bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interfacing HDF5 with a scalable object‐centric storage system on hierarchical storage
Authors: Mu Jingqing , Soumagne Jerome , Byna Suren , Koziol Quincey , Tang Houjun , Warren Richard 
Published: March 2020

SummaryObject storage technologies that take advantage of multitier storage on HPC systems are emerging. However, to use these technologies at present, applications have to be modified significantly from current I/O libraries. HDF5, a widely used I/O middleware on HPC systems, provides a virtual object layer (VOL) that allows applications to connect to different storage mechanisms transparently without requiring significant code modifications. We recently designed the proactive data containers (PDC) object‐centric storage system that provides the capabilities of transparent, asynchronous, and autonomous data movement taking advantage of multiple storage tiers—a decision that has so far been left upon the user on most current systems. To enable PDC's features through HDF5 without modifying application codes, we have developed an HDF5 VOL connector that interfaces with PDC. We present in this article the connector interface and evaluate its performance on Cori, a Cray XC40 supercomputer located at the National Energy Research Scientific Computing Center (NERSC). Our evaluation demonstrates up to an 8× improvement compared with HDF5 that has the most recent optimizations.
Unconventional Pyridyl Ligand Inclusion within a Flexible Metal‐Organic Framework Bearing an N,N′‐Diethylformamide (DEF)‐Solvated Cd5 Cluster Secondary Building Unit
Authors: Chao Meng‐Yao , Chen Jing , Wu Xiao‐Yu , Wang Rui‐Yao , Wang Pei‐Pei , Ding Lifeng , Young David J. , Zhang Wen‐Hua 
Published: March 2020

AbstractA cationic three‐dimensional (3D) metal‐organic framework (MOF) sustained by an N,N′‐diethylformamide (DEF)‐solvated zigzag‐shaped Cd5 cluster secondary building unit (SBU), [Et2NH2]2[Cd5(BTB)4(DEF)2] ⋅ 4.75DEF (1 a, H3BTB=benzene‐1,3,5‐tribenzoic acid) shows flexible framework behavior and undergoes solvate exchange with CHCl3 to yield [Et2NH2]2[Cd5(BTB)4(DEF)2] ⋅ xCHCl3 (1 b) accompanied by changes to pore sizes and shapes. Unexpectedly, the DEF solvates coordinated to the central Cd2+ could not be replaced by strongly donor pyridyl and dipyridyl ligands. Additionally, more electron‐deficient pyridyls preferentially coordinated to the flanking Cd2+ of the Cd5 SBU, as exemplified by [Et2NH2]2[Cd5(BTB)4(DEF)2(PyCHO)2] ⋅ xSol (2 a, PyCHO=4‐pyridinealdehyde) and [Et2NH2]2[Cd5(BTB)4(DEF)2(PyAc)2] ⋅ xSol (2 b, PyAc=4‐acetylpyridine). Density functional theory (DFT) calculations were used to understand these counterintuitive observations.
Multigene Engineering by GoldenBraid Cloning: From Plants to Filamentous Fungi and Beyond
Authors: Vazquez‐Vilar Marta , Gandía Mónica , García‐Carpintero Victor , Marqués Eric , Sarrion‐Perdigones Alejandro , Yenush Lynne , Polaina Julio , Manzanares Paloma , Marcos Jose F. , Orzaez Diego 
Published: March 2020

