bluuebunny/crossref_metadata_2025 huggingface dataset:
Implementation of distortion symmetry for the nudged elastic band method with DiSPy
Authors: Munro Jason M. , Liu Vincent S. , Gopalan Venkatraman , Dabo Ismaila
Published: April 2019

The nudged elastic band (NEB) method is a commonly used approach for the calculation of minimum energy pathways of kinetic processes. However, the final paths obtained rely heavily on the nature of the initially chosen path. This often necessitates running multiple calculations with differing starting points in order to obtain accurate results. Recently, it has been shown that the NEB algorithm can only conserve or raise the distortion symmetry exhibited by an initial pathway. Using this knowledge, symmetry-adapted perturbations can be generated and used as a tool to systematically lower the initial path symmetry, enabling the exploration of other low-energy pathways that may exist. Here, the group and representation theory details behind this process are presented and implemented in a standalone piece of software (DiSPy). The method is then demonstrated by applying it to the calculation of ferroelectric switching pathways in LiNbO3. Previously reported pathways are more easily obtained, with new paths also being found which involve a higher degree of atomic coordination.
Investigation of chloride-induced depassivation of iron in alkaline media by reactive force field molecular dynamics
Authors: DorMohammadi Hossein , Pang Qin , Murkute Pratik , Árnadóttir Líney , Isgor O. Burkan
Published: April 2019

The passivity of iron in alkaline media enables the use of carbon steel as reinforcement in concrete, which makes up the majority of modern infrastructure. However, chlorides, mainly from deicing chemicals or marine salts, can break down the iron passive film and cause active corrosion. Despite recent advances in nanoscale characterization of iron passivity, significant gaps exist in our understanding of the dynamic processes that lead to the chloride-induced breakdown of passive films. In this study, chloride-induced depassivation of iron in pH 13.5 NaOH solution is studied using reactive force field molecular dynamics. The depassivation process initiates by local acidification of the electrolyte near the film surface, followed by iron dissolution into the electrolyte, and iron vacancy formation in the passive film. Chlorides do not penetrate the passive film, but mainly act as a catalyst for the formation of iron vacancies, which diffuse toward the metal/oxide interface, suggesting a depassivation mechanism consistent with the point-defect model.
Magnetic states of coupled spin tubes with frustrated geometry in CsCrF4
Authors: Hagihala Masato , Hayashida Shohei , Avdeev Maxim , Manaka Hirotaka , Kikuchi Hodaka , Masuda Takatsugu
Published: April 2019

When a theoretical model is realized in nature, small perturbation terms play important roles in the selection of the ground state in geometrically frustrated magnets. In case of a triangular spin tube, the two-dimensional network of the inter-tube interaction forms characteristic lattices. Among them Kagome-Triangular (KT) lattice is known to exhibit an enriched phase diagram including various types of non-trivial structures: non-coplanar cuboc structure, coplanar 120° structure with the two-dimensional propagation vector of $${\boldsymbol{k}}_{2\mathrm{D}}$$

k

2
D

 = (0, 0), $$\sqrt 3 \times \sqrt 3$$

3

×

3

structure with $${\boldsymbol{k}}_{2{\mathrm{D}}}$$

k

2

D

 = (1/3, 1/3), and incommensurate structure. We investigate the magnetic state in the model material CsCrF4 by using neutron diffraction technique. Combination of representation analysis and Rietveld refinement reveals that a very rare structure, i.e., a quasi-120° structure with $${\boldsymbol{k}}_{2{\mathrm{D}}}$$

k

2

D

 = (1/2, 0), is realized at the base temperature. The classical calculation of the phase diagram elucidates that CsCrF4 is the first experimental realization of the KT lattice having ferromagnetic Kagome bond. A single-ion anisotropy and Dzyaloshinskii-Moriya interaction play key roles in the selection of the ground state. Furthermore, a successive phase transition having an intermediate state represented by $${\boldsymbol{k}}_{2{\mathrm{D}}}$$

k

2

D

 = (1/3, 1/3) is observed. The intermediate state is a partially ordered 120° structure which is induced by thermal fluctuation.
Mistletoe extract Fraxini inhibits the proliferation of liver cancer by down-regulating c-Myc expression
Authors: Yang Peiying , Jiang Yan , Pan Yong , Ding Xiaoping , Rhea Patrea , Ding Jibin , Hawke David H. , Felsher Dean , Narla Goutham , Lu Zhimin , Lee Richard T.
Published: April 2019

Mistletoe (Viscum album) is a type of parasitic plant reported to have anticancer activity including in hepatocellular carcinoma (HCC). However, the mechanism of mistletoe’s anticancer activity, and its effectiveness in treating HCC are not fully understood. We report here that mistletoe extracts, including Fraxini (grown on ash trees) and Iscador Q and M (grown on oak and maple trees), exert strong antiproliferative activity in Hep3B cells, with median inhibitory concentrations (IC50) of 0.5 µg/mL, 7.49 µg/mL, and 7.51 µg/mL, respectively. Results of Reversed Phase Proteomic Array analysis (RPPA) suggests that Fraxini substantially down-regulates c-Myc expression in Hep3B cells. Fraxini-induced growth inhibition (at a concentration of 1.25 μg/ml) was less pronounced in c-Myc knockdown Hep3B cells than in control cells. Furthermore, in the Hep3B xenograft model, Fraxini-treated (8 mg/kg body weight) mice had significantly smaller tumors (34.6 ± 11.9 mm3) than control mice (161.6 ± 79.4 mm3, p < 0.036). Similarly, c-Myc protein expression was reduced in Fraxini treated Hep3B cell xenografts compared to that of control mice. The reduction of c-Myc protein levels in vitro Hep3B cells appears to be mediated by the ubiquitin-proteasome system. Our results suggest the importance of c-Myc in Fraxini’s antiproliferative activity, which warrants further investigation.
Characterization of Three Novel H3F3A-mutated Giant Cell Tumor Cell Lines and Targeting of Their Wee1 Pathway
Authors: Lübbehüsen Christoph , Lüke Julian , Seeling Carolin , Mellert Kevin , Marienfeld Ralf , von Baer Alexandra , Schultheiss Markus , Möller Peter , Barth Thomas F. E.
Published: April 2019

