Miracle-dz/UniFAR-FTUs huggingface dataset:
Title Changes in expression levels of ERCC1, DPYD, and VEGFA mRNA after first-line chemotherapy of metastatic colorectal cancer: Results of a multicenter study

Our previous study showed that administering oxaliplatin as first-line chemotherapy increased ERCC1 and DPD levels in liver colorectal cancers (CRCs) metastases. Second, whether the anti-VEGF monoclonal antibody bevacizumab alters tumoral VEGFA levels is unknown. We conducted this multicenter observational study to validate our previous findings on ERCC1 and DPD, and clarify the response of
ShapeClip: Towards Rapid Prototyping with Shape-Changing Displays for Designers

This paper presents ShapeClip: a modular tool capable of transforming any computer screen into a z-actuating shape-changing display. This enables designers to produce dynamic physical forms by "clipping" actuators onto screens. ShapeClip displays are portable, scalable, fault-tolerant, and support runtime re-arrangement. Users are not required to have knowledge of electronics or programming, and can develop motion designs with presentation software, image editors, or web-technologies. To evaluate ShapeClip we carried out a full-day workshop with expert designers. Participants were asked to generate shape-changing designs and then construct them using ShapeClip. ShapeClip enabled participants to rapidly and successfully transform their ideas into functional systems.
Learning Markov graphs up to edit distance

This paper presents a rate distortion approach to Markov graph learning. It provides lower bounds on the number of samples required for any algorithm to learn the Markov graph structure of a probability distribution, up to edit distance. We first prove a general result for any probability distribution, and then specialize it for Ising and Gaussian models. In particular, for both Ising and Gaussian models on p variables with degree at most d, we show that at least Ω((d - s/p)log p) samples are required for any algorithm to learn the graph structure up to edit distance s. Our bounds represent a strong converse; i.e., we show that for a lower number of samples, the probability of error goes to 1 as the problem size increases. These results show that substantial gains in sample complexity may not be possible without paying a significant price in edit distance error.
Binary Darboux–Bäcklund transformations for the Manin–Radul super KdV hierarchy

We construct the supersymmetric extensions of the Darboux–Backlund transformations (DBTs) for the Manin–Radul super Korteweg–de Vries (KdV) hierarchy using the super-pseudo-differential operators. The elementary DBTs are triggered by the gauge operators constructed from the wave functions and adjoint wave functions of the hierarchy. Iterating these elementary DBTs, we obtain not only Wronskian-type but also binary-type superdeterminant representations of the solutions.
Fusion categories and homotopy theory

We apply the yoga of classical homotopy theory to classification problems of G-extensions of fusion and braided fusion categories, where G is a finite group. Namely, we reduce such problems to classification (up to homotopy) of maps from BG to classifiying spaces of certain higher groupoids. In particular, to every fusion category C we attach the 3-groupoid BrPic(C) of invertible C-bimodule categories, called the Brauer-Picard groupoid of C, such that equivalence classes of G-extensions of C are in bijection with homotopy classes of maps from BG to the classifying space of BrPic(C). This gives rise to an explicit description of both the obstructions to existence of extensions and the data parametrizing them; we work these out both topologically and algebraically. One of the central results of the paper is that the 2-truncation of BrPic(C) is canonically the 2-groupoid of braided autoequivalences of the Drinfeld center Z(C) of C. In particular, this implies that the Brauer-Picard group BrPic(C) (i.e., the group of equivalence classes of invertible C-bimodule categories) is naturally isomorphic to the group of braided autoequivalences of Z(C). Thus, if C=Vec(A), where A is a finite abelian group, then BrPic(C) is the orthogonal group O(A+A^*). This allows one to obtain a rather explicit classification of extensions in this case; in particular, in the case G=Z/2, we rederive (without computations) the classical result of Tambara and Yamagami. Moreover, we explicitly describe the category of all (Vec(A1),Vec(A2))-bimodule categories (not necessarily invertible ones) by showing that it is equivalent to the hyperbolic part of the category of Lagrangian correspondences.
An Experimental Comparison of Dynamic Routing Protocols in Mobile Networks

The paper deals with the research of dynamic attributes of routing protocols in the vehicle’s movement simulation in urban environment. Simulation environment allows to modify the volume of the transmitted data, transmission speed, failures’ character and intensity. The research was performed for OLSR and B.A.T.M.A.N. protocols. The obtained results permit to formulate optimal conditions for using these protocols on the vehicle’s board.
Space-efficient approximate Voronoi diagrams

