bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deer antler stem cells are a novel type of cells that sustain full regeneration of a mammalian organ—deer antler
Authors: Wang Datao , Berg Debbie , Ba Hengxing , Sun Hongmei , Wang Zhen , Li Chunyi 
Published: June 2019

AbstractDeer antlers are extraordinary mammalian organs that can fully regenerate annually. Antler renewal is a stem cell-based epimorphic process and antler stem (AS) cells can initiate de novo generation of antlers in postnatal mammals. However, although being called stem cells, the AS cells have not been characterized at molecular level based on the stem cell criteria. Comprehensive characterization of the AS cells would undoubtedly help to decipher the mechanism underlying the full regeneration of deer antlers, the only case of stem cell-based epimorphic regeneration in mammals. In the present study, three types of AS cells (antlerogenic periosteal cells APCs, for initial pedicle and first antler formation; pedicle periosteal cells PPC, for annual antler regeneration; and reserve mesenchyme cells RMCs, for rapid antler growth), were isolated for comprehensive molecular characterization. A horn-growth-related gene, RXFP2, was found to be expressed only in AS cells lineages but not in the facial periosteal cells (FPCs, locates geographically in the vicinity of the APCs or PPCs), suggesting the RXFP2 might be a specific marker for the AS cell lineage in deer. Our results demonstrated that AS cells expressed classic MSC markers including surface markers CD73, CD90, CD105 and Stro-1. They also expressed some of the markers including Tert, Nestin, S100A4, nucleostemin and C-Myc, suggesting that they have some attributes of the ESCs. Microinjection of male APC into deer blastocysts resulted in one female foetus (110 days gestation) recovered with obvious pedicle primordia with both male and female genotype detected in the ovary. In conclusion, the AS cells should be defined as MSCs but with partial attributes of ESCs.
Bogoliubov waves and distant transport of magnon condensate at room temperature
Authors: Bozhko Dmytro A. , Kreil Alexander J. E. , Musiienko-Shmarova Halyna Yu. , Serga Alexander A. , Pomyalov Anna , L’vov Victor S. , Hillebrands Burkard 
Published: June 2019

AbstractA macroscopic collective motion of a Bose–Einstein condensate (BEC) is commonly associated with phenomena such as superconductivity and superfluidity, often generalised by the term supercurrent. Another type of motion of a quantum condensate is second sound—a wave of condensate’s parameters. Recently, we reported on the decay of a BEC of magnons caused by a supercurrent outflow of the BEC from the locally heated area of a room temperature magnetic film. Here, we present the observation of a macroscopic BEC transport mechanism related to the excitation of second sound. The condensed magnons, being propelled out of the heated area, form compact humps of BEC density, which propagate many hundreds of micrometers in the form of distinct second sound—Bogoliubov waves. This discovery advances the physics of quasiparticles and allows for the application of related transport phenomena for low-loss data transfer in magnon spintronics devices.
Disordered RNA chaperones can enhance nucleic acid folding via local charge screening
Authors: Holmstrom Erik D. , Liu Zhaowei , Nettels Daniel , Best Robert B. , Schuler Benjamin 
Published: June 2019

AbstractRNA chaperones are proteins that aid in the folding of nucleic acids, but remarkably, many of these proteins are intrinsically disordered. How can these proteins function without a well-defined three-dimensional structure? Here, we address this question by studying the hepatitis C virus core protein, a chaperone that promotes viral genome dimerization. Using single-molecule fluorescence spectroscopy, we find that this positively charged disordered protein facilitates the formation of compact nucleic acid conformations by acting as a flexible macromolecular counterion that locally screens repulsive electrostatic interactions with an efficiency equivalent to molar salt concentrations. The resulting compaction can bias unfolded nucleic acids towards folding, resulting in faster folding kinetics. This potentially widespread mechanism is supported by molecular simulations that rationalize the experimental findings by describing the chaperone as an unstructured polyelectrolyte.
Speaker-normalized sound representations in the human auditory cortex
Authors: Sjerps Matthias J. , Fox Neal P. , Johnson Keith , Chang Edward F. 
Published: June 2019

