bluuebunny/crossref_metadata_2025 huggingface dataset:
On the need for a new generation of coastal change models for the 21st century
Authors: Ranasinghe Roshanka
Published: February 2020

The combination of climate change impacts, declining fluvial sediment supply, and heavy human utilization of the coastal zone, arguably the most populated and developed land zone in the world, will very likely lead to massive socio-economic and environmental losses in the coming decades. Effective coastal planning/management strategies that can help circumvent such losses require reliable local scale (<~10 km) projections of coastal change resulting from the integrated effect of climate change driven variations in mean sea level, storm surge, waves, and riverflows. Presently available numerical models are unable to adequately fulfill this need. A new generation of multi-scale, probabilistic coastal change models is urgently needed to comprehensively assess and optimise coastal risk at local scale, enabling risk informed, climate proof adaptation measures that strike a good balance between risk and reward.
Pentatricopeptide repeat protein MID1 modulates nad2 intron 1 splicing and Arabidopsis development
Authors: Zhao Peng , Wang Fang , Li Na , Shi Dong-Qiao , Yang Wei-Cai
Published: February 2020

As one of the best-studied RNA binding proteins in plant, pentatricopeptide repeats (PPRs) protein are mainly targeted to mitochondria and/or chloroplasts for RNA processing to regulate the biogenesis and function of the organelles, but its molecular mechanism and role in development remain to be further revealed. Here, we identified a mitochondria-localized P-type small PPR protein, MITOCHONDRION-MEDIATED GROWTH DEFECT 1 (MID1) that is crucial forArabidopsisdevelopment. Mutation inMID1causes retarded embryo development and stunted plant growth with defects in cell expansion and proliferation. Molecular experiments showed thatMID1is required for the splicing of thenad2intron 1 in mitochondria. Consistently,mid1plants display significant reduction in the abundance and activity of mitochondrial respiration complex I, accompanied by abnormal mitochondrial morphology and energy metabolism. Furthermore, MID1 is associated with othertrans-factors involved inNICOTINAMIDE ADENINE DINUCLEOTIDE HYDROGEN(NADH)DEHYDROGENASE SUBUNIT 2(nad2) intron 1 splicing, and interacts directly with itself and MITOCHONDRIAL STABILITY FACTOR 1 (MTSF1). This suggests that MID1 most likely functions as a dimer fornad2intron 1 splicing. Together, we characterized a novel PPR protein MID1 fornad2intron 1 splicing.
A Cyclic-di-GMP signalling network regulates biofilm formation and surface associated motility of Acinetobacter baumannii 17978
Authors: Ahmad Irfan , Nygren Evelina , Khalid Fizza , Myint Si Lhyam , Uhlin Bernt Eric
Published: February 2020

Acinetobacter baumannii has emerged as an increasing multidrug-resistant threat in hospitals and a common opportunistic nosocomial pathogen worldwide. However, molecular details of the pathogenesis and physiology of this bacterium largely remain to be elucidated. Here we identify and characterize the c-di-GMP signalling network and assess its role in biofilm formation and surface associated motility. Bioinformatic analysis revealed eleven candidate genes for c-di-GMP metabolizing proteins (GGDEF/EAL domain proteins) in the genome of A. baumannii strain 17978. Enzymatic activity of the encoded proteins was assessed by molecular cloning and expression in the model organisms Salmonella typhimurium and Vibrio cholerae. Ten of the eleven GGDEF/EAL proteins altered the rdar morphotype of S. typhimurium and the rugose morphotype of V. cholerae. The over expression of three GGDEF proteins exerted a pronounced effect on colony formation of A. baumannii on Congo Red agar plates. Distinct panels of GGDEF/EAL proteins were found to alter biofilm formation and surface associated motility of A. baumannii upon over expression. The GGDEF protein A1S_3296 appeared as a major diguanylate cyclase regulating macro-colony formation, biofilm formation and the surface associated motility. AIS_3296 promotes Csu pili mediated biofilm formation. We conclude that a functional c-di-GMP signalling network in A. baumannii regulates biofilm formation and surface associated motility of this increasingly important opportunistic bacterial pathogen.
A combined Far-FTIR, FTIR Spectromicroscopy, and DFT Study of the Effect of DNA Binding on the [4Fe4S] Cluster Site in EndoIII
Authors: Hassan Ayaz , Macedo Lucyano J. A. , Souza João C. P. de , Lima Filipe C. D. A. , Crespilho Frank N.
Published: February 2020

Endonuclease III (EndoIII) is a DNA glycosylase that contains the [4Fe4S] cluster, which is essential for the protein to bind to damaged DNA in a process called base excision repair (BER). Here we propose that the change in the covalency of Fe–S bonds of the [4Fe4S] cluster caused by double-stranded (ds)-DNA binding is accompanied by a change in their strength, which is due to alterations of the electronic structure of the cluster. Micro-FTIR spectroscopy in the mid-IR region and FTIR spectroscopy in the far IR (450 and 300 cm−1) were used independently to study the structural changes in EndoIII and the behavior of the [4Fe4S] cluster it contains, in the native form and upon its binding to ds-DNA. Structural changes in the DNA itself were also examined. The characteristics vibrational modes, corresponding to Fe–S (sulfide) and Fe–S (thiolate) bonds were identified in the cluster through far IR spectroscopy as well through quantum chemistry calculations. Based on the experimental results, these vibrational modes shift in their spectral positions caused by negatively charged DNA in the vicinity of the cluster. Modifications of the Fe–S bond lengths upon DNA binding, both of the Fe–S (sulfide) and Fe–S (thiolate) bonds in the [4Fe4S] cluster of EndoIII are responsible for the stabilization of the cluster towards higher oxidation state (3+), and hence its redox communication along the ds-DNA helix.
Automated high-throughput heartbeat quantification in medaka and zebrafish embryos under physiological conditions
Authors: Gierten Jakob , Pylatiuk Christian , Hammouda Omar T. , Schock Christian , Stegmaier Johannes , Wittbrodt Joachim , Gehrig Jochen , Loosli Felix
Published: February 2020

