bluuebunny/crossref_metadata_2025 huggingface dataset:
Preparation and characterization of magnetic theranostic nanoparticles for curcumin delivery and evaluation as MRI contrast agent
Authors: Nosrati Hamed , Charmi Jalil , Abedini Somayeh , Rashidi Nafis , Attari Elahe , Davaran Soodabeh , Danafar Hossein , Kheiri Manjili Hamidreza
Published: October 2018

In this study we described the production of curcumin (CUR) loaded L‐tyrosine (Tyr coated Fe3O4 magnetic nanoparticles. CUR loaded Tyr modified Fe3O4 nanoparticles (F@Tyr@CUR NPs) were analyzed by transmission electron microscopy, fourier transform infrared spectroscopy, thermo gravimetric analysis, vibrating sample magnetometer, X‐ray diffraction and dynamic light scattering techniques. The dynamic light scattering results showed that the ζ‐potential of F@Tyr@CUR NPs was about −15.4 mV. Also, the internal average size was about 25.81 ± 3.31 (mean ± SD (n = 30)) nm. The drug loading and encapsulation efficiency were 8.87 ± 0.09% and 35.21 ± 0.41%, respectively. In addition, hemolysis test on human red blood cells were conducted to determine the hemocompatibility of F@Tyr@CUR NPs. Next, MTT assays on HEK‐293 were conducted to determine the toxicity of F@Tyr@CUR NPs. Lastly, the potential anticancer effect of F@Tyr@CUR NPs was considered on MCF‐7 cancer cell line. The outcomes indicated that these F@Tyr@CUR NPs are appropriate for delivery of CUR anticancer drug. Also, the MRI training established the effectiveness of Fe3O4 magnetic nanoparticles as contrast agent for the revealing of tumor as evidenced from the phantom images as well as higher T2 relaxivity.
Fabrication of noble‐metal‐free g‐C3N4‐MIL‐53(Fe) composite for enhanced photocatalytic H2‐generation performance
Authors: Bai Chunpeng , Bi Jingce , Wu Junbiao , Meng Hao , Xu Yan , Han Yide , Zhang Xia
Published: October 2018

In this paper, we reported that g‐C3N4/MIL‐53(Fe) composites were successfully fabricated through a simple grinding method, and they were used as photocatalysts to generate H2 from water under simulated sunlight irradiation. The introduction of g‐C3N4 into MIL‐53(Fe) could efficiently improve the H2 evolution rate from splitting water, which was attributed to the charge spatial separation between g‐C3N4 and MIL‐53(Fe). Impressively, g‐C3N4/MIL‐53(Fe)‐0.5 composite displayed the highest H2 evolution rate (0.9054 mmol g−1 h−1), about 335 and 47 times higher than that of pristine MIL‐53(Fe) 0.0027 mmol g−1 h−1 and g‐C3N4 (0.0193 mmol g−1 h−1), respectively. Further investigation demonstrated that an intimate interfacial contact, more active sites and well‐matched energy level were responsible for the enhancement of photocatalytic H2 evolution over g‐C3N4/MIL‐53(Fe) composites. To the best of our knowledge, this is the first report about using g‐C3N4/MIL‐53(Fe) composite as photocatalyst for H2 evolution. Thus, this study might open an avenue to fabricate the novel photocatalysts with superior activity.
Thermal stability enhancement of guar‐based hydraulic fracturing fluids by phosphate treatment
Authors: Ma X. , Wang H. , Boyd W. W. , Cheng M. , Yao C. , Lei G.
Published: October 2018

Guar gum (GG), along with its derivatives [e.g., hydroxypropyl guar (HPG)], is an important thickening agent in the hydraulic fracturing fluid system. However, as the oil reservoir gets deeper, GG is unable to tolerate the elevated temperature. In this study, the thermal stability of GG and HPG can be increased up to 95% and 80%, respectively, when phosphates are used as thermal stabilizer. The thermal stability is highest when the usage of phosphate is 1.84 mmol L−1 KH2PO4 for GG and 2.27 mmol L−1 K2HPO4 for HPG and the pH is 6.25–6.90 for GG and 6.25–8.75 for HPG. Furthermore, the heated GG with phosphate treatment demonstrates excellent crosslinking ability, which suggests that phosphate can be a good alternative for current thermal stabilizers and has potential application in the high‐temperature formation oil or gas production. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019, 136, 47119.
Encapsulation ofN,N‐diethyl‐meta‐toluamide (DEET) via miniemulsion polymerization for temperature controlled release
Authors: Gomes G. M. , Bigon J. P. , Montoro F. E. , Lona L. M. F.
Published: October 2018

N,N‐diethyl‐meta‐toluamide (DEET), an insect repellent, can be successfully encapsulated in poly(n‐butyl methacrylate‐co‐methyl methacrylate) nanospheres via direct miniemulsion polymerization. Stable and low polydisperse nanospheres with a number average diameter of 114 ± 37 nm were obtained. It is shown that DEET is an effective costabilizer and that sodium lauryl sulfate is a suitable surfactant. The nanospheres glass‐transition temperature (Tg) can be tuned by adjusting the ratio betweenn‐butyl methacrylate and methyl methacrylate in the monomer formulation. The repellent reduced the polymerization reaction rate and the copolymer molecular weight, and changed the nanoparticle morphology. The release rate of the encapsulated DEET provides repellency for over 9 h and is and more controlled when compared to the free DEET. Results show the mechanism of release is temperature dependent. At temperatures close to and lower than the polymerTg, polymer relaxation is the limiting mechanism. At higher temperatures, Fickian diffusion limits the overall release. Thus, the DEET release rate can be tuned by adjusting the copolymerTg. This ensures this material a great potential as temperature‐dependent delivery system. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci.2019,136, 47139.
Sunlight photodepolymerization of transient polymers
Authors: Phillips O. , Engler A. , Schwartz J. M. , Jiang J. , Tobin C. , Guta Y. A. , Kohl P. A.
Published: October 2018