AbstractThe acoustic dimensions that distinguish speech sounds (like the vowel differences in “boot” and “boat”) also differentiate speakers’ voices. Therefore, listeners must normalize across speakers without losing linguistic information. Past behavioral work suggests an important role for auditory contrast enhancement in normalization: preceding context affects listeners’ perception of subsequent speech sounds. Here, using intracranial electrocorticography in humans, we investigate whether and how such context effects arise in auditory cortex. Participants identified speech sounds that were preceded by phrases from two different speakers whose voices differed along the same acoustic dimension as target words (the lowest resonance of the vocal tract). In every participant, target vowels evoke a speaker-dependent neural response that is consistent with the listener’s perception, and which follows from a contrast enhancement model. Auditory cortex processing thus displays a critical feature of normalization, allowing listeners to extract meaningful content from the voices of diverse speakers.
Impact of molecular quadrupole moments on the energy levels at organic heterojunctions
Authors: Schwarze Martin , Schellhammer Karl Sebastian , Ortstein Katrin , Benduhn Johannes , Gaul Christopher , Hinderhofer Alexander , Perdigón Toro Lorena , Scholz Reinhard , Kublitski Jonas , Roland Steffen , Lau Matthias , Poelking Carl , Andrienko Denis , Cuniberti Gianaurelio , Schreiber Frank , Neher Dieter , Vandewal Koen , Ortmann Frank , Leo Karl 
Published: June 2019

AbstractThe functionality of organic semiconductor devices crucially depends on molecular energies, namely the ionisation energy and the electron affinity. Ionisation energy and electron affinity values of thin films are, however, sensitive to film morphology and composition, making their prediction challenging. In a combined experimental and simulation study on zinc-phthalocyanine and its fluorinated derivatives, we show that changes in ionisation energy as a function of molecular orientation in neat films or mixing ratio in blends are proportional to the molecular quadrupole component along the π-π-stacking direction. We apply these findings to organic solar cells and demonstrate how the electrostatic interactions can be tuned to optimise the energy of the charge-transfer state at the donor−acceptor interface and the dissociation barrier for free charge carrier generation. The confirmation of the correlation between interfacial energies and quadrupole moments for other materials indicates its relevance for small molecules and polymers.
Replication termination without a replication fork trap
Authors: Galli Elisa , Ferat Jean-Luc , Desfontaines Jean-Michel , Val Marie-Eve , Skovgaard Ole , Barre François-Xavier , Possoz Christophe 
Published: June 2019

AbstractBacterial chromosomes harbour a unique origin of bidirectional replication, oriC. They are almost always circular, with replication terminating in a region diametrically opposite to oriC, the terminus. The oriC-terminus organisation is reflected by the orientation of the genes and by the disposition of DNA-binding protein motifs implicated in the coordination of chromosome replication and segregation with cell division. Correspondingly, the E. coli and B. subtilis model bacteria possess a replication fork trap system, Tus/ter and RTP/ter, respectively, which enforces replication termination in the terminus region. Here, we show that tus and rtp are restricted to four clades of bacteria, suggesting that tus was recently domesticated from a plasmid gene. We further demonstrate that there is no replication fork system in Vibrio cholerae, a bacterium closely related to E. coli. Marker frequency analysis showed that replication forks originating from ectopic origins were not blocked in the terminus region of either of the two V. cholerae chromosomes, but progressed normally until they encountered an opposite fork. As expected, termination synchrony of the two chromosomes is disrupted by these ectopic origins. Finally, we show that premature completion of the primary chromosome replication did not modify the choreography of segregation of its terminus region.
Co-subsistence of avian influenza virus subtypes of low and high pathogenicity in Bangladesh: Challenges for diagnosis, risk assessment and control
Authors: Parvin Rokshana , Begum Jahan Ara , Chowdhury Emadadul Haque , Islam Mohammed Rafiqul , Beer Martin , Harder Timm 
Published: June 2019

