bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design of defect spins in piezoelectric aluminum nitride for solid-state hybrid quantum technologies
Authors: Seo Hosung , Govoni Marco , Galli Giulia 
Published: February 2016

AbstractSpin defects in wide-band gap semiconductors are promising systems for the realization of quantum bits, or qubits, in solid-state environments. To date, defect qubits have only been realized in materials with strong covalent bonds. Here, we introduce a strain-driven scheme to rationally design defect spins in functional ionic crystals, which may operate as potential qubits. In particular, using a combination of state-of-the-artab-initiocalculations based on hybrid density functional and many-body perturbation theory, we predicted that the negatively charged nitrogen vacancy center in piezoelectric aluminum nitride exhibits spin-triplet ground states under realistic uni- and bi-axial strain conditions; such states may be harnessed for the realization of qubits. The strain-driven strategy adopted here can be readily extended to a wide range of point defects in other wide-band gap semiconductors, paving the way to controlling the spin properties of defects in ionic systems for potential spintronic technologies.
Evidence of disrupted high-risk human papillomavirus DNA in morphologically normal cervices of older women
Authors: Leonard Sarah M. , Pereira Merlin , Roberts Sally , Cuschieri Kate , Nuovo Gerard , Athavale Ramanand , Young Lawrence , Ganesan Raji , Woodman Ciarán B. 
Published: February 2016

AbstractHigh-risk human papillomavirus (HR-HPV) causes nearly 100% of cervical carcinoma. However, it remains unclear whether HPV can establish a latent infection, one which may be responsible for the second peak in incidence of cervical carcinoma seen in older women. Therefore, using Ventana in situ hybridisation (ISH), quantitative PCR assays and biomarkers of productive and transforming viral infection, we set out to provide the first robust estimate of the prevalence and characteristics of HPV genomes in FFPE tissue from the cervices of 99 women undergoing hysterectomy for reasons unrelated to epithelial abnormality. Our ISH assay detected HR-HPV in 42% of our study population. The majority of ISH positive samples also tested HPV16 positive using sensitive PCR based assays and were more likely to have a history of preceding cytological abnormality. Analysis of subsets of this population revealed HR-HPV to be transcriptionally inactive as there was no evidence of a productive or transforming infection. Critically, the E2 gene was always disrupted in those HPV16 positive cases which were assessed. These findings point to a reservoir of transcriptionally silent, disrupted HPV16 DNA in morphologically normal cervices, re-expression of which could explain the increase in incidence of cervical cancer observed in later life.
Endocardial Remodeling in Heart Failure Patients with Impaired and Preserved Left Ventricular Systolic Function-A Magnetic Resonance Image Study
Authors: Lin Lian-Yu , Su Mao-Yuan M. , Pham Van-Truong , Tran Thi-Thao , Wang Yung-Hung , Tseng Wen-Yih I. , Lo Men-Tzung , Lin Jiunn-Lee 
Published: February 2016

AbstractLeft ventricular (LV) trabeculation has been studied in certain forms of cardiomyopathy. However, the changes of LV endocardial trabeculation during the remodeling process leading to heart failure (HF) are unclear. Seventy-four patients with systolic heart failure (SHF), 65 with heart failure with preserved ejection fraction (HFpEF) and 61 without HF were prospectively enrolled. All subjects received magnetic resonance imaging (MRI) study including cine, T1 and late gadolinium enhancement (LGE) images. Trabecular-papillary muscle (TPM) mass, fractal dimension (FD) and extracellular volume (ECV) were derived. The results showed that TPM mass index was higher in patients with SHF than that in patients with HFpEF and non-HF. The TPM mass-LV mass ratio (TPMm/LVM) was higher in SHF group than that in HFpEF and non-HF. FD was not different among groups. The presence of LGE was inversely associated with TPM mass index and TPMm/LVM while the ECV were positively associated with TPMm/LVM. The FD was positively associated with LV chamber size. In conclusion, TPM increases in patients with SHF and are probably related to myocardial cell hypertrophy and fibrotic repair during remodeling. The FD increases with the dilatation of LV chamber but remain unchanged with the deterioration of LV function.
Ribosomal small subunit domains radiate from a central core
Authors: Gulen Burak , Petrov Anton S. , Okafor C. Denise , Vander Wood Drew , O’Neill Eric B. , Hud Nicholas V. , Williams Loren Dean 
Published: February 2016

