bluuebunny/crossref_metadata_2025 huggingface dataset:
Deep optimization for spectrum repacking
Authors: Newman Neil , Fréchette Alexandre , Leyton-Brown Kevin
Published: December 2017

Over 13 months in 2016--17 the U.S. Federal Communications Commission conducted an "incentive auction" to repurpose radio spectrum from broadcast television to wireless internet. In the end, the auction yielded $19.8 bn, $10.05 bn of which was paid to 175 broadcasters for voluntarily relinquishing their licenses across 14 Ultra High Frequency (UHF) channels. Stations that continued broadcasting were assigned potentially new channels to fit as densely as possible into the channels that remained. The government netted more than $7 bn (used to pay down the national debt) after covering costs (including retuning). A crucial element of the auction design was the construction of a solver, dubbed SAT-based Feasibility Checker (SATFC), that determined whether sets of stations could be "repacked" in this way; it needed to run every time a station was given a price quote. This paper describes the process by which we built SATFC. We adopted an approach we dub "deep optimization," taking a data-driven, highly parametric, and computationally intensive approach to solver design. More specifically, to build SATFC we designed software that could pair both complete and local-search SAT-encoded feasibility checking with a wide range of domain-specific techniques, such as constraint graph decomposition and novel caching mechanisms that allow for reuse of partial solutions from related, solved problems. We then used automatic algorithm configuration techniques to construct a portfolio of 8 complementary algorithms to be run in parallel, aiming to achieve good performance on instances that arose in proprietary auction simulations. To evaluate the impact of our solver in this paper, we built an open-source reverse auction simulator. We found that within the short time budget required in practice, SATFC solved more than 95% of the problems it encountered. Furthermore, the incentive auction paired with SATFC produced nearly optimal allocations in a restricted setting and substantially outperformed other alternatives at national scale.
Halide
Authors: Ragan-Kelley Jonathan , Adams Andrew , Sharlet Dillon , Barnes Connelly , Paris Sylvain , Levoy Marc , Amarasinghe Saman , Durand Frédo
Published: December 2017

Writing high-performance code on modern machines requires not just locally optimizing inner loops, but globally reorganizing computations to exploit parallelism and locality---doing things such as tiling and blocking whole pipelines to fit in cache. This is especially true for image processing pipelines, where individual stages do much too little work to amortize the cost of loading and storing results to and from off-chip memory. As a result, the performance difference between a naive implementation of a pipeline and one globally optimized for parallelism and locality is often an order of magnitude. However, using existing programming tools, writing high-performance image processing code requires sacrificing simplicity, portability, and modularity. We argue that this is because traditional programming models conflate the computations defining the
algorithm
with decisions about intermediate storage and the order of computation, which we call the
schedule.

We propose a new programming language for image processing pipelines, called Halide, that separates the algorithm from its schedule. Programmers can change the schedule to express many possible organizations of a single algorithm. The Halide compiler then synthesizes a globally combined loop nest for an entire algorithm, given a schedule. Halide models a space of schedules which is expressive enough to describe organizations that match or outperform state-of-the-art hand-written implementations of many computational photography and computer vision algorithms. Its model is simple enough to do so often in only a few lines of code, and small changes generate efficient implementations for x86, ARM, Graphics Processors (GPUs), and specialized image processors, all from a single algorithm.

Halide has been public and open source for over four years, during which it has been used by hundreds of programmers to deploy code to tens of thousands of servers and hundreds of millions of phones, processing billions of images every day.
Feeling sounds, hearing sights
Authors: Mone Gregory
Published: December 2017

A new wave of sensory substitution devices work to assist people who are blind or deaf.
Smartphone science
Authors: Wright Alex
Published: December 2017

A new generation of portable scientific instruments is taking shape, thanks to mobile processors and innovative data-gathering techniques.
Popularity spikes hurt future chances for viral propagation of protomemes
Authors: Coscia Michele
Published: December 2017

Once a meme gets popular, it will have to evolve to keep being popular.
User-Generated Content in Pervasive Games
Authors: Kasapakis Vlasios , Gavalas Damianos
Published: December 2017

User-generated content (UGC) is already incorporated in several computer game instances wherein the players may create, edit and release their own content to the game world, thus influencing the game's evolution as well as the experience of other players. Lately, pervasive games have emerged as an exciting new development in gaming extending the boundaries of play out in the real word. The effectiveness of pervasive games in creating immersive live-action game experiences principally depends on the correlation of the game content with actual physical elements. To address this issue, most pervasive game prototypes so far have been bound to specific locations, while game content has been manually edited by the developers; they have also been heavily dependent on the mediation of orchestration teams. Nevertheless, the capacity of pervasive games to be staged anywhere (i.e. their portability) is critical for their wider adoption and commercial success. Since the manual creation of game content is not feasible in portable games, UGC remains as the only practical option for content provision. Notably, the impact of UGC has not been studied so far in the pervasive games literature. This article introduces
Barbarossa
, a pervasive role-playing game based on UGC.
Barbarossa
serves as a testbed for investigating the effect of UGC under diverse technical, functional and game play characteristics. The user trials of
Barbarossa
confirmed that the effective use of UGC can enhance the quality of experience perceived by players and indirectly serve as a useful orchestration tool. We also document best practices with respect to the effective use of UGC in pervasive games, which could be useful to future developers.
How law and computer science can work together to improve the information society
Authors: Marsden Chris
Published: December 2017

