bluuebunny/crossref_metadata_2025 huggingface dataset:
High levels of multiple paternity in a spermcast mating freshwater mussel
Authors: Wacker Sebastian , Larsen Bjørn Mejdell , Jakobsen Per , Karlsson Sten
Published: July 2018

Multiple paternity is an important characteristic of the genetic mating system and common across a wide range of taxa. Multiple paternity can increase within‐population genotypic diversity, allowing selection to act on a wider spectre of genotypes, and potentially increasing effective population size. While the genetic mating system has been studied in many species with active mating behavior, little is known about multiple paternity in sessile species releasing gametes into the water. In freshwater mussels, males release sperm into the water, while eggs are retained and fertilized inside the female (spermcast mating). Mature parasitic glochidia are released into the water and attach to the gills of fish where they are encapsulated until settling in the bottom substrate. We used 15 microsatellite markers to detect multiple paternity in a wild population of the freshwater pearl mussel (Margaritifera margaritifera). We found multiple paternity in all clutches for which more than two offspring were genotyped, and numbers of sires were extremely high. Thirty‐two sires had contributed to the largest clutch (43 offspring sampled). This study provides the first evidence of multiple paternity in the freshwater pearl mussel, a species that has experienced dramatic declines across Europe. Previous studies on other species of freshwater mussels have detected much lower numbers of sires. Multiple paternity in freshwater pearl mussels may be central for maintaining genetic variability in small and fragmented populations and for their potential to recover after habitat restoration and may also be important in the evolutionary arms race with their fish host with a much shorter generation time.
Latitudinal effects on crown shape evolution
Authors: Lindh Magnus , Falster Daniel S. , Zhang Lai , Dieckmann Ulf , Brännström Åke
Published: July 2018

Large variations in crown shape are observed across the globe, from plants with wide and deep crowns to those with leaves clustered at the top. While there have been advances in the large‐scale monitoring of forests, little is known about factors driving variations in crown shape with environmental conditions. Previous theoretical research suggests a gradient in crown shape with latitude, due to the effects of sun angle. Yet, it remains unclear whether such changes are also predicted under competition. Using a size‐structured forest‐growth model that incorporates self‐shading from plants and competitive shading from their neighbors, we investigate how changes in site productivity and sun angle shape crown evolution. We consider evolution in two traits describing the top‐heaviness and width‐to‐height ratio of crowns, shaped by trade‐offs reflecting the costs and benefits of alternative architectures. In top‐heavy trees, most of the leaves are at the top half of the trunk. We show that, contrary to common belief, the angle of sun beams per se has only a weak influence on crown shapes, except at low site productivity. By contrast, reduced site productivity has a strong effect, with trees growing in less productive sites keeping their leaves closer to the ground. The crown width‐to‐height ratio is generally higher at a lower site productivity, but this trait is not strongly influenced by any environmental factor. This theoretical analysis brings into question established beliefs about the effects of latitude on crown shapes. By introducing geometry‐related growth constraints caused by shading from both the surrounding forest and the tree on itself, and costs for constructing and maintaining a three‐dimensional crown, our analysis suggests crown shapes may vary with latitude, mostly via effects on overall site productivity, and less because of the angle of the sun.
RAD sequencing resolved phylogenetic relationships in European shrub willows (Salix L. subg. Chamaetia and subg. Vetrix) and revealed multiple evolution of dwarf shrubs
Authors: Wagner Natascha Dorothea , Gramlich Susanne , Hörandl Elvira
Published: July 2018

The large and diverse genus Salix L. is of particular interest for decades of biological research. However, despite the morphological plasticity, the reconstruction of phylogenetic relationships was so far hampered by the lack of informative molecular markers. Infrageneric classification based on morphology separates dwarf shrubs (subg. Chamaetia) and taller shrubs (subg. Vetrix), while previous phylogenetic studies placed species of these two subgenera just in one largely unresolved clade. Here we want to test the utility of genomic RAD sequencing markers for resolving relationships at different levels of divergence in Salix. Based on a sampling of 15 European species representing 13 sections of the two subgenera, we used five different RAD sequencing datasets generated by Ipyrad to conduct phylogenetic analyses. Additionally we reconstructed the evolution of growth form and analyzed the genetic composition of the whole clade. The results showed fully resolved trees in both ML and BI analysis with high statistical support. The two subgenera Chamaetia and Vetrix were recognized as nonmonophyletic, which suggests that they should be merged. Within the Vetrix/Chamaetia clade, a division into three major subclades could be observed. All species were confirmed to be monophyletic. Based on our data, arctic‐alpine dwarf shrubs evolved four times independently. The structure analysis showed five mainly uniform genetic clusters which are congruent in sister relationships observed in the phylogenies. Our study confirmed RAD sequencing as a useful genomic tool for the reconstruction of relationships on different taxonomic levels in the genus Salix.
Sexual and temporal variations in floral scent in the subdioecious shrub Eurya japonica Thunb
Authors: Wang Hui , Zheng Peiming , Aoki Dan , Miyake Takashi , Yagami Sachie , Matsushita Yasuyuki , Fukushima Kazuhiko , Nakagawa Michiko
Published: July 2018

