Miracle-dz/UniFAR-FTUs huggingface dataset:
The Research of Paper Influence Based on Citation Context - A Case Study of the Nobel Prize Winner's Paper

Citation context was used to measure the influence of highly cited papers. The themes of citation context were analyzed with bibliometrics methods. The citation context was classified into three categories as positive, negative and neutral. And the neutral citations were also classified into three sub categories, related work in background or introduction, theoretical foundation, and experimental foundation. The citation contexts of a highly cited paper of O’Keefe were extracted as the experiment data set. The results showed that the co-occurrence method was very useful for describing the themes of the citation contexts. The citation contexts of the selected paper were divided into five themes. The classification of citation contexts could provide more information about how and why a paper was highly cited. There was no negative citation in this experiment, and more than 10% citation contexts were positive citation. About 50% of the neutral citations were belonging to related work in background or introduction. The detailed influence of the target paper was also illustrated in our research.
The aminoglycoside antibiotic dihydrostreptomycin rapidly enters mouse outer hair cells through the mechano  ‐electrical transducer channels

The most serious side‐effect of the widely used aminoglycoside antibiotics is irreversible intracellular damage to the auditory and vestibular hair cells of the inner ear. The mechanism of entry into the hair cells has not been unequivocally resolved. Here we report that extracellular dihydrostreptomycin not only blocks the mechano‐electrical transducer channels of mouse outer hair cells at negative membrane potentials, as previously shown, but also enters the cells through these channels, which are located in the cells' mechanosensory hair bundles. The voltage‐dependent blocking kinetics indicate an open‐channel block mechanism, which can be well described by a two barrier–one binding site model, quantifying the antibiotic's block of the channel as well as its permeation in terms of the associated rate constants. The results identify the open transducer channels as the main route for aminoglycoside entry. Intracellularly applied dihydrostreptomycin also blocks the transducer channels, but at positive membrane potentials. However, the potency of the block was two orders of magnitude lower than that due to extracellular dihydrostreptomycin. Extracellular Ca2+ increases the free energy of the barrier nearest the extracellular side and of the binding site for dihydrostreptomycin. This reduces both the entry of dihydrostreptomycin into the channel and the channel's affinity for the drug. In vivo, where the extracellular Ca2+ concentration in the endolymph surrounding the hair bundles is < 100 μm, we predict that some 9000 dihydrostreptomycin molecules per second enter each hair cell at therapeutic drug concentrations.
Distributed transmit beamforming based on a 3-bit feedback system

A distributed transmit beamforming technique is developed for both a static and a time-varying channel in a wireless sensor network. This algorithm is based on an iterative procedure that synchronizes the transmitters to send a common message signal coherently to the receiver, using a 3-bit feedback in each timeslot. Results show that the received power increases quadratically with number of transmitters, and there is a substantially improved performance over a 1-bit feedback system and system without feedback.
Practical aspects of Compressed Suffix Arrays and FM-Index in Searching DNA Sequences

Searching patterns in the DNA sequence is an important step in biological research. To speed up the search process, one can index the DNA sequence. However, classical indexing data structures like suffix trees and suffix arrays are not feasible for indexing DNA sequences due to main memory requirement, as DNA sequences can be very long. In this paper, we evaluate the performance of two compressed data structures, Compressed Suffix Array (CSA) and FM-index, in the context of searching and indexing DNA sequences. Our results show that CSA is better than FM-index for searching long patterns. We also investigate other practical aspects of the data structures such as the memory requirement for building the indexes.
Reverse transcription–polymerase chain reaction molecular testing of cytology specimens: Pre‐analytic and analytic factors

