bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biogeography of the Caribbean Cyrtognatha spiders
Authors: Čandek Klemen , Agnarsson Ingi , Binford Greta J. , Kuntner Matjaž 
Published: January 2019

AbstractIsland systems provide excellent arenas to test evolutionary hypotheses pertaining to gene flow and diversification of dispersal-limited organisms. Here we focus on an orbweaver spider genusCyrtognatha(Tetragnathidae) from the Caribbean, with the aims to reconstruct its evolutionary history, examine its biogeographic history in the archipelago, and to estimate the timing and route of Caribbean colonization. Specifically, we test ifCyrtognathabiogeographic history is consistent with an ancient vicariant scenario (the GAARlandia landbridge hypothesis) or overwater dispersal. We reconstructed a species level phylogeny based on one mitochondrial (COI) and one nuclear (28S) marker. We then used this topology to constrain a time-calibrated mtDNA phylogeny, for subsequent biogeographical analyses in BioGeoBEARS of over 100 originally sampledCyrtognathaindividuals, using models with and without a founder event parameter. Our results suggest a radiation of CaribbeanCyrtognatha, containing 11 to 14 species that are exclusively single island endemics. Although biogeographic reconstructions cannot refute a vicariant origin of the Caribbean clade, possibly an artifact of sparse outgroup availability, they indicate timing of colonization that is much too recent for GAARlandia to have played a role. Instead, an overwater colonization to the Caribbean in mid-Miocene better explains the data. From Hispaniola,Cyrtognathasubsequently dispersed to, and diversified on, the other islands of the Greater, and Lesser Antilles. Within the constraints of our island system and data, a model that omits the founder event parameter from biogeographic analysis is less suitable than the equivalent model with a founder event.
Habitat management as a safe and effective approach for improving yield and quality of tea (Camellia sinensis) leaves
Authors: Li Jianlong , Zhou Ying , Zhou Bo , Tang Hao , Chen Yiyong , Qiao Xiaoyan , Tang Jinchi 
Published: January 2019

AbstractTea (Camellia sinensis) leaves are used to make the most widely consumed beverage globally after water. Therefore, the safety and quality of raw tea leaves are important indices for making tea and related products. Habitat management has been widely used as an environmentally friendly method to control pests in agroecosystems. To investigate the impact of habitat management on tea plantation ecosystems, a habitat management approach with intercropping was established. The function of habitat management on pest control was evaluated. Furthermore, metabolome and transcriptome analysis were applied to assay changes in quality-related metabolites. The habitat management approach was found to maintain arthropod biodiversity and develop natural arthropod enemies in the tea plantation. Therefore, the yield of the habitat management-treated tea plantation was increased. Metabolome analysis showed that epigallocatechin-3-gallate, the major catechin in tea leaves, has a significantly increased content in leaves of tea plants under habitat management compared with those in the control tea plantation. The content of L-theanine, the major amino acid in tea leaves, was not significantly changed in tea plants under habitat management. Furthermore, aroma compounds were more abundant in tea leaves from the habitat management-treated tea plantation than those from the chemical pesticide-treated tea plantation. Therefore, habitat management is reported for the first time as a safe and effective approach to improving the yield and quality of tea leaves.
Enhancement of superconducting properties and flux pinning mechanism on Cr0.0005NbSe2 single crystal under Hydrostatic pressure
Authors: Arumugam S. , Krishnan Manikandan , Ishigaki Kent , Gouchi Jun , Pervin Rukshana , Selvan G. Kalai , Shirage Parasharam M. , Uwatoko Y. 
Published: January 2019