Seeking to remedy bad legislation with good science.
Phase-amplitude coupling within the anterior thalamic nuclei during seizures
Authors: Ibrahim George M. , Wong Simeon , Morgan Benjamin R. , Lipsman Nir , Fallah Aria , Weil Alexander G. , Krishna Vibhor , Wennberg Richard A. , Lozano Andres A.
Published: December 2017

Cross-frequency phase-amplitude coupling (cfPAC) subserves an integral role in the hierarchical organization of interregional neuronal communication and is also expressed by epileptogenic cortex during seizures. Here, we sought to characterize patterns of cfPAC expression in the anterior thalamic nuclei during seizures by studying extra-operative recordings in patients implanted with deep brain stimulation electrodes for intractable epilepsy. Nine seizures from two patients were analyzed in the peri-ictal period. CfPAC was calculated using the modulation index and interregional functional connectivity was indexed using the phase-locking value. Statistical analysis was performed within subjects on the basis of nonparametric permutation and corrected with Gaussian field theory. Five of the nine analyzed seizures demonstrated significant cfPAC. Significant cfPAC occurred during the pre-ictal and ictal periods in three seizures, as well as the postictal windows in four seizures. The preferred phase at which cfPAC occurred differed 1) in space, between the thalami of the epileptogenic and nonepileptogenic hemispheres; and 2) in time, at seizure termination. The anterior thalamic nucleus of the epileptogenic hemisphere also exhibited altered interregional phase-locking synchrony concurrent with the expression of cfPAC. By analyzing extraoperative recordings from the anterior thalamic nuclei, we show that cfPAC associated with altered interregional phase synchrony is lateralized to the thalamus of the epileptogenic hemisphere during seizures. Electrophysiological differences in cfPAC, including preferred phase of oscillatory interactions may be further investigated as putative targets for individualized neuromodulation paradigms in patients with drug-resistant epilepsy.

NEW & NOTEWORTHY The association between fast brain activity and slower oscillations is an integral mechanism for hierarchical neuronal communication, which is also manifested in epileptogenic cortex. Our data suggest that the same phenomenon occurs in the anterior thalamic nuclei during seizures. Further, the preferred phase of modulation shows differences in space, between the epileptogenic and nonepileptogenic hemispheres and time, as seizures terminate. Our data encourage the study of cross-frequency coupling for targeted, individualized closed-loop stimulation paradigms.
Navel Orange Maturity Classification by Multispectral Indexes Based on Hyperspectral Diffuse Transmittance Imaging
Authors: Wei Xuan , He Jin-Cheng , Ye Da-Peng , Jie Deng-Fei
Published: December 2017

Maturity grading is important for the quality of fruits. Nondestructive maturity detection can be greatly beneficial to the consumer and fruit industry. In this paper, a hyperspectral image of navel oranges was obtained using a diffuse transmittance imaging based system. Multispectral indexes were built to identify the maturity with the hyperspectral technique. Five indexes were proposed to combine the spectra at wavelengths of 640, 760 nm (red edges), and 670 nm (for chlorophyll content) to grade the navel oranges into three maturity stages. The index of (T670+T760-T640)/(T670+T760+T640) seemed to be more appropriate to classify maturity, especially to distinguish immature oranges that can be straightly identified in accordance with the value of this index ((T670+T760-T640)/(T670+T760+T640)). Different indexes were used as the input of linear discriminate analysis (LDA) and of k-nearest neighbor (k-NN) algorithm to identify the maturity, and it was found that k-NN with (T670+T760-T640)/(T670+T760+T640) could reach the highest correct classification rate of 96.0%. The results showed that the built index was feasible and accurate in the nondestructive classification of oranges based on the hyperspectral diffuse transmittance imaging. It will greatly help to develop low-cost and real-time multispectral imaging systems for the nondestructive detection of fruit quality in the industry.
Oxidative Stress in Patients Undergoing Peritoneal Dialysis: A Current Review of the Literature
Authors: Liakopoulos Vassilios , Roumeliotis Stefanos , Gorny Xenia , Eleftheriadis Theodoros , Mertens Peter R.
Published: December 2017

Peritoneal dialysis (PD) patients manifest excessive oxidative stress (OS) compared to the general population and predialysis chronic kidney disease patients, mainly due to the composition of the PD solution (high‐glucose content, low pH, elevated osmolality, increased lactate concentration and glucose degradation products). However, PD could be considered a more biocompatible form of dialysis compared to hemodialysis (HD), since several studies showed that the latter results in an excess accumulation of oxidative products and loss of antioxidants. OS in PD is tightly linked with chronic inflammation, atherogenesis, peritoneal fibrosis, and loss of residual renal function. Although exogenous supplementation of antioxidants, such as vitamins E and C, N‐acetylcysteine, and carotenoids, in some cases showed potential beneficial effects in PD patients, relevant recommendations have not been yet adopted in everyday clinical practice.
Analytic Method on Characteristic Parameters of Bacteria in Water by Multiwavelength Transmission Spectroscopy
Authors: Hu Yuxia , Zhao Nanjing , Gan Tingting , Duan Jingbo , Yu Hui Juan , Meng Deshuo , Liu Jianguo , Liu Wenqing
Published: December 2017

