bluuebunny/crossref_metadata_2025 huggingface dataset:
Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses
Authors: Amemiya Takayuki , Gromiha M. Michael , Horimoto Katsuhisa , Fukui Kazuhiko
Published: January 2019

To detect drug candidates for dengue haemorrhagic fever (DHF), we employed a computational drug repositioning method to perform an integrated multiple omics analysis based on transcriptomic, proteomic, and interactomic data. We identified 3,892 significant genes, 389 proteins, and 221 human proteins by transcriptomic analysis, proteomic analysis, and human–dengue virus protein–protein interactions, respectively. The drug candidates were selected using gene expression profiles for inverse drug–disease relationships compared with DHF patients and healthy controls as well as interactomic relationships between the signature proteins and chemical compounds. Integrating the results of the multiple omics analysis, we identified eight candidates for drug repositioning to treat DHF that targeted five proteins (ACTG1, CALR, ERC1, HSPA5, SYNE2) involved in human–dengue virus protein–protein interactions, and the signature proteins in the proteomic analysis mapped to significant pathways. Interestingly, five of these drug candidates, valparoic acid, sirolimus, resveratrol, vorinostat, and Y-27632, have been reported previously as effective treatments for flavivirus-induced diseases. The computational approach using multiple omics data for drug repositioning described in this study can be used effectively to identify novel drug candidates.
TaME-seq: An efficient sequencing approach for characterisation of HPV genomic variability and chromosomal integration
Authors: Lagström Sonja , Umu Sinan Uğur , Lepistö Maija , Ellonen Pekka , Meisal Roger , Christiansen Irene Kraus , Ambur Ole Herman , Rounge Trine B.
Published: January 2019

HPV genomic variability and chromosomal integration are important in the HPV-induced carcinogenic process. To uncover these genomic events in an HPV infection, we have developed an innovative and cost-effective sequencing approach named TaME-seq (tagmentation-assisted multiplex PCR enrichment sequencing). TaME-seq combines tagmentation and multiplex PCR enrichment for simultaneous analysis of HPV variation and chromosomal integration, and it can also be adapted to other viruses. For method validation, cell lines (n = 4), plasmids (n = 3), and HPV16, 18, 31, 33 and 45 positive clinical samples (n = 21) were analysed. Our results showed deep HPV genome-wide sequencing coverage. Chromosomal integration breakpoints and large deletions were identified in HPV positive cell lines and in one clinical sample. HPV genomic variability was observed in all samples allowing identification of low frequency variants. In contrast to other approaches, TaME-seq proved to be highly efficient in HPV target enrichment, leading to reduced sequencing costs. Comprehensive studies on HPV intra-host variability generated during a persistent infection will improve our understanding of viral carcinogenesis. Efficient identification of both HPV variability and integration sites will be important for the study of HPV evolution and adaptability and may be an important tool for use in cervical cancer diagnostics.
Optimization of Normal Human Bronchial Epithelial (NHBE) Cell 3D Cultures for in vitro Lung Model Studies
Authors: Rayner Rachael E. , Makena Patrudu , Prasad Gaddamanugu L. , Cormet-Boyaka Estelle
Published: January 2019

Robust in vitro lung models are required for risk assessment to measure key events leading to respiratory diseases. Primary normal human bronchial epithelial cells (NHBE) represent a good lung model but obtaining well-differentiated 3D cultures can be challenging. Here, we evaluated the ability to expand primary NHBE cells in different culture conditions while maintaining their 3D culture characteristics such as ciliated and goblet cells, and ion channel function. Differentiated cultures were optimally obtained with PneumaCult-Ex Plus (expansion medium)/PneumaCult-ALI (differentiation medium). Primary cells passaged up to four times maintained airway epithelial characteristics as evidenced by ciliated pseudostratified columnar epithelium with goblet cells, trans-epithelial electrical resistance (TEER) (>400 Ohms.cm2), and cystic fibrosis transmembrane conductance regulator-mediated short-circuit currents (>3 µA/cm2). No change in ciliary beat frequency (CBF) or airway surface liquid (ASL) meniscus length was observed up to passage six. For the first time, this study demonstrates that CFTR ion channel function and normal epithelial phenotypic characteristics are maintained in passaged primary NHBE cells. Furthermore, this study highlights the criticality of evaluating expansion and differentiation conditions for achieving optimal phenotypic and functional endpoints (CBF, ASL, ion channel function, presence of differentiated cells, TEER) when developing in vitro lung models.
Sensitive Molybdenum Disulfide Based Field Effect Transistor Sensor for Real-time Monitoring of Hydrogen Peroxide
Authors: Zheng Chao , Jin Xin , Li Yutao , Mei Junchi , Sun Yujie , Xiao Mengmeng , Zhang Hong , Zhang Zhiyong , Zhang Guo-Jun
Published: January 2019

A reliable and highly sensitive hydrogen peroxide (H2O2) field effect transistor (FET) sensor is reported, which was constructed by using molybdenum disulfide (MoS2)/reduced graphene oxide (RGO). In this work, we prepared MoS2 nanosheets by a simple liquid ultrasonication exfoliation method. After the RGO-based FET device was fabricated, MoS2 was assembled onto the RGO surface for constructing MoS2/RGO FET sensor. The as-prepared FET sensor showed an ultrahigh sensitivity and fast response toward H2O2 in a real-time monitoring manner with a limit of detection down to 1 pM. In addition, the constructed sensor also exhibited a high specificity toward H2O2 in complex biological matrix. More importantly, this novel biosensor was capable of monitoring of H2O2 released from HeLa cells in real-time. So far, this is the first report of MoS2/RGO based FET sensor for electrical detection of signal molecules directly from cancer cells. Hence it is promising as a new platform for the clinical diagnosis of H2O2-related diseases.
Effects of circadian misalignment on cognition in chronic shift workers
Authors: Chellappa Sarah L. , Morris Christopher J. , Scheer Frank A. J. L.
Published: January 2019