The giant cell tumor of bone (GCTB) is a locally aggressive primary bone tumor that is composed of mononuclear stroma cells, scattered macrophages, and multinucleated osteoclast-like giant cells which cause pathologic osteolysis. The stroma cells represent the neoplastic population of the tumor and are characterized by the H3F3A mutation G34W. This point mutation is regarded as the driver mutation of GCTB. We have established three new stable H3F3A mutated GCTB cell lines: U-GCT1, U-GCT2, and U-GCT3M. MK-1775 is a Wee1-kinase inhibitor which has been used for blocking of sarcoma growth. In the cell lines we detected Wee1, Cdk1, Cyclin B1, H3K36me3, and Rrm2 as members of the Wee1 pathway. We analyzed the effect of MK-1775 and gemcitabine, alone and in combination, on the growth of the cell lines. The cell lines showed a significant reduction in cell proliferation when treated with MK-1775 or gemcitabine. The combination of both agents led to a further significant reduction in cell proliferation compared to the single agents. Immunohistochemical analysis of 13 GCTB samples revealed that Wee1 and downstream-relevant members are present in GCTB tissue samples. Overall, our work offers valuable new tools for GCTB studies and presents a description of novel biomarkers and molecular targeting strategies.
Body mass index in young men and risk of inflammatory bowel disease through adult life: A population-based Danish cohort study
Authors: Mendall Michael A. , Jensen Camilla B. , Sørensen Thorkild I. A. , Ängquist Lars H. , Jess Tine
Published: April 2019

Body mass index (BMI) is associated with increased future risk of inflammatory bowel disease(IBD) particularly Crohn’s disease(CD), where associations with high and low BMI have been observed. Most studies are based on adult women. We aimed to explore the impact of BMI in men entering adult life on their long-term risk of developing IBD. A total of 377,957 men born during 1939–1959, with BMI measured at draft boards at mean age 19, were followed from 1977, or time of examination, to end of 2015. Risk of IBD was assessed using Cox regression. During 13 million person-years of follow-up, 1,523 developed CD and 3,323 UC. Using normal weight as reference, for CD the following HRs were observed: BMI < 18.5, 1.35; 95% CI, 1.12–1.62, BMI 25–29.9; 0.83; 95% CI, 0.68–1.02. and BMI > 30 1.20; 95% CI, 0.75–1.90). The increased risk of CD in underweight was maintained up until age 60 not explained by known effects of smoking. For UC, minor inverse associations were observed. Restricted cubic splines revealed a U-shape association between BMI and CD, but not UC. Low BMI of men entering adult life is associated with an increased incidence of CD and UC up to 40 years later.
Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat
Authors: Bhat Basharat , Singh Ashutosh , Iqbal Zaffar , Kaushik Jai K. , Rao A. R. , Ahmad Syed Mudasir , Bhat Hina , Ayaz Aadil , Sheikh F. D. , Kalra Shalini , Shanaz Syed , Mir Masood Salim , Agarwal Pawan Kumar , Mohapatra Trilochan , Ganai Nazir A.
Published: April 2019

The genetics of coat color variation remains a classic area. Earlier studies have focused on a limited number of genes involved in color determination; however, the complete set of trait determinants are still not well known. In this study, we used high-throughput sequencing technology to identify and characterize intricate interactions between genes that cause complex coat color variation in Changthangi Pashmina goats, producer of finest and costly commercial animal fiber. We systematically identified differentially expressed mRNAs and lncRNAs from black, brown and white Pashmina goat skin samples by using RNA-sequencing technique. A pairwise comparison of black, white and brown skin samples yielded 2479 significantly dysregulated genes (2422 mRNA and 57 lncRNAs). Differentially expressed genes were enriched in melanin biosynthesis, melanocyte differentiation, developmental pigmentation, melanosome transport activities GO terms. Our analysis suggested the potential role of lncRNAs on color coding mRNAs in cis and trans configuration. We have also developed online data repository as a component of the study to provide a central location for data access, visualization and interpretation accessible through http://pcd.skuastk.org/.
A concept for single-shot volumetric fluorescence imaging via orthogonally polarized excitation lattices
Authors: Ströhl Florian , Kaminski Clemens F.
Published: April 2019

The deconvolution of widefield fluorescence images provides only guesses of spatial frequency information along the optical axis due to the so called missing cone in the optical transfer function. Retaining the single-shot imaging speed of deconvolution microscopy while gaining access to missing cone information is thus highly desirable for microscopy of volumetric samples. Here, we present a concept that superimposes two orthogonally polarized excitation lattices with a phase-shift of p between them. In conjunction with a non-iterative image reconstruction algorithm this permits the restoration of missing cone information. We show how fluorescence anisotropy could be used as a method to encode and decode the patterns simultaneously and develop a rigorous theoretical framework for the method. Through in-silico experiments and imaging of fixed biological cells on a structured illumination microscope that emulates the proposed setup we validate the feasibility of the method.
Survey on Heavy Metals Contamination and Health Risk Assessment in Commercially Valuable Asian Swamp Eel, Monopterus albus from Kelantan, Malaysia
Authors: Sow Ai Yin , Ismail Ahmad , Zulkifli Syaizwan Zahmir , Amal Mohammad Noor , Hambali Kamarul Ariffin
Published: April 2019