An analytic method together with the Mie scattering theory and Beer-Lambert law is proposed for the characteristic parameter determination of bacterial cells (Escherichia coli10389) from multiwavelength transmission spectroscopy measurements. We calculate the structural parameters ofE. colicells, and compared with the microscopy, the relative error of cell volume is 7.90%, the cell number is compared with those obtained by plate counting, the relative error is l.02%, and the nucleic content and protein content of singleE. colicells are consistent with the data reported elsewhere. The proposed method can obtain characteristic parameters of bacteria as an excellent candidate for the rapid detection and identification of bacteria in the water.
Effects of TLR3 and TLR9 Signaling Pathway on Brain Protection in Rats Undergoing Sevoflurane Pretreatment during Cardiopulmonary Bypass
Authors: Nan Zhou , Jin Zhou , Huijuan Cao , Tiezheng Zhang , Keyan Chen
Published: December 2017

Objective. To investigate the effects of TLR3 and TLR9 signaling pathway on brain injury during CPB in rats pretreated with sevoflurane and its possible molecular mechanism.Methods. SD rats were randomly assigned to sham group, CPB group, and Sev group. Brain tissue was obtained at before CPB (T0), at CPB for 30 minutes (T1), 1 hour after CPB (T3), and 3 hours after CPB (T5). ELISA was used to measure S100-βand IL-6. Western blot was utilized to determine TLR3 and TLR9 expression. TUNEL was applied to detect neuronal apoptosis.Results. Compared with CPB group, atT1, at termination after 1 hour of CPB (T2),T3, 2 hours after CPB (T4) andT5, S100-βand IL-6 decreased in Sev group. Compared with CPB group, IFN-βwere increased in Sev group, exceptT0. Compared with CPB group, TLR3 expression increased, and TLR9 and NF-κB decreased in Sev group. The apoptotic neurons were less in Sev group than in CPB group (P<0.05).Conclusion. Sevoflurane intervention can activate TLR3 and TLR9 signaling pathway, upregulate TLR3 expression and downstream TRIF expression, decrease TLR9 expression, and downregulate downstream NF-κB expression in CPB rat models, thereby mitigating brain injury induced by inflammatory response during CPB.
Expression of Cancer Stem Cell Marker CD44 and Its Polymorphisms in Patients with Chronic Gastritis, Precancerous Gastric Lesion, and Gastric Cancer: A Cross-Sectional Multicenter Study in Thailand
Authors: Tongtawee Taweesak , Wattanawongdon Wareeporn , Simawaranon Theeraya , Kaewpitoon Soraya , Kaengpenkae Sivamate , Jintabanditwong Nichaphat , Tangjanyatham Pakorn , Ratchapol Warisara , Kangwantas Kokiet , Dechsukhum Chavaboon , Leeanansaksiri Wilairat , Kaewpitoon Natthawut , Matrakool Likit , Panpimanmas Sukij
Published: December 2017

Here we investigated CD44 protein expression and its polymorphisms in patients with chronic gastritis, precancerous gastric lesions, and gastric cancer; and we evaluated our result with the risk of CD44 protein expression and clinicopathological characteristics. Our results obtained by analyzing 162 gastric cancer patients, 125 chronic gastritis, and 165 precancerous gastric lesions from three study centers in Thailand showed that CD44 expression was significantly higher in patients with precancerous gastric lesions and gastric cancer while patients with chronic gastritis were negative for CD44 staining (p=0.036). We further observed the significant association of variant genotype; gastric cancer patients carrying AG or GG of CD44 rs187116 had more increased risk of CD44 expression than wild-type (WT) carriers (AG: odds ratio (OR) = 5.67; 95% CI = 1.57–7.23; p=0.024 and GG: OR = 8.32; 95% CI = 2.94–11.42; p=0.016), but no significant difference in the risk of CD44 expression due to polymorphism in patients with precancerous gastric lesions. Our results suggested that CD44 expression could be used as a marker for the prediction of gastric cancer development, particularly in patients with precancerous gastric lesions carrying AG or GG, who were selected to surveillance follow-up for gastric cancer prevention.
Correlation between Pathological Characteristics and Young’s Modulus Value of Spastic Gastrocnemius in a Spinal Cord Injury Rat Model
Authors: Jiang Li , Wang Yu-jue , Wang Qiao-yuan , Wang Qing , Wei Xiao-mei , Li Na , Guo Wei-ping , Dou Zu-lin
Published: December 2017

The goal of the present study were (1) to investigate the pathological characteristics of gastrocnemius muscle (GM) and quantitatively assess GM tissue stiffness in rat models with spinal cord injury (SCI) and (2) to explore the correlation between pathological characteristics changes and Young’s modulus value of GM. 24 Sprague Dawley male rats were allocated into normal control groups and SCI model subgroups, respectively. GM stiffness was assessed with shear wave sonoelastography technology. All GMs were further analyzed by pathological examinations. GM weights were decreased, the ratio of type I fibers was decreased, and the ratio of type II fibers was increased in the GM in the model group. MyHC-I was decreased, while MyHC-II was increased according to the electrophoretic analysis in model subgroups. The elastic modulus value of GM was increased in the model group. A significant negative correlation was found between Young’s modulus value of GM and the ratio of type I fibers of GM in model subgroup. Our studies showed that the stiffness of GM is correlated with pathological characteristics during the initial stages of SCI in rats. We also identified shear wave sonoelastography technology as a useful tool to assess GM stiffness in SCI rat models.
Immunomodulatory Effect of Flavonoids of Blueberry (Vaccinium corymbosum L.) Leaves via the NF-κB Signal Pathway in LPS-Stimulated RAW 264.7 Cells
Authors: Shi Dazhi , Xu Mengyi , Ren Mengyue , Pan Enshan , Luo Chaohua , Zhang Wei , Tang Qingfa
Published: December 2017

