bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subtle left-right asymmetry of gene expression profiles in embryonic and foetal human brains
Authors: de Kovel Carolien G. F. , Lisgo Steven N. , Fisher Simon E. , Francks Clyde 
Published: August 2018

AbstractLeft-right laterality is an important aspect of human –and in fact all vertebrate– brain organization for which the genetic basis is poorly understood. Using RNA sequencing data we contrasted gene expression in left- and right-sided samples from several structures of the anterior central nervous systems of post mortem human embryos and foetuses. While few individual genes stood out as significantly lateralized, most structures showed evidence of laterality of their overall transcriptomic profiles. These left-right differences showed overlap with age-dependent changes in expression, indicating lateralized maturation rates, but not consistently in left-right orientation over all structures. Brain asymmetry may therefore originate in multiple locations, or if there is a single origin, it is earlier than 5 weeks post conception, with structure-specific lateralized processes already underway by this age. This pattern is broadly consistent with the weak correlations reported between various aspects of adult brain laterality, such as language dominance and handedness.
Targeting protein-protein interactions for therapeutic discovery via FRET-based high-throughput screening in living cells
Authors: Stroik Daniel R. , Yuen Samantha L. , Janicek Kevyn A. , Schaaf Tory M. , Li Ji , Ceholski Delaine K. , Hajjar Roger J. , Cornea Razvan L. , Thomas David D. 
Published: August 2018

AbstractWe have developed a structure-based high-throughput screening (HTS) method, using time-resolved fluorescence resonance energy transfer (TR-FRET) that is sensitive to protein-protein interactions in living cells. The membrane protein complex between the cardiac sarcoplasmic reticulum Ca-ATPase (SERCA2a) and phospholamban (PLB), its Ca-dependent regulator, is a validated therapeutic target for reversing cardiac contractile dysfunction caused by aberrant calcium handling. However, efforts to develop compounds with SERCA2a-PLB specificity have yet to yield an effective drug. We co-expressed GFP-SERCA2a (donor) in the endoplasmic reticulum membrane of HEK293 cells with RFP-PLB (acceptor), and measured FRET using a fluorescence lifetime microplate reader. We screened a small-molecule library and identified 21 compounds (Hits) that changed FRET by >3SD. 10 of these Hits reproducibly alter SERCA2a-PLB structure and function. One compound increases SERCA2a calcium affinity in cardiac membranes but not in skeletal, suggesting that the compound is acting specifically on the SERCA2a-PLB complex, as needed for a drug to mitigate deficient calcium transport in heart failure. The excellent assay quality and correlation between structural and functional assays validate this method for large-scale HTS campaigns. This approach offers a powerful pathway to drug discovery for a wide range of protein-protein interaction targets that were previously considered “undruggable”.
Flood inundation assessment for the Hanoi Central Area, Vietnam under historical and extreme rainfall conditions
Authors: Luo Pingping , Mu Dengrui , Xue Han , Ngo-Duc Thanh , Dang-Dinh Kha , Takara Kaoru , Nover Daniel , Schladow Geoffrey 
Published: August 2018

AbstractFlash floods have long been common in Asian cities, with recent increases in urbanization and extreme rainfall driving increasingly severe and frequent events. Floods in urban areas cause significant damage to infrastructure, communities and the environment. Numerical modelling of flood inundation offers detailed information necessary for managing flood risk in such contexts. This study presents a calibrated flood inundation model using referenced photos, an assessment of the influence of four extreme rainfall events on water depth and inundation area in the Hanoi central area. Four types of historical and extreme rainfall were input into the inundation model. The modeled results for a 2008 flood event with 9 referenced stations resulted in an R2 of 0.6 compared to observations. The water depth at the different locations was simulated under the four extreme rainfall types. The flood inundation under the Probable Maximum Precipitation presents the highest risk in terms of water depth and inundation area. These results provide insights into managing flood risk, designing flood prevention measures, and appropriately locating pump stations.
Genomic and molecular analysis of conserved and unique features of soybean PIF4
Authors: Arya Hina , Singh Mohan B. , Bhalla Prem L. 
Published: August 2018