AbstractSuperconducting properties of Cr0.0005NbSe2 (Tc~6.64 K) single crystals have been investigated through the temperature dependent resistivity (~8 GPa) and DC magnetization (~1 GPa) measurements. Further, the critical current density (Jc) as a function of applied magnetic field has been studied from magnetic isotherms. The vortex pinning mechanisms have also been systematically analyzed using weak collective pinning theory as a function of pressure. The Jc corresponds to the flux flow enhanced by the application of pressure due to increase of Tc and vortex changes. We found that the pressure is responsible for the spatial variations in the charge carrier mean free path (δl pinning). We find that core point pinning is more dominant than surface pinning which is caused by the application of pressure. In addition, Jc(H = 0) increases from 3.9 × 105 (0 GPa) to 1.3 × 106 (1.02 GPa) A/cm2 at 2 K as the pressure is increased from normal pressure to 1.02 GPa. The pressure dependence of Tc (dTc/dP) becomes 0.91 K/GPa and 0.75 K/GPa from magnetization and resistivity measurements respectively. We found that the pressure promotes the anisotropy nature, and decrease of coherence length and resulting in pathetic interface of the vortex core with pinning centers.
Physical characteristics not psychological state or trait characteristics predict motion during resting state fMRI
Authors: Ekhtiari Hamed , Kuplicki Rayus , Yeh Hung-wen , Paulus Martin P. 
Published: January 2019

AbstractHead motion (HM) during fMRI acquisition can significantly affect measures of brain activity or connectivity even after correction with preprocessing methods. Moreover, any systematic relationship between HM and variables of interest can introduce systematic bias. There is a large and growing interest in identifying neural biomarkers for psychiatric disorders using resting state fMRI (rsfMRI). However, the relationship between HM and different psychiatric symptoms domains is not well understood. The aim of this investigation was to determine whether psychiatric symptoms and other characteristics of the individual predict HM during rsfMRI. A sample of n = 464 participants (174 male) from the Tulsa1000, a naturalistic longitudinal study recruiting subjects with different levels of severity in mood/anxiety/substance use disorders based on the dimensional NIMH Research Domain Criteria framework was used for this study. Based on a machine learning (ML) pipeline with nested cross-validation to avoid overfitting, the stacked model with 15 anthropometric (like body mass index, BMI) and demographic (age and sex) variables identifies BMI and weight as the most important variables and explained 10.9 percent of the HM variance (95% CI: 9.9–11.8). In comparison ML models with 105 self-report measures for state and trait psychological characteristics identified nicotine and alcohol use variables as well as impulsivity inhibitory control variables but explain only 5 percent of HM variance (95% CI: 3.5–6.4). A combined ML model using all 120 variables did not perform significantly better than the model using only 15 physical variables (combined model 95% confidence interval: 10.2–12.4). Taken together, after considering physical variables, state or trait psychological characteristics do not provide additional power to predict motion during rsfMRI.
Structural features distinguishing infectious ex vivo mammalian prions from non-infectious fibrillar assemblies generated in vitro
Authors: Terry Cassandra , Harniman Robert L. , Sells Jessica , Wenborn Adam , Joiner Susan , Saibil Helen R. , Miles Mervyn J. , Collinge John , Wadsworth Jonathan D. F. 
Published: January 2019

AbstractSeeded polymerisation of proteins forming amyloid fibres and their spread in tissues has been implicated in the pathogenesis of multiple neurodegenerative diseases: so called “prion-like” mechanisms. While ex vivo mammalian prions, composed of multichain assemblies of misfolded host-encoded prion protein (PrP), act as lethal infectious agents, PrP amyloid fibrils produced in vitro generally do not. The high-resolution structure of authentic infectious prions and the structural basis of prion strain diversity remain unknown. Here we use cryo-electron microscopy and atomic force microscopy to examine the structure of highly infectious PrP rods isolated from mouse brain in comparison to non-infectious recombinant PrP fibrils generated in vitro. Non-infectious recombinant PrP fibrils are 10 nm wide single fibres, with a double helical repeating substructure displaying small variations in adhesive force interactions across their width. In contrast, infectious PrP rods are 20 nm wide and contain two fibres, each with a double helical repeating substructure, separated by a central gap of 8–10 nm in width. This gap contains an irregularly structured material whose adhesive force properties are strikingly different to that of the fibres, suggestive of a distinct composition. The structure of the infectious PrP rods, which cause lethal neurodegeneration, readily differentiates them from all other protein assemblies so far characterised in other neurodegenerative diseases.
Geometric Determinants of In-Situ Direct Laser Writing
Authors: Lamont Andrew C. , Alsharhan Abdullah T. , Sochol Ryan D. 
Published: January 2019