This work investigates the metals concentration in the tissues of Asian swamp eel, Monopterus albus. Five selected tissues, including liver, gill, bone, skin, and muscle were examined for the concentration of Zn, Cu, Cd, Pb, and Ni. The concentrations of Cd and Pb were found high in the muscle tissues of the eels. Additionally, high amounts of Zn and Cu metals were observed in the liver, whereas the Cd, Pb, and Ni metals were highly detected in gill. The accumulation of Zn, Cu, Cd, Pb, and Ni in both skin and bone of the eel seems to vary between seasons. Low levels of Zn, Cu, and Ni were identified in the muscle tissues of the eels. This study revealed that the concentration of Cd and Pb in the muscle tissues of Asian swamp eels exceeded the permissible limits by the US EPA, suggesting the consumption of the muscle may be hazardous and can severely affect one’s health.
K1 gene transformation activities in AIDS-related and classic type Kaposi’s sarcoma: Correlation with clinical presentation
Authors: Tamanaha-Nakasone Ayumi , Uehara Karina , Tanabe Yasuka , Ishikawa Haruna , Yamakawa Natsuko , Toyoda Zensei , Kurima Kiyoto , Kina Shinichiro , Tsuneki Masayuki , Okubo Yuko , Yamaguchi Sayaka , Utsumi Daisuke , Takahashi Kenzo , Arakawa Hirofumi , Arasaki Akira , Kinjo Takao
Published: April 2019

Kaposi’s sarcoma-associated herpesvirus (KSHV) causes both AIDS-related Kaposi’s sarcoma (KS) and classic KS, but their clinical presentations are different, and respective mechanisms remain to be elucidated. The KSHV K1 gene is reportedly involved in tumorigenesis through the immunoreceptor tyrosine-based activation motif (ITAM). Since we found the sequence variations in the K1 gene of KSHV isolated from AIDS-related KS and classic KS, we hypothesized that the transformation activity of the K1 gene contributes to the different clinical presentations. To evaluate our hypothesis, we compared the transformation activities of the K1 gene between AIDS-related KS and classic KS. We also analyzed ITAM activities and the downstream AKT and NF-κB. We found that the transformation activity of AIDS-related K1 was greater than that of classic K1, and that AIDS-related K1 induced higher ITAM activity than classic K1, causing more potent Akt and NF-κB activities. K1 downregulation by siRNA in AIDS-related K1 expressing cells induced a loss of transformation properties and decreased both Akt and NF-κB activities, suggesting a correlation between the transformation activity of K1 and ITAM signaling. Our study indicates that the increased transformation activity of AIDS-related K1 is associated with its clinical aggressiveness, whereas the weak transformation activity of classic type K1 is associated with a mild clinical presentation and spontaneous regression. The mechanism of spontaneous regression of classic KS may provide new therapeutic strategy to cancer.
Identification of Prolyl isomerase Pin1 as a novel positive regulator of YAP/TAZ in breast cancer cells
Authors: Khanal Prem , Yeung Benjamin , Zhao Yulei , Yang Xiaolong
Published: April 2019

The Hippo signalling pathway plays very important roles in tumorigenesis, metastasis, organ size control, and drug resistance. Although, it has been shown that the two major components of Hippo pathway, YAP and TAZ, play very crucial role in tumorigenesis and drug resistance, the exact molecular mechanisms are still unknown. Recently, we have shown that the prolyl isomerase Pin1 regulates the activity of Hippo pathway through interaction with Hippo component LATS kinase. Thus we asked if Pin1 is also able to interact with other Hippo pathway components. Therefore, in order to investigate whether Pin1 can interacts with other components of the Hippo pathway, we performed GST-pull down and co-immunoprecipitation (Co-IP) assays and have identified two Hippo components YAP and TAZ oncoproteins as novel binding partner of Pin1. We found that Pin1 interacts with YAP/TAZ in a phosphorylation-independent manner and WW domain of Pin1 is necessary for this interaction. Moreover, by using real time qRT-PCR, Cycloheximide chase, luciferase reporter, cell viability and soft agar assays, we have shown that Pin1 increases the tumorigenic and drug-resistant activity of YAP/TAZ through stabilization of YAP/TAZ at protein levels. Together, we have identified Pin1 as a novel positive regulator of YAP/TAZ in tumorigenesis and drug resistance of breast cancer cells. These findings will provide a significant contribution for targeting the Pin1-YAP/TAZ signaling for the successful treatment of tumorigenesis and drug resistance of breast and other cancers in the future.
Multi-platform imaging in ABCA4-Associated Disease
Authors: Chen Lijuan , Lee Winston , de Carvalho Jose Ronaldo Lima , Chang Stanley , Tsang Stephen H. , Allikmets Rando , Sparrow Janet R.
Published: April 2019