AbstractMany synthetic biologists have adopted methods based on Type IIS restriction enzymes and Golden Gate technology in their cloning procedures, as these enable the combinatorial assembly of modular elements in a very efficient way following standard rules. GoldenBraid (GB) is a Golden Gate–based modular cloning system that, in addition, facilitates the engineering of large multigene constructs and the exchange of DNA parts as result of its iterative cloning scheme. GB was initially developed specifically for plant synthetic biology, and it has been subsequently extended and adapted to other organisms such as Saccharomyces cerevisiae, filamentous fungi, and human cells by incorporating a number of host‐specific features into its basic scheme. Here we describe the general GB cloning procedure and provide detailed protocols for its adaptation to filamentous fungi—a GB variant known as FungalBraid. The assembly of a cassette for gene disruption by homologous recombination, a fungal‐specific extension of the GB utility, is also shown. Development of FungalBraid was relatively straightforward, as both plants and fungi can be engineered using the same binary plasmids via Agrobacterium‐mediated transformation. We also describe the use of a set of web‐based tools available at the GB website that assist users in all cloning procedures. The availability of plant and fungal versions of GB will facilitate genetic engineering in these industrially relevant organisms. © 2020 by John Wiley & Sons, Inc.Basic Protocol 1: Software‐assisted modular DNA assembly of a two gene expression‐cassette with GBBasic Protocol 2: Agrobacterium tumefaciens–mediated transformation of filamentous fungiBasic Protocol 3: Software‐assisted modular DNA assembly of a gene disruption‐cassette using GBBasic Protocol 4: Obtaining disruption transformants
Electron Transfer Mediated by Iron Carbonyl Clusters Enhance Light‐Driven Hydrogen Evolution in Water by Quantum Dots
Authors: Li Chuanshuai , Rahaman Ahibur , Lin Weihua , Mourad Hassan , Meng Jie , Honarfar Alireza , Abdellah Mohamed , Guo Meiyuan , Richmond Michael G. , Zheng Kaibo , Nordlander Ebbe 
Published: March 2020

AbstractPhotocatalytic water splitting has become a promising strategy for converting solar energy into clean and carbon‐neutral solar fuels in a low‐cost and environmentally benign way. Hydrogen gas is such a potential solar fuel/energy carrier. In a classical artificial photosynthetic system, a photosensitizer is generally associated with a co‐catalyst to convert photogenerated charge into (a) chemical bond(s). In the present study, assemblies consisting of CdSe quantum dots that are coupled with one of two molecular complexes/catalysts, that is, [Fe2S2(CO)6] or [Fe3Te2(CO)9], using an interface‐directed approach, have been tested as catalytic systems for hydrogen production in aqueous solution/organic solution. In the presence of ascorbic acid as a sacrificial electron donor and proton source, these assemblies exhibit enhanced activities for the rate of hydrogen production under visible light irradiation for 8 h in aqueous solution at pH 4.0 with up to 110 μmol of H2 per mg of assembly, almost 8.5 times that of pure CdSe quantum dots under the same conditions. Transient absorption and time‐resolved photoluminescence spectroscopies have been used to investigate the charge carrier transfer dynamics in the quantum dot/iron carbonyl cluster assemblies. The spectroscopic results indicate that effective electron transfer from the molecular iron complex to the valence band of the excited CdSe quantum dots significantly inhibits the recombination of photogenerated charge carriers, boosting the photocatalytic activity for hydrogen generation; that is, the iron clusters function as effective intermediaries for electron transfer from the sacrificial electron donor to the valence band of the quantum dots.
Behavior underpins the predictive power of a trait‐based model of butterfly movement
Authors: Evans Luke C. , Sibly Richard M. , Thorbek Pernille , Sims Ian , Oliver Tom H. , Walters Richard J. 
Published: March 2020

Abstract

Dispersal ability is key to species persistence in times of environmental change. Assessing a species' vulnerability and response to anthropogenic changes is often performed using one of two methods: correlative approaches that infer dispersal potential based on traits, such as wingspan or an index of mobility derived from expert opinion, or a mechanistic modeling approach that extrapolates displacement rates from empirical data on short‐term movements.

Here, we compare and evaluate the success of the correlative and mechanistic approaches using a mechanistic random‐walk model of butterfly movement that incorporates relationships between wingspan and sex‐specific movement behaviors.

The model was parameterized with new data collected on four species of butterfly in the south of England, and we observe how wingspan relates to flight speeds, turning angles, flight durations, and displacement rates.

We show that flight speeds and turning angles correlate with wingspan but that to achieve good prediction of displacement even over 10 min the model must also include details of sex‐ and species‐specific movement behaviors.

We discuss what factors are likely to differentially motivate the sexes and how these could be included in mechanistic models of dispersal to improve their use in ecological forecasting.
Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia)
Authors: Limmon Gino , Delrieu‐Trottin Erwan , Patikawa Jesaya , Rijoly Frederik , Dahruddin Hadi , Busson Frédéric , Steinke Dirk , Hubert Nicolas 
Published: March 2020

AbstractThe Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass‐based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass‐based approaches. Recent meta‐analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.
Quality of life in heart failure with preserved ejection fraction: importance of obesity, functional capacity, and physical inactivity
Authors: Reddy Yogesh N.V. , Rikhi Aruna , Obokata Masaru , Shah Sanjiv J. , Lewis Gregory D. , AbouEzzedine Omar F. , Dunlay Shannon , McNulty Steven , Chakraborty Hrishikesh , Stevenson Lynne W. , Redfield Margaret M. , Borlaug Barry A. 
Published: March 2020