AbstractThe domain architecture of a large RNA can help explain and/or predict folding, function, biogenesis and evolution. We offer a formal and general definition of an RNA domain and use that definition to experimentally characterize the rRNA of the ribosomal small subunit. Here the rRNA comprising a domain is compact, with a self-contained system of molecular interactions. A given rRNA helix or stem-loop must be allocated uniquely to a single domain. Local changes such as mutations can give domain-wide effects. Helices within a domain have interdependent orientations, stabilities and interactions. With these criteria we identify a core domain (domain A) of small subunit rRNA. Domain A acts as a hub, linking the four peripheral domains and imposing orientational and positional restraints on the other domains. Experimental characterization of isolated domain A, and mutations and truncations of it, by methods including selective 2′OH acylation analyzed by primer extension and circular dichroism spectroscopy are consistent with our architectural model. The results support the utility of the concept of an RNA domain. Domain A, which exhibits structural similarity to tRNA, appears to be an essential core of the small ribosomal subunit.
Conformational plasticity of RepB, the replication initiator protein of promiscuous streptococcal plasmid pMV158
Authors: Boer D. Roeland , Ruiz-Masó José Angel , Rueda Manuel , Petoukhov Maxim V. , Machón Cristina , Svergun Dmitri I. , Orozco Modesto , del Solar Gloria , Coll Miquel 
Published: February 2016

AbstractDNA replication initiation is a vital and tightly regulated step in all replicons and requires an initiator factor that specifically recognizes the DNA replication origin and starts replication. RepB from the promiscuous streptococcal plasmid pMV158 is a hexameric ring protein evolutionary related to viral initiators. Here we explore the conformational plasticity of the RepB hexamer by i) SAXS, ii) sedimentation experiments, iii) molecular simulations and iv) X-ray crystallography. Combining these techniques, we derive an estimate of the conformational ensemble in solution showing that the C-terminal oligomerisation domains of the protein form a rigid cylindrical scaffold to which the N-terminal DNA-binding/catalytic domains are attached as highly flexible appendages, featuring multiple orientations. In addition, we show that the hinge region connecting both domains plays a pivotal role in the observed plasticity. Sequence comparisons and a literature survey show that this hinge region could exists in other initiators, suggesting that it is a common, crucial structural element for DNA binding and manipulation.
Wharton’s jelly-derived mesenchymal stem cells combined with praziquantel as a potential therapy for Schistosoma mansoni-induced liver fibrosis
Authors: Hammam Olfat A. , Elkhafif Nagwa , Attia Yasmeen M. , Mansour Mohamed T. , Elmazar Mohamed M. , Abdelsalam Rania M. , Kenawy Sanaa A. , El-Khatib Aiman S. 
Published: February 2016

AbstractLiver fibrosis is one of the most serious consequences of S. mansoni infection. The aim of the present study was to investigate the potential anti-fibrotic effect of human Wharton’s jelly-derived mesenchymal stem cells (WJMSCs) combined with praziquantel (PZQ) in S. mansoni-infected mice. S. mansoni-infected mice received early (8th week post infection) and late (16th week post infection) treatment with WJMSCs, alone and combined with oral PZQ. At the 10th month post infection, livers were collected for subsequent flow cytometric, histopathological, morphometric, immunohistochemical, gene expression, and gelatin zymographic studies. After transplantation, WJMSCs differentiated into functioning liver-like cells as evidenced by their ability to express human hepatocyte-specific markers. Regression of S. mansoni-induced liver fibrosis was also observed in transplanted groups, as evidenced by histopathological, morphometric, and gelatin zymographic results besides decreased expression of three essential contributors to liver fibrosis in this particular model; alpha smooth muscle actin, collagen-I, and interleukin-13. PZQ additionally enhanced the beneficial effects observed in WJMSCs-treated groups. Our results suggest that combining WJMSCs to PZQ caused better enhancement in S. mansoni-induced liver fibrosis, compared to using each alone.
An Ultra-thin Amniotic Membrane as Carrier in Corneal Epithelium Tissue-Engineering
Authors: Zhang Liying , Zou Dulei , Li Sanming , Wang Junqi , Qu Yangluowa , Ou Shangkun , Jia Changkai , Li Juan , He Hui , Liu Tingting , Yang Jie , Chen Yongxiong , Liu Zuguo , Li Wei 
Published: February 2016