AbstractPhytochrome-interacting factor 4 (PIF4) participates in light signaling by interacting with photoreceptors, phytochromes, and cryptochromes. Although well characterized in Arabidopsis, PIF4′s role in crop plants is unknown. Here we performed the first integrated genomics, transcriptomics, and molecular characterization of PIF4 in soybean (Glycine max) plants. Fifteen identified Glycine max PIFs (GmPIFs) grouped into PIF3, PIF4, and PIF8 subfamilies based on their phylogenetic relationships. The GmPIF4 subfamily formed two distinct clades (GmPIF4 I and GmPIF4 II) with different amino acid sequences in the conserved bHLH region. Quantitative transcriptional analysis of soybean plants exposed to different photoperiods and temperatures indicated that all PIF4 I clade GmPIF4s conserved PIF4-like expression. Three out of four GmPIF4 transcripts of the GmPIF4 I clade increased at 35 °C compared to 25 °C under short day conditions. RNA sequencing of soybeans undergoing floral transition showed differential regulation of GmPIF4b, and ectopic GmPIF4b expression in wild type Arabidopsis resulted in an early flowering phenotype. Complementation of GmPIF4b in Arabidopsis pif4-101 mutants partially rescued the mutant phenotype. PIF4 protein levels peaked before dawn, and a GmPIF4b protein variant was observed in soybean plants treated at high temperatures.
Optical Characterization of Neurosurgical Operating Microscopes: Quantitative Fluorescence and Assessment of PpIX Photobleaching
Authors: Belykh Evgenii , Miller Eric J. , Patel Arpan A. , Bozkurt Baran , Yağmurlu Kaan , Robinson Timothy R. , Nakaji Peter , Spetzler Robert F. , Lawton Michael T. , Nelson Leonard Y. , Seibel Eric J. , Preul Mark C. 
Published: August 2018

AbstractProtoporphyrin IX (PpIX) induced by 5-aminolevulinic acid (5-ALA) is increasingly used as a fluorescent marker for fluorescence-guided resection of malignant gliomas. Understanding how the properties of the excitation light source and PpIX fluorescence interact with the surgical microscope is critical for effective use of the fluorescence-guided tumor resection technique. In this study, we performed a detailed assessment of the intensity of the emitted blue light and white light and the light beam profile of clinical grade operating microscopes used for PpIX visualization. These measurements revealed both recognized fluorescence photobleaching limitations and unrecognized limitations that may alter quantitative observations of PpIX fluorescence obtained with the operating microscope with potential impact on research and clinical uses. We also evaluated the optical properties of a photostable fluorescent standard with an excitation-emission profile similar to PpIX. In addition, we measured the time-dependent dynamics of 5-ALA-induced PpIX fluorescence in an animal glioma model. Finally, we developed a ratiometric method for quantification of the PpIX fluorescence that uses the photostable fluorescent standard to normalize PpIX fluorescence intensity. This method increases accuracy and allows reproducible and direct comparability of the measurements from multiple samples.
Impact of iterative model reconstruction combined with dose reduction on the image quality of head and neck CTA in children
Authors: Cheng Bochao , Xing Haoyang , Lei Du , Guo Yingkun , Ning Gang , Gong Qiyong , Cai Wu 
Published: August 2018

AbstractThis study aimed to evaluate the imaging quality of head and neck computed tomographic angiography (CTA) in pediatric patients at a lowered radiation dose by combining an iterative model reconstruction (IMR) with low voltage scanning. Eighty-three pediatric patients were randomized into two groups as follows: Group A (n = 42), 100 kV/50 ml contrast media (CM), using filtered back projection (FBP); and Group B (n = 41), 80 kV/30 ml CM, using IMR. The enhanced CT value of the arteries, the image noise, the signal-to-noise ratio (SNR)/contrast-to-noise ratio (CNR), the image quality, the effective radiation dose (ED) and the iodine intake were compared between the two groups. The mean ED and iodine intake of group B were reduced by 69.8% and 40.0%, respectively, compared to those of group A. The mean CT values of the arteries in group B were higher than those in group A (p < 0.01), whereas the image noise of group B was lower than that of group A (p < 0.01). Group B exhibited a better image quality and a higher mean CNR/SNR than that of group A (p < 0.01). Compared to FBP, IMR in head and neck CTA enables a significant reduction in the radiation dose while preserving the diagnostic image quality. Thus, IMR, combined with low tube voltage scanning, provided an excellent solution for improving the image quality of craniocervical vessels in children.
Modelling electron-phonon interactions in graphene with curved space hydrodynamics
Authors: Giordanelli Ilario , Mendoza Miller , Herrmann Hans Jürgen 
Published: August 2018

