bluuebunny/crossref_metadata_2025 huggingface dataset:
An Advanced Deep Learning Approach for Ki-67 Stained Hotspot Detection and Proliferation Rate Scoring for Prognostic Evaluation of Breast Cancer
Authors: Saha Monjoy , Chakraborty Chandan , Arun Indu , Ahmed Rosina , Chatterjee Sanjoy
Published: June 2017

Being a non-histone protein, Ki-67 is one of the essential biomarkers for the immunohistochemical assessment of proliferation rate in breast cancer screening and grading. The Ki-67 signature is always sensitive to radiotherapy and chemotherapy. Due to random morphological, color and intensity variations of cell nuclei (immunopositive and immunonegative), manual/subjective assessment of Ki-67 scoring is error-prone and time-consuming. Hence, several machine learning approaches have been reported; nevertheless, none of them had worked on deep learning based hotspots detection and proliferation scoring. In this article, we suggest an advanced deep learning model for computerized recognition of candidate hotspots and subsequent proliferation rate scoring by quantifying Ki-67 appearance in breast cancer immunohistochemical images. Unlike existing Ki-67 scoring techniques, our methodology uses Gamma mixture model (GMM) with Expectation-Maximization for seed point detection and patch selection and deep learning, comprises with decision layer, for hotspots detection and proliferation scoring. Experimental results provide 93% precision, 0.88% recall and 0.91% F-score value. The model performance has also been compared with the pathologists’ manual annotations and recently published articles. In future, the proposed deep learning framework will be highly reliable and beneficial to the junior and senior pathologists for fast and efficient Ki-67 scoring.
Motor errors lead to enhanced performance in older adults
Authors: Levy-Tzedek S.
Published: June 2017

Young individuals make larger and faster forearm movements when visual feedback about the movement is not available, compared to when it is. We set out to test whether this behavior persists with aging. We tested 40 participants, 20 in each age group – young and old, on a task that required making rhythmic movements of the forearm with and without visual feedback. Surprisingly, we found that older adults increased the speed and the amplitude of their movements to an even greater extent than did the young adults. Furthermore, we found that the increase in speed and amplitude during the non-vision trial segments improved their performance on the task, and they were able to leverage the change in these movement parameters (speed and amplitude) to improve their performance during subsequent trial segments that did include visual feedback. The improvement in accuracy on the task was accompanied by a decrease in path variability. The results indicate that older adults can adapt their movement parameters to enhance performance following a motor perturbation. They further suggest that motor variability in old age can be advantageous under certain circumstances.
Role of the stability of charge ordering in exchange bias effect in doped manganites
Authors: Dasgupta Papri , Das Kalipada , Pakhira Santanu , Mazumdar Chandan , Mukherjee S. , Mukherjee S. , Poddar A.
Published: June 2017

In this work we have carried out an elaborate study on the magnetic properties and investigated the exchange bias phenomena of some charge-ordered (CO) manganites. The detailed study of Sm1−xCaxMnO3(x = 0.5, 0.55, 0.6, 0.65, 0.7) compounds shows that Sm0.4Ca0.6MnO3, which is the most robust charge ordered material studied here, shows significantly large exchange bias field (HE) as compared to the other compounds. Our experimental results and analysis indicate that TCO, which reflects the stability of the charge-ordered state, is one of the key parameters for the exchange bias effect. Similar behaviour is found in other rare-earth analogues,viz., La1−xCaxMnO3and Pr1−xCaxMnO3compounds as well. We also found that with increasing stability of CO states in Sm1−xCaxMnO3compounds, HEenhances due to increase in number and reduction in size of ferromagnetic clusters.
Chronic vitamin D deficiency induces lung fibrosis through activation of the renin-angiotensin system
Authors: Shi Yongyan , Liu Tianjing , Yao Li , Xing Yujiao , Zhao Xinyi , Fu Jianhua , Xue Xindong
Published: June 2017

Pulmonary fibrosis, which influences lung function and exacerbates a patient’s condition, is the ultimate stage of many lung diseases. Vitamin D deficiency is associated with pulmonary fibrosis and impaired lung function, but the underlying mechanism has not yet been fully elucidated. Moreover, vitamin D deficiency may cause over-activation of the renin-angiotensin system (RAS), which aggravates extracellular matrix (ECM) deposition and lung fibrosis. This study aims to investigate the effect of chronic vitamin D deficiency on lung fibrosis in otherwise healthy mice and to explore the role of RAS in this process. Mice were depleted of vitamin D through diet control and were compared with healthy subjects. Chronic vitamin D deficiency destructs lung structures, impairs lung development and stimulates ECM deposition. RAS components are also found to increase. These effects seem to worsen with prolonged vitamin D deficiency. By giving RAS blockers, these changes can be largely rescued. However, a smooth muscle relaxant whose regulatory effect on blood pressure is independent of RAS does not show similar effects. This study demonstrated that chronic vitamin D deficiency may induce RAS activation, which subsequently stimulates the expression of profibrotic factors and activates the fibrotic cascade. This profibrotic effect of RAS is independent of elevated blood pressure.
Effect of hydrogen on semiconductive properties of passive film on ferrite and austenite phases in a duplex stainless steel
Authors: Guo L. Q. , Qin S. X. , Yang B. J. , Liang D. , Qiao L. J.
Published: June 2017

