bluuebunny/crossref_metadata_2025 huggingface dataset:
Contrast sensitivity isocontours of the central visual field
Authors: Choi Agnes Y. J. , Nivison-Smith Lisa , Phu Jack , Zangerl Barbara , Khuu Sieu K. , Jones Bryan W. , Pfeiffer Rebecca L. , Marc Robert E. , Kalloniatis Michael
Published: August 2019

Standard automated perimetry (SAP), the most common form of perimetry used in clinical practice, is associated with high test variability, impacting clinical decision making and efficiency. Contrast sensitivity isocontours (CSIs) may reduce test variability in SAP by identifying regions of the visual field with statistically similar patterns of change that can be analysed collectively and allow a point (disease)-to-CSI (normal) comparison in disease assessment as opposed to a point (disease)-to-point (normal) comparison. CSIs in the central visual field however have limited applicability as they have only been described using visual field test patterns with low, 6° spatial sampling. In this study, CSIs were determined within the central 20° visual field using the 10-2 test grid paradigm of the Humphrey Field Analyzer which has a high 2° sampling frequency. The number of CSIs detected in the central 20° visual field was greater than previously reported with low spatial sampling and stimulus size dependent: 6 CSIs for GI, 4 CSIs for GII and GIII, and 3 CSIs for GIV and GV. CSI number and distribution were preserved with age. Use of CSIs to assess visual function in age-related macular degeneration (AMD) found CSI guided analysis detected a significantly greater deviation in sensitivity of AMD eyes from normal compared to a standard clinical pointwise comparison (−1.40 ± 0.15 dB vs −0.96 ± 0.15 dB; p < 0.05). This work suggests detection of CSIs within the central 20° is dependent on sampling strategy and stimulus size and normative distribution limits of CSIs can indicate significant functional deficits in diseases affecting the central visual field such as AMD.
Fibrinogen binding is affected by amino acid substitutions in C-terminal repeat region of fibronectin binding protein A
Authors: Casillas-Ituarte Nadia N. , DiBartola Alex C. , Broughton Megan J. , Pérez-Guzmán Lumarie , Wheeler Robert M. , Ibaraki Makoto , Lower B. Alexis , Dunn James A. , Lower Brian H. , Fowler Vance G. , Hӧӧk Magnus , McIntyre Lauren M. , Lower Steven K. , Sharma-Kuinkel Batu K.
Published: August 2019

Fibronectin-binding protein A (FnBPA), a protein displayed on the outer surface of Staphylococcus aureus, has a structured A-domain that binds fibrinogen (Fg) and a disordered repeat-region that binds fibronectin (Fn). Amino acid substitutions in Fn-binding repeats (FnBRs) have previously been linked to cardiovascular infection in humans. Here we used microtiter and atomic force microscopy (AFM) to investigate adhesion by variants of full-length FnBPA covalently anchored in the outer cell wall of Lactococcus lactis, a Gram-positive surrogate that otherwise lacks adhesins to mammalian ligands. Fn adhesion increased in five of seven FnBPA variants under static conditions. The bond targeting Fn increased its strength with load under mechanical dissociation. Substitutions extended bond lifetime (1/koff) up to 2.1 times for FnBPA-Fn. Weaker adhesion was observed for Fg in all FnBPA variants tested with microtiter. However, mechanical dissociation with AFM showed significantly increased tensile strength for Fg interacting with the E652D/H782Q variant. This is consistent with a force-induced mechanism and suggests that the dock, lock, and latch (DLL) mechanism is favored for Fg-binding under mechanical stress. Collectively, these experiments reveal that FnBPA exhibits bimodal, ligand-dependent adhesive behavior. Amino acid substitutions in the repeat-region of FnBPA impact binding to both ligands. This was unexpected for Fg since all variants have the same A-domain sequence, and the Fg-binding site is distant from the repeat region. This indicates that FnBRs may fold back on the A-domain in a way that impacts the DLL binding mechanism for Fg.
Major lithogenic contributions to the distribution and budget of iron in the North Pacific Ocean
Authors: Zheng Linjie , Sohrin Yoshiki
Published: August 2019

Recent studies have elucidated that iron (Fe) is a critical trace metal that influences the productivity of marine ecosystems and the biogeochemical cycles of other elements in the modern ocean. However, our understanding of the biogeochemistry of Fe remains incomplete. Herein, we report basin-scale and full-depth sectional distributions of total dissolvable iron (tdFe), dissolved iron (dFe), and labile particulate iron (lpFe = tdFe – dFe) in the North Pacific Ocean, as observed during three cruises of the GEOTRACES Japan program. We found that lpFe dominates tdFe and is significantly correlated with labile particulate aluminum (lpAl): lpFe [nmol kg−1] = (0.544 ± 0.005) lpAl [nmol kg−1] + 0.11 ± 0.04, r2 = 0.968, n = 432. The results indicate a major lithogenic contribution to the distribution of particulate Fe. For dFe, the unique distribution is attributed to the combined effects of biogeochemical cycling, manganese reduction, and lithogenic contribution. Based on concurrent observations of Fe, Al, and manganese (Mn), we infer that the width of the boundary scavenging zone is approximately 500 km off the Aleutian shelf. We estimate the inventory of tdFe in the North Pacific as 1.1 × 1012 mol, which is approximately four times that of dFe. Our results emphasize the potential importance of lpFe in the ocean’s iron cycle.
Endothelial RhoA GTPase is essential for in vitro endothelial functions but dispensable for physiological in vivo angiogenesis
Authors: Zahra Fatema Tuz , Sajib Md Sanaullah , Ichiyama Yusuke , Akwii Racheal Grace , Tullar Paul E. , Cobos Christopher , Minchew Shelby A. , Doçi Colleen L. , Zheng Yi , Kubota Yoshiaki , Gutkind J. Silvio , Mikelis Constantinos M.
Published: August 2019

