bluuebunny/crossref_metadata_2025_split huggingface dataset:
A serine protease KLK8 emerges as a regulator of regulators in memory: Microtubule protein dependent neuronal morphology and PKA-CREB signaling
Authors: Konar Arpita , Kumar Ashish , Maloney Bryan , Lahiri Debomoy K. , Thakur Mahendra K. 
Published: June 2018

AbstractThe multitude of molecular pathways underlying memory impairment in neurological disorders and aging-related disorders has been a major hurdle against therapeutic targeting. Over the years, neuronal growth promoting factors, intracellular kinases, and specific transcription factors, particularly cyclic AMP response element-binding protein (CREB), have emerged as crucial players of memory storage, and their disruption accompanies many cognitive disabilities. However, a molecular link that can influence these major players and can be a potential recovery target has been elusive. Recent reports suggest that extracellular cues at the synapses might evoke an intracellular signaling cascade and regulate memory function. Herein, we report novel function of an extracellular serine protease, kallikrein 8 (KLK8/Neuropsin) in regulating the expression of microtubule associated dendrite growth marker microtubule-associated protein (MAP2)c, dendrite architecture and protein kinase A (PKA)-CREB signaling. Both knockdown of KLK8 via siRNA transfection in mouse primary hippocampal neurons and via intra-hippocampal administration of KLK8 antisense oligonucleotides in vivo reduced expression of MAP2c, dendrite length, dendrite branching and spine density. The KLK8 mediated MAP2c deficiency in turn inactivated PKA and downstream transcription factor phosphorylated CREB (pCREB), leading to downregulation of memory-linked genes and consequent impaired memory consolidation. These findings revealed a protease associated novel pathway of memory impairment in which KLK8 may act as a “regulator of regulators”, suggesting its exploration as an important therapeutic target of memory disorders.
T315I mutation of BCR-ABL1 into human Philadelphia chromosome-positive leukemia cell lines by homologous recombination using the CRISPR/Cas9 system
Authors: Tamai Minori , Inukai Takeshi , Kojika Satoru , Abe Masako , Kagami Keiko , Harama Daisuke , Shinohara Tamao , Watanabe Atsushi , Oshiro Hiroko , Akahane Koshi , Goi Kumiko , Sugihara Eiji , Nakada Shinichiro , Sugita Kanji 
Published: June 2018

AbstractIn many cancers, somatic mutations confer tumorigenesis and drug-resistance. The recently established clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system is a potentially elegant approach to functionally evaluate mutations in cancers. To reproduce mutations by homologous recombination (HR), the HR pathway must be functional, but DNA damage repair is frequently impaired in cancers. Imatinib is a tyrosine kinase inhibitor for BCR-ABL1 in Philadelphia chromosome-positive (Ph+) leukemia, and development of resistance due to kinase domain mutation is an important issue. We attempted to introduce the T315I gatekeeper mutation into three Ph+ myeloid leukemia cell lines with a seemingly functional HR pathway due to resistance to the inhibitor for poly (ADP) ribose polymerase1. Imatinib-resistant sublines were efficiently developed by the CRISPR/Cas9 system after short-term selection with imatinib; resulting sublines acquired the T315I mutation after HR. Thus, the usefulness of CRISPR/Cas9 system for functional analysis of somatic mutations in cancers was demonstrated.
Death-associated protein kinase 1 mediates interleukin-1β production through regulating inlfammasome activation in Bv2 microglial cells and mice
Authors: Song Limin , Pei Lei , Hu Lisha , Pan Shangwen , Xiong Wei , Liu Min , Wu Yan , Shang You , Yao Shanglong 
Published: June 2018

AbstractInterleukin-1β (IL-1β) plays a crucial role in mediating inflammation and innate immunity response in the central nervous system. Death-associated protein kinase 1 (DAPK1) was shown to be involved in several cellular processes. Here, we investigated the effects of DAPK1 on IL-1β production in microglial cells. We used a combination of in vitro (Bv2 microglial cell cultures) and in vivo (mice injected with amyloid-β (Aβ)) techniques to address the role of caspase-1 activation in release of IL-1β. DAPK1 involvement was postulated through genetic approaches and pharmacological blockade of this enzyme. We found that Aβ25–35 stimulation induced IL-1β production and caspase-1 activation in LPS-primed Bv2 cells and mice. DAPK1 knockdown and catalytic activity inhibition reduced IL-1β maturation and caspase-1 activation, nevertheless, DAPK1 overexpression attenuated these effects. Aβ25–35-induced lysosomal cathepsin B leakage was required for DAPK1 activation. Furthermore, repeated DAPK1 inhibitor treatment ameliorated the memory impairment in Aβ25–35-injected mice. Taken together, our findings suggest that DAPK1 facilitates Aβ25–35-induced IL-1β production through regulating caspase-1 activation in microglial cells.
An ultra-fast mechanically active cell culture substrate
Authors: Poulin Alexandre , Imboden Matthias , Sorba Francesca , Grazioli Serge , Martin-Olmos Cristina , Rosset Samuel , Shea Herbert 
Published: June 2018