The introduction of molecular testing into cytopathology laboratory practice has expanded the types of samples considered feasible for identifying genetic alterations that play an essential role in cancer diagnosis and treatment. Reverse transcription–polymerase chain reaction (RT‐PCR), a sensitive and specific technical approach for amplifying a defined segment of RNA after it has been reverse‐transcribed into its DNA complement, is commonly used in clinical practice for the identification of recurrent or tumor‐specific fusion gene events. Real‐time RT‐PCR (quantitative RT‐PCR), a technical variation, also permits the quantitation of products generated during each cycle of the polymerase chain reaction process. This review addresses qualitative and quantitative pre‐analytic and analytic considerations of RT‐PCR as they relate to various cytologic specimens. An understanding of these aspects of genetic testing is central to attaining optimal results in the face of the challenges that cytology specimens may present. Cancer Cytopathol 2017;125:11‐19. © 2016 American Cancer Society.
Meta-Analysis of the Cystatin C(CST3) Gene G73A Polymorphism and Susceptibility to Alzheimer's Disease

ABSTRACT Background: The association between cystatin C(CST3) gene (rs1064039) G73A polymorphism and Alzheimer's disease (AD) is controversial. The objective of the study was to investigate the possible association between CST3 G73A polymorphism and AD. Method: We performed a meta-analysis pooling data from all relevant studies including 2,410 cases and 2,539 controls. We applied a random-effects or fixed-effects model to combine odds ratio (OR) and 95% confidence intervals (95% CI). Results: Positive associations of the CST3 G73A polymorphism with AD risk were found in allele comparison A versus G (OR = 1.61, 95% CI = 1.19–2.18), dominant model AG + GG versus AA (OR = 0.63, 95% CI = 0.47–0.86), and homozygote comparison AA versus GG (OR = 1.61, 95% CI = 1.19–2.18). In subgroup analysis stratified by ethnicity, significant associations were also demonstrated in Caucasians under allele comparison (OR = 1.17, 95% CI = 1.02–1.33), dominant genetic (OR = 0.59, 95% CI = 0.40–0.86) model, and homozygote comparison (OR = 1.73, 95% CI = 1.18–2.54), but not in Asians. In subgroup analysis according to the age of onset, 73A allele (A versus G) was significantly associated with susceptibility to AD in Caucasians (OR = 1.26, 95% CI = 1.06–1.50), However, no association was found in Asians. Conclusion: The CST3 G73A polymorphism is associated with AD in Caucasian populations, but not in Asians.
MDG-1, a Potential Regulator of PPARα and PPARγ, Ameliorates Dyslipidemia in Mice

Hyperlipidemia is a serious epidemic disease caused by lipid metabolism disorder, which is harmful to human health. MDG-1, a β-d-fructan polysaccharide extracted from Ophiopogon japonicus, has been shown to improve abnormal blood lipid levels and alleviate diabetes. However, the underlying mechanism on hyperlipidemia is largely unknown. In this study, male C57BL/6 mice were randomly separated into three groups, respectively: low-fat diet (Con), high-fat diet (HFD), and high-fat diet plus 5‰ MDG-1 (HFD + MDG-1). Body weight was measured and the serum lipid levels were analyzed. Using gene microarray, various core pathways, together with levels of gene expression within hepatocytes, were analyzed. RT-PCR was used to confirm the identity of the differentially expressed genes. MDG-1 could prevent obesity in HFD-induced mice and improve abnormal serum lipids. Besides, MDG-1 could regulate hyperlipidemia symptoms, specifically, and decrease fasting blood glucose, improve glucose tolerance, and ameliorate insulin resistance. According to results from gene microarray, most of the identified pathways were involved in the digestion and absorption of fat, biosynthesis, and catabolism of fatty acids as well as the secretion and biological synthesis of bile acids. Furthermore, MDG-1 may act upon peroxisome proliferator-activated receptors (PPAR) α and γ, activating PPARα whilst inhibiting PPARγ, thus having a potent hypolipidemic effect.
A unified digital watermarking interface for eCommerce scenarios

There is an increased interest, by content creators and owners, in content protection systems that provide the ability to control or restrict the content that can be shared on peer-to-peer file sharing systems. At the same time, there is much debate that argues that content protection in peer-to-peer systems will unfairly restrict the users’ ability to share content. We explore the issue of content protection in peer-to-peer systems. We examine the benefits that it would provide to many parties including peer-to-peer network operators, individual and institutional content providers, and ultimately end-users. We then examine the challenges involved–the often conflicting goals of content providers and users. We explore how a content protection system can maintain the features that interest end-users such as an open peer-to-peer sharing experience, privacy, and flexible business models. We outline the design objectives of such a protection system. We discuss how previous attempts at content protection in peer-topeer systems only supported basic business models and show how protection systems can provide the flexibility necessary to support common content distribution business models. We explain the design space and examine proposed systems for centralized and decentralized content protection systems.
Ethnoecology of the Ozark Highlands' Agricultural Encounter

