bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fast sintering of silver nanoparticle and flake layers by infrared module assistance in large area roll-to-roll gravure printing system
Authors: Park Janghoon , Kang Hyi Jae , Shin Kee-Hyun , Kang Hyunkyoo 
Published: October 2016

AbstractWe present fast sintering for silver (Ag) nanoparticle (NP) and flake layers printed using roll-to-roll (R2R) gravure printing. An infrared (IR) sintering module was applied to an R2R system to shorten the sintering duration of an R2R gravure-printed Ag layer. IR sintering of the conductive layer was improved by optimising the process condition. After printing of the Ag NP and Ag flake layers, additional IR sintering was performed in the R2R system. The lowest sheet resistance obtained in the Ag NP layer was 0.294 Ω/□, the distance between the substrate and lamp was 50-mm long, the IR lamp power was 500 W, and the sintering time was 5.4 s. The fastest sintering of 0.34 Ω/□ was achieved with 50-mm distance, 1,000-W IR lamp power, and 1.08-s sintering time. In the Ag flake layer, the lowest sheet resistance obtained was 0.288 Ω/□ with a 20-mm distance, 1,000-W IR lamp power, and 10.8-s sintering time. Meanwhile, the fastest sintering was obtained with a 3.83 Ω/□ sheet resistance, 20-mm distance, 1000-W IR lamp, and 1.08-s sintering time. Thus, the IR sintering module can easily be employed in an R2R system to obtain excellent layer sheet resistance.
Computational prediction shines light on type III secretion origins
Authors: Goldberg Tatyana , Rost Burkhard , Bromberg Yana 
Published: October 2016

AbstractType III secretion system is a key bacterial symbiosis and pathogenicity mechanism responsible for a variety of infectious diseases, ranging from food-borne illnesses to the bubonic plague. In many Gram-negative bacteria, the type III secretion system transports effector proteins into host cells, converting resources to bacterial advantage. Here we introduce a computational method that identifies type III effectors by combining homology-based inference with de novo predictions, reaching up to 3-fold higher performance than existing tools. Our work reveals that signals for recognition and transport of effectors are distributed over the entire protein sequence instead of being confined to the N-terminus, as was previously thought. Our scan of hundreds of prokaryotic genomes identified previously unknown effectors, suggesting that type III secretion may have evolved prior to the archaea/bacteria split. Crucially, our method performs well for short sequence fragments, facilitating evaluation of microbial communities and rapid identification of bacterial pathogenicity – no genome assembly required. pEffect and its data sets are available at http://services.bromberglab.org/peffect.
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
Authors: Hölzer Martin , Krähling Verena , Amman Fabian , Barth Emanuel , Bernhart Stephan H. , Carmelo Victor A. O. , Collatz Maximilian , Doose Gero , Eggenhofer Florian , Ewald Jan , Fallmann Jörg , Feldhahn Lasse M. , Fricke Markus , Gebauer Juliane , Gruber Andreas J. , Hufsky Franziska , Indrischek Henrike , Kanton Sabina , Linde Jörg , Mostajo Nelly , Ochsenreiter Roman , Riege Konstantin , Rivarola-Duarte Lorena , Sahyoun Abdullah H. , Saunders Sita J. , Seemann Stefan E. , Tanzer Andrea , Vogel Bertram , Wehner Stefanie , Wolfinger Michael T. , Backofen Rolf , Gorodkin Jan , Grosse Ivo , Hofacker Ivo , Hoffmann Steve , Kaleta Christoph , Stadler Peter F. , Becker Stephan , Marz Manja 
Published: October 2016

AbstractThe unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.
Intrinsic noise and deviations from criticality in Boolean gene-regulatory networks
Authors: Villegas Pablo , Ruiz-Franco José , Hidalgo Jorge , Muñoz Miguel A. 
Published: October 2016

AbstractGene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline between their ordered and disordered phases. Critical networks have been argued to lead to a number of functional advantages such as maximal dynamical range, maximal sensitivity to environmental changes, as well as to an excellent tradeoff between stability and flexibility. Here, we study the effect of noise within the context of Boolean networks trained to learn complex tasks under supervision. We verify that quasi-critical networks are the ones learning in the fastest possible way –even for asynchronous updating rules– and that the larger the task complexity the smaller the distance to criticality. On the other hand, when additional sources of intrinsic noise in the network states and/or in its wiring pattern are introduced, the optimally performing networks become clearly subcritical. These results suggest that in order to compensate for inherent stochasticity, regulatory and other type of biological networks might become subcritical rather than being critical, all the most if the task to be performed has limited complexity.
Antiestrogen Resistant Cell Lines Expressing Estrogen Receptor α Mutations Upregulate the Unfolded Protein Response and are Killed by BHPI
Authors: Mao Chengjian , Livezey Mara , Kim Ji Eun , Shapiro David J. 
Published: October 2016