AbstractAimsPatient‐reported quality of life (QOL) is a highly prognostic and clinically relevant endpoint in patients with heart failure (HF) with preserved ejection fraction (HFpEF). The relationships between QOL and different markers of HF severity remain unclear, particularly as they relate to functional capacity and directly measured activity levels. We hypothesized that QOL would demonstrate a stronger relationship with measures of exercise capacity and adiposity compared to other disease measures.Methods and resultsThis is a secondary analysis of the National Heart, Lung, and Blood Institute‐sponsored RELAX, NEAT‐HFpEF and INDIE‐HFpEF trials to determine the relationships between QOL (assessed by the Kansas City Cardiomyopathy Questionnaire and Minnesota Living with Heart Failure Questionnaire) and different domains reflecting HF severity, including maximal aerobic capacity (peak oxygen consumption), submaximal exercise capacity (6‐min walk distance), volume of daily activity (accelerometry), physician‐estimated functional class, resting echocardiography, and plasma natriuretic peptide levels. A total of 408 unique patients with chronic HFpEF were split into tertiles of QOL scores defined as QOLworst, QOLintermediate, QOLbest. The QOLworst HFpEF group was youngest, with a higher body mass index, greater prevalence of class II obesity and diabetes, and the lowest N‐terminal pro‐brain natriuretic peptide (NT‐proBNP) levels. After adjustment for age, sex and body mass index, poorer QOL was associated with worse physical capacity and activity levels, assessed by peak oxygen consumption, 6‐min walk distance and actigraphy, but was not associated with NT‐proBNP or indices from resting echocardiography. QOL was similarly reduced in patients with and without prior HF hospitalization.ConclusionsQuality of life in HFpEF is poorest in patients who are young, obese and have diabetes, and is more robustly tied to measures reflecting functional capacity and daily activity levels rather than elevations in NT‐proBNP or prior HF hospitalization. These findings have major implications for the understanding of QOL in HFpEF and for the design of future clinical trials targeting symptom improvement in HFpEF.Clinical Trial Registration: RELAX, NCT00763867; NEAT‐HFpEF, NCT02053493; INDIE‐HFpEF, NCT02742129.
Impact of Carbon Porosity on the Performance of Cathode Microporous Layers in Proton Exchange Membrane Fuel Cells
Authors: Govindarajan R. , Payoyo J. , Fang B. , Bonakdarpour A. , Wilkinson D. P. 
Published: March 2020

AbstractAcetylene black carbons were activated under flowing CO2 atmosphere at 900 °C for different treatment times. The impact of this heat treatment on the porosity, hydrophilicity, and surface oxygen groups was carefully examined. Longer periods of activation led to increases in the surface area and porosity of the samples. Pore size distributions of the samples showed an increase in micropores, followed by a rise in mesopores, which indicated the occurrence of pore widening with a longer activation period. When used as a microporous layer for H2/air fuel cells, samples with higher levels of porosity showed, in general, reduced mass transport performance due to the formation of pooling locations for water. These results highlight the importance of textural pores in carbon structures on the water management in hydrogen fuel cell when operating under high humidity conditions.
Temporospatial distribution and transcriptional profile of retinal microglia in the oxygen‐induced retinopathy mouse model
Authors: Boeck Myriam , Thien Adrian , Wolf Julian , Hagemeyer Nora , Laich Yannik , Yusuf Dilmurat , Backofen Rolf , Zhang Peipei , Boneva Stefaniya , Stahl Andreas , Hilgendorf Ingo , Agostini Hansjürgen , Prinz Marco , Wieghofer Peter , Schlunck Günther , Schlecht Anja , Lange Clemens 
Published: March 2020