Accurate quantification of heartbeats in fish models is an important readout to study cardiovascular biology, disease states and pharmacology. However, dependence on anaesthesia, laborious sample orientation or requirement for fluorescent reporters have hampered the use of high-throughput heartbeat analysis. To overcome these limitations, we established an efficient screening assay employing automated label-free heart rate determination of randomly oriented, non-anesthetized medaka (Oryzias latipes) and zebrafish (Danio rerio) embryos in microtiter plates. Automatically acquired bright-field data feeds into an easy-to-useHeartBeatsoftware with graphical user interface for automated quantification of heart rate and rhythm. Sensitivity of the assay was demonstrated by profiling heart rates during entire embryonic development. Our analysis revealed rapid adaption of heart rates to temperature changes, which has implications for standardization of experimental layout. The assay allows scoring of multiple embryos per well enabling a throughput of >500 embryos per 96-well plate. In a proof of principle screen for compound testing, we captured concentration-dependent effects of nifedipine and terfenadine over time. Our novel assay permits large-scale applications ranging from phenotypic screening, interrogation of gene functions to cardiovascular drug development.
Developing a xenograft model of human vasculature in the mouse ear pinna
Authors: Meehan Gavin R. , Scales Hannah E. , Osii Rowland , De Niz Mariana , Lawton Jennifer C. , Marti Matthias , Garside Paul , Craig Alister , Brewer James M.
Published: February 2020

Humanised xenograft models allow for the analysis of human tissue within a physiological environmentin vivo. However, current models often rely on the angiogenesis and ingrowth of recipient vasculature to perfuse tissues, preventing analysis of biological processes and diseases involving human blood vessels. This limits the effectiveness of xenografts in replicating human physiology and may lead to issues with translating findings into human research. We have designed a xenograft model of human vasculature to address this issue. Human subcutaneous fat was culturedin vitroto promote blood vessel outgrowth prior to implantation into immunocompromised mice. We demonstrate that implants survived, retained human vasculature and anastomosed with the circulatory system of the recipient mouse. Significantly, by performing transplants into the ear pinna, this system enabled intravital observation of xenografts by multiphoton microscopy, allowing us to visualise the steps leading to vascular cytoadherence of erythrocytes infected with the human parasitePlasmodium falciparum. This model represents a useful tool for imaging the interactions that occur within human tissuesin vivoand permits visualization of blood flow and cellular recruitment in a system which is amenable to intervention for various studies in basic biology together with drug evaluation and mechanism of action studies.
High-throughput DNA barcoding of oligochaetes for abundance-based indices to assess the biological quality of sediments in streams and lakes
Authors: Vivien Régis , Apothéloz-Perret-Gentil Laure , Pawlowski Jan , Werner Inge , Lafont Michel , Ferrari Benoit J. D.
Published: February 2020

Aquatic oligochaete communities are valuable indicators of the biological quality of sediments in streams and lakes, but identification of specimens to the species level based on morphological features requires solid expertise in taxonomy and is possible only for a fraction of specimens present in a sample. The identification of aquatic oligochaetes using DNA barcodes would facilitate their use in biomonitoring and allow a wider use of this taxonomic group for ecological diagnoses. Previous approaches based on DNA metabarcoding of samples composed of total sediments or pools of specimens have been proposed for assessing the biological quality of ecosystems, but such methods do not provide precise information on species abundance, which limits the value of resulting ecological diagnoses. Here, we tested how a DNA barcoding approach based on high-throughput sequencing of sorted and genetically tagged specimens performed to assess oligochaete species diversity and abundance and the biological quality of sediments in streams and lakes. We applied both molecular and morphological approaches at 13 sites in Swiss streams and at 7 sites in Lake Geneva. We genetically identified 33 or 66 specimens per site. For both approaches, we used the same index calculations. We found that the ecological diagnoses derived from the genetic approach matched well with those of the morphological approach and that the genetic identification of only 33 specimens per site provided enough ecological information for correctly estimating the biological quality of sediments in streams and lakes.
Coalescence dynamics of 3D islands on weakly-interacting substrates
Authors: Gervilla V. , Almyras G. A. , Lü B. , Sarakinos K.
Published: February 2020