In many flowering plants, floral scents are a significant trait for visitors, playing an important role in attracting pollinators and/or detracting herbivores. The evolution of flowering plants from hermaphroditism to dioecy is often accompanied by sexual dimorphism in floral scent. In this study, floral scents emitted by different sexual morphs of the subdioecious shrub Eurya japonica Thunb. were collected using a dynamic headspace method, and sexual and temporal variations were evaluated by gas chromatography–mass spectrometry (GC–MS). Two volatiles, α‐pinene and linalool, were identified as the major components of floral scents in females, hermaphrodites, and males. The males emit higher amounts of floral scents, particularly α‐pinene, compared to females or hermaphrodites. Floral scents emitted by males generally decrease as flowers enter senescence, whereas those from females or hermaphrodites do not significantly differ. Intraspecific variations in floral scents of subdioecious species provided by this study would contribute to better understanding of sexual dimorphism in floral scent.
Human activities accelerated the degradation of saline seepweed red beaches by amplifying top‐down and bottom‐up forces
Authors: Lu Weizhi , Xiao Jingfeng , Lei Wei , Du Jinqiu , Li Zhengjie , Cong Pifu , Hou Wenhao , Zhang Jialin , Chen Luzhen , Zhang Yihui , Liao Guoxiang
Published: July 2018

Salt marshes dominated by saline seepweed (Suaeda heteroptera) provide important ecosystem services such as sequestering carbon (blue carbon), maintaining healthy fisheries, and protecting shorelines. These salt marshes also constitute stunning red beach landscapes, and the resulting tourism significantly contributes to the local economy. However, land use change and degradation have led to a substantial loss of the red beach area. It remains unclear how human activities influence the top‐down and bottom‐up forces that regulate the distribution and succession of these salt marshes and lead to the degradation of the red beaches. We examined how bottom‐up forces influenced the germination, emergence, and colonization of saline seepweed with field measurements and a laboratory experiment. We also examined whether top‐down forces affected the red beach distribution by conducting a field survey for crab burrows and density, laboratory feeding trials, and waterbird investigations. The higher sediment accretion rate induced by human activities limited the establishment of new red beaches. The construction of tourism facilities and the frequent presence of tourists reduced the density of waterbirds, which in turn increased the density of crabs, intensifying the top‐down forces such as predators and herbivores that drive the degradation of the coastal red beaches. Our results show that sediment accretion and plant–herbivory changes induced by human activities were likely the two primary ecological processes leading to the degradation of the red beaches. Human activities significantly shaped the abundance and distribution of the red beaches by altering both top‐down and bottom‐up ecological processes. Our findings can help us better understand the dynamics of salt marshes and have implications for the management and restoration of coastal wetlands.
Species richness and turnover among indigenous and introduced plants and insects of the Southern Ocean Islands
Authors: Leihy Rachel I. , Duffy Grant A. , Chown Steven L.
Published: July 2018

Simultaneously investigating variation in species richness and turnover for indigenous and introduced communities holds great promise as a means to understand the relative contributions of ecological processes to community structure. Such insight will advance understanding of the ways in which environmental change may affect future community dynamics. Using a recently developed multi‐site turnover metric, zeta diversity (ζ), we explored species turnover patterns across indigenous and introduced insect and vascular plant communities of the Southern Ocean Islands. In addition, we used updated species occurrence and high‐resolution environmental data to reexamine previously described patterns and drivers of species richness across the region. Species richness variation in indigenous insect and vascular plant communities was largely explained by island isolation and temperature, whereas human visitation frequency was strongly associated with introduced species diversity of both groups. Indigenous communities of both plants and insects had faster rates of species turnover across sites and less inter‐island connectivity than their introduced counterparts. Zeta diversity analyses suggested that stochastic processes were more influential than niche‐related processes on the observed patterns of turnover of indigenous insects. Meanwhile, turnover patterns of introduced insects and indigenous and introduced vascular plants were indicative of the dominance of niche‐related processes. These outcomes highlight very different diversity patterns across indigenous and alien communities and indicate that different ecological processes may underlie diversity variation across these islands and taxonomic groups.
What would you choose: Online or Offline or Mixed services? Feasibility of online HIV counselling and testing among Thai men who have sex with men and transgender women and factors associated with service uptake
Authors: Phanuphak Nittaya , Anand Tarandeep , Jantarapakde Jureeporn , Nitpolprasert Chattiya , Himmad Kanittha , Sungsing Thanthip , Trachunthong Deondara , Phomthong Sangusa , Phoseeta Petchfa , Tongmuang Sumitr , Mingkwanrungruang Pravit , Meekrua Dusita , Sukthongsa Supachai , Hongwiangchan Somporn , Upanun Nutchanin , Barisri Jiranuwat , Pankam Tippawan , Phanuphak Praphan
Published: July 2018

Introduction

HIV testing coverage remains low among men who have sex with men (MSM) and transgender women (TGW). We studied characteristics of Thai MSM and TGW who chose online and/or offline platforms for HIV counselling and testing and the feasibility of integrating online technologies and HIV self‐testing to create service options.

Methods

From December 2015 to June 2017, MSM and TGW enrolled from Bangkok Metropolitan Region and Pattaya could choose between: offline HIV counselling and testing (Offline group), online pre‐test counselling and offline HIV testing (Mixed group), and online counselling and online, supervised, HIV self‐testing (Online group). Sociodemographic data, risk behaviour and social network use characteristics were collected by self‐administered questionnaires. Logistic regression models identified covariates for service preferences.

