bluuebunny/crossref_metadata_2025_split huggingface dataset:
Knockdown of HIF-1α by siRNA-expressing plasmid delivered by attenuated Salmonella enhances the antitumor effects of cisplatin on prostate cancer
Authors: Gu Junlian , Li Yang , Zeng Jun , Wang Bo , Ji Kun , Tang Yufeng , Sun Qing 
Published: August 2017

AbstractResistance to cisplatin (DDP) and dose-related toxicity remain two important obstacles in the treatment of prostate cancer (PCa) patients with DDP-based chemotherapy. We have investigated whether the knockdown of hypoxia-inducible factor-1 alpha (HIF-1α) by siRNA could enhance the antitumor activity of DDP, and aimed to determine the underlying mechanisms. Intravenous injection of attenuated Salmonella carrying a HIF-1α siRNA-expressing plasmid was used to knockdown HIF-1α in a PC-3 xenograft model. The in vitro and in vivo effects of HIF-1α siRNA treatment and/or DPP on PCa cell proliferation, apoptosis, glycolysis, and production of reactive oxygen species (ROS) were assessed by examining molecular markers specific to each process. The results demonstrated that the treatment of tumor-bearing mice with attenuated Salmonella carrying the HIF-1α siRNA plasmid greatly enhanced the antitumor effects of low-dose DDP. Further mechanistic studies demonstrated that knockdown of HIF-1α improved the response of PCa cells to DDP by redirecting aerobic glycolysis toward mitochondrial oxidative phosphorylation, leading to cell death through overproduction of ROS. Our findings indicate that DDP-based chemotherapy combined with targeting the HIF-1α-regulated cancer metabolism pathway might be an ideal strategy to treat PCa.
Three TF Co-expression Modules Regulate Pressure-Overload Cardiac Hypertrophy in Male Mice
Authors: Chang Yao-Ming , Ling Li , Chang Ya-Ting , Chang Yu-Wang , Li Wen-Hsiung , Shih Arthur Chun-Chieh , Chen Chien-Chang 
Published: August 2017

AbstractPathological cardiac hypertrophy, a dynamic remodeling process, is a major risk factor for heart failure. Although a number of key regulators and related genes have been identified, how the transcription factors (TFs) dynamically regulate the associated genes and control the morphological and electrophysiological changes during the hypertrophic process are still largely unknown. In this study, we obtained the time-course transcriptomes at five time points in four weeks from male murine hearts subjected to transverse aorta banding surgery. From a series of computational analyses, we identified three major co-expression modules of TF genes that may regulate the gene expression changes during the development of cardiac hypertrophy in mice. After pressure overload, the TF genes in Module 1 were up-regulated before the occurrence of significant morphological changes and one week later were down-regulated gradually, while those in Modules 2 and 3 took over the regulation as the heart size increased. Our analyses revealed that the TF genes up-regulated at the early stages likely initiated the cascading regulation and most of the well-known cardiac miRNAs were up-regulated at later stages for suppression. In addition, the constructed time-dependent regulatory network reveals some TFs including Egr2 as new candidate key regulators of cardiovascular-associated (CV) genes.
A family of archaea-like carboxylesterases preferentially expressed in the symbiotic phase of the mycorrhizal fungus Tuber melanosporum
Authors: Cavazzini Davide , Grossi Guido , Levati Elisabetta , Vallese Francesca , Montanini Barbara , Bolchi Angelo , Zanotti Giuseppe , Ottonello Simone 
Published: August 2017