AbstractWe present a mechanically active cell culture substrate that produces complex strain patterns and generates extremely high strain rates. The transparent miniaturized cell stretcher is compatible with live cell microscopy and provides a very compact and portable alternative to other systems. A cell monolayer is cultured on a dielectric elastomer actuator (DEA) made of a 30 μm thick silicone membrane sandwiched between stretchable electrodes. A potential difference of several kV’s is applied across the electrodes to generate electrostatic forces and induce mechanical deformation of the silicone membrane. The DEA cell stretcher we present here applies up to 38% tensile and 12% compressive strain, while allowing real-time live cell imaging. It reaches the set strain in well under 1 ms and generates strain rates as high as 870 s−1, or 87%/ms. With the unique capability to stretch and compress cells, our ultra-fast device can reproduce the rich mechanical environment experienced by cells in normal physiological conditions, as well as in extreme conditions such as blunt force trauma. This new tool will help solving lingering questions in the field of mechanobiology, including the strain-rate dependence of axonal injury and the role of mechanics in actin stress fiber kinetics.
Three-stage vertical distribution of seawater conductivity
Authors: Zheng Zeyu , Fu Yang , Liu Kaizhou , Xiao Rui , Wang Xiaohui , Shi Haibo 
Published: June 2018

AbstractSeawater conductivity is an important indicator of ocean electromagnetic properties and directly impacts the electromagnetic attenuation characteristics and phase distribution features of the ocean. Few studies have considered how the combined effects of salinity, temperature and pressure affect the vertical conductivity distribution and its formation mechanisms. Here, we analyse the vertical distributions of seawater conductivity from the sea surface to a maximum depth of 7062 m at five different locations. Electric conductivity profiles show similar vertical structures at all locations. Electric conductivity decreases with increasing depth first and then slowly increases from approximately 2000 m to the seabed. We observe an exponential relationship between the conductivity minimum and the water depth. At all five measurement locations, seawater conductivity measurements show a stable three-stage vertical distribution on logarithmic scales, with the middle stage satisfying a power law relationship. We analyse the vertical distribution of temperature in the second stage and investigate the relationship between temperature and conductivity. The results show that temperature also exhibits a power-law relationship with depth and a high linear correlation exists between temperature and conductivity. Our findings suggest that the vertical structure of conductivity is largely temperature dependent.
Variability Assessment of Aromatic Rice Germplasm by Pheno-Genomic traits and Population Structure Analysis
Authors: Islam M. Z. , Khalequzzaman M. , Bashar M. K. , Ivy N. A. , Mian M. A. K. , Pittendrigh B. R. , Haque M. M. , Ali M. P. 
Published: June 2018

AbstractWhile the pleasant scent of aromatic rice is making it more popular, with demand for aromatic rice expected to rise in future, varieties of this have low yield potential. Genetic diversity and population structure of aromatic germplasm provide valuable information for yield improvement which has potential market value and farm profit. Here, we show diversity and population structure of 113 rice germplasm based on phenotypic and genotypic traits. Phenotypic traits showed that considerable variation existed across the germplasm. Based on Shannon–Weaver index, the most variable phenotypic trait was lemma-palea color. Detecting 140 alleles, 11 were unique and suitable as a germplasm diagnostic tool. Phylogenetic cluster analysis using genotypic traits classified germplasm into three major groups. Moreover, model-based population structure analysis divided all germplasm into three groups, confirmed by principal component and neighbors joining tree analyses. An analysis of molecular variance (AMOVA) and pairwise FST test showed significant differentiation among all population pairs, ranging from 0.023 to 0.068, suggesting that all three groups differed. Significant correlation coefficient was detected between phenotypic and genotypic traits which could be valuable to select further improvement of germplasm. Findings from this study have the potential for future use in aromatic rice molecular breeding programs.
Effects of Mild Blast Traumatic Brain Injury on Cognitive- and Addiction-Related Behaviors
Authors: Muelbl Matthew J. , Slaker Megan L. , Shah Alok S. , Nawarawong Natalie N. , Gerndt Clayton H. , Budde Matthew D. , Stemper Brian D. , Olsen Christopher M. 
Published: June 2018