Throughout the twentieth century, many farm families in the Missouri Ozarks, USA, significantly changed their practices or abandoned agriculture as an occupation altogether. Researchers, farmers, and the general public assume the shift was an inevitable process of increasing economic efficiency. This article utilizes ethnoecology to demonstrate the importance of the overlooked cognitive aspects of agricultural modernization and to elucidate contemporary agricultural heterogeneity in the Ozark Mineral Area of southeast Missouri. Research included two years of participant observation, agro-ecosystem analysis, and ethno-ecological and semi-structured interviews to document Ozark farmers’ perceptions of their farming environments and their agroecological practices. While some farmers’ perceptions of their farming environments have changed with agricultural modernization, removing traditional morality from agricultural decisions, other farmers maintain traditional practices within their agroecological landscape.
Improving Digital Predistortion Mismatch Sensitivity Using Tunable Matching Networks

Digital predistortion (DPD) is a well-known method to reduce non-linear distortion in RF power amplifiers (PAs). In this paper, we present a study on the sensitivity of this linearization technique under large mismatch conditions, and how this sensitivity can be improved using a tunable matching network (TMN). Under different load conditions, PA behavior may change significantly making more complicated the DPD solution convergence, reducing its performance or even disabling its correct operation. Using a TMN the load impedance variation effect can be reduced, observing improvements in adjacent channel power ratio (ACPR) and regions of DPD convergence in the Smith chart.
Simplifying flexible isosurfaces using local geometric measures

The contour tree, an abstraction of a scalar field that encodes the nesting relationships of isosurfaces, can be used to accelerate isosurface extraction, to identify important isovalues for volume-rendering transfer functions, and to guide exploratory visualization through a flexible isosurface interface. Many real-world data sets produce unmanageably large contour trees which require meaningful simplification. We define local geometric measures for individual contours, such as surface area and contained volume, and provide an algorithm to compute these measures in a contour tree. We then use these geometric measures to simplify the contour trees, suppressing minor topological features of the data. We combine this with a flexible isosurface interface to allow users to explore individual contours of a dataset interactively.
Transcription elongation factor P‐TEFb mediates Tat activation of HIV‐1 transcription at multiple stages

Tat stimulates human immunodeficiency virus type 1 (HIV‐1) transcription elongation through recognition of the transactivation response (TAR) RNA stem–loop structure at the 5′ end of nascent viral transcripts. Recently, a human transcription elongation factor P‐TEFb, consisting of CDK9 kinase, cyclin T and other associated factors, has been shown to interact with Tat to restore Tat activation in HeLa nuclear extract depleted of P‐TEFb. Here, we report the purification of a P‐TEFb complex fraction containing epitope‐tagged wild‐type CDK9 or kinase‐inactive CDK9 and five tightly associated polypeptides. Only wild‐type P‐TEFb complex with an active CDK9 kinase was able to hyperphosphorylate the C‐terminal domain of RNA polymerase II and mediate Tat transactivation in P‐TEFb‐depleted HeLa nuclear extract. Tat also stimulated transcription elongation by recruitment of the P‐TEFb complex to the HIV‐1 promoter through a Tat–TAR interaction. A possible mechanism for P‐TEFb to become associated with polymerase elongation complexes and function as a general elongation factor was demonstrated by an interaction of P‐TEFb with double‐stranded RNA molecules through an 87 kDa subunit. Finally, P‐TEFb was found to interact with and phosphorylate Tat‐SF1, a Tat cofactor required for Tat transactivation. Our data indicate that the various subunits of the human P‐TEFb complex may play distinct roles at multiple stages to mediate Tat activation of HIV‐1 transcription elongation.
Endothelial nitric oxide synthase-related mechanotransduction changes in aged porcine angular aqueous plexus cells.