Imbalanced angiogenesis is a characteristic of several diseases. Rho GTPases regulate multiple cellular processes, such as cytoskeletal rearrangement, cell movement, microtubule dynamics, signal transduction and gene expression. Among the Rho GTPases, RhoA, Rac1 and Cdc42 are best characterized. The role of endothelial Rac1 and Cdc42 in embryonic development and retinal angiogenesis has been studied, however the role of endothelial RhoA is yet to be explored. Here, we aimed to identify the role of endothelial RhoA in endothelial cell functions, in embryonic and retinal development and explored compensatory mechanisms. In vitro, RhoA is involved in cell proliferation, migration and tube formation, triggered by the angiogenesis inducers Vascular Endothelial Growth Factor (VEGF) and Sphingosine-1 Phosphate (S1P). In vivo, through constitutive and inducible endothelial RhoA deficiency we tested the role of endothelial RhoA in embryonic development and retinal angiogenesis. Constitutive endothelial RhoA deficiency, although decreased survival, was not detrimental for embryonic development, while inducible endothelial RhoA deficiency presented only mild deficiencies in the retina. The redundant role of RhoA in vivo can be attributed to potential differences in the signaling cues regulating angiogenesis in physiological versus pathological conditions and to the alternative compensatory mechanisms that may be present in the in vivo setting.
Alterations in lipid metabolism of spinal cord linked to amyotrophic lateral sclerosis
Authors: Chaves-Filho Adriano Britto , Pinto Isabella Fernanda Dantas , Dantas Lucas Souza , Xavier Andre Machado , Inague Alex , Faria Rodrigo Lucas , Medeiros Marisa H. G. , Glezer Isaias , Yoshinaga Marcos Yukio , Miyamoto Sayuri
Published: August 2019

Amyotrophic lateral sclerosis (ALS) is characterized by progressive loss of upper and lower motor neurons leading to muscle paralysis and death. While a link between dysregulated lipid metabolism and ALS has been proposed, lipidome alterations involved in disease progression are still understudied. Using a rodent model of ALS overexpressing mutant human Cu/Zn-superoxide dismutase gene (SOD1-G93A), we performed a comparative lipidomic analysis in motor cortex and spinal cord tissues of SOD1-G93A and WT rats at asymptomatic (~70 days) and symptomatic stages (~120 days). Interestingly, lipidome alterations in motor cortex were mostly related to age than ALS. In contrast, drastic changes were observed in spinal cord of SOD1-G93A 120d group, including decreased levels of cardiolipin and a 6-fold increase in several cholesteryl esters linked to polyunsaturated fatty acids. Consistent with previous studies, our findings suggest abnormal mitochondria in motor neurons and lipid droplets accumulation in aberrant astrocytes. Although the mechanism leading to cholesteryl esters accumulation remains to be established, we postulate a hypothetical model based on neuroprotection of polyunsaturated fatty acids into lipid droplets in response to increased oxidative stress. Implicated in the pathology of other neurodegenerative diseases, cholesteryl esters appear as attractive targets for further investigations.
Glycan-immobilized dual-channel field effect transistor biosensor for the rapid identification of pandemic influenza viral particles
Authors: Hideshima Sho , Hayashi Hiroki , Hinou Hiroshi , Nambuya Shunsuke , Kuroiwa Shigeki , Nakanishi Takuya , Momma Toshiyuki , Nishimura Shin-Ichiro , Sakoda Yoshihiro , Osaka Tetsuya
Published: August 2019

Pandemic influenza, triggered by the mutation of a highly pathogenic avian influenza virus (IFV), has caused considerable damage to public health. In order to identify such pandemic IFVs, antibodies that specifically recognize viral surface proteins have been widely used. However, since the analysis of a newly discovered virus is time consuming, this delays the availability of suitable detection antibodies, making this approach unsuitable for the early identification of pandemic IFVs. Here we propose a label-free semiconductor-based biosensor functionalized with sialic-acid-containing glycans for the rapid identification of the pandemic IFVs present in biological fluids. Specific glycans are able to recognize wild-type human and avian IFVs, suggesting that they are useful in discovering pandemic IFVs at the early stages of an outbreak. We successfully demonstrated that a dual-channel integrated FET biosensing system, which were modified with 6′-sialyllactose and 3′-sialyllactose for each gate area, can directly and specifically detect human H1N1 and avian H5N1 IFV particles, respectively, present in nasal mucus. Furthermore, to examine the possibility of identifying pandemic IFVs, the signal attributed to the detection of Newcastle disease virus (NDV) particles, which was selected as a prime model of a pandemic IFV, was clearly observed from both sensing gates. Our findings suggest that the proposed glycan-immobilized sensing system could be useful in identifying new pandemic IFVs at the source of an outbreak.
Worldwide human mitochondrial haplogroup distribution from urban sewage
Authors: Pipek Orsolya Anna , Medgyes-Horváth Anna , Dobos László , Stéger József , Szalai-Gindl János , Visontai Dávid , Kaas Rolf S. , Koopmans Marion , Hendriksen Rene S. , Aarestrup Frank M. , Csabai István
Published: August 2019