AbstractWe introduce a different perspective describing electron-phonon interactions in graphene based on curved space hydrodynamics. Interactions of phonons with charge carriers increase the electrical resistivity of the material. Our approach captures the lattice vibrations as curvature changes in the space through which electrons move following hydrodynamic equations. In this picture, inertial corrections to the electronic flow arise naturally effectively producing electron-phonon interactions. The strength of the interaction is controlled by a coupling constant, which is temperature independent. We apply this model to graphene and recover satisfactorily the linear scaling law for the resistivity that is expected at high temperatures. Our findings open up a new perspective of treating electron-phonon interactions in graphene, and also in other materials where electrons can be described by the Fermi liquid theory.
Assessment of Corneal Stromal Remodeling and Regeneration after Photorefractive Keratectomy
Authors: Kivanany Pouriska B. , Grose Kyle C. , Tippani Madhavi , Su Shan , Petroll W. Matthew 
Published: August 2018

AbstractThis study utilizes high resolution multi-dimensional imaging to identify temporal and spatial changes in cell/extracellular matrix (ECM) patterning mediating cell migration, fibrosis, remodeling and regeneration during wound healing. Photorefractive keratectomy (PRK) was performed on rabbits. In some cases, 5([4,6-dichlorotriazin-2yl]-amino)fluorescein (DTAF) was applied immediately after surgery to differentiate native vs. cell-secreted collagen. Corneas were assessed 3–180 days postoperatively using in vivo confocal microscopy, and cell/ECM patterning was evaluated in situ using multiphoton and second harmonic generation (SHG) imaging. 7 days post-PRK, migrating fibroblasts below the ablation site were co-aligned with the stromal lamellae. At day 21, randomly patterned myofibroblasts developed on top of the ablation site; whereas cells underneath were elongated, co-aligned with collagen, and lacked stress fibers. Over time, fibrotic tissue was remodeled into more transparent stromal lamellae. By day 180, stromal thickness was almost completely restored. Stromal regrowth occurred primarily below the ablation interface, and was characterized by co-localization of gaps in DTAF labeling with elongated cells and SHG collagen signaling. Punctate F-actin labeling was detected along cells co-aligned with DTAF and non-DTAF labeled collagen, suggesting cell-ECM interactions. Overall, collagen lamellae appear to provide a template for fibroblast patterning during wound healing that mediates stromal repopulation, regeneration and remodeling.
Improvement of vascular dysfunction by argirein through inhibiting endothelial cell apoptosis associated with ET-1/Nox4 signal pathway in diabetic rats
Authors: Su Jie , An Xing-Rong , Li Qing , Li Xiao-Xue , Cong Xiao-dong , Xu Ming 
Published: August 2018

AbstractEndothelial cell apoptosis plays an important role in the pathophysiological mechanism of vascular complications in type 2 diabetes mellitus (T2DM). Argirein, a new synthetic compound was demonstrated to inactivate NADPH oxidase to alleviate cardiac dysfunction in T2DM. Here, we investigated whether argirein medication attenuated the vascular dysfunction in T2DM by inhibiting endothelial cell apoptosis which was associated with NADPH oxidase. The rat aortic endothelial cells (RAECs) were incubated with glucose (30 mM) for 48 hour in vitro. It was shown that high glucose significantly increased the protein expression of BAX (Bcl-2 Associated X protein) and Caspase-3 and decreased Bcl2 (B-Cell Leukemia/Lymphoma 2) protein level in RAECs, which was normalized by argirein medication. The annexin V-FITC bound cell percentage and DNA fragments in agarose electrophoresis were markedly suppressed by argirein to confirm the anti-apoptotic property of argirein in RAECs. Furthermore, we found that argirein blocked the endothelin (ET)-1/Nox4 signal-dependent superoxide (O2−.) generation, which regulated endothelial cell apoptosis in RAECs. In vivo, argirein intervention relieved the vasodilatory response to acetylcholine and restored the expressions of Nox4 and BAX in the aorta endothelium of high-fat diet (HFD)-fed rats following streptozocin (STZ) injection. For the first time, we demonstrated that argirein could inhibit vascular endothelial cell apoptosis, which was attributed to blocking ET-1/Nox4 signal-dependent O2− generation in RAECs. This current study revealed the therapeutic effects of argirein to prevent the vascular complication in T2DM through inhibiting endothelial cell apoptosis which was associated with the anti-oxidative property of argirein.
Ndr kinases regulate retinal interneuron proliferation and homeostasis
Authors: Léger Hélène , Santana Evelyn , Leu N. Adrian , Smith Eliot T. , Beltran William A. , Aguirre Gustavo D. , Luca Francis C. 
Published: August 2018