Hydrogen effect on semiconductivity and compositions of passive films formed on ferrite and austenite phases in a duplex stainless steel were investigated by current sensing atomic force microscopy and X-ray photoelectron spectroscopy. It is demonstrated that hydrogen significantly increases the conductivity of passive film due to the increase of OH−/O2− ratio. The passive film on austenite has higher conductivity than that on ferrite after hydrogen charging due to more hydrogen in austenite. The presence of hydrogen causes an inversion of conductivity type of passive film from p-type to n-type, attributed to the chemical composition change.
Visuotactile integration modulates motor performance in a perceptual decision-making task
Authors: Grechuta Klaudia , Guga Jelena , Maffei Giovanni , Rubio Ballester Belen , Verschure Paul F. M. J.
Published: June 2017

Body ownership is critically dependent on multimodal integration as for instance revealed in the Rubber Hand Illusion (RHI) and a number of studies which have addressed the neural correlates of the processes underlying this phenomenon. Both experimental and clinical research have shown that the structures underlying body ownership seem to significantly overlap with those of motor control including the parietal and ventral premotor cortices, Temporal Parietal Junction (TPJ) and the insula. This raises the question of whether this structural overlap between body ownership and motor control structures is of any functional significance. Here, we investigate the specific question of whether experimentally induced ownership over a virtual limb can modulate the performance of that limb in a simple sensorimotor task. Using a Virtual reality (VR) environment we modulate body ownership in three experimental conditions with respect to the (in)congruence of stimulus configurations. Our results show that the degree of ownership directly modulates motor performance. This implies that body ownership is not exclusively a perceptual and/or subjective multimodal state but that it is tightly coupled to systems for decision-making and motor control.
Single-stranded RNA viruses infecting the invasive Argentine ant, Linepithema humile
Authors: Gruber Monica A. M. , Cooling Meghan , Baty James W. , Buckley Kevin , Friedlander Anna , Quinn Oliver , Russell Jessica F. E. J. , Sébastien Alexandra , Lester Philip J.
Published: June 2017

Social insects host a diversity of viruses. We examined New Zealand populations of the globally widely distributed invasive Argentine ant (Linepithema humile) for RNA viruses. We used metatranscriptomic analysis, which identified six potential novel viruses in the Dicistroviridae family. Of these, three contigs were confirmed by Sanger sequencing as Linepithema humile virus-1 (LHUV-1), a novel strain of Kashmir bee virus (KBV) and Black queen cell virus (BQCV), while the others were chimeric or misassembled sequences. We extended the known sequence of LHUV-1 to confirm its placement in the Dicistroviridae and categorised its relationship to closest relatives, which were all viruses infecting Hymenoptera. We examined further for known viruses by mapping our metatranscriptomic sequences to all viral genomes, and confirmed KBV, BQCV, LHUV-1 and Deformed wing virus (DWV) presence using qRT-PCR. Viral replication was confirmed for DWV, KBV and LHUV-1. Viral titers in ants were higher in the presence of honey bee hives. Argentine ants appear to host a range of’ honey bee’ pathogens in addition to a virus currently described only from this invasive ant. The role of these viruses in the population dynamics of the ant remain to be determined, but offer potential targets for biocontrol approaches.
Enhanced derivation of human pluripotent stem cell-derived cortical glutamatergic neurons by a small molecule
Authors: Cao Shi-Ying , Hu Yao , Chen Cheng , Yuan Fang , Xu Min , Li Qi , Fang Kai-Heng , Chen Yaoyu , Liu Yan
Published: June 2017

Human pluripotent stem cells (hPSCs) play important role in studying the function of human glutamatergic neurons and related disease pathogenesis. However, the current hPSC-derived cortical system produced a significant number of inhibitory GABAergic neurons that reduced the purity of excitatory neurons. In this study, we established a robust hPSC-derived cortical neurogenesis system by applying the SHH inhibitor cyclopamine. Cyclopamine specified the dorsal cortical fate in a dose-dependent manner and enhanced the generation of cortical glutamatergic neurons, expressing PAX6, TBR1, TBR2, CTIP2, SATB2, and vesicular glutamate transporters (vGLUT). In contrast, the ventral patterning was inhibited and the GABAergic neurons were significantly reduced to 12% with the treatment of cyclopamine. In addition, we applied our current method to generate trisomy 21 iPSC-derived glutamatergic neurons that showed a robust reduction of vesicular glutamate transporters in the glutamatergic neurons with trisomy 21, revealing the developmental deficits in cortical glutamatergic neurons. Our method enriched the generation of cortical glutamatergic neurons which may facilitate the study of human neurological diseases and cell therapy.
Effective Adsorption and Removal of Phosphate from Aqueous Solutions and Eutrophic Water by Fe-based MOFs of MIL-101
Authors: Xie Qiying , Li Yan , Lv Zhaoling , Zhou Hang , Yang Xiangjun , Chen Jing , Guo Hong
Published: June 2017

Although many efforts have been devoted to the adsorptive removal of phosphate from aqueous solutions and eutrophic water, it is still highly desirable to develop novel adsorbents with high adsorption capacities. In this study, Fe-based metal-organic frameworks (MOFs), MIL-101 and NH2-MIL-101, are fabricated through a general facile strategy. Their performance as an adsorbent for phosphate removal is investigated. Experiments are performed to study the effects of various factors on the phosphate adsorption, including adsorbent dosage, contact time and co-existing ions. Both MIL-101(Fe) and NH2-MIL-101(Fe) show highly effective removal of phosphates from aqueous solutions, and the concentration of phosphates decrease sharply from the initial 0.60 mg·L−1 to 0.045 and 0.032 mg·L−1, respectively, within just 30 min of exposure. The adsorption kinetics and adsorption isotherms reveal that NH2-MIL-101(Fe) has higher adsorption capacity than MIL-101(Fe) possibly due to the amine group. Furthermore, the Fe-based MOFs also exhibit a high selectivity towards phosphate over other anions such as chloride, bromide, nitrate and sulfate. Particularly, the prepared Fe-based MIL-101 materials are also capable of adsorbing phosphate in an actual eutrophic water sample and display better removal effect.
Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China
Authors: Zhou Jing , Jiang Xin , Wei Dan , Zhao Baisuo , Ma Mingchao , Chen Sanfeng , Cao Fengming , Shen Delong , Guan Dawei , Li Jun
Published: June 2017

Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.
Differences in pharmacodynamic responses to rocuronium in normal or injured orbicularis oris are associated with expression of acetylcholine receptor subunits
Authors: Huang Yong , Xing Yian , Wang Hong , Chen Lianhua , Li Shitong
Published: June 2017

Previous research has indicated that differences in sensitivities to muscle relaxants exist between facial nerve- and somatic nerve-innervated muscles. Here, we report that the 50% inhibitory concentration (IC50) values for rocuronium were significantly larger in the normal orbicularis oris than those in the gastrocnemius. Increased IC50 values and reduced twitch tension were observed after facial nerve injury. The normal orbicularis oris had a smaller muscle fiber cross-sectional area (CSA) and a larger ratio of endplate surface area (ESA) to muscle fiber CSA (ESA/CSA), but no difference was found in the density of nicotinic acetylcholine receptor (nAChR) subunits on endplates between normal orbicularis oris and gastrocnemius. Expression of the nAChR α1, β1, δ, ε, and γ subunits increased significantly on the postsynaptic membranes of endplates and extra-junctional muscle membranes after facial nerve injury. Our results suggest that facial nerve-innervated muscle was less sensitive than somatic nerve-innervated muscle, and the mechanisms underlying this result may be related to muscle fiber CSA and the ESA/CSA ratio, but not to the density of nAChR subunits on endplates. Facial nerve injury caused the resistance to neuromuscular blockers and reduced twitch tension, which was related to qualitative, quantitative, and locational changes in nAChR subunits.
WSMD: weakly-supervised motif discovery in transcription factor ChIP-seq data
Authors: Zhang Hongbo , Zhu Lin , Huang De-Shuang
Published: June 2017

Although discriminative motif discovery (DMD) methods are promising for eliciting motifs from high-throughput experimental data, due to consideration of computational expense, most of existing DMD methods have to choose approximate schemes that greatly restrict the search space, leading to significant loss of predictive accuracy. In this paper, we propose Weakly-Supervised Motif Discovery (WSMD) to discover motifs from ChIP-seq datasets. In contrast to the learning strategies adopted by previous DMD methods, WSMD allows a “global” optimization scheme of the motif parameters in continuous space, thereby reducing the information loss of model representation and improving the quality of resultant motifs. Meanwhile, by exploiting the connection between DMD framework and existing weakly supervised learning (WSL) technologies, we also present highly scalable learning strategies for the proposed method. The experimental results on both real ChIP-seq datasets and synthetic datasets show that WSMD substantially outperforms former DMD methods (including DREME, HOMER, XXmotif, motifRG and DECOD) in terms of predictive accuracy, while also achieving a competitive computational speed.
MatureP: prediction of secreted proteins with exclusive information from their mature regions
Authors: Orfanoudaki Georgia , Markaki Maria , Chatzi Katerina , Tsamardinos Ioannis , Economou Anastassios
Published: June 2017

More than a third of the cellular proteome is non-cytoplasmic. Most secretory proteins use the Sec system for export and are targeted to membranes using signal peptides and mature domains. To specifically analyze bacterial mature domain features, we developed MatureP, a classifier that predicts secretory sequences through features exclusively computed from their mature domains. MatureP was trained using Just Add Data Bio, an automated machine learning tool. Mature domains are predicted efficiently with ~92% success, as measured by the Area Under the Receiver Operating Characteristic Curve (AUC). Predictions were validated using experimental datasets of mutated secretory proteins. The features selected by MatureP reveal prominent differences in amino acid content between secreted and cytoplasmic proteins. Amino-terminal mature domain sequences have enhanced disorder, more hydroxyl and polar residues and less hydrophobics. Cytoplasmic proteins have prominent amino-terminal hydrophobic stretches and charged regions downstream. Presumably, secretory mature domains comprise a distinct protein class. They balance properties that promote the necessary flexibility required for the maintenance of non-folded states during targeting and secretion with the ability of post-secretion folding. These findings provide novel insight in protein trafficking, sorting and folding mechanisms and may benefit protein secretion biotechnology.
Aerobic biogenesis of selenium nanoparticles by Enterobacter cloacae Z0206 as a consequence of fumarate reductase mediated selenite reduction
Authors: Song Deguang , Li Xiaoxiao , Cheng Yuanzhi , Xiao Xiao , Lu Zeqing , Wang Yizhen , Wang Fengqin
Published: June 2017