The study and development of transient devices is an emerging field where the disposal of a device after use is desired to avoid reverse engineering and minimize the environmental impact. Polyaldehydes with phototriggers have been investigated because the radiation wavelength can be adjusted to meet the transient application. Polynuclear aromatic hydrocarbons (PAHs) were used as the optical sensitizer for photoacid generators (PAGs). Photoinduced electron transfer (PET) with an iodonium‐based PAG was used to expand the spectral sensitivity range. Anthracene, tetracene, and pentacene derivatives were synthesized with appended phenylethynyl groups to improve the solubility of the sensitizer and adjust the absorption wavelength. Sensitization of the iodonium‐based PAG with the PAH derivatives was found to have thermodynamically favorable PET reactions for depolymerization of poly(propylene carbonate) and poly(phthalaldehyde) (PPHA). The Rehm–Weller equation and Stern–Volmer analysis were used to study the electron transfer and the fluorescence quenching rates of the PAHs with the iodonium salts, respectively. The photosensitivity, efficiency, and byproducts of the PET reactions in the decomposable polymer films are reported. A rapid photoreaction is reported for the depolymerization of PPHA exposed to a sunlight dose of <6 J cm−2 (i.e., 1 min of direct sunlight) with a pentacene‐based sensitizer. © 2018 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019, 136, 47141.
Otitis media, antibiotics, and risk of autism spectrum disorder
Authors: Wimberley Theresa , Agerbo Esben , Pedersen Carsten B. , Dalsgaard Søren , Horsdal Henriette Thisted , Mortensen Preben B. , Thompson Wesley K. , Köhler‐Forsberg Ole , Yolken Robert H.
Published: October 2018

Otitis media infections and antibiotic treatment have been linked to the risk of developing autism spectrum disorder. Broad‐spectrum antibiotics may alter the composition of the gut flora microbiota, which is hypothesized to be involved in the regulation of the immune system. This study examines the interplay among otitis media, antibiotics, and the subsequent risk of developing autism. Based on the entire Danish population, 780,547 children were followed from birth (January 1, 1997 to December 31, 2008) until December 31, 2012. We calculated adjusted hazard ratios and absolute risks of autism with 95% confidence intervals (CIs) related to previous otitis media diagnoses and antibiotic prescriptions redeemed at Danish pharmacies. The absolute risk of autism before age 10 was increased among children with otitis media (1.2% for females and 3.3% for males) and in children who had redeemed an antibiotic prescription (0.6% and 2.7% for females and males) compared to children without a history of otitis media and antibiotics usage (0.4% for females and 1.9% for males). Similarly, we found an increased hazard ratio of autism associated with otitis media (1.83 95% CI 1.71–1.95) and antibiotics usage (1.29 95% CI 1.17–1.43). A history of both otitis media and antibiotic treatment did not further increase the risk of autism. Although the risk of autism was associated with otitis media and treatment with antibiotics, we found little evidence of a synergistic effect between otitis media infections and treatment with antibiotics. Autism Res 2018, 11: 1432–1440. © 2018 International Society for Autism Research, Wiley Periodicals, Inc.

Lay Summary

We investigated whether otitis media ear infections and antibiotic treatment were associated with autism spectrum disorder. Autism was more common in children who had had an otitis media infection or who had been treated with antibiotics. Given the observational nature of our data, our study cannot be used to conclude that otitis media or use of antibiotics cause autism, as our findings may be subject to unobserved confounding.
Chemical cross‐linking of a variety of green fluorescent proteins as Förster resonance energy transfer donors for Yukon orange fluorescent protein: A project‐based undergraduate laboratory experience
Authors: Marchioretto Mira K. , Horton Jacqueline T. , Berstler Calvin A. , Humphries Joseph B. , Koloditch Isaac J. , Voss Samuel D. , de La Harpe Kimberly , Hicks Barry W. , Jefferies Latisha R.
Published: October 2018

Förster resonance energy transfer (FRET) is the basis for many techniques used in biomedical research. Due to its wide use in molecular sensing, FRET is commonly introduced in many biology, chemistry, and physics courses. While FRET is of great importance in the biophysical sciences, the complexity and difficulty of constructing FRET experiments has resulted in limited usage in undergraduate laboratory settings. Here, we present a practical undergraduate laboratory experiment for teaching FRET using a diverse set of green‐emitting fluorescent proteins (FPs) as donors for a cross‐linked Yukon orange FP. This laboratory experiment enables students to make the connection of basic lab procedures to real world applications and can be applied to molecular biology, biochemistry, physical chemistry, and biophysical laboratory courses. Published 2018. This article is a U.S. Government work and is in the public domain in the USA., 46(5):516–522, 2018.
Detection of aquaporin‐4 antibodies for patients with CNS inflammatory demyelinating diseases other than typical MS in Lithuania
Authors: Sakalauskaitė‐Juodeikienė Eglė , Armalienė Giedrė , Kizlaitienė Rasa , Bagdonaitė Loreta , Giedraitienė Nataša , Mickevičienė Dalia , Rastenytė Daiva , Kaubrys Gintaras , Jatužis Dalius
Published: October 2018

Objectives

Neuromyelitis optica (NMO) is frequently associated with aquaporin‐4 autoantibodies (AQP4‐Ab); however, studies of NMO in Lithuania are lacking. Therefore, the main objective of our study is to assess positivity for AQP4‐Ab in patients presenting with inflammatory demyelinating central nervous system (CNS) diseases other than typical multiple sclerosis (MS) in Lithuania.