Results

Of 472 MSM and 99 TGW enrolled, 202 self‐selected the Offline group, 158 preferred the Mixed group, and 211 chose the Online group. The Online group had the highest proportion of first‐time testers (47.3% vs. 42.4% vs. 18.1%, p < 0.001) and reported highest HIV prevalence (15.9% vs. 13.0% vs. 3.4%, p = 0.001) as compared to Offline and Mixed groups, respectively. Having tested for HIV twice or more (OR 2.57, 95% CI 1.03 to 6.41, p = 0.04) increased the likelihood to choose online pre‐test counselling. Being TGW (OR 6.66, 95% CI 2.91 to 15.25, p < 0.001) and using social media from four to eight hours (OR 2.82, 95% CI 1.48 to 5.37, p = 0.002) or >8 hours (OR 2.33, 95% CI 1.05 to 5.16, p = 0.04) increased selection of online, supervised, HIV self‐testing. Providers primarily used smartphones (79.2%) and laptops (37.5%) to deliver online services. Self‐testing strip image sharpness and colour quality were rated “good” to “excellent” by all providers. Most participants (95.1%) agreed that online supervision and HIV self‐testing guidance offered were satisfactory and well delivered.

Conclusions

Online HIV services among MSM and TGW are feasible in Thailand and have the potential to engage high proportions of first‐time testers and those with high HIV prevalence. When designing public health interventions, integrating varied levels of online HIV services are vital to engage specific sections of MSM and TGW populations in HIV services.

Clinical Trial Number

NCT03203265
Uptake of HIV self‐testing and linkage to treatment among men who have sex with men (MSM) in Nigeria: A pilot programme using key opinion leaders to reach MSM
Authors: Tun Waimar , Vu Lung , Dirisu Osasuyi , Sekoni Adekemi , Shoyemi Elizabeth , Njab Jean , Ogunsola Sade , Adebajo Sylvia
Published: July 2018

Introduction

HIV self‐testing (HIVST) offers an alternative to facility‐based HIV testing services, particularly for populations such as men who have sex with men (MSM) who may fear accessing testing due to stigma, discrimination and criminalization. Innovative HIV testing approaches are needed to meet the goal of 90% of people living with HIV being diagnosed. This study piloted an intervention to distribute oral HIVST kits to MSM through key opinion leaders (KOLs) in Lagos, Nigeria and assessed the feasibility, acceptability, uptake of HIVST and linkage to HIV treatment.

Methods

A cohort study was conducted (May through September 2017) with 319 participants who were recruited by 12 KOLs through their networks. A baseline survey was conducted at the time of the oral HIVST kit (OraQuick® HIV antibody test) distribution to eligible MSM followed by a 3‐month follow‐up survey to assess usage of and experience with the HIVST kits. Each participant was given two kits.

Results

The median age of the participants was 25 years, 88.7% were literate and 17.9% were first‐time testers. Of the 257 participants (80.7% retention) who completed the three‐month follow‐up interview, 97.7% reported using the HIVST kit and 14 (5.6%) self‐reported an HIV positive result. A quarter (22.7%) tested themselves the same day they received the kit, and 49.4% tested within one week. Almost all participants reported that the HIVST kit instructions were easy or somewhat easy to understand (99.6%) and perform the test (98.0%). The most common reasons they liked the test were ease of use (87.3%), confidentiality/privacy (82.1%), convenience (74.1%) and absence of needle pricks (64.9%). All 14 participants who tested positive had sought confirmatory testing and initiated HIV treatment by the time of the three‐month survey.

Conclusions

HIVST distribution through KOLs was feasible and oral self‐testing was highly acceptable among this urban MSM population. Despite concerns about linkage to treatment when implementing self‐testing, this study showed that linkage to treatment can be achieved with active follow‐up and access to a trusted MSM‐friendly community clinic that offers HIV treatment. HIVST should be considered as an additional option to standard HIV testing models for MSM.
Changes in engagement in HIV prevention and care services among female sex workers during intensified community mobilization in 3 sites in Zimbabwe, 2011 to 2015
Authors: Ndori‐Mharadze Tendayi , Fearon Elizabeth , Busza Joanna , Dirawo Jeffrey , Musemburi Sithembile , Davey Calum , Acharya Xeno , Mtetwa Sibongile , Hargreaves James R , Cowan Frances
Published: July 2018

Introduction

‘Sisters with a Voice’, Zimbabwe's nationally scaled comprehensive programme for female sex workers (FSWs), intensified community mobilization activities in three sites to increase protective behaviours and utilization of clinical services. We compare indicators among FSWs at the beginning and after implementation.

Methods

We used mixed methods to collect data at three sites: in‐depth interviews (n = 22) in 2015, routine clinical data from 2010 to 2015, and two respondent driven sampling surveys in 2011 and 2015, in which participants completed an interviewer‐administered questionnaire and provided a finger prick blood sample for HIV antibody testing. Estimates were weighted using RDS‐1 and estimate convergence assessed in both years. We assessed differences in six indicators between 2011 and 2015 using logistic regression adjusted for age, duration in sex work and education.