PURPOSE To investigate effects of aging on endothelial nitric oxide synthase (eNOS) expression and signaling in angular aqueous plexus (AAP) (functional equivalent to human Schlemm's canal) cells subjected to shear stress. METHODS The AAP cells were isolated differentially from porcine outflow tissues using puromycin selection. Cell aging was induced by culturing cells in hyperoxia condition (40% oxygen and 5% carbon dioxide) for 14 days. The AAP cells grown in chamber slides were exposed to a shear stress of 8 dynes/cm(2) for 24 hours. Expression of eNOS, eNOS-phospho Thr495, eNOS-phospho Ser1177, and Akt-phospho was tested by Western blot analysis and immunofluorescence staining. Nitric oxide (NO) levels were measured using the Griess assay. RESULTS Compared with control, eNOS levels in aged cells were significantly reduced by 60% (P < 0.05; n = 6). Phosphorylation of eNOS at Ser1177 and Akt at Ser473 was 63% and 80% lower in aged cells, respectively, whereas phosphorylation of the eNOS inhibition site (Thr495) increased by 6.1-fold (P < 0.05; n = 6). Shear stress (8 dynes/cm(2) for 24 hours) increased eNOS abundance (total protein and at cell borders) and phosphorylation at Ser1177 by 1.7-fold and 1.8-fold, respectively (P < 0.05; n = 6), whereas aged cells were unresponsive. In control cells exposed to shear stress, the NO concentration was 1.8-fold higher than in the static group (P < 0.05; n = 4); however, aged cells were unresponsive to shear stress (mean ± SD, 4.3 ± 1.3 vs. 4.1 ± 1.4 μM). CONCLUSIONS Aged AAP cells appear compromised in their mechanotransduction machinery involving eNOS, the protein product of the gene, NOS3, polymorphisms of which impart a risk for the development of glaucoma.
Random Accessible Mesh Compression Using Mesh Chartification

Previous mesh compression techniques provide decent properties such as high compression ratio, progressive decoding, and out-of-core processing. However, only a few of them supports the random accessibility in decoding, which enables the details of any specific part to be available without decoding other parts. This paper proposes an effective framework for the random accessibility of mesh compression. The key component of the framework is a wire-net mesh constructed from a chartification of the given mesh. Charts are compressed separately for random access to mesh parts and a wire-net mesh provides an indexing and stitching structure for the compressed charts. Experimental results show that random accessibility can be achieved with competent compression ratio, which is only a little worse than single-rate and comparable to progressive encoding. To demonstrate the merits of the framework, we apply it to process huge meshes in an out-of-core manner, such as out-of-core rendering and out-of-core editing.
N1-Src Kinase Is Required for Primary Neurogenesis in Xenopus tropicalis

The presence of the neuronal-specific N1-Src splice variant of the C-Src tyrosine kinase is conserved through vertebrate evolution, suggesting an important role in complex nervous systems. Alternative splicing involving an N1-Src-specific microexon leads to a 5 or 6 aa insertion into the SH3 domain of Src. A prevailing model suggests that N1-Src regulates neuronal differentiation via cytoskeletal dynamics in the growth cone. Here we investigated the role of n1-src in the early development of the amphibian Xenopus tropicalis, and found that n1-src expression is regulated in embryogenesis, with highest levels detected during the phases of primary and secondary neurogenesis. In situ hybridization analysis, using locked nucleic acid oligo probes complementary to the n1-src microexon, indicates that n1-src expression is highly enriched in the open neural plate during neurula stages and in the neural tissue of adult frogs. Given the n1-src expression pattern, we investigated a possible role for n1-src in neurogenesis. Using splice site-specific antisense morpholino oligos, we inhibited n1-src splicing, while preserving c-src expression. Differentiation of neurons in the primary nervous system is reduced in n1-src-knockdown embryos, accompanied by a severely impaired touch response in later development. These data reveal an essential role for n1-src in amphibian neural development and suggest that alternative splicing of C-Src in the developing vertebrate nervous system evolved to regulate neurogenesis. SIGNIFICANCE STATEMENT The Src family of nonreceptor tyrosine kinases acts in signaling pathways that regulate cell migration, cell adhesion, and proliferation. Srcs are also enriched in the brain, where they play key roles in neuronal development and neurotransmission. Vertebrates have evolved a neuron-specific splice variant of C-Src, N1-Src, which differs from C-Src by just 5 or 6 aa. N1-Src is poorly understood and its high similarity to C-Src has made it difficult to delineate its function. Using antisense knockdown of the n1-src microexon, we have studied neuronal development in the Xenopus embryo in the absence of n1-src, while preserving c-src. Loss of n1-src causes a striking absence of primary neurogenesis, implicating n1-src in the specification of neurons early in neural development.
Freeform Image