Fundus autofluorescence (FAF) imaging is crucial to the diagnosis and monitoring of recessive Stargardt disease (STGD1). In a retrospective cohort study of 34 patients, we compared FAF imaging platforms varying in field size (30° and 55°: blue/SW-AF and NIR-AF; 200°: ultrawide-field, UWF-AF), excitation wavelength (488 nm, blue/SW-AF; 532 nm, UWF-AF and 787 nm, NIR-AF) and image processing. Due to reduced absorption of 532 nm and 787 nm light by macular pigment, foveal sparing was more readily demonstrable by green/UWF-AF and NIR-AF imaging. Prominent in green/UWF-AF images is a central zone of relatively elevated AF that is continuous inferonasal with a demarcation line bordering lower AF nasally and higher AF temporally. This zone and border are more visible in STGD1 than in healthy eyes and more visible with green/UWF-AF. With the development of AF flecks, inferonasal retina is initially spared. Central atrophic areas were larger in NIR-AF images than in blue/SW-AF and green/UWF-AF images and the presence of a contiguous hyperAF ring varied with imaging modality. Flecks visible as hyperAF foci in blue/SW-AF images were also visible in green/UWF-AF but were often hypoAF in NIR-AF. Since disease in STGD1 often extends beyond the 30° and 55° fields, green/UWF-AF has advantages including for pediatric patients. The imaging platforms examined provided complementary information.
Revisiting Fragmentation Reactions of Protonated α-Amino Acids by High-Resolution Electrospray Ionization Tandem Mass Spectrometry with Collision-Induced Dissociation
Authors: Zhang Pengwei , Chan Wan , Ang Irene L. , Wei Rui , Lam Melody M. T. , Lei Kate M. K. , Poon Terence C. W.
Published: April 2019

Fragmentation reactions of protonated α-amino acids (AAs) were studied previously using tandem mass spectrometry (MS/MS) of unit mass resolution. Isobaric fragmentation products and minor fragmentation products could have been overlooked or misannotated. In the present study, we examined the fragmentation patterns of 19 AAs using high-resolution electrospray ionization MS/MS (HR-ESI-MS/MS) with collision-induced dissociation (CID). Isobaric fragmentation products from protonated Met and Trp were resolved and identified for the first time. Previously unreported fragmentation products from protonated Met, Cys, Gln, Arg, and Lys were observed. Additionally, the chemical identity of a fragmentation product from protonated Trp that was incorrectly annotated in previous investigations was corrected. All previously unreported fragmentation products and reactions were verified by pseudo MS3 experiments and/or MS/MS analyses of deuterated AAs. Clearer pictures of the fragmentation reactions for Met, Cys, Trp, Gln, Arg and Lys were obtained in the present study.
Correlative 3D Imaging and Microfluidic Modelling of Human Pulmonary Lymphatics using Immunohistochemistry and High-resolution μCT
Authors: Robinson Stephanie K. , Ramsden Jonathan J. , Warner Jane , Lackie Peter M. , Roose Tiina
Published: April 2019

Lung lymphatics maintain fluid homoeostasis by providing a drainage system that returns fluid, cells and metabolites to the circulatory system. The 3D structure of the human pulmonary lymphatic network is essential to lung function, but it is poorly characterised. Image-based 3D mathematical modelling of pulmonary lymphatic microfluidics has been limited by the lack of accurate and representative image geometries. This is due to the microstructural similarity of the lymphatics to the blood vessel network, the lack of lymphatic-specific biomarkers, the technical limitations associated with image resolution in 3D, and sectioning artefacts present in 2D techniques. We present a method that combines lymphatic specific (D240 antibody) immunohistochemistry (IHC), optimised high-resolution X-ray microfocus computed tomography (μCT) and finite-element mathematical modelling to assess the function of human peripheral lung tissue. The initial results identify lymphatic heterogeneity within and between lung tissue. Lymphatic vessel volume fraction and fractal dimension significantly decreases away from the lung pleural surface (p < 0.001, n = 25 and p < 0.01, n = 20, respectively). Microfluidic modelling successfully shows that in lung tissue the fluid derived from the blood vessels drains through the interstitium into the lymphatic vessel network and this drainage is different in the subpleural space compared to the intralobular space. When comparing lung tissue from health and disease, human pulmonary lymphatics were significantly different across five morphometric measures used in this study (p ≤ 0.0001). This proof of principle study establishes a new engineering technology and workflow for further studies of pulmonary lymphatics and demonstrates for the first time the combination of correlative μCT and IHC to enable 3D mathematical modelling of human lung microfluidics at micrometre resolution.
Dengue virus reduces expression of low-density lipoprotein receptor-related protein 1 to facilitate replication in Aedes aegypti
Authors: Tree Maya O. , Londono-Renteria Berlin , Troupin Andrea , Clark Kellie M. , Colpitts Tonya M. , Conway Michael J.
Published: April 2019

Aedes aegypti is the primary vector of a number of viruses pathogenic to humans including dengue virus (DENV). DENV infection leads to widespread transcriptomic and proteomic alterations in mosquito cells. Here we identified alterations to the mosquito cell secretome during DENV infection by performing liquid chromatography tandem mass spectrometry. We found that an extracellular fragment of low-density lipoprotein receptor-related protein 1 (LRP-1) was present during infection. Previous literature suggests that LRP-1 regulates cholesterol homeostasis. Therefore, we hypothesized that DENV modifies LRP-1 protein expression to maintain host-derived intracellular cholesterol, which would facilitate virus replication within membrane-associated replication compartments. Accordingly, stimuli that are present during flavivirus infection reduced LRP-1 protein expression. We also found that dsRNA knockdown of LRP-1 increased intracellular cholesterol and DENV viral RNA. Further, depletion of intracellular lipids reduced infection. Together, these data suggest that DENV reduces LRP-1 protein expression, possibly through regulated intramembrane proteolysis (RIP), to increase intracellular cholesterol and facilitate replication in Ae. aegypti.
Fine root lignin content is well predictable with near-infrared spectroscopy
Authors: Elle Oliver , Richter Ronny , Vohland Michael , Weigelt Alexandra
Published: April 2019