Results

870 FSWs were recruited from the three sites in 2011 and 915 in 2015. Using logistic regression to adjust for socio‐demographic differences, we found higher estimates of the proportion of HIV‐positive FSWs and HIV‐positive FSWs who knew their status and reported being on ART in Mutare and Victoria Falls in 2015 compared to 2011. Reported condom use with clients did not differ by year; however, condom use with regular partners was higher in 2015 in Mutare and Hwange. Reported HIV testing in the last six months among HIV‐negative FSWs was higher in 2015 across sites: for instance, in Victoria Falls it was 13.4% (95% CI 8.7% to 19.9%) in 2011 and 80.8% (95% CI 74.0 to 87.7) in 2015. FSWs described positive perceptions of the Sisters programme, ease of engaging with health services, and improved solidarity among peers. Programme data showed increases in service use by 2015 across all sites.

Conclusions

Improvements in key HIV care engagement indicators were observed among FSWs in two sites and in testing and prevention indicators across the three sites after implementation of an intensified community mobilization intervention. Engagement with services for FSWs is critical for countries to reach 90‐90‐90 targets.
Molecular dynamics simulation on the allosteric analysis of the c‐di‐GMP class I riboswitch induced by ligand binding
Authors: Li Chaoqun , Zhao Xiaojia , Xie Pengtao , Hu Junping , Bi Huimin
Published: July 2018

Riboswitches are RNA molecules that regulate gene expression using conformation change, affected by binding of small molecule ligands. Although a number of ligand‐bound aptamer complex structures have been solved, it is important to know ligand‐free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, we use dynamics simulations on a series of models to characterize the ligand‐free and ligand‐bound aptamer domain of the c‐di‐GMP class I (GEMM‐I) riboswitch. The results revealed that the ligand‐free aptamer has a stable state with a folded P2 and P3 helix, an unfolded P1 helix and open binding pocket. The first Mg ions binding to the aptamer is structurally favorable for the successive c‐di‐GMP binding. The P1 helix forms when c‐di‐GMP is successive bound. Three key junctions J1/2, J2/3 and J1/3 in the GEMM‐I riboswitch contributing to the formation of P1 helix have been found. The binding of the c‐di‐GMP ligand to the GEMM‐I riboswitch induces the riboswitch's regulation through the direct allosteric communication network in GEMM‐I riboswitch from the c‐di‐GMP binding sites in the J1/2 and J1/3 junctions to the P1 helix, the indirect ones from those in the J2/3 and P2 communicating to P1 helix via the J1/2 and J1/3 media.
In vivo sliding distance on the metal‐on‐polyethylene total hip arthroplasty articulation using patient‐specific gait analysis
Authors: Peng Yun , Arauz Paul , An Shuai , Kwon Young‐Min
Published: July 2018

Metal‐on‐polyethylene (MoP) is the most commonly used bearing surface in primary total hip arthroplasty (THA). Polyethylene wear debris remains a major concern. Studies investigating the wear performance based on patient‐specific in vivo kinematics and component orientation remains largely lacking. The primary goal of this study was to identify patterns of the distribution of sliding distance and cross‐shear ratio among THA patients. A validated approach combining dual fluoroscopic imaging system and computed‐tomography was utilized to quantify in vivo gait kinematics and component orientations in 48 total hips. The distribution of accumulated sliding distance and cross‐shear ratio over the polyethylene bearing surface was calculated and analyzed using principal component analysis (PCA). Strong patient‐specific variation in sliding distance and cross‐shear ratio was observed. PCA detected two principal components (PCs) of the sliding distance that together contribute to 94.8% of the total variation. PCA detected four PCs that together contribute to 86% of the total variation of the cross‐shear ratio. Regression analysis identified a positive association between cross‐shear magnitude and axial and frontal range of motion (RoM). Increased cup inclination, stem anteversion, and reduced cup anteversion may lead to superiorly distributed high cross‐shear region, potentially accelerating wear. Our study investigated, in vivo sliding distance and cross‐shear pattern using a comprehensive patient‐specific dataset and detected several wear indicators under in vivo conditions. These findings provided useful reference values that may help to assess wear in MoP THA patients. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:3151–3160, 2018.
Polystyrene Foam with High Cell Density and Small Cell Size by Compression‐Injection Molding and Core Back Foaming Technique: Evolution of Cells in Cavity
Authors: Bai Tiantian , Dong Binbin , Xiao Mengjun , Liu Hu , Wang Ning , Wang Yaming , Wang Chao , Liu Chuntai , Cao Wei , Zhang Jiaoxia , Ma Yong , Guo Zhanhu
Published: July 2018

Many efforts have been made to obtain uniform cell structures from foam injection molding techniques. However, cell nucleation mechanism and complex dynamics during the cell formation have rarely been well understood. Here, high‐pressure foam injection molding (HPFIM) is achieved by combining the injection–compression molding with core back foaming (ICMCBF) technique. The influences of compression pressure and time on the cell structure of polystyrene foam during the foaming process are studied. Compared with low pressure for conventional foam injection molding, high compression pressure (200 bar) and fast pressure drop rate of ICMCBF endow the foam with the highest cell density (1.59 × 107 cells cm−3), and the smallest cell size (15 µm). The tensile strength and impact strength are enhanced by about 60% (from 22.3 to 35.6 MPa) and 80% (from 3.6 to 6.8 MPa), respectively. This study gives a critical understanding of the cell nucleation and growth mechanism of the foam injection molding and supplies a new strategy for the fabrication of foam with uniform cell structure.
Barley Products of Different Fiber Composition Selectively Change Microbiota Composition in Rats
Authors: Teixeira Cristina , Prykhodko Olena , Alminger Marie , Fåk Hållenius Frida , Nyman Margareta
Published: July 2018

Scope

Several dietary fiber properties are suggested to be important for the profiling of the microbiota composition, but those characteristics are rather unclear. Whether different physico‐chemical properties of barley dietary fiber influence the gut microbiota composition is investigated.