Shift work is associated with increased human operational errors, presumably due to the circadian timing system that inhibits optimal cognitive function during the night. Circadian misalignment, which is the misalignment between the circadian pacemaker and behavioral/environmental cycles, impairs cognitive performance in non-shift workers. However, it remains uncertain whether the adverse cognitive consequences of circadian misalignment are also observed in chronic shift workers. Thus, we investigated the effects of circadian misalignment on cognitive performance in chronic shift workers. Using a randomized, cross-over design that simulated day shift work (circadian alignment) and night shift work (circadian misalignment), we show that circadian misalignment increases cognitive vulnerability on sustained attention, information processing and visual-motor performance, particularly after more than 10 hours of scheduled wakefulness. Furthermore, their increased levels of subjective sleepiness and their decreased sleep efficiency were significantly associated with impaired sustained attention and visual-motor performance. Our data suggest that circadian misalignment dramatically deteriorates cognitive performance in chronic shift workers under circadian misalignment. This increased cognitive vulnerability may have important safety consequences, given the increasing number of nighttime jobs that crucially rely on the availability of cognitive resources.
Urbanization threaten the pollination of Gentiana dahurica
Authors: Hou Qin-zheng , Pang Xia , Wang Yu-pei , Sun Kun , Jia Ling-yun , Zhang Shi-hu , Li Qiao-xia
Published: January 2019

With rapid spread of the urbanization, many environmental factors, such as climate, soil pH and nutrients have been changed. However, the plant pollination affected by urbanization was seldom conducted. Here, we studied the flower visitation rates, seed production, pollen limitation and flower morphological characters of Gentiana dahurica at 3 populations along an urban-peri-urban gradient around Xi’ning over 4 consecutive years, aiming to test the effects of urbanization on plant pollination service. Our results showed that the pollinator visit frequencies, interannual stability of pollinator assemblages and visit frequencies declined with the intensification of urbanization. As urbanization intensified, plant borne more flowers and the flower morphological sizes became “longer” (the length of flowers, filaments and styles were increased, but the width of flowers kept stable at the 3 populations); the flower duration, especially the female phase duration prolonged. The seed-set ratio of G. dahurica in natural condition decreased and more severe pollen limitation occurred in more urbanized populations. Also, an interannual variation of seed-set ratio and index of pollen limitation (IPL), which related with the variation of pollinator visit frequencies, were found in this study. These results suggest that the pollination service can be threatened by urbanization over a long-time interval for G. dahurica. This finding highlights the importance of pollinator affections acting on plant pollination system. Additionally, as pollinator assemblages and visit frequencies interannually changed, a long-time scale observation is needed to understand the plant-pollinator relationships.
Combination of polyetherketoneketone scaffold and human mesenchymal stem cells from temporomandibular joint synovial fluid enhances bone regeneration
Authors: Lin Yi , Umebayashi Mayumi , Abdallah Mohamed-Nur , Dong Guoying , Roskies Michael G. , Zhao Yaoyao Fiona , Murshed Monzur , Zhang Zhiguang , Tran Simon D.
Published: January 2019

Therapies using human mesenchymal stem cells (MSCs) combined with three-dimensional (3D) printed scaffolds are a promising strategy for bone grafting. But the harvest of MSCs still remains invasive for patients. Human synovial fluid MSCs (hSF-MSCs), which can be obtained by a minimally invasive needle-aspiration procedure, have been used for cartilage repair. However, little is known of hSF-MSCs in bone regeneration. Polyetherketoneketone (PEKK) is an attractive bone scaffold due to its mechanical properties comparable to bone. In this study, 3D-printed PEKK scaffolds were fabricated using laser sintering technique. hSF-MSCs were characterized and cultured on PEKK to evaluate their cell attachment, proliferation, and osteogenic potential. Rabbit calvarial critical-sized bone defects were created to test the bone regenerative effect of PEKK with hSF-MSCs. In vitro results showed that hSF-MSCs attached, proliferated, and were osteogenic on PEKK. In vivo results indicated that PEKK seeded with hSF-MSCs regenerated twice the amount of newly formed bone when compared to PEKK seeded with osteogenically-induced hSF-MSCs or PEKK scaffolds alone. These results suggested that there was no need to induce hSF-MSCs into osteoblasts prior to their transplantations in vivo. In conclusion, the combined use of PEKK and hSF-MSCs was effective in regenerating critical-sized bone defects.
Robot-assisted Tongue Base Resection ensures favorable therapeutic outcome to Obstructive Sleep Apnea patients with Lingual tonsil hypertrophy
Authors: Cho Sung-Woo , Hong Seung-No , Han Doo Hee , Won Tae-Bin , Kim Dong-Young , Kim Hyun Jik
Published: January 2019