1. Root lignin is a key driver of root decomposition, which in turn is a fundamental component of the terrestrial carbon cycle and increasingly in the focus of ecologists and global climate change research. However, measuring lignin content is labor-intensive and therefore not well-suited to handle the large sample sizes of most ecological studies. To overcome this bottleneck, we explored the applicability of high-throughput near infrared spectroscopy (NIRS) measurements to predict fine root lignin content. 2. We measured fine root lignin content in 73 plots of a field biodiversity experiment containing a pool of 60 grassland species using the Acetylbromid (AcBr) method. To predict lignin content, we established NIRS calibration and prediction models based on partial least square regression (PLSR) resulting in moderate prediction accuracies (RPD = 1.96, R2 = 0.74, RMSE = 3.79). 3. In a second step, we combined PLSR with spectral variable selection. This considerably improved model performance (RPD = 2.67, R2 = 0.86, RMSE = 2.78) and enabled us to identify chemically meaningful wavelength regions for lignin prediction. 4. We identified 38 case studies in a literature survey and quantified median model performance parameters from these studies as a benchmark for our results. Our results show that the combination Acetylbromid extracted lignin and NIR spectroscopy is well suited for the rapid analysis of root lignin contents in herbaceous plant species even if the amount of sample is limited.
Functional Printing of Conductive Silver-Nanowire Photopolymer Composites
Authors: Glier Tomke E. , Akinsinde Lewis , Paufler Malwin , Otto Ferdinand , Hashemi Maryam , Grote Lukas , Daams Lukas , Neuber Gerd , Grimm-Lebsanft Benjamin , Biebl Florian , Rukser Dieter , Lippmann Milena , Ohm Wiebke , Schwartzkopf Matthias , Brett Calvin J. , Matsuyama Toru , Roth Stephan V. , Rübhausen Michael
Published: April 2019

We investigated the fabrication and functional behaviour of conductive silver-nanowire-polymer composites for prospective use in printing applications. Silver-nanowires with an aspect ratio of up to 1000 were synthesized using the polyol route and embedded in a UV-curable and printable polymer matrix. Sheet resistances in the composites down to 13 Ω/sq at an optical transmission of about 90% were accomplished. The silver-nanowire composite morphology and network structure was investigated by electron microscopy, atomic force microscopy, profilometry, ellipsometry as well as surface sensitive X-ray scattering. By implementing different printing applications, we demonstrate that our silver nanowires can be used in different polymer composites. On the one hand, we used a tough composite for a 2D-printed film as top contact on a solar cell. On the other hand, a flexible composite was applied for a 3D-printed flexible capacitor.
Gut bacteria of the cowpea beetle mediate its resistance to dichlorvos and susceptibility to Lippia adoensis essential oil
Authors: Akami Mazarin , Njintang Nicolas Yanou , Gbaye Olajire A. , Andongma Awawing A. , Rashid Muhammad Adnan , Niu Chang-Ying , Nukenine Elias Nchiwan
Published: April 2019

Bacteria inhabiting the gut of insects provide many benefits to their hosts, such as aiding in food digestion, reproduction, and immunity, tissue homeostasis, adaptation to environment and resistance to pathogen and pesticides. The cowpea beetle, Callosobruchus maculatus, is a serious cosmopolitan pest of pulses. This beetle has lent itself as a guinea pig for several ecological studies. It harbors a consortium of bacterial communities in its gut, but the evidence for their role in its physiology is fragmentary. In this work, we hypothesized that gut microbiota mediates C. maculatus resistance to dichlorvos (DDVP or O,O-dimethyl O-2,2-dichlorovinylphosphate) and represent the target of Lippia adoensis (Gambian Tea Bush) essential oil (EO). Symbiotic and aposymbiotic beetles were exposed to artificial cowpea seeds earlier treated with DDVP or EO. Adult mortality and changes in gut bacterial community composition and abundance were examined at F1 and F5 generations. The susceptibility of experimental beetles to DDVP was significantly affected by their symbiotic status. The adult mortality decreased across generations in DDVP treatments, and remained significantly higher in aposymbiotic groups. In EO treatments, the mortality was consistent irrespective of symbiotic status and experimental generations. When compared to DDVP and the Control, EO treatments had significantly lower bacterial richness and diversity, as well as lower abundance of Proteobacteria, Firmicutes, and Bacteroidetes. These results support our hypothesis and describe the responses of gut microbial communities to pesticide treatments. This could be of interest for developing new management strategies of this pest.
Egocentrically-stable discriminative stimulus-based spatial navigation in mice: implementation and comparison with allocentric cues
Authors: Chun Jinsung , Kim Youngsoo , Choi Jin Woo , Kim Daesoo , Jo Sungho
Published: April 2019