AbstractOutgrowth of metastases expressing ERα mutations Y537S and D538G is common after endocrine therapy for estrogen receptor α (ERα) positive breast cancer. The effect of replacing wild type ERα in breast cancer cells with these mutations was unclear. We used the CRISPR-Cas9 genome editing system and homology directed repair to isolate and characterize 14 T47D cell lines in which ERαY537S or ERαD538G replace one or both wild-type ERα genes. In 2-dimensional, and in quantitative anchorage-independent 3-dimensional cell culture, ERαY537S and ERαD538G cells exhibited estrogen-independent growth. A progestin further increased their already substantial proliferation in micromolar 4-hydroxytamoxifen and fulvestrant/ICI 182,780 (ICI). Our recently described ERα biomodulator, BHPI, which hyperactivates the unfolded protein response (UPR), completely blocked proliferation. In ERαY537S and ERαD538G cells, estrogen-ERα target genes were constitutively active and partially antiestrogen resistant. The UPR marker sp-XBP1 was constitutively activated in ERαY537S cells and further induced by progesterone in both cell lines. UPR-regulated genes associated with tamoxifen resistance, including the oncogenic chaperone BiP/GRP78, were upregulated. ICI displayed a greater than 2 fold reduction in its ability to induce ERαY537S and ERαD538G degradation. Progestins, UPR activation and perhaps reduced ICI-stimulated ERα degradation likely contribute to antiestrogen resistance seen in ERαY537S and ERαD538G cells.
The phasor-FLIM fingerprints reveal shifts from OXPHOS to enhanced glycolysis in Huntington Disease
Authors: Sameni Sara , Syed Adeela , Marsh J. Lawrence , Digman Michelle A. 
Published: October 2016

AbstractHuntington disease (HD) is an autosomal neurodegenerative disorder caused by the expansion of Polyglutamine (polyQ) in exon 1 of the Huntingtin protein. Glutamine repeats below 36 are considered normal while repeats above 40 lead to HD. Impairment in energy metabolism is a common trend in Huntington pathogenesis; however, this effect is not fully understood. Here, we used the phasor approach and Fluorescence Lifetime Imaging Microscopy (FLIM) to measure changes between free and bound fractions of NADH as a indirect measure of metabolic alteration in living cells. Using Phasor-FLIM, pixel maps of metabolic alteration in HEK293 cell lines and in transgenic Drosophila expressing expanded and unexpanded polyQ HTT exon1 in the eye disc were developed. We found a significant shift towards increased free NADH, indicating an increased glycolytic state for cells and tissues expressing the expanded polyQ compared to unexpanded control. In the nucleus, a further lifetime shift occurs towards higher free NADH suggesting a possible synergism between metabolic dysfunction and transcriptional regulation. Our results indicate that metabolic dysfunction in HD shifts to increased glycolysis leading to oxidative stress and cell death. This powerful label free method can be used to screen native HD tissue samples and for potential drug screening.
Marangoni effect visualized in two-dimensions Optical tweezers for gas bubbles
Authors: Miniewicz A. , Bartkiewicz S. , Orlikowska H. , Dradrach K. 
Published: October 2016

AbstractIn the report we demonstrate how, using laser light, effectively trap gas bubbles and transport them through a liquid phase to a desired destination by shifting the laser beam position. The physics underlying the effect is complex but quite general as it comes from the limited to two-dimension, well-known, Marangoni effect. The experimental microscope-based system consists of a thin layer of liquid placed between two glass plates containing a dye dissolved in a solvent and a laser light beam that is strongly absorbed by the dye. This point-like heat source locally changes surface tension of nearby liquid-air interface. Because of temperature gradients a photo-triggered Marangoni flows are induced leading to self-amplification of the effect and formation of large-scale whirls. The interface is bending toward beam position allowing formation of a gas bubble upon suitable beam steering. Using various techniques (employing luminescent particles or liquid crystals), we visualize liquid flows propelled by the tangential to interface forces. This helped us to understand the physics of the phenomenon and analyze accompanying effects leading to gas bubble trapping. The manipulation of sessile droplets moving on the glass surface induced via controlled with laser light interface bending (i.e. “droplet catapult”) is demonstrated as well.
Zika virus infection during the period of maximal brain growth causes microcephaly and corticospinal neuron apoptosis in wild type mice
Authors: Huang Wen-Chin , Abraham Rachy , Shim Byoung-Shik , Choe Hyeryun , Page Damon T. 
Published: October 2016