In the present study, we examined the ability of Enterobacter cloacae Z0206 to reduce toxic sodium selenite and mechanism of this process. E. cloacae Z0206 was found to completely reduce up to 10 mM selenite to elemental selenium (Se°) and form selenium nanoparticles (SeNPs) under aerobic conditions. The selenite reducing effector of E. cloacae Z0206 cell was to be a membrane-localized enzyme. iTRAQ proteomic analysis revealed that selenite induced a significant increase in the expression of fumarate reductase. Furthermore, the addition of fumarate to the broth and knockout of fumarate reductase (frd) both significantly decreased the selenite reduction rate, which revealed a previously unrecognized role of E. cloacae Z0206 fumarate reductase in selenite reduction. In contrast, glutathione-mediated Painter-type reactions were not the main pathway of selenite reducing. In conclusion, E. cloacae Z0206 effectively reduced selenite to Se° using fumarate reductase and formed SeNPs; this capability may be employed to develop a bioreactor for treating Se pollution and for the biosynthesis of SeNPs in the future.
Analysis of the brain palmitoyl-proteome using both acyl-biotin exchange and acyl-resin-assisted capture methods
Authors: Edmonds Matthew J. , Geary Bethany , Doherty Mary K. , Morgan Alan
Published: June 2017

Palmitoylation is a reversible post-translational protein modification in which palmitic acid is added to cysteine residues, allowing association with different cellular membranes and subdomains. Recently, techniques have been developed to identify palmitoylation on a proteome-wide scale in order to reveal the full cellular complement of palmitoylated proteins. However, in the studies reported to date, there is considerable variation between the sets of identified palmitoyl-proteins and so there remains some uncertainty over what constitutes the definitive complement of palmitoylated proteins even in well-studied tissues such as brain. To address this issue, we used both acyl-biotin exchange and acyl-resin-assisted capture approaches using rat brain as a common protein source. The palmitoyl-proteins identified from each method by mass spectrometry were then compared with each other and previously published studies. There was generally good agreement between the two methods, although many identifications were unique to one method, indicating that at least some of the variability in published palmitoyl proteomes is due to methodological differences. By combining our new data with previous publications using mammalian cells/tissues, we propose a high confidence set of bona fide palmitoylated proteins in brain and provide a resource to help researchers prioritise candidate palmitoyl-proteins for investigation.
Vertical crustal motions across Eastern Tibet revealed by topography-dependent seismic tomography
Authors: Zhang Xinyan , Wang Yanghua , Gao Rui , Xu Tao , Bai Zhiming , Tian Xiaobo , Li Qiusheng
Published: June 2017

Using a topography-dependent tomographic scheme, the seismic velocity structure of the Eastern Tibetan Plateau, including the uplifted Longmenshan (LMS) orogenic belt, is accurately imaged in spite of the extreme topographic relief in the LMS region and thick sedimentary covers in the neighbouring Sichuan Basin. The obtained image shows a high-resolution upper crustal structure on a 500 km-long profile that is perpendicular to the LMS. The image clearly shows that the crystalline basement was uplifted within the LMS orogenic belt, and that the neighbouring Songpan-Ganzi Terrane was covered by a thick flysch belt, with evidence of near-surface thrust faults caused by convergence between Eastern Tibet and the Sichuan Basin. The indication that the lower crust beneath the LMS was folded and pushed upwards and the upper crust was removed by exhumation, supports the concept of a lower crustal channel flow beneath Eastern Tibet. The image also reveals that the destructive Wenchuan earthquake of year 2008 occurred in the upper crust, directly at the structural discontinuity between Eastern Tibet Plateau and the Sichuan Basin.
New noninvasive index for predicting liver fibrosis in Asian patients with chronic viral hepatitis
Authors: Wang Hung-Wei , Peng Cheng-Yuan , Lai Hsueh-Chou , Su Wen-Pang , Lin Chia-Hsin , Chuang Po-Heng , Chen Sheng-Hung , Chen Ching-Hsiang , Hsu Wei-Fan , Huang Guan-Tarn
Published: June 2017

We developed an optimal noninvasive index comprising routine laboratory parameters for predicting cirrhosis in chronic hepatitis B (CHB) and chronic hepatitis C (CHC) patients. This study included 992 CHB patients and 1,284 CHC patients who received liver biopsy. We developed the new index, named modified Fibrosis-4 (mFIB-4) according to four independent variables of the model: age, aspartate aminotransferase (AST), alanine aminotransferase (ALT), and platelet count. The formula of the mFIB-4 index is 10 × Age(years) × AST(U/L)/Platelet count(109/L) × ALT(U/L). For predicting cirrhosis, the bootstrap areas under the receiver operating characteristic curve for platelet count, AST/ALT ratio (AAR), AAR/platelet ratio index (AARPRI), AST/platelet ratio index (APRI), FIB-4, Pohl score, age-platelet (AP) index, Lok index, fibrosis quotient (FibroQ), and mFIB-4 were 0.7680, 0.7400, 0.8070, 0.6090, 0.7690, 0.6990, 0.7850, 0.7960, 0.8110, and 0.8070 in CHB patients, and 0.8170, 0.7210, 0.8400, 0.7310, 0.8310, 0.6730, 0.8220, 0.8440, 0.8570, and 0.8480 in CHC patients, respectively. FibroQ and mFIB-4 exhibited the highest diagnostic performance levels for liver cirrhosis in CHB and CHC despite the inclusion of the international normalised ratio in the formulation of FibroQ. Thus, mFIB-4 is a simple, inexpensive, and readily available method for assessing the liver fibrosis stage of Asian patients with CHB or CHC.
Temperature gradients assist carbohydrate allocation within trees
Authors: Sperling Or , Silva Lucas C. R. , Tixier Aude , Théroux-Rancourt Guillaume , Zwieniecki Maciej A.
Published: June 2017