AbstractTraumatic brain injury (TBI) commonly results in cognitive and psychiatric problems. Cognitive impairments occur in approximately 30% of patients suffering from mild TBI (mTBI), and correlational evidence from clinical studies indicates that substance abuse may be increased following mTBI. However, understanding the lasting cognitive and psychiatric problems stemming from mTBI is difficult in clinical settings where pre-injury assessment may not be possible or accurate. Therefore, we used a previously characterized blast model of mTBI (bTBI) to examine cognitive- and addiction-related outcomes. We previously demonstrated that this model leads to bilateral damage of the medial prefrontal cortex (mPFC), a region critical for cognitive function and addiction. Rats were exposed to bTBI and tested in operant learning tasks several weeks after injury. bTBI rats made more errors during acquisition of a cue discrimination task compared to sham treated rats. Surprisingly, we observed no differences between groups in set shifting and delayed matching to sample, tasks known to require the mPFC. Separate rats performed cocaine self-administration. No group differences were found in intake or extinction, and only subtle differences were observed in drug-primed reinstatement 3–4 months after injury. These findings indicate that bTBI impairs acquisition of a visual discrimination task and that bTBI does not significantly increase the ability of cocaine exposure to trigger drug seeking.
Different concentrations of lipopolysaccharide regulate barrier function through the PI3K/Akt signalling pathway in human pulmonary microvascular endothelial cells
Authors: Zheng Xia , Zhang Wang , Hu Xiaotong 
Published: June 2018

AbstractLipopolysaccharide (LPS) can lead to vascular endothelial barrier dysfunction, which often results in acute lung injury and acute respiratory distress syndrome. However, the effects of different concentrations of LPS on human pulmonary microvascular endothelial barrier function and the involvement of the phosphatidylinositol-3-kinase-serine/threonine kinase (PI3K/Akt) pathway in this process remain unclear. Human pulmonary microvascular endothelial cells (HPMECs) were stimulated with different doses of LPS, and barrier function was examined by determining cell monolayer permeability, cell migration, and the expression of intercellular junction proteins (VE-Cadherin, Claudin-5, and Connexin-43). LY294002 was used to inhibit PI3K to verify the role of the PI3K/Akt pathway in the regulation of barrier function in HPMECs stimulated by LPS. Low doses of LPS increased HPMEC migration, up-regulated VE-Cadherin and Claudin-5 expression, down-regulated Connexin-43 expression, and promoted Akt phosphorylation, which could collectively decrease monolayer permeability. In contrast, high doses of LPS suppressed HPMEC migration, down-regulated the expression of VE-Cadherin and Claudin-5, up-regulated Connexin-43 expression, and reduced Akt phosphorylation, which could collectively increase monolayer permeability. LPS has a biphasic effect on HPMEC barrier function through the PI3K/Akt pathway, and this effect is concentration-dependent.
Ascertaining when a basin is Wada: the merging method
Authors: Daza Alvar , Wagemakers Alexandre , Sanjuán Miguel A. F. 
Published: June 2018

AbstractTrying to imagine three regions separated by a unique boundary seems a difficult task. However, this is exactly what happens in many dynamical systems showing Wada basins. Here, we present a new perspective on the Wada property: A Wada boundary is the only one that remains unaltered under the action of merging the basins. This observation allows to develop a new method to test the Wada property, which is much faster than the previous ones. Furthermore, another major advantage of the merging method is that a detailed knowledge of the dynamical system is not required.
Investigation of drug release modulation from poly(2-oxazoline) micelles through ultrasound
Authors: Salgarella Alice Rita , Zahoranová Anna , Šrámková Petra , Majerčíková Monika , Pavlova Ewa , Luxenhofer Robert , Kronek Juraj , Lacík Igor , Ricotti Leonardo 
Published: June 2018

