bluuebunny/crossref_metadata_2025 huggingface dataset:
On-Chip Inverted Emulsion Method for Fast Giant Vesicle Production, Handling, and Analysis
Authors: Yandrapalli Naresh , Seemann Tina , Robinson Tom
Published: March 2020

Liposomes and giant unilamellar vesicles (GUVs) in particular are excellent compartments for constructing artificial cells. Traditionally, their use requires bench-top vesicle growth, followed by experimentation under a microscope. Such steps are time-consuming and can lead to loss of vesicles when they are transferred to an observation chamber. To overcome these issues, we present an integrated microfluidic chip which combines GUV formation, trapping, and multiple separate experiments in the same device. First, we optimized the buffer conditions to maximize both the yield and the subsequent trapping of the vesicles in micro-posts. Captured GUVs were monodisperse with specific size of 18 ± 4 µm in diameter. Next, we introduce a two-layer design with integrated valves which allows fast solution exchange in less than 20 s and on separate sub-populations of the trapped vesicles. We demonstrate that multiple experiments can be performed in a single chip with both membrane transport and permeabilization assays. In conclusion, we have developed a versatile all-in-one microfluidic chip with capabilities to produce and perform multiple experiments on a single batch of vesicles using low sample volumes. We expect this device will be highly advantageous for bottom-up synthetic biology where rapid encapsulation and visualization is required for enzymatic reactions.
Evaluation of Performance and Tunability of a Co-Flow Inertial Microfluidic Device
Authors: Bogseth Amanda , Zhou Jian , Papautsky Ian
Published: March 2020

Microfluidics has gained a lot of attention for biological sample separation and purification methods over recent years. From many active and passive microfluidic techniques, inertial microfluidics offers a simple and efficient method to demonstrate various biological applications. One prevalent limitation of this method is its lack of tunability for different applications once the microfluidic devices are fabricated. In this work, we develop and characterize a co-flow inertial microfluidic device that is tunable in multiple ways for adaptation to different application requirements. In particular, flow rate, flow rate ratio and output resistance ratio are systematically evaluated for flexibility of the cutoff size of the device and modification of the separation performance post-fabrication. Typically, a mixture of single size particles is used to determine cutoff sizes for the outlets, yet this fails to provide accurate prediction for efficiency and purity for a more complex biological sample. Thus, we use particles with continuous size distribution (2–32 μm) for separation demonstration under conditions of various flow rates, flow rate ratios and resistance ratios. We also use A549 cancer cell line with continuous size distribution (12–27 μm) as an added demonstration. Our results indicate inertial microfluidic devices possess the tunability that offers multiple ways to improve device performance for adaptation to different applications even after the devices are prototyped.
Buoyancy-Free Janus Microcylinders as Mobile Microelectrode Arrays for Continuous Microfluidic Biomolecule Collection within a Wide Frequency Range: A Numerical Simulation Study
Authors: Liu Weiyu , Ren Yukun , Tao Ye , Yan Hui , Xiao Congda , Wu Qisheng
Published: March 2020

We numerically study herein the AC electrokinetic motion of Janus mobile microelectrode (ME) arrays in electrolyte solution in a wide field frequency, which holds great potential for biomedical applications. A fully coupled physical model, which incorporates the fluid-structure interaction under the synergy of induced-charge electroosmotic (ICEO) slipping and interfacial Maxwell stress, is developed for this purpose. A freely suspended Janus cylinder free from buoyancy, whose main body is made of polystyrene, while half of the particle surface is coated with a thin conducting film of negligible thickness, will react actively on application of an AC signal. In the low-frequency limit, induced-charge electrophoretic (ICEP) translation occurs due to symmetric breaking in ICEO slipping, which renders the insulating end to move ahead. At higher field frequencies, a brand-new electrokinetic transport phenomenon called “ego-dielectrophoresis (e-DEP)” arises due to the action of the localized uneven field on the inhomogeneous particle dipole moment. In stark contrast with the low-frequency ICEP translation, the high-frequency e-DEP force tends to drive the asymmetric dipole moment to move in the direction of the conducting end. The bidirectional transport feature of Janus microspheres in a wide AC frequency range can be vividly interpreted as an array of ME for continuous loading of secondary bioparticles from the surrounding liquid medium along its direction-controllable path by long-range electroconvection. These results pave the way for achieving flexible and high-throughput on-chip extraction of nanoscale biological contents for subsequent on-site bioassay based upon AC electrokinetics of Janus ME arrays.
Photonic Crystal Stimuli-Responsive Chromatic Sensors: A Short Review
Authors: Chiappini Andrea , Tran Lam Thi Ngoc , Trejo-García Pablo Marco , Zur Lidia , Lukowiak Anna , Ferrari Maurizio , Righini Giancarlo C.
Published: March 2020