Objective. This study aimed to explore the immunoregulatory effect of flavonoids of blueberry (Vaccinium corymbosum L.) leaves (FBL). Methods. The flavonoids of blueberry leaves were prepared with 70% ethanol and were identified by ultraperformance liquid chromatography/quadrupole-time-of-flight mass spectrometry (UPLC/Q-Tof-MS). The immunoregulatory effect and possible regulatory mechanisms of FBL were investigated in lipopolysaccharide- (LPS-) induced RAW 264.7 cells. Results. According to the results of UPLC/Q-Tof-MS, nine flavonoids of blueberry leaves were identified. FBL showed a significant reduction in the production of TNF-α in LPS-stimulated RAW 264.7 cells. FBL significantly decreased the expression of NF-κB p65 and P-NF-κB p65 in LPS-induced RAW 264.7 cells in a dose-dependent manner. Conclusion. Our study showed the immunoregulatory effect of FBL through the suppression of TNF-α via the NF-κB signal pathway.
Modulation of Tumor-Associated Macrophages (TAM) Phenotype by Platelet-Activating Factor (PAF) Receptor
Authors: da Silva Junior Ildefonso Alves , Stone Simone Cardozo , Rossetti Renata Marques , Jancar Sonia , Lepique Ana Paula
Published: December 2017

Platelet-activating factor (PAF) plays an important role in the pathogenesis of several types of tumors. The biological effects of PAF are mediated by the PAF receptor (PAFR), which can be expressed by tumor cells and host cells that infiltrate the tumor microenvironment. In the present study, we investigated the role of PAFR expressed by leukocytes that infiltrate two types of tumors, one that expresses PAFR (TC-1 carcinoma) and another that does not express the receptor (B16F10 melanoma) implanted in mice that express the receptor or not (PAFR KO). It was found that both tumors grew significantly less in PAFR KO than inwild-type(WT) mice. Analysis of the leukocyte infiltration shown in PAFR KO increased the frequency of neutrophils (Gr1+) and of CD8+lymphocytes in B16F10 tumors and of CD4+lymphocytes in TC-1 tumors. PAFR KO also had a higher frequency of M1-like (CD11c+) and lower M2-like (CD206+) macrophages infiltrated in both tumors. This was confirmed in macrophages isolated from the tumors that showed higher iNOS, lower arginase activity, and lower IL10 expression in PAFR KO tumors than WT mice. These data suggest that in the tumor microenvironment, endogenous PAF-like activity molecules bind PAFR in macrophages which acquire an M2-like profile and this promotes tumor growth.
Automated Epileptic Seizure Detection in Scalp EEG Based on Spatial-Temporal Complexity
Authors: Zhu Xinzhong , Xu Huiying , Zhao Jianmin , Tian Jie
Published: December 2017

Epilepsy is a group of neurological disorders characterized by epileptic seizures, wherein electroencephalogram (EEG) is one of the most common technologies used to diagnose, monitor, and manage patients with epilepsy. A large number of EEGs have been recorded in clinical applications, which leads to visual inspection of huge volumes of EEG not routinely possible. Hence, automated detection of epileptic seizure has become a goal of many researchers for a long time. A novel method is therefore proposed to construct a patient-specific detector based on spatial-temporal complexity analysis, involving two commonly used entropy-based complexity analysis methods, which are permutation entropy (PE) and sample entropy (SE). The performance of spatial-temporal complexity method is evaluated on a shared dataset. Results suggest that the proposed epilepsy detectors achieve promising performance: the average sensitivities of PE and SE in 23 patients are 99% and 96.6%, respectively. Moreover, both methods can accurately recognize almost all the seizure-free EEG. The proposed method not only obtains a high accuracy rate but also meets the real-time requirements for its application on seizure detection, which suggests that the proposed method has the potential of detecting epileptic seizures in real time.
PSBinder: A Web Service for Predicting Polystyrene Surface-Binding Peptides
Authors: Li Ning , Kang Juanjuan , Jiang Lixu , He Bifang , Lin Hao , Huang Jian
Published: December 2017

Polystyrene surface-binding peptides (PSBPs) are useful as affinity tags to build a highly effective ELISA system. However, they are also a quite common type of target-unrelated peptides (TUPs) in the panning of phage-displayed random peptide library. As TUP, PSBP will mislead the analysis of panning results if not identified. Therefore, it is necessary to find a way to quickly and easily foretell if a peptide is likely to be a PSBP or not. In this paper, we describe PSBinder, a predictor based on SVM. To our knowledge, it is the first web server for predicting PSBP. The SVM model was built with the feature of optimized dipeptide composition and 87.02% (MCC = 0.74; AUC = 0.91) of peptides were correctly classified by fivefold cross-validation. PSBinder can be used to exclude highly possible PSBP from biopanning results or to find novel candidates for polystyrene affinity tags. Either way, it is valuable for biotechnology community.
HIV-Stigma in Nigeria: Review of Research Studies, Policies, and Programmes
Authors: Odimegwu Clifford O. , Akinyemi Joshua O. , Alabi Olatunji O.
Published: December 2017