AbstractAmong external stimuli used to trigger release of a drug from a polymeric carrier, ultrasound has gained increasing attention due to its non-invasive nature, safety and low cost. Despite this attention, there is only limited knowledge about how materials available for the preparation of drug carriers respond to ultrasound. This study investigates the effect of ultrasound on the release of a hydrophobic drug, dexamethasone, from poly(2-oxazoline)-based micelles. Spontaneous and ultrasound-mediated release of dexamethasone from five types of micelles made of poly(2-oxazoline) block copolymers, composed of hydrophilic poly(2-methyl-2-oxazoline) and hydrophobic poly(2-n-propyl-2-oxazoline) or poly(2-butyl-2-oxazoline-co-2-(3-butenyl)-2-oxazoline), was studied. The release profiles were fitted by zero-order and Ritger-Peppas models. The ultrasound increased the amount of released dexamethasone by 6% to 105% depending on the type of copolymer, the amount of loaded dexamethasone, and the stimulation time point. This study investigates for the first time the interaction between different poly(2-oxazoline)-based micelle formulations and ultrasound waves, quantifying the efficacy of such stimulation in modulating dexamethasone release from these nanocarriers.
Recognition of candidate transcription factors related to bilberry fruit ripening by de novo transcriptome and qRT-PCR analyses
Authors: Nguyen Nga , Suokas Marko , Karppinen Katja , Vuosku Jaana , Jaakola Laura , Häggman Hely 
Published: June 2018

AbstractBilberry (Vaccinium myrtillus L.) fruits are an excellent natural resource for human diet because of their special flavor, taste and nutritional value as well as medical properties. Bilberries are recognized for their high anthocyanin content and many of the genes involved in the anthocyanin biosynthesis have been characterized. So far, neither genomic nor RNA-seq data have been available for the species. In the present study, we de novo sequenced two bilberry fruit developmental stages, unripe green (G) and ripening (R). A total of 57,919 unigenes were assembled of which 80.2% were annotated against six public protein databases. The transcriptome served as exploratory data to identify putative transcription factors related to fruit ripening. Differentially expressed genes (DEGs) between G and R stages were prominently upregulated in R stage with the functional annotation indicating their main roles in active metabolism and catalysis. The unigenes encoding putative ripening-related regulatory genes, including members of NAC, WRKY, LOB, ERF, ARF and ABI families, were analysed by qRT-PCR at five bilberry developmental stages. Our de novo transcriptome database contributes to the understanding of the regulatory network associated with the fruit ripening in bilberry and provides the first dataset for wild Vaccinium species acquired by NGS technology.
Dependence and Homeostasis of Membrane Impedance on Cell Morphology in Cultured Hippocampal Neurons
Authors: Matsumura Ryosuke , Yamamoto Hideaki , Hayakawa Takeshi , Katsurabayashi Shutaro , Niwano Michio , Hirano-Iwata Ayumi 
Published: June 2018

AbstractThe electrical impedance of cell membranes is important for excitable cells, such as neurons, because it strongly influences the amount of membrane potential change upon a flow of ionic current across the membrane. Here, we report on an investigation of how neuronal morphology affects membrane impedance of cultured hippocampal neurons. Microfabricated substrates with patterned scaffolding molecules were used to restrict the neurite growth of hippocampal neurons, and the impedance was measured via whole-cell patch-clamp recording under the inhibition of voltage-dependent ion channels. Membrane impedance was found to depend inversely on the dendrite length and soma area, as would be expected from the fact that its electrical property is equivalent to a parallel RC circuit. Moreover, we found that in biological neurons, the membrane impedance is homeostatically regulated to impede changes in the membrane area. The findings provide direct evidence on cell-autonomous regulation of neuronal impedance and pave the way towards elucidating the mechanism responsible for the resilience of biological neuronal networks.
Predicting reference soil groups using legacy data: A data pruning and Random Forest approach for tropical environment (Dano catchment, Burkina Faso)
Authors: Hounkpatin Kpade O. L. , Schmidt Karsten , Stumpf Felix , Forkuor Gerald , Behrens Thorsten , Scholten Thomas , Amelung Wulf , Welp Gerhard 
Published: June 2018