Materials and methods

Data were collected from the two largest University hospitals in Lithuania. During the study period, there were 121 newly diagnosed typical MS cases, which were included in the MS registry database. After excluding these typical MS cases, we analyzed the remaining 29 cases of other CNS inflammatory demyelinating diseases, including atypical MS (n = 14), acute transverse myelitis, TM (n = 8), acute disseminated encephalomyelitis, ADEM (n = 3), clinically isolated syndrome, CIS (n = 2), atypical optic neuritis, ON (n = 1), and NMO (n = 1). We assessed positivity for AQP4‐Ab for the 29 patients and evaluated clinical, laboratory, and instrumental differences between AQP4‐Ab seropositive and AQP4‐Ab seronegative patient groups.

Results

AQP4‐Ab test was positive for three (10.3%) patients in our study, with initial diagnoses of atypical MS (n = 2) and ADEM (n = 1). One study patient was AQP4‐Ab negative despite being previously clinically diagnosed with NMO. There were no significant clinical, laboratory, or instrumental differences between the groups of AQP4‐Ab positive (3 [10.3%]) and negative (26 [89.7%]) patients.

Conclusions

AQP4‐Ab test was positive for one‐tenth of patients with CNS inflammatory demyelinating diseases other than typical MS in our study. AQP4‐Ab testing is highly recommended for patients presenting with not only TM and ON but also an atypical course of MS and ADEM.
Achieving greater efficiency and higher confidence in single‐cell cloning by combining cell printing and plate imaging technologies
Authors: Yim Mandy , Shaw David
Published: October 2018

In recent years, health authorities have increased emphasis on demonstrating that a cell line, which is used for the generation of biologics, is clonally derived. Within the past few years, single‐cell manipulation technologies, especially microfluidic drop‐on‐demand dispensing, have gained increased attention in the biopharmaceutical industry. This work discusses the development and characterization of a single‐cell printing workflow followed by plate imaging. By combining single‐cell printing and plate imaging with manual image verification it is possible to, (1) dramatically reduce the number of microtiter plates needed during the single‐cell cloning of clinical cell lines, as compared with a limiting‐dilution single‐cell cloning workflow, and therefore reduce the number of high‐resolution images acquired and stored and (2) achieve >99.99% assurance that the cell lines derived from this workflow are clonally derived. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 34:1454–1459, 2018
Design, Synthesis and Molecular Docking Studies of Some Tetrahydropyrimidine Derivatives as Possible Fascin Inhibitors
Authors: Riahi Narges , Kefayat Amirhosein , Ghasemi Ahmad , Asgarshamsi Mohammadhosein , Panjehpoor Mojtaba , Fassihi Afshin
Published: October 2018

Eight derivatives of tetrahydropyrimidine scaffold were designed and prepared as hybrid compounds possessing the structural features of both monastrol as an anticancer drug and nifedipine as a fascin blocking agent. All of the compounds were evaluated for their cytotoxic potency and the ability to inhibit 4T1 breast cancer cells migration. Then, they were investigated in silico for their ability to inhibit the fascin protein using molecular docking simulation. The most potent compound was 4d and the weakest one was 4a according to the in vitro cytotoxicity assay. The corresponding IC50 values were 193.70 and 248.75 μm, respectively. The least cytotoxic compound (4a) was one of the strongest ones in binding to the fascin binding site according to the molecular docking results. 4a and 4e inhibited the 4T1 cells migration better than other compounds. They were more potent than nifedipine in inhibiting the migration process. In silico studies proved 4h to be the most potent fascin inhibitor in terms of ΔGbind although it was not inhibiting migration. The controversy between the in vitro and in silico results may cancel the theory of the involvement of the fascin inhibition in the migration inhibition. However, the considerable antimigratory effects of some of the synthesized compounds encourage performing further in vivo experiments to introduce novel tumor metastasis inhibitors.
Substrate Preference Pattern of Agaricus meleagris Pyranose Dehydrogenase Evaluated through Bioelectrochemical Flow Injection Amperometry
Authors: Rafighi Parvin , Bollella Paolo , Pankratova Galina , Peterbauer Clemens K. , Conghaile Peter Ó , Leech Dónal , Haghighi Behzad , Gorton Lo
Published: October 2018

Pyranose dehydrogenase (PDH) is a quinone‐dependent extracellular flavoglycoprotein mainly produced by litter‐decomposing fungi and contributes to the degradation of lignocellulose. PDH in terms of structure and catalytic features pertains to the glucose methanol‐choline oxidoreductase family and oxidizes a wide substrate range of aldopyranoses including hexoses, pentoses, disaccharides and oligosaccharides with a high degree of regioselectivity. The purpose of this study was to rationalize the preference of PDH immobilized on an electrode with the structural features of various substrates and thus the kinetic constants were measured for various sugars. PDH was co‐immobilized on the electrode with an osmium redox polymer. Response currents for different sugars were measured using flow injection amperometry at +0.3 V vs. Ag|AgCl, KCl (0.1 M). The Michaelis‐Menten constants, the turnover numbers and the catalytic efficiency were calculated and revealed that type, orientation and configuration of the substituent play a major role on substrate preference. An OH‐group at C‐1 and C‐6 are not essential and substrate specificities are little affected by the substitution at C‐1. The presence and orientation of OH− at C‐2 and C‐3 are relevant for reactivity. Orientation of OH− at the C‐4 position has little effect, and sugars with a substitution below the plane at C‐5 are not suitable as substrate. Highest activity for oxidation of glucose, mannose and sucrose was detected at pH 8.5.
Effect of sulphation on the catalytic activity of MIL‐101 and the activation energy of an esterification reaction
Authors: Yılmaz Esra , Sert Emine , Atalay Ferhan Sami
Published: October 2018