We use kinetic Monte Carlo simulations and analytical modelling to study coalescence of three-dimensional (3D) nanoscale faceted silver island pairs on weakly-interacting fcc(111) substrates, with and without concurrent supply of mobile adatoms from the vapor phase. Our simulations show that for vapor flux arrival rates F < 1 monolayer/second (ML/s) coalescence manifests itself by one of the islands absorbing the other via sidewall facet migration. This process is mediated by nucleation and growth of two-dimensional (2D) layers on the island facets, while the supply of mobile atoms increases the nucleation probability and shortens the time required for coalescence completion. When F is increased above 1 ML/s, coalescence is predominantly governed by deposition from the vapor phase and the island pair reaches a compact shape via agglomeration. The crucial role of facets for the coalescence dynamics is further supported by a mean-field thermodynamic description of the nucleation energetics and kinetics. Our findings explain experimental results which show that two-dimensional film growth morphology on weakly-interacting substrates is promoted when the rate of island coalescence is suppressed. The present study also highlights that deviations of experimentally reported film morphological evolutions in weakly-interacting film/substrate systems from predictions based on the sintering and particle growth theories may be understood in light of the effect of deposition flux atoms on the energetics and kinetics of facet-layer nucleation during coalescence.
DeepBTS: Prediction of Recurrence-free Survival of Non-small Cell Lung Cancer Using a Time-binned Deep Neural Network
Authors: Lee Bora , Chun Sang Hoon , Hong Ji Hyung , Woo In Sook , Kim Seoree , Jeong Joon Won , Kim Jae Jun , Lee Hyun Woo , Na Sae Jung , Beck Kyongmin Sarah , Gil Bomi , Park Sungsoo , An Ho Jung , Ko Yoon Ho
Published: February 2020

Accurate prediction of non-small cell lung cancer (NSCLC) prognosis after surgery remains challenging. The Cox proportional hazard (PH) model is widely used, however, there are some limitations associated with it. In this study, we developed novel neural network models called binned time survival analysis (DeepBTS) models using 30 clinico-pathological features of surgically resected NSCLC patients (training cohort, n = 1,022; external validation cohort, n = 298). We employed the root-mean-square error (in the supervised learning model, s- DeepBTS) or negative log-likelihood (in the semi-unsupervised learning model, su-DeepBTS) as the loss function. The su-DeepBTS algorithm achieved better performance (C-index = 0.7306; AUC = 0.7677) than the other models (Cox PH: C-index = 0.7048 and AUC = 0.7390; s-DeepBTS: C-index = 0.7126 and AUC = 0.7420). The top 14 features were selected using su-DeepBTS model as a selector and could distinguish the low- and high-risk groups in the training cohort (p = 1.86 × 10−11) and validation cohort (p = 1.04 × 10−10). When trained with the optimal feature set for each model, the su-DeepBTS model could predict the prognoses of NSCLC better than the traditional model, especially in stage I patients. Follow-up studies using combined radiological, pathological imaging, and genomic data to enhance the performance of our model are ongoing.
Upregulation of GPNCA is associated with poor prognosis through enhancement of tumor growth via regulating GSK3B
Authors: Liao Weijie , Liu Fuhai , Zhang Haowei , Liao Weifang , Xu Naihan , Xie Weidong , Zhang Yaou
Published: February 2020

GPNCA is a long non-coding RNA with unknown functions. In this study, using data from 9 cancers obtained from The Cancer Genome Atlas (TCGA), GPNCA was identified as overexpressed in cancer vs. normal tissues. The upregulation of GPNCA was associated with poor overall prognosis in colon, liver, renal clear cell and breast cancers. The upregulation of GPNCA was partly due to enhanced H3K27ac occupancy on its promoter region via EP300 and KAT2A/GCN5. The overexpression of GPNCA was positively related to tumor metastasis in colon cancer and poor disease-free and recurrence-free survival in colon and liver cancer. Both gene ontology (GO) enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis indicated that GPNCA was closely linked to regulation of gene transcription and post-transcriptional modifications, which was further supported by in vitro cell cytoplasmic and nuclear RNA purification assessments. Furthermore, GPNCA was associated with cell growth. Our in vitro experiments demonstrated that GPNCA silencing inhibited tumor growth via inhibiting its nearby gene GSK3B. Taken together, these findings highlight GPNCA as a biomarker for cancer diagnosis and a potential target for future cancer drug development.
Leveraging Signatures of Plant Functional Strategies in Wood Density Profiles of African Trees to Correct Mass Estimations From Terrestrial Laser Data
Authors: Momo Stéphane Takoudjou , Ploton Pierre , Martin-Ducup Olivier , Lehnebach Romain , Fortunel Claire , Sagang Le Bienfaiteur Takougoum , Boyemba Faustin , Couteron Pierre , Fayolle Adeline , Libalah Moses , Loumeto Joel , Medjibe Vincent , Ngomanda Alfred , Obiang Diosdado , Pélissier Raphaël , Rossi Vivien , Yongo Olga ,   PREREDD Collaborators, Bocko Yannick , Fonton Noël , Kamdem Narcisse , Katembo John , Kondaoule Henriette Josiane , Maïdou Hervé Martial , Mankou Géraud , Mbasi Michel , Mengui Thomas , Mofack Gislain I. I. , Moundounga Cynel , Moundounga Quentin , Nguimbous Lydie , Ncham Norberto Nsue , Asue Francisco Ondo Meye , Senguela Yvon-Patrick , Viard Lionel , Zapfack Louis , Sonké Bonaventure , Barbier Nicolas
Published: February 2020