AbstractEndemic co-circulation of potentially zoonotic avian influenza viruses (AIV) of subtypes H5N1 and H9N2 (G1 lineage) in poultry in Bangladesh accelerated diversifying evolution. Two clinical samples from poultry obtained in 2016 yielded five different subtypes (highly pathogenic [HP] H5N1, HP H5N2, HP H7N1, HP H7N2, H9N2) and eight genotypes of AIV by plaque purification. H5 sequences grouped with clade 2.3.2.1a viruses while N1 was related to an older, preceding clade, 2.2.2. The internal genome segments of the plaque-purified viruses originated from clade 2.2.2 of H5N1 or from G1/H9N2 viruses. H9 and N2 segments clustered with contemporary H9N2 strains. In addition, HP H7 sequences were detected for the first time in samples and linked to Pakistani HP H7N3 viruses of 2003. The unexpected findings of mixtures of reassorted HP H5N1 and G1-like H9N2 viruses, which carry genome segments of older clades in association with the detection of HP H7 HA segments calls for confirmation of these results by targeted surveillance in the area of origin of the investigated samples. Hidden niches and obscured transmission pathways may exist that retain or re-introduce genome segments of older viruses or reassortants thereof which causes additional challenges for diagnosis, risk assessment and disease control.
Rapid evolutionary responses to insecticide resistance management interventions by the German cockroach (Blattella germanica L.)
Authors: Fardisi Mahsa , Gondhalekar Ameya D. , Ashbrook Aaron R. , Scharf Michael E. 
Published: June 2019

AbstractThe German cockroach (Blattella germanica L.) is a worldwide pest that lives exclusively in human environments. B. germanica threatens human health by producing asthma-triggering allergens, vectoring pathogenic/antibiotic-resistant microbes, and by contributing to unhealthy indoor environments. While insecticides are essential for reducing cockroach populations and improving health outcomes, insecticide resistance has been a consistent barrier to cockroach control since the 1950s. We conducted seminal field studies to compare three insecticide resistance intervention strategies for cockroaches and evaluated resistance evolution across multiple generations. Using pre-treatment resistance assessment to drive decisions, we found that single active ingredient (AI) treatments can successfully eliminate cockroaches if starting resistance levels are low. We further established that rotation treatments intuitively reduce selection pressure, and are effective when insecticides with no/low resistance are used. We also found that mixture products containing thiamethoxam + λ-cyhalothrin AIs were universally ineffective and highly repellent; and finally, evolution of cross-resistance among AIs is a significant, previously unrealized challenge.
Assessment of 213Bi-anti-EGFR MAb treatment efficacy in malignant cancer cells with [1-13C]pyruvate and [18F]FDG
Authors: Feuerecker Benedikt , Michalik Michael , Hundshammer Christian , Schwaiger Markus , Bruchertseifer Frank , Morgenstern Alfred , Seidl Christof 
Published: June 2019

AbstractEvaluation of response to therapy is among the key objectives of oncology. A new method to evaluate this response includes magnetic resonance spectroscopy (MRS) with hyperpolarized 13C-labelled metabolites, which holds promise to provide new insights in terms of both therapeutic efficacy and tumor cell metabolism. Human EJ28Luc urothelial carcinoma and LN18 glioma cells were treated with lethal activity concentrations of a 213Bi-anti-EGFR immunoconjugate. Treatment efficacy was controlled via analysis of DNA double-strand breaks (immunofluorescence γH2AX staining) and clonogenic survival of cells. To investigate changes in metabolism of treated cells vs controls we analyzed conversion of hyperpolarized [1-13C]pyruvate to [1-13C]lactate via MRS as well as viability of cells, lactate formation and lactate dehydrogenase activity in the cellular supernatants and [18F]FDG uptake in treated cells vs controls, respectively. Treatment of malignant cancer cells with 213Bi-anti-EGFR-MAb induced intense DNA double-strand breaks, resulting in cell death as monitored via clonogenic survival. Moreover, treatment of EJ28Luc bladder cancer cells resulted in decreased cell viability, [18F]FDG-uptake and an increased lactate export. In both EJ28Luc and LN18 carcinoma cells treatment with 213Bi-anti-EGFR-MAb triggered a significant increase in lactate/pyruvate ratios, as measured with hyperpolarized [1-13C]pyruvate. Treatment with 213Bi-anti-EGFR-MAb resulted in an effective induction of cell death in EJ28Luc and LN18 cells. Lactate/pyruvate ratios of hyperpolarized [1-13C]pyruvate proved to detect early treatment response effects, holding promise for future clinical applications in early therapy monitoring.
Effect of de novo transcriptome assembly on transcript quantification
Authors: Hsieh Ping-Han , Oyang Yen-Jen , Chen Chien-Yu 
Published: June 2019