Methods and results

Seven diets containing equal amounts of dietary fiber from barley malts, brewer's spent grain (BSG), and barley extracts, resulting in varying amounts of β‐glucan, soluble arabinoxylan, and insoluble arabinoxylan in the diets were given to conventional rats. Malts increased microbiota alpha diversity more than BSG and the extracts. The intake of soluble arabinoxylan was related to Akkermansia and propionic acid formation in the cecum of rats, whereas β‐glucan and/or insoluble arabinoxylan were attributed to some potentially butyrate‐producing bacteria (e.g., Lactobacillus, Blautia, and Allobaculum).

Conclusion

This study demonstrates that there is a potential to stimulate butyrate‐ and propionate‐producing bacteria in the cecum of rats with malt products of specific fiber properties. Moreover, BSG, a by product from beer production, added to malt can possibly be used to further modulate the microbiota composition, toward a higher butyric acid formation. A complex mixture of fiber as in the malts is of greater importance for microbiota diversity than purer fiber extracts.
The Impact of Nutritional Interventions in Pregnant Women on DNA Methylation Patterns of the Offspring: A Systematic Review
Authors: Andraos Stephanie , de Seymour Jamie Violet , O'Sullivan Justin Martin , Kussmann Martin
Published: July 2018

Epidemiological studies have consistently demonstrated that environmental exposures in early life are associated with later‐life health status and disease susceptibility. Epigenetic modifications, such as DNA methylation, have been suggested as potential mechanisms linking the intrauterine environment with offspring health status. The present systematic review compiles peer‐reviewed randomized controlled trials assessing the impact of maternal nutritional interventions on DNA methylation patterns of the offspring. The results of the included trials are consistent with micronutrient supplementation not significantly affecting offspring tissue DNA methylation patterns, yet subgrouping by sex, BMI, and smoking status increased the significance of nutritional supplementation on DNA methylation. Maternal BMI and smoking status as well as offspring sex were factors influencing offspring DNA methylation responsiveness to nutritional interventions during pregnancy. Future research should aim at assessing the impact of nutritional interventions on DNA methylation patterns of neonates comparing single versus multi‐micronutrient supplementation, within populations having high versus low baseline nutritional statuses.
Scaling limits to large area perovskite solar cell efficiency
Authors: Wilkinson Ben , Chang Nathan L. , Green Martin A. , Ho‐Baillie Anita W.Y.
Published: July 2018

Perovskite solar cells have demonstrated efficiencies over 20%, but this has not been reproduced at large areas. We explore the theoretical limit to single large area perovskite solar cell efficiency, with different front conductive layers: first, the standard n‐i‐p structure with a transparent conductive electrode (TCE) at the substrate, and then structures that include a front metal grid. We model and optimize the impact of the thickness of the TCE and the dimensions of the grid elements to balance series resistance, parasitic absorption in the TCE layer, and shading losses to maximize efficiency. The results of the optimization suggest that the efficiency of the standard design can be significantly improved simply by selecting the optimum TCE thicknesses for the cell size. However, the poor scaling of the standard design prevents the fabrication of efficient large area cells. Adding a metal grid allows the efficiency of large area cells (156 mm × 156 mm) to approach that of small cells and exceed 20%. The maximum efficiency is limited by the minimum width of the metal grid elements and the sheet resistance of the metal grid material. In this context, the performances of fluorine‐doped tin oxide and indium tin oxide as TCE materials were compared, with indium tin oxide found to be superior. We also explore the limits of performance when connecting multiple cells in series to form a large area minimodule and determine the conditions when a front grid is beneficial. Design rules are presented that allow researchers to calculate the optimum cell parameters for high efficiency.
Machine learning PV system performance analyser
Authors: Rodrigues Sandy , Ramos Helena Geirinhas , Morgado‐Dias Fernando
Published: July 2018