Trees experience two distinct environments: thermally-variable air and thermally-buffered soil. This generates intra-tree temperature gradients, which can affect carbon metabolism and water transport. In this study, we investigated whether carbohydrate allocation within trees is assisted by temperature gradients. We studied pistachio (Pistacia integerrima) to determine: (1) temperature-induced variation in xylem sugar concentration in excised branches; (2) changes in carbon allocation in young trees under simulated spring and fall conditions; and (3) seasonal variability of starch levels in mature orchard trees under field conditions. We found that warm branches had less sugar in perfused sap than cold branches due to increasing parenchyma storage. Simulated spring conditions promoted allocation of carbohydrates from cold roots to warm canopy and explained why starch levels surged in canopies of orchard trees during early spring. This driving force of sugar transport is interrupted in fall when canopies are colder than roots and carbohydrate redistribution is compartmentalized. On the basis of these findings, we propose a new mechanistic model of temperature-assisted carbohydrate allocation that links environmental cues and tree phenology. This data-enabled model provides insights into thermal “fine-tuning” of carbohydrate metabolism and a warning that the physiological performance of trees might be impaired by climatic changes.
Resolving phylogenetic relationships of Delphacini and Tropidocephalini (Hemiptera: Delphacidae: Delphacinae) as inferred from four genetic loci
Authors: Huang Yi-Xin , Zheng Li-Fang , Bartlett Charles R. , Qin Dao-Zheng
Published: June 2017

This paper explores the phylogeny of the delphacid subfamily Delphacinae based on nuclear ribosomal and mitochondrial DNA sequences of four genetic loci (16S rDNA, 28S rDNA,Cytochrome oxidase IandCytochrome b). Maximum likelihood and Bayesian analyses yield robust phylogenetic trees. The topologies support the monophyly of Delphacinae and its basal split into three tribes, and provisionally support subdividing Delphacini into three clades, including a more broadly defined Numatina. The tribe Tropidocephalini is divided into two clades. In addition,Paranectopiais transferred from Tropidocephalini to Delphacini andHarmaliasyn. nov. is regarded as a junior synonym ofOpiconsiva. The generaBambusiphaga,MegadelphaxandMuirodelphaxare found to be paraphyletic. The estimated time to the most recent common ancestor of Delphacinae is roughly at 90 million years ago in Late Cretaceous.
West Nile virus infectious replicon particles generated using a packaging-restricted cell line is a safe reporter system
Authors: Li Wei , Ma Le , Guo Li-Ping , Wang Xiao-Lei , Zhang Jing-Wei , Bu Zhi-Gao , Hua Rong-Hong
Published: June 2017

West Nile virus (WNV) is a neurotropic pathogen which causes zoonotic disease in humans. Recently, there have been an increasing number of infected cases and there are no clinically approved vaccines or effective drugs to treat WNV infections in humans. The purpose of this study was to facilitate vaccine and antiviral drug discovery by developing a packaging cell line-restricted WNV infectious replicon particle system. We constructed a DNA-based WNV replicon lacking the C-prM-E coding region and replaced it with a GFP coding sequence. To produce WNV replicon particles, cell lines stably-expressing prM-E and C-prM-E were constructed. When the WNV replicon plasmid was co-transfected with a WNV C-expressing plasmid into the prM-E-expressing cell line or directly transfected the C-prM-E expressing cell line, the replicon particle was able to replicate, form green fluorescence foci, and exhibit cytopathic plaques similar to that induced by the wild type virus. The infectious capacity of the replicon particles was restricted to the packaging cell line as the replicons demonstrated only one round of infection in other permissive cells. Thus, this system provides a safe and convenient reporter WNV manipulating tool which can be used to study WNV viral invasion mechanisms, neutralizing antibodies and antiviral efficacy.
DATS, the data tag suite to enable discoverability of datasets
Authors: Sansone Susanna-Assunta , Gonzalez-Beltran Alejandra , Rocca-Serra Philippe , Alter George , Grethe Jeffrey S. , Xu Hua , Fore Ian M. , Lyle Jared , Gururaj Anupama E. , Chen Xiaoling , Kim Hyeon-eui , Zong Nansu , Li Yueling , Liu Ruiling , Ozyurt I. Burak , Ohno-Machado Lucila
Published: June 2017

Today’s science increasingly requires effective ways to find and access existing datasets that are distributed across a range of repositories. For researchers in the life sciences, discoverability of datasets may soon become as essential as identifying the latest publications via PubMed. Through an international collaborative effort funded by the National Institutes of Health (NIH)’s Big Data to Knowledge (BD2K) initiative, we have designed and implemented the DAta Tag Suite (DATS) model to support the DataMed data discovery index. DataMed’s goal is to be for data what PubMed has been for the scientific literature. Akin to the Journal Article Tag Suite (JATS) used in PubMed, the DATS model enables submission of metadata on datasets to DataMed. DATS has a core set of elements, which are generic and applicable to any type of dataset, and an extended set that can accommodate more specialized data types. DATS is a platform-independent model also available as an annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex.
The modulation of adult neuroplasticity is involved in the mood-improving actions of atypical antipsychotics in an animal model of depression
Authors: Morais M , Patrício P , Mateus-Pinheiro A , Alves N D , Machado-Santos A R , Correia J S , Pereira J , Pinto L , Sousa N , Bessa J M
Published: June 2017

