bluuebunny/crossref_metadata_2025 huggingface dataset:
High‐Resolution Protein 3D Structure Determination in Living Eukaryotic Cells
Authors: Tanaka Takashi , Ikeya Teppei , Kamoshida Hajime , Suemoto Yusuke , Mishima Masaki , Shirakawa Masahiro , Güntert Peter , Ito Yutaka
Published: April 2019

Proteins in living cells interact specifically or nonspecifically with an enormous number of biomolecules. To understand the behavior of proteins under intracellular crowding conditions, it is indispensable to observe their three‐dimensional (3D) structures at the atomic level in a physiologically natural environment. We demonstrate the first de novo protein structure determinations in eukaryotes with the sf9 cell/baculovirus system using NMR data from living cells exclusively. The method was applied to five proteins, rat calmodulin, human HRas, human ubiquitin, T. thermophilus HB8 TTHA1718, and Streptococcus protein G B1 domain. In all cases, we could obtain structural information from well‐resolved in‐cell 3D nuclear Overhauser effect spectroscopy (NOESY) data, suggesting that our method can be a standard tool for protein structure determinations in living eukaryotic cells. For three proteins, we achieved well‐converged 3D structures. Among these, the in‐cell structure of protein G B1 domain was most accurately determined, demonstrating that a helix‐loop region is tilted away from a β‐sheet compared to the conformation in diluted solution.
Polymeric Design for Electron Transfer in Photoinduced Hydrogen Generation through a Coil–Globule Transition
Authors: Okeyoshi Kosuke , Yoshida Ryo
Published: April 2019

To realize a renewable energy society, a polymeric system for photoinduced hydrogen generation utilizing a copolymer containing an electron acceptor was designed. In this system, the redox changes of viologen introduced into poly(N‐isopropylacrylamide) cause cyclic conformational changes owing to the shifting of the phase transition temperature (PTT). The polymeric coil–globule transitions with hydrophilic/hydrophobic changes accelerate the electron transfer for hydrogen generation. In particular, hydrogen generation using visible‐light energy with high efficiency is achieved around the PTT. In contrast to conventional solution systems, our polymeric system enables efficient hydrogen generation in a close molecular arrangement without the aggregation of catalytic nanoparticles. The utilization of conformational changes will provide a new strategy for synthesizing artificial photosynthetic hydrogels that split water to generate both hydrogen and oxygen.
Inorganic Salts Induce Thermally Reversible and Anti‐Freezing Cellulose Hydrogels
Authors: Zhang Xiong‐Fei , Ma Xiaofeng , Hou Ting , Guo Kechun , Yin Jiayu , Wang Zhongguo , Shu Lian , He Ming , Yao Jianfeng
Published: April 2019

Inspired by the anti‐freezing mechanisms found in nature, ionic compounds (ZnCl2/CaCl2) are integrated into cellulose hydrogel networks to enhance the freezing resistance. In this work, cotton cellulose is dissolved by a specially designed ZnCl2/CaCl2 system, which endows the cellulose hydrogels specific properties such as excellent freeze‐tolerance, good ion conductivity, and superior thermal reversibility. Interestingly, the rate of cellulose coagulation could be promoted by the addition of extra water or glycerol. This new type of cellulose‐based hydrogel may be suitable for the construction of flexible devices used at temperature as low as −70 °C.
Narrowing Segments of Helical Carbon Nanotubes with Curved Aromatic Panels
Authors: Kogashi Kanako , Matsuno Taisuke , Sato Sota , Isobe Hiroyuki
Published: April 2019

Rigid molecular cylinders with a 1 nm diameter were synthesized by assembling arylene panels with Pt‐mediated macrocylization. Chrysenylene panels that previously participated in tetrameric macrocyclization were contorted by the addition of two benzo groups on the sides to form dibenzochrysenylene, which allowed for a reduction in the numbers of participating panels to three. Consequently, narrowed cyclochrysenylene congeners were obtained. The narrowed chiral cylinders possessed width‐dependent chiroptical properties. The magnetic transition dipole moment was dictated by the radius of a ring‐current‐like circle that was formed by local electric transition dipole moments on the cylinder.
Identifying breach mechanism during air‐gap spinning of lignin–cellulose ionic‐liquid solutions
Authors: Bengtsson Jenny , Jedvert Kerstin , Köhnke Tobias , Theliander Hans
Published: April 2019

To be able to produce highly oriented and strong fibers from polymer solutions, a high elongational rate during the fiber‐forming process is necessary. In the air‐gap spinning process, a high elongational rate is realized by employing a high draw ratio, the ratio between take‐up and extrusion velocity. Air‐gap spinning of lignin–cellulose ionic‐liquid solutions renders fibers that are promising to use as carbon fiber precursors. To further improve their mechanical properties, the polymer orientation should be maximized. However, achieving high draw ratios is limited by spinning instabilities that occur at high elongational rates. The aim of this experimental study is to understand the link between solution properties and the critical draw ratio during air‐gap spinning. A maximum critical draw ratio with respect to temperature is found. Two mechanisms that limit the critical draw ratio are proposed, cohesive breach and draw resonance, the latter identified from high‐speed videos. The two mechanisms clearly correlate with different temperature regions. The results from this work are not only of value for future work within the studied system but also for the design of air‐gap spinning processes in general. © 2019 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2019, 136, 47800.
Next‐Generation Additive Manufacturing: Tailorable Graphene/Polylactic(acid) Filaments Allow the Fabrication of 3D Printable Porous Anodes for Utilisation within Lithium‐Ion Batteries
Authors: Foster Christopher W. , Zou Guo‐Qiang , Jiang Yunling , Down Michael P. , Liauw Christopher M. , Garcia‐Miranda Ferrari Alejandro , Ji Xiaobo , Smith Graham C. , Kelly Peter J. , Banks Craig E.
Published: April 2019