Wood density (WD) relates to important tree functions such as stem mechanics and resistance against pathogens. This functional trait can exhibit high intraindividual variability both radially and vertically. With the rise of LiDAR-based methodologies allowing nondestructive tree volume estimations, failing to account for WD variations related to tree function and biomass investment strategies may lead to large systematic bias in AGB estimations. Here, we use a unique destructive dataset from 822 trees belonging to 51 phylogenetically dispersed tree species harvested across forest types in Central Africa to determine vertical gradients in WD from the stump to the branch tips, how these gradients relate to regeneration guilds and their implications for AGB estimations. We find that decreasing WD from the tree base to the branch tips is characteristic of shade-tolerant species, while light-demanding and pioneer species exhibit stationary or increasing vertical trends. Across all species, the WD range is narrower in tree crowns than at the tree base, reflecting more similar physiological and mechanical constraints in the canopy. Vertical gradients in WD induce significant bias (10%) in AGB estimates when using database-derived species-average WD data. However, the correlation between the vertical gradients and basal WD allows the derivation of general correction models. With the ongoing development of remote sensing products providing 3D information for entire trees and forest stands, our findings indicate promising ways to improve greenhouse gas accounting in tropical countries and advance our understanding of adaptive strategies allowing trees to grow and survive in dense rainforests.
Crystallization Mechanism in Spark Plasma Sintered Bulk Metallic Glass Analyzed using Small Angle Neutron Scattering
Authors: Paul Tanaji , Singh Ashish , Littrell Kenneth C. , Ilavsky Jan , Harimkar Sandip P.
Published: February 2020

Understanding the thermal stability of metallic glasses is critical to determining their safe temperatures of service. In this paper, the crystallization mechanism in spark plasma sintered Fe48Cr15Mo14Y2C15B6 metallic glass is established by analyzing the crystal size distribution using x-ray diffraction, transmission electron microscopy and in-situ small angle neutron scattering. Isothermal annealing at 700 °C and 725 °C for 100 min resulted in the formation of (Fe,Cr)23C6 crystals, measured from transmission electron micrographs, to be from 10 to 30 nm. The small angle neutron scattering intensity measured in-situ, over a Q-range of 0.02 to 0.3 Å−1, during isothermal annealing of the sintered samples, confirmed the presence of (Fe,Cr)23C6 crystals. The measured scattering intensity, fitted by the maximum entropy model, over the Q-range of 0.02 to 0.06 Å−1, revealed that the crystals had radii ranging from 3 to 18 nm. The total volume fraction of crystals were estimated to be 0.13 and 0.22 upon isothermal annealing at 700 °C and 725 °C for 100 min respectively. The mechanism of crystallization in this spark plasma sintered iron based metallic glass was established to be from pre-existing nuclei as confirmed by Avrami exponents of 0.25 ± 0.01 and 0.39 ± 0.01 at the aforesaid temperatures.
Hepatitis C Virus Clearance with Glucose Improvement and Factors Affecting the Glucose Control in Chronic Hepatitis C Patients
Authors: Yuan Man , Zhou Juan , Du Lingyao , Yan Libo , Tang Hong
Published: February 2020

The study aimed to investigate whether the glucose level improves and what factors affect the improvement in glucose control after the eradication of hepatitis C virus (HCV). A total of 1090 patients with HCV infections were enrolled, among which 278 (25.5%) patients were diagnosed with prediabetes, and 89 (8.16%) patients were diagnosed with diabetes. In the cohort, 990 patients belonged to sustained virological response (SVR) group and 100 belonged to non-SVR group. Decreases in the fasting plasma glucose (FPG) level were found in the SVR group but not in the non-SVR group (p < 0.001; p = 0.267). In the SVR group, subjects with baseline FPG ≥ 5.6 mmol/L were further stratified into glycometabolism-improved (N = 182) and unimproved (N = 150) groups according to their FPG after viral eradication. Multivariate analysis showed that older age, higher baseline HCV RNA, glucose, total bilirubin and alanine aminotransferase levels were independent risk factors for insufficient glucose improvement. In conclusion, patients with HCV infection had a higher prevalence of abnormal glycometabolism. It could be improved after viral eradication, indicating that HCV may influence glycometabolism. Moreover, Age, baseline HCV RNA, glucose, total bilirubin and alanine aminotransferase levels were impact factor for glycometabolism improvement after viral eradication.
Probing phase transition in VO2 with the novel observation of low-frequency collective spin excitation
Authors: Basu Raktima , Srihari V. , Sardar Manas , Srivastava Sachin Kumar , Bera Santanu , Dhara Sandip
Published: February 2020

VO2 is well known for its first order, reversible, metal-to-insulator transition (MIT) along with a simultaneous structural phase transition (SPT) from a high-temperature metallic rutile tetragonal (R) to an insulating low-temperature monoclinic (M1) phase via two other insulating metastable phases of monoclinic M2 and triclinic T. At the same time, VO2 gains tremendous attention because of the half-a-century-old controversy over its origin, whether electron-electron correlation or electron-phonon coupling trigger the phase transition. In this regard, V1-xMgxO2 samples were grown in stable phases of VO2 (M1, M2, and T) by controlled doping of Mg. We have observed a new collective mode in the low-frequency Raman spectra of all three insulating M1, M2 and T phases. We identify this mode with the breather (singlet spin excitation) mode about a spin-Pierls dimerized one dimensional spin ½ Heisenberg chain. The measured frequencies of these collective modes are phenomenologically consistent with the superexchange coupling strength between V spin ½ moments in all three phases. The significant deviation of Stokes to anti-Stokes intensity ratio of this low-frequency Raman mode from the usual thermal factor exp(hʋ/KBT) for phonons, and the orthogonal dependency of the phonon and spinon vibration in the polarized Raman study confirm its origin as spin excitations. The shift in the frequency of spin-wave and simultaneous increase in the transition temperature in the absence of any structural change confirms that SPT does not prompt MIT in VO2. On the other hand, the presence of spin-wave confirms the perturbation due to spin-Peierls dimerization leading to SPT. Thus, the observation of spin-excitations resulting from 1-D Heisenberg spin-½ chain can finally resolve the years-long debate in VO2 and can be extended to oxide-based multiferroics, which are useful for various potential device applications.
Shoes with active insoles mitigate declines in balance after fatigue
Authors: Moon Jeongin , Pathak Prabhat , Kim Sudeok , Roh Se-gon , Roh Changhyun , Shim Youngbo , Ahn Jooeun
Published: February 2020