AbstractCorrect quantification of transcript expression is essential to understand the functional elements in different physiological conditions. For the organisms without the reference transcriptome, de novo transcriptome assembly must be carried out prior to quantification. However, a large number of erroneous contigs produced by the assemblers might result in unreliable estimation. In this regard, this study investigates how assembly quality affects the performance of quantification based on de novo transcriptome assembly. We examined the over-extended and incomplete contigs, and demonstrated that assembly completeness has a strong impact on the estimation of contig abundance. Then we investigated the behavior of the quantifiers with respect to sequence ambiguity which might be originally presented in the transcriptome or accidentally produced by assemblers. The results suggested that the quantifiers often over-estimate the expression of family-collapse contigs and under-estimate the expression of duplicated contigs. For organisms without reference transcriptome, it remains challenging to detect the inaccurate estimation on family-collapse contigs. On the contrary, we observed that the situation of under-estimation on duplicated contigs can be warned through analyzing the read proportion of estimated abundance (RPEA) of contigs in the connected component inferenced by the quantifiers. In addition, we suggest that the estimated quantification results on the connected component level have better accuracy over sequence level quantification. The analytic results conducted in this study provides valuable insights for future development of transcriptome assembly and quantification.
Variable osteogenic performance of MC3T3-E1 subclones impacts their utility as models of osteoblast biology
Authors: Hwang Phillip W. , Horton Jason A. 
Published: June 2019

AbstractThe spontaneously immortalized murine calvarial cell line MC3T3-E1 and its derivative subclones are widely used models of osteoblast biology. Many investigators have reported conflicting data under seemingly similar experimental conditions, though the specific subclone studied is often not specified. The purpose of this study was to directly compare the commercially available MC3T3-E1 subclones 4, 14, and 24 in terms of responsiveness to osteogenic induction media and/or stimulation with rhPTH[1–34]. We assayed osteogenic gene expression, capacity to deposit and mineralize a collagenous matrix, and the expression and signaling function of PTH1R. Our data demonstrate that each subclone bears little functional resemblance to the others, or to primary calvarial osteoblasts. Specifically, whereas subclone 4 is responsive to PTH stimulation and capable of matrix mineralization, subclones 14 and 24 do not faithfully replicate these key aspects of osteoblast biology. Furthermore, little overlap was observed between the gene expression profile of subclone 4 and primary calvarial osteoblasts. Our experience working with these cell lines demonstrates that the MC3T3-E1 derived cell lines are imperfect models of osteoblast biology, and reinforce the importance of clearly articulating selection and reporting of research materials.
Effects of system response delays on elderly humans’ cognitive performance in a virtual training scenario
Authors: Wirzberger Maria , Schmidt René , Georgi Maria , Hardt Wolfram , Brunnett Guido , Rey Günter Daniel 
Published: June 2019

AbstractObserved influences of system response delay in spoken human-machine dialogues are rather ambiguous and mainly focus on perceived system quality. Studies that systematically inspect effects on cognitive performance are still lacking, and effects of individual characteristics are also often neglected. Building on benefits of cognitive training for decelerating cognitive decline, this Wizard-of-Oz study addresses both issues by testing 62 elderly participants in a dialogue-based memory training with a virtual agent. Participants acquired the method of loci with fading instructional guidance and applied it afterward to memorizing and recalling lists of German nouns. System response delays were randomly assigned, and training performance was included as potential mediator. Participants’ age, gender, and subscales of affinity for technology (enthusiasm, competence, positive and negative perception of technology) were inspected as potential moderators. The results indicated positive effects on recall performance with higher training performance, female gender, and less negative perception of technology. Additionally, memory retention and facets of affinity for technology moderated increasing system response delays. Participants also provided higher ratings in perceived system quality with higher enthusiasm for technology but reported increasing frustration with a more positive perception of technology. Potential explanations and implications for the design of spoken dialogue systems are discussed.
Genetic comparisons of fall armyworm populations from 11 countries spanning sub-Saharan Africa provide insights into strain composition and migratory behaviors
Authors: Nagoshi Rodney N. , Goergen Georg , Plessis Hannalene Du , van den Berg Johnnie , Meagher Robert 
Published: June 2019