Tongue base (TB) narrowing is recognized as a significant site of upper airway collapse during sleep in obstructive sleep apnea (OSA) patients and robot technology is expected to have promising clinical utility in OSA patients with TB narrowing. The purpose of our study is to demonstrate the better therapeutic conditions and favorable indications of robot-assisted TB resection (TBR) in OSA. We performed robot-assisted TBR combined with nasal and palatal surgery in 16 OSA patients with any of the following characteristics: severe TB narrowing (over grade II) and moderate or severe OSA. The preoperative median AHI was 48.8/hr and the median lowest SaO2 was 82.0%. The median AHI decreased to 18.7/hr and ten patients (62.5%) were included in the responder group following robot-assisted TBR combined with nasal and palatal surgery. The lowest SaO2 improved to 90.5% and the posterior airway space (PAS) was significantly increased following robot-assisted TBR. Cephalometric results showed that wider PAS were observed in responders compared to non-responders prior to robot-assisted TBR. Interestingly, there was greater improvement in the objective parameters including PAS in the OSA patients with lingual tonsilar hypertrophy than they were in those without and all patients with lingual tonsillar hypertrophy (n = 6) responded to robot-assisted TBR. Robot-assisted TBR exhibited minimal morbidity and postoperative complications in OSA patients. Robot-assisted TBR can be considered a promising and innovative surgical option to reduce TB volume and improve sleep parameters in OSA patients with TB narrowing. OSA patient with TB narrowing due to lingual tonsil hypertrophy shows greater therapeutic outcome and lingual tonsil hypertrophy appears to be most favorable surgical indications of robot-assisted TBR.
Bio-inspired synthesis of aqueous nanoapatite liquid crystals
Authors: Tan Junjun , Jin Xiaoying , Chen Minfang
Published: January 2019

The macroscopically ordered structure of rod-like nanoapatites within the collagen matrix is of great significance for the mechanical performance of bones and teeth. However, the synthesis of macroscopically ordered nanoapatite remains a challenge. Inspired by the effect of citrate molecules on apatite crystals in natural bone and the similarities between these ordered rod-like nanoapatites and the nematic phase of inorganic liquid crystals (LCs), we synthesized aqueous liquid crystal from rod-like nanoapatites with the aid of sodium citrate. Following a similar procedure, aqueous Mg(OH)2 and Mg3(PO4)2 LCs were also prepared. These findings lay the foundation for the fabrication of macroscopically assembled nanoapatite-based functional materials for biomedical applications and offer a green chemical synthesis platform for the development of new types of inorganic LCs. This process may reduce the difficulties in synthesizing large quantities of inorganic LCs so that they can be applied to the fabrication of functional materials.
Cellular and animal models of skin alterations in the autism-related ADNP syndrome
Authors: Mollinedo Pilar , Kapitansky Oxana , Gonzalez-Lamuño Domingo , Zaslavsky Adi , Real Pedro , Gozes Illana , Gandarillas Alberto , Fernandez-Luna Jose L.
Published: January 2019

Mutations in ADNP have been recently associated with intellectual disability and autism spectrum disorder. However, the clinical features of patients with this syndrome are not fully identified, and no treatment currently exists for these patients. Here, we extended the ADNP syndrome phenotype describing skin abnormalities in both a patient with ADNP syndrome and an Adnp haploinsufficient mice. The patient displayed thin dermis, hyperkeratotic lesions in periarticular areas and delayed wound healing. Patient-derived skin keratinocytes showed reduced proliferation and increased differentiation. Additionally, detection of cell cycle markers indicated that mutant cells exhibited impaired cell cycle progression. Treatment of ADNP-deficient keratinocytes with the ADNP-derived NAP peptide significantly reduced the expression of differentiation markers. Sonography and immunofluorescence staining of epidermal layers revealed that the dermis was thinner in the patient than in a healthy control. Adnp haploinsufficient mice (Adnp+/−) mimicked the human condition showing reduced dermal thickness. Intranasal administration of NAP significantly increased dermal thickness and normalized the levels of cell cycle and differentiation markers. Our observations provide a novel activity of the autism-linked ADNP in the skin that may serve to define the clinical phenotype of patients with ADNP syndrome and provide an attractive therapeutic option for skin alterations in these patients.
Defect Chemistry and Li-ion Diffusion in Li2RuO3
Authors: Kuganathan Navaratnarajah , Kordatos Apostolos , Chroneos Alexander
Published: January 2019

Layered Li2RuO3 is an important candidate cathode material in rechargeable lithium ion batteries because of its novel anionic redox process and high reversible capacity. Atomistic scale simulations are used to calculate the intrinsic defect process, favourable dopants and migration energies of lithium ion diffusions together with migration paths in Li2RuO3. The Li Frenkel is calculated to be the most favourable intrinsic defect type. The cation anti-site defect, in which Li and Ru ions exchange their positions is 1.89 eV/defect suggesting that this defect would be observed at high temperatures. Long range vacancy assisted lithium diffusion paths were calculated and it is confirmed that the lowest overall activation energy (0.73 eV) migration path is along the ab plane. Trivalent dopants (Al3+, Co3+, Sc3+, In3+, Y3+, Gd3+ and La3+) were considered to create additional Li in Li2RuO3. Here we show that Al3+ or Co3+ are the ideal dopants and this is in agreement with the experimental studies reported on Co3+ doping in Li2RuO3.
Traction force microscopy with optimized regularization and automated Bayesian parameter selection for comparing cells
Authors: Huang Yunfei , Schell Christoph , Huber Tobias B. , Şimşek Ahmet Nihat , Hersch Nils , Merkel Rudolf , Gompper Gerhard , Sabass Benedikt
Published: January 2019