Community level genetic information can be essential to direct health measures and study demographic tendencies but is subject to considerable ethical and legal challenges. These concerns become less pronounced when analyzing urban sewage samples, which are ab ovo anonymous by their pooled nature. We were able to detect traces of the human mitochondrial DNA (mtDNA) in urban sewage samples and to estimate the distribution of human mtDNA haplogroups. An expectation maximization approach was used to determine mtDNA haplogroup mixture proportions for samples collected at each different geographic location. Our results show reasonable agreement with both previous studies of ancient evolution or migration and current US census data; and are also readily reproducible and highly robust. Our approach presents a promising alternative for sample collection in studies focusing on the ethnic and genetic composition of populations or diseases associated with different mtDNA haplogroups and genotypes.
LncRNA SAMD12-AS1 promotes cell proliferation and inhibits apoptosis by interacting with NPM1
Authors: Liu Qi , Liu Ningning , Shangguan Qilin , Zhang Fang , Chai Wenjia , Tong Xiaomei , Zhao Xin , Li Zhiwei , Qi Dandan , Ye Xin
Published: August 2019

Chronic hepatitis B virus infection is a major risk factor for hepatocellular carcinoma. HBV infection affects lncRNA expression in infected cells, but the detailed mechanism and biological significance are not yet clear. In this study, we focused on exploring the function of the HBV-upregulated lncRNA SAMD12-AS1 in cell proliferation. We found that there is a higher level of SAMD12-AS1 expression in tumors than in adjacent nontumorous liver tissues. We showed that ectopic expression of SAMD12-AS1 promotes cell growth and blocks apoptosis, while knockdown of SAMD12-AS1 inhibits cell proliferation and enhances etoposide-induced apoptosis. Using RNA immunoprecipitation and mass spectrometry, we determined that SAMD12-AS1 interacts with NPM1 and confirmed that SAMD12-AS1(1-350) is required for the interaction with NPM1. As it is known that NPM1 interacts with the E3 ligase HDM2 and reduces HDM2-mediated p53 degradation, we examined whether SAMD12-AS1 can affect p53 stability. Overexpression of SAMD12-AS1 caused a reduction in p53 protein levels by shortening its half-life. Conversely, knockdown of SAMD12-AS1 prolonged the half-life of p53. We further demonstrated that SAMD12-AS1 increased the interaction of HDM2 and p53 and enhanced p53 ubiquitination. Our findings reveal that HBV-upregulated SAMD12-AS1 regulates cell proliferation and apoptosis via the NPM1-HDM2-p53 axis.
Pore water pressure responses in silty sediment bed under random wave action
Authors: Niu Jianwei , Xu Jishang , Dong Ping , Li Guangxue
Published: August 2019

We studied pore water pressure responses in silty seabed under random wave action through a series of experiments in a wide wave flume. Unlike previous experiments involving regular waves, we focus on random waves including wind-induced short waves and long waves so as to gain further insights into seabed responses and liquefaction risks posed by random waves. In particular, the study investigated how the secondary long waves that were induced by incident short wave groups affected the seabed responses. The test results revealed that these long waves could cause much larger seabed responses than the short waves (eight times larger in our flume tests). Although they had smaller wave heights than the short waves, the long waves were found to contribute much more significantly to the cumulative pore pressure than previously recognized. The likely reason is that the long waves are disproportionally effective in generating cumulative excess pore pressure, confirming qualitatively some of the earlier theoretical predictions. One of the implications from these research findings is that the existing design methods when applied to random waves could grossly underestimate liquefaction potential in silty sediment bed if either spectrum-based mean wave parameters or significant wave parameters were used.
Thermodynamic evidence of giant salt deposit formation by serpentinization: an alternative mechanism to solar evaporation
Authors: Debure Mathieu , Lassin Arnault , Marty Nicolas C. , Claret Francis , Virgone Aurélien , Calassou Sylvain , Gaucher Eric C.
Published: August 2019

The evaporation of seawater in arid climates is currently the main accepted driving mechanism for the formation of ancient and recent salt deposits in shallow basins. However, the deposition of huge amounts of marine salts, including the formation of tens of metres of highly soluble types (tachyhydrite and bischofite) during the Aptian in the South Atlantic and during the Messinian Salinity Crisis, are inconsistent with the wet and warm palaeoclimate conditions reconstructed for these periods. Recently, a debate has been developed that opposes the classic model of evaporite deposition and argues for the generation of salt by serpentinization. The products of the latter process can be called “dehydratites”. The associated geochemical processes involve the consumption of massive amounts of pure water, leading to the production of concentrated brines. Here, we investigate thermodynamic calculations that account for high salinities and the production of soluble salts and MgCl2-rich brines through sub-seafloor serpentinization processes. Our results indicate that salt and brine formation occurs during serpentinization and that the brine composition and salt assemblages are dependent on the temperature and CO2 partial pressure. Our findings help explain the presence and sustainability of highly soluble salts that appear inconsistent with reconstructed climatic conditions and demonstrate that the presence of highly soluble salts probably has implications for global tectonics and palaeoclimate reconstructions.
Clinical Trial to Evaluate Safety and Efficacy of Transdermal Electrical Stimulation on Visual Functions of Patients with Retinitis Pigmentosa
Authors: Miura Gen , Sugawara Takeshi , Kawasaki Yohei , Tatsumi Tomoaki , Nizawa Tomohiro , Baba Takayuki , Hanaoka Hideki , Yamamoto Shuichi
Published: August 2019