Animals are capable of using visual cues to find the correct route during navigation. These visual cues, which contain spatial information on the direction towards the goal point, are perceived either allocentrically or egocentrically. In this study, we examined how navigating with these two types of visual cues affects the learning processes of rodents. To present egocentrically-stable spatial cues, we devised a head-mounted device that provided discriminative orientation cues that indicated the correct choice at a fork within a double Y-maze. For allocentrically-stable spatial cues, LEDs serving as external route-mark cues were attached to the walls of the double Y-maze and illuminated to indicate the correct pathway. To rule out the possibility of the mice using extra-maze cues, we rotated the entire maze and used different start and goal sites for every trial. Our results revealed that mice using egocentric cues and external route-mark cues both showed a sigmoidal learning process for spatial navigation and that external route mark-based learning, surprisingly, learned faster than egocentric stimulus-based learning in egocentric space.
Influence of ordered L12 precipitation on strain-rate dependent mechanical behavior in a eutectic high entropy alloy
Authors: Gwalani Bharat , Gangireddy Sindhura , Zheng Yufeng , Soni Vishal , Mishra Rajiv S. , Banerjee Rajarshi
Published: April 2019

Recent studies indicate that eutectic high-entropy alloys can simultaneously possess high strength and high ductility, which have potential industrial applications. The present study focuses on Al0.7CoCrFeNi, a lamellar dual-phase (fcc + B2) precipitation-strengthenable eutectic high entropy alloy. This alloy exhibits an fcc + B2 (B2 with bcc nano-precipitates) microstructure resulting in a combination of the soft and ductile fcc phase together with hard B2 phase. Low temperature annealing leads to the precipitation of ordered L12 intermetallic precipitates within the fcc resulting in enhanced strength. The strengthening contribution due to fine scale L12 is modeled using Orowan dislocation bowing and by-pass mechanism. The alloy was tested under quasi-static (strain-rate = 10−3 s−1) tensile loading and dynamic (strain-rate = 103 s−1) compressive loading. Due to the fine lamellar microstructure with a large number of fcc-bcc interfaces, the alloy show relatively high flow-stresses, ~1400 MPa under quasi-static loading and in excess of 1800 MPa under dynamic loading. Interestingly, the coherent nano-scale L12 precipitate caused a significant rise in the yield strength, without affecting the strain rate sensitivity (SRS) significantly. These lamellar structures had higher work hardening due to their capability for easily storing higher dislocation densities. The back-stresses from the coherent L12 precipitate were insufficient to cause improvement in twin nucleation, owing to elevated twinning stress under quasi-static testing. However, under dynamic testing high density of twins were observed.
Particle velocity controls phase transitions in contagion dynamics
Authors: Rodríguez Jorge P. , Ghanbarnejad Fakhteh , Eguíluz Víctor M.
Published: April 2019

Interactions often require the proximity between particles. The movement of particles, thus, drives the change of the neighbors which are located in their proximity, leading to a sequence of interactions. In pathogenic contagion, infections occur through proximal interactions, but at the same time, the movement facilitates the co-location of different strains. We analyze how the particle velocity impacts on the phase transitions on the contagion process of both a single infection and two cooperative infections. First, we identify an optimal velocity (close to half of the interaction range normalized by the recovery time) associated with the largest epidemic threshold, such that decreasing the velocity below the optimal value leads to larger outbreaks. Second, in the cooperative case, the system displays a continuous transition for low velocities, which becomes discontinuous for velocities of the order of three times the optimal velocity. Finally, we describe these characteristic regimes and explain the mechanisms driving the dynamics.
SMAD3 directly regulates cell cycle genes to maintain arrest in granulosa cells of mouse primordial follicles
Authors: Granados-Aparici Sofia , Hardy Kate , Franks Stephen , Sharum Isam B. , Waite Sarah L. , Fenwick Mark A.
Published: April 2019

Primordial follicles, consisting of granulosa cell (GC)-enveloped oocytes are maintained in a state of developmental arrest until activated to grow. The mechanism that operates to maintain this arrested state in GCs is currently unknown. Here, we show the TGFβ-activated transcription factor SMAD3 is expressed in primordial GC nuclei alongside the cell cycle proteins, cyclin D2 (CCND2) and P27. Using neonatal C57/Bl6 mouse ovaries densely populated with primordial follicles, CCND2 protein co-localised and was detected in complex with P27 by immunofluorescence and co-immunoprecipitation, respectively. In the same tissue, SMAD3 co-precipitated with DNA sequences upstream of Ccnd2 and Myc transcription start sites implicating both as direct SMAD3 targets. In older ovaries follicle growth was associated with nuclear exclusion of SMAD3 and reduced P27 and CCND2 in GCs, alongside elevated Myc expression. Brief (2 H) exposure of neonatal ovaries to TGFβ1 (10 ng/ml) in vitro led to immediate dissociation of SMAD3 from the Ccnd2 and Myc promoters. This coincided with elevated Myc and phospho-S6, an indicator of mTOR signalling, followed by a small increase in mean primordial GC number after 48 H. These findings highlight a concentration-dependent role for TGFβ signalling in the maintenance and activation of primordial follicles, through SMAD-dependent and independent signalling pathways, respectively.
Evaluation of a Chicken 600K SNP genotyping array in non-model species of grouse
Authors: Minias Piotr , Dunn Peter O. , Whittingham Linda A. , Johnson Jeff A. , Oyler-McCance Sara J.
Published: April 2019