AbstractThe recent discovery of fall armyworm (Spodoptera frugiperda, J.E. Smith) in Africa presents a significant threat to that continent’s food security. The species exhibits several traits in the Western Hemisphere that if transferred to Africa would significantly complicate control efforts. These include a broad host range, long-distance migratory behavior, and resistance to multiple pesticides that varies by regional population. Therefore, determining which fall armyworm subpopulations are present in Africa could have important implications for risk assessments and mitigation efforts. The current study is an extension of earlier surveys that together combine the collections from 11 nations to produce the first genetic description of fall armyworm populations spanning the sub-Saharan region. Comparisons of haplotype frequencies indicate significant differences between geographically distant populations. The haplotype profile from all locations continue to identify Florida and the Caribbean regions as the most likely Western Hemisphere origins of the African infestations. The current data confirm the uncertainty of fall armyworm strain identification in Africa by genetic methods, with the possibility discussed that the African infestation may represent a novel interstrain hybrid population of potentially uncertain behavioral characteristics.
A new analytical model for flow in acidized fractured-vuggy porous media
Authors: Lei Gang , Liao Qinzhuo , Zhang Dongxiao 
Published: June 2019

AbstractAcidizing is one of the widely used technologies that makes the development of naturally fractured-vuggy reservoirs effective. During the process of acidizing, carbonate minerals are dissolved by hydrochloric acid, which can create high conductivity channels and wormholes to connect fractures and pores. In this work, a new analytical model, incorporating the heterogeneity of the pore networks into acidizing region, is proposed to study the flow characteristics in acidized fractured-vuggy reservoirs. The model is coupled by an acidized inner region and a conceptualized outer region of common triple medium. The porosity and permeability of inner region, which are rather heterogeneous and disordered when observed at different length scales, can be well addressed by fractal theory. The properties of the outer region can be described with three basic parameters: the matrix block size LM, the space interval of fracture LF and the radius of the vug Lv. Results show that the flow characteristic curves can be characterized by six flow stages (i.e. wellbore storage stage, radial flow stage in the interior region, fracture-vug inter-porosity flow stage, transition flow stage, fracture-matrix inter-porosity flow stage and external boundary response stage). It can be applied to estimate reservoir parameters for uncertainty reduction using inverse modeling.
Development of a rapid, simple and efficient one-pot cloning method for a reverse genetics system of broad subtypes of influenza A virus
Authors: Choi Won-Suk , Jeong Ju Hwan , Lloren Khristine Kaith S. , Ahn Su Jeong , Antigua Khristine Joy C. , Kim Young-il , Si Young-Jae , Baek Yun Hee , Choi Young Ki , Song Min-Suk 
Published: June 2019

AbstractThe reverse genetics (RG) system of influenza A viruses is well established. However, the conventional sequence-dependent method for cloning influenza genome segments is time-consuming and requires multiple processes (eg. enzyme digestion and ligation) and exhibits low cloning efficiency compared to the sequence-independent cloning method. In this study, we improved influenza genome cloning into the pHW2000 vector for an RG system by incorporating a sequence-independent circular polymerase extension cloning (CPEC) approach which requires only 2 steps (reverse transcription and one-pot CPEC-PCR) and takes about 4 hours before the transformation. The specifically designed viral gene and vector primers used for CPEC-PCR have improved cloning efficiency ranging from 63.6 to 100% based on the results of gene-specific colony PCR which was additionally confirmed by enzyme digestion. We successfully cloned all genes from broad subtypes of influenza A viruses (H1-H12, N1-N9) and rescued by the RG system. Our results demonstrate that this method—one-Pot cloning for influenza A virus—was efficient in terms of required time and cloning rate. In conclusion, the novel cloning method for influenza A virus will contribute to a significant reduction in the time required for genetic studies of emerging influenza viruses.