Adherent cells exert traction forces on to their environment which allows them to migrate, to maintain tissue integrity, and to form complex multicellular structures during developmental morphogenesis. Traction force microscopy (TFM) enables the measurement of traction forces on an elastic substrate and thereby provides quantitative information on cellular mechanics in a perturbation-free fashion. In TFM, traction is usually calculated via the solution of a linear system, which is complicated by undersampled input data, acquisition noise, and large condition numbers for some methods. Therefore, standard TFM algorithms either employ data filtering or regularization. However, these approaches require a manual selection of filter- or regularization parameters and consequently exhibit a substantial degree of subjectiveness. This shortcoming is particularly serious when cells in different conditions are to be compared because optimal noise suppression needs to be adapted for every situation, which invariably results in systematic errors. Here, we systematically test the performance of new methods from computer vision and Bayesian inference for solving the inverse problem in TFM. We compare two classical schemes, L1- and L2-regularization, with three previously untested schemes, namely Elastic Net regularization, Proximal Gradient Lasso, and Proximal Gradient Elastic Net. Overall, we find that Elastic Net regularization, which combines L1 and L2 regularization, outperforms all other methods with regard to accuracy of traction reconstruction. Next, we develop two methods, Bayesian L2 regularization and Advanced Bayesian L2 regularization, for automatic, optimal L2 regularization. Using artificial data and experimental data, we show that these methods enable robust reconstruction of traction without requiring a difficult selection of regularization parameters specifically for each data set. Thus, Bayesian methods can mitigate the considerable uncertainty inherent in comparing cellular tractions in different conditions.
Quantitative analysis, pharmacokinetics and metabolomics study for the comprehensive characterization of the salt-processing mechanism of Psoraleae Fructus
Authors: Li Kai , Zhou Ning , Zheng Xiao-Ke , Feng Wei-Sheng , Li Fei , Zhang Zhen-Ling , Lu Ya-Qi
Published: January 2019

Research based on quantitative analysis, pharmacokinetics and metabolomics was conducted to explore the effects of salt-processing on Psoraleae Fructus (PF). Quantitative analysis showed that the contents of bioactive components were higher in salt-processed Psoraleae Fructus (SPF) extract than in PF extract. Pharmacokinetics indicated that the overall AUC and tmax levels was higher, while Cmax was lower in the SPF group. In the metabolomics study, the differential influences of PF and SPF on 22 common biomarkers and associated metabolic pathways showed that salt-processing could enhance the effect of PF and reduce toxicity in the cardiovascular and renal systems. The internal correlations among these results, together with the influence of salt-processing, suggested that the effects of heating and newly generated surfactants during the salt-processing procedure were the primary causes of the changes in chemical composition and absorption characteristics, as well as the subsequent enhanced efficacy and minor toxicity.
DNA damage and transcriptional regulation in iPSC-derived neurons from Ataxia Telangiectasia patients
Authors: Corti Alessandro , Sota Raina , Dugo Matteo , Calogero Raffaele A. , Terragni Benedetta , Mantegazza Massimo , Franceschetti Silvana , Restelli Michela , Gasparini Patrizia , Lecis Daniele , Chrzanowska Krystyna H. , Delia Domenico
Published: January 2019

Ataxia Telangiectasia (A-T) is neurodegenerative syndrome caused by inherited mutations inactivating the ATM kinase, a master regulator of the DNA damage response (DDR). What makes neurons vulnerable to ATM loss remains unclear. In this study we assessed on human iPSC-derived neurons whether the abnormal accumulation of DNA-Topoisomerase 1 adducts (Top1ccs) found in A-T impairs transcription elongation, thus favoring neurodegeneration. Furthermore, whether neuronal activity-induced immediate early genes (IEGs), a process involving the formation of DNA breaks, is affected by ATM deficiency. We found that Top1cc trapping by CPT induces an ATM-dependent DDR as well as an ATM-independent induction of IEGs and repression especially of long genes. As revealed by nascent RNA sequencing, transcriptional elongation and recovery were found to proceed with the same rate, irrespective of gene length and ATM status. Neuronal activity induced by glutamate receptors stimulation, or membrane depolarization with KCl, triggered a DDR and expression of IEGs, the latter independent of ATM. In unperturbed A-T neurons a set of genes (FN1, DCN, RASGRF1, FZD1, EOMES, SHH, NR2E1) implicated in the development, maintenance and physiology of central nervous system was specifically downregulated, underscoring their potential involvement in the neurodegenerative process in A-T patients.
Identifying outbreaks of Porcine Epidemic Diarrhea virus through animal movements and spatial neighborhoods
Authors: Machado Gustavo , Vilalta Carles , Recamonde-Mendoza Mariana , Corzo Cesar , Torremorell Montserrat , Perez Andrez , VanderWaal Kimberly
Published: January 2019

The spread of pathogens in swine populations is in part determined by movements of animals between farms. However, understanding additional characteristics that predict disease outbreaks and uncovering landscape factors related to between-farm spread are crucial steps toward risk mitigation. This study integrates animal movements with environmental risk factors to identify the occurrence of porcine epidemic diarrhea virus (PEDV) outbreaks. Using weekly farm-level incidence data from 332 sow farms, we applied machine-learning algorithms to quantify associations between risk factors and PEDV outbreaks with the ultimate goal of training predictive models and to identify the most important factors associated with PEDV occurrence. Our best algorithm was able to correctly predict whether an outbreak occurred during one-week periods with >80% accuracy. The most important predictors included pig movements into neighboring farms. Other important neighborhood attributes included hog density, environmental and weather factors such as vegetation, wind speed, temperature, and precipitation, and topographical features such as slope. Our neighborhood-based approach allowed us to simultaneously capture disease risks associated with long-distance animal movement as well as local spatial dynamics. The model presented here forms the foundation for near real-time disease mapping and will advance disease surveillance and control for endemic swine pathogens in the United States.
Production and characterization of biocontrol fertilizer from brewer’s spent grain via solid-state fermentation
Authors: Qiu Lei , Li Jiao-Jiao , Li Zhen , Wang Juan-Juan
Published: January 2019