The use of single nucleotide polymorphism (SNP) arrays to generate large SNP datasets for comparison purposes have recently become an attractive alternative to other genotyping methods. Although most SNP arrays were originally developed for domestic organisms, they can be effectively applied to wild relatives to obtain large panels of SNPs. In this study, we tested the cross-species application of the Affymetrix 600K Chicken SNP array in five species of North American prairie grouse (Centrocercus and Tympanuchus genera). Two individuals were genotyped per species for a total of ten samples. A high proportion (91%) of the total 580 961 SNPs were genotyped in at least one individual (73–76% SNPs genotyped per species). Principal component analysis with autosomal SNPs separated the two genera, but failed to clearly distinguish species within genera. Gene ontology analysis identified a set of genes related to morphogenesis and development (including genes involved in feather development), which may be primarily responsible for large phenotypic differences between Centrocercus and Tympanuchus grouse. Our study provided evidence for successful cross-species application of the chicken SNP array in grouse which diverged ca. 37 mya from the chicken lineage. As far as we are aware, this is the first reported application of a SNP array in non-passerine birds, and it demonstrates the feasibility of using commercial SNP arrays in research on non-model bird species.
Biological activity of Dittrichia viscosa (L.) Greuter extracts against adult Sitophilus granarius (L.) (Coleoptera, Curculionidae) and identification of active compounds
Authors: Rotundo Giuseppe , Paventi Gianluca , Barberio Antonia , De Cristofaro Antonio , Notardonato Ivan , Russo Mario V. , Germinara Giacinto S.
Published: April 2019

Dittrichia viscosa (L.) Greuter, a perennial weed of the Mediterranean area, was reported to be source of active substances. Here, by means of both ingestion and contact assays, the biological activity of three different extracts (n-hexane, methanol, and distilled water) of D. viscosa aerial part has been evaluated against Sitophilus granarius (L.) adults, an important pest of stored grains. Ingestion assays showed negligible mortality and food deterrence for all the extracts, whereas only a slight reduction of some nutritional parameters (relative growth rate, relative consumption rate, food efficiency conversion) was recorded for water extract. High contact toxicity was found only for the n-hexane extract (24 h median lethal dose LD50 = 53.20 μg/adult). This extract was further subfractioned by silica gel column chromatography and then by thin layer chromatography. Further contact toxicity bioassays highlighted two active subfractions which were analyzed by GC-MS. This revealed the occurrence, in both subfractions, of two major peaks that were identified as α- and γ- costic acid isomers. Moreover, D. viscosa active subfractions, did not cause acetylcholinesterase (AChE) inhibition; therefore, in the light of progressive limitation of compounds acting by this mechanism of action, D. viscosa represents a promising eco-sustainable source of natural products for pest control.
Positive verbal suggestion optimizes postural control
Authors: Villa-Sánchez Bernardo , Emadi Andani Mehran , Menegaldo Giulia , Tinazzi Michele , Fiorio Mirta
Published: April 2019

Balance is a very important function that allows maintaining a stable stance needed for many daily life activities and for preventing falls. We investigated whether balance control could be improved by a placebo procedure consisting of verbal suggestion. Thirty healthy volunteers were randomized in two groups (placebo and control) and asked to perform a single-leg stance task in which they had to stand as steadily as possible on the dominant leg. The task was repeated in three sessions (T0, T1, T2). At T1 and T2 an inert treatment was applied on the leg, by informing the placebo group that it was effective in improving balance. The control group was overtly told that treatment was inert. An accelerometer applied on participants’ leg allowed to measure body sways in different directions. Subjective parameters, like perception of stability, were also collected. Results showed that the placebo group had less body sways than the control group at T2, both in the three-dimensional space and in the anterior-posterior direction. Furthermore, the placebo group perceived to be more stable than the control group. This study represents the first evidence that placebo effect optimizes posture, with a potential translational impact in patients with postural and gait disturbances.
Pharmacological boost of DNA damage response and repair by enhanced biogenesis of DNA damage response RNAs
Authors: Gioia Ubaldo , Francia Sofia , Cabrini Matteo , Brambillasca Silvia , Michelini Flavia , Jones-Weinert Corey W. , d’Adda di Fagagna Fabrizio
Published: April 2019

A novel class of small non-coding RNAs called DNA damage response RNAs (DDRNAs) generated at DNA double-strand breaks (DSBs) in a DROSHA- and DICER-dependent manner has been shown to regulate the DNA damage response (DDR). Similar molecules were also reported to guide DNA repair. Here, we show that DDR activation and DNA repair can be pharmacologically boosted by acting on such non-coding RNAs. Cells treated with enoxacin, a compound previously demonstrated to augment DICER activity, show stronger DDR signalling and faster DNA repair upon exposure to ionizing radiations compared to vehicle-only treated cells. Enoxacin stimulates DDRNA production at chromosomal DSBs and at dysfunctional telomeres, which in turn promotes 53BP1 accumulation at damaged sites, therefore in a miRNA-independent manner. Increased 53BP1 occupancy at DNA lesions induced by enoxacin ultimately suppresses homologous recombination, channelling DNA repair towards faster and more accurate non-homologous end-joining, including in post-mitotic primary neurons. Notably, augmented DNA repair stimulated by enoxacin increases the survival also of cancer cells treated with chemotherapeutic agents.
Phenotypic characteristics and transcriptome profile of Cryptococcus gattii biofilm
Authors: Tavares Eliandro Reis , Gionco Bárbara , Morguette Ana Elisa Belotto , Andriani Gabriella Maria , Morey Alexandre Tadachi , do Carmo Anderson Oliveira , de Pádua Pereira Ulisses , Andrade Galdino , de Oliveira Admilton Gonçalves , Pinge-Filho Phileno , Nakamura Celso Vataru , Yamauchi Lucy Megumi , Yamada-Ogatta Sueli Fumie
Published: April 2019