Photonic crystals (PhC) are spatially ordered structures with lattice parameters comparable to the wavelength of propagating light. Their geometrical and refractive index features lead to an energy band structure for photons, which may allow or forbid the propagation of electromagnetic waves in a limited frequency range. These unique properties have attracted much attention for both theoretical and applied research. Devices such as high-reflection omnidirectional mirrors, low-loss waveguides, and high- and low-reflection coatings have been demonstrated, and several application areas have been explored, from optical communications and color displays to energy harvest and sensors. In this latter area, photonic crystal fibers (PCF) have proven to be very suitable for the development of highly performing sensors, but one-dimensional (1D), two-dimensional (2D) and three-dimensional (3D) PhCs have been successfully employed, too. The working principle of most PhC sensors is based on the fact that any physical phenomenon which affects the periodicity and the refractive index of the PhC structure induces changes in the intensity and spectral characteristics of the reflected, transmitted or diffracted light; thus, optical measurements allow one to sense, for instance, temperature, pressure, strain, chemical parameters, like pH and ionic strength, and the presence of chemical or biological elements. In the present article, after a brief general introduction, we present a review of the state of the art of PhC sensors, with particular reference to our own results in the field of mechanochromic sensors. We believe that PhC sensors based on changes of structural color and mechanochromic effect are able to provide a promising, technologically simple, low-cost platform for further developing devices and functionalities.
How to Ease the Pain of Taking a Diagnostic Point of Care Test to the Market: A Framework for Evidence Development
Authors: Graziadio Sara , Winter Amanda , Lendrem B. , Suklan Jana , Jones William , Urwin Samuel , O’Leary Rachel , Dickinson Rachel , Halstead Anna , Kurowska Kasia , Green Kile , Sims Andrew , Simpson A. , Power H. , Allen A.
Published: March 2020

Bringing a diagnostic point of care test (POCT) to a healthcare market can be a painful experience as it requires the manufacturer to meet considerable technical, financial, managerial, and regulatory challenges. In this opinion article we propose a framework for developing the evidence needed to support product development, marketing, and adoption. We discuss each step in the evidence development pathway from the invention phase to the implementation of a new POCT in the healthcare system. We highlight the importance of articulating the value propositions and documenting the care pathway. We provide guidance on how to conduct care pathway analysis as little has been published on this. We summarize the clinical, economic and qualitative studies to be considered for developing evidence, and provide useful links to relevant software, on-line applications, websites, and give practical advice. We also provide advice on patient and public involvement and engagement (PPIE), and on product management. Our aim is to help device manufacturers to understand the concepts and terminology used in evaluation of in vitro diagnostics (IVDs) so that they can communicate effectively with evaluation methodologists, statisticians, and health economists. Manufacturers of medical tests and devices can use the proposed framework to plan their evidence development strategy in alignment with device development, applications for regulatory approval, and publication.
Insights into Thermophilic Plant Biomass Hydrolysis from Caldicellulosiruptor Systems Biology
Authors: Blumer-Schuette Sara E.
Published: March 2020

Plant polysaccharides continue to serve as a promising feedstock for bioproduct fermentation. However, the recalcitrant nature of plant biomass requires certain key enzymes, including cellobiohydrolases, for efficient solubilization of polysaccharides. Thermostable carbohydrate-active enzymes are sought for their stability and tolerance to other process parameters. Plant biomass degrading microbes found in biotopes like geothermally heated water sources, compost piles, and thermophilic digesters are a common source of thermostable enzymes. While traditional thermophilic enzyme discovery first focused on microbe isolation followed by functional characterization, metagenomic sequences are negating the initial need for species isolation. Here, we summarize the current state of knowledge about the extremely thermophilic genus Caldicellulosiruptor, including genomic and metagenomic analyses in addition to recent breakthroughs in enzymology and genetic manipulation of the genus. Ten years after completing the first Caldicellulosiruptor genome sequence, the tools required for systems biology of this non-model environmental microorganism are in place.
Distinct Roles of Acidophiles in Complete Oxidation of High-Sulfur Ferric Leach Product of Zinc Sulfide Concentrate
Authors: Muravyov Maxim , Panyushkina Anna
Published: March 2020

A two-step process, which involved ferric leaching with biologically generated solution and subsequent biooxidation with the microbial community, has been previously proposed for the processing of low-grade zinc sulfide concentrates. In this study, we carried out the process of complete biological oxidation of the product of ferric leaching of the zinc concentrate, which contained 9% of sphalerite, 5% of chalcopyrite, and 29.7% of elemental sulfur. After 21 days of biooxidation at 40 °C, sphalerite and chalcopyrite oxidation reached 99 and 69%, respectively, while the level of elemental sulfur oxidation was 97%. The biooxidation residue could be considered a waste product that is inert under aerobic conditions. The results of this study showed that zinc sulfide concentrate processing using a two-step treatment is efficient and promising. The microbial community, which developed during biooxidation, was dominated by Acidithiobacillus caldus, Leptospirillum ferriphilum, Ferroplasma acidiphilum, Sulfobacillus thermotolerans, S. thermosulfidooxidans, and Cuniculiplasma sp. At the same time, F. acidiphilum and A. caldus played crucial roles in the oxidation of sulfide minerals and elemental sulfur, respectively. The addition of L. ferriphilum to A. caldus during biooxidation of the ferric leach product proved to inhibit elemental sulfur oxidation.
Melting Curve of Potassium Chloride from in situ Ionic Conduction Measurements
Authors: Zhou Dongyuan , Dong Junjie , Si Yanhan , Zhu Feng , Li Jie
Published: March 2020