To evaluate the safety and efficacy of transdermal electrical stimulation (TdES) with skin electrodes on improving the visual functions of patients with retinitis pigmentosa (RP), twenty eyes of 10 patients with RP underwent TdES (10-ms biphasic pulses, 20 Hz, 30 min) 6 times at 2 week intervals. All patients were stimulated bilaterally with 1.0 mA pulses. The primary endpoint was safety, and the secondary endpoints were the changes in the best-corrected visual acuity (BCVA), visual fields determined by the Humphrey field analyzer (HFA) 10-2 and Goldmann perimetry, and answers to the Visual Function Questionnaire-25. All of the 10 enrolled patients completed the study according to the protocol. No adverse events related to the treatments were reported during the follow-up examinations. The mean BCVA and Early Treatment Diabetic Retinopathy Study visual acuity were significantly improved after the TdES (P = 0.0078 and P = 0.001, respectively). The mean deviation of the HFA 10-2 was also significantly improved (P = 0.0076). We conclude that TdES with skin electrode is a safe therapeutic option and should be considered as a treatment option for patients with RP.
Effectiveness of acid suppressants and other mucoprotective agents in reducing the risk of occult gastrointestinal bleeding in nonsteroidal anti-inflammatory drug users
Authors: Kim Tae Jun , Kim Eun Ran , Hong Sung Noh , Kim Young-Ho , Lee Yeong Chan , Kim Hye Seung , Kim Kyunga , Chang Dong Kyung
Published: August 2019

Acid suppressants such as histamine-2 receptor antagonists (H2RAs) and proton pump inhibitors (PPIs) are effective in preventing gastrointestinal (GI) bleeding in nonsteroidal anti-inflammatory drugs (NSAIDs) users. Despite widespread acid suppressant use, there remain concerns about several potential risks of long-term use. Therefore, we investigated whether gastroprotective agents (GPAs) other than acid suppression therapy are effective in preventing NSAID-related GI injury. To this end, we studied 9,133 patients with osteoarthritis or rheumatoid arthritis who used NSAIDs for ≥1 month. A decrease of 2 g/dL or more in the hemoglobin level was considered a GI injury indicator. The GPAs included acid suppressants and other mucoprotective agents. Acid suppressants included PPIs and H2RAs. Other mucoprotective agents included misoprostol, rebamipide, and eupatilin. During a median follow-up period of 27 (range, 4.3-51.3) weeks, occult GI bleeding occurred in 1,191 (13%) patients. A comparison of patients who used GPAs concomitantly with that of nonusers in a multivariable analysis revealed the hazard ratios (HRs; 95% confidence intervals [CIs]) for occult GI bleeding were 0.30 (0.20-0.44), 0.35 (0.29-0.43), 0.47 (0.23-0.95), 0.43 (0.35-0.51), and 0.98 (0.86-1.12) for PPIs, H2RAs, misoprostol, rebamipide, and eupatilin, respectively. Compared to PPI co-treatment, H2RA, misoprostol, rebamipide, and eupatilin co-treatments were associated with occult GI bleeding HRs (95% CIs) of 1.19 (0.79-1.79), 1.58 (0.72-3.46), 1.44 (0.96-2.16), and 3.25 (2.21-4.77), respectively. Our findings suggest that mucoprotective agents, such as rebamipide and misoprostol, as well as acid suppressants, are effective in reducing the risk for GI injury in NSAID users.
A thermosensitive electromechanical model for detecting biological particles
Authors: SoltanRezaee Masoud , Bodaghi Mahdi , Farrokhabadi Amin
Published: August 2019

Miniature electromechanical systems form a class of bioMEMS that can provide appropriate sensitivity. In this research, a thermo-electro-mechanical model is presented to detect biological particles in the microscale. Identification in the model is based on analyzing pull-in instability parameters and frequency shifts. Here, governing equations are derived via the extended Hamilton’s principle. The coupled effects of system parameters such as surface layer energy, electric field correction, and material properties are incorporated in this thermosensitive model. Afterward, the accuracy of the present model and obtained results are validated with experimental, analytical, and numerical data for several cases. Performing a parametric study reveals that mechanical properties of biosensors can significantly affect the detection sensitivity of actuated ultra-small detectors and should be taken into account. Furthermore, it is shown that the number or dimension of deposited particles on the sensing zone can be estimated by investigating the changes in the threshold voltage, electrode deflection, and frequency shifts. The present analysis is likely to provide pertinent guidelines to design thermal switches and miniature detectors with the desired performance. The developed biosensor is more appropriate to detect and characterize viruses in samples with different temperatures.
The relationship between chronic perceived stress and error processing: evidence from event-related potentials
Authors: Wu Jianhui , Feng Mengjiao , Liu Yutong , Fang Huihua , Duan Hongxia
Published: August 2019

Prolonged exposure to stress has a wide effect on the brain and cognition. Error processing, as one of the crucial components of executive function, plays an important role in cognitive and behavior control. However, to date, there is little research addressing the relationship between chronic perceived stress and error processing. The present study aims to explore the relationship between chronic perceived stress by the Cohen Perceived Stress Scale (PSS) and different stages of error processing by the method of Event-Related Potential (ERP). The error processing was tested in a classical auditory Go/NoGo paradigm, and ERP components including early Error-related Negativity (ERN) and late Error Positivity (Pe) were computed as the indices of error processing. The results showed that the PSS score was positively correlated with the Pe amplitude but not with the ERN amplitude. The correlation between PSS and the Pe amplitude holds true even after controlling the trait anxiety and depression symptoms. These results suggest that the higher the chronic stress level, the more sensitive the individuals are to their own errors as well as the more emotional/motivated attention the individuals distributed to their own errors.
Testing performance of large-scale surveys in determining trends for the critically endangered Great Indian Bustard Ardeotis nigriceps
Authors: Khan Shaheer , Chatterjee Nilanjan , Habib Bilal
Published: August 2019