Nigeria has about 3.8 million people living with HIV, the second largest globally. Stigma and discrimination are major barriers to testing, treatment uptake, and adherence. In this review, we synthesized information on research studies, policies, and programmes related to HIV-stigma in Nigeria. This was with a view to identify critical areas that research and programmes must address in order to accelerate the progress towards zero (new infections, discrimination, and death) target by year 2030. Existing studies were mostly devoted to stigma assessment using varieties of measures. Research, policies, and programmes in the past two decades have made very useful contributions to stigma reduction. We identified the need for a consistent, valid, and objective measure of stigma at different levels of the HIV response. Nigeria does not lack relevant policies; what needs to be strengthened are design, planning, implementation, monitoring, and evaluation of context-specific stigma reduction programmes.
Approximate Path Searching Method for Single‐Satellite Observation and Transmission Task Planning Problem
Authors: Peng Shuang , Chen Hao , Li Jun , Jing Ning
Published: December 2017

Satellite task planning not only plans the observation tasks to collect images of the earth surface, but also schedules the transmission tasks to download images to the ground station for users’ using, which plays an important role in improving the efficiency of the satellite observation system. However, most of the work to our knowledge, scheduling the observation and transmission tasks separately, ignores the correlation between them in resource (e.g., energy and memory) consumption and acquisition. In this paper, we study the single‐satellite observation and transmission task planning problem under a more accurate resource usage model. Two preprocessing strategies including graph partition and nondominated subpaths selection are used to decompose the problem, and an improved label‐setting algorithm with the lower bound cutting strategy is proposed to maximize the total benefit. Finally, we compare the proposed method with other three algorithms based on three data sets, and the experimental result shows that our method can find the near‐optimal solution in much less time.
Icariin Regulates the Bidirectional Differentiation of Bone Marrow Mesenchymal Stem Cells through Canonical Wnt Signaling Pathway
Authors: Huang Jun-ming , Bao Yuan , Xiang Wei , Jing Xing-zhi , Guo Jia-chao , Yao Xu-dong , Wang Rui , Guo Feng-jin
Published: December 2017

Fat infiltration within the bone marrow is easily observed in some postmenopausal women. Those fats are mainly derived from bone marrow mesenchymal stem cells (BMMSCs). The increment of adipocytes derived from BMMSCs leads to decreased osteoblasts derived from BMMSCs, so the bidirectional differentiation of BMMSCs significantly contributes to osteoporosis. Icariin is the main extractive of Herba Epimedii which is widely used in traditional Chinese medicine. In this experiment, we investigated the effect of icariin on the bidirectional differentiation of BMMSCs through quantitative real‐time PCR, immunofluorescence, western blot, and tissue sections in vitro and in vivo. We found that icariin obviously promotes osteogenesis and inhibits adipogenesis through detecting staining and gene expression. Micro‐CT analysis showed that icariin treatment alleviated the loss of cancellous bone of the distal femur in ovariectomized (OVX) mice. H&E staining analysis showed that icariin‐treated OVX mice obtained higher bone mass and fewer bone marrow lipid droplets than OVX mice. Western blot and immunofluorescence showed that icariin regulates the bidirectional differentiation of BMMSCs via canonical Wnt signaling. This study demonstrates that icariin exerts its antiosteoporotic effect by regulating the bidirectional differentiation of BMMSCs through the canonical Wnt signaling pathway.
Macrophage Polarization in Cerebral Aneurysm: Perspectives and Potential Targets
Authors: Shao Lingmin , Qin Xingping , Liu Jia , Jian Zhihong , Xiong Xiaoxing , Liu Renzhong
Published: December 2017

Cerebral aneurysms (CAs) have become a health burden not only because their rupture is life threatening, but for a series of devastating complications left in survivors. It is well accepted that sustained chronic inflammation plays a crucial role in the pathology of cerebral aneurysms. In particular, macrophages have been identified as critical effector cells orchestrating inflammation in CAs. In recent years, dysregulated M1/M2 polarization has been proposed to participate in the progression of CAs. Although the pathological mechanisms of M1/M2 imbalance in CAs remain largely unknown, recent advances have been made in the understanding of the molecular basis and other immune cells involving in this sophisticated network. We provide a concise overview of the mechanisms associated with macrophage plasticity and the emerging molecular targets.
Connecting Patterns Inspire Link Prediction in Complex Networks
Authors: Zhou Ming-Yang , Liao Hao , Xiong Wen-Man , Wu Xiang-Yang , Wei Zong-Wen
Published: December 2017

Link prediction uses observed data to predict future or potential relations in complex networks. An underlying hypothesis is that two nodes have a high likelihood of connecting together if they share many common characteristics. The key issue is to develop different similarity-evaluating approaches. However, in this paper, by characterizing the differences of the similarity scores of existing and nonexisting links, we find an interesting phenomenon that two nodes with some particular low similarity scores also have a high probability to connect together. Thus, we put forward a new framework that utilizes an optimal one-variable function to adjust the similarity scores of two nodes. Theoretical analysis suggests that more links of low similarity scores (long-range links) could be predicted correctly by our method without losing accuracy. Experiments in real networks reveal that our framework not only enhances the precision significantly but also predicts more long-range links than state-of-the-art methods, which deepens our understanding of the structure of complex networks.
Nesprin-2 Interacts with Condensin Component SMC2
Authors: Xing Xin , Mroß Carmen , Hao Linlin , Munck Martina , Herzog Alexandra , Mohr Clara , Unnikannan C. P. , Kelkar Pranav , Noegel Angelika A. , Eichinger Ludwig , Neumann Sascha
Published: December 2017