Depression is a prevalent psychiatric disorder with an increasing impact in global public health. However, a large proportion of patients treated with currently available antidepressant drugs fail to achieve remission. Recently, antipsychotic drugs have received approval for the treatment of antidepressant-resistant forms of major depression. The modulation of adult neuroplasticity, namely hippocampal neurogenesis and neuronal remodeling, has been considered to have a key role in the therapeutic effects of antidepressants. However, the impact of antipsychotic drugs on these neuroplastic mechanisms remains largely unexplored. In this study, an unpredictable chronic mild stress protocol was used to induce a depressive-like phenotype in rats. In the last 3 weeks of stress exposure, animals were treated with two different antipsychotics: haloperidol (a classical antipsychotic) and clozapine (an atypical antipsychotic). We demonstrated that clozapine improved both measures of depressive-like behavior (behavior despair and anhedonia), whereas haloperidol aggravated learned helplessness in the forced-swimming test and behavior flexibility in a cognitive task. Importantly, an upregulation of adult neurogenesis and neuronal survival was observed in animals treated with clozapine, whereas haloperidol promoted a downregulation of these processes. Furthermore, clozapine was able to re-establish the stress-induced impairments in neuronal structure and gene expression in the hippocampus and prefrontal cortex. These results demonstrate the modulation of adult neuroplasticity by antipsychotics in an animal model of depression, revealing that the atypical antipsychotic drug clozapine reverts the behavioral effects of chronic stress by improving adult neurogenesis, cell survival and neuronal reorganization.
Neuroimaging studies of GABA in schizophrenia: a systematic review with meta-analysis
Authors: Egerton A , Modinos G , Ferrera D , McGuire P
Published: June 2017

Data from animal models and from postmortem studies suggest that schizophrenia is associated with brain GABAergic dysfunction. The extent to which this is reflected in data from in vivo studies of GABA function in schizophrenia is unclear. The Medline database was searched to identify articles published until 21 October 2016. The search terms included GABA, proton magnetic resonance spectroscopy (1H-MRS), positron emission tomography (PET), single photon emission computed tomography (SPECT), schizophrenia and psychosis. Sixteen GABA 1H-MRS studies (538 controls, 526 patients) and seven PET/SPECT studies of GABAA/benzodiazepine receptor (GABAA/BZR) availability (118 controls, 113 patients) were identified. Meta-analyses of 1H-MRS GABA in the medial prefrontal cortex (mPFC), parietal/occipital cortex (POC) and striatum did not show significant group differences (mFC: g=−0.3, 409 patients, 495 controls, 95% confidence interval (CI): −0.6 to 0.1; POC: g=−0.3, 139 patients, 111 controls, 95% CI: −0.9 to 0.3; striatum: g=−0.004, 123 patients, 95 controls, 95% CI: −0.7 to 0.7). Heterogeneity across studies was high (I2>50%), and this was not explained by subsequent moderator or meta-regression analyses. There were insufficient PET/SPECT receptor availability studies for meta-analyses, but a systematic review did not suggest replicable group differences in regional GABAA/BZR availability. The current literature does not reveal consistent alterations in in vivo GABA neuroimaging measures in schizophrenia, as might be hypothesized from animal models and postmortem data. The analysis highlights the need for further GABA neuroimaging studies with improved methodology and addressing potential sources of heterogeneity.
Comparison of multivariate classification algorithms using EEM fluorescence data to distinguish Cryptococcus neoformans and Cryptococcus gattii pathogenic fungi
Authors: Costa Fernanda S. L. , Silva Priscila P. , Morais Camilo L. M. , Theodoro Raquel C. , Arantes Thales D. , Lima Kássio M. G.
Published: June 2017

Cryptococcus neoformansandCryptococcus gattiiare the etiologic agents of cryptococcosis, whose suitable treatment depends on rapid and correct detection and differentiation of theCryptococcusspecies.
A novel turn-on fluorescent sensor for highly selective detection of Al(iii) in an aqueous solution based on simple electrochemically synthesized carbon dots
Authors: Fu Xu-Cheng , Jin Jiang-Zhou , Wu Ju , Jin Jun-Cheng , Xie Cheng-Gen
Published: June 2017

Photoluminescent C-dots made by a one-step electrolysis method make a selective fluorescent sensor for Al3+ over other metal ions.
A novel electrochemiluminescence sensor for bisphenol A determination based on graphene–palladium nanoparticles/polyvinyl alcohol hybrids
Authors: Hu Yijie , Liu Zhimin , Zhan Haijun , Hu Leqian , Cui Lin , Wang Kang
Published: June 2017

Herein, graphene–palladium nanoparticles (PdNP–GR) were synthesized and dispersed in polyvinyl alcohol (PVA) to obtain a PdNP–GR/PVA composite.
Long alkyl side-chains impede exciton interaction in organic light harvesting crystals
Authors: Nagarajan Kalaivanan , Gopan Gopika , Cheriya Rijo T. , Hariharan Mahesh
Published: June 2017

First report on the effect of side-chain induced perturbations on exciton interactions in an organic light harvesting crystal.
Thermal ring-opening polymerization of an unsymmetrical silicon-bridged [1]ferrocenophane in coordination nanochannels
Authors: Kobayashi Yuichiro , Honjo Kayako , Kitagawa Susumu , Gwyther Jessica , Manners Ian , Uemura Takashi
Published: June 2017

Thermal ring-opening polymerization of the unsymmetrically substituted [1]ferrocenophane was performed in one-dimensional nanochannels of porous coordination polymers (PCPs).
Improved catalytic performance of porous metal–organic frameworks for the ring opening of styrene oxide
Authors: Julião Diana , Barbosa André D. S. , Peixoto Andreia F. , Freire Cristina , de Castro Baltazar , S. Balula Salete , Cunha-Silva Luís
Published: June 2017