We report experimental constraints on the melting curve of potassium chloride (KCl) between 3.2 and 9 GPa from in situ ionic conduction measurements using a multi-anvil apparatus. On the basis of concurrent measurements of KCl and sodium chloride (NaCl) at 1 bar using the differential thermal analysis (DTA) method and Pt sphere marker, we show that the peak rate of increase in ionic current with temperature upon heating coincides with latent heat ledge and fall of Pt sphere, thus establishing the criterion for melting detection from ionic conduction measurements. Applying this criterion to high pressures, we found that the melting point of KCl rose steeply with increasing pressure to exceed 2443 ± 100 K at 9 GPa. Fitting the results of this study together with existing data at pressures below 4 GPa and above 20 GPa, we obtained the Simon’s melting equation for KCl in the simple cubic B2 structure between 1.8 and 50 GPa: T m = 1323 ( P − 1.87 2.2 ( 1 ) + 1 ) 1 2.7 ( 1 ) , where T is in K and P is in GPa. Starting at 1 bar, the melting point of KCl increases at an average rate of ~150 K/GPa to cross that of Pt near 9 GPa. The highly refractory nature of KCl makes it a sensitive pressure calibrant for the large-volume pressure at moderate pressures and a potential sample container for experiments at moderate pressures and very high temperatures.
Optimization of Operating Parameters on Dry Grinding of Calcite in a Stirred Media Mill Using the Box-Behnken Design
Authors: Katircioglu-Bayel Diler
Published: March 2020

The optimization of the operating parameters of a stirred media mill in the dry grinding of calcite was investigated. A three-level Box-Behnken design was used for the purpose of examining the impact of four independent factors, the stirrer speed (SS), grinding time (GT), media filling ratio (MFR), and solid mass fraction (SMF), on the product particle size (d50). For the purpose of establishing an empirical correlation between operating parameters and responses, a series of experiments were carried out. Variance analysis showed a reasonably good value for d50 (R2 = 0.965). According to the software solutions, the optimum conditions for minimizing the d50 size were found to be 573 rpm stirrer speed, 11.18 min grinding time, 63% media filling ratio, and 11.52% solid mass fraction, with 3.78 µm for the d50 size. To verify the improvement of grinding, verification tests were performed using the above-mentioned optimum conditions and the average d50 size and standard deviation were found to be 3.83 µm and 0.025, respectively. The average d50 value obtained was smaller than those obtained in the 27 tests. Furthermore, when the optimum result obtained from the experiments was compared with the result obtained using the software, a 22% energy saving was achieved. The impacts of grinding on the structural characteristics of calcite particles were characterized by XRD analysis. XRD measurements indicated that no change was observed in the peak areas of ground calcite specimens compared to the untreated calcite specimen.
Sonochemical Synthesis of Copper-doped BiVO4/g-C3N4 Nanocomposite Materials for Photocatalytic Degradation of Bisphenol A under Simulated Sunlight Irradiation
Authors: Lee Gang-Juan , Lee Xin-Yu , Lyu Cong , Liu Na , Andandan Sambandam , Wu Jerry J.
Published: March 2020

Copper-doped bismuth vanadate/graphitic carbon nitride (BiVO4/g-C3N4) nanocomposite materials were successfully fabricated using a sonochemical approach. Cu-doped BiVO4/g-C3N4 nanocomposite photocatalysts could improve electron/hole (e−/h+) pair separation, stability, and light-harvesting efficiency compared to pristine BiVO4 or g-C3N4, resulting in the enhancement of photocatalytic activity. The optimal parameters, such as pH value at 10, photocatalyst dosage of 0.4 g L−1, and 10 mol% Cu-doped BiVO4/g-C3N4 photocatalyst, were determined to degrade initial concentration of 20 ppm Bisphenol A, which could be completely removed after 90 min. Furthermore, the excessive doping of copper (> 10 mol%) could not synthesize the pure monoclinic scheelite phase, which substantially resulted in the reduction of the photocatalytic activity.
An Ultrasensitive Non-Enzymatic Sensor for Quantitation of Anti-Cancer Substance Chicoric Acid Based on Bimetallic Nanoalloy with Polyetherimide-Capped Reduced Graphene Oxide
Authors: Jiao Jun , Pan Meixin , Liu Xinran , Liu Jian , Li Binshuai , Chen Qiang
Published: March 2020

Exploiting effective therapies to fight tumor growth is an important part of modern cancer research. The anti-cancer activities of many plant-derived substances are well known, in part because the substances are often extensively distributed. Chicoric acid, a phenolic compound widely distributed in many plants, has drawn widespread attention in recent years because of its extraordinary anti-cancer activities. However, traditional methods for quantifying chicoric acid are inefficient and time-consuming. In this study, an ultrasensitive non-enzymatic sensor for the determination of chicoric acid was developed based on the use of an Au@Pt-polyetherimide-reduced graphene oxide (PEI-RGO) nanohybrid-modified glassy carbon electrode. Owing to the considerable conductivity of PEI-functionalized RGO and the efficient electrocatalytic activity of Au@Pt nanoalloys, the designed sensor exhibited a high capacity for chicoric acid measurement, with a low detection limit of 4.8 nM (signal-to-noise ratio of 3) and a broad linear range of four orders of magnitude. With the advantages provided by the synergistic effects of Au@Pt nanocomposites and PEI-RGO, the developed sensor also revealed exceptional electrochemical characteristics, including superior sensitivity, fast response, acceptable long-term stability, and favorable selectivity. This work provides a powerful new platform for the highly accurate measurement of chicoric acid quantities, facilitating further research into its potential as a cancer treatment.
The Use of Vitamins and Coenzyme Q10 for the Treatment of Vascular Occlusion Diseases Affecting the Retina
Authors: Fernández-Vega Beatriz , Nicieza Javier , Álvarez-Barrios Ana , Álvarez Lydia , García Montserrat , Fernández-Vega Carlos , Vega José A. , González-Iglesias Héctor
Published: March 2020