Brewer’s spent grain (BSG) is a promising substrate for the production of biocontrol fertilizer (BF). The effects of temperature, water content and fermentation time on the conidiation and germination rate of the entomopathogenic fungi Beauveria bassiana (BbQLU1) were modeled in a 3 × 3 × 3 factorially designed experiment. The optimum conditions for BF production (60% water content at 25 °C for 12 days) resulted in a conidiation of 0.85 × 108 spores/g and a germination rate of 98.68%. BF at a concentration of 1 × 10−2 g/ml prompted plant growth and exhibited high toxicity against Galleria mellonella with an LT50 of 3.6 days. GC-MS analysis found 2-piperidone; benzoic acid, 3-methyl-, methyl ester; and other compounds to be potentially related to the toxicity and enhanced plant growth. These findings provide substantial evidence to support the production of BF.
Calcite fibre formation in modern brachiopod shells
Authors: Simonet Roda Maria , Griesshaber Erika , Ziegler Andreas , Rupp Ulrich , Yin Xiaofei , Henkel Daniela , Häussermann Vreni , Laudien Jürgen , Brand Uwe , Eisenhauer Anton , Checa Antonio G. , Schmahl Wolfgang W.
Published: January 2019

The fibrous calcite layer of modern brachiopod shells is a hybrid composite material and forms a substantial part of the hard tissue. We investigated how cells of the outer mantle epithelium (OME) secrete calcite material and generate the characteristic fibre morphology and composite microstructure of the shell. We employed AFM, FE-SEM, and TEM imaging of embedded/etched, chemically fixed/decalcified and high-pressure frozen/freeze substituted samples. Calcite fibres are secreted by outer mantle epithelium (OME) cells. Biometric analysis of TEM micrographs indicates that about 50% of these cells are attached via hemidesmosomes to an extracellular organic membrane present at the proximal, convex surface of the fibres. At these sites, mineral secretion is not active. Instead, ion transport from OME cells to developing fibres occurs at regions of closest contact between cells and fibres, however only at sites where the extracellular membrane at the proximal fibre surface is not developed yet. Fibre formation requires the cooperation of several adjacent OME cells. It is a spatially and temporally changing process comprising of detachment of OME cells from the extracellular organic membrane, mineral secretion at detachment sites, termination of secretion with formation of the extracellular organic membrane, and attachment of cells via hemidesmosomes to this membrane.
The protective value of a defensive display varies with the experience of wild predators
Authors: Umbers Kate D. L. , White Thomas E. , De Bona Sebastiano , Haff Tonya , Ryeland Julia , Drinkwater Eleanor , Mappes Johanna
Published: January 2019

Predation has driven the evolution of diverse adaptations for defence among prey, and one striking example is the deimatic display. While such displays can resemble, or indeed co-occur with, aposematic ‘warning’ signals, theory suggests deimatic displays may function independently of predator learning. The survival value of deimatic displays against wild predators has not been tested before. Here we used the mountain katydid Acripeza reticulata to test the efficacy of a putative deimatic display in the wild. Mountain katydids have a complex defence strategy; they are camouflaged at rest, but reveal a striking red-, blue-, and black-banded abdomen when attacked. We presented live katydids to sympatric (experienced) and allopatric (naive) natural predators, the Australian magpie Cracticus tibicen, and observed bird reactions and katydid behaviors and survival during repeated interactions. The efficacy of the katydids’ defence differed with predator experience. Their survival was greatest when faced with naïve predators, which provided clear evidence of the protective value of the display. In contrast, katydid survival was consistently less likely when facing experienced predators. Our results suggest that sympatric predators have learned to attack and consume mountain katydids despite their complex defense, and that their post-attack display can be an effective deterrent, particularly against naïve predators. These results suggest that deimatism does not require predator learning to afford protection, but that a predator can learn to expect the display and subsequently avoid it or ignore it. That sympatric predators learn to ignore the defense is a possible explanation for the mountain katydid’s counter-intuitive behavior of revealing warning colors only after tactile stimuli from predator attack.
A combination of yeast beta-glucan and milk hydrolysate is a suitable alternative to zinc oxide in the race to alleviate post-weaning diarrhoea in piglets
Authors: Mukhopadhya Anindya , O’Doherty John V. , Sweeney Torres
Published: January 2019