Herein, we report the fabrication and application of Li‐ion anodes for utilisation within Li‐ion batteries, which are fabricated via additive manufacturing/3D printing (fused deposition modelling) using a bespoke graphene/polylactic acid (PLA) filament, where the graphene content can be readily tailored and controlled over the range 1–40 wt. %. We demonstrate that a graphene content of 20 wt. % exhibits sufficient conductivity and critically, effective 3D printability for the rapid manufacturing of 3D printed freestanding anodes (3DAs); simplifying the components of the Li‐ion battery negating the need for a copper current collector. The 3DAs are physicochemically and electrochemically characterised and possess sufficient conductivity for electrochemical studies. Critically, it is found that if the 3DAs are used in Li‐ion batteries the specific capacity is very poor but can be significantly improved through the use of a chemical pre‐treatment. Such treatment induces an increased porosity, which results in a 200‐fold increase (after anode stabilisation) of the specific capacity (ca. 500 mAh g−1 at a current density of 40 mA g−1). This work significantly enhances the field of additive manufacturing/3D printed graphene based energy storage devices demonstrating that useful 3D printable batteries can be realised.
Using auditory feedback to improve striking for mixed martial artists
Authors: Krukauskas Frank , Miltenberger Raymond , Gavoni Paul
Published: April 2019

The purpose of this study was to evaluate auditory feedback to increase the effectiveness of throwing a “right cross.” Auditory feedback, implemented by the mixed martial arts coach, was evaluated in multiple baselines across participants design with four mixed martial arts students, two males and two females, 25–54 years old. The target behavior was the percentage of correct steps in the 20‐step task analysis of throwing a right cross. In the auditory feedback procedure, the coach used a handheld clicker and make the clicking sound as a reinforcer each time the participant performed a specific step in the task analysis correctly. This process continued until all steps were performed correctly. The percentage of correct steps of the right cross improved substantially during assessment sessions following the introduction of the auditory feedback and maintained at 90% or more for all participants during follow‐up. Improvements were also noted in the social validity assessment.
Consumers' corporate social responsibility and corporate ability associations as predictors of reputation: Developing countries under analysis
Authors: Contini Michele , Annunziata Eleonora , Rizzi Francesco , Frey Marco
Published: April 2019

This study investigates the effect of corporate social responsibility (CSR) and corporate ability (CA) associations on perceived corporate reputation (PCR) and the relationship between the two associations in different cultural environments. By focusing on electricity providers, we carried out a questionnaire survey within BRICS capital cities—that is, Brazil, Russia, India, China, and South Africa—and tested a conceptual model via structural equation modelling. Results showed that, grouping BRICS together, CSR and CA associations predicted PCR, and CA association partially mediated the relationship between CSR association and PCR. When analysing each country separately, these relations were confirmed only for Brazil, China, and South Africa. These findings extend the literature on consumers' corporate associations by differentiating between CSR and CA among different cultural environments. Managers should avoid replicating business strategies in different cultural systems, coordinating such strategies to maximise PCR. The paper concludes with suggestions for coordinating CSR and CA within business development strategies.
Simulation‐based learning modules for undergraduate engineering dynamics
Authors: Karadoğan Ernur , Karadoğan Figen
Published: April 2019

In this paper, we describe software modules that provide both visual and haptic feedback to the student, and evaluate their effectiveness. The system integrates software modules with a haptic interface that can augment teaching and learning in a required undergraduate engineering Dynamics course. Students can change parameters, predict answers, compare outcomes, interact with animations, and feel the results using a haptic interface. Three software modules were evaluated in two separate studies. The first study focused on subjective ratings based on student opinions. The second study assessed the effect of the modules on students' conceptual understanding for force and motion using a pretest/posttest design. The results revealed that the practice with the modules significantly improved the conceptual understanding of the targeted concepts. In addition, students showed a significant preference by stating that the modules would increase their interest in Dynamics as a subject and their engagement in the Dynamics course.
Branched DNA Architectures Produced by PCR‐Based Assembly as Gene Compartments for Cell‐Free Gene‐Expression Reactions
Authors: Guo Xiaocui , Bai Lihui , Li Feng , Huck Wilhelm T. S. , Yang Dayong
Published: April 2019