Nutritional supplementation with antioxidants and vitamins is widely recommended in the treatment of vascular disorders affecting the retina, although there is insufficient evidence on its effectiveness. The vitamin-like compound coenzyme Q10 (CoQ10) is a nutritional supplement of current interest to treat neurodegenerative diseases. Here, we report a retrospective clinical case series study of 48 patients diagnosed with retinal vascular diseases, including non-arteritic ischemic optic neuropathy (NAION), retinal artery occlusion (RAO), and homonymous hemianopia or quadrantanopia following stroke, treated with oral supplementation with CoQ10 (100 mg per day) and vitamins. Patient follow-up was performed using the Humphrey field analyzer and 30-2 testing algorithm to determine the visual field index (VFI) and progression rates. All treated patients showed positive VFI progression rates per year: +11.5 ± 15% for NAION patients (n = 18), +22 ± 17% for RAO patients (n = 7), +9.3 ± 10.5% for hemianopia/quadrantanopia patients (n = 10), and +11 ± 21% for patients with other conditions (n = 13). The interruption of CoQ10 supplementation in one patient resulted in a pronounced decrease of the VFI, which was partially recovered when treatment was restored. This study supports the role of CoQ10 as a nutritional therapeutic agent for vascular diseases affecting the retina. Owing to decreased VFI after interruption of CoQ10, its beneficial effects may be reversible.
Lifestyle Patterns Begin in Early Childhood, Persist and Are Socioeconomically Patterned, Confirming the Importance of Early Life Interventions
Authors: Lioret Sandrine , Campbell Karen J. , McNaughton Sarah A. , Cameron Adrian J. , Salmon Jo , Abbott Gavin , Hesketh Kylie D.
Published: March 2020

Traditional approaches to understanding the behavioural determinants of adiposity have considered diet, physical activity and sedentary behaviour in isolation. Although integrative approaches have identified a variety of lifestyle patterns in children at preschool-age or older, along with some variability by socio-economic positions, this has rarely been examined in younger cohorts. We aimed to identify lifestyle patterns at 1.5, 3.5 and 5 years, including dietary intake, outdoor time and television viewing time, to assess associations with maternal education (as a proxy for socio-economic position), and to investigate their persistence between toddlerhood and preschool age. Participants were 417 and 293 children aged 1.5 y from the Melbourne Infant Feeding Activity and Nutrition Trial (InFANT) and InFANT Extend Programs, respectively. Data were collected using questionnaires at child ages 1.5, 3.5 and 5 y (InFANT); and 1.5 and 3.5 y (InFANT Extend). Principal component analysis was undertaken at each time point on the separate and pooled datasets. Associations between the lifestyle patterns scores and maternal education were assessed with multivariable regression analysis. Two lifestyle patterns (“Discretionary consumption and TV” and “Fruit, vegetables and outdoor”) were identified as early as 1.5 y. They remained consistent across ages and were evident in both datasets. These patterns were inversely and positively associated with maternal education, respectively. Such early clustering of obesity related energy balance behaviours and tracking during early childhood suggests there may be shared antecedents common to the individual behaviours that could be targeted for intervention. Our findings provide support for interventions targeting multiple behaviours and tailored to the level of family socio-economic disadvantage.
Antrodia cinnamomea Confers Obesity Resistance and Restores Intestinal Barrier Integrity in Leptin-deficient Obese Mice
Authors: Tsai Yi-Ting , Ruan Jhen-Wei , Chang Cherng-Shyang , Ko Mei-Lan , Chou Hsiu-Chuan , Lin Chi-Chien , Lin Chiao-Mei , Huang Chih-Ting , Wei Yu-Shan , Liao En-Chi , Chen Hsin-Yi , Kao Cheng-Yuan , Chan Hong-Lin
Published: March 2020

Obesity is associated with metabolic disorders. Thus, obesity prevention and treatment are essential for health. Antrodia cinnamomea (AC) is a multifunctional medicinal fungus used for the treatment of various diseases and for preventing diet-induced obesity. Leptin deficiency causes over-eating and spontaneous obesity. The concomitant metabolic symptoms are more severe than diet-induced obesity. Here, we used leptin-deficient (ob/ob) mice as an animal model for over-feeding to study the effect of AC on obesity. We fed C57BL/6 mice (WT, ob+/+) and ob/ob mice with AC for four weeks before performing qRT-PCR and immunoblot analysis to elaborate AC-modulated mechanisms. Further, we used Caco-2 cells as a human intestinal epithelial barrier model to examine the effect of AC on intestinal permeability. Our results suggested that AC reduces lipid deposits of the liver and epididymal white adipose tissue (EWAT) by promoting lipid metabolism and inhibiting lipogenesis-associated genes and proteins in ob/ob mice. Moreover, AC effectively repaired intestinal-barrier injury caused by leptin deficiency and enhanced intestinal barrier integrity in Caco-2 cells. Interestingly, AC significantly reduced body weight and EWAT with no compromise on food intake in ob/ob mice. Thus, AC effectively reduced obesity caused by leptin-deficiency and can potentially be used as a nutraceutical for treating obesity.
The Metabolic Syndrome: Emerging Novel Insights Regarding the Relationship between the Homeostasis Model Assessment of Insulin Resistance and other Key Predictive Markers in Young Adults of Western Algeria
Authors: Belhayara Mohammed Ilyes , Mellouk Zoheir , Hamdaoui Mohammed Seddik , Bachaoui Malika , Kheroua Omar , Malaisse Willy J.
Published: March 2020