An emerging strategy to improve the performance of porous metal–organic framework (MOF) materials as heterogeneous catalysts is reported.
Does H4SO5 exist?
Authors: Murillo Fernando , Vargas-Caamal Alba , Pan Sudip , Cabellos José Luis , Mora-Fonz Miguel J. , Muñoz-Castro Alvaro , Restrepo Albeiro , Merino Gabriel
Published: June 2017

The possible existence of H4SO5 in aqueous sulfuric acid is analyzed in detail.
Femtosecond to nanosecond studies of octupolar molecules and their quadrupolar and dipolar analogues
Authors: Seintis K. , Agathangelou D. , Cvejn D. , Almonasy N. , Bureš F. , Giannetas V. , Fakis M.
Published: June 2017

The fs–ps anisotropy dynamics of octupolar, quadrupolar and dipolar molecules with different π-bridges.
The maximum predicted content of cation vacancies in inorganic and organic–inorganic perovskites: the role of the tolerance factor
Authors: Ji D. H. , Wang S. L. , Ge X. Z. , Zhang Q. Q. , Zhang C. M. , Zeng Z. W. , Bai Y.
Published: June 2017

Curves of the maximum or minimum valuesversusthe different ratio of cation at the A sites for A1−h1PbX3hybrid perovskites.
Room temperature sintering of polar ZnO nanosheets: II-mechanism
Authors: Fernández-Pérez Amparo , Rodríguez-Casado Verónica , Valdés-Solís Teresa , Marbán Gregorio
Published: June 2017

Zn interstitials flow from the non-polar region towards the polar surface of the small mesopores.
Swelling of micro-hydrogels with a crosslinker gradient
Authors: Boon Niels , Schurtenberger Peter
Published: June 2017

The swollen structure of microgels with a crosslinked-polymer backbone is recovered by considering the crosslinker gradient inside the particles.
Thermal stability and thermal conductivity of phosphorene in phosphorene/graphene van der Waals heterostructures
Authors: Pei Qing-Xiang , Zhang Xiaoliang , Ding Zhiwei , Zhang Ying-Yan , Zhang Yong-Wei
Published: June 2017

We investigated the thermal stability and thermal conductivity of phosphorene in phosphorene/graphene heterostructures using molecular dynamics simulations.
Electrochemical CO2 reduction on Au surfaces: mechanistic aspects regarding the formation of major and minor products
Authors: Cave Etosha R. , Montoya Joseph H. , Kuhl Kendra P. , Abram David N. , Hatsukade Toru , Shi Chuan , Hahn Christopher , Nørskov Jens K. , Jaramillo Thomas F.
Published: June 2017

A detailed look at CO2 electroreduction on a polycrystalline gold surface and a mechanistic discussion on the formation of methanol.
N-Pyrrolylphosphines as ligands for highly regioselective rhodium-catalyzed 1-butene hydroformylation: effect of water on the reaction selectivity
Authors: Alsalahi W. , Grzybek R. , Trzeciak A. M.
Published: June 2017

Addition of water to the hydroformylation of 1-butene resulted in an increase of n/iso up to 50.
Time-resolved SERS study of the oxygen reduction reaction in ionic liquid electrolytes for non-aqueous lithium–oxygen cells
Authors: Radjenovic Petar M. , Hardwick Laurence J.
Published: June 2017

We use the Raman active bands of O2˙− to probe its changing Lewis basicity through its interaction with various ionic liquid electrolytes at the electrode surface.
Alleviation of metabolic syndrome by monascin and ankaflavin: the perspective of Monascus functional foods
Authors: Lin Chih-Hui , Lin Tzu-Hsing , Pan Tzu-Ming
Published: June 2017

The metabolites ofMonascuswith multiple benefits are popular subjects for the development of functional foods.
A hydrogel-based solidification method for the direct analysis of liquid samples by laser-induced breakdown spectroscopy
Authors: Lin Qingyu , Bian Fang , Wei Zhimei , Wang Shuai , Duan Yixiang
Published: June 2017

A simple, fast, and direct method based on hydrogel-based solidification technique has been developed for determining metallic elements in liquid samples using laser-induced breakdown spectroscopy (LIBS).
Depth profile analysis of rare earth elements in corroded steels by pulsed glow discharge – time of flight mass spectrometry
Authors: Muñiz Rocío , Lobo Lara , Kerry Timothy , Sharrad Clint A. , Pereiro Rosario
Published: June 2017

Depth profiling with PP-TOFMS of REEs (as substitutes of radioactive elements) in studies of stainless steel corrosion and contaminant uptake.
The memristive effect as a novelty in drug monitoring
Authors: Tzouvadaki Ioulia , Aliakbarinodehi Nima , De Micheli Giovanni , Carrara Sandro
Published: June 2017

Coupling of the memristive effect and DNA-aptamer properties for novel and effective monitoring of therapeutic compounds.
A paper-based touch sensor with an embedded micro-probe array fabricated by double-sided laser printing
Authors: Huang Gui-Wen , Li Na , Xiao Hong-Mei , Feng Qing-Ping , Fu Shao-Yun
Published: June 2017

Herein, we demonstrated a low-cost and flexible paper-based touch sensor, which was fabricated via an original highly efficient double-sided laser printing technique.
Carpatizine, a novel bridged oxazine derivative generated by non-enzymatic reactions
Authors: Fu Peng , MacMillan John B.
Published: June 2017

Non-enzymatic reactions were used to improve the structurally diverse natural products.
RAFT multiblock reactor telescoping: from monomers to tetrablock copolymers in a continuous multistage reactor cascade
Authors: Baeten Evelien , Haven Joris J. , Junkers Tanja
Published: June 2017