The physical distance between genes plays important roles in controlling gene expression reactions in vivo. Herein, we report the design and synthesis of a branched gene architecture in which three transcription units are integrated into one framework through assembly based on the polymerase chain reaction (PCR), together with the exploitation of these constructs as “gene compartments” for cell‐free gene expression reactions, probing the impact of this physical environment on gene transcription and translation. We find that the branched gene system enhances gene expression yields, in particular at low concentrations of DNA and RNA polymerase (RNAP); furthermore, in a crowded microenvironment that mimics the intracellular microenvironment, gene expression from branched genes maintains a relatively high level. We propose that the branched gene assembly forms a membrane‐free gene compartment that resembles the nucleoid of prokaryotes and enables RNAP to shuttle more efficiently between neighboring transcription units, thus enhancing gene expression efficiency. Our branched DNA architecture provides a valuable platform for studying the influence of “cellular” physical environments on biochemical reactions in simplified cell‐free systems.
Phase‐Dependent Stability and Substrate‐Induced Deactivation by Strong Metal‐Support Interaction of Ru/TiO2 Catalysts for the Hydrogenation of Levulinic Acid
Authors: Liu Fang , Ftouni Jamal , Bruijnincx Pieter C. A. , Weckhuysen Bert M.
Published: April 2019

The choice of support type has a profound influence on catalyst performance in liquid phase hydrogenation reactions, including the catalytic hydrogenation of biomass‐derived levulinic acid (LA) to γ‐valerolactone (GVL). Catalytic performance, including stability, of three Ru/TiO2 catalysts, having a similar mean Ru metal nanoparticle size but supported on three types of TiO2, namely P25, rutile and anatase, is evaluated by multiple reuse under batch reactor conditions. T3he catalysts’ physicochemical properties before and after recycling are characterized by XRD, STEM, TGA and FT‐IR after CO stepwise adsorption. The results show that the deactivation seen for (mixed) anatase‐supported catalysts in dioxane can be attributed to strong metal‐support interaction (SMSI) rather than coke formation or metal sintering, with the rutile‐based catalyst being more resistant against such support reduction. Notably, SMSI formation under the applied, relatively mild conditions only occurs in the presence of organic acids, such as LA or valeric acid.
How Do Vortex Structures Influence Boundary Layer Dynamics in Gas‐Liquid Systems?
Authors: Rüttinger Sophie , Hoffmann Marko , Schlüter Michael
Published: April 2019

In many process engineering applications, the dynamics of gas‐liquid two‐phase flows plays a crucial role. The transfer of mass from the gaseous phase into the liquid phase is often a limiting step. This communication deals with the question how vortex structures, which are ubiquitous in engineering fluid flows, influence the transport processes of mass and momentum close to the interface. The question is approached by means of a methodical series of experiments with increasing optical access. By utilizing particle image velocimetry and laser‐induced fluorescence, detailed investigations of hydrodynamics and mass transfer are carried out.
Suspension and Mixing Characterization of Intermittent Agitation Modes in DASGIP Bioreactors
Authors: Samaras Jasmin Jade , Micheletti Martina , Ducci Andrea
Published: April 2019

Intermittent agitation strategies have been increasingly used for a range of process development applications, i.e., to modulate physical cues, to improve stem cell differentiation yields, and to control hydrodynamic shear stresses in microcarrier suspension; however, there is a distinct lack of characterization. Both continuous and intermittent agitation modes in relation to suspension and mixing dynamics within a DASGIP bioreactor were characterized. Suspension dynamics were found to be affected by microcarrier porosity and the degree of settling was found to be more pronounced at the top of the bioreactor. Mixing time characterization showed a marked improvement in mixing efficiency for intermittent agitation, with an overall dependence on the timing of tracer insertion.
Statistical analysis and heuristic identification of unexpected interactions from the neurokinase‐inhibitor interactome in trigeminal neuralgia pharmacological intervention
Authors: Liu Lei , Chen Xiaobing , Liu Weiju , Yu Hui , Liu Fangming
Published: April 2019

The cell signaling pathways of human trigeminal neuralgia (TN) are orchestrated by a variety of protein kinase‐elicited phosphorylation events. However, a majority of TN‐related neurokinases have not yet been revealed and still remain largely unexplored. Here, a systematic kinase‐inhibitor interactome for 601 small‐molecule inhibitors across 51 human neurokinases is created via a high‐throughput molecular docking procedure; the inhibitors are reversible, ATP competitive, and commercially available, while the kinases are enriched by gene ontology (GO) to be semantically relevant with TN and have cocrystallized structures with their cognate ligands. Heuristic clustering and statistical analysis identify 35 hit inhibitors from the interactome profile, which are potential to target TN‐related kinases. The intermolecular interactions of four promising inhibitors with the array of 51 TN‐related kinases are investigated in detail at molecular level using dynamics simulation and energetics analysis. Consequently, a total of nine protein kinases are inferred as high‐affinity cotargets of these potent inhibitors, in which fours have already been established as sophisticated targets for TN therapy, while others are still unclear about their therapeutic implications underlying the disease. Some candidates are selected as representatives to perform kinase assay. It is found that some putative kinase targets can be inhibited effectively by noncognate inhibitors; the activity values are comparable with or even better than known cognate inhibitors. Structural examination of a potent kinase‐inhibitor complex identifies a number of noncovalent interactions such as hydrogen bonds, cation‐π stacking, and hydrophobic contacts at the tightly packed complex interface, conferring both stability and specificity to the complex recognition and interaction.
Mechanistic Insights into the Self‐Assembly of an Acid‐Sensitive Photoresponsive Supramolecular Polymer
Authors: Kartha Kalathil K. , Allampally Naveen Kumar , Yagai Shiki , Albuquerque Rodrigo Q. , Fernández Gustavo
Published: April 2019