In this paper we present a technique for image deformation in which the user is given flexible control over what kind of deformation to perform. Freeform image extends available image deformation techniques in that it provides a palette of intuitive tools including interactive object segmentation, stiffness editing and force-based controls to achieve both a natural look and realistic animations of deforming parts. The model underlying our approach is physics-based and it is amenable to a variety of different kinds of image manipulations ranging from as-rigid- as-possible to fully elastic deformations. We have developed a multigrid solver for quadrangular finite elements, which achieves real-time performance for high resolution pixel grids. On recent CPUs this solver can handle about 16K co-rotated finite elements at roughly 60 ms.
Multiobjective Identification of Controlling Areas in Neuronal Networks

In this paper, we investigate the multiobjective identification of controlling areas in the neuronal network of a cat's brain by considering two measures of controllability simultaneously. By utilizing nondominated sorting mechanisms and composite differential evolution (CoDE), a reference-point-based nondominated sorting composite differential evolution (RP-NSCDE) is developed to tackle the multiobjective identification of controlling areas in the neuronal network. The proposed RP-NSCDE shows its promising performance in terms of accuracy and convergence speed, in comparison to nondominated sorting genetic algorithms II. The proposed method is also compared with other representative statistical methods in the complex network theory, single objective, and constraint optimization methods to illustrate its effectiveness and reliability. It is shown that there exists a tradeoff between minimizing two objectives, and therefore pareto fronts (PFs) can be plotted. The developed approaches and findings can also be applied to coordination control of various kinds of real-world complex networks including biological networks and social networks, and so on.
Riverine Bacterial Communities Reveal Environmental Disturbance Signatures within the Betaproteobacteria and Verrucomicrobia

Riverine bacterial communities play an essential role in the biogeochemical coupling of terrestrial and marine environments, transforming elements and organic matter in their journey from land to sea. However, precisely due to the fact that rivers receive significant terrestrial input, the distinction between resident freshwater taxa vs. land-derived microbes can often become ambiguous. Furthermore, ecosystem perturbations could introduce allochthonous microbial groups and reshape riverine bacterial communities. Using full- and partial-length 16S ribosomal RNA gene sequences, we analyzed the composition of bacterial communities in the Tar River of North Carolina from November 2010 to November 2011, during which a natural perturbation occurred: the inundation of the lower reaches of an otherwise drought-stricken river associated with Hurricane Irene, which passed over eastern North Carolina in late August 2011. This event provided the opportunity to examine the microbiological, hydrological, and geochemical impacts of a disturbance, defined here as the large freshwater influx into the Tar River, superimposed on seasonal changes or other ecosystem variability independent of the hurricane. Our findings demonstrate that downstream communities are more taxonomically diverse and temporally variable than their upstream counterparts. More importantly, pre- vs. post-disturbance taxonomic comparison of the freshwater-dominant Betaproteobacteria class and the phylum Verrucomicrobia reveal a disturbance signature of previously undetected taxa of diverse origins. We use known traits of closely-related taxa to interpret the ecological function of disturbance-associated bacteria, and hypothesize that carbon cycling was enhanced post-disturbance in the Tar River, likely due to the flux of organic carbon into the system associated with the large freshwater pulse. Our analyses demonstrate the importance of geochemical and hydrological alterations in structuring bacterial communities, and illustrate the response of temperate riverine bacteria on fine taxonomic scales to a disturbance.