Fatigue can induce postural instability and even lead to falls. However, most current methods to delay or reduce fatigue require long preparatory time, or large and expensive equipment. We propose a convenient method to alleviate postural instability due to fatigue. We paid attention to that fatigue and aging share similar neurophysiological deterioration of sensory-motor function. Considering that stochastic resonance via sub-sensory mechanical vibration increases postural stability in the elderly, we propose that sub-sensory insole vibration reduces the negative effect of fatigue on postural control. We performed experiments with 21 young and healthy adult participants, and demonstrated that insole vibration compensates for the loss of balance ability due to fatigue. The sub-sensory insole vibration restored both the area of center of pressure and the complexity of the time series of the motor output after fatigue to the pre-fatigue levels. The insole units generating the vibration were completely concealed in shoes and controlled by a smart phone. This compact implementation contrasts with the cumbersome procedure of current solutions to fatigue-induced postural instability.
Organelle inheritance and genome architecture variation in isogamous brown algae
Authors: Choi Ji Won , Graf Louis , Peters Akira F. , Cock J. Mark , Nishitsuji Koki , Arimoto Asuka , Shoguchi Eiichi , Nagasato Chikako , Choi Chang Geun , Yoon Hwan Su
Published: February 2020

Among the brown algal lineages, Ectocarpales species have isogamous fertilization in which male and female gametes are morphologically similar. In contrast, female gametes are much larger than male gametes in the oogamous species found in many other brown algal lineages. It has been reported that the plastids of isogamous species are biparentally inherited whereas the plastids of oogamous species are maternally inherited. In contrast, in both isogamous and oogamous species, the mitochondria are usually inherited maternally. To investigate whether there is any relationship between the modes of inheritance and organellar genome architecture, we sequenced six plastid genomes (ptDNA) and two mitochondrial genomes (mtDNA) of isogamous species from the Ectocarpales and compared them with previously sequenced organellar genomes. We found that the biparentally inherited ptDNAs of isogamous species presented distinctive structural rearrangements whereas maternally inherited ptDNAs of oogamous species showed no rearrangements. Our analysis permits the hypothesis that structural rearrangements in ptDNAs may be a consequence of the mode of inheritance.
Ultrasonically and Iontophoretically Enhanced Drug-Delivery System Based on Dissolving Microneedle Patches
Authors: Bok Moonjeong , Zhao Zhi-Jun , Jeon Sohee , Jeong Jun-Ho , Lim Eunju
Published: February 2020

A multifunctional system comprised of hyaluronic acid microneedles was developed as an effective transdermal delivery platform for rapid local delivery. The microneedles can regulate the filling amount on the tip, by controlling the concentration of hyaluronic acid solution. Ultrasonication induces dissolution of the HA microneedles via vibration of acoustic pressure, and AC iontophoresis improves the electrostatic force-driven diffusion of HA ions and rhodamine B. The effect of ultrasound on rhodamine release was analyzed in vitro using a gelatin hydrogel. The frequency and voltage dependence of the AC on the ion induction transfer was also evaluated experimentally. The results showed that the permeability of the material acts as a key material property. The delivery system based on ultrasonication and iontophoresis in microneedles increases permeation, thus resulting in shorter initial delivery time than that required by delivery systems based on passive or ultrasonication alone. This study highlights the significance of the combination between ultrasonic waves and iontophoresis for improving the efficiency of the microneedles, by shortening the reaction duration. We anticipate that this system can be extended to macromolecular and dependence delivery, based on drug response time.
Impacts of climate change on tropical cyclones and induced storm surges in the Pearl River Delta region using pseudo-global-warming method
Authors: Chen Jilong , Wang Ziqian , Tam Chi-Yung , Lau Ngar-Cheung , Lau Dick-Shum Dickson , Mok Hing-Yim
Published: February 2020

We have investigated changes of western North Pacific land-falling tropical cyclone (TC) characteristics due to warmer climate conditions, using the pseudo-global-warming (PGW) technique. Historical simulations of three intense TCs making landfall in Pearl River Delta (PRD) were first conducted using the Weather Research and Forecasting (WRF) model. The same cases were then re-simulated by superimposing near- (2015–2039) and far- (2075–2099) future temperature and humidity changes onto the background climate; these changes were derived from the Coupled Model Intercomparison Project phase 5 (CMIP5) multi-model projections according to the Representative Concentration Pathway (RCP) 8.5 scenario. Peak intensities of TCs (maximum surface wind in their lifetimes) are expected to increase by ~ (3) 10% in the (near) far future. Further experiments indicate that surface warming alone acts to intensify TCs by enhancing sea surface heat flux, while warmer atmosphere acts in the opposite way by increasing the stability. In the far future, associated storm surges are also estimated to increase by about 8.5%, computed by the Sea, Lake, and Overland Surges from Hurricanes (SLOSH) model. Combined with sea level rise and estimated land vertical displacement, TC-induced storm tide affecting PRD will increase by ~1 m in the future 2075–2099 period.
The vocal organ of hummingbirds shows convergence with songbirds
Authors: Riede Tobias , Olson Christopher R.
Published: February 2020