Great Indian Bustard (GIB) is listed as Critically Endangered, with less than 250 individuals surviving in three fragmented populations. The species is under tremendous threat due to various anthropogenic pressures. Effective management and conservation of GIB requires a proper monitoring protocol, which we propose using an occupancy framework approach to detect changes in the species’ population. We used occupancy estimates from various landscape level surveys and simulated scenarios to evaluate the effectiveness of the proposed protocol. Our result showed there is >70% chance of detecting 100% change in the occupancy with 100 sampling sites and 10 temporal replicates. While with double sampling sites, the same change can be detected with 4–6 temporal replicates. In absence of a robust population estimation method, we argue for the use of occupancy as a surrogate to detect change in population as it provides better insights for rare elusive species such as GIB. Our proposed methodological framework is more precise than previous methods, which will help in evaluating efficacy of management interventions proposed and the implementation of species recovery plans.
Investigation of antireflective and hydrophobic properties in polycrystalline GaN films with dual porosity produced by CVD
Authors: Mena Gómez Josue , Carvajal Joan J. , Bilousov Oleksandr , Díaz Francesc , Aguiló Magdalena
Published: August 2019

We optimized the deposition conditions of polycrystalline nanoporousGaN coatings produced by Chemical Vapor Deposition on Si substrates, by exploring the effect produced by the Ga holder shape, the initial amount of Ga, the reaction deposition time and the metallic catalyst used. Such polycrystalline films probed to act as antireflective coatings by reducing the reflectance of Si substrates by 50% or more, and that of flat GaN samples by 40% in the UV and 83% in the visible, at the same time that they exhibit an almost constant reflectance from 400 to 800 nm, important to develop UV sensors with enhanced sensitivity. Furthermore, the polycrystalline nanoporous coatings we developed exhibit hydrophobic behaviour, with a static contact angle of 119°, and a contact angle hysteresis of 4.5°, which might contribute to enlarge the durability of such functional films, by the self cleaning effect induced.
Synergistic silencing of α-globin and induction of γ-globin by histone deacetylase inhibitor, vorinostat as a potential therapy for β-thalassaemia
Authors: Mettananda Sachith , Yasara Nirmani , Fisher Christopher A. , Taylor Stephen , Gibbons Richard , Higgs Doug
Published: August 2019

β-Thalassaemia is one of the most common monogenic diseases with no effective cure in the majority of patients. Unbalanced production of α-globin in the presence of defective synthesis of β-globin is the primary mechanism for anaemia in β-thalassaemia. Clinical genetic data accumulated over three decades have clearly demonstrated that direct suppression of α-globin and induction of γ-globin are effective in reducing the globin chain imbalance in erythroid cells hence improving the clinical outcome of patients with β-thalassaemia. Here, we show that the histone deacetylase inhibitor drug, vorinostat, in addition to its beneficial effects for patients with β-thalassaemia through induction of γ-globin, has the potential to simultaneously suppress α-globin. We further show that vorinostat exhibits these synergistic beneficial effects in globin gene expression at nanomolar concentrations without perturbing erythroid expansion, viability, differentiation or the transcriptome. This new evidence will be helpful for the interpretation of existing clinical trials and future clinical studies that are directed towards finding a cure for β-thalassaemia using vorinostat.
Dissipation of the Insecticide Cyantraniliprole and Its Metabolite IN-J9Z38 in Proso Millet during Cultivation
Authors: Lee Jonghwa , Jung Min Woo , Lee Junghak , Lee Jiho , Shin Yongho , Kim Jeong-Han
Published: August 2019

The dissipation patterns of cyantraniliprole and its metabolite IN-J9Z38 were investigated using proso millet (Panicum miliaceum) under open-field conditions to establish a pre-harvest interval. A simple and sensitive analytical method was developed for analyzing residues using ultra-high performance liquid chromatography coupled with tandem mass spectrometry (UHPLC-MS/MS) for multiple reaction monitoring of target compounds. The analytical method was validated in terms of the instrumental limit of quantitation, method limit of quantitation, linearity, accuracy, and precision. The method was successfully applied to the analysis of cyantraniliprole and IN-J9Z38 residues in the field samples of four plots, which were treated twice with an oil dispersion formulation, according to the date of pesticide treatment before harvest. In the case of cyantraniliprole in grain and straw, there was a 91.1 and 89.1% decrease, respectively, from the initial residues (14–7 days) to the final plot (40–30 days before harvest). However, IN-J9Z38 gradually increased over time, indicating that cyantraniliprole transformed into IN-J9Z38 during cultivation. The biological half-lives of total cyantraniliprole were 11.3 and 9.4 days for grain and straw, respectively. The results obtained in this study will inform regulation and management of pesticide use for the minor crop proso millet.
Co-carcinogenic effects of vitamin E in prostate
Authors: Vivarelli Fabio , Canistro Donatella , Cirillo Silvia , Papi Alessio , Spisni Enzo , Vornoli Andrea , Croce Clara M. Della , Longo Vincenzo , Franchi Paola , Filippi Sandra , Lucarini Marco , Zanzi Cristina , Rotondo Francesca , Lorenzini Antonello , Marchionni Silvia , Paolini Moreno
Published: August 2019