Several biological markers have been identified as risk factors for cardiovascular disease and are associated with increased risk of metabolic syndrome (MetS). This study provides a factual information on promising biomarkers that are associated with MetS and can aid in early detection and management of MetS in young adults of Western Algeria. We studied a total of one hundred subjects aged between thirty and forty years with MetS, in which anthropometric measurements, insulin resistance, C peptide and HbA1c, lipid profile, circulating adipokines and glucagon-like peptide-1 were measured by suitable methods, in comparison to two groups of control. MetS is closely linked to altered glucose homeostasis, the plasma insulin/glucose ratio; i.e., the insulinogenic index helps to estimate the level of insulin secretion and also for assessing β-cell function. The correlation between homeostasis model assessment insulin resistance index (HOMA-IR) and HbA1c, body mass index or plasma triglycerides yielded positive and significant values. Biomarkers with a known and predictable association with MetS can provide a means to detect those at risk and intervene as needed. This could significantly decrease the burden complications impose on patients and the healthcare system.
Effect of Quercetin Treatment on Mitochondrial Biogenesis and Exercise-Induced AMP-Activated Protein Kinase Activation in Rat Skeletal Muscle
Authors: Koshinaka Keiichi , Honda Asuka , Masuda Hiroyuki , Sato Akiko
Published: March 2020

The purpose of this study was to evaluate the effect of chronic quercetin treatment on mitochondrial biogenesis, endurance exercise performance and activation levels of AMP-activated protein kinase (AMPK) in rat skeletal muscle. Rats were assigned to a control or quercetin group and were fed for 7 days. Rats treated with quercetin showed no changes in the protein levels of citrate synthase or cytochrome C oxidase IV or those of sirtuin 1, peroxisome proliferator-activated receptor gamma coactivator-1α or phosphorylated AMPK. After endurance swimming exercise, quercetin-treated rats demonstrated no differences in blood and muscle lactate levels or glycogen utilization speed compared to control rats. These results indicate that quercetin treatment does not stimulate mitochondrial biogenesis in skeletal muscle and does not influence metabolism in a way that might enhance endurance exercise capacity. On the other hand, the AMPK phosphorylation level immediately after exercise was significantly lower in quercetin-treated muscles, suggesting that quercetin treatment might provide a disadvantage to muscle adaptation when administered with exercise training. The molecular results of this study indicate that quercetin treatment may not be advantageous for improving endurance exercise performance, at least after high-dose and short-term therapy.
Binge Drinking and Risk of Breast Cancer: Results from the SUN (‘Seguimiento Universidad de Navarra’) Project
Authors: Sánchez-Bayona Rodrigo , Gea Alfredo , Gardeazabal Itziar , Romanos-Nanclares Andrea , Martínez-González Miguel Ángel , Bes-Rastrollo Maira , Santisteban Marta , Toledo Estefanía
Published: March 2020

Alcohol intake is associated with the risk of breast cancer. Different patterns of alcohol-drinking may have different effects on breast cancer even when keeping constant the total amount of alcohol consumed. We aimed to assess the association between binge drinking and breast cancer risk. The SUN Project is a Spanish dynamic prospective cohort of university graduates initiated in 1999. In the 556-item lifestyle baseline questionnaire a validated food-frequency questionnaire was embedded. Participants completed biennial follow-up questionnaires. Cox regression models were used to estimate the hazard ratio (HR) for breast cancer associated with the exposure to binge drinking. A stratified analysis was performed according to menopausal status. We included 9577 women (mean age = 34 years, SD = 10 years), with a median follow-up of 11.8 years. Among 104,932 women-years of follow-up, we confirmed 88 incident cases of breast cancer. Women in the binge drinking group showed a higher risk of breast cancer (HR = 1.76; 95% CI: 1.03–2.99) compared to women in the non-binge drinking category. In the stratified analysis, a 2-fold higher risk for premenopausal breast cancer was associated with binge drinking habit (HR = 2.06; 95% CI: 1.11–3.82). This study adds new evidence on the association of binge drinking with breast cancer risk.
Improved Metagenomic Taxonomic Profiling Using a Curated Core Gene-Based Bacterial Database Reveals Unrecognized Species in the Genus Streptococcus
Authors: Chalita Mauricio , Ha Sung-min , Kim Yeong Ouk , Oh Hyun-Seok , Yoon Seok-Hwan , Chun Jongsik
Published: March 2020