AbstractAmniotic membranes (AMs) are widely used as a corneal epithelial tissue carrier in reconstruction surgery. However, the engineered tissue transparency is low due to the translucent thick underlying AM stroma. To overcome this drawback, we developed an ultra-thin AM (UAM) by using collagenase IV to strip away from the epithelial denuded AM (DAM) some of the stroma. By thinning the stroma to about 30 μm, its moist and dry forms were rendered acellular, optically clear and its collagen framework became compacted and inerratic. Engineered rabbit corneal epithelial cell (RCEC) sheets generated through expansion of limbal epithelial cells on UAM were more transparent and thicker than those expanded on DAM. Moreover, ΔNp63 and ABCG2 gene expression was greater in tissue engineered cell sheets expanded on UAM than on DAM. Furthermore, 2 weeks after surgery, the cornea grafted with UAM based cell sheets showed higher transparency and more stratified epithelium than the cornea grafted with DAM based cell sheets. Taken together, tissue engineered corneal epithelium generated on UAM has a preferable outcome because the transplanted tissue is more transparent and better resembles the phenotype of the native tissue than that obtained by using DAM for this procedure. UAM preserves compact layer of the amniotic membrane and maybe an ideal substrate for corneal epithelial tissue engineering.
Community Sewage Sensors towards Evaluation of Drug Use Trends: Detection of Cocaine in Wastewater with DNA-Directed Immobilization Aptamer Sensors
Authors: Yang Zhugen , Castrignanò Erika , Estrela Pedro , Frost Christopher G. , Kasprzyk-Hordern Barbara 
Published: February 2016

AbstractIllicit drug use has a global concern and effective monitoring and interventions are highly required to combat drug abuse. Wastewater-based epidemiology (WBE) is an innovative and cost-effective approach to evaluate community-wide drug use trends, compared to traditional population surveys. Here we report for the first time, a novel quantitative community sewage sensor (namely DNA-directed immobilization of aptamer sensors, DDIAS) for rapid and cost-effective estimation of cocaine use trends via WBE. Thiolated single-stranded DNA (ssDNA) probe was hybridized with aptamer ssDNA in solution, followed by co-immobilization with 6-mercapto-hexane onto the gold electrodes to control the surface density to effectively bind with cocaine. DDIAS was optimized to detect cocaine at as low as 10 nM with a dynamic range from 10 nM to 5 μM, which were further employed for the quantification of cocaine in wastewater samples collected from a wastewater treatment plant in seven consecutive days. The concentration pattern of the sampling week is comparable with that from mass spectrometry. Our results demonstrate that the developed DDIAS can be used as community sewage sensors for rapid and cost-effective evaluation of drug use trends, and potentially implemented as a powerful tool for on-site and real-time monitoring of wastewater by un-skilled personnel.
Genome wide transcriptome profiling reveals differential gene expression in secondary metabolite pathway of Cymbopogon winterianus
Authors: Devi Kamalakshi , Mishra Surajit K. , Sahu Jagajjit , Panda Debashis , Modi Mahendra K. , Sen Priyabrata 
Published: February 2016

AbstractAdvances in transcriptome sequencing provide fast, cost-effective and reliable approach to generate large expression datasets especially suitable for non-model species to identify putative genes, key pathway and regulatory mechanism. Citronella (Cymbopogon winterianus) is an aromatic medicinal grass used for anti-tumoral, antibacterial, anti-fungal, antiviral, detoxifying and natural insect repellent properties. Despite of having number of utilities, the genes involved in terpenes biosynthetic pathway is not yet clearly elucidated. The present study is a pioneering attempt to generate an exhaustive molecular information of secondary metabolite pathway and to increase genomic resources in Citronella. Using high-throughput RNA-Seq technology, root and leaf transcriptome was analysed at an unprecedented depth (11.7 Gb). Targeted searches identified majority of the genes associated with metabolic pathway and other natural product pathway viz. antibiotics synthesis along with many novel genes. Terpenoid biosynthesis genes comparative expression results were validated for 15 unigenes by RT-PCR and qRT-PCR. Thus the coverage of these transcriptome is comprehensive enough to discover all known genes of major metabolic pathways. This transcriptome dataset can serve as important public information for gene expression, genomics and function genomics studies in Citronella and shall act as a benchmark for future improvement of the crop.
A CAPS-based binding assay provides semi-quantitative validation of protein-DNA interactions
Authors: Xie Yongyao , Zhang Yaling , Zhao Xiucai , Liu Yao-Guang , Chen Letian 
Published: February 2016