AbstractAn increasing number of esterases is being revealed by (meta) genomic sequencing projects, but few of them are functionally/structurally characterized, especially enzymes of fungal origin. Starting from a three-member gene family of secreted putative “lipases/esterases” preferentially expressed in the symbiotic phase of the mycorrhizal fungusTuber melanosporum(“black truffle”), we show here that these enzymes (TmelEST1-3) are dimeric, heat-resistant carboxylesterases capable of hydrolyzing various short/medium chain p-nitrophenyl esters. TmelEST2 was the most active (kcat = 2302 s−1for p-nitrophenyl-butyrate) and thermally stable (T50 = 68.3 °C), while TmelEST3 was the only one displaying some activity on tertiary alcohol esters. X-ray diffraction analysis of TmelEST2 revealed a classical α/β hydrolase-fold structure, with a network of dimer-stabilizing intermolecular interactions typical of archaea esterases. The predicted structures of TmelEST1 and 3 are overall quite similar to that of TmelEST2 but with some important differences. Most notably, the much smaller volume of the substrate-binding pocket and the more acidic electrostatic surface profile of TmelEST1. This was also the only TmelEST capable of hydrolyzing feruloyl-esters, suggestinng a possible role in root cell-wall deconstruction during symbiosis establishment. In addition to their potential biotechnological interest, TmelESTs raise important questions regarding the evolutionary recruitment of archaea-like enzymes into mesophilic subterranean fungi such as truffles.
Prediction of infarction volume and infarction growth rate in acute ischemic stroke
Authors: Kamran Saadat , Akhtar Naveed , Alboudi Ayman , Kamran Kainat , Ahmad Arsalan , Inshasi Jihad , Salam Abdul , Shuaib Ashfaq , Qidwai Uvais 
Published: August 2017

AbstractThe prediction of infarction volume after stroke onset depends on the shape of the growth dynamics of the infarction. To understand growth patterns that predict lesion volume changes, we studied currently available models described in literature and compared the models with Adaptive Neuro-Fuzzy Inference System [ANFIS], a method previously unused in the prediction of infarction growth and infarction volume (IV). We included 67 patients with malignant middle cerebral artery [MMCA] stroke who underwent decompressive hemicraniectomy. All patients had at least three cranial CT scans prior to the surgery. The rate of growth and volume of infarction measured on the third CT was predicted with ANFIS without statistically significant difference compared to the ground truth [P = 0.489]. This was not possible with linear, logarithmic or exponential methods. ANFIS was able to predict infarction volume [IV3] over a wide range of volume [163.7–600 cm3] and time [22–110 hours]. The cross correlation [CRR] indicated similarity between the ANFIS-predicted IV3 and original data of 82% for ANFIS, followed by logarithmic 70%, exponential 63% and linear 48% respectively. Our study shows that ANFIS is superior to previously defined methods in the prediction of infarction growth rate (IGR) with reasonable accuracy, over wide time and volume range.
Determination of the endothelin-1 recognition sites of endothelin receptor type A by the directed-degeneration method
Authors: Han Seong-Gu , Ko Sanghwan , Lee Won-Kyu , Jung Sang Taek , Yu Yeon Gyu 
Published: August 2017

AbstractG-protein coupled receptors (GPCRs) play indispensable physiological roles in cell proliferation, differentiation, and migration; therefore, identifying the mechanisms by which ligands bind to GPCRs is crucial for developing GPCR-targeting pharmaceutics and for understanding critical biological functions. Although some structural information is available regarding the interactions between GPCRs and their small molecule ligands, knowledge of how GPCRs interact with their corresponding macromolecule ligands, such as peptides and proteins, remains elusive. In this study, we have developed a novel strategy to investigate the precise ligand recognition mechanisms involved in the interaction of endothelin receptor type A (ETA) with its ligand, endothelin-1 (ET-1); we call this method “directed degeneration” method. Through flow cytometric screening of a randomized ETA library, statistical analysis of the identified sequences, and biochemical studies, the ligand interaction map was successfully obtained.
Self-controlled wave propagation in hyperelastic media
Authors: Xin Fengxian , Lu Tian Jian 
Published: August 2017

AbstractWe demonstrate theoretically that an ultrasonic wave propagating in a hyperelastic medium can self-control its phase velocities. This phenomenon occurs because the propagation of the ultrasonic wave generates acoustic radiation stresses in the medium, which can induce large deformation of the medium with significant stiffening effect. In turn, such deformation reshapes the wave propagation while the deformation stiffening changes significantly the phase velocities of the wave till the acoustic radiation stresses are balanced by elastic stresses in the current configuration of the hyperelastic medium. As a result of deformation stiffening, an initially isotropic medium becomes anisotropic, thus enabling self-control or self-bending of the wave propagation. We further reveal that, due to snap-through instability of acoustomechanical deformation in the hyperelastic medium, the ultrasonic wave can discontinuously switch its phase velocities from one state to another by jumping over a large unstable regime. This self-control and switchable mechanism of ultrasonic wave propagation in homogenous hyperelastic media offers innovative design opportunities for phononic, thermal and acoustic materials and devices.
Anti-SmD1 antibodies are associated with renal disorder, seizures, and pulmonary arterial hypertension in Chinese patients with active SLE
Authors: Hu Chaojun , Li Mengtao , Liu Jian , Qian Junyan , Xu Dong , Zhang Shulan , Li Ping , Zhao Jiulang , Tian Xinping , Zeng Xiaofeng 
Published: August 2017