AbstractMyeloid cells such as resident retinal microglia (MG) or infiltrating blood‐derived macrophages (Mϕ) accumulate in areas of retinal ischemia and neovascularization (RNV) and modulate neovascular eye disease. Their temporospatial distribution and biological function in this process, however, remain unclarified. Using state‐of‐the‐art methods, including cell‐specific reporter mice and high‐throughput RNA sequencing (RNA Seq), this study determined the extent of MG proliferation and Mϕ infiltration in areas with retinal ischemia and RNV in Cx3cr1CreERT2:Rosa26‐tdTomato mice and examined the transcriptional profile of MG in the mouse model of oxygen‐induced retinopathy (OIR). For RNA Seq, tdTomato‐positive retinal MG were sorted by flow cytometry followed by Gene ontology (GO) cluster analysis. Furthermore, intraperitoneal injections of the cell proliferation marker 5‐ethynyl‐2′‐deoxyuridine (EdU) were performed from postnatal day (p) 12 to p16. We found that MG is the predominant myeloid cell population while Mϕ rarely appears in areas of RNV. Thirty percent of retinal MG in areas of RNV were EdU‐positive indicating a considerable local MG cell expansion. GO cluster analysis revealed an enrichment of clusters related to cell division, tubulin binding, ATPase activity, protein kinase regulatory activity, and chemokine receptor binding in MG in the OIR model compared to untreated controls. In conclusion, activated retinal MG alter their transcriptional profile, exhibit considerable proliferative ability and are by far the most frequent myeloid cell population in areas of ischemia and RNV in the OIR model thus presenting a potential target for future therapeutic approaches.
The biofilm‐associated bacterial infections unrelated to indwelling devices
Authors: Mirzaei Rasoul , Mohammadzadeh Rokhsareh , Alikhani Mohammad Yousef , Shokri Moghadam Mohammad , Karampoor Sajad , Kazemi Sima , Barfipoursalar Alireza , Yousefimashouf Rasoul 
Published: March 2020

AbstractBiofilms are microbial communities established in the self‐produced extracellular substances that include up to 80% of associated microbial infections. During biofilm formation, bacterial cells shift from the planktonic forms to aggregated forms surrounded by an extracellular polymeric substance. The bacterial biofilm shows resistance against immune reactions as well as antibiotics and is potentially able to cause disorders by both device‐related and nondevice‐related infections. The nondevice‐related bacterial biofilm infections include dental plaque, urinary tract infections, cystic fibrosis, otitis media, infective endocarditis, tonsillitis, periodontitis, necrotizing fasciitis, osteomyelitis, infectious kidney stones, and chronic inflammatory diseases. In this review, we will summarize and examine the literature about bacterial biofilm infections unrelated to indwelling devices.
Elevated microRNA‐20b‐3p and reduced thioredoxin‐interacting protein ameliorate diabetic retinopathy progression by suppressing the NLRP3 inflammasomes
Authors: Wang Shuai , Du Shanshan , Lv Yong , Wang Wenzhan , Zhang Fengyan 
Published: March 2020

AbstractOver the years, microRNA‐20b‐3p (miR‐20b‐3p) has been found to play an essential role in human diseases; we aimed to investigate the effect of miR‐20b‐3p on the progression of diabetic retinopathy (DR). The DR rat models were established by streptozotocin injection and treated with miR‐20b‐3p mimics, silenced, or overexpressed thioredoxin‐interacting protein (TXNIP). Afterward, the expression of miR‐20b‐3p and TXNIP, visual function, inflammatory factors, microvascular injury, vascular permeability, cell apoptosis, and angiogenesis in rats' retinal tissues were assessed. The target relation between miR‐20b‐3p and TXNIP was confirmed by dual luciferase reporter gene assay. MiR‐20b‐3p was poorly expressed while TXNIP was highly expressed in DR rats' retinal tissues. Elevated miR‐20b‐3p and inhibited TXNIP promoted the visual function, and restricted the inflammatory reaction, microvascular injury, vascular permeability, cell apoptosis, and angiogenesis in DR rats, thereby decelerating the development of DR. Furthermore, TXNIP was targeted by miR‐20b‐3p. We have found in this study that elevated miR‐20b‐3p could repress the levels of inflammatory factors by inhibiting TXNIP, thus attenuating the pathology of retina in DR rats, which provided new candidates for DR treatment.
Periodontal soft‐ and hard‐tissue changes after augmented corticotomy in Chinese adult patients with skeletal Angle Class III malocclusion: A non‐randomized controlled trial
Authors: Jing Wu‐di , Jiao Jian , Xu Li , Hou Jian‐xia , Li Xiao‐tong , Wang Xiao‐xia , Xu Xiao , Mao Ming‐xin 
Published: March 2020