How sound is generated in the hummingbird syrinx is largely unknown despite their complex vocal behavior. To fill this gap, syrinx anatomy of four North American hummingbird species were investigated by histological dissection and contrast-enhanced microCT imaging, as well as measurement of vocalizations in a heliox atmosphere. The placement of the hummingbird syrinx is uniquely located in the neck rather than inside the thorax as in other birds, while the internal structure is bipartite with songbird-like anatomical features, including multiple pairs of intrinsic muscles, a robust tympanum and several accessory cartilages. Lateral labia and medial tympaniform membranes consist of an extracellular matrix containing hyaluronic acid, collagen fibers, but few elastic fibers. Their upper vocal tract, including the trachea, is shorter than predicted for their body size. There are between-species differences in syrinx measurements, despite similar overall morphology. In heliox, fundamental frequency is unchanged while upper-harmonic spectral content decrease in amplitude, indicating that syringeal sounds are produced by airflow-induced labia and membrane vibration. Our findings predict that hummingbirds have fine control of labia and membrane position in the syrinx; adaptations that set them apart from closely related swifts, yet shows convergence in their vocal organs with those of oscines.
A five-year longitudinal observational study in morbidity and mortality of negative appendectomy in Sulaimani teaching Hospital/Kurdistan Region/Iraq
Authors: Ahmed Hiwa Omer , Muhedin Rizgar , Boujan Amir , Aziz Aso Hama Saeed , Abdulla Ara muhamad , Hardi Rezan Ahmed , Abdulla Aso Ahmed , Sidiq Taban Aziz
Published: February 2020

The most common surgical emergency is suspected acute appendicitis, the lifetime risk of acute appendicitis is estimated to be 8.6% for men and 6.7% for women, with a male to female ratio of 1.4:1; correct diagnosis can be made in 70–80% of patients after the operations about 32% of appendectomies revealed normal appendices and meanwhile appendectomy has a considerable morbidity and mortality. The aim is to explore potential morbidity and mortality associated with negative appendectomy. Prospective case series study, including 5847 patients, who were suspected to have acute appendicitis over a period of five years from 1st December 2013 to 30th November 2018, in emergency department of Sulaimani Teaching Hospital. All the collected data were collected, organized then analyzed by Statistical Package for the Social Sciences version 21. Morbidity in the patients with negative appendectomies occurred in patients in the form of 90 (01.91%) wound infection, 48 (01.02%) intestinal obstruction and last 15 (00.32%) patients developed septicemia. While mortality in negative appendectomy patients was 21, (00.45%). Negative appendectomies have high rates of morbidity and mortality, knowing real rates may help in considering various policies and may be helpful to elude avoidable complications and potential mortality.
Impact of Bayesian Inference on the Selection of Psidium guajava
Authors: da Silva Flavia Alves , Viana Alexandre Pio , Corrêa Caio Cezar Guedes , Carvalho Beatriz Murizini , de Sousa Carlos Misael Bezerra , Amaral Bruno Dias , Ambrósio Moisés , Glória Leonardo Siqueira
Published: February 2020

Perennial breeding species demand substantial investment in various resources, mainly the required time to obtain adult and productive plants. Estimating several genetic parameters in these species, in a more confidence way, means saving resources when selecting a new genotype. A model using the Bayesian approach was compared with the frequentist methodology for selecting superior genotypes. A population of 17 families of full-siblings of guava tree was evaluated, and the yield, fruit mass, and pulp mass were measured. The Bayesian methodology suggest more accurate estimates of variance components, as well as better results to fit of model in a cross-validation. Proper priori for Bayesian model is very important to convergency of chains, mainly for small datasets. Even with poor priori, Bayesian was better than frequentist approach.
Apoptosis of vaginal epithelial cells in clinical samples from women with diagnosed bacterial vaginosis
Authors: Roselletti Elena , Sabbatini Samuele , Perito Stefano , Mencacci Antonella , Vecchiarelli Anna , Monari Claudia
Published: February 2020

Bacterial vaginosis (BV) is one of the most common vaginal infections among women of childbearing age. Gardnerella vaginalis (G. vaginalis) is a keystone microorganism present in more than 95% of all BV cases. The first step of the infection process in BV is mediated by interaction of microorganisms with epithelial cells (ECs). However, the role of these cells in BV pathogenesis is largely unknown. The present study aimed to investigate the vaginal EC response during BV. Twenty healthy women and 34 women with BV were enrolled in this study. The number of ECs in the vaginal swab was counted and analyzed for intracellular signals and apoptosis by flow cytometry. Cell damage was evaluated by lactate dehydrogenase assay. Compared to that in healthy donors, the percentage of exfoliated vaginal ECs was increased in women with BV, and an absence of neutrophils was observed in both groups. Activation signals, such as p-IκBα and c-Fos were unmodulated in the vaginal ECs of women with BV. Moreover, EC damage and apoptosis were significantly increased in patients with BV. Apoptosis was related to caspase-3 activation and the presence of G. vaginalis. This study provides the first evidence of a direct involvement of G. vaginalis in the apoptotic process of vaginal ECs during BV. This effect was mediated by caspase-3 activation, and G. vaginalis appeared to be one of causes for inducing EC apoptosis in BV. Hence, our findings suggest a possible explanation for the increased exfoliation of ECs in the vagina during BV.
On-site single pollen metabolomics reveals varietal differences in phosphatidylinositol synthesis under heat stress conditions in rice
Authors: Wada Hiroshi , Hatakeyama Yuto , Nakashima Taiken , Nonami Hiroshi , Erra-Balsells Rosa , Hakata Makoto , Nakata Keisuke , Hiraoka Kenzo , Onda Yayoi , Nakano Hiroshi
Published: February 2020