AbstractDirect laser writing (DLW) is a three-dimensional (3D) manufacturing technology that offers significant geometric versatility at submicron length scales. Although these characteristics hold promise for fields including organ modeling and microfluidic processing, difficulties associated with facilitating the macro-to-micro interfaces required for fluid delivery have limited the utility of DLW for such applications. To overcome this issue, here we report an in-situ DLW (isDLW) strategy for creating 3D nanostructured features directly inside of—and notably, fully sealed to—sol-gel-coated elastomeric microchannels. In particular, we investigate the role of microchannel geometry (e.g., cross-sectional shape and size) in the sealing performance of isDLW-printed structures. Experiments revealed that increasing the outward tapering of microchannel sidewalls improved fluidic sealing integrity for channel heights ranging from 10 μm to 100 μm, which suggests that conventional microchannel fabrication approaches are poorly suited for isDLW. As a demonstrative example, we employed isDLW to 3D print a microfluidic helical coil spring diode and observed improved flow rectification performance at higher pressures—an indication of effective structure-to-channel sealing. We envision that the ability to readily integrate 3D nanostructured fluidic motifs with the entire luminal surface of elastomeric channels will open new avenues for emerging applications in areas such as soft microrobotics and biofluidic microsystems.
Hope4Genes: a Hopfield-like class prediction algorithm for transcriptomic data
Authors: Cantini Laura , Caselle Michele 
Published: January 2019

AbstractAfter its introduction in 1982, the Hopfield model has been extensively applied for classification and pattern recognition. Recently, its great potential in gene expression patterns retrieval has also been shown. Following this line, we develop Hope4Genes a single-sample class prediction algorithm based on a Hopfield-like model. Differently from previous works, we here tested the performances of the algorithm for class prediction, a task of fundamental importance for precision medicine and therapeutic decision-making. Hope4Genes proved better performances than the state-of-art methodologies in the field independently of the size of the input dataset, its profiling platform, the number of classes and the typical class-imbalance present in biological data. Our results provide encoraging evidence that the Hopfield model, together with the use of its energy for the estimation of the false discoveries, is a particularly promising tool for precision medicine.
Involvement of CTCF in transcription regulation of EGR1 at early G1 phase as an architecture factor
Authors: Sekiya Takeshi , Kato Kohsuke , Kawaguchi Atsushi , Nagata Kyosuke 
Published: January 2019

AbstractEarly growth response 1 (EGR1) is a transcription factor and regulates cellular processes such as proliferation, differentiation, and apoptosis. The expression of EGR1 is rapidly induced in response to several stimuli, and it activates the expression of downstream target genes involved in signaling cascades. EGR1 gene is also known to be transcribed in early G1 phase. However, the regulation of EGR1 transcription in early G1 phase is not clarified well. Here we found that CCCTC-binding factor (CTCF), a chromatin binding protein, is required to transcribe EGR1 gene at the onset of early G1 phase. We found that CTCF mediated the formation of higher-order chromatin structures among CTCF binding sites located in the EGR1 locus. Disruption of the CTCF-dependent higher-order chromatin structure using nuclease-dead Cas9 (dCas9)-mediated interference reduced the EGR1 transcription in early G1 phase. Collectively, we propose that CTCF has functional roles for the temporal expression of EGR1 in early G1 phase through regulation of higher-order chromatin structure organization.
Sex differences in early sensorimotor processing for speech discrimination
Authors: Thornton David , Harkrider Ashley W. , Jenson David E. , Saltuklaroglu Tim 
Published: January 2019