Shotgun metagenomics is of great importance in order to understand the composition of the microbial community associated with a sample and the potential impact it may exert on its host. For clinical metagenomics, one of the initial challenges is the accurate identification of a pathogen of interest and ability to single out that pathogen within a complex community of microorganisms. However, in absence of an accurate identification of those microorganisms, any kind of conclusion or diagnosis based on misidentification may lead to erroneous conclusions, especially when comparing distinct groups of individuals. When comparing a shotgun metagenomic sample against a reference genome sequence database, the classification itself is dependent on the contents of the database. Focusing on the genus Streptococcus, we built four synthetic metagenomic samples and demonstrated that shotgun taxonomic profiling using the bacterial core genes as the reference database performed better in both taxonomic profiling and relative abundance prediction than that based on the marker gene reference database included in MetaPhlAn2. Additionally, by classifying sputum samples of patients suffering from chronic obstructive pulmonary disease, we showed that adding genomes of genomospecies to a reference database offers higher taxonomic resolution for taxonomic profiling. Finally, we show how our genomospecies database is able to identify correctly a clinical stool sample from a patient with a streptococcal infection, proving that genomospecies provide better taxonomic coverage for metagenomic analyses.
Fatty Acid Amides Synthesized from Andiroba Oil (Carapa guianensis Aublet.) Exhibit Anticonvulsant Action with Modulation on GABA-A Receptor in Mice: A Putative Therapeutic Option
Authors: Rodrigues de Oliveira Fábio , Eleuterio Rodrigues Keuri , Hamoy Moisés , Rodrigues Sarquis Ícaro , Otake Hamoy Akira , Elena Crespo Lopez Maria , Maciel Ferreira Irlon , de Matos Macchi Barbarella , Luiz Martins do Nascimento José
Published: March 2020

Epilepsy is a chronic neurological disease characterized by excessive neuronal activity leading to seizure; about 30% of affected patients suffer from the refractory and pharmacoresistant form of the disease. The anticonvulsant drugs currently used for seizure control are associated with adverse reactions, making it important to search for more effective drugs with fewer adverse reactions. There is increasing evidence that endocannabinoids can pharmacologically modulate action against seizure and antiepileptic disorders. Therefore, the objective of this study is to investigate the anticonvulsant effects of fatty acid amides (FAAs) in a pentylenetetrazole (PTZ)-induced seizure model in mice. FAAs (FAA1 and FAA2) are obtained from Carapa guianensis oil by biocatalysis and are characterized by Fourier Transform Infrared Analysis (FT-IR) and Gas Chromatography-Mass Spectrometry (GC-MS). Only FAA1 is effective in controlling the increased latency time of the first myoclonic jerk and in significantly decreasing the total duration of tonic-clonic seizures relative to the pentylenetetrazol model. Also, electrocortical alterations produced by pentylenetetrazol are reduced when treated by FAA1 that subsequently decreased wave amplitude and energy in Beta rhythm. The anticonvulsant effects of FAA1 are reversed by flumazenil, a benzodiazepine antagonist on Gamma-Aminobutyric Acid-A (GABA-A) receptors, indicating a mode of action via the benzodiazepine site of these receptors. To conclude, the FAA obtained from C. guianensis oil is promising against PTZ-induced seizures.
Targeting a Subset of the Membrane Proteome for Top–Down Mass Spectrometry: Introducing the Proteolipidome
Authors: Whitelegge Julian
Published: March 2020

A subsection of integral membrane proteins partition into chloroform during a chloroform/methanol/water extraction primarily designed to extract lipids. Traditionally, these proteins were called proteolipids due to their lipid-like properties; the c-subunit of the ATP synthase integral FO component is the best known due to its abundance. In this manuscript, we investigate purification of proteolipid proteins away from lipids for high-resolution mass spectrometry. Size-exclusion chromatography on silica beads using a chloroform/methanol/aqueous formic acid (4/4/1; v/v) mobile phase allowed the separation of larger proteins (>3 kDa) from lipids (<1.5 kDa) and analysis by online electrospray ionization mass spectrometry. Fraction collection for mass spectrometry was limited by presence of plasticizers and other contaminants solubilized by chloroform. Drying down of the protein sample followed by resuspension in formic acid (70%) allowed reverse-phase chromatography on a polymeric support at elevated temperature, as described previously. Fractions collected in this way could be stored for extended periods at −80 °C without adducts or contaminants. Top–down mass spectrometry enabled the definition of PsaI as a novel proteolipid of spinach thylakoid membrane. Proteolipid preparation worked similarly when total membranes from mouse brains were extracted with chloroform. While it might be tempting to use the described extraction, we prefer to broaden the meaning of the term, whereby the proteolipidome is defined as a novel biological membrane proteome that includes the full complement of membrane proteins, their binding partners/ligands and their tightly bound structural lipids that constitute each protein–lipid complex’s functional unit; that is, a complete description of a biological membrane.
To Spite the Devil: Martin Luther and Katharina von Bora’s Wedding as Reform and Resistance
Authors: Bowers Diane V.
Published: March 2020

The basis of Martin Luther’s decision to marry Katharina von Bora on 13 June 1525, stemmed from his public, theological position that unless one were a particular exception, all men and women should marry. However, Luther’s decision to marry when he did was controversial because the Peasants’ Revolt raged, and it was surprising because up until November of 1524 Luther had stated that he was in his mind averse to marriage (for himself). Yet in May of 1525 Luther stated that he intended to take “his Katie” to wife, and in June, he did so. Why did Luther change his mind, and marry precisely when he did? I argue that the timing of his decision was influenced by Luther’s apocalyptic sensibility that he was living in the last days, the immediate political context of the Peasants’ Revolt, and the death of Elector Frederick the Wise of Saxony, Luther’s patron and protector. The reason for his choice of Katharina von Bora as his wife included the need to secure for her financial support, but no less, her exercise of her own agency in choosing him as a husband. Can we say that Luther also personally warmed to the idea of marriage, drawn to the companionship of bed and table that it provided? There is certainly support for answering “yes.” Luther’s decision to marry was a theological, confessional, and political act, and yet these do not preclude the very human, personal, and relational factors in his decision.
Situating Pārśva’s Biography in Varanasi
Authors: Gough Ellen
Published: March 2020