The supramolecular polymerization of an acid‐sensitive pyridyl‐based ligand (L1) bearing a photoresponsive azobenzene moiety was elucidated by mechanistic studies. Addition of trifluoroacetic acid (TFA) led to the transformation of the antiparallel H‐bonded fibers of L1 in methylcyclohexane into superhelical braid‐like fibers stabilized by H‐bonding of parallel‐stacked monomer units. Interestingly, L1 dimers held together by unconventional pyridine–TFA N⋅⋅⋅H⋅⋅⋅O bridges represent the main structural elements of the assembly. UV‐light irradiation caused a strain‐driven disassembly and subsequent aggregate reconstruction, which ultimately led to short fibers. The results allowed to understand the mechanism of mutual influence of acid and light stimuli on supramolecular polymerization processes, thus opening up new possibilities to design advanced stimuli‐triggered supramolecular systems.
Antibacterial Small Molecules That Potently Inhibit Staphylococcus aureus Lipoteichoic Acid Biosynthesis
Authors: Naclerio George A. , Karanja Caroline W. , Opoku‐Temeng Clement , Sintim Herman O.
Published: April 2019

The rise of antibiotic resistance, especially in Staphylococcus aureus, and the increasing death rate due to multiresistant bacteria have been well documented. The need for new chemical entities and/or the identification of novel targets for antibacterial drug development is high. Lipoteichoic acid (LTA), a membrane‐attached anionic polymer, is important for the growth and virulence of many Gram‐positive bacteria, and interest has been high in the discovery of LTA biosynthesis inhibitors. Thus far, only a handful of LTA biosynthesis inhibitors have been described with moderate (MIC=5.34 μg mL−1) to low (MIC=1024 μg mL−1) activities against S. aureus. Herein we describe the identification of novel compounds that potently inhibit LTA biosynthesis in S. aureus, displaying impressive antibacterial activities (MIC as low as 0.25 μg mL−1) against methicillin‐resistant S. aureus (MRSA). Under similar in vitro assay conditions, these compounds are 4‐fold more potent than vancomycin and 8‐fold more potent than linezolid against MRSA.
Time‐critical data management in clouds: Challenges and a Dynamic Real‐Time Infrastructure Planner (DRIP) solution
Authors: Koulouzis Spiros , Martin Paul , Zhou Huan , Hu Yang , Wang Junchao , Carval Thierry , Grenier Baptiste , Heikkinen Jani , de Laat Cees , Zhao Zhiming
Published: April 2019

The increasing volume of data being produced, curated, and made available by research infrastructures in the environmental science domain require services that are able to optimize the delivery and staging of data for researchers and other users of scientific data. Specialized data services for managing data life cycle, for creating and delivering data products, and for customized data processing and analysis all play a crucial role in how these research infrastructures serve their communities, and many of these activities are time‐critical—needing to be carried out frequently within specific time windows. We describe our experiences identifying the time‐critical requirements of environmental scientists making use of computational research support environments. We present a microservice‐based infrastructure optimization suite, the Dynamic Real‐Time Infrastructure Planner, used for constructing virtual infrastructures for research applications on demand. We provide a case study whereby our suite is used to optimize runtime service quality for a data subscription service provided by the Euro‐Argo using EGI Federated Cloud and EUDAT's B2SAFE services, and to consider how such a case study relates to other application scenarios.
Non‐blocking two‐phase commit using blockchain
Authors: Ezhilchelvan Paul , Aldweesh Amjad , van Moorsel Aad
Published: April 2019

The two‐phase commit (2PC) protocol has long been known to have a provably inevitable vulnerability to blocking or non‐progress amidst server crashes, even when the distributed database system guarantees the most demanding timing‐related or “synchrony” requirements. Our aim here is to eliminate this vulnerability by using a blockchain for coordinating 2PC execution. We present the impossibilities, the possibilities, the cost, and the trade‐offs in this blockchain‐based approach to blocking‐free management of distributed transactions. We prove that a non‐blocking and blockchain‐coordinated 2PC protocol can exist only if both the blockchain and distributed database systems meet synchrony requirements; otherwise, although blocking remains eliminated, transactions can unnecessarily abort. We present a blockchain‐coordinated 2PC protocol and provide rigorous arguments for its correctness under the synchrony requirements. We then implement this protocol on the Ethereum Testnet and demonstrate, through our experiments, that the monetary cost of executing smart contracts is quite small, that the protocol performance slows down when using a public blockchain like Ethereum, and that even major violations of synchrony requirements lead only to relatively small increases in unnecessary aborts. We thus identify a trade‐off between improving protocol performance and admitting a risk that transactions could occasionally abort unnecessarily.
Integrated positioning algorithm based on GPS/WLAN
Authors: Li Dengao , Wei Zheng , Zhao Jumin , Cheng Junbing , Ma Zhiying
Published: April 2019