The nuclear envelope proteins, Nesprins, have been primarily studied during interphase where they function in maintaining nuclear shape, size, and positioning. We analyze here the function of Nesprin-2 in chromatin interactions in interphase and dividing cells. We characterize a region in the rod domain of Nesprin-2 that is predicted as SMC domain (aa 1436–1766). We show that this domain can interact with itself. It furthermore has the capacity to bind to SMC2 and SMC4, the core subunits of condensin. The interaction was observed during all phases of the cell cycle; it was particularly strong during S phase and persisted also during mitosis. Nesprin-2 knockdown did not affect condensin distribution; however we noticed significantly higher numbers of chromatin bridges in Nesprin-2 knockdown cells in anaphase. Thus, Nesprin-2 may have an impact on chromosomes which might be due to its interaction with condensins or to indirect mechanisms provided by its interactions at the nuclear envelope.
Temporal Regulation offimGenes in UropathogenicEscherichia coliduring Infection of the Murine Urinary Tract
Authors: Schwan William R. , Ding Hua
Published: December 2017

UropathogenicEscherichia coli(UPEC) adhere to cells in the human urinary tract via type 1 pili that undergo phase variation where a 314-bpfimSDNA element flips between Phase-ON and Phase-OFF orientations through two site-specific recombinases, FimB and FimE. Threefim-luxoperon transcriptional fusions were created and moved into the clinical UPEC isolate NU149 to determine their temporal regulation in UPEC growing in the urinary tract. Within murine urinary tracts, the UPEC strains demonstrated elevated transcription offimAandfimBearly in the infection, but lower transcription by the fifth day in murine kidneys. In contrast,fimEtranscription was much lower than eitherfimAorfimBearly, increased markedly at 24 h after inoculation, and then dropped five days after inoculation. Positioning offimSwas primarily in the Phase-ON position over the time span in UPEC infected bladders, whereas in UPEC infected murine kidneys the Phase-OFF orientation was favored by the fifth day after inoculation. Hemagglutination titers with guinea pig erythrocytes remained constant in UPEC growing in infected murine bladders but fell substantially in UPEC infected kidneys over time. Our results show temporalin vivoregulation offimgene expression in different environmental niches when UPEC infects the murine urinary tract.
High Sensitivity of Human Adipose Stem Cells to Differentiate into Myofibroblasts in the Presence of C. aspersa Egg Extract
Authors: García-Honduvilla Natalio , Cifuentes Alberto , Ortega Miguel A. , Delgado Arancha , González Salvador , Bujan Julia , Alvarez-Mon Melchor
Published: December 2017

Introduction. Regeneration therapy using adipose-derived stem cells (ADSC) has been proposed in the treatment of skin aging. Myofibroblast plays a relevant role in the organization of the extracellular matrix of the damaged skin. A natural extract was derived from the eggs of the mollusk Cryptomphalus aspersa (e-CAF) that seems to play a role on skin repair. We have investigated the potential effects of e-CAF in the differentiation of ADSC. Materials and methods. ADSC were cultured in the absence or presence of e-CAF (50 and 200 μg/mL) for 24 hours and 7 days. Real-time cell assay, morphological, immunofluorescence, and RT-PCR techniques were used to evaluate the cell culture and expression of αSMA, collagen I, and tropoelastin. Results. e-CAF induced significant reduction in the rate of growth of ADSC from 24 hours to 7 days of culture. e-CAF also induced bigger sizes, higher levels of cytoplasmic refringence and complexity, and a more polyhedral morphological changes in the cultured ADSC. The protein and mRNA expression of αSMA was significantly increased in e-CAF-cultured ADSC. Conclusion. e-CAF promotes ADSC differentiation to myofibroblasts and should be considered as a potential agent for the prevention and treatment of skin aging.
Acoustic Emission Monitoring and Failure Precursors of Sandstone Samples under Various Loading and Unloading Paths
Authors: Xu Jie , Jiang Jingdong , Zuo Lingling , Gao Yufeng
Published: December 2017

To explore the failure precursors of hard rock, a series of triaxial loading and unloading experiments were carried out on sandstone sample using the acoustic emission systems. The extreme-point symmetric mode decomposition method (ESMD method) was used to denoise and reconstruct the AE data. The AE quiet period in Scheme I becomes much more obvious with the confining pressure increasing, which can be regarded as the precursor information of the sample failure under conventional triaxial compression. Unlike Scheme I, there are no obvious precursory characteristics before failure in Schemes II and III, and the count rate reaches the maximum at the peak point. When the stress ratio ranges from 0.8 to 1.0, the fractal values of acoustic emission can be used to investigate the failure precursors of samples at a lower confining pressure. When the time ratio is greater than 0.8 under higher confining pressures, the fractal values of sandstone samples under unloading paths are rapidly reduced, which can be used to predict rock failure at higher confining pressures.
First records of the Indo-Pacific Finless Porpoise Neophocaena phocaenoides (G. Cuvier, 1829) (Cetartiodactyla: Phocoenidae) from Sri Lanka
Authors: Nanayakkara Ranil P. , Jefferson Thomas A. , Abayaratne Sandaruwan
Published: December 2017