Well-defined multiblock copolymers were synthesized via reversible addition-fragmentation chain transfer radical polymerization in a fully continuous multireactor cascade.
Ring-expansion cationic polymerization of vinyl ethers
Authors: Ouchi Makoto , Kammiyada Hajime , Sawamoto Mitsuo
Published: June 2017

Ring-expansion cationic polymerization of vinyl ethers with a hemiacetal ester-embedded cyclic initiator allows precise syntheses of ring-based architectures due to the controlled propagation as well as the monomer pendant design.
Bioinspired polydopamine-induced assembly of ultrafine Fe(OH)3 nanoparticles on halloysite toward highly efficient fire retardancy of epoxy resin via an action of interfacial catalysis
Authors: Li Zhi , Liu Lejing , Jiménez González Alejandro , Wang De-Yi
Published: June 2017

Halloysite nanotubes were functionalized with polydopamine and ultrafine Fe(OH)3 nanoparticles to impart epoxy resin with highly efficient fire retardancy via interfacial catalysis.
Poly(o-aminophenol) prepared by Cu(ii) catalyzed air oxidation and its use as a bio-sensing architecture
Authors: Bicak Tugrul Cem , Soylemez Saniye , Buber Ece , Toppare Levent , Yagci Yusuf
Published: June 2017

A novel procedure for the preparation of organosoluble poly(o-aminophenol) is described.
Self-assembly and disassembly of stimuli responsive tadpole-like single chain nanoparticles using a switchable hydrophilic/hydrophobic boronic acid cross-linker
Authors: Zhang Junliang , Tanaka Joji , Gurnani Pratik , Wilson Paul , Hartlieb Matthias , Perrier Sébastien
Published: June 2017

pH/sugar responsive behaviour of tadpole-like single chain nanoparticles based on a switchable hydrophilic/hydrophobic boronic acid cross-linker is described.
Gd(OH)3with multiform morphologies and MRI contrast agent properties by different solvents
Authors: Park Sung Jun , Park Jin Young , Yang Hyun Kyoung , Je Jae-Yong
Published: June 2017

The morphology of Gd(OH)3is changed from nanorods to microrods, nanoparticles and nanoplates by different solvents, which affects the MRI signal intensity.
Investigating students' similarity judgments in organic chemistry
Authors: Graulich N. , Bhattacharyya G.
Published: June 2017

Organic chemistry is possibly the most visual science of all chemistry disciplines. The process of scientific inquiry in organic chemistry relies on external representations, such as Lewis structures, mechanisms, and electron arrows. Information about chemical properties or driving forces of mechanistic steps is not available through direct perception, and thus looking beyond the respresentation is challenging for learners. In this study, we investigated the categorization behavior of undergraduate students enrolled in an organic chemistry course when engaged in various categorization tasks involving electrophilic addition reactions to alkenes. The critical attribute a student chose to make a category out of a set of reactions was classified as perceptual or relational and gave insights into how students process and store information about reactions at an early level of expertise. Our results support the notion that students are prone to the surface level of representations and make sense of reactions depicted in a very minimalistic fashion. Implications for approaching this phenomenon in teaching are discussed.
Surface engineering of graphitic carbon nitride polymers with cocatalysts for photocatalytic overall water splitting
Authors: Zhang Guigang , Lan Zhi-An , Wang Xinchen
Published: June 2017

Overall water splitting for the stoichiometric generation of H2 and O2 has been achieved by rational cocatalyst modification of g-C3N4 polymers to modulate the surface redox reaction kinetics.
Rh-promoted mixed oxides for “low-temperature” methane partial oxidation in the absence of gaseous oxidants
Authors: Shafiefarhood Arya , Zhang Junshe , Neal Luke Michael , Li Fanxing
Published: June 2017

Rh promoted mixed-oxides show a syngas productivity of 7.9 mmol g−1at 600 °C in the absence of gaseous oxidants.
Enhanced charge collection with passivation of the tin oxide layer in planar perovskite solar cells
Authors: Lee Yonghui , Paek Sanghyun , Cho Kyung Taek , Oveisi Emad , Gao Peng , Lee Seunghwan , Park Jin-Seong , Zhang Yi , Humphry-Baker Robin , Asiri Abdullah M. , Nazeeruddin Mohammad Khaja
Published: June 2017

The morphological, opto-physical and electrical properties of the SnO2layer in perovskite solar cells are investigated.
Gradient release of cardiac morphogens by photo-responsive polymer micelles for gradient-mediated variation of embryoid body differentiation
Authors: Gupta Mukesh K. , Balikov Daniel A. , Lee Yunki , Ko Edward , Yu Christopher , Chun Young Wook , Sawyer Douglas B. , Kim Won Shik , Sung Hak-Joon
Published: June 2017

Illustration of photo-gradient mediated release of retinoic acid from polymer micelles upon photo-irradiation (365 nm).
Solution–solid–solid growth of metastable wurtzite γ-MnS nanowires with controlled length
Authors: Zhang Yongliang , Xu Rui , Chen Wenmiao , Zhuo Ou , Wu Qiang , Cai Jing , Wang Xizhang , Hu Zheng
Published: June 2017

Uniform metastable wurtzite γ-MnS nanowires were synthesized via solution–solid–solid (SSS) growth in a mixed solvent of 1-dodecylamine and 1-dodecanethiol. The length of the γ-MnS nanowires can be well controlled by adjusting the amount ratio of [(C4H9)2NCS2]2Mn precursors to Ag2S catalysts.