In complex urban environment, GPS signals are susceptible to occlusion and interference; the positioning accuracy will be reduced or even impossible to locate. Today, Wireless Local Area Network (WLAN) localization technology can effectively supplement the blind spot of GPS signals. However, due to the instability of received signal strength (RSS), the positioning accuracy of WLAN is seriously affected. To solve the aforementioned problems, a GPS/WLAN integrated location algorithm based on particle filter is proposed. In our method, the federated Kalman filter is used to fuse the location information of GPS and WLAN, and then the important sampling function of the particle filter is generated by the fusion result. The updating of the particle weights is accomplished by the results of federated Kalman filter and map information. With the complementary characteristics of GPS and WLAN positioning technology, the experimental results show that our algorithm can effectively improves the coverage rate of GPS and the positioning accuracy of pedestrians in complex urban environment. Compared with GPS and WLAN single system and traditional fusion algorithm, the positioning accuracy of the proposed algorithm is significantly improved.
In Situ Synthesis of NiCoP Nanoparticles Supported on Reduced Graphene Oxide for the Catalytic Hydrolysis of Ammonia Borane
Authors: Yang Chenlu , Men Yana , Xu Yuezhi , Liang Lijing , Cai Ping , Luo Wei
Published: April 2019

Developing highly efficient and stable noble‐metal‐free catalysts toward catalytic hydrolysis of ammonia borane (AB) for hydrogen storage is highly desirable, but still remains challenging. We report a simple and in situ co‐reduction approach to synthesize bimetallic NiCoP nanoparticles (NPs) supported on reduced graphene oxide (rGO). Thanks to the strong electronic interaction between Ni, Co, and P, the as‐synthesized Co89.8Ni10.2P11.7/rGO catalyst exhibits superior catalytic performance towards hydrolysis of AB, with the turnover frequency value (TOF) of 18.6 min−1, which is about 2.5 times higher than that of NiCo/rGO.
A Semitransparent Nitride Photoanode Responsive up to λ=600 nm Based on a Carbon Nanotube Thin Film Electrode
Authors: Akagi Daijiro , Kageshima Yosuke , Hashizume Yuta , Aoi Shigeki , Sasaki Yutaka , Kaneko Hiroyuki , Higashi Tomohiro , Hisatomi Takashi , Katayama Masao , Minegishi Tsutomu , Noda Suguru , Domen Kazunari
Published: April 2019

The development of semitransparent photoanodes is required for the construction of tandem photoelectrochemical (PEC) water splitting cells incorporating photocathodes. However, the poor stability of transparent conductive oxides at high temperatures hampers the growth of non‐oxide photoanodes with intense visible light absorption. In this work, semitransparent Ta3N5 thin film photoanodes were prepared on quartz glass substrates coated with carbon nanotubes (CNTs) by sputtering and thermal nitridation. This process makes use of the high thermal and chemical stability as well as the tunable conductivity and transmittance of CNT substrates. The photoanodic current produced by these Ta3N5 photoanodes at negative potentials is also enhanced by surface modification with Mg species. Conductive semitransparent CNT substrates such as these will assist in the development of new tandem PEC cells for water splitting.
A double‐blind, placebo‐controlled study of vortioxetine in the treatment of binge‐eating disorder
Authors: Grant Jon E. , Valle Stephanie , Cavic Elizabeth , Redden Sarah A. , Chamberlain Samuel R.
Published: April 2019

Background

Binge‐eating disorder (BED) is associated with impaired quality of life and has a number of untoward public health associations. There are few established pharmacological treatments for BED, and available options are not suitable for all individuals. Vortioxetine is a recently developed pharmacological agent with effects on the serotonergic but also other neurochemical systems, which has yet to be evaluated in this context.

Method

Eighty adults with BED were recruited for a double‐blind, placebo‐controlled study. Participants received 12‐week treatment with vortioxetine (10 mg/day for 1 week, then increasing to 20 mg/day) or placebo in a parallel design. The primary efficacy outcome measures were binge‐eating frequency and weight. Safety data were collected. Effects of active versus placebo treatment were characterized using linear repeated measures models.

Results

Both vortioxetine and placebo treatment were associated with significant reductions in binge‐eating frequency. Vortioxetine did not differentiate significantly from placebo on any efficacy measure. Frequency of adverse events did not differ between groups.

Discussion

Vortioxetine was not more effective than placebo in the treatment of BED. The ability to detect pharmacological treatment benefit may have been hindered by the relatively high placebo response and drop out. Future work should seek to better understand and predict placebo response in BED, with a view to more targeted treatment interventions and, potentially, sample enrichment.
Exploring the community phylogenetic structure along the slope aspect of subalpine meadows in the eastern Qinghai–Tibetan Plateau, China
Authors: Liu Minxia , Che Yingdi , Jiao Jiao , Li Lirong , Jiang Xiaoxuan
Published: April 2019