Metal organic frameworks have been recently highlighted as promising materials for heterogeneous catalysts. In this study, MIL‐101, a chromium‐based metal organic framework was synthesized using the solvothermal method and functionalized through sulphation. The catalytic activities of MIL‐101 and sulphated MIL‐101 (MIL‐101s) were tested in the esterification of acetic acid. The conversion of acetic acid increased from 73.7 to 86.2 % after sulphation at 363 K. These results prove that the sulphation of MIL‐101 is an effective way to enhance the acidity and catalytic activity of MIL‐101.

The characterization of MIL‐101 and MIL‐101s was performed using FTIR, BET, XRD, TG‐DTA, SEM/EDX, XPS, and potentiometric titration methods. A BET analysis showed that MIL‐101 maintained its porosity after sulphation. The sulphation reduced the surface area and pore volume but increased the acidity.
Analysis of Cysteine Post Translational Modifications Using Organic Mercury Resin
Authors: Doulias Paschalis‐Thomas , Gould Neal S.
Published: October 2018

The wide reactivity of the thiol group enables the formation of a variety of reversible, covalent modifications on cysteine residues. S‐nitrosylation, like many other post‐translational modifications, is site selective, reversible, and necessary for a wide variety of fundamental cellular processes. The overall abundance of S‐nitrosylated proteins and reactivity of the nitrosyl group necessitates an enrichment strategy for accurate detection with adequate depth. Herein, a method is presented for the enrichment and detection of endogenous protein S‐nitrosylation from complex mixtures of cell or tissue lysate utilizing organomercury resin. Minimal adaptations to the method also support the detection of either S‐glutathionylation or S‐acylation using the same enrichment platform. When coupled with high accuracy mass spectrometry, these methods enable a site‐specific level of analysis, facilitating the curation comparable datasets of three separate cysteine post‐translational modifications. © 2018 by John Wiley & Sons, Inc.
Genetic Engineering of Human Pluripotent Stem Cells Using PiggyBac Transposon System
Authors: Park Mi Ae , Jung Ho Sun , Slukvin Igor
Published: October 2018

Human pluripotent stem cells (hPSCs) emerged as an important tool to investigate human development and disease. These studies often require genetically engineering hPSCs to stably express a transgene, which remains functional in various hPSC progeny. PiggyBac transposon is a highly effective and technically simple vector system with large cargo space available for permanent gene delivery. This unit describes the use of PiggyBac transposons to genetically engineer hPSCs to introduce conditionally expressed transgene or reporter to effectively monitor gene expression during differentiation. Both methods enable robust generation of stable hPSC lines within 1 month. © 2018 by John Wiley & Sons, Inc.
Investigation of the antimicrobial and anticancer activity of aminonaphthoquinones
Authors: Wellington Kevin W. , Kolesnikova Natasha I. , Nyoka Nomgqibelo B. P. , McGaw Lyndy J.
Published: October 2018

In this study, we report on the inhibitory activity of synthesized aminonaphthoquinones against two bacterial and one fungal species to determine their antimicrobial properties. A minimum inhibitory concentration (MIC) of 7.8 μg/mL was obtained against the fungus, Candida albicans, which was better than that of Amphotericin B (MIC = 31.25 μg/mL). Escherichia coli (Gram ‐), was inhibited at a MIC of 23.4 μg/mL and Staphylococcus aureus (Gram +) at a MIC of 31.3 μg/mL. The aminonaphthoquinones were also screened against HCT116 colon, PC3 prostate and HepG2 liver cancer cell lines to evaluate their cytostatic effects. They had potent activity (GI50 = 5.87–9.90 μM) which was about three‐6‐fold better than that of parthenolide (GI50 = 25.97 μM) against the prostate cancer cell line. These compounds were generally more selective for cancer cells than for normal human lung fetal fibroblasts (WI‐38).
Morphological and biological characterization of a light‐colored mutant in the multicolored Asian lady beetle,Harmonia axyridis
Authors: Sun Yuan‐Xing , Hao Ya‐Nan , Yan Yu , Zhang Yi , Feng Yi , Liu Tong‐Xian
Published: October 2018

Insect cuticle color formed with melanin pigments has numerous types of mutants which usually cause pleiotropic effects. Melanism has been widely studied, but mutants with light‐colored phenotype as well as the consequent fitness changes have rarely been reported.

Here, in the laboratory strain ofHarmonia axyridis, we found a novel mutantgrand confirmed that the mutation was inherited in a simple Mendelian autosomal recessive manner. This mutant (HAM) continuously displayed a light‐colored pigmentation versus dark blackish in the wild phenotype (HAW). L‐DOPAand dopamine are melanin precursors, and less L‐DOPAwas present in the cuticle of larval and adultHAMmutants compared toHAWwild type, but more dopamine was detected in the larval cuticle ofHAM(p ≤ 0.0235). For the orange background of elytra, the composition as well as total concentration of carotenoids was different betweenHAMandHAW, which resulted in significantly lower saturation value but significantly higher hue value inHAMthan inHAW(p < 0.0001).

