatin regions and TF footprints.
Growth arrest in the active rare biosphere
Authors: Hausmann Bela , Pelikan Claus , Rattei Thomas , Loy Alexander , Pester Michael 
Published: March 2018

AbstractMicrobial diversity in the environment is mainly concealed within the rare biosphere, which is arbitrarily defined as all species with <0.1% relative abundance. While dormancy explains a low-abundance state very well, the cellular mechanisms leading to rare but active microorganisms are not clear. We used environmental systems biology to genomically and metabolically characterize a cosmopolitan sulfate reducer that is of low abundance but highly active in peat soil, where it contributes to counterbalance methane emissions. We obtained a 98%-complete genome of this low-abundance species, Candidatus Desulfosporosinus infrequens, by metagenomics. To test for environmentally relevant metabolic activity of Ca. D. infrequens, anoxic peat soil microcosms were incubated under diverse in situ-like conditions for 36 days and analyzed by metatranscriptomics. Compared to the no-substrate control, transcriptional activity of Ca. D. infrequens increased 56- to 188-fold in incubations with sulfate and acetate, propionate, lactate, or butyrate, revealing a versatile substrate use. Cellular activation was due to a significant overexpression of genes encoding ribosomal proteins, dissimilatory sulfate reduction, and carbon-degradation pathways, but not of genes encoding DNA or cell replication. We show for the first time that a rare biosphere member transcribes metabolic pathways relevant for carbon and sulfur cycling over prolonged time periods while being growth-arrested in its lag phase.SignificanceThe microbial rare biosphere represents the largest pool of biodiversity on Earth and constitutes, in sum of all its members, a considerable part of a habitat’s biomass. Dormancy or starvation are typically used to explain a low-abundance state. We show that low-abundance microorganisms can be highly metabolically active while being growth-arrested over prolonged time periods. We show that this is true for microbial keystone species, such as a cosmopolitan but low-abundance sulfate reducer in wetlands that is involved in counterbalancing greenhouse gas emission. Our results challenge the central dogmas “metabolic activity translates directly into growth” as well as “low abundance equals little ecosystem impact” and provide an important step forward in understanding rare biosphere members relevant for ecosystem functions.
Thy1transgenic mice expressing the red fluorescent calcium indicator jRGECO1a for neuronal population imagingin vivo
Authors: Dana Hod , Novak Ondrej , Guardado-Montesino Michael , Fransen James W. , Hu Amy , Borghuis Bart G. , Guo Caiying , Kim Douglas S. , Svoboda Karel 
Published: March 2018

AbstractCalcium imaging is commonly used to measure the neural activity of large groups of neurons in mice. Genetically encoded calcium indicators (GECIs) can be delivered for this purpose using non-invasive genetic methods. Compared to viral gene transfer, transgenic targeting of GECIs provides stable long-term expression and obviates the need for invasive viral injections. Transgenic mice expressing the green GECI GCaMP6 are already widely used. Here we present the generation and characterizarion of transgenic mice expressing the sensitive red GECI jRGECO1a, driven by theThy1promoter. Four transgenic lines with different expression patterns showed sufficiently high expression for cellularin vivoimaging. We used two-photon microscopy to characterize visual responses of individual neurons in the visual cortexin vivo. The signal-to-noise ratio in transgenic mice was comparable to, or better than, for mice transduced with adeno-associated virus. We also show thatThy1-jRGECO1a transgenic mice are useful for transcranial population imaging and functional mapping using widefield fluorescecnce microscopy. We also demonstrate imaging of visual responses in retinal ganglion cells.Thy1-jRGECO1a transgenic mice are therefore a useful addition to the toolbox for imaging activity in intact neural networks.