A large number of basic researches and observational studies suggested the cancer preventive activity of vitamin E, but large-scale human intervention trials have yielded disappointing results and actually showed a higher incidence of prostate cancer although the mechanisms underlying the increased risk remain largely unknown. Here we show through in vitro and in vivo studies that vitamin E produces a marked inductive effect on carcinogen-bioactivating enzymes and a pro-oxidant status promoting both DNA damage and cell transformation frequency. First, we found that vitamin E in the human prostate epithelial RWPE-1 cell line has the remarkable ability to upregulate the expression of various phase-I activating cytochrome P450 (CYP) enzymes, including activators of polycyclic aromatic hydrocarbons (PAHs), giving rise to supraphysiological levels of reactive oxygen species. Furthermore, our rat model confirmed that vitamin E in the prostate has a powerful booster effect on CYP enzymes associated with the generation of oxidative stress, thereby favoring lipid-derived electrophile spread that covalently modifies proteins. We show that vitamin E not only causes DNA damage but also promotes cell transformation frequency induced by the PAH-prototype benzo[a]pyrene. Our findings might explain why dietary supplementation with vitamin E increases the prostate cancer risk among healthy men.
Differential neural dynamics underlying pragmatic and semantic affordance processing in macaque ventral premotor cortex
Authors: Maranesi Monica , Bruni Stefania , Livi Alessandro , Donnarumma Francesco , Pezzulo Giovanni , Bonini Luca
Published: August 2019

Premotor neurons play a fundamental role in transforming physical properties of observed objects, such as size and shape, into motor plans for grasping them, hence contributing to “pragmatic” affordance processing. Premotor neurons can also contribute to “semantic” affordance processing, as they can discharge differently even to pragmatically identical objects depending on their behavioural relevance for the observer (i.e. edible or inedible objects). Here, we compared the response of monkey ventral premotor area F5 neurons tested during pragmatic (PT) or semantic (ST) visuomotor tasks. Object presentation responses in ST showed shorter latency and lower object selectivity than in PT. Furthermore, we found a difference between a transient representation of semantic affordances and a sustained representation of pragmatic affordances at both the single neuron and population level. Indeed, responses in ST returned to baseline within 0.5 s whereas in PT they showed the typical sustained visual-to-motor activity during Go trials. In contrast, during No-go trials, the time course of pragmatic and semantic information processing was similar. These findings suggest that premotor cortex generates different dynamics depending on pragmatic and semantic information provided by the context in which the to-be-grasped object is presented.
Effects of Earthworms and Agricultural Plant Species on the Soil Nematode Community in a Microcosm Experiment
Authors: Niu Xinli , Zhai Peipei , Zhang Weixin , Gu Yanfang
Published: August 2019

Both earthworms and plants may affect the soil nematode community. However, the effects of earthworms and plant species interactions on soil nematode community are poorly understood. We explored how an epigeic earthwormEisenia fetidaaffects the soil nematode community in systems with three representative plants (wheat, cotton and cabbage) which were grown in pots with or without added earthworms under greenhouse conditions. Earthworm presence decreased the abundance of total nematode and all four nematode trophic groups, except for the fungivore and predator/omnivore nematodes in wheat systems, but increased the genus richness of nematode in all treatments. Due to plant identity and different root exudates, plants had significant effects on soil nematode abundance. Compared with the no plant and without earthworm treatment, wheat and cabbage had the higher stimulation of the abundance of total nematode, bacterivores and fungivores, and cotton had the higher stimulation of the abundance of fungivores and predators-omnivores; whereas earthworm presence mostly weakened the stimulation effects of plant species on soil nematode abundance which indicated earthworms had the enhanced effects in the presence of plants. The interaction affected soil nematode abundance (total nematodes, bacterivore, fungivore and omnivore-predators) and community diversity indices (diversity indexH′, evenness indexJ′, community maturity index ∑MI, Simpson dominance index λ and nematode channel ratio NCR). Principal component analysis showed that plant species affected soil nematode community composition. Redundancy analysis indicated plant species and biomass accounted for 41.60% and 34.13% of the variation in soil nematode community structure, respectively; while earthworms explained only 6.13%. Overall, current study suggest that earthworm could inhibit nematode abundance; whereas, plants have exerted greater influences on nematode community structure than earthworm presence due to their species-specific effects on different trophic groups of nematodes.
Exploring evolution and diversity of Chinese Dipterocarpaceae using next-generation sequencing
Authors: Cvetković Tijana , Hinsinger Damien Daniel , Strijk Joeri Sergej
Published: August 2019

Tropical forests, a key-category of land ecosystems, are faced with the world’s highest levels of habitat conversion and associated biodiversity loss. In tropical Asia, Dipterocarpaceae are one of the economically and ecologically most important tree families, but their genomic diversity and evolution remain understudied, hampered by a lack of available genetic resources. Southern China represents the northern limit for Dipterocarpaceae, and thus changes in habitat ecology, community composition and adaptability to climatic conditions are of particular interest in this group. Phylogenomics is a tool for exploring both biodiversity and evolutionary relationships through space and time using plastome, nuclear and mitochondrial genome. We generated full plastome and Nuclear Ribosomal Cistron (NRC) data for Chinese Dipterocarpaceae species as a first step to improve our understanding of their ecology and evolutionary relationships. We generated the plastome of Dipterocarpus turbinatus, the species with the widest distribution using it as a baseline for comparisons with other taxa. Results showed low level of genomic diversity among analysed range-edge species, and different evolutionary history of the incongruent NRC and plastome data. Genomic resources provided in this study will serve as a starting point for future studies on conservation and sustainable use of these dominant forest taxa, phylogenomics and evolutionary studies.
NGSReadsTreatment – A Cuckoo Filter-based Tool for Removing Duplicate Reads in NGS Data
Authors: Gaia Antonio Sérgio Cruz , de Sá Pablo Henrique Caracciolo Gomes , de Oliveira Mônica Silva , Veras Adonney Allan de Oliveira
Published: August 2019