AbstractNdr2/Stk38l encodes a protein kinase associated with the Hippo tumor suppressor pathway and is mutated in a naturally-occurring canine early retinal degeneration (erd). To elucidate the retinal functions of Ndr2 and its paralog Ndr1/Stk38, we generated Ndr1 and Ndr2 single knockout mice. Although retinal lamination appeared normal in these mice, Ndr deletion caused a subset of Pax6-positive amacrine cells to proliferate in differentiated retinas, while concurrently decreasing the number of GABAergic, HuD and Pax6-positive amacrine cells. Retinal transcriptome analyses revealed that Ndr2 deletion increased expression of neuronal stress genes and decreased expression of synaptic organization genes. Consistent with the latter, Ndr deletion dramatically reduced levels of Aak1, an Ndr substrate that regulates vesicle trafficking. Our findings indicate that Ndr kinases are important regulators of amacrine and photoreceptor cells and suggest that Ndr kinases inhibit the proliferation of a subset of terminally differentiated cells and modulate interneuron synapse function via Aak1.
Li2SnO3 as a Cathode Material for Lithium-ion Batteries: Defects, Lithium Ion Diffusion and Dopants
Authors: Kuganathan Navaratnarajah , Kordatos Apostolos , Chroneos Alexander 
Published: August 2018

AbstractTin-based oxide Li2SnO3 has attracted considerable interest as a promising cathode material for potential use in rechargeable lithium batteries due to its high- capacity. Static atomistic scale simulations are employed to provide insights into the defect chemistry, doping behaviour and lithium diffusion paths in Li2SnO3. The most favourable intrinsic defect type is Li Frenkel (0.75 eV/defect). The formation of anti-site defect, in which Li and Sn ions exchange their positions is 0.78 eV/defect, very close to the Li Frenkel. The present calculations confirm the cation intermixing found experimentally in Li2SnO3. Long range lithium diffusion paths via vacancy mechanisms were examined and it is confirmed that the lowest activation energy migration path is along the c-axis plane with the overall activation energy of 0.61 eV. Subvalent doping by Al on the Sn site is energetically favourable and is proposed to be an efficient way to increase the Li content in Li2SnO3. The electronic structure calculations show that the introduction of Al will not introduce levels in the band gap.
A peculiar case of Campylobacter jejuni attenuated aspartate chemosensory mutant, able to cause pathology and inflammation in avian and murine model animals
Authors: Hartley-Tassell L. E. , Day C. J. , Semchenko E. A. , Tram G. , Calderon-Gomez L. I. , Klipic Z. , Barry A. M. , Lam A. K. , McGuckin M. A. , Korolik V. 
Published: August 2018

AbstractAn attenuated Campylobacter jejuni aspartate chemoreceptor ccaA mutant caused gross pathological changes despite reduced colonisation ability in animal models. In chickens, the pathological changes included connective tissue and thickening of the mesenteric fat, as well as the disintegration of the villus tips in the large intestine, whereas in mice, hepatomegaly occurred between 48–72 hours post infection and persisted for the six days of the time course. In addition, there was a significant change in the levels of IL-12p70 in mice infected with the C. jejuni ccaA mutant. CcaA isogenic mutant was hyper-invasive in cell culture and microscopic examination revealed that it had a “run” bias in its “run-and-tumble” chemotactic behaviour. The mutant cells also exhibited lower level of binding to fucosylated and higher binding to sialylated glycan structures in glycan array analysis. This study highlights the importance of investigating phenotypic changes in C. jejuni, as we have shown that specific mutants can cause pathological changes in the host, despite reduction in colonisation potential.
Genome-wide mRNA expression analysis of peripheral blood from patients with obsessive-compulsive disorder
Authors: Song Yuqing , Liu Yansong , Wu Panpan , Zhang Fuquan , Wang Guoqiang 
Published: August 2018