AbstractSensorimotor activity in speech perception tasks varies as a function of context, cognitive load, and cognitive ability. This study investigated listener sex as an additional variable. Raw EEG data were collected as 21 males and 21 females discriminated /ba/ and /da/ in quiet and noisy backgrounds. Independent component analyses of data from accurately discriminated trials identified sensorimotor mu components with characteristic alpha and beta peaks from 16 members of each sex. Time-frequency decompositions showed that in quiet discrimination, females displayed stronger early mu-alpha synchronization, whereas males showed stronger mu-beta desynchronization. Findings indicate that early attentional mechanisms for speech discrimination were characterized by sensorimotor inhibition in females and predictive sensorimotor activation in males. Both sexes showed stronger early sensorimotor inhibition in noisy discrimination conditions versus in quiet, suggesting sensory gating of the noise. However, the difference in neural activation between quiet and noisy conditions was greater in males than females. Though sex differences appear unrelated to behavioral accuracy, they suggest that males and females exhibit early sensorimotor processing for speech discrimination that is fundamentally different, yet similarly adaptable to adverse conditions. Findings have implications for understanding variability in neuroimaging data and the male prevalence in various neurodevelopmental disorders with inhibitory dysfunction.
CGRP-CRLR/RAMP1 signal is important for stress-induced hematopoiesis
Authors: Suekane Akira , Saito Yusuke , Nakahata Shingo , Ichikawa Tomonaga , Ogoh Honami , Tsujikawa Kazutake , Morishita Kazuhiro 
Published: January 2019

AbstractEcotropic viral integration site-1 (EVI1) has a critical role in normal and malignant hematopoiesis. Since we previously identified high expression of calcitonin receptor like receptor (CRLR) in acute myeloid leukemia (AML) with high EVI1 expression, we here characterized the function of CRLR in hematopoiesis. Since higher expression of CRLR and receptor activity modifying protein 1 (RAMP1) was identified in immature hematopoietic bone marrow (BM) cells, we focused on calcitonin gene-related peptide (CGRP), a specific ligand for the CRLR/RAMP1 complex. To elucidate the role of CGRP in hematopoiesis, Ramp1-deficient (Ramp1−/−) mice were used. The steady-state hematopoiesis was almost maintained in Ramp1−/− mice; however, the BM repopulation capacity of Ramp1−/− mice was significantly decreased, and the transplanted Ramp1−/− BM mononuclear cells had low proliferation capacity with enhanced reactive oxygen species (ROS) production and cell apoptosis. Thus, CGRP is important for maintaining hematopoiesis during temporal exposures with proliferative stress. Moreover, continuous CGRP exposure to mice for two weeks induced a reduction in the number of BM immature hematopoietic cells along with differentiated myeloid cells. Since CGRP is known to be increased under inflammatory conditions to regulate immune responses, hematopoietic exhaustion by continuous CGRP secretion under chronic inflammatory conditions is probably one of the important mechanisms of anti-inflammatory responses.
Rapid Data Analytics to Relate Sugarcane Aphid [(Melanaphis sacchari (Zehntner)] Population and Damage on Sorghum (Sorghum bicolor (L.) Moench)
Authors: Uchimiya Minori , Knoll Joseph E. 
Published: January 2019

AbstractSugarcane aphid [(Melanaphis sacchari (Zehntner)] emerged in the United States in 2013 as a new pest infesting sorghum (Sorghum bicolor (L.) Moench). Aphid population and plant damage are assessed by field scouting with mean comparison tests or repeated regression analysis. Because of inherently large replication errors from the field and interactions between treatments, new data analytics are needed to rapidly visualize the pest emergence trend and its impact on plant damage. This study utilized variable importance in the projection (VIP) and regression vector statistics of partial least squares (PLS) modeling to deduce directional relationships between aphid population and leaf damage from biweekly field monitoring (independent variable) and chemical composition (dependent variable) of 24 sweet sorghum cultivars. Regardless of environment, aphid population increase preceded the maximum damage rating. Greater damage rating at earlier growth stage in 2015 than 2016 led to an overall higher damage rating in 2015 than 2016. This trend in damage coincided with higher concentrations of trans-aconitic acid and polyphenolic secondary products in stem juice in 2016 than 2015, at the expense of primary sugar production. Developed rapid data analytics could be extended to link phenotypes to perturbation parameters (e.g., cultivar and growth stage), enabling integrated pest management.
Stereolithographic 3D printing of extrinsically self-healing composites
Authors: Sanders Polly , Young Adam J. , Qin Yang , Fancey Kevin S. , Reithofer Michael R. , Guillet-Nicolas Rémy , Kleitz Freddy , Pamme Nicole , Chin Jia Min 
Published: January 2019

