Miracle-dz/UniFAR-FTUs huggingface dataset:
Jovian Dynamics. Part II: The Genesis and Equilibration of Vortex Sets

Abstract To extend studies of the dynamics of thin atmospheric layers, the generation and equilibration of multiple anticyclonic vortex sets associated with long solitary baroclinic Rossby waves are examined numerically using a primitive equation model with Jovian parameters subject to a simple heating function. We seek primarily to model the three main groups of anticyclones seen on Jupiter, namely, the Great Red Spot, the three White Ovals, and the dozen or so Small Ovals that occur at latitudes of −21°, −33°, and −41°, respectively. The motions are confined to thin upper layers by exponential vertical structures that favor absolute vortex stability. Calculations are also made to examine the regeneration, intrazonal and interscale interactions, and propagation rates of vortices. Vortex sets resembling the three main Jovian groups in scale, form, and number can be simultaneously generated and maintained in a steady configuration by a heating that produces stable westerly and weakly unstable easterly jets.
EXPERIMENTAL STUDIES OF ADAPTATION IN CLARKIA XANTIANA. I. SOURCES OF TRAIT VARIATION ACROSS A SUBSPECIES BORDER

Abstract Both genetic differentiation and phenotypic plasticity might be expected to affect the location of geographic range limits. Co-gradient variation (CoGV), plasticity that is congruent with genetic differentiation, may enhance performance at range margins, whereas its opposite, counter-gradient variation (CnGV) may hinder performance. Here we report findings of reciprocal transplant experiments intended to tease apart the roles of differentiation and plasticity in producing phenotypic variation across a geographic border between two plant subspecies. Clarkia xantiana ssp. xantiana and C. xantiana ssp. parviflora are California-endemic annuals that replace each other along a west–east gradient of declining precipitation. We analyzed variation in floral traits, phenological traits, and vegetative morphological and developmental traits by sowing seeds of 18 populations (six of ssp. xantiana and 12 of ssp. parviflora) at three sites (one in each subspecies' exclusive range and one in the subspecies' contact zone), in two growing seasons (an exceptionally wet El Niño winter and a much drier La Niña winter). Significant genetic differences between subspecies appeared in 11 of 12 traits, and differences were of the same sign as in nature. These findings are consistent with the hypothesis that selection is responsible for subspecies differences. Geographic variation within subspecies over part of the spatial gradient mirrored between-subspecies differences present at a larger scale. All traits showed significant plasticity in response to spatial and temporal environmental variation. Plasticity patterns ranged from spatial and temporal CoGV (e.g., in node of first flower), to spatial CnGV (e.g., in flowering time), to patterns that were neither CoGV nor CnGV (the majority of traits). Instances of CoGV may reflect adaptive plasticity and may serve to increase performance under year-to-year environmental variation and at sites near the subspecies border. However, the presence of spatial CnGV in some critical traits suggests that subspecies ranges may also be constrained by patterns of plasticity.
An improved voltage balancing method of modular multilevel converters

In this paper, an improved voltage balancing method of modular multilevel converters (MMCs) is proposed. This method divides sub-modules in same arm into several groups which voltage balancing is based on. The voltage balancing between groups is based on the sorting result of group sub-module average voltage and the voltage balancing within group is based on the sorting result of sub-module voltages in group. The proposed method can save sorting time greatly compared with the conventional method. Simulation results on a MMC based three-phase inverter show validity of the proposed method.
The Phenolic Recognition Profiles of the Agrobacterium tumefaciens VirA Protein Are Broadened by a High Level of the Sugar Binding Protein ChvE