In this study, we characterized Cryptococcus gattii biofilm formation in vitro. There was an increase in the density of metabolically active sessile cells up to 72 h of biofilm formation on polystyrene and glass surfaces. Scanning electron microscopy and confocal laser scanning microscopy analysis revealed that in the early stage of biofilm formation, yeast cells adhered to the abiotic surface as a monolayer. After 12 h, extracellular fibrils were observed projecting from C. gattii cells, connecting the yeast cells to each other and to the abiotic surface; mature biofilm consisted of a dense network of cells deeply encased in an extracellular polymeric matrix. These features were also observed in biofilms formed on polyvinyl chloride and silicone catheter surfaces. We used RNA-Seq-based transcriptome analysis to identify changes in gene expression associated with C. gattii biofilm at 48 h compared to the free-floating planktonic cells. Differential expression analysis showed that 97 and 224 transcripts were up-regulated and down-regulated in biofilm, respectively. Among the biological processes, the highest enriched term showed that the transcripts were associated with cellular metabolic processes, macromolecule biosynthetic processes and translation.
Ferroelectric order driven Eu3+ photoluminescence in BaZrxTi1−xO3 perovskite
Authors: Canu Giovanna , Bottaro Gregorio , Buscaglia Maria Teresa , Costa Chiara , Condurache Oana , Curecheriu Lavinia , Mitoseriu Liliana , Buscaglia Vincenzo , Armelao Lidia
Published: April 2019

The ability to tune and enhance the properties of luminescent materials is essential for enlarging their application potential. Recently, the modulation of the photoluminescence emission of lanthanide-doped ferroelectric perovskites by applying an electric field has been reported. Herein, we show that the ferroelectric order and, more generally the polar order, has a direct effect on the photoluminescence of Eu3+ in the model BaZrxTi1−xO3 perovskite even in the absence of an external field. The dipole arrangement evolves with increasing x from long-range ferroelectric order to short-range order typical of relaxors until the non-polar paraelectric BaZrO3 is achieved. The cooperative polar interactions existing in the lattice (x < 1) promote the off-center displacement of the Eu3+ ion determining a change of the lanthanide site symmetry and, consequently, an abrupt variation of the photoluminescence emission with temperature. Each type of polar order is characterized by a distinct photoluminescence behaviour.
Mechanistic modelling supports entwined rather than exclusively competitive DNA double-strand break repair pathway
Authors: Ingram S. P. , Warmenhoven J. W. , Henthorn N. T. , Smith E. A. K. , Chadwick A. L. , Burnet N. G. , Mackay R. I. , Kirkby N. F. , Kirkby K. J. , Merchant M. J.
Published: April 2019

Following radiation induced DNA damage, several repair pathways are activated to help preserve genome integrity. Double Strand Breaks (DSBs), which are highly toxic, have specified repair pathways to address them. The main repair pathways used to resolve DSBs are Non-Homologous End Joining (NHEJ) and Homologous Recombination (HR). Cell cycle phase determines the availability of HR, but the repair choice between pathways in the G2 phases where both HR and NHEJ can operate is not clearly understood. This study compares several in silico models of repair choice to experimental data published in the literature, each model representing a different possible scenario describing how repair choice takes place. Competitive only scenarios, where initial protein recruitment determines repair choice, are unable to fit the literature data. In contrast, the scenario which uses a more entwined relationship between NHEJ and HR, incorporating protein co-localisation and RNF138-dependent removal of the Ku/DNA-PK complex, is better able to predict levels of repair similar to the experimental data. Furthermore, this study concludes that co-localisation of the Mre11-Rad50-Nbs1 (MRN) complexes, with initial NHEJ proteins must be modeled to accurately depict repair choice.
Comparison of Multipulse Laser Vaporesection versus Plasmakinetic Resection for Treatment of Benign Prostate Obstruction
Authors: Hsu Fu-Shun , Chou Chen-Wei , Chang Hong-Chiang , Tu Yuan-Po , Sha Shing-Jia , Chung Huang-Hsin , Huang Kuo-How
Published: April 2019

We aimed to compare the efficacy and safety of Multipulse laser vaporesection of the prostate (MPVP) versus plasmakinetic resection of the prostate (PKRP) for treatment of patients with benign prostate obstruction (BPO) in a prospective trial. From January 2016 to April 2017, a total of 144 patients were included in the cohort study, of whom 73 patients underwent MPVP and 71 underwent PKRP. All patients received pre-operative evaluation and followed up at 1, 3, 6 and 12 months postoperatively. Baseline characteristics, perioperative data and postoperative outcomes were compared. Early (within 30 days postoperatively) and late complications were also recorded. Preoperative data, including age, prostate volume, international prostate symptom score (IPSS), International Index of Erectile Function Questionnaires (IIEF-5), the rate of anticoagulants use, Charlson comorbidity index were similar in two groups. Peri-operative parameters, including the rate of transfusion, and decrease in hemoglobin level were comparable. The operative time, the duration of catheterization and length of hospital stay were significantly shorter in the MPVP group. The voiding parameters and the quality-of-life scores (QoL) improved significantly in both groups postoperatively. There was a significantly difference in QoL at 1-year in the MPVP group (p < 0.001), under mixed model analysis with random effect and Bonferroni correction. There were no significant differences in improvement of IPSS, Qmax, IIEF-5, residual prostate volume ratio and PSA level reduction at the 1-year follow-up. MPVP was significantly superior to PKRP in terms of a reduction in overall complication rate (21.9% vs 45.0%, p = 0.004). Both treatments led to comparable symptomatic improvements. MPVP demonstrates satisfactory efficiency, shorter catheterization time and shorter hospital stay. Our data revealed that MPVP may be a promising technique which is safe and favorable alternative for patients with BPO.