AbstractBackgroundTo investigate soft‐ and hard‐tissue changes after augmented corticotomy in Chinese adult patients with skeletal Angle Class III malocclusion.MethodsThis non‐randomized controlled trial included 357 anterior teeth from 30 Chinese adult patients with skeletal Angle Class III malocclusion for whom the proposed treatment was augmented corticotomy. Jaws receiving surgery were allocated to a test group (S, surgical group, n = 47) and jaws not receiving surgery were allocated to a control group (NS, non‐surgical group, n = 13). Changes in the periodontal biotype, width of the keratinized gingiva (WKG), and labial and lingual horizontal bone thicknesses (BTs) were compared 6 months after surgery by univariate and multivariate analyses.ResultsAfter adjustment for confounding variables, average gains of 0.473 mm in the WKG and 0.649 mm in the labial BT were found in the S group relative to the NS group (P <0.05). The odds of transition from a thin periodontal biotype to a thick biotype in the S group were about 230 times those in the NS group, and the odds of the reverse biotype transition in the NS group were about 83 times those in the S group (P <0.05).ConclusionsWithin the limitations of the present study, augmented corticotomy is a promising approach to improve insufficient periodontal soft and hard tissues in Chinese adult patients with skeletal Angle Class III malocclusion.
Interfacial Activity of Bitumen Components
Authors: Stammitti Aurelio , Bhanot Ashutosh , Boza Americo , Ng Samson , Acosta Edgar 
Published: March 2020

AbstractThe interfacial activity of asphaltenes, naphthenic acids, and naphthenates has been amply studied in the literature, as they are involved in the formation and stabilization of bitumen and heavy crude oil emulsions. While most of the literature evaluates one component at a time, in this work these bitumen components were separated one at a time from Athabasca bitumen, and the surface activity of the resulting fraction was evaluated as a function of pH, solvent aromaticity (heptane/toluene mixtures, known as heptol, at volume ratios 50/50 and 80/20), and temperature for selected systems. The interfacial activity was evaluated in two ways: via dynamic interfacial tension during adsorption on a bitumen drop of constant volume, and via dynamic interfacial tension during drop volume cycling. The adsorption data were interpreted using a model that combined multicomponent adsorption kinetics inspired by Langmuir–Freundlich kinetics with the Fainerman surface equation of state. The volume cycling experiments were interpreted using the compression relaxation model, which segregates adsorption/relaxation effects from elastic phenomena at interfaces. Overall, the adsorption data confirmed that naphthenic acids are the fastest adsorbing species that tend to dominate the interface, but that asphaltenes adsorb, almost irreversibly, at longer time scales and likely forming a sublayer previously proposed in the literature. The dilatational elasticity of the interface seems to be highly influenced by that asphaltene sublayer, which softens at high pH at room temperature, or at 80 °C independently of the pH of the system.
Postharvest benzothiazole treatment enhances healing in mechanically damaged sweet potato by activating the phenylpropanoid metabolism
Authors: Wang Caixia , Chen Lin , Peng Chunlin , Shang Xiaoqing , Lv Xiaolong , Sun Jie , Li Cheng , Wei Lei , Liu Xiaoli 
Published: March 2020

AbstractBACKGROUNDSweet potato often suffers mechanical damage during harvest, handling, and transportation. Infections, water loss, and quality changes of sweet potato caused by mechanical damage pose great financial losses. Wound healing is an effective method to alleviate such problems. In this study, the effects of postharvest treatment with benzothiazole (BTH) on wound healing of sweet potato was investigated.RESULTSPostharvest BTH treatment of sweet potatoes promoted lignin accumulation in wounded tissues, and 100 mg L−1 BTH exhibited better effects than 50 mg L−1 or 150 mg L−1 BTH. The biosynthesis of lignin in wounded tissues significantly decreased the weight loss of sweet potatoes. An increase in respiration intensity after BTH treatment was observed. The total phenolic and flavonoid contents and the activity of phenylalanine ammonia‐lyase, peroxidase, and polyphenol oxidase were increased in BTH‐treated sweet potatoes. This suggests that BTH increases phenylpropanoid metabolism.CONCLUSIONPostharvest 100 mg L−1 BTH treatment could promote wound healing in mechanically damaged sweet potatoes. The activation of the phenylpropanoid metabolism might be the mechanism of action of BTH in wound healing. © 2020 Society of Chemical Industry