AbstractDetection of autoantibodies in systemic lupus erythematosus (SLE) plays an important role in timely diagnosis and earlier treatment of SLE. In this study, we used a SmD1 polypeptide-based ELISA to determine anti-SmD1 antibody in 269 SLE, including100 naïve (had not been treated with steroids or immunosuppressants at study inception) SLE patients and 169 non-naive SLE patients; 233 controls with other rheumatic diseases (RDC) (70 RA, 40 AS, 73SSc, and 50 SS), and 110 healthy controls (HC) group. The positive rate of anti-SmD1 among all SLE patients was 60.97%, higher than that in the RDC group (13.30%,P = 0.000) or the HC group (9.09%,P = 0.000). The positive rate of anti-SmD1 in non-naive SLE patients was higher than that for anti-dsDNA antibodies (44.97%,P = 0.03). Positivity for anti-SmD1 only was found in 14.00% of naive SLE patients and 16.00% of non-naive SLE patients. In naive SLE patients, the serum concentration of anti-SmD1 was lower after treatment than before treatment (P = 0.039). Active SLE patients positive for anti-SmD1 were more likely to have malar rash, rash, nonscarring alopecia, PAH and hypocomplementemia. High positivity for anti-SmD1 only in patients with SLE indicated the importance and necessity of detection of anti-SmD1 in patients with SLE.
Wheat TaPUB1 modulates plant drought stress resistance by improving antioxidant capability
Authors: Zhang Guangqiang , Zhang Meng , Zhao Zhongxian , Ren Yuanqing , Li Qinxue , Wang Wei 
Published: August 2017

AbstractE3 ligases play significant roles in plant stress tolerance by targeting specific substrate proteins for post-translational modification. In a previous study, we cloned TaPUB1 from Triticum aestivum L., which encodes a U-box E3 ligase. Real-time polymerase chain reaction revealed that the gene was up-regulated under drought stress. To investigate the function of TaPUB1 in the response of plants to drought, we generated transgenic Nicotiana benthamiana (N. benthamiana) plants constitutively expressing TaPUB1 under the CaMV35S promoter. Compared to wild type (WT), the transgenic plants had higher germination and seedling survival rates as well as higher photosynthetic rate and water retention, suggesting that the overexpression of TaPUB1 enhanced the drought tolerance of the TaPUB1 overexpressing (OE) plants. Moreover, less accumulation of reactive oxygen species (ROS) and stronger antioxidant capacity were detected in the OE plants than in the WT plants. To characterize the mechanisms involved, methyl viologen (MV) was used to induce oxidative stress conditions and we identified the functions of this gene in the plant tolerance to oxidative stress. Our results suggest that TaPUB1 positively modulates plant drought stress resistance potential by improving their antioxidant capacity.
A novel missense variant in the nuclear localization signal of POU4F3 causes autosomal dominant non-syndromic hearing loss
Authors: Lin Yin-Hung , Lin Yi-Hsin , Lu Ying-Chang , Liu Tien-Chen , Chen Chien-Yu , Hsu Chuan-Jen , Chen Pei-Lung , Wu Chen-Chi 
Published: August 2017

AbstractAutosomal dominant non-syndromic hearing loss (ADNSHL) is genetically heterogeneous with more than 35 genes identified to date. Using a massively parallel sequencing panel targeting 159 deafness genes, we identified a novel missense variant of POU4F3 (c.982A>G, p.Lys328Glu) which co-segregated with the deafness phenotype in a three-generation Taiwanese family with ADNSHL. This variant could be classified as a “pathogenic variant” according to the American College of Medical Genetics and Genomics guidelines. We then performed subcellular localization experiments and confirmed that p.Lys328Glu compromised transportation of POU4F3 from the cytoplasm to the nucleus. POU3F4 p.Lys328Glu was located within a bipartite nuclear localization signal (NLS), and was the first missense variant in bipartite NLS of POU4F3 validated in functional studies. These findings expanded the mutation spectrum of POU4F3 and provided insight into the pathogenesis associated with aberrant POU4F3 localization.
Network-based machine learning and graph theory algorithms for precision oncology
Authors: Zhang Wei , Chien Jeremy , Yong Jeongsik , Kuang Rui 
Published: August 2017