AbstractInvestigation of protein-DNA interactions provides crucial information for understanding the mechanisms of gene regulation. Current methods for studying protein-DNA interactions, such as DNaseI footprinting or gel shift assays, involve labeling DNA with radioactive or fluorescent tags, making these methods costly, laborious and potentially damaging to the environment. Here, we describe a novel cleaved amplified polymorphic sequence (CAPS)-based binding assay (CBA), which is a label-free method that can simplify the semi-quantitative validation of protein-DNA interactions. The CBA tests the interaction between a protein and its target DNA, based on the CAPS pattern produced due to differences in the accessibility of a restriction endonuclease site (intrinsic or artificial) in amplified DNA in the presence and absence of the protein of interest. Thus, the CBA can produce a semi-quantitative readout of the interaction strength based on the dose of the binding protein. We demonstrate the principle and feasibility of CBA using B3, MADS3 proteins and the corresponding RY or CArG-box containing DNAs.
Association between Functional MICA-TM and Behcet’s Disease: A Systematic Review and Meta-analysis
Authors: Zhang Jun , Liao Dan , Yang Lu , Hou Shengping 
Published: February 2016

AbstractThe relationships between polymorphisms of the trans-membrane(TM) region located in the major histocompatibility complex (MHC) class I chain–related gene A (MICA) and Behcet’s disease (BD) have been discussed previously, however, the results were contradictory. In this study, we thoroughly assess whether MICA-TM gene variants are associated with BD by means of a systematic review and meta-analysis. Our study focused on the effects of polymorphisms of MICA-A4, A5, A5.1, A6 and A9 from the included articles. Sixteen previous original publications representing 1,555 BD patients and 2,086 unrelated healthy controls analyzed the association of BD with MICA-TM gene polymorphisms. For the five alleles, MICA-A6 showed a strongly positive correlation with BD patients and could be viewed as an increased risk factor of BD (OR = 2.34, 95%CI: 2.02–2.70). Furthermore, MICA-A4, A5, A5.1 and A9 exhibited negative associations with BD (OR = 0.71, 95%CI: 0.58–0.86; OR = 0.75, 95%CI: 0.63–0.90; OR = 0.63, 95%CI: 0.44–0.91; OR = 0.70, 95%CI: 0.58–0.84, respectively). Our meta-analysis confirmed MICA-A6 could be responsible for BD in three ethnic regions and should probably be treated as a risk factor for BD. MICA-A4, A5, A5.1 and A9 could be regarded as protective factors, especially in the Middle East and East Asia.
Periodic, Quasi-periodic and Chaotic Dynamics in Simple Gene Elements with Time Delays
Authors: Suzuki Yoko , Lu Mingyang , Ben-Jacob Eshel , Onuchic José N. 
Published: February 2016

AbstractRegulatory gene circuit motifs play crucial roles in performing and maintaining vital cellular functions. Frequently, theoretical studies of gene circuits focus on steady-state behaviors and do not include time delays. In this study, the inclusion of time delays is shown to entirely change the time-dependent dynamics for even the simplest possible circuits with one and two gene elements with self and cross regulations. These elements can give rise to rich behaviors including periodic, quasi-periodic, weak chaotic, strong chaotic and intermittent dynamics. We introduce a special power-spectrum-based method to characterize and discriminate these dynamical modes quantitatively. Our simulation results suggest that, while a single negative feedback loop of either one- or two-gene element can only have periodic dynamics, the elements with two positive/negative feedback loops are the minimalist elements to have chaotic dynamics. These elements typically have one negative feedback loop that generates oscillations and another unit that allows frequent switches among multiple steady states or between oscillatory and non-oscillatory dynamics. Possible dynamical features of several simple one- and two-gene elements are presented in details. Discussion is presented for possible roles of the chaotic behavior in the robustness of cellular functions and diseases, for example, in the context of cancer.
Assembly of coupled redox fuel cells using copper as electron acceptors to generate power and its in-situ retrieval
Authors: Zhang Hui-Min , Xu Wei , Li Gang , Liu Zhan-Meng , Wu Zu-Cheng , Li Bo-Geng 
Published: February 2016