Thirty species of marine mammals have been recorded from Sri Lanka.  Amongst them the Indo-Pacific Finless Porpoise Neophocaena phocaenoides is the only representative of the family Phocoenidae.  The only previous record from Sri Lanka was a specimen caught on the Wadge Bank by a Smithsonian Carangid Survey team in 1970.  Wadge Bank is west of the island and is, in fact, in Indian territorial waters.  Here we present the first legitimate records of the Finless Porpoise from Sri Lanka, based on one stranding and three live sightings.  Furthermore, the occurrence of threatened species such as the Indo-Pacific Finless Porpoise in the waters of the Palk Bay and the Gulf of Mannar indicates that a cross boundary research initiative between Indian and Sri Lankan scientists, simultaneously focusing on the conservation of the species, is essential.  We believe, through such an initiative, a more holistic approach could be adopted when studying and conserving the species, which could then be expanded to encapsulate many other marine species and ecosystems.
Nyctibatrachus mewasinghi, a new species of night frog (Amphibia: Nyctibatrachidae) from Western Ghats of Kerala, India
Authors: Krutha Keerthi , Dahanukar Neelesh , Molur Sanjay
Published: December 2017

A new species Nyctibatrachus mewasinghi is described from the Malabar Wildlife Sanctuary of Western Ghats of Kozhikode District, Kerala.  The new species can be distinguished from known congeners based on small adult size, head equal to or slightly wider than long, less wrinkled dorsal skin with prominent granular projections, absence of dorso-lateral glandular folds, a ridge extending from the lip over the tip of the snout to between the nostrils bifurcate posteriorly producing an inverted ‘Y’, finger and toe discs well developed with dorso-terminal groove, cover rounded distally, third finger disc slightly wider than finger width and fourth toe disc almost equal to or slightly wider than toe width, presence of two palmar tubercles, moderate webbing and thigh, shank and foot almost of equal length.  Molecular phylogeny based on two mitochondrial genes (ND1 and 16S rRNA) reveals that the species is genetically distinct from others within the genus, and is a sister taxon to N. athirappillyensis and N. kempholeyensis.  Multivariate morphometric analysis clearly distinguishes the new night frog species Nyctibatrachus mewasinghi from N. athirappillyensis and N. kempholeyensis.
Phenology and seed germination of the Indian Screw Tree Helicteres isora L. (Malvales: Malvaceae)
Authors: Muthukumar Mariappan , Kumar Thiruppathi Senthil , Rao Mandali Venkateswara
Published: December 2017

Helicteres isora L. (Malvaceae), a medicinally important tree species used in Ayurveda as well as by folklore practitioners, is studied for its phenology, associated problems with the environment and anthropogenic effects.  In Helicteres isora, flower buds are initiated by the end of July and flowering occurs during the middle of August to late October.  Fruits mature during late January to early April.  In between various factors like blister beetles, unidentified worms, deficit rainfall, early summer affect the flowering and seed setting, which cause 35–45 % loss.  Seed viability of mature seeds were recorded 88.2% at fresh collection and decreases over period of time. In vitro, among the various treatments, acid treated seeds (H2SO4, 98.0%; 1 min) resulted in the best germination response of 84.5%.  Sterile wet cotton soaked with sterile distilled water was found suitable for germination compared to other substratum, while half-strength MS medium with 2.0% sucrose was suitable for seedling development.
Notes on taxonomy and captive development of the Rattus andamanensis (Blyth, 1860) (Rodentia: Muridae) from southern Andamans, India
Authors: Talmale S. S. , Bharathimeena T.
Published: December 2017

Studies on mammalian fauna from the Andaman & Nicobar Islands have been done by various researchers but meager information is available on rodent fauna from these Islands.  Morphometric and cranial details of fresh specimens of one of the rodent species, Rattus andamanensis (Blyth, 1860) of family Muridae, collected from its type locality in southern Andamans has been reported in the present paper.  Morphological variations within the population are discussed.  Observations on in-captivity-development of the young ones of the species in the laboratory are also recorded.
First record of migratory Grey-necked Bunting Emberiza buchanani Blyth, 1844 (Aves: Passeriformes: Emberizidae) as a winter visitor in Tiruchirappalli District, Tamil Nadu, India
Authors: Siva T. , Neelanarayanan P.
Published: December 2017

The Grey-necked Bunting or Grey-hooded Bunting is a New World sparrow and a winter visitor to India, particularly Gujarat region.  Earlier, sightings of this species were rarely reported from other parts of India.  In this communication the Grey-necked Bunting is reported for the first time with photographic evidence in Tiruchirappalli District, Tamil Nadu.  The bird was observed in dry open areas and small hillocks. Detailed information on this species is wanting.
MUSCLEMOTION
Authors: Sala Luca , van Meer Berend J. , Tertoolen Leon G.J. , Bakkers Jeroen , Bellin Milena , Davis Richard P. , Denning Chris , Dieben Michel A.E. , Eschenhagen Thomas , Giacomelli Elisa , Grandela Catarina , Hansen Arne , Holman Eduard R. , Jongbloed Monique R.M. , Kamel Sarah M. , Koopman Charlotte D. , Lachaud Quentin , Mannhardt Ingra , Mol Mervyn P.H. , Mosqueira Diogo , Orlova Valeria V. , Passier Robert , Ribeiro Marcelo C. , Saleem Umber , Smith Godfrey L. , Burton Francis L. , Mummery Christine L.
Published: December 2017

Rationale:

There are several methods to measure cardiomyocyte and muscle contraction, but these require customized hardware, expensive apparatus, and advanced informatics or can only be used in single experimental models. Consequently, data and techniques have been difficult to reproduce across models and laboratories, analysis is time consuming, and only specialist researchers can quantify data.