Extensive fitness changes were detected inHAM. (a)HAMlarvae had similar predation capacity and preimaginal development time asHAW, but the newly emerged adults were much smaller (p < 0.0001). (b) Both fecundity and egg hatch rate in cross ♀(HAM) × ♂(HAM) were significantly lower than those in ♀(HAW) × ♂(HAW) (p ≤ 0.0087), but were not different with those in ♀(HAW) × ♂(HAM). (c)HAMhad weaker resistance to desiccation and ultraviolet irradiation compared toHAW(p ≤ 0.0115).

These results indicated that the novel light‐colored mutant (HAM) was highly correlated with fitness changes, and it would be a perfect model to study molecular mechanisms of melanism and how a gene results in pleiotropic effects.
Host specificity driving genetic structure and diversity in ectoparasite populations: Coevolutionary patterns in Apodemus mice and their lice
Authors: Martinů Jana , Hypša Václav , Štefka Jan
Published: October 2018

A degree of host specificity, manifested by the processes of host–parasite cospeciations and host switches, is assumed to be a major determinant of parasites’ evolution. To understand these patterns and formulate appropriate ecological hypotheses, we need better insight into the coevolutionary processes at the intraspecific level, including the maintenance of genetic diversity and population structure of parasites and their hosts. Here, we address these questions by analyzing large‐scale molecular data on the louse Polyplax serrata and its hosts, mice of the genus Apodemus, across a broad range of European localities. Using mitochondrial DNA sequences and microsatellite data, we demonstrate the general genetic correspondence of the Apodemus/Polyplax system to the scenario of the postglacial recolonization of Europe, but we also show several striking discrepancies. Among the most interesting are the evolution of different degrees of host specificity in closely related louse lineages in sympatry, or decoupled population structures of the host and parasites in central Europe. We also find strong support for the prediction that parasites with narrower host specificity possess a lower level of genetic diversity and a deeper pattern of interpopulation structure as a result of limited dispersal and smaller effective population size.
Implications of survey effort on estimating demographic parameters of a long‐lived marine top predator
Authors: Symons John , Sprogis Kate R. , Bejder Lars
Published: October 2018

Effective management of wildlife populations rely on knowledge of their abundance, survival, and reproductive rates. Maintaining long‐term studies capable of estimating demographic parameters for long‐lived, slow‐reproducing species is challenging. Insights into the effects of research intensity on the statistical power to estimate demographic parameters are limited. Here, we investigate implications of survey effort on estimating abundance, home range sizes, and reproductive output of Indo‐Pacific bottlenose dolphins (Tursiops aduncus), using a 3‐year subsample of a long‐term, capture–recapture study off Bunbury, Western Australia. Photo‐identification on individual dolphins was collected following Pollock's Robust Design, where seasons were defined as “primary periods”, each consisting of multiple “secondary periods.” The full dataset consisted of 12 primary periods and 72 secondary periods, resulting in the study area being surveyed 24 times/year. We simulated reduced survey effort by randomly removing one, two, or three secondary periods per primary period. Capture–recapture models were used to assess the effect of survey intensity on the power to detect trends in population abundance, while individual dolphin sighting histories were used to assess the ability to conduct home range analyses. We used sighting records of adult females and their calving histories to assess survey effort on quantifying reproductive output. A 50% reduction in survey effort resulted in (a) up to a 36% decline in population abundance at the time of detection; (b) a reduced ability to estimate home range sizes, by increasing the time for individuals to be sighted on ≥30 occasions (an often‐used metric for home range analyses) from 7.74 to 14.32 years; and (c) 33%, 24%, and 33% of annual calving events across three years going undocumented, respectively. Results clearly illustrate the importance of survey effort on the ability to assess demographic parameters with clear implications for population viability analyses, population forecasting, and conservation efforts to manage human–wildlife interactions.
DNA barcoding the flowering plants from the tropical coral islands of Xisha (China)
Authors: Li Shengchun , Qian Xin , Zheng Zexin , Shi Miaomiao , Chang Xiaoyu , Li Xiaojuan , Liu Junfang , Tu Tieyao , Zhang Dianxiang
Published: October 2018

Aim

DNA barcoding has been widely applied to species diversity assessment in various ecosystems, including temperate forests, subtropical forests, and tropical rain forests. However, tropical coral islands have never been barcoded before due to the difficulties in field exploring. This study aims at barcoding the flowering plants from a unique ecosystem of the tropical coral islands in the Pacific Ocean and supplying valuable evolutionary information for better understanding plant community assembly of those particular islands in the future.

Location

Xisha Islands, China.

Methods

This study built a DNA barcode database for 155 plant species from the Xisha Islands using three DNA markers (ITS, rbcL, and matK). We applied the sequence similarity method and a phylogenetic‐based method to assess the barcoding resolution.

Results

All the three DNA barcodes showed high levels of PCR success (96%–99%) and sequencing success (98%–100%). ITS performed the highest rate of species resolution (>95%) among the three markers, while plastid markers delivered a relatively poor species resolution (85%–90%). Our analyses obtained a marginal increase in species resolution when combining the three DNA barcodes.