AbstractThe onset of obsessive-compulsive disorder (OCD) involves the interaction of heritability and environment. The aim of this study is to identify the global messenger RNA (mRNA) expressed in peripheral blood from 30 patients with OCD and 30 paired healthy controls. We generated whole-genome gene expression profiles of peripheral blood mononuclear cells (PBMCs) from all the subjects using microarrays. The expression of the top 10 mRNAs was verified by real-time quantitative PCR (qRT-PCR) analysis. We also performed an enrichment analysis of the gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotations of the differentially expressed mRNAs. We identified 51 mRNAs that were significantly differentially expressed between the subjects with OCD and the controls (fold change ≥1.5; false discovery rate <0.05); 45 mRNAs were down-regulated and 6 mRNAs were up-regulated. The qRT-PCR analysis of 10 selected genes showed that they were all up-regulated, which was opposite to the results obtained from the microarrays. The GO and KEGG enrichment analysis showed that ribosomal pathway was the most enriched pathway among the differentially expressed mRNAs. Our findings support the idea that altered genome expression profiles may underlie the development of OCD.
Measuring the mutual diffusion coefficient of heavy water in normal water using a double liquid-core cylindrical lens
Authors: Meng Weidong , Xia Yan , Chen Yan , Pu Xiaoyun 
Published: August 2018

AbstractThe mutual diffusion coefficient of heavy water in normal water is measured over a temperature range of 20 to 40 °C using a novel method called the shift of equivalent refractive index slice (SERIS). The measured values range from 1.9086 × 10−5 to 3.0860 × 10−5 cm2/s and fit the Arrhenius equation well, and the calculated data from the equation are consistent with the literature values obtained by the interference method. The SERIS method is based on a double liquid-core cylindrical lens (DLCL); the front liquid core of the DLCL is used as both a liquid diffusion cell and a key imaging lens, and the resolvable minimum of liquid refractive index is δn = 6.15 × 10−5. The rear liquid core is used as an aplanatic lens, and the transversal spherical aberration is less than 1 μm. The SERIS method provides a new way to measure mutual diffusion coefficients of liquid and has the following advantages: visual measurement, use of a simplified device, and easy operation.
Detection and biochemical characterization of insecticide resistance in field populations of Asian citrus psyllid in Guangdong of China
Authors: Tian Fajun , Mo Xiufang , Rizvi Syed Arif Hussain , Li Chaofeng , Zeng Xinnian 
Published: August 2018

AbstractThe Asian citrus psyllid, Diaphorina citri Kuwayama, is one of the most damaging pests of citrus-producing regions throughout the world. The use of insecticides is the main strategy for controlling psyllid and has increased year by year. In this study, four field populations of D. citri were evaluated for resistance to nine different insecticides using the leaf-dip method. The results showed that the highest level of resistance for D. citri was found in imidacloprid with a resistance ratio of 15.12 in the Zengcheng population compared with the laboratory susceptible population. This was followed by chlorpyriphos (6.47), dinotefuran (6.16), thiamethoxam (6.04), lambda-cyhalothrin (4.78), and bifenthrin (4.16). Piperonyl butoxide (PBO) and triphenyl phosphate (TPP) showed significant synergism on imidacloprid effects in the Zengcheng population (3.84- and 2.46-fold, respectively). Nevertheless, diethyl maleate (DEM) had no synergism on imidacloprid. Biochemical enzyme assays suggested that general esterase, glutathione S-transferase and cytochrome P450 monooxygenase activities were higher in the field-collected populations than in the laboratory susceptible population. However, glutathione S-transferase may play a minor role in the resistance of adult D. citri to insecticides. At the molecular level, resistance of D. citri to imidacloprid is mainly related to the increased expression of CYP4C68 and CYP4G70 (>5-fold).
Impact of finger biophysical properties on touch gestures and tactile perception: Aging and gender effects
Authors: Abdouni A. , Vargiolu R. , Zahouani H. 
Published: August 2018

AbstractThe human finger plays an extremely important role in tactile perception, but little is known about the role of its biophysical properties (mechanical properties, contact properties and surface topography) in tactile perception. In addition, the touch gestures used to perceive an object’s properties differ among people. We combined studies on the biophysical properties and the vibrations measured from the human finger to understand the age and gender effects on the tactile perception and the difference between the touch gestures. In addition, a new algorithm, Mel-frequency cepstral coefficients (MFCCs), was used to analyze the vibratory signal obtained from the physical contact of the finger, and a surface is proposed and validated. The values obtained regarding the correlation between the tribohaptic system results and the biophysical properties show that the Young’s modulus and the surface topography are the most important. An inverse correlation was observed between the MFCC and the tactile perception. This last observation explained the results of better tactile perception with left to right touch gestures. It also demonstrated a better tactile perception for women.