Zinc oxide (ZnO) is currently used as a dietary supplement to support gut homeostasis during the standard ‘abrupt’ weaning practices in commercial pig production. However, a replacement is urgently required as a ban on ZnO usage is imminent. The objective of this study was to explore the potential of a bovine casein hydrolysate (5kDaR) and yeast β-glucan, and their combination, as an alternative to ZnO. Eighty 21d old male piglets received a basal diet or supplemented with 5kDaR and yeast β-glucan alone or in combination, or ZnO from the day of weaning and were monitored for 10 days (n = 8/group; dietary groups: control diet; control diet + 5kDaR; control diet + yeast β-glucan; control diet + 5kDaR + yeast β-glucan; control diet + ZnO). Individually, supplement yeast β-glucan or 5kDaR did not improve gut health. In contrast, the yeast β-glucan + 5kDaR combination supplement supported a healthy gut, indicated by healthy faecal scores and improved growth parameters; similar to ZnO inclusion (P > 0.05). There was no negative effect on the gut microbiota with yeast β-glucan + 5kDaR supplementation; while ZnO negatively affected theBifidobacterium spp. abundance (P < 0.05). The inflammatory NFκB pathway was suppressed by yeast β-glucan + 5kDaR supplementation, similar to ZnO (P > 0.05). In conclusion, the dietary supplement yeast β-glucan + 5kDaR restored homeostasis of the newly weaned piglet gut similar to the widely used ZnO, and can potentially replace ZnO.
Nonlinear Imaging using Object-Dependent Illumination
Authors: Lu Jen-Tang , Goy Alexandre S. , Fleischer Jason W.
Published: January 2019

Nonlinear imaging systems can surpass the limits of linear optics, but nearly all rely on physical media and atomic/molecular response to work. These materials are constrained by their physical properties, such as frequency selectivity, environmental sensitivity, time behavior, and fixed nonlinear response. Here, we show that electro-optic spatial light modulators (SLMs) can take the place of traditional nonlinear media, provided that there is a feedback between the shape of the object and the pattern on the modulator. This feedback creates a designer illumination that generalizes the field of adaptive optics to include object-dependent patterns. Unlike physical media, the SLM response can provide a wide range of mathematical functions, operate over broad bandwidths at high speeds, and work equally well at high power and single-photon levels. We demonstrate the method experimentally for both coherent and incoherent light.
Superficial sedimentary stocks and sources of carbon and nitrogen in coastal vegetated assemblages along a flow gradient
Authors: Santos Rui , Duque-Núñez Natalia , de los Santos Carmen B. , Martins Márcio , Carrasco A. Rita , Veiga-Pires Cristina
Published: January 2019

Coastal vegetated ecosystems are major organic carbon (OC) and total nitrogen (TN) sinks, but the mechanisms that regulate their spatial variability need to be better understood. Here we assessed how superficial sedimentary OC and TN within intertidal vegetated assemblages (saltmarsh and seagrass) vary along a flow gradient, which is a major driver of sediment grain size, and thus of organic matter (OM) content. A significant relationship between flow current velocity and OC and TN stocks in the seagrass was found, but not in the saltmarsh. OC and TN stocks of the saltmarsh were larger than the seagrass, even though that habitat experiences shorter hydroperiods. Mixing models revealed that OM sources also varied along the flow gradient within the seagrass, but not in the saltmarsh, showing increasing contributions of microphytobenthos (17–32%) and decreasing contributions of POM (45–35%). As well, OM sources varied vertically as microphytobenthos contribution was highest at the higher intertidal saltmarsh (48%), but not POM (39%). Macroalgae, seagrass and saltmarsh showed low contributions. Local trade-offs between flow current velocities, hydroperiod and structural complexity of vegetation must be considered, at both horizontal and vertical (elevation) spatial dimensions, for better estimates of blue carbon and nitrogen in coastal ecosystems.
Liposome-based transfection enhances RNAi and CRISPR-mediated mutagenesis in non-model nematode systems
Authors: Adams Sally , Pathak Prachi , Shao Hongguang , Lok James B. , Pires-daSilva Andre
Published: January 2019

Nematodes belong to one of the most diverse animal phyla. However, functional genomic studies in nematodes, other than in a few species, have often been limited in their reliability and success. Here we report that by combining liposome-based technology with microinjection, we were able to establish a wide range of genomic techniques in the newly described nematode genus Auanema. The method also allowed heritable changes in dauer larvae of Auanema, despite the immaturity of the gonad at the time of the microinjection. As proof of concept for potential functional studies in other nematode species, we also induced RNAi in the free-living nematode Pristionchus pacificus and targeted the human parasite Strongyloides stercoralis.
Controlling the Polarity of the Molecular Beam Epitaxy Grown In-Bi Atomic Film on the Si(111) Surface
Authors: Lin Cho-Ying , Hsu Chia-Hsiu , Huang Yu-Zhang , Hsieh Shih-Ching , Chen Han-De , Huang Li , Huang Zhi-Quan , Chuang Feng-Chuan , Lin Deng-Sung
Published: January 2019

Synchrotron radiation core-level photoemission spectroscopy, scanning tunneling microscopy (STM), and first-principles calculations have been utilized to explore the growth processes and the atomic structure of the resulting films during the two-step molecular beam epitaxy (MBE) of In and Bi on the Si(111) surface. Deposition of 1.0-ML Bi on the In/Si(111)-(4 × 1) surface at room temperature results in Bi-terminated BiIn-(4 × 3) structures, which are stable up to ~300 °C annealing. By contrast, deposition of In on the β-Bi/Si(111)-(√3 × √3) surface at room temperature results in three dimensional (3D) In islands. In both cases, annealing at 460 °C results in the same In-terminated In0.75Bi/Si(111)-(2 × 2) surface. Our DFT calculations confirm that the surface energy of In-terminated In0.75Bi/Si(111)-(2 × 2) system is lower than that of Bi-terminated Bi0.75In/Si(111)-(2 × 2). These findings provide means for the control of the polarity of the MBE In-Bi atomically thick films.
TMEM16F activation by Ca2+ triggers plasma membrane expansion and directs PD-1 trafficking
Authors: Bricogne Christopher , Fine Michael , Pereira Pedro M. , Sung Julia , Tijani Maha , Wang Youxue , Henriques Ricardo , Collins Mary K. , Hilgemann Donald W.
Published: January 2019