Machine learning techniques (MLTs) can create accurate predictions of solar outputs that are used in photovoltaic system performance analysis. The issue with MLT application is the requirement for large amounts of historical data for training the prediction models that is not always available. Since the photovoltaic system behaviour is non‐linear due to the unpredictable nature of the weather conditions throughout the year, MLT training requires annual historical data to create the prediction model. The photovoltaic system production meters only store up to 3 months of historical power values. This information served as motivation to research different types of MLTs, in search of one that would accurately predict the daily solar energy values of a photovoltaic system based on the available 3‐month historical data. The aim of this work is to implement a photovoltaic system performance analyser that estimates daily solar alternating current energy outputs for any rooftop photovoltaic system, based on daily solar irradiation values, without being influenced by the seasons of the year nor the photovoltaic system installation location. Therefore, 5 MLTs were studied and compared, which include the regression tree, artificial neural network, multigene genetic programming, Gaussian process, and the support vector machine for regression. Results show that the regression tree MLT provides acceptable results to be used in all locations and all seasons of the year, while the support vector machine for regression is best for spring and summer training dataset months, and the Gaussian process is best for the autumn and winter training dataset months.
The Sperm Proteome of the Echiuran Urechis unicinctus (Annelida, Echiura)
Authors: Qin Zhenkui , Zhang Yanjie , Mu Huawei , Zhang Zhifeng , Qiu Jian‐Wen
Published: July 2018

Sperm proteins presumably play critical roles in reproduction, but in many non‐model animals their identities are unknown. A total of 147 sperm proteins from the echiuran worm Urechis unicinctus, the first sperm proteome in the phylum Annelida, are reported. The echiuran sperm proteome can be classified into diverse functional groups: energy metabolism (31%), protein synthesis and degradation (18%), spermatogenesis and sperm motility (12%), signal pathway (11%), ion channel and transport proteins (6%), cytoskeleton (4%), immunity and stress responses (3%), and fertilization (1%). These results will facilitate studies of mechanisms of fertilization in echiurans, as well as comparative studies of reproduction and evolution across lophotrochozoans. Data are available via ProteomeXchange with identifier PXD009176.
Simultaneous Quantification of the Acetylome and Succinylome by ‘One‐Pot’ Affinity Enrichment
Authors: Basisty Nathan , Meyer Jesse G , Wei Lei , Gibson Bradford W , Schilling Birgit
Published: July 2018

Protein posttranslational modifications (PTMs) are of increasing interest in biomedical research, yet studies rarely examine more than one PTM. One barrier to multi‐PTM studies is the time cost for both sample preparation and data acquisition, which scale linearly with the number of modifications. The most prohibitive requirement is often the need for large amounts of sample, which must be increased proportionally with the number of PTM enrichment steps. Here, a streamlined, quantitative label‐free proteomic workflow—“one‐pot” PTM enrichment—that enables comprehensive identification and quantification of peptides containing acetylated and succinylated lysine residues from a single sample containing as little as 1 mg mitochondria protein is described. Coupled with a label‐free, data‐independent acquisition (DIA), 2235 acetylated and 2173 succinylated peptides with the one‐pot method are identified and quantified and peak areas are shown to be highly correlated between the one‐pot and traditional single‐PTM enrichments. The ‘one‐pot’ method makes possible detection of multiple PTMs occurring on the same peptide, and it is shown that it can be used to make unique biological insights into PTM crosstalk. Compared to single‐PTM enrichments, the one‐pot workflow has equivalent reproducibility and enables direct assessment of PTM crosstalk from biological samples in less time from less tissue.
Quantitative Proteomic Analysis of Cell Responses to Electroporation, a Classical Gene Delivery Approach
Authors: Zhao Minzhi , Zhao Deyao , Ma Yan , Hu Zhiyuan , Wei Zewen
Published: July 2018

Electroporation, as an established nonviral technology for breaching cell membrane, has been accepted for the delivery of nucleic acids. Despite satisfactory delivery efficiencies have been achieved on multiple cell kinds by simply exhausting all possible electrical parameters, electroporation is still inefficient, or even invalid, for various kinds of cells. This is largely due to the lack of comprehensive understanding of cell responses to electrical stimulation at biological aspect. Moreover, a systematically investigation of protein variation of electroporated cells is also required for biosafety evaluation before clinically applying electroporation. By employing quantitative proteomic analysis, the biological mechanism of electroporation is explored from the molecular level. The results reveal that electrical stimulations widely influence many biological processes including nucleic acid stabilization, protein synthesis, cytoskeleton dynamic, inflammation, and cell apoptosis. It is found that several antivirus‐related processes appeared in the enrichment results. Moreover, SAMD9, a broad spectrum antiviral and antitumor factor, is dramatically downregulated on easy‐to‐transfect cells while electroporation can not alter SAMD9 expression on hard‐to‐transfect cells, hinting that electroporation, a pure physical treatment, can induce antivirus‐like defensive responses and the altering of SAMD9 can be used to predict the effectiveness of electroporation on transfecting specific kinds of cells.
Fabrication of Ultra‐Fine TATB/HMX Cocrystal Using a Compound Solvent
Authors: Hou Conghua , Zhang Yuanping , Chen Yunge , Jia Xinlei , Zhang Shimin , Tan Yingxin
Published: July 2018