AbstractWe demonstrate for the first time the direct stereolithographic 3D printing of an extrinsically self-healing composite, comprised of commercial photocurable resin modified with anisole and PMMA-filled microcapsules. The composites demonstrate solvent-welding based autonomous self-healing to afford 87% recovery of the initial critical toughness. This work illustrates the potential of stereolithographic printing to fabricate self-healing composites with user-defined structures, avoiding the need for extensive rheological optimization of printing inks, like in direct-write 3D printing. Importantly, this work also demonstrates the inclusion of microcapsules into 3D printing resins to incorporate additional functionality into printed composites, which could be adapted for applications beyond self-healing materials.
Controllable Tunneling Triboelectrification of Two-Dimensional Chemical Vapor Deposited MoS2
Authors: Wang He , Huang Chung-Che , Polcar Tomas 
Published: January 2019

AbstractTunneling triboelectrification of chemical vapor deposited monolayer MoS2has been characterized at nanoscale with contact-mode atomic force microscopy (AFM) and Kelvin force microscopy (KFM). Although charges can be trapped on insulators like SiO2by conventional triboelectrification, triboelectric charges tunneling through MoS2and localized at the underlying substrate exhibit more than two orders of magnitude longer lifetime. Their polarity and density can be modified by triboelectric process with various bias voltages applied to Pt-coated AFM tips, and the saturated density is almost 30 times higher than the reported result of SiO2. Thus, the controllable tunneling triboelectric properties of MoS2on insulating substrates can provide guidance to build a new class of two-dimensional (2D) MoS2-based nanoelectronic devices.
Identification of candidate neoantigens produced by fusion transcripts in human osteosarcomas
Authors: Rathe Susan K. , Popescu Flavia E. , Johnson James E. , Watson Adrienne L. , Marko Tracy A. , Moriarity Branden S. , Ohlfest John R. , Largaespada David A. 
Published: January 2019

AbstractOsteosarcomas are characterized by highly disrupted genomes. Although osteosarcomas lack common fusions, we find evidence of many tumour specific gene-gene fusion transcripts, likely due to chromosomal rearrangements and expression of transcription-induced chimeras. Most of the fusions result in out-of-frame transcripts, potentially capable of producing long novel protein sequences and a plethora of neoantigens. To identify fusions, we explored RNA-sequencing data to obtain detailed knowledge of transcribed fusions, by creating a novel program to compare fusions identified by deFuse to de novo transcripts generated by Trinity. This allowed us to confirm the deFuse results and identify unusual splicing patterns associated with fusion events. Using various existing tools combined with this custom program, we developed a pipeline for the identification of fusion transcripts applicable as targets for immunotherapy. In addition to identifying candidate neoantigens associated with fusions, we were able to use the pipeline to establish a method for measuring the frequency of fusion events, which correlated to patient outcome, as well as highlight some similarities between canine and human osteosarcomas. The results of this study of osteosarcomas underscores the numerous benefits associated with conducting a thorough analysis of fusion events within cancer samples.
Discovery and evaluation of inhibitor of LARP6 as specific antifibrotic compound
Authors: Stefanovic Branko , Manojlovic Zarko , Vied Cynthia , Badger Crystal-Dawn , Stefanovic Lela 
Published: January 2019

AbstractFibrosis is characterized by excessive production of type I collagen. Biosynthesis of type I collagen in fibrosis is augmented by binding of protein LARP6 to the 5′ stem-loop structure (5′SL), which is found exclusively in type I collagen mRNAs. A high throughput screen was performed to discover inhibitors of LARP6 binding to 5′SL, as potential antifibrotic drugs. The screen yielded one compound (C9) which was able to dissociate LARP6 from 5′ SL RNA in vitro and to inactivate the binding of endogenous LARP6 in cells. Treatment of hepatic stellate cells (liver cells responsible for fibrosis) with nM concentrations of C9 reduced secretion of type I collagen. In precision cut liver slices, as an ex vivo model of hepatic fibrosis, C9 attenuated the profibrotic response at 1 μM. In prophylactic and therapeutic animal models of hepatic fibrosis C9 prevented development of fibrosis or hindered the progression of ongoing fibrosis when administered at 1 mg/kg. Toxicogenetics analysis revealed that only 42 liver genes changed expression after administration of C9 for 4 weeks, suggesting minimal off target effects. Based on these results, C9 represents the first LARP6 inhibitor with significant antifibrotic activity.