The Next-Generation Sequencing (NGS) platforms provide a major approach to obtaining millions of short reads from samples. NGS has been used in a wide range of analyses, such as for determining genome sequences, analyzing evolutionary processes, identifying gene expression and resolving metagenomic analyses. Usually, the quality of NGS data impacts the final study conclusions. Moreover, quality assessment is generally considered the first step in data analyses to ensure the use of only reliable reads for further studies. In NGS platforms, the presence of duplicated reads (redundancy) that are usually introduced during library sequencing is a major issue. These might have a serious impact on research application, as redundancies in reads can lead to difficulties in subsequent analysis (e.g., de novo genome assembly). Herein, we present NGSReadsTreatment, a computational tool for the removal of duplicated reads in paired-end or single-end datasets. NGSReadsTreatment can handle reads from any platform with the same or different sequence lengths. Using the probabilistic structure Cuckoo Filter, the redundant reads are identified and removed by comparing the reads with themselves. Thus, no prerequisite is required beyond the set of reads. NGSReadsTreatment was compared with other redundancy removal tools in analyzing different sets of reads. The results demonstrated that NGSReadsTreatment was better than the other tools in both the amount of redundancies removed and the use of computational memory for all analyses performed. Available in https://sourceforge.net/projects/ngsreadstreatment/.
Staurosporine from Streptomyces sanyensis activates Programmed Cell Death in Acanthamoeba via the mitochondrial pathway and presents low in vitro cytotoxicity levels in a macrophage cell line
Authors: Cartuche Luis , Sifaoui Ines , Cruz Darío , Reyes-Batlle María , López-Arencibia Atteneri , Javier Fernández José , Díaz-Marrero Ana R. , Piñero José E. , Lorenzo-Morales Jacob
Published: August 2019

Recently, the search for novel therapeutic agents against Acanthamoeba species has been focused on the evaluation of natural resources. Among them, marine microorganisms have risen as a source of bioactive compounds with the advantage of the ability to obtain unlimited and constant amounts of the compounds in contrast to other natural sources such as plants. Furthermore, marine actinomycetes have recently been reported as highly rich in bioactive agents including salinosporamides, xiamycines, indolocarbazoles, naphtyridines, phenols, dilactones such as antimycines and macrolides among others. In this study, staurosporine (STS) was isolated from a strain of Streptomyces sanyensis and tested against Acanthamoeba to characterize the therapeutic potential of STS against this protozoan parasite. We have established that STS is active against both stages of the Acanthamoeba life cycle, by the activation of Programmed Cell Death via the mitochondrial pathway of the trophozoite. We have also established that STS has relatively low toxicity towards a macrophage cell line. However, previous studies have highlighted higher toxicity levels induced on other vertebrate cell lines and future research to lower these toxicity issues should be developed.
Shift of Sensitivity in Botrytis cinerea to Benzimidazole Fungicides in Strawberry Greenhouse Ascribing to the Rising-lowering of E198A Subpopulation and its Visual, On-site Monitoring by Loop-mediated Isothermal Amplification
Authors: Liu Y. H. , Yuan S. K. , Hu X. R. , Zhang C. Q.
Published: August 2019

Grey mold disease results from Botrytis cinerea, a classical “high-risk” plant pathogenic fungus in meaning of resistance development to fungicides, and its management depends largely on the frequent applications of fungicides. The evolution of resistance to benzimidazole chemicals during 2008 and 2016 was monitored continuously in strawberry greenhouses located in Zhejiang province. Results showed that extensive applications of the mixture of carbendazim and diethofencarb caused the rapid spread of Ben MR subpopulation. The withdraw of this mixture lead to the sharply decrease of Ben MR and re-dominance of Ben HR isolates of B. cinerea with the E198A mutation in β-tubulin gene. The LAMP primers, based on the E198A point mutation, were designed to detect the E198A genotype specifically. HNB (Hydroxynaphthol blue), a metalion indicator, acted as a visual LAMP reaction indicator that turned the violet colored into a sky-blue color. The detection limit of concentration of DNA was 100 × 10−2 ng/μL and this LAMP assay could be applied to detect the E198A genotype with 100% accuracy in strawberry greenhouses of three Province and was more rapid and easier to operate. In summary, we establish a simple and sensitive on-field LAMP assay which can be adopted to determine within 1.5 h whether the benzimidazoles or the mixture of a benzimidazole fungicide and diethofencarb is suitable for management of B. cinerea.
Light needle microscopy with spatially transposed detection for axially resolved volumetric imaging
Authors: Kozawa Yuichi , Sato Shunichi
Published: August 2019

The demand for rapid three-dimensional volumetric imaging is increasing in various fields, including life science. Laser scanning fluorescence microscopy has been widely employed for this purpose; however, a volumetric image is constructed by two-dimensional image stacking with a varying observation plane, ultimately limiting the acquisition speed. Here we propose a method enabling axially resolved volumetric imaging without a moving observation plane in the framework of laser scanning microscopy. A scanning light needle spot with an extended focal depth provides excitation, which normally produces a deep focus image with a loss of depth information. In our method, the depth information is retrieved from transposed lateral information on an array detector by utilising non-diffracting and self-bending characteristics imposed on fluorescent signals. This technique, implemented in two-photon microscopy, achieves truly volumetric images constructed from a single raster scan of a light needle, which has the capability to significantly reduce the acquisition time.
Supratentorial Cerebral Arterial Territories for Computed Tomograms: A Mapping Study in 1160 Large Artery Infarcts
Authors: Kim Dong-Eog , Jang Jinseong , Schellingerhout Dawid , Ryu Wi-Sun , Park Jong-Ho , Lee Su-Kyoung , Kim Dongmin , Bae Hee-Joon
Published: August 2019