Although a loss of healthy pollen grains induced by metabolic heat responses has been indicated to be a major cause of heat-induced spikelet sterility under global climate change, to date detailed information at pollen level has been lacking due to the technical limitations. In this study, we used picolitre pressure-probe-electrospray-ionization mass spectrometry (picoPPESI-MS) to directly determine the metabolites in heat-treated single mature pollen grains in two cultivars, heat-tolerant cultivar, N22 and heat-sensitive cultivar, Koshihikari. Heat-induced spikelet fertility in N22 and Koshihikari was 90.0% and 46.8%, respectively. While no treatment difference in in vitro pollen viability was observed in each cultivar, contrasting varietal differences in phosphatidylinositol (PI)(34:3) have been detected in mature pollen, together with other 106 metabolites. Greater PI content was detected in N22 pollen regardless of the treatment, but not for Koshihikari pollen. In contrast, there was little detection for phosphoinositide in the single mature pollen grains in both cultivars. Our findings indicate that picoPPESI-MS analysis can efficiently identify the metabolites in intact single pollen. Since PI is a precursor of phosphoinositide that induces multiple signaling for pollen germination and tube growth, the active synthesis of PI(34:3) prior to germination may be closely associated with sustaining spikelet fertility even at high temperatures.
Associations of a vegan diet with inflammatory biomarkers
Authors: Menzel Juliane , Biemann Ronald , Longree Alessa , Isermann Berend , Mai Knut , Schulze Matthias B. , Abraham Klaus , Weikert Cornelia
Published: February 2020

Vegetarian or vegan nutrition might influence inflammatory processes, thereby reducing the risk of chronic diseases. As the vegan diet becomes more importance in modern societies, data from the “Risks and Benefits of a Vegan Diet”-study has been used to investigate the associations of veganism with a comprehensive spectrum of inflammatory biomarkers, compared to omnivores. This cross-sectional study comprises 36 vegans and 36 omnivores (18 men and 18 women each) aged 30–60 years. No significant differences in any of the investigated inflammatory biomarkers (high-sensitivity C-reactive protein (hsCRP), interleukin-18 (IL-18), interleukin-1 receptor antagonist (IL-1 RA), intercellular adhesion molecule-1 (ICAM-1), adiponectin, omentin-1 and resistin) were observed between vegans and omnivores. However, the duration of a vegan diet was positively correlated with resistin (Spearman r = 0.59), IL-18 concentrations (Spearman r = 0.44) and IL-1 RA (Spearman r = 0.34). Moreover, the present study supports BMI and waist circumference as important factors influencing the inflammatory state. Further research is needed to evaluate associations between a vegan diet and inflammatory biomarkers to provide more evidence about the inflammatory state as underlying mechanisms of a vegan diet to influence the risk of numerous chronic diseases.
Generation of mouse model of TGFBI-R124C corneal dystrophy using CRISPR/Cas9-mediated homology-directed repair
Authors: Kitamoto Kohdai , Taketani Yukako , Fujii Wataru , Inamochi Aya , Toyono Tetsuya , Miyai Takashi , Yamagami Satoru , Kuroda Masahiko , Usui Tomohiko , Ouchi Yasuo
Published: February 2020

Mutations in transforming growth factor-beta-induced (TGFBI) gene cause clinically distinct types of corneal dystrophies. To delineate the mechanisms driving these dystrophies, we focused on the R124C mutation in TGFBI that causes lattice corneal dystrophy type1 (LCD1) and generated novel transgenic mice harbouring a single amino acid substitution of arginine 124 with cysteine in TGFBI via ssODN-mediated base-pair substitution using CRISPR/Cas9 technology. Eighty percent of homozygous and 9.1% of heterozygous TGFBI-R124C mice developed a corneal opacity at 40 weeks of age. Hematoxylin and eosin and Masson trichrome staining showed eosinophilic deposits in subepithelial corneal stroma that stained negative for Congo-red. Although amyloid deposition was not observed in TGFBI-R124C mice, irregular amorphous deposits were clearly observed via transmission electron microscopy near the basement membrane. Interestingly, we found that the corneal deposition of TGFBI protein (TGFBIp) was significantly increased in homozygous TGFBI-R124C mice, suggesting a pathogenic role for the mutant protein accumulation. Furthermore, as observed in the LCD1 patients, corneal epithelial wound healing was significantly delayed in TGFBI-R124C mice. In conclusion, our novel mouse model of TGFBI-R124C corneal dystrophy reproduces features of the human disease. This mouse model will help delineate the pathogenic mechanisms of human corneal dystrophy.
Comparative transcriptome profiling of selected osmotic regulatory proteins in the gill during seawater acclimation of chum salmon (Oncorhynchus keta) fry
Authors: Lee Sang Yoon , Lee Hwa Jin , Kim Yi Kyung
Published: February 2020