Objective:

Here, we describe and validate an automated, open-source software tool (MUSCLEMOTION) adaptable for use with standard laboratory and clinical imaging equipment that enables quantitative analysis of normal cardiac contraction, disease phenotypes, and pharmacological responses.

Methods and Results:

MUSCLEMOTION allowed rapid and easy measurement of movement from high-speed movies in (1) 1-dimensional in vitro models, such as isolated adult and human pluripotent stem cell-derived cardiomyocytes; (2) 2-dimensional in vitro models, such as beating cardiomyocyte monolayers or small clusters of human pluripotent stem cell-derived cardiomyocytes; (3) 3-dimensional multicellular in vitro or in vivo contractile tissues, such as cardiac “organoids,” engineered heart tissues, and zebrafish and human hearts. MUSCLEMOTION was effective under different recording conditions (bright-field microscopy with simultaneous patch-clamp recording, phase contrast microscopy, and traction force microscopy). Outcomes were virtually identical to the current gold standards for contraction measurement, such as optical flow, post deflection, edge-detection systems, or manual analyses. Finally, we used the algorithm to quantify contraction in in vitro and in vivo arrhythmia models and to measure pharmacological responses.

Conclusions:

Using a single open-source method for processing video recordings, we obtained reliable pharmacological data and measures of cardiac disease phenotype in experimental cell, animal, and human models.
Embodiment and the Prophetic Message in Isaiah’s Memoir
Authors: Grey Jacqueline
Published: December 2017

In the Isaiah memoir, the prophet refers to three children that function as signs that embody his message. The signs of all three children are connected to the political situation of the Syro-Ephraimite Crisis preoccupying Judah at that time. The physical presence of Shear-Jashub (Isa 7:1–9) emphasized the immanence of the prophetic word. It highlights a value of the prophetic community of Isaiah: that a prophetic word, like embodiment, is present. The second child, Immanuel (Isa 7:10–16), highlights the importance of the physical presence of bearers of the prophetic message as imperative to the prophetic message. That is, the message of Isaiah relied upon the prophet and those that embodied his signs to be visible in the community, even when their presence was uncomfortable and unwanted. The third sign (Isa 8:1–4) is produced by the collaboration of Isaiah and the woman-prophet. This highlights the prophetic community of Isaiah as a discerning community that emphasized inclusivity as imperative. Like Isaiah’s community, the pentecostal family both historically and today identifies itself as a prophetic community. Isaiah’s memoir reminds us that prophetic communication should be relevant and immediate. A prophetic community addresses real-world problems and offers solutions that promote the holistic well-being of people and creation in their context. A prophetic community is committed to embodying its message. Yet, while this community is embodied and located in a culture, it needs to see beyond its own culture and the political challenges of its location. While it is important to identify and address the theological and social issues of each location, however, this should not be the sole lens through which we envision the future of Pentecostalism and the future of the Society for Pentecostal Studies.
Reading the Epistle of James with Socioeconomically Marginalized Immigrants in the Southern United States
Authors: Autero Esa
Published: December 2017

The themes of possessions and socioeconomic injustice have caught the attention of scholars of the Epistle of James in recent years. Nevertheless, most biblical scholars still focus primarily on the epistle’s historical aspects, a notable exception being Latin American scholars. Yet, even though many of these have interpreted James from the perspective of their context of socioeconomic exploitation, their readings do not report how people themselves understand and use biblical texts.1 This article explores the themes of wealth, poverty, and marginality in James using empirical hermeneutics. For this purpose, a group of Latino/a pentecostal believers in the southern United States read James 1:1–11 and 5:1–8 in a small Bible study group from the perspective of their religious experience, social marginalization, and economic exploitation. This article includes a report of the group’s reading of the above-mentioned passages, along with theological and practical reflections aimed at churches and practitioners.
Two New Rock-cut Tombs in the Bārāndūz Valley, Iran
Authors: Dan Roberto , Khan Mohammadi Behrouz , Haji Mohammadi Keomars
Published: December 2017

The article presents a newly discovered site with a fortress and a rock-cut complex in the Lake Urmiya basin. The site is located approximately 1 kilometre north-west of the village of Sydk/Sīdak in the Bārāndūz River valley, about 30 km south-west of the city of Urmiya.
On the Third Dagestani Campaign of Nadir Shah Afshar (1741): The Letters of Ibrahim of Urada
Authors: Aytberov Timirlan
Published: December 2017

The article presents the English translation with commentaries of three messages in Arabic by Ibrahim of Urada addressed to the people of Avaristan during the campaign of Nadir Shah to Dagestan. They provide important data elucidating the details of this poorly studied historical event that took place in the fall of 1741.
Bezeichnungen von Wurfwaffen und Belagerungsgeschützen im Iranischen I: Iranica mutuata II
Authors: Buyaner David B.
Published: December 2017

The paper focuses on two words of obscure etymology occurring in the Pahlavi text of presumably Parthian origin Draxt ī asūrīg, namely  and . For the former, numerous related forms in Classical Armenian, Old Georgian and New Persian are considered, and a new suggestion is made as regards the ultimate, i. e. Old Iranian, etymology of the term and the way by which it entered Middle West Iranian, as well as in respect of a subgroup of the forms discussed, which turns out to have derived from a variety of the etymon characterised by certain semantic and phonetic features. For both terms Sogdian origin is established and some further etymological considerations are made.