AbstractZika virus (ZIKV) infection in pregnant women has been established as a cause of microcephaly in newborns. Here we test the hypothesis that neurodevelopmental stages when the brain is undergoing rapid growth are particularly vulnerable to the effects of ZIKV infection. We injected ZIKV intracranially into wild type C57BL/6 mice at two different time points: early postnatal development, when the brain is growing at its maximal rate, and at weaning, when the brain has largely reached adult size. Both time points showed widespread immunoreactivity for ZIKV and cleaved caspase 3 (CC3, a marker of apoptosis) throughout the brain. However, in early postnatal ZIKV injected mice, some brain areas and cell types display particularly large increases in apoptosis that we did not observe in older animals. Corticospinal pyramidal neurons, a cell type implicated in human microcephaly associated with ZIKV infection, are an example of one such cell type. Proliferating cells in the ventricular zone stem cell compartment are also depleted. These findings are consistent with the hypothesis that periods of rapid brain growth are especially susceptible to neurodevelopmental effects of ZIKV infection, and establish a valuable model to investigate mechanisms underlying neurodevelopmental effects of ZIKV infection and explore candidate therapeutics.
Islanding the power grid on the transmission level: less connections for more security
Authors: Mureddu Mario , Caldarelli Guido , Damiano Alfonso , Scala Antonio , Meyer-Ortmanns Hildegard 
Published: October 2016

AbstractIslanding is known as a management procedure of the power system that is implemented at the distribution level to preserve sensible loads from outages and to guarantee the continuity in electricity supply, when a high amount of distributed generation occurs. In this paper we study islanding on the level of the transmission grid and shall show that it is a suitable measure to enhance energy security and grid resilience. We consider the German and Italian transmission grids. We remove links either randomly to mimic random failure events, or according to a topological characteristic, their so-called betweenness centrality, to mimic an intentional attack and test whether the resulting fragments are self-sustainable. We test this option via the tool of optimized DC power flow equations. When transmission lines are removed according to their betweenness centrality, the resulting islands have a higher chance of being dynamically self-sustainable than for a random removal. Less connections may even increase the grid’s stability. These facts should be taken into account in the design of future power grids.
New interpretation of the Gran Dolina-TD6 bearing Homo antecessor deposits through sedimentological analysis
Authors: Campaña I. , Pérez-González A. , Benito-Calvo A. , Rosell J. , Blasco R. , de Castro J. M. Bermúdez , Carbonell E. , Arsuaga J. L. 
Published: October 2016

AbstractGran Dolina is a cavity infilled by at least 25 m of Pleistocene sediments. This sequence contains the TD6 stratigraphic unit, whose records include around 170 hominin bones that have allowed the definition of a new species, Homo antecessor. This fossil accumulation was studied as a single assemblage and interpreted as a succession of several human home bases. We propose a complete stratigraphic context and sedimentological interpretation for TD6, analyzing the relationships between the sedimentary facies, the clasts and archaeo-palaeontological remains. The TD6 unit has been divided into three sub-units and 13 layers. Nine sedimentary facies have been defined. Hominin remains appear related to three different sedimentary facies: debris flow facies, channel facies and floodplain facies. They show three kinds of distribution: first a group of scattered fossils, then a group with layers of fossils in fluvial facies, and third a group with a layer of fossils in mixed fluvial and gravity flow facies. The results of this work suggest that some of these hominin remains accumulated in the cave by geological processes, coming from the adjacent slope above the cave or the cave entry, as the palaeogeography and sedimentary characteristics of these allochthonous facies suggest.
Versatile members of the DNAJ family show Hsp70 dependent anti-aggregation activity on RING1 mutant parkin C289G
Authors: Kakkar Vaishali , Kuiper E. F. Elsiena , Pandey Abhinav , Braakman Ineke , Kampinga Harm H. 
Published: October 2016

AbstractParkinson’s disease is one of the most common neurodegenerative disorders and several mutations in different genes have been identified to contribute to the disease. A loss of function parkin RING1 domain mutant (C289G) is associated with autosomal-recessive juvenile-onset Parkinsonism (AR-JP) and displays altered solubility and sequesters into aggregates. Single overexpression of almost each individual member of the Hsp40 (DNAJ) family of chaperones efficiently reduces parkin C289G aggregation and requires interaction with and activity of endogenously expressed Hsp70 s. For DNAJB6 and DNAJB8, potent suppressors of aggregation of polyglutamine proteins for which they rely mainly on an S/T-rich region, it was found that the S/T-rich region was dispensable for suppression of parkin C289G aggregation. Our data implies that different disease-causing proteins pose different challenges to the protein homeostasis system and that DNAJB6 and DNAJB8 are highly versatile members of the DNAJ protein family with multiple partially non-overlapping modes of action with respect to handling disease-causing proteins, making them interesting potential therapeutic targets.
Computational identification of putative lincRNAs in mouse embryonic stem cell
Authors: Liu Hui , Lyu Jie , Liu Hongbo , Gao Yang , Guo Jing , He Hongjuan , Han Zhengbin , Zhang Yan , Wu Qiong 
Published: October 2016