AbstractNetwork-based analytics plays an increasingly important role in precision oncology. Growing evidence in recent studies suggests that cancer can be better understood through mutated or dysregulated pathways or networks rather than individual mutations and that the efficacy of repositioned drugs can be inferred from disease modules in molecular networks. This article reviews network-based machine learning and graph theory algorithms for integrative analysis of personal genomic data and biomedical knowledge bases to identify tumor-specific molecular mechanisms, candidate targets and repositioned drugs for personalized treatment. The review focuses on the algorithmic design and mathematical formulation of these methods to facilitate applications and implementations of network-based analysis in the practice of precision oncology. We review the methods applied in three scenarios to integrate genomic data and network models in different analysis pipelines, and we examine three categories of network-based approaches for repositioning drugs in drug–disease–gene networks. In addition, we perform a comprehensive subnetwork/pathway analysis of mutations in 31 cancer genome projects in the Cancer Genome Atlas and present a detailed case study on ovarian cancer. Finally, we discuss interesting observations, potential pitfalls and future directions in network-based precision oncology.
Embedded gate CVD MoS2 microwave FETs
Authors: Sanne Atresh , Park Saungeun , Ghosh Rudresh , Yogeesh Maruthi Nagavalli , Liu Chison , Mathew Leo , Rao Rajesh , Akinwande Deji , Banerjee Sanjay Kumar 
Published: August 2017

AbstractRecent studies have increased the cut off frequencies achievable by exfoliated MoS2 by employing a combination of channel length scaling and geometry modification. However, for industrial scale applications, the mechanical cleavage process is not scalable but, thus far, the same device improvements have not been realized on chemical vapor deposited MoS2. Here we use a gate-first process flow with an embedded gate geometry to fabricate short channel chemical vapor deposited MoS2 radio frequency transistors with a notable fT of 20 GHz and fmax of 11.4 GHz, and the largest high-field saturation velocity, vsat = 1.88 × 106 cm/s, in MoS2 reported so far. The gate-first approach, facilitated by cm-scale chemical vapor deposited MoS2, offers enhancement mode operation, ION/IOFF ratio of 108, and a transconductance (gm) of 70 μS/μm. The intrinsic fT (fmax) obtained here is 3X (2X) greater than previously reported top-gated chemical vapor deposited MoS2 radio frequency field-effect transistors. With as-measured S-parameters, we demonstrate the design of a GHz MoS2-based radio frequency amplifier. This amplifier has gain greater then 15 dB at 1.2 GHz, input return loss  > 10 dB, bandwidth  > 200 MHz, and DC power consumption of ~10 mW.
Peptide Functionalized Gold Nanorods for the Sensitive Detection of a Cardiac Biomarker Using Plasmonic Paper Devices
Authors: Tadepalli Sirimuvva , Kuang Zhifeng , Jiang Qisheng , Liu Keng-Ku , Fisher Marilee A. , Morrissey Jeremiah J. , Kharasch Evan D. , Slocik Joseph M. , Naik Rajesh R. , Singamaneni Srikanth 
Published: August 2017

AbstractThe sensitivity of localized surface plasmon resonance (LSPR) of metal nanostructures to adsorbates lends itself to a powerful class of label-free biosensors. Optical properties of plasmonic nanostructures are dependent on the geometrical features and the local dielectric environment. The exponential decay of the sensitivity from the surface of the plasmonic nanotransducer calls for the careful consideration in its design with particular attention to the size of the recognition and analyte layers. In this study, we demonstrate that short peptides as biorecognition elements (BRE) compared to larger antibodies as target capture agents offer several advantages. Using a bioplasmonic paper device (BPD), we demonstrate the selective and sensitive detection of the cardiac biomarker troponin I (cTnI). The smaller sized peptide provides higher sensitivity and a lower detection limit using a BPD. Furthermore, the excellent shelf-life and thermal stability of peptide-based LSPR sensors, which precludes the need for special storage conditions, makes it ideal for use in resource-limited settings.
Real‐time implementation of three‐phase single‐stage SPV grid‐tied system using TL‐VSC
Authors: Hussain Ikhlaq , Kandpal Maulik , Singh Bhim 
Published: August 2017