Exploring the community assembly has been important for explaining the maintenance mechanisms of biodiversity and species coexistence, in that it is a central issue in community ecology. Here, we examined patterns of the community phylogenetic structure of the subalpine meadow plant community along the slope gradient in the Qinghai–Tibetan Plateau of China. We surveyed all species and constructed the phylogenetic tree of the plant community based on data from the Angiosperm Phylogeny Group III. We selected the net relative index (NRI) and evaluated the community phylogenetic structure along the five slope plants communities. We found that the phylogenetic structure varied from phylogenetic clustering to phylogenetic overdispersion with the slope aspect from north to south. In the north slope, the community phylogenetically cluster indicated that the limiting similarity played a leading role in the community assembly and the maintenance of biodiversity. Community phylogenetic overdispersion in the east, southeast, and south slopes indicated that habitat filtration was the driving force for community assembly. The NRI index of the northeast slope was close to zero, implying random dispersion. But it may be driven by the neutral process or limiting similarity, in that the community assembly process was the result of a combination of several ecological factors and thus required further study.
Comparative genomics of 10 newCaenorhabditisspecies
Authors: Stevens Lewis , Félix Marie-Anne , Beltran Toni , Braendle Christian , Caurcel Carlos , Fausett Sarah , Fitch David , Frézal Lise , Gosse Charlie , Kaur Taniya , Kiontke Karin , Newton Matthew D. , Noble Luke M. , Richaud Aurélien , Rockman Matthew V. , Sudhaus Walter , Blaxter Mark
Published: April 2019

The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for 10 new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We reveal extensive variation in genome size and investigate the molecular processes that underlie this variation. We show unexpected complexity in the evolutionary history of key developmental pathway genes. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.
Induction therapy in acute myeloid leukemia: Is it time to put aside standard 3 + 7?
Authors: Ferrara Felicetto , Vitagliano Orsola
Published: April 2019

For more than 30 years after its introduction, the combination of an anthracycline, usually daunorubicin, given for 3 days with continuous infusion of cytarabine for 7 days (3 + 7) has been the standard induction regimen for patients with acute myeloid leukemia (AML). In the last decade, there has been a progressive understanding of the molecular pathogenesis of the disease, which has led to discovery of potential therapeutic targets, resulting in selective treatment approaches aimed at rational and personalized treatment strategies. In the last 2 years, different new agents for AML have become widely available for newly diagnosed or relapsing/refractory patients, and others are object of clinical investigation. For most treatment‐naïve patients, it is now evident that standard 3 + 7 represents undertreatment in that the addition of new compounds results in better quality of response and improved survival. Hopefully, within few years, no patients with AML will be given standard 3 + 7 in the daily practice and a personalized approach targeting driving mutations will be widely applied.
Visualizing astrocytes in the deep mouse brain in vivo
Authors: Liu Hongji , Wang Jiaqi , Zhuang Ziwei , He Jiexing , Wen Wenhui , Qiu Ping , Wang Ke
Published: April 2019

Astrocytes play a key role in the central nervous system. However, methods of visualizing astrocytes in the deep brain in vivo have been lacking. 3‐photon fluorescence imaging of astrocytes labeled by sulforhodamine 101 (SR101) is demonstrated in deep mouse brain in vivo. Excitation wavelength selection was guided by wavelength‐dependent 3‐photon action cross section (ησ
3) measurement of SR101. 3‐photon fluorescence imaging of the SR101‐labeled vasculature enabled an imaging depth of 1340‐μm into the mouse brain. This justifies the deep imaging capability of the technique and indicates that the imaging depth is not determined by the signal‐to‐background ratio limit encountered in 2‐photon fluorescence imaging. Visualization of astrocytes 910 μm below the surface of the mouse brain in vivo is demonstrated, 30% deeper than that using 2‐photon fluorescence microscopy. Through quantitative comparison of the signal difference between the SR101‐labeled blood vessels and astrocytes, the challenges of visualizing astrocytes below the white matter is further elucidated.
Association between the flap endonuclease 1 gene polymorphisms and cancer susceptibility: An updated meta‐analysis
Authors: Moazeni‐Roodi Abdolkarim , Ghavami Saeid , Ansari Hossein , Hashemi Mohammad
Published: April 2019

Flap endonuclease 1 (FEN1) has emerged as an important enzyme in the maintenance of genomic instability and preventing carcinogenesis. The relationship between FEN1 −69G>A (rs174538)+4150G>T (rs4246215) polymorphisms and cancer susceptibility has been reported; however, results were inconclusive. In the present study, a meta‐analysis of data from eligible reports was carried out to summarize the possible relationship between FEN1 polymorphisms and cancer risk. A total of 11 articles, including 20 studies with 7366 cases and 9028 controls and 18 studies with 6649 cases and 8325 controls for FEN1 rs174538 and FEN1 rs4246215 polymorphisms, respectively, were recruited for meta‐analysis. Overall, meta‐analyses showed that FEN1 rs174538 and rs4246215 polymorphisms are significantly associated with the decreased risk of cancer. The stratified analysis proposed that both variants were associated with protection against gastrointestinal cancer, breast cancer, hepatocellular cancer, esophageal cancer, gastric cancer, colorectal cancer, and lung cancer. In conclusion, this meta‐analysis revealed an association between FEN1 polymorphisms and cancer risk. Additional studies in a larger study population that include subjects from a variety of ethnicities are warranted to further verify our findings.
Weighted gene coexpression network analysis identifies specific transcriptional modules and hub genes related to intramuscular fat traits in chicken breast muscle
Authors: Li Guoxi , Zhao Yinli , Li Yuanfang , Chen Yi , Jin Wenjiao , Sun Guirong , Han Ruili , Tian Yadong , Li Hong , Kang Xiangtao
Published: April 2019