We recently generated a high-resolution supratentorial vascular topographic atlas using diffusion-weighed MRI in a population of large artery infarcts. These MRI-based topographic maps are not easily applicable to CT scans, because the standard-reference-lines for axial image orientation (i.e., anterior-posterior commissure line versus orbito-meatal line, respectively) are ‘not parallel’ to each other. Moreover, current, widely-used CT-based vascular topographic diagrams omit demarcation of the inter-territorial border-zones. Thus, we aimed to generate a CT-specific high-resolution atlas, showing the supratentorial cerebrovascular territories and the inter-territorial border-zones in a statistically rigorous way. The diffusion-weighted MRI lesion atlas is based on 1160 patients (67.0 ± 13.3 years old, 53.7% men) with acute (<1-week) cerebral infarction due to significant (>50%) stenosis or occlusion of a single large cerebral artery: anterior, middle, or posterior cerebral artery. We developed a software package enabling the transformation of our MR-based atlas into a re-oriented CT space corresponding to the axial slice orientations used in clinical practice. Infarct volumes are individually mapped to the three vascular territories on the CT template-set, generating brain maps showing the voxelwise frequency of infarct by the affected parent vessel. We then mapped the three vascular territories collectively, generating a dataset of Certainty-Index (CI) maps to reflect the likelihood of a voxel being a member of a specific vascular territory. Border-zones could be defined by using either relative infarct frequencies or CI differences. The topographic vascular territory atlas, revised for CT, will allow for easier and more accurate delineation of arterial territories and borders on CT images.
Trichoderma harzianum favours the access of arbuscular mycorrhizal fungi to non-host Brassicaceae roots and increases plant productivity
Authors: Poveda Jorge , Hermosa Rosa , Monte Enrique , Nicolás Carlos
Published: August 2019

The family Brassicaceae includes plants that are non-host for arbuscular mycorrhizal fungi (AMF) such as the model plantArabidopsis thaliana(arabidopsis) and the economically important crop plantBrassica napus(rapeseed). It is well known thatTrichodermaspecies have the ability to colonize the rhizosphere of Brassicaceae plants, promoting growth and development as well as stimulating systemic defenses. The aim of the present work is to ascertain that Brassicaceae plants increase productivity when AMF andTrichodermaare combinedly applied, and how such an effect can be ruled. This simultaneous application of aTrichoderma harzianumbiocontrol strain and an AMF formulation produces a significant increase in the colonization byTrichodermaand the presence of AMF in arabidopsis and rapeseed roots, such colonization accompanied by improved productivity in both Brassicaceae species. Expression profiling of defense-related marker genes suggests that the phytohormone salicylic acid plays a key role in the modulation of the root colonization process when both fungi are jointly applied.
Proteomics-based functional studies reveal that galectin-3 plays a protective role in the pathogenesis of intestinal Behçet’s disease
Authors: Lee Hyun Jung , Kim Jae Hyeon , Hong Sujeong , Hwang Inhwa , Park Soo Jung , Kim Tae Il , Kim Won Ho , Yu Je-Wook , Kim Seung Won , Cheon Jae Hee
Published: August 2019

The pathogenesis of intestinal Behçet’s disease (BD) remains poorly understood. Therefore, we aimed to discover and validate biomarkers using proteomics analysis and subsequent functional studies. After two-dimensional electrophoresis, candidate proteins were identified using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF MS). We validated these results by evaluating the protein levels and their functions in vitro using HT-29 colorectal cancer cells, colon tissues from patients and mice, and murine bone marrow derived macrophages (BMDMs). Of the 30 proteins differentially expressed in intestinal BD tissues, we identified seven using MALDI-TOF/TOF MS. Focusing on galectin-3, we found that TGF-B and IL-10 expression was significantly lower in shLGALS3-transfected cells. Expression of GRP78 and XBP1s and apoptosis rates were all higher in shLGALS3-transfected cells upon the induction of endoplasmic reticulum stress. In response to lipopolysaccharide stimulation, microtubule-associated protein 1 light chain 3B accumulated and lysosomes decreased in these cells. Finally, Salmonella typhimurium infection induced caspase-1 activation and increased IL-1β production, which facilitated activation of the NLRC4 inflammasome, in Lgals3−/− murine BMDMs compared to wild type BMDMs. Our data suggest that galectin-3 may play a protective role in the pathogenesis of intestinal BD via modulation of ER stress, autophagy, and inflammasome activation.
Chemometric analysis of enantioselective Raman spectroscopy data enables enantiomeric ratio determination
Authors: Rullich Claudia C. , Kiefer Johannes
Published: August 2019

Enantioselective Raman spectroscopy data are evaluated using PLSR to yield the enantiomeric ratio of chiral solutions.
A weighted ensemble method based on wavelength selection for near-infrared spectroscopic calibration
Authors: Yu Shaohui , Liu Jing
Published: August 2019

A weighted clustering and pruning of wavelength variables-partial least squares (WCPV-PLS) method was proposed.