This study shows how Varanasi, a site that many people understand to be a sacred Hindu city, has been made “Jain” through its association with the lives of four of the twenty-four enlightened founders of Jainism, the jinas or tīrthaṅkaras. It provides an overview of the Jain sites of worship in Varanasi, focusing especially on how events in the life of the twenty-third tīrthaṅkara Pārśva were placed in the city from the early modern period to the present day in order to bring Jain wealth and resources to the city. It examines the temple-building programs of two Śvetāmbara renunciants in particular: the temple-dwelling Kuśalacandrasūri of the Kharataragaccha (initiated in 1778), and the itinerant Ācārya Rājayaśasūri of the Tapāgaccha (b. 1945). While scholars and practitioners often make a strong distinction between the temple-dwelling monks (yatis) who led the Śvetāmbara community in the early modern period and the peripatetic monks (munis) who emerged after reforms in the late nineteenth-century—casting the former as clerics and the latter as true renunciants—ultimately, the lifestyles of Kuśalacandrasūri and Rājayaśasūri appear to be quite similar. Both these men have drawn upon the wealth of Jain merchants and texts—the biographies of Pārśva—to establish their lineage’s presence in Varanasi through massive temple-building projects.
“True, Masculine Men Are Not Like Women!”: Salafism between Extremism and Democracy
Authors: Olsson Susanne
Published: March 2020

Whether we should understand Salafism in general as a security threat, as extremist, and as un-democratic and of concern to authorities is a debated question. In the article, this policy-oriented objective is addressed through an analysis of a specific non-violent Salafi ideology in Sweden, which is compared to the Swedish government’s definition of gender equality. The basic argument in this article is that we can use words like “extreme” as relational concepts, which makes them analytically useful, i.e., when the benchmark is clearly defined.
Tales of Endings and Beginnings: Cycles of Violence as a Leitmotif in the Narrative Structure of the Bhadrakāḷīmāhātmya
Authors: van Brussel Noor
Published: March 2020

The asura’s demise at the hands of the goddess is a theme frequently revisited in Hindu myth. It is the chronicle of a death foretold. So too is the Bhadrakāḷīmāhātmya, a sixteenth century regional purāṇa from Kerala, that narrates the tale of fierce goddess Bhadrakāḷī and her predestined triumph over asura king Dārika. Violence is ubiquitous in this narrative, which was designed with one goal in mind: glorifying the ultimate act of defeating the asura enemy. In its course the story exhibits many kinds of violence: self-harm, cosmic warfare, murder, etc. This paper argues that (1) violence comes to serve as a structural aspect in the text. Reappearing consistently at key moments in the narrative, violence both frames and structures the goddess’s tale. Yet, it is not only the violent act that dominates, it is its accompaniment by equal acts of regeneration that dictates the flow of the narrative, creating a pulsating course of endings and beginnings; (2) these cycles, that strategically occur throughout the narrative, come to serve as a Leitmotif referring to the cyclic tandem of destruction and regeneration that has dominated post-Vedic Hindu myth in many forms. The pulsating dynamic of death and revival thus becomes a specific narrative design that aims to embed the regional goddess within a grander framework of Time.
The Least Square Adjustment for Estimating the Tropical Peat Depth Using LiDAR Data
Authors: Cahyono Bambang Kun , Aditya Trias , Istarno
Published: March 2020

High-accuracy peat maps are essential for peatland restoration management, but costly, labor-intensive, and require an extensive amount of peat drilling data. This study offers a new method to create an accurate peat depth map while reducing field drilling data up to 75%. Ordinary least square (OLS) adjustments were used to estimate the elevation of the mineral soil surface based on the surrounding soil parameters. Orthophoto and Digital Terrain Models (DTMs) from LiDAR data of Tebing Tinggi Island, Riau, were used to determine morphology, topography, and spatial position parameters to define the DTM and its coefficients. Peat depth prediction models involving 100%, 50%, and 25% of the field points were developed using the OLS computations, and compared against the field survey data. Raster operations in a GIS were used in processing the DTM, to produce peat depth estimations. The results show that the soil map produced from OLS provided peat depth estimations with no significant difference from the field depth data at a mean absolute error of ±1 meter. The use of LiDAR data and the OLS method provides a cost-effective methodology for estimating peat depth and mapping for the purpose of supporting peat restoration.
Determining the Suitable Number of Ground Control Points for UAS Images Georeferencing by Varying Number and Spatial Distribution
Authors: Oniga Valeria-Ersilia , Breaban Ana-Ioana , Pfeifer Norbert , Chirila Constantin
Published: March 2020