Main conclusions

This study provides the first plant DNA barcode data for the unique ecosystem of tropical coral islands and considerably supplements the DNA barcode library for the flowering plants on the oceanic islands. Based on the PCR and sequencing success rates, and the discriminatory power of the three DNA regions, we recommend ITS as the most successful DNA barcode to identify the flowering plants from Xisha Islands. Due to its high sequence variation and low fungal contamination, ITS could be a preferable candidate of DNA barcode for plants from other tropical coral islands as well. Our results also shed lights on the importance of biodiversity conservation of tropical coral islands.
Can AI predict animal movements? Filling gaps in animal trajectories using inverse reinforcement learning
Authors: Hirakawa Tsubasa , Yamashita Takayoshi , Tamaki Toru , Fujiyoshi Hironobu , Umezu Yuta , Takeuchi Ichiro , Matsumoto Sakiko , Yoda Ken
Published: October 2018

Focal animal sampling and continuous recording of behavior in situ are essential in the study of ecology. However, observation gaps and missing records are unavoidable because the focal individual can move out of sight and recording devices do not always work properly. Using an inverse reinforcement learning (IRL) framework, we have developed a novel gap‐filling method to predict the most likely route that an animal would have traveled; within this framework, an algorithm learns a reward function from animal trajectories to find the environmental features preferred by the animal. We applied this approach to GPS trajectories obtained from streaked shearwaters (Calonectris leucomelas) and provide evidence of the advantages of the IRL approach over previously used interpolation methods. These advantages are as follows: (1) No assumptions about the parametric distribution governing movements are needed, (2) no assumptions regarding landscape preferences and restrictions are needed, and (3) large spatiotemporal gaps can be filled. This work demonstrates how IRL can enhance the ability to fill gaps in animal trajectories and construct reward‐space maps in heterogeneous environments. The proposed methodology can assist movement research, which seeks to understand phenomena that are ecologically and evolutionarily significant, such as habitat selection and migration.
Development of discrete CoFFWA for distribution network reconfigurations
Authors: Ikegami Hiromitsu , Mori Hiroyuki
Published: October 2018

In this article, an efficient Discrete CoFFWA method is proposed to deal with distribution network reconfigurations. It is useful for minimizing the active power network losses by switching on/off sectionalizing switches and shunt capacitors. The mathematical formulation may be expressed as one of combinatorial optimization problems. This article presents a discrete version of cooperative framework for fireworks algorithm (CoFFWA) of advanced metaheuristics to solve distribution network reconfigurations efficiently. It is one of the efficient Fireworks Algorithms that imitate the behavior of firework explosion. To improve the solution accuracy, CoFFWA makes use of new strategies such as the independent selection method and the crowdness‐avoiding cooperative strategy. The proposed method transforms CoFFWA into discrete one with multipoint mutation. The proposed method is successfully applied to the IEEE 69‐node and 119‐node distribution networks.
Estimation of the solar radiation based on air temperature in tunisia
Authors: Ayadi Ahmed , Driss Zied , Bouabidi Abdallah , Abid Mohamed Salah
Published: October 2018

This article focuses on the estimation of the solar global daily radiation using the values of the air temperature. The reason for choosing this environmental parameter is that the data of the air temperature are available worldwide and are easy to be recorded from the local meteorological station. Specified models were developed to estimate the global solar radiation data in considered cities in Tunisia, North Africa. A site‐independent model was proposed to estimate the solar radiation using only the minimum and the maximum daily air temperature. By using five statistical indicators, the proposed models were assessed in order to present the best model for each region in Tunisia. Acceptable values of the indicators were recorded. The presented statistical test is based on recorded data from meteorological stations implemented in Tunis, Kairouan, Sfax, Gabes, and Kebili. The choice of the five selected cities is based on the availability of the metrological measurements. The assessment of the potential of the solar energy in the considered cities was presented. Zoning the assessment of the solar radiation would give a better understanding of the distribution of solar radiation and an overview of the general solar radiation climatic conditions within Tunisia. © 2018 American Institute of Chemical Engineers Environ Prog, 38: 600–607, 2019
Postprocessing‐based interpolation schemes for nested Cartesian finite difference grids of different size
Authors: Figueroa Alejandro , Löhner Rainald
Published: October 2018

Nested Cartesian grid systems by design require interpolation of solution fields from coarser to finer grid systems. While several choices are available, preserving accuracy, stability, and efficiency at the same time require careful design of the interpolation schemes. Given this context, a series of interpolation algorithms based on postprocessing halo information on nested Cartesian finite difference grids of different size were developed and tested. The results obtained indicate that most of these do not yield the expected improvement, and some even tend to make the solver unstable. However, some third‐ and fourth‐order interpolation functions do yield considerable accuracy improvement, are stable, and are worth implementing.
Calcium‐regulated mitochondrial ATP‐Mg/Pi carriers evolved from a fusion of an EF‐hand regulatory domain with a mitochondrial ADP/ATP carrier‐like domain
Authors: Harborne Steven P. D. , Kunji Edmund R. S.
Published: October 2018