Salmonid fishes, chum salmon (Oncorhynchus keta) have the developed adaptive strategy to withstand wide salinity changes from the early life stage. This study investigated gene expression patterns of cell membrane proteins in the gill of chum salmon fry on the transcriptome level by tracking the salinity acclimation of the fish in changing environments ranging from freshwater (0 ppt) to brackish water (17.5 ppt) to seawater (35 ppt). Using GO analysis of DEGs, the known osmoregulatory genes and their functional groups such as ion transport, transmembrane transporter activity and metal ion binding were identified. The expression patterns of membrane protein genes, including pump-mediated protein (NKA, CFTR), carrier-mediated protein (NKCC, NHE3) and channel-mediated protein (AQP) were similar to those of other salmonid fishes in the smolt or adult stages. Based on the protein-protein interaction analysis between transmembrane proteins and other related genes, we identified osmotic-related genes expressed with salinity changes and analyzed their expression patterns. The findings of this study may facilitate the disentangling of the genetic basis of chum salmon and better able an understanding of the osmophysiology of the species.
Predictive context biases binocular rivalry in children and adults with no positive relation to two measures of social cognition
Authors: Valuch Christian , Kulke Louisa
Published: February 2020

Integration of prior experience and contextual information can help to resolve perceptually ambiguous situations and might support the ability to understand other peoples’ thoughts and intentions, called Theory of Mind. We studied whether the readiness to incorporate contextual information for resolving binocular rivalry is positively associated with Theory-of-Mind-related social cognitive abilities. In children (12 to 13 years) and adults (18 to 25 years), a predictive temporal context reliably modulated the onset of binocular rivalry to a similar degree. In contrast, adult participants scored better on measures of Theory of Mind compared to children. We observed considerable interindividual differences regarding the influence of a predictive context on binocular rivalry, which were associated with differences in sensory eye dominance. The absence of a positive association between predictive effects on perception and Theory of Mind performance suggests that predictive effects on binocular rivalry and higher-level Theory-of-Mind-related abilities stem from different neurocognitive mechanisms. We conclude that the influence of predictive contextual information on basic visual processes is fully developed at an earlier age, whereas social cognitive skills continue to evolve from adolescence to adulthood.
Numerical Analysis of Airway Mucus Clearance Effectiveness Using Assisted Coughing Techniques
Authors: Ren Shuai , Li Wei , Wang Lin , Shi Yan , Cai Maolin , Hao Liming , Luo Zihao , Niu Jinglong , Xu Weiqing , Luo Zujin
Published: February 2020

Cough is a protective respiratory reflex used to clear respiratory airway mucus. For patients with cough weakness, such as chronic obstructive pulmonary disease, neuromuscular weakness disease and other respiratory diseases, assisted coughing techniques are essential to help them clear mucus. In this study, the Eulerian wall film model was applied to simulate the coughing clearance process through a computational fluid dynamics methodology. Airway generation 0 to generation 2 based on realistic geometry is considered in this study. To quantify cough effectiveness, cough efficiency was calculated. Moreover, simulations of four different coughing techniques applied for chronic obstructive pulmonary disease and neuromuscular weakness disease were conducted. The influences of mucus film thickness and mucus viscosity on cough efficiency were analyzed. From the simulation results, we found that with increasing mucus film thickness and decreasing mucus viscosity, cough efficiency improved accordingly. Assisted coughing technologies have little influence on the mucus clearance of chronic obstructive pulmonary disease models. Finally, it was observed that the cough efficiency of the mechanical insufflation-exsufflation technique (MIE) is more than 40 times the value of an unassisted coughing technique, which indicates that the MIE technology has a great effect on airway mucus clearance for neuromuscular weakness disease models.
Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer
Authors: Szczerba Hubert , Komoń-Janczara Elwira , Krawczyk Mariusz , Dudziak Karolina , Nowak Anna , Kuzdraliński Adam , Waśko Adam , Targoński Zdzisław
Published: February 2020

Enterobacter aerogenes LU2 was isolated from cow rumen and recognized as a potential succinic acid producer in our previous study. Here, we present the first complete genome sequence of this new, wild strain and report its basic genetic features from a biotechnological perspective. The MinION single-molecule nanopore sequencer supported by the Illumina MiSeq platform yielded a circular 5,062,651 bp chromosome with a GC content of 55% that lacked plasmids. A total of 4,986 genes, including 4,741 protein-coding genes, 22 rRNA-, 86 tRNA-, and 10 ncRNA-encoding genes and 127 pseudogenes, were predicted. The genome features of the studied strain and other Enterobacteriaceae strains were compared. Functional studies on the genome content, metabolic pathways, growth, and carbon transport and utilization were performed. The genomic analysis indicates that succinic acid can be produced by the LU2 strain through the reductive branch of the tricarboxylic acid cycle (TCA) and the glyoxylate pathway. Antibiotic resistance genes were determined, and the potential for bacteriocin production was verified. Furthermore, one intact prophage region of length ~31,9 kb, 47 genomic islands (GIs) and many insertion sequences (ISs) as well as tandem repeats (TRs) were identified. No clustered regularly interspaced short palindromic repeats (CRISPRs) were found. Finally, comparative genome analysis with well-known succinic acid producers was conducted. The genome sequence illustrates that the LU2 strain has several desirable traits, which confirm its potential to be a highly efficient platform for the production of bulk chemicals.