AbstractEnergy extraction from waste has attracted much interest nowadays. Herein, a coupled redox fuel cell (CRFC) device using heavy metals, such as copper, as an electron acceptor is assembled to testify the recoveries of both electricity and the precious metal without energy consumption. In this study, a NaBH4-Cu(II) CRFC was employed as an example to retrieve copper from a dilute solution with self-electricity production. The properties of the CRFC have been characterized, and the open circuit voltage was 1.65 V with a maximum power density of 7.2 W m−2 at an initial Cu2+ concentration of 1,600 mg L−1 in the catholyte. 99.9% of the 400 mg L−1 copper was harvested after operation for 24 h, and the product formed on the cathode was identified as elemental copper. The CRFC demonstrated that useful chemicals were recovered and the electricity contained in the chemicals was produced in a self-powered retrieval process.
Maintenance of aversive memories shown by fear extinction-impaired phenotypes is associated with increased activity in the amygdaloid-prefrontal circuit
Authors: Laricchiuta Daniela , Saba Luana , De Bartolo Paola , Caioli Silvia , Zona Cristina , Petrosini Laura 
Published: February 2016

AbstractAlthough aversive memory has been mainly addressed by analysing the changes occurring in average populations, the study of neuronal mechanisms of outliers allows understanding the involvement of individual differences in fear conditioning and extinction. We recently developed an innovative experimental model of individual differences in approach and avoidance behaviors, classifying the mice as Approaching, Balancing or Avoiding animals according to their responses to conflicting stimuli. The approach and avoidance behaviors appear to be the primary reactions to rewarding and threatening stimuli and may represent predictors of vulnerability (or resilience) to fear. We submitted the three mice phenotypes to Contextual Fear Conditioning. In comparison to Balancing animals, Approaching and Avoiding mice exhibited no middle- or long-term fear extinction. The two non-extinguishing phenotypes exhibited potentiated glutamatergic neurotransmission (spontaneous excitatory postsynaptic currents/spinogenesis) of pyramidal neurons of medial prefrontal cortex and basolateral amygdala. Basing on the a priori individuation of outliers, we demonstrated that the maintenance of aversive memories is linked to increased spinogenesis and excitatory signaling in the amygdala-prefrontal cortex fear matrix.
Observation of the Kibble–Zurek Mechanism in Microscopic Acoustic Crackling Noises
Authors: Ghaffari H. O. , Griffth W. A. , Benson P.M. , Xia K. , Young R. P. 
Published: February 2016

AbstractCharacterizing the fast evolution of microstructural defects is key to understanding “crackling” phenomena during the deformation of solid materials. For example, it has been proposed using atomistic simulations of crack propagation in elastic materials that the formation of a nonlinear hyperelastic or plastic zone around moving crack tips controls crack velocity. To date, progress in understanding the physics of this critical zone has been limited due to the lack of data describing the complex physical processes that operate near microscopic crack tips. We show, by analyzing many acoustic emission events during rock deformation experiments, that the signature of this nonlinear zone maps directly to crackling noises. In particular, we characterize a weakening zone that forms near the moving crack tips using functional networks and we determine the scaling law between the formation of damages (defects) and the traversal rate across the critical point of transition. Moreover, we show that the correlation length near the transition remains effectively frozen. This is the main underlying hypothesis behind the Kibble-Zurek mechanism (KZM) and the obtained power-law scaling verifies the main prediction of KZM.
Spectral variation of fluorescence lifetime near single metal nanoparticles
Authors: Li Jia , Krasavin Alexey V. , Webster Linden , Segovia Paulina , Zayats Anatoly V. , Richards David 
Published: February 2016

AbstractWe explore the spectral dependence of fluorescence enhancement and the associated lifetime modification of fluorescent molecules coupled to single metal nanoparticles. Fluorescence lifetime imaging microscopy and single-particle dark-field spectroscopy are combined to correlate the dependence of fluorescence lifetime reduction on the spectral overlap between the fluorescence emission and the localised surface plasmon (LSP) spectra of individual gold nanoparticles. A maximum lifetime reduction is observed when the fluorescence and LSP resonances coincide, with good agreement provided by numerical simulations. The explicit comparison between experiment and simulation, that we obtain, offers an insight into the spectral engineering of LSP mediated fluorescence and may lead to optimized application in sensing and biomedicine.