Intramuscular fat (IMF) traits are important factors that influence meat quality. However, the molecular regulatory mechanisms that underlie this trait in chickens are still poorly understood at the gene coexpression level. Here, we performed a weighted gene coexpression network analysis between IMF traits and transcriptome profile in breast muscle in the Chinese domestic Gushi chicken breed at 6, 14, 22, and 30 weeks. A total of 26 coexpressed gene modules were identified. Six modules, which included the dark gray, purple, cyan, pink, light cyan, and blue modules, showed a significant positive correlation (P < 0.05) with IMF traits. The strongest correlation was observed between the dark gray module and IMF content (r = 0.85; P = 4e‐04) and between the blue module and different fatty acid content (r = 0.87~0.91; P = 5e‐05~2e‐04). Enrichment analysis showed that the enrichment of biological processes, such as fatty acid metabolic process, fat cell differentiation, acylglycerol metabolic process, and glycerolipid metabolism were significantly different in the six modules. In addition, the 32, 24, 4, 7, 6, and 25 hub genes were identified from the blue, pink, light cyan, cyan, dark gray, and purple modules, respectively. These hub genes are involved in multiple links to fatty acid metabolism, phospholipid metabolism, cholesterol metabolism, diverse cellular behaviors, and cell events. These results provide novel insights into the molecular regulatory mechanisms for IMF‐related traits in chicken and may also help to uncover the formation mechanism for excellent meat quality traits in local breeds of Chinese chicken.
Upregulation of circular RNA circ_0034642 indicates unfavorable prognosis in glioma and facilitates cell proliferation and invasion via the miR‐1205/BATF3 axis
Authors: Yi Chao , Li Hongbin , Li Dan , Qin Xiangying , Wang Jun , Liu Yang , Liu Zengliang , Zhang Jiewen
Published: April 2019

Accumulating studies demonstrate the critical role of circular RNAs (circRNAs) in the pathogenesis of various types of cancers. Previously, hsa_circ_0034642 has been found elevated in glioma tissues compared with the normal tissues, as proved by high‐throughput microarray. We further investigated its expression level in 52 paired tissues and different glioma cell lines by quantitative reverse transcription‐polymerase chain reaction. In addition, Fisher's exact test, Kaplan‐Meier curves, and Cox analyses were performed to elucidate the clinical significance of hsa_circ_0034642. For the part of functional assays, gain/loss‐of‐function assays were conducted to measure cell growth, apoptosis, and metastatic properties affected by hsa_circ_0034642. Furthermore, the mechanisms of hsa_circ_0034642 were investigated by dual‐luciferase reporter assays. As the results demonstrated, hsa_circ_0034642 was boosted in glioma tissues and cells. Overexpression of hsa_circ_0034642 was associated with clinical severity and poor prognosis. What is more, elevated hsa_circ_0034642 strikingly facilitated cell proliferation, migratory and invasive capacities, and decreased apoptotic cells. Mechanistically, hsa_circ_0034642 sponges miR‐1205. miR‐1205 regulates BATF3 level through targeting its 3′‐untranslated region. In summary, hsa_circ_0034642 might play a key role in this malignancy.
Description of noncovalent interactions involving π‐system with high precision: An assessment of RPA, MP2, and DFT‐D methods
Authors: Su He , Wang Hui , Wang Hongyan , Lu Yunxiang , Zhu Zhengdan
Published: April 2019

Efficient approaches with high precision are essential for understanding the formation and stability of noncovalent interaction complexes. Here, 21 noncovalent interaction complexes involving π‐system are selected and grouped in three subsets according to ETS–NOCV method: dispersion‐dominated, electrostatic‐dominated, and mixed. We mainly focus on examining the performance of random‐phase approximation (RPA) on these π systems. The tested RPA‐based method includes standard RPA and its variants including the related single excitations (SEs), renormalized single excitations (rSEs), second‐order screened exchange (SOSEX), and the renormalized second‐order perturbation theory (rPT2). The routine second‐order Møller–Plesset perturbation theory (MP2) and three popular DFT‐D functionals (M06‐2X‐D3, ωB97XD, and PBE‐D3(BJ)) are also assessed for comparison. In this work, besides the calculation of interaction energies at Dunning‐type aug‐cc‐pVDZ and aug‐cc‐pVTZ basis set, we also present a larger database of interaction energies calculated using MP2 and RPA methods with Dunning‐type aug‐cc‐pVQZ basis set. An accurate CCSD(T)/CBS scheme is used to provide benchmark database. In addition to the high‐level results, we also provide potential energy surfaces (PES) of different interaction type. Among all the tested methods, MP2 has a satisfactory performance on electrostatic‐dominated and mixed‐type systems, except for dispersion‐dominated systems. DFT‐D functionals, especially ωB97XD functional, has a balanced performance across all the tested systems. Importantly, for RPA‐based methods, the calculation accuracy can be dramatically improved by taking into account SE or exchange effects, especially in the mixed complexes. We conclude that rPT2 among all the test RPA‐based methods gives an overall satisfactory performance across different interaction types. © 2019 Wiley Periodicals, Inc.
PE_PGRS62 promotes the survival of Mycobacterium smegmatis within macrophages via disrupting ER stress‐mediated apoptosis
Authors: Long Quanxin , Xiang Xiaohong , Yin Qingqin , Li Shuangjiang , Yang Wenmin , Sun Hang , Liu Qi , Xie Jianping , Deng Wanyan
Published: April 2019