Currently, products that are obtained by Unmanned Aerial Systems (UAS) image processing based on structure-from-motion photogrammetry (SfM) are being investigated for use in high precision projects. Independent of the georeferencing process being done directly or indirectly, Ground Control Points (GCPs) are needed to increase the accuracy of the obtained products. A minimum of three GCPs is required to bring the results into a desired coordinate system through the indirect georeferencing process, but it is well known that increasing the number of GCPs will lead to a higher accuracy of the final results. The aim of this study is to find the suitable number of GCPs to derive high precision results and what is the effect of GCPs systematic or stratified random distribution on the accuracy of the georeferencing process and the final products, respectively. The case study involves an urban area of about 1 ha that was photographed with a low-cost UAS, namely, the DJI Phantom 3 Standard, at 28 m above ground. The camera was oriented in a nadiral position and 300 points were measured using a total station in a local coordinate system. The UAS images were processed using the 3DF Zephyr software performing a full BBA with a variable number of GCPs i.e., from four up to 150, while the number and the spatial location of check points (ChPs) was kept constant i.e., 150 for each independent distribution. In addition, the systematic and stratified random distribution of GCPs and ChPs spatial positions was analysed. Furthermore, the point clouds and the mesh surfaces that were automatically derived were compared with a terrestrial laser scanner (TLS) point cloud while also considering three test areas: two inside the area defined by GCPs and one outside the area. The results expressed a clear overview of the number of GCPs needed for the indirect georeferencing process with minimum influence on the final results. The RMSE can be reduced down to 50% when switching from four to 20 GCPs, whereas a higher number of GCPs only slightly improves the results.
A Bayesian Three-Cornered Hat (BTCH) Method: Improving the Terrestrial Evapotranspiration Estimation
Authors: He Xinlei , Xu Tongren , Xia Youlong , Bateni Sayed M. , Guo Zhixia , Liu Shaomin , Mao Kebiao , Zhang Yuan , Feng Huaize , Zhao Jingxue
Published: March 2020

In this study, a Bayesian-based three-cornered hat (BTCH) method is developed to improve the estimation of terrestrial evapotranspiration (ET) by integrating multisource ET products without using any a priori knowledge. Ten long-term (30 years) gridded ET datasets from statistical or empirical, remotely-sensed, and land surface models over contiguous United States (CONUS) are integrated by the BTCH and ensemble mean (EM) methods. ET observations from eddy covariance towers (ETEC) at AmeriFlux sites and ET values from the water balance method (ETWB) are used to evaluate the BTCH- and EM-integrated ET estimates. Results indicate that BTCH performs better than EM and all the individual parent products. Moreover, the trend of BTCH-integrated ET estimates, and their influential factors (e.g., air temperature, normalized differential vegetation index, and precipitation) from 1982 to 2011 are analyzed by the Mann–Kendall method. Finally, the 30-year (1982 to 2011) total water storage anomaly (TWSA) in the Mississippi River Basin (MRB) is retrieved based on the BTCH-integrated ET estimates. The TWSA retrievals in this study agree well with those from the Gravity Recovery and Climate Experiment (GRACE).
Accuracy Verification of Airborne Large-Footprint Lidar based on Terrain Features
Authors: Lian Weiqi , Li Shaoning , Zhang Guo , Wang Yanan , Chen Xinyang , Cui Hao
Published: March 2020

Accuracy verification of airborne large-footprint lidar data is important for proper data application but is difficult when ground-based laser detectors are not available. Therefore, we developed a novel method for lidar accuracy verification based on the broadened echo pulse caused by signal saturation over water. When an aircraft trajectory crosses both water and land, this phenomenon and the change in elevation between land and water surfaces can be used to verify the plane and elevation accuracy of the airborne large-footprint lidar data in conjunction with a digital surface model (DSM). Due to the problem of echo pulse broadening, the center-of-gravity (COG) method was proposed to optimize the processing flow. We conducted a series of experiments on terrain features (i.e., the intersection between water and land) in Xiangxi, Hunan Province, China. Verification results show that the elevation accuracy obtained in our experiments was better than 1 m and the plane accuracy was better than 5 m, which is well within the design requirements. Although this method requires specific terrain conditions for optimum applicability, the results can lead to valuable improvements in the flexibility and quality of lidar data collection.
Quantifying Information Content in Multispectral Remote-Sensing Images Based on Image Transforms and Geostatistical Modelling
Authors: Zhang Ying , Zhang Jingxiong , Yang Wenjing
Published: March 2020

Quantifying information content in remote-sensing images is fundamental for information-theoretic characterization of remote sensing information processes, with the images being usually information sources. Information-theoretic methods, being complementary to conventional statistical methods, enable images and their derivatives to be described and analyzed in terms of information as defined in information theory rather than data per se. However, accurately quantifying images’ information content is nontrivial, as information redundancy due to spectral and spatial dependence needs to be properly handled. There has been little systematic research on this, hampering wide applications of information theory. This paper seeks to fill this important research niche by proposing a strategy for quantifying information content in multispectral images based on information theory, geostatistics, and image transformations, by which interband spectral dependence, intraband spatial dependence, and additive noise inherent to multispectral images are effectively dealt with. Specifically, to handle spectral dependence, independent component analysis (ICA) is performed to transform a multispectral image into one with statistically independent image bands (not spectral bands of the original image). The ICA-transformed image is further normal-transformed to facilitate computation of information content based on entropy formulas for Gaussian distributions. Normal transform facilitates straightforward incorporation of spatial dependence in entropy computation for the aforementioned double-transformed image bands with inter-pixel spatial correlation modeled via variograms. Experiments were undertaken using Landsat ETM+ and TM image subsets featuring different dominant land cover types (i.e., built-up, agricultural, and hilly). The experimental results confirm that the proposed methods provide more objective estimates of information content than otherwise when spectral dependence, spatial dependence, or non-normality is not accommodated properly. The differences in information content between image subsets obtained with ETM+ and TM were found to be about 3.6 bits/pixel, indicating the former’s greater information content. The proposed methods can be adapted for information-theoretic analyses of remote sensing information processes.