AbstractPredicting taxonomic classes can be challenging with dataset subject to substantial irregularities due to the involvement of many surveyors. A data pruning approach was used in the present study to reduce such source errors by exploring whether different data pruning methods, which result in different subsets of a major reference soil groups (RSG) – the Plinthosols – would lead to an increase in prediction accuracy of the minor soil groups by using Random Forest (RF). This method was compared to the random oversampling approach. Four datasets were used, including the entire dataset and the pruned dataset, which consisted of 80% and 90% respectively, and standard deviation core range of the Plinthosols data while cutting off all data points belonging to the outer range. The best prediction was achieved when RF was used with recursive feature elimination along with the non-oversampled 90% core range dataset. This model provided a substantial agreement to observation, with a kappa value of 0.57 along with 7% to 35% increase in prediction accuracy for smaller RSG. The reference soil groups in the Dano catchment appeared to be mainly influenced by the wetness index, a proxy for soil moisture distribution.
Analysis of Purines and Pyrimidines distribution over miRNAs of Human, Gorilla, Chimpanzee, Mouse and Rat
Authors: Das Jayanta Kumar , Choudhury Pabitra Pal , Chaudhuri Adwitiya , Hassan Sk. Sarif , Basu Pallab 
Published: June 2018

AbstractMeaningful words in English need vowels to break up the sounds that consonants make. The Nature has encoded her messages in RNA molecules using only four alphabets A, U, C and G in which the nine member double-ring bases (adenine (A) and Guanine (G)) are purines, while the six member single-ring bases (cytosine (C) and uracil (U)) are pyrimidines. Four bases A, U, C and G of RNA sequences are divided into three kinds of classifications according to their chemical properties. One of the three classifications, the purine-pyrimidine class is important. In understanding the distribution (organization) of purines and pyrimidines over some of the non-coding RNAs, all miRNAs of the three species (human, gorilla and chimpanzee) of Hominidae family and two species (mouse and rat) from of Muridae family are considered. The distribution of purines and pyrimidines over miRNA shows deviation from randomness. Based on the quantitative metrics (fractal dimension, Hurst exponent, Hamming distance, distance pattern of purine-pyrimidine, density distribution of purine-pyrimidine and Shannon entropy) five different clusters have been made for the five species. We have observed some couple of results including the closeness of different clusters among the five species.
Identification of Biomarkers Based on Differentially Expressed Genes in Papillary Thyroid Carcinoma
Authors: Han Jun , Chen Meijun , Wang Yihan , Gong Boxuan , Zhuang Tianwei , Liang Lingyu , Qiao Hong 
Published: June 2018

AbstractThe incidence of papillary thyroid carcinoma (PTC) is increasing rapidly throughout the world. Hence, there is an urgent need for identifying more specific and sensitive biomarkers to explorate the pathogenesis of PTC. In this study, three pairs of stage I PTC tissues and matched normal adjacent tissues were sequenced by RNA-Seq, and 719 differentially expressed genes (DEGs) were screened. KEGG pathway enrichment analyses indicated that the DEGs were significantly enriched in 28 pathways. A total of 18 nodes consisting of 20 DEGs were identified in the top 10% of KEGG integrated networks. The functions of DEGs were further analysed by GO. The 13 selected genes were confirmed by qRT-PCR in 16 stage I PTC patients and by The Cancer Genome Atlas (TCGA) database. The relationship interactions between DEGs were analysed by protein-protein interaction networks and chromosome localizations. Finally, four newly discovered genes, COMP, COL3A1, ZAP70, and CD247, were found to be related with PTC clinical phenotypes, and were confirmed by Spearman’s correlation analyses in TCGA database. These four DEGs might be promising biomarkers for early-stage PTC, and provide an experimental foundation for further exploration of the pathogenesis of early-stage PTC.
Social information can potentiate understanding despite inhibiting cognitive effort
Authors: Derex Maxime , Boyd Robert 
Published: June 2018

AbstractBoth reasoning ability and social learning play a crucial role in human adaptation. Cognitive abilities like enhanced reasoning skills have combined with cumulative cultural adaptation to allow our species to dominate the world like no other. Thus, understanding how social learning interacts with individual reasoning ability is crucial for unravelling our evolutionary history. Here we describe a laboratory experiment designed to investigate the effect of social learning on individuals’ ability to infer a general rule about unfamiliar problems. In this experiment, social information had both positive and negative effects on individuals’ likelihood of inferring the rule. Social learners required more evidence to infer the rule than did individual learners, suggesting that social learning inhibits cognitive effort but social learning provided individuals with information that individual learners were unlikely to gather on their own, especially as the task became more difficult. When individuals are unlikely to discover useful information by themselves, social learning can potentiate understanding even though it reduces individual cognitive effort.