Mycobacterium tuberculosis, the leading causative agent of tuberculosis, remains one of the most deadly infectious pathogens. PE_PGRS proteins become a new focus as their species specificity in mycobacteria, especially in pathogenic mycobacteria. Despite intensive research, PE_PGRS proteins are still a mysterious aspect of mycobacterial pathogenesis with unknown mechanism. Herein, we focused on a PE_PGRS member from M. tuberculosis, PE_PGRS62, characterized by a surface‐exposed protein function in disrupting phagolysosome maturation. Expression of PE_PGRS62 in Mycobacterium smegmatis, a nonpathogenic species naturally deficient in PE_PGRS genes, resulted in enhanced resistance to various in vitro stresses and cellular survival in macrophage. As a consequence, the cytokine profiles of macrophage were disturbed and cell apoptosis were inhibited via decreasing endoplasmic reticulum stress response.
New developmental syndromes: Understanding the family experience
Authors: Inglese Cara N. , Elliott Alison M. ,   CAUSES Study, Lehman Anna
Published: April 2019

Increased application of next generation sequencing has led to the discovery of a multitude of new neurodevelopmental syndromes, contributing to an increased diagnostic rate for exome sequencing from 25% originally to 40% currently. Owing to the recent recognition of these syndromes, as well as the types of large‐scale studies (with limited phenotype information) often making these discoveries, these disorders may be poorly characterized clinically. As a result there is very limited information and disorder‐specific support available to patients and families. We used a qualitative approach to explore how families experience a diagnosis of a new syndrome. We conducted semi‐structured telephone interviews with parents and adult siblings of children who received a diagnosis of a new syndrome after whole exome sequencing (WES) performed through a translational research study. The interviews were recorded, transcribed verbatim, and transcripts were analyzed using grounded theory methods. Analysis of the 12 interviews revealed that a lack of information about the child's condition continues to play a large role in these families' experiences even after diagnosis. Almost all (92%) participants expressed ongoing uncertainty about their child's health and future. Most (83%) participants were interested in identifying other families with the same syndrome, which was related to both social support and seeking of information. Interestingly, 33% of participants worried about the child's risk for cancer due to their syndrome. Our results highlight some of the needs of families of children with new syndromes, and emphasize important issues care providers should address in pre‐ and post‐test genetic counseling for WES and whole genome sequencing.
Synthesis, 3H‐labelling and in vitro evaluation of a substituted dipiperidine alcohol as a potential ligand for chemokine receptor 2
Authors: Artelsmair Markus , Miranda‐Azpiazu Patricia , Kingston Lee , Bergare Jonas , Schou Magnus , Varrone Andrea , Elmore Charles S.
Published: April 2019

The immune system is implicated in the pathology of neurodegenerative disorders. The C‐C chemokine receptor 2 (CCR2) is one of the key targets involved in the activation of the immune system. A suitable ligand for CCR2 could be a useful tool to study immune activation in central nervous system (CNS) disorders. Herein, we describe the synthesis, tritium radiolabelling, and preliminary in vitro evaluation in post‐mortem human brain tissue of a known potent small molecule antagonist for CCR2. The preparation of a tritium‐labelled analogue for the autoradiography (ARG) study gave rise to an intriguing and unexpected side reaction profile through a novel amination of ethanol and methanol in the presence of tritium. After successful preparation of the tritiated radioligand, in vitro ARG measurements on human brain sections revealed nonspecific binding properties of the selected antagonist in the CNS.
Solidification of floating organic droplet microextraction for determination of seven insecticides in fruit juice, vegetables and agricultural runoff using gas chromatography with flame ionization and mass spectrometry detection
Authors: Hoisang Watcharaporn , Nacapricha Duangjai , Wilairat Prapin , Tiyapongpattana Warawut
Published: April 2019

Liquid microextraction employing solidification of the floating organic droplet, with vortexing and heating to optimize extraction efficiency, was developed for the determination of seven insecticides in fruit juice, vegetables, and agricultural runoff water. The extracts were analyzed by gas chromatography with both flame ionization and mass spectrometry detection for the determination of chlorpyrifos, prothiofos, profenofos, ethion, λ‐cyhalothrin, permethrin, and cypermethrin, respectively. Using 20 μL of 1‐undecanol in 10 mL of aqueous solution containing 1% w/v sodium chloride provided preconcentration factor of 500. The enrichment factor of the analytes was in the range of 355 to 509 with extraction recovery >71%. The linearity ranges were 4–200 μg/kg for gas chromatography with flame ionization detection and 1–100 μg/kg for gas chromatography with mass spectrometry, with limits of detection ranging from 0.04 to 1.2 μg/kg, which are lower than the international maximum residue limits for vegetables and fruit juice. Intra‐day and inter‐day precisions are less than 5.4 and 7.0% relative standard deviation, respectively. The method was successfully applied to the determination of the seven insecticides in samples of vegetables, fruit juice and agricultural runoff, with recoveries ranging from 61.7 to 120.8%. The extraction method is simple, efficient and environmentally friendly.