ABSTRACT The formation of crown gall tumors by Agrobacterium tumefaciens requires that the virulence (vir) genes be induced by chemical signals which consist of specific phenolic compounds and monosaccharides, synthesized at plant wound sites. Signal transduction in the activation of these genes is mediated by the VirA-VirG two-component regulatory system, together with ChvE, a glucose-galactose binding protein which interacts with VirA. We have previously presented genetic evidence that virA senses phenolic compounds directly (Y.-W. Lee, S. Jin, W.-S. Sim, and E. W. Nester, Proc. Natl. Acad. Sci. USA 92:12245–12249, 1995). The vir genes of strain KU12 can be induced by 4-hydroxyacetophenone, p-coumaric acid, and phenol, whereas these same phenolic compounds are weak inducers of the virgenes of strain A6. In this report, we show that a specific inducing sugar can broaden the specificity of the phenolic compound which VirA senses. 4-Hydroxyacetophenone and other related phenolic compounds function as inducing phenolic compounds with the virA gene of A6 if arabinose replaces glucose as the inducing sugar. We further demonstrate that this broadened specificity for phenolic inducers results from the increased level of ChvE through induction by arabinose via the regulatory protein GbpR. If high levels of ChvE are present, then poorly inducing phenolic compounds can induce the virgenes to high levels in combination with glucose. Comparing the induction response of the wild type and that of a VirA mutant with a mutation in its receiver domain revealed that the activity of the receiver domain is controlled by the periplasmic domain. We discuss these observations in terms of how VirA senses and transduces signals elicited by the two classes of plant signal molecules.
Pro-necrotic molecules impact local immunosurveillance in human breast cancer

ABSTRACT Necrosis culminates in spilling cellular content through the permeabilized plasma membrane, thereby releasing potentially immunostimulatory molecules in the pericellular space of dead cells. Accordingly, molecules involved in necroptotic signaling, such as receptor-interacting serine/threonine-protein kinase 3 (RIPK3) and mixed lineage kinase-like (MLKL) have been found to stimulate anticancer immune responses in mouse models of chemotherapy. mRNAs encoding prominent pro-necrotic gene products (RIPK1, RIPK3, MLKL, PGAM5 and DFNA5) were correlated with immune-related metagenes in several cancer types (breast, colorectal, lung, ovary, melanoma), revealing the strongest associations in breast cancer. In two independent breast cancer cohorts, the expression of MLKL and DFNA5 was decreased at the mRNA levels in tumor as compared with normal tissues. Moreover, MLKL expression exhibited a strong positive correlation with genes reflecting the presence of B, NK and T lymphocytes in the tumor bed, in multiple distinct breast cancer subtypes. In contrast, the positive correlation between RIPK3 and lymphoid cells was restricted to HER2+ and triple negative/basal-like breast cancer. Moreover, the expression of DFNA5, which mediates post-apoptotic secondary necrosis, mostly correlated with the monocytic lineage and macrophages in ER+/luminal A breast cancers. MLKL (and to some extent RIPK1 and RIPK3) was strongly associated with the local expression of genes involved in interferon-α and interferon-γ responses. Altogether, these results support the idea that pro-necrotic signaling facilitates intratumoral immune responses in human breast cancer.
FPGA interconnect sizing using extended logical effort model

The proposed XLE model will enable us to calculate the delay of FPGA interconnect and determine closed form expressions for optimal transistor size, sensitivity and a minimal bound on delay. We will further extend it to cover process variations, resulting in a tool that can compare the statistical properties of different architectures. The models are simple and relatively technology independent and hence can be used to gain better intuition into the major causes of delay. Such a delay model can be used in optimization models and CAD tools as well as aid designers in developing new FPGA interconnect schemes.
Flexible Music Retrieval in Sublinear Time

Music sequences can be treated as texts in order to perform music retrieval tasks on them. However, the text search problems that result from this modeling are unique to music retrieval. Up to date, several approaches derived from classical string matching have been proposed to cope with the new search problems, yet each problem had its own algorithms. In this paper we show that a technique recently developed for multipattern approximate string matching is flexible enough to be successfully extended to solve many different music retrieval problems, as well as combinations thereof not addressed before. We show that the resulting algorithms are average-optimal in many cases and close to average-optimal otherwise. Empirically, they are much better than existing approaches in many practical cases.
Portable and transparent software managed scheduling on accelerators for fair resource sharing