TMEM16F is a Ca2+-gated ion channel that is required for Ca2+-activated phosphatidylserine exposure on the surface of many eukaryotic cells. TMEM16F is widely expressed and has roles in platelet activation during blood clotting, bone formation and T cell activation. By combining microscopy and patch clamp recording we demonstrate that activation of TMEM16F by Ca2+ionophores in Jurkat T cells triggers large-scale surface membrane expansion in parallel with phospholipid scrambling. With continued ionophore application,TMEM16F-expressing cells then undergo extensive shedding of ectosomes. The T cell co-receptor PD-1 is selectively incorporated into ectosomes. This selectivity depends on its transmembrane sequence. Surprisingly, cells lacking TMEM16F not only fail to expand surface membrane in response to elevated cytoplasmic Ca2+, but instead undergo rapid massive endocytosis with PD-1 internalisation. These results establish a new role for TMEM16F as a regulator of Ca2+activated membrane trafficking.
Metabolic Syndrome and Incidence of Laryngeal Cancer: A Nationwide Cohort Study
Authors: Kim Sang-Yeon , Han Kyung-do , Joo Young-Hoon
Published: January 2019

It is unknown whether the presence of metabolic syndrome (MetS) affects the incidence of laryngeal cancer. The aim of this national population-based retrospective study was to analyze the relationship between MetS and the incidence of laryngeal cancer. Patients with laryngeal cancer (ICD-10: C32) between 2009 and 2010 were retrospectively identified and tracked until 2015 using the Korean Health Insurance claims database. During the seven-year follow-up period, 5,322 subjects were newly diagnosed with larynx cancer. The mean age of people with laryngeal cancer was much higher than those without (63.29 vs. 47.7 years, p < 0.0001), and the incidence of larynx cancer in men was much higher than that in women (93.16% vs. 6.84%, p < 0.0001). Age, gender, smoking status, alcohol intake, and exercise-adjusted hazard ratios indicated that participants with MetS had a 1.13-fold higher hazard of having larynx cancer than those without MetS. The number of MetS components was a strong risk factor for laryngeal cancer with a higher risk estimate of this cancer in both ex- and current smokers as well as people who have never smoked. MetS was found to be an independent risk factor for the incidence of laryngeal cancer. In Korea, MetS and its components are significantly associated with the development of laryngeal cancer.
Local anaesthetics upregulate nitric oxide generation in cord blood and adult human neutrophils
Authors: Kulinska Karolina I. , Billert Maria , Sawinski Krzysztof , Czerniak Katarzyna , Gaca Michał , Kusza Krzysztof , Nowak Krzysztof W. , Siemionow Maria , Billert Hanna
Published: January 2019

Nitric oxide (NO) generation by systemic neonatal neutrophils is not clarified. It is also not known whether local anaesthetics (LAs) transferred to the fetal systemic circulation following maternal epidural blockade may affect this process. In the present study, NO generation was evaluated in neutrophils from cord blood (CB, n = 11) and adult blood (n = 10) following exposure to bupivacaine (0.0005, 0.005, 1 mM), lidocaine (0.002, 0.02, 4 mM) and ropivacaine (0.0007, 0.007, 1.4 mM) using flow cytometry, as well as indirectly by determining nitrite concentrations in cell incubation media. To determine the role of NO synthase (NOS) isoforms in NO generation following exposure to LAs, experiments were repeated in the presence of the NOS inhibitors, NG-nitro-L-arginine methyl ester and aminoguanidine; in addition, the expression of NOS isoforms was analysed. CB neutrophils produced less NO than adult neutrophils. LAs, especially ropivacaine and lidocaine, stimulated neutrophil NO generation, but in CB neutrophils this effect was negligible at clinically relevant drug concentrations. A mechanism involving NOS activity was responsible for the observed phenomena. In conclusion, LAs are able to upregulate neutrophil NO production, but in neonates this effect is likely to be clinically insignificant.
Ag fiber/IZO Composite Electrodes: Improved Chemical and Thermal Stability and Uniform Light Emission in Flexible Organic Light-Emitting Diodes
Authors: Choi Junhee , Park Cheol Hwee , Kwack Jin Ho , Lee Dong Jun , Kim Jae Geun , Choi Jaemyeong , Bae Bong Han , Park Soo Jong , Kim Enjung , Park Young Wook , Ju Byeong-Kwon
Published: January 2019

Electrospun metal fiber is a promising flexible transparent electrode owing to its extremely long length and facile fabrication process. However, metal-fiber electrodes have problems with chemical and thermal stability and nonuniform emission in organic light-emitting diode (OLED) at low luminance. In this study, we proposed a Ag fiber/IZO composite electrode with high stability. Ag fiber/IZO composite electrodes exhibited chemical and thermal stability. In addition, it was demonstrated that the OLED with the Ag fiber/IZO composite electrode operated stably, and the uniform emission of the OLED with metal-fiber electrodes improved by using highly conductive IZO film.
Characterization of drug binding within the HCN1 channel pore
Authors: Tanguay Jérémie , Callahan Karen M. , D’Avanzo Nazzareno
Published: January 2019