A novel energetic cocrystal predicted to exhibit greater power and lower sensitivity, consisting of 1,3,5‐triamino‐2,4,6‐trinitrobenzene (TATB) and cyclotetramethylenetetranitramine (HMX) is presented. The TATB/HMX cocrystals were prepared using a compound solvent of [Emim]Ac and DMSO at 80 °C by recrystallization. Structural characterizations and thermal properties of the raw materials and cocrystals were systematically investigated by scanning electron microscopy (SEM), X‐ray diffraction, fourier‐transform infrared spectroscopy, fourier transform raman spectroscopy and differential scanning calorimetry. The SEM results indicated that microparticles are hexagonal in shape and ∼2 μm in size. The formation of cocrystals originates from the N−H⋅⋅⋅O hydrogen bonding between ‐NO2 (HMX) and ‐NH2 (TATB). Naturally, compared to raw HMX, the impact sensitivity of the cocrystals is reduced. The EXPLO5 program showed TATB/HMX with desirable detonation performance.
Genomic screening of new putative antiviral lectins from Amazonian cyanobacteria based on a bioinformatics approach
Authors: Siqueira Andrei Santos , Lima Alex Ranieri Jerônimo , Aguiar Delia Cristina Figueira , Santos Alberdan Silva , Vianez Júnior João Lídio da Silva Gonçalves , Gonçalves Evonnildo Costa
Published: July 2018

Lectins are proteins of nonimmune origin, which are capable of recognizing and binding to glycoconjugate moieties. Some of them can block the interaction of viral glycoproteins to the host cell receptors acting as antiviral agents. Although cyanobacterial lectins have presented broad biotechnological potential, little research has been directed to Amazonian Cyanobacterial diversity. In order to identify new antiviral lectins, we performed genomic analysis in seven cyanobacterial strains from Coleção Amazônica de Cianobactérias e Microalgas (CACIAM). We found 75 unique CDS presenting one or more lectin domains. Since almost all were annotated as hypothetical proteins, we used homology modeling and molecular dynamics simulations to evaluate the structural and functional properties of three CDS that were more similar to known antiviral lectins. Nostoc sp. CACIAM 19 as well as Tolypothrix sp. CACIAM 22 strains presented cyanovirin‐N homologues whose function was confirmed by binding free energy calculations. Asn, Glu, Thr, Lys, Leu, and Gly, which were described as binding residues for cyanovirin, were also observed on those structures. As for other known cyanovirins, those residues in both our models also made favorable interactions with dimannose. Finally, Alkalinema sp. CACIAM 70d presented one CDS, which was identified as a seven‐bladed beta‐propeller structure with binding sites predicted for sialic acid and N‐acetylglucosamine. Despite its singular structure, our analysis suggested this molecule as a new putative antiviral lectin. Overall, the identification and the characterization of new lectins and their homologues are a promising area in antiviral research, and Amazonian cyanobacteria present biotechnological potential to be explored in this regard.
DrugMetab: An Integrated Machine Learning and Lexicon Mapping Named Entity Recognition Method for Drug Metabolite
Authors: Wu Heng‐Yi , Lu Deshun , Hyder Mustafa , Zhang Shijun , Quinney Sara K. , Desta Zeruesenay , Li Lang
Published: July 2018

Drug metabolites (DMs) are critical in pharmacology research areas, such as drug metabolism pathways and drug‐drug interactions. However, there is no terminology dictionary containing comprehensive drug metabolite names, and there is no named entity recognition (NER) algorithm focusing on drug metabolite identification. In this article, we developed a novel NER system, DrugMetab, to identify DMs from the PubMed abstracts. DrugMetab utilizes the features characterized from the Part‐of‐Speech, drug index, and pre/suffix, and determines DMs within context. To evaluate the performance, a gold‐standard corpus was manually constructed. In this task, DrugMetab with sequential minimal optimization (SMO) classifier achieves 0.89 precision, 0.77 recall, and 0.83 F‐measure in the internal testing set; and 0.86 precision, 0.85 recall, and 0.86 F‐measure in the external validation set. We further compared the performance between DrugMetab and whatizitChemical, which was designed for identifying small molecules or chemical entities. DrugMetab outperformed whatizitChemical, which had a lower recall rate of 0.65.
Voltage Induced by Superconducting Vortices in Open Nanostructured Microtubes
Authors: Rezaev Roman , Posenitskiy Evgeny , Smirnova Ekaterina , Levchenko Evgenii , Schmidt Oliver G. , Fomin Vladimir M.
Published: July 2018

Using the finite‐difference time‐domain simulation, voltage induced by moving vortices as a function of the transport current and magnetic field is analyzed for rolled up nanostructured microtubes. Open superconductor tubes are shown to produce less dissipation as compared to the planar structures under the same magnetic field and transport current. The induced voltage as a function of the magnetic field provides information about the vortex pattern. In particular, an increase of the number of vortex chains in the tube results in a sixfold decrease of a slope of the induced voltage as a linear function of the magnetic field.
Scour depths at sites selected for spawning by brown trout (Salmo trutta) along a longitudinal gradient of a North American mountain river
Authors: Meredith C. S. , Budy P. , Schmidt J. C.
Published: July 2018