Accelerators, such as Graphic Processing Units (GPUs), are popular components of modern parallel systems. Their energy-efficient performance make them attractive components for modern data center nodes. However, they lack control for fair resource sharing amongst multiple users. This paper presents a runtime and Just In Time compiler that enables resource sharing control and software managed scheduling on accelerators. It is portable and transparent, requiring no modification or recompilation of existing systems or user applications. We provide an extensive evaluation of our scheme with over 40,000 different workloads on 2 platforms and we deliver fairness improvements ranging from 6.8× to 13.66×. In addition, we also deliver system throughput speedups ranging from 1.13× to 1.31×.
A mechanism for enhanced symmetric key encryption based mixnet

Anonymous networks enable entities to send messages without disclosing their identities. Many anonymous networks had been proposed already, such as Mixnet, DC-net, Crowds, etc. However, they still have serious drawbacks. Namely, they require tremendous computation overheads to transmit messages over networks. That is because asymmetric key encryption algorithms are used. This paper proposes a new mechanism for anonymous communication that removes these drawbacks while exploiting symmetric key encryption algorithms.
Amino acid activation in subcellular fractions of Tetrahymena pyriformis.

SYNOPSIS. The presence of amino acid activating enzymes was demonstrated in the ciliated protozoan Tetrahymena pyriformis. By employing a sensitive hydroxamate assay procedure, the activation of L-valine was assayed in various subcellular fractions of the ciliate, and some characteristics of the enzyme activity in the most active fraction were determined. Most of the activity resided in pH 5 fractions isolated from high speed supernatants of ciliates disrupted by various physical and chemical methods. No activity could be demonstrated in isolated cilia, in pellicles with attached kinetosomes, in microsomes or in macronuclei, providing these organelles were thoroughly washed. A washed mitochondrial preparation isolated by the Mager and Lipmann procedure activated L-valine; mitochondria isolated by the procedure of Hogg and Kornberg did not. The pH 5 fraction isolated from the 102,000 X g supernatant of digitonin-lysed ciliates was stable for several weeks when stored in 0.1 M Tris buffer, pH 7.6 at – 25 C. The activity of this fraction with respect to L-valine activation was dependent on the presence of ATP1 and magnesium in the reaction mixture. The optimal concentrations of these components and of L-valine and hydroxylamine were determined, and the linearity of activity with time and enzyme concentration was demonstrated. Valine activation was not modified by dialysis of the pH 5 fraction, or treatment with RNase, or the addition of boiled pH 5 fraction.
CS 224 W : Regarding spread of influence and its maximization in Social Networks

Understanding the spread of influence and how to maximize it in social networks is an important and relevant topic in social network analysis. There are numerous practical business applications such as viral marketing and understanding where to seed stories to maximize impact. Existing techniques exist for influence maximization such as the independent cascade model and use of the greedy hill climbing algorithm. These techniques, however, are run on graphs that are static. Additionally, many of these algorithms are very expensive to run. In today’s rapidly changing online environment, graphs are seldom static and also the cardinality of the seed set could change. Even a short delay in analysis of this evolving graphs can lead to unfavorable results.
Evaluating Safety, Soundness and Sensibleness of Obfuscation Systems

Author masking is the task of paraphrasing a document so that its writing style no longer matches that of its original author. This task was introduced as part of the 2016 PAN Lab on Digital Text Forensics, for which a total of three research teams submitted their results. This work describes our methodology to evaluate the submitted obfuscation systems based on their safety, soundness and sensibleness. For the first two dimensions, we introduce automatic evaluation measures and for sensibleness we report our manual evaluation results.
Discovery of VHEγ-rays from the blazar 1ES 1215+303 with the MAGIC telescopes and simultaneous multi-wavelength observations