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels mediate rhythmic electrical activity of cardiac pacemaker cells, and in neurons play important roles in setting resting membrane potentials, dendritic integration, neuronal pacemaking, and establishing action potential threshold. Block of HCN channels slows the heart rate and is currently used to treat angina. However, HCN block also provides a promising approach to the treatment of neuronal disorders including epilepsy and neuropathic pain. While several molecules that block HCN channels have been identified, including clonidine and its derivative alinidine, lidocaine, mepivacaine, bupivacaine, ZD7288, ivabradine, zatebradine, and cilobradine, their low affinity and lack of specificity prevents wide-spread use. Different studies suggest that the binding sites of these inhibitors are located in the inner vestibule of HCN channels, but the molecular details of their binding remain unknown. We used computational docking experiments to assess the binding sites and mode of binding of these inhibitors against the recently solved atomic structure of human HCN1 channels, and a homology model of the open pore derived from a closely related CNG channel. We identify a possible hydrophobic groove in the pore cavity that plays an important role in conformationally restricting the location and orientation of drugs bound to the inner vestibule. Our results also help explain the molecular basis of the low-affinity binding of these inhibitors, paving the way for the development of higher affinity molecules.
Can electric fields explain inter-individual variability in transcranial direct current stimulation of the motor cortex?
Authors: Laakso Ilkka , Mikkonen Marko , Koyama Soichiro , Hirata Akimasa , Tanaka Satoshi
Published: January 2019

The effects of transcranial direct current stimulation (tDCS) on motor cortical excitability are highly variable between individuals. Inter-individual differences in the electric fields generated in the brain by tDCS might play a role in the variability. Here, we explored whether these fields are related to excitability changes following anodal tDCS of the primary motor cortex (M1). Motor evoked potentials (MEPs) were measured in 28 healthy subjects before and after 20 min sham or 1 mA anodal tDCS of right M1 in a double-blind crossover design. The electric fields were individually modelled based on magnetic resonance images. Statistical analysis indicated that the variability in the MEPs could be partly explained by the electric fields, subjects with the weakest and strongest fields tending to produce opposite changes in excitability. To explain the findings, we hypothesized that the likely locus of action was in the hand area of M1, and the effective electric field component was that in the direction normal to the cortical surface. Our results demonstrate that a large part of inter-individual variability in tDCS may be due to differences in the electric fields. If this is the case, electric field dosimetry could be useful for controlling the neuroplastic effects of tDCS.
A pathogenic haplotype, common in Europeans, causes autosomal recessive albinism and uncovers missing heritability in OCA1
Authors: Grønskov Karen , Jespersgaard Cathrine , Bruun Gitte Hoffmann , Harris Pernille , Brøndum-Nielsen Karen , Andresen Brage S. , Rosenberg Thomas
Published: January 2019

Oculocutaneous albinism (OCA) is a genetically heterogeneous disorder. Six genes are associated with autosomal recessive OCA (TYR, OCA2, TYRP1, SLC45A2, SLC24A5 and LRMDA), and one gene, GPR143, is associated with X-linked ocular albinism (OA). Molecular genetic analysis provides a genetic diagnosis in approximately 60% of individuals with clinical OA/OCA. A considerably number of the remaining 40% are heterozygous for a causative sequence variation in TYR. To identify missing causative sequence variants in these, we used a NGS based approach, genotyping and segregation analysis. We report two putative pathogenic haplotypes which only differ by two extremely rare SNVs, indicating that the haplotypes have a common derivation. Both haplotypes segregate consistent with an autosomal recessive inheritance pattern and include the allele p.S192Y-p.R402Q. An explanation for the pathogenicity of the haplotypes could be the combination of p.S192Y and p.R402Q. Homozygosity for the pathogenic haplotypes causes a partial albinism phenotype. In our cohort, 15% of affected individuals had a molecular genetic diagnosis involving the pathogenic haplotype. Consequently, the prevalence of albinism seems to be substantially underestimated, and children with unexplained bilateral subnormal vision and/or nystagmus should be analysed clinically and molecularly for albinism.
A Combined Targeted and Whole Exome Sequencing Approach Identified Novel Candidate Genes Involved in Heritable Pulmonary Arterial Hypertension
Authors: Barozzi Chiara , Galletti Margherita , Tomasi Luciana , De Fanti Sara , Palazzini Massimiliano , Manes Alessandra , Sazzini Marco , Galiè Nazzareno
Published: January 2019

The pathogenesis of idiopathic and heritable forms of pulmonary arterial hypertension is still not completely understood, even though several causative genes have been proposed, so that a third of patients remains genetically unresolved. Here we applied a multistep approach to extend identification of the genetic bases of such a disease by searching for novel candidate genes/pathways. Twenty-eight patients belonging to 18 families were screened for BMPR2 mutations and BMPR2-negative samples were tested for 12 additional candidate genes by means of a specific massive parallel sequencing-based assay. Finally, whole exome sequencing was performed on four patients showing no mutations at known disease genes, as well as on their unaffected parents. In addition to EIF2AK4, which has been already suggested to be associated with pulmonary veno-occlusive disease, we identified the novel candidate genes ATP13A3, CD248, EFCAB4B, involved in lung vascular remodeling that represent reliable drivers contributing to the disease according to their biological functions/inheritance patterns. Therefore, our results suggest that combining gene panel and whole exome sequencing provides new insights useful for the genetic diagnosis of familial and idiopathic pulmonary arterial hypertension, as well as for the identification of biological pathways that will be potentially targeted by new therapeutic strategies.