In the Intermountain West, USA, fry of fall‐spawning brown trout (Salmo trutta) are susceptible to scour‐related mortality because they are still in the gravel during spring snowmelt run‐off events. The goal of our research was to understand patterns of gravel scour on the Logan River, Utah, in relation to brown trout spawning and whether mobility of spawning gravels could explain the absence of brown trout from higher elevations. We collected data to characterize local entrainment potential at spawning gravels longitudinally on the Logan River during 2009 and 2010 spring flood events. We used scour chains to measure scour depth at spawning locations, and we also examined the position of redds in channel cross sections in relation to the centre line. The flood magnitude in both years approximated the 2‐year flood magnitude, but the flood in 2009 was much longer in duration. Scour at 27% of scour chain locations exceeded the estimated median upper limit of developing fry in 2009, whereas scour at 0% of locations exceeded this depth in 2010. Brown trout spawned in locations with similar entrainment potential at both mid and high elevations, which contributed to a lack of trend in scour depth with elevation. In addition, the majority of areas chosen for spawning were channel margins. The relationship between local entrainment potential at spawning gravels and scour depth was similar for the mid‐elevation canyon zone with medium brown trout density and the high‐elevation noncanyon zone with low brown trout density. In a low‐elevation backwater zone containing high densities of brown trout, scour was high despite low levels of entrainment potential. Overall, findings suggest that spawning gravel scour is not limiting brown trout abundance at high elevations in this system given shallow scour depths overall and a general lack of increase in scour depth with increasing elevation/distance upstream.
Flexible, Flame‐Resistant, and Dendrite‐Impermeable Gel‐Polymer Electrolyte for Li–O2/Air Batteries Workable Under Hurdle Conditions
Authors: Zou Xiaohong , Lu Qian , Zhong Yijun , Liao Kaiming , Zhou Wei , Shao Zongping
Published: July 2018

Gel‐polymer electrolytes are considered as a promising candidate for replacing the liquid electrolytes to address the safety concerns in Li–O2/air batteries. In this work, by taking advantage of the hydrogen bond between thermoplastic polyurethane and aerogel SiO2 in gel polymer, a highly crosslinked quasi‐solid electrolyte (FST‐GPE) with multifeatures of high ionic conductivity, high mechanical flexibility, favorable flame resistance, and excellent Li dendrite impermeability is developed. The resulting gel‐polymer Li–O2/air batteries possess high reaction kinetics and stabilities due to the unique electrode–electrolyte interface and fast O2 diffusion in cathode, which can achieve up to 250 discharge–charge cycles (over 1000 h) in oxygen gas. Under ambient air atmosphere, excellent performances are observed for coin‐type cells over 20 days and for prototype cells working under extreme bending conditions. Moreover, the FST‐GPE electrolyte also exhibits durability to protect against fire, dendritic Li, and H2O attack, demonstrating great potential for the design of practical Li–O2/air batteries.
The Effects of International Accents and Shared First Language on Listening Comprehension Tests
Authors: Kang Okim , Thomson Ron , Moran Meghan
Published: July 2018

This study examines the effect of incorporating a variety of international English accents into a simulated TOEFL listening comprehension test in growing recognition of internationalization of language teaching and learning in the field of TESOL. Although some high‐stakes English proficiency exams have begun incorporating speech samples produced by speakers from a range of inner circle English‐speaking backgrounds (e.g., Britain, the United States, Australia), the inclusion of samples produced by speakers of outer and expanding circle English varieties (e.g., India, Nigeria, Mexico, South Korea) has been largely avoided. For this study the researchers recruited speakers from six distinct English varieties to produce speech samples for a mock TOEFL iBT listening exam. Listeners who spoke with the same six international English accents were then recruited to take the resulting tests. Results indicate that when accented English is highly comprehensible, listening test scores for stimuli based on high‐proficiency speakers of outer and expanding circle varieties of English are not significantly lower than they are in response to stimuli based on inner circle varieties of English. With respect to a shared first language effect on test scores when test materials are spoken in the test taker's own accent, results are complex but inconclusive.
New Group 14 Element Substituted Phosphaalkenes
Authors: Balmer Markus , von Hänisch Carsten
Published: July 2018

A new way is presented to prepare group 14 compounds substituted with a terminal NHC stabilized phosphenidenyl substituent. On this occasion, it is shown that depending on the chain length of the group 14 element dichlorides in reaction with SIMesPK a mono‐ or disubstitution can be observed. Starting from Me2SiCl2 or tBu2SnCl2 a single substitution occurred. Longer chains of group 14 dihalides like (SiMe2Cl)2 or O(SiMe2SiMe2Cl)2 lead to silicon bridged bisphosphinidenyl compounds.
A Novel Approach for Prediction of Sensitivity toward the Electrical Discharge of Quaternary Ammonium‐based Energetic Ionic Liquids or Salts
Authors: Nazari Behzad , Keshavarz Mohammad Hossein , Jafari Mohammad , Jafari Fatemeh
Published: July 2018

Sensitivity toward electrical discharge (electric spark or electrostatic sensitivity) is an important safety parameter for assessment of working with new energetic compounds including ionic molecular energetic materials. This work introduces a novel simple correlation to assess the electrostatic sensitivity of quaternary ammonium‐based energetic ionic liquids or salts, which are based on elemental composition and the structure parameters of specific cations and anions. For 66 ionic molecular systems as a training set, the Root Mean Square Error (RMSE), Mean Absolute Error (MAE), and Maximum of Errors (Max Error) of predictions for the new model are 0.17, 0.15, and 0.31 J, respectively. The reliability of models was also tested for further 21 ionic compounds, which give the values of RMSE, MAE, and Max Error of 0.13, 0.11, and 0.25 J, respectively. Thus, the accuracy of the novel method for prediction of the electrostatic sensitivity of quaternary ammonium‐based energetic ionic liquids or salts is relatively good with respect to high uncertainties in experimental data.