Context. We present the discovery of very high energy (VHE, E > 100 GeV) gamma-ray emission from the BL Lac object 1ES 1215+303 by the MAGIC telescopes and simultaneous multi-wavelength data in a broad energy range from radio to gamma-rays. Aims. We study the VHE gamma-ray emission from 1ES 1215+303 and its relation to the emissions in other wavelengths. Methods. Triggered by an optical outburst, MAGIC observed the source in 2011 January-February for 20.3 h. The target was monitored in the optical R-band by the KVA telescope that also performed optical polarization measurements. We triggered target of opportunity observations with the Swift satellite and obtained simultaneous and quasi-simultaneous data from the Fermi Large Area Telescope and from the Metsahovi radio telescope. We also present the analysis of older MAGIC data taken in 2010. Results. The MAGIC observations of 1ES 1215+303 carried out in 2011 January-February resulted in the first detection of the source at VHE with a statistical significance of 9.4 sigma. Simultaneously, the source was observed in a high optical and X-ray state. In 2010 the source was observed in a lower state in optical, X-ray, and VHE, while the GeV gamma-ray flux and the radio flux were comparable in 2010 and 2011. The spectral energy distribution obtained with the 2011 data can be modeled with a simple one zone SSC model, but it requires extreme values for the Doppler factor or the electron energy distribution.
Genetic identification and structure of Clarias batrachus (Linnaeus, 1758) from Southeast Asia using a mitochondrial DNA marker.

A phylogenetic tree and median-joining network based on cytochrome b sequence data revealed clades consistent with morphological differences and geographical distribution of Clarias batrachus (Linnaeus, 1758) in Southeast Asia. AMOVA analysis for variation was significant among populations (P<0.05) and was in agreement with morphological differences. Pairwise differences were significant between Java and Brunei/Borneo, Brunei/Borneo and west Malaysia, and Java and west Malaysia samples (P < 0.05). Closest relationships were found between samples from Brunei/Borneo and Java, and between west Malaysia and Laos-Sumatra. Nine haplotypes were unique to geographical regions. The Java species had high haplotype (1.000 ± 0.126) but low nucleotide (0.017) diversities, suggesting a population bottleneck followed by expansion. However, SSD and Hri (P=0.5) did not support demographic expansion. Instead, purifying selection where mutations occur and accumulate at silent sites is a more acceptable explanation.
Proteomics of Secretory and Endocytic Organelles in Giardia lamblia

Giardia lamblia is a flagellated protozoan enteroparasite transmitted as an environmentally resistant cyst. Trophozoites attach to the small intestine of vertebrate hosts and proliferate by binary fission. They access nutrients directly via uptake of bulk fluid phase material into specialized endocytic organelles termed peripheral vesicles (PVs), mainly on the exposed dorsal side. When trophozoites reach the G2/M restriction point in the cell cycle they can begin another round of cell division or encyst if they encounter specific environmental cues. They induce neogenesis of Golgi-like organelles, encystation-specific vesicles (ESVs), for regulated secretion of cyst wall material. PVs and ESVs are highly simplified and thus evolutionary diverged endocytic and exocytic organelle systems with key roles in proliferation and transmission to a new host, respectively. Both organelle systems physically and functionally intersect at the endoplasmic reticulum (ER) which has catabolic as well as anabolic functions. However, the unusually high degree of sequence divergence in Giardia rapidly exhausts phylogenomic strategies to identify and characterize the molecular underpinnings of these streamlined organelles. To define the first proteome of ESVs and PVs we used a novel strategy combining flow cytometry-based organelle sorting with in silico filtration of mass spectrometry data. From the limited size datasets we retrieved many hypothetical but also known organelle-specific factors. In contrast to PVs, ESVs appear to maintain a strong physical and functional link to the ER including recruitment of ribosomes to organelle membranes. Overall the data provide further evidence for the formation of a cyst extracellular matrix with minimal complexity. The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD000694.
Dual-Server Public-Key Encryption With Keyword Search for Secure Cloud Storage