The mitochondrial ATP‐Mg/Pi carrier is responsible for the calcium‐dependent regulation of adenosine nucleotide concentrations in the mitochondrial matrix, which allows mitochondria to respond to changing energy requirements of the cell. The carrier is expressed in mitochondria of fungi, plants and animals and belongs to the family of mitochondrial carriers. The carrier is unusual as it consists of three separate domains: (i) an N‐terminal regulatory domain with four calcium‐binding EF‐hands similar to calmodulin, (ii) a loop domain containing an amphipathic α‐helix and (iii) a mitochondrial carrier domain related to the mitochondrial ADP/ATP carrier. This striking example of three domains coming together from different origins to provide new functions represents an interesting quirk of evolution. In this review, we outline how the carrier was identified and how its physiological role was established with a focus on human isoforms. We exploit the sequence and structural information of the domains to explore the similarities and differences to their closest counterparts; mitochondrial ADP/ATP carriers and proteins with four EF‐hands. We discuss how their combined function has led to a mechanism for calcium‐regulated transport of adenosine nucleotides. Finally, we compare the ATP‐Mg/Pi carrier with the mitochondrial aspartate/glutamate carrier, the only other mitochondrial carrier regulated by calcium, and we will argue that they have arisen by convergent rather than divergent evolution. © 2018 The Authors. IUBMB Life published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology, 70(12):1222–1232, 2018
Does mitochondrial DNA evolution in metazoa drive the origin of new mitochondrial proteins?
Authors: van Esveld S. L. , Huynen M. A.
Published: October 2018

Most eukaryotic cells contain mitochondria with a genome that evolved from their α‐proteobacterial ancestor. In the course of eukaryotic evolution, the mitochondrial genome underwent a dramatic reduction in size, caused by the loss and translocation of genes. This required adjustments in mitochondrial gene expression mechanisms and resulted in a complex collaborative system of mitochondrially encoded transfer RNAs and ribosomal RNAs with nuclear encoded proteins to express the mitochondrial encoded oxidative phosphorylation (OXPHOS) proteins. In this review, we examine mitochondrial gene expression from an evolutionary point of view: to what extent can we correlate changes in the mitochondrial genome in the evolutionary lineage leading to human with the origin of new nuclear encoded proteins. We dated the evolutionary origin of mitochondrial proteins that interact with mitochondrial DNA or its RNA and/or protein products in a systematic manner and compared them with documented changes in the mitochondrial DNA. We find anecdotal but accumulating evidence that metazoan RNA‐interacting proteins arose in conjunction with changes of the mitochondrial DNA. We find no substantial evidence for such compensatory evolution in new OXPHOS proteins, which appear to be constrained by the ability to form supercomplexes. © 2018 IUBMB Life, 70(12):1240–1250, 2018
NT5E inhibition suppresses the growth of sunitinib‐resistant cells and EMT course and AKT/GSK‐3β signaling pathway in renal cell cancer
Authors: Peng Dan , Hu Zhiquan , Wei Xian , Ke Xinwen , Shen Yuanqing , Zeng Xing
Published: October 2018

We aimed to explore the mechanisms of sunitinib‐resistance in renal cell cancer (RCC) and provide new therapeutic evidence and biomarkers for RCC treatment using human clear‐cell renal cell carcinoma (ccRCC) cell line, 786‐O. Microarray analysis, quantitative real time PCR (qRT‐PCR), Western blot, and immunohistochemistry were used to detect Ecto‐5′‐nucleotidase (NT5E) expressions in sunitinib‐resistant tissues in RCC. 3‐(4,5‐dimethyl‐2‐thiazolyl)‐2,5‐diphenyl‐2‐H‐tetrazolium bromide, Thiazolyl Blue Tetrazolium Bromide (MTT), cell‐count kit 8 (CCK‐8), wound healing, and Transwell assays were used to investigate the influences of sunitinib and NT5E on 786‐O cell line and sunitinib‐resistant 786‐O cell line (S786‐O). Protein expressions related to epithelial–mesenchymal transition (EMT) and AKT/GSK‐3β signaling pathway in 786‐O cells and S786‐O cells were determined by Western blot. In vivo experiment was performed using NCr‐nu/nu mice to explore the effects of NT5E on cell growth and EMT signal in sunitinib environment. NT5E expression was upregulated in sunitinib‐resistant RCC tissues and cells. NT5E downregulation repressed RCC cell proliferation, migration as well as invasion. EMT course and AKT/GSK‐3β signal pathway both in vitro and in vivo in sunitinib environment was suppressed to varying degrees via NT5E inhibition. NT5E inhibition could suppress the growth of sunitinib‐resistant RCC cells and restrain EMT course and AKT/GSK‐3β signal pathway in sunitinib environment in RCC. © 2018 IUBMB Life, 71(1):113–124, 2019
Poly r(C) Binding Protein 1 Regulates Posttranscriptional Expression of the Ubiquitin Ligase TRIM56 in Ovarian Cancer
Authors: Zhao Lei , Wang Zhi‐gang , Zhang Ping , Yu Xiu‐feng , Su Xiao‐jie
Published: October 2018