AbstractAs the regulatory factors, lncRNAs play critical roles in embryonic stem cells. And lincRNAs are most widely studied lncRNAs, however, there might still might exist a large member of uncovered lncRNAs. In this study, we constructed the de novo assembly of transcriptome to detect 6,701 putative long intergenic non-coding transcripts (lincRNAs) expressed in mouse embryonic stem cells (ESCs), which might be incomplete with the lack coverage of 5′ ends assessed by CAGE peaks. Comparing the TSS proximal regions between the known lincRNAs and their closet protein coding transcripts, our results revealed that the lincRNA TSS proximal regions are associated with the characteristic genomic and epigenetic features. Subsequently, 1,293 lincRNAs were corrected at their 5′ ends using the putative lincRNA TSS regions predicted by the TSS proximal region prediction model based on genomic and epigenetic features. Finally, 43 putative lincRNAs were annotated by Gene Ontology terms. In conclusion, this work provides a novel catalog of mouse ESCs-expressed lincRNAs with the relatively complete transcript length, which might be useful for the investigation of transcriptional and post-transcriptional regulation of lincRNA in mouse ESCs and even mammalian development.
AML1/ETO accelerates cell migration and impairs cell-to-cell adhesion and homing of hematopoietic stem/progenitor cells
Authors: Saia Marco , Termanini Alberto , Rizzi Nicoletta , Mazza Massimiliano , Barbieri Elisa , Valli Debora , Ciana Paolo , Gruszka Alicja M. , Alcalay Myriam 
Published: October 2016

AbstractThe AML1/ETO fusion protein found in acute myeloid leukemias functions as a transcriptional regulator by recruiting co-repressor complexes to its DNA binding site. In order to extend the understanding of its role in preleukemia, we expressed AML1/ETO in a murine immortalized pluripotent hematopoietic stem/progenitor cell line, EML C1, and found that genes involved in functions such as cell-to-cell adhesion and cell motility were among the most significantly regulated as determined by RNA sequencing. In functional assays, AML1/ETO-expressing cells showed a decrease in adhesion to stromal cells, an increase of cell migration rate in vitro, and displayed an impairment in homing and engraftment in vivo upon transplantation into recipient mice. Our results suggest that AML1/ETO expression determines a more mobile and less adherent phenotype in preleukemic cells, therefore altering the interaction with the hematopoietic niche, potentially leading to the migration across the bone marrow barrier and to disease progression.
Moku virus; a new Iflavirus found in wasps, honey bees and Varroa
Authors: Mordecai Gideon J , Brettell Laura E , Pachori Purnima , Villalobos Ethel M. , Martin Stephen J , Jones Ian M , Schroeder Declan C 
Published: October 2016

AbstractThere is an increasing global trend of emerging infectious diseases (EIDs) affecting a wide range of species, including honey bees. The global epidemic of the single stranded RNA Deformed wing virus (DWV), driven by the spread of Varroa destructor has been well documented. However, DWV is just one of many insect RNA viruses which infect a wide range of hosts. Here we report the full genome sequence of a novel Iflavirus named Moku virus (MV), discovered in the social wasp Vespula pensylvanica collected in Hawaii. The novel genome is 10,056 nucleotides long and encodes a polyprotein of 3050 amino acids. Phylogenetic analysis showed that MV is most closely related to Slow bee paralysis virus (SBPV), which is highly virulent in honey bees but rarely detected. Worryingly, MV sequences were also detected in honey bees and Varroa from the same location, suggesting that MV can also infect other hymenopteran and Acari hosts.
A novel proposal of a simplified bacterial gene set and the neo-construction of a general minimized metabolic network
Authors: Ye Yuan-Nong , Ma Bin-Guang , Dong Chuan , Zhang Hong , Chen Ling-Ling , Guo Feng-Biao 
Published: October 2016

AbstractA minimal gene set (MGS) is critical for the assembly of a minimal artificial cell. We have developed a proposal of simplifying bacterial gene set to approximate a bacterial MGS by the following procedure. First, we base our simplified bacterial gene set (SBGS) on experimentally determined essential genes to ensure that the genes included in the SBGS are critical. Second, we introduced a half-retaining strategy to extract persistent essential genes to ensure stability. Third, we constructed a viable metabolic network to supplement SBGS. The proposed SBGS includes 327 genes and required 431 reactions. This report describes an SBGS that preserves both self-replication and self-maintenance systems. In the minimized metabolic network, we identified five novel hub metabolites and confirmed 20 known hubs. Highly essential genes were found to distribute the connecting metabolites into more reactions. Based on our SBGS, we expanded the pool of targets for designing broad-spectrum antibacterial drugs to reduce pathogen resistance. We also suggested a rough semi-de novo strategy to synthesize an artificial cell, with potential applications in industry.