Searchable encryption is of increasing interest for protecting the data privacy in secure searchable cloud storage. In this paper, we investigate the security of a well-known cryptographic primitive, namely, public key encryption with keyword search (PEKS) which is very useful in many applications of cloud storage. Unfortunately, it has been shown that the traditional PEKS framework suffers from an inherent insecurity called inside keyword guessing attack (KGA) launched by the malicious server. To address this security vulnerability, we propose a new PEKS framework named dual-server PEKS (DS-PEKS). As another main contribution, we define a new variant of the smooth projective hash functions (SPHFs) referred to as linear and homomorphic SPHF (LH-SPHF). We then show a generic construction of secure DS-PEKS from LH-SPHF. To illustrate the feasibility of our new framework, we provide an efficient instantiation of the general framework from a Decision Diffie-Hellman-based LH-SPHF and show that it can achieve the strong security against inside the KGA.
Dynamics Calibration of a Redundant Flexible Joint Robot based on Gyroscopes and Encoders

In this paper we show the identification of the dynamic parameters of a redundant flexible joint robot with a flexible bearing in the first joint. The bearing leads to distortions of the link velocities measured by gyroscopes. The bearing flexibility is not modeled explicitly, resulting in a very simple model. For the joint positions encoders are used. We show how to pack the calibration problem into the sparse least-squares on manifolds toolkit (SLOM) and present the results. For verification we compare the measured data with the predicted data computed using the identified dynamic parameters.
Scalable exfoliation for large-size boron nitride nanosheets by low temperature thermal expansion-assisted ultrasonic exfoliation

Hexagonal boron nitride nanosheets (BNNSs) hold great potential in many applications due to their intriguing properties. However, the high-yield preparation of large-size BNNSs still remains a key challenge. Herein, we report a scalable exfoliation process, named as ‘low temperature thermal expansion-assisted ultrasonic exfoliation’, to prepare BNNSs. This method firstly utilizes hydrogen induced low temperature thermal reduction of hydroxyl-functionalized bulk hexagonal boron nitride (BN-OH) to weaken interlayer interaction between adjacent layers, and then employs a brief sonication to completely exfoliate BNNSs from their bulk materials. Few-layer and large-size BNNSs with a high yield of 26% are successfully prepared by this method. Moreover, the large-area BNNSs can effectively enhance the thermal conductivity of thermoplastic polyurethane elastomer on account of the decrease of interfacial thermal resistance. Low temperature thermal expansion-assisted ultrasonic exfoliation can thus provide an efficient approach to scalable fabrication of high-quality BNNSs. Furthermore, this method is promising for the high-yield production of other nanosheets.
Retrieving Product Features and Opinions from Customer Reviews

A new methodology based on language models retrieves product features and opinions from a collection of free-text customer reviews about a product or service. The proposal relies on a language-modeling framework that can be applied to reviews in any domain and language provided with a minimal knowledge source of sentiments or opinions (that is, a minimal seed set of opinion words).
A Mobile Device Prototype Application for the Detection and Prediction of Node Faults in Wireless Sensor Networks

Various implementations of wireless sensor networks (i.e. personal area-, wireless body area- networks) are prone to node and network failures by such characteristics as limited node energy resources and hardware damage incurred from their surrounding environment (i.e. flooding, forest fires, a patient falling). This may jeopardize their reliability to act as early warning systems, monitoring systems for patients and athletes, and industrial and environmental observation networks. Following the current trend and widespread use of hand held, mobile communication devices, we outline an application architecture designed to detect and predict faulty nodes in wireless sensor networks. Furthermore, we implement our design as a proof of concept prototype for Android-based smartphones, which may be extended to develop other applications used for monitoring networked wireless personal area and body sensors used in other capacities. We have conducted several preliminary experiments to demonstrate the use of our design, which is capable of monitoring networks of wireless sensor devices and predicting node faults based on several localized metrics. As attributes of such networks may change over time, any models generated when the application is initialized must be updated periodically such that the applied machine learning algorithm maintains high levels of both accuracy and precision. The application is designed to discover node faults and, once identified, alert the user so that appropriate action may be taken.