Our earlier work has shown that the E3 ligase TRIM56 messenger RNA (mRNA) level and vimentin protein expression followed an inverse correlation in ovarian carcinoma patients; however, the regulatory mechanisms underlying TRIM56 expression is unclear. Steady state expression of TRIM56 mRNA expression in the normal ovarian cell line Moody and ovarian cancer cell lines SKOV‐3, A2780, and Caov‐3 were not significantly different; however, TRIM56 protein expression was significantly lower in the ovarian cancer cell lines compared to the Moody cell line. Polysome profiling showed significant increase in translation of TRIM56 messenger RNA in the Moody cells compared to the SKOV‐3 cells. We performed RNA‐affinity pulldown using biotinylated TRIM56 5 ‘and 3’‐UTR and postnuclear extracts from Moody and SKOV‐3 cells. Whereas no notable difference was observed in affinity pull‐down obtained with the 5’‐UTR, there was obvious difference in protein binding patterns with the 3’‐UTR. Mass spectrometry was used to determine the most differentially binding protein as poly r (c) binding protein 1 (PCBP1). PCBP1 expression and binding to the 3’‐UTR was both higher in SKOV‐3 cells compared to the Moody cells. Silencing of TRIM56 in Moody cells cause an increase in in vitro migration and invasion, and a similar effect was mimicked by overexpression of PCBP1. Conversely, silencing of PCBP1 or overexpression of TRIM56 in SKOV‐3 cells significantly decreased in vitro migration and invasion. In xenograft assays, SKOV‐3 cells stably overexpressing shRNA targeting PCBP1 decreased metastasis, whereas shRNA‐targeting TRIM56 potentiated detection of metastatic lesions, compared to the parental SKOV‐3 cells themselves. Taken together our results reveal a yet undefined posttranscriptional regulatory mechanism underlying low expression of TRIM56 in ovarian cancer. © 2018 IUBMB Life, 71(1):177–182, 2019
Impact of Body Weight Dynamics Following Intentional Weight Loss on Fracture Risk: Results from The Action for Health in Diabetes Study
Authors: Beavers Kristen M , Neiberg Rebecca H , Johnson Karen C , Davis C Hunter , Casanova Ramon , Schwartz Ann V , Crandall Carolyn J , Lewis Cora E , Pi‐Sunyer Xavier , Kritchevsky Stephen B ,   the Look AHEAD Research Group
Published: October 2018

The purpose of this study is to explore the impact of body weight change following intentional weight loss on incident fracture and bone mineral density (BMD) in overweight and obese adults with diabetes. A total of 1885 individuals with type 2 diabetes (baseline age: 58.5 ± 6.7 years, 58% women, body mass index: 35.7 ± 6.0 kg/m2) who participated in the Look AHEAD study and lost any weight 1 year after being randomized to an intensive lifestyle intervention were assessed. Body weight was measured annually and participants were categorized as weight regainers, weight cyclers, or continued losers/maintainers based on a ±3% annual change in weight from year 1 to year 4. Adjudicated overall fracture incidence was captured from years 4 through 13 (median follow‐up duration 11.5 years). Hip and spine BMD was assessed in a subset of participants at baseline, year 4 (n = 468), and year 8 (n = 354), using dual‐energy X‐ray absorptiometry. Cox proportional hazards and linear regression models, adjusted for relevant covariates, were performed for fracture and BMD outcomes, respectively. Fifty‐eight percent, 22%, and 20% of participants were classified as weight regainers, weight cyclers, and continued losers/maintainers, respectively; and 217 fractures (men n = 63; women n = 154) were recorded during the follow‐up period. There were no statistically significant differences in total incident fracture rates for weight regainers (HR [95% CI]: 1.01 [95% CI, 0.71 to 1.44]) or weight cyclers (HR [95% CI]: 1.02 [95% CI, 0.68 to 1.53]) when compared to continued losers/maintainers (p = 0.99). Similarly, follow‐up BMD estimates did not significantly vary by weight pattern group, although consistent trends for lowered BMD in the hip region were noted for continued losers/maintainers and weight cyclers compared with weight regainers. Patterns of weight change in the 3 years following 1 year of intentional weight loss were not associated with subsequent fracture or significantly reduced BMD in this cohort of overweight and obese adults with type 2 diabetes. © 2018 The Authors. JBMR Plus Published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.
PyDEF 2.0: An Easy to Use Post‐treatment Software for Publishable Charts Featuring a Graphical User Interface
Authors: Stoliaroff Adrien , Jobic Stéphane , Latouche Camille
Published: October 2018

Herein we present an open‐source program automating the post‐treatment of solid‐state ab initio calculations performed with VASP, the most used solid‐state simulation package. The program plots Density of States (DOS) and Band Diagrams, enabling the user to conduct efficiently a detailed study of electronic properties of a material. Our tool includes a complete module dedicated to point defects studies, proposing various corrections which can be activated at will and innovative property calculations such as defect concentrations. This is the first program of its kind to offer a direct plot of the stability domain of the studied matrix with respect to its components’ chemical potentials. We also implemented the retrieval of optical indices ɛ1 and ɛ2, the computation of the refractive and extinction coefficients (n, k) and the reflexivity R of the material. All features of the piece of software are available through a thoroughly designed user‐friendly, elegant and efficient Graphical User Interface (GUI) to be accessible to material scientists with various expertises, from both the experimental and theoretical sides. All figures are of publishable quality and can be customized as desired. © 2018 Wiley Periodicals, Inc.
Simulations of NaCl Aggregation from Solution: Solvent Determines Topography of Free Energy Landscape
Authors: Patel Lara A. , Kindt James T.
Published: October 2018

The partition‐enabled analysis of cluster histograms (PEACH) method is used to calculate the free energy surface of NaCl aggregation using cluster statistics from MD simulations of small systems (40–90 ions plus solvent) in four solvents. In all cases (pure methanol, pure water, and two methanol/water mixtures) NaCl clusters show a transition from amorphous to rocksalt structure with increasing cluster size. The crossover sizes, and the apparent kinetic barrier to ordering, increase with increasing water content. Implications for the proposed two‐step mechanism of NaCl crystal nucleation (in which the ordered structure emerges from a large disordered cluster), and how this mechanism might depend on solvent and on degree of supersaturation, are discussed. In pure water, nonideal crowding effects that promote clustering are identified from systematic concentration‐dependent deviations between simulation results and the PEACH model fit. In contrast, the ability of PEACH to fit aggregation statistics in mixed solvents is consistent with negligible interactions between ions in different clusters. © 2018 Wiley Periodicals, Inc.