This work deals with real‐time implementation of a three‐phase single‐stage solar photovoltaic (SPV) grid‐tied system using a three‐level voltage source converter (TL‐VSC) working at lower switching frequency of 900 Hz under varying solar intensity levels for large power applications. The proposed system consists of SPV array, TL‐VSC, interfacing inductors, and three‐phase AC grid. The decoupled current controller with the capacitor voltage balancing control and an incremental conductance maximum power point tracking (IC‐MPPT)‐based algorithms are used to control the TL‐VSC to track and transfer maximum active power to AC grid at unity power factor from SPV array. Owing to low switching frequency and single‐stage topology, the efficacy of the system is increased. The performance of SPV grid integrated system using TL‐VSC is validated under varying solar intensity levels in the laboratory at different switching frequencies and interfacing inductors in accordance to IEEE 519 standard.
Wafer‐level vacuum‐encapsulated silicon resonators with arc‐welded electrodes
Authors: Xereas George , Chodavarapu Vamsy P. 
Published: August 2017

This work presents wafer‐level vacuum‐encapsulated silicon resonators that utilise movable electrodes and arc welding in order to achieve deep sub‐micron transduction gaps. The devices are fabricated using micro‐electro‐mechanical systems (MEMS) integrated design for inertial sensors (MIDIS) process, a commercial pure‐play MEMS process, offered by Teledyne DALSA Semiconductor Inc.. The default minimum transduction gap in the MIDIS process is 1.5 μm. Here, the work introduces a technique to permanently reduce the transduction gap of the resonator using localised arc welding to a designed width of ∼200 nm. The prototype Lamé mode resonators are encapsulated in an ultra‐clean 10 mTorr vacuum cavity that ensures long‐term stability. The quality factor was measured to be 1.37 million at a resonance frequency of 6.89 MHz. With the narrower gap, the motional resistance of the resonators is reduced by a factor of ten times.
Polyaromatic disordered carbon grains as carriers of the UV bump: Far-UV to mid-IR spectroscopy of laboratory analogs
Authors: Gavilan L. , Le K. C. , Pino T. , Alata I. , Giuliani A. , Dartois E. 
Published: August 2017

Context. A multiwavelength study of laboratory carbons with varying degrees of hydrogenation and sp2 hybridization is required to characterize the structure of the carbonaceous carriers of interstellar and circumstellar extinction.
Aims. We study the spectral properties of carbonaceous dust analogs from the far-ultraviolet to the mid-infrared and correlate features in both spectral ranges to the aromatic/aliphatic degree.
Methods. Analogs to carbonaceous interstellar dust encountered in various phases of the interstellar medium have been prepared in the laboratory. These are amorphous hydrogenated carbons (a-C:H), analogs to the diffuse interstellar medium component, and soot particles, analogs to the polyaromatic component. Thin films (d < 100 nm) have been measured in transmission in the vacuum-ultraviolet (VUV; 120–210 nm) within the atmospheric pressure experiment (APEX) chamber of the DISCO beam line at the SOLEIL synchrotron radiation facility. Spectra of these films were further measured through the UV-Vis (210 nm–1 μm) and in the mid-infrared (3–15 μm).
Results. Tauc optical gaps, Eg, are derived from the visible spectra. The major spectral features are fitted through the VUV to the mid-infrared to obtain positions, full-widths at half maximum (FWHM), and integrated intensities. These are plotted against the position of the π-π∗ electronic transitions peak. Unidentified or overlapping features in the UV are identified by correlations with complementary infrared data. A correlation between the optical gap and position of the π-π∗ electronic transitions peak is found. The latter is also correlated to the position of the sp3 carbon defect band at ~8 μm, the aromatic C=C stretching mode position at ~6 μm, and the H/C ratio.
Conclusions. Ultraviolet and infrared spectroscopy of structurally diverse carbon samples are used to constrain the nanostructural properties of carbon carriers of both circumstellar and interstellar extinction, such as the associated coherent lengths and the size of polyaromatic units. Our study suggests that carriers of the interstellar UV bump should exhibit infrared bands akin to the A/B classes of the aromatic infrared bands, while the circumstellar bump carriers should exhibit bands corresponding to the B/C classes.