(MATH) Given a set $S$ of $n$ points in $\IR^d$, a {\em $(t,\epsilon)$-approximate Voronoi diagram (AVD)} is a partition of space into constant complexity cells, where each cell $c$ is associated with $t$ representative points of $S$, such that for any point in $c$, one of the associated representatives approximates the nearest neighbor to within a factor of $(1+\epsilon)$. Like the Voronoi diagram, this structure defines a spatial subdivision. It also has the desirable properties of being easy to construct and providing a simple and practical data structure for answering approximate nearest neighbor queries. The goal is to minimize the number and complexity of the cells in the AVD. (MATH) We assume that the dimension $d$ is fixed. Given a real parameter $\gamma$, where $2 \le \gamma \le 1/\epsilon$, we show that it is possible to construct a $(t,\epsilon)$-AVD consisting of \[O(n \epsilon^{\frac{d-1}{2}} \gamma^{\frac{3(d-1)}{2}} \log \gamma) \] cells for $t = O(1/(\epsilon \gamma)^{(d-1)/2})$. This yields a data structure of $O(n \gamma^{d-1} \log \gamma)$ space (including the space for representatives) that can answer $\epsilon$-NN queries in time $O(\log(n \gamma) + 1/(\epsilon \gamma)^{(d-1)/2})$. (Hidden constants may depend exponentially on $d$, but do not depend on $\epsilon$ or $\gamma$). (MATH) In the case $\gamma = 1/\epsilon$, we show that the additional $\log \gamma$ factor in space can be avoided, and so we have a data structure that answers $\epsilon$-approximate nearest neighbor queries in time $O(\log (n/\epsilon))$ with space $O(n/\epsilon^{d-1})$, improving upon the best known space bounds for this query time. In the case $\gamma = 2$, we have a data structure that can answer approximate nearest neighbor queries in $O(\log n + 1/\epsilon^{(d-1)/2})$ time using optimal $O(n)$ space. This dramatically improves the previous best space bound for this query time by a factor of $O(1/\epsilon^{(d-1)/2})$. (MATH) We also provide lower bounds on the worst-case number of cells assuming that cells are axis-aligned rectangles of bounded aspect ratio. In the important extreme cases $\gamma \in \{2, 1/\epsilon\}$, our lower bounds match our upper bounds asymptotically. For intermediate values of $\gamma$ we show that our upper bounds are within a factor of $O((1/\epsilon)^{(d-1)/2}\log \gamma)$ of the lower bound.
Human cytomegalovirus: demonstration of permissive epithelial cells and nonpermissive fibroblastic cells in a survey of human cell lines

To more clearly define the characteristics which render a cell permissive for human cytomegalovirus (HCMV), we screened a panel of human cell lines differing in morphology, ploidy, and extent of differentiation for the ability to sustain productive HCMV replication. Cells were exposed to HCMV at 5 to 20 PFU per cell and examined at 4 to 14 days postinfection to detect the production of infectious virus by a plaque assay and the assembly of progeny virions by electron microscopy. By these criteria, high-titer HCMV replication (10(6) to 10(7) PFU/ml) occurred in a well-differentiated, diploid, epithelial cell line, HCMC, which had been derived from normal human colonic mucosa. In contrast, all aneuploid human cell types proved to be nonpermissive, including a fibroblastic cell line designated HT-144. These results indicate that HCMV replication in cultures is not strictly limited to fibroblasts and conversely that not all human fibroblastic cells are permissive for HCMV. Nonpermissive cell types were further investigated by attempts to chemically induce HCMV replication. Treatment of nonpermissive cell types with 25 to 500 micrograms of 5-iodo-2'-deoxyuridine per ml prior to infection did not convert them to the permissive state. The implications of these findings for the possible mechanisms maintaining the nonpermissive state are discussed.
Similarities in 2- and 6-Line Ferrihydrite Based on Pair Distribution Function Analysis of X-ray Total Scattering

Iron(III) hydroxides are abundant in near-surface natural environments and play an important role in geochemical processes and the fate of contaminants. The issue of the structure of the common nanophase material ferrihydrite (ferric hydroxide) is controversial and has been debated in the literature for many years without definitive resolution. At least two types of ferrihydrite, the 2-line and 6-line forms, are conventionally recognized. It has been suggested that these forms possess different structures built up by different mixtures of distinct nanophase components. However, traditional crystallographic methods provide depictions of structure that are most sensitive either to short-range order (X-ray absorption) or long-range periodicity (X-ray diffraction or electron diffraction). We used high-energy X-ray total scattering for pair distribution function analysis to observe both the short- and intermediate-range ordering (exceeding similar to 15 angstrom) of synthetic ferrihydrite with three distinct average domain sizes of 2, 3, and 6 nm. We show that there are no significant differences in the underlying structures of these materials and that the differences in the diffraction patterns can be entirely interpreted by variations in the average size of the coherent scattering domains. The average crystallite sizes inferred from the PDF analysis are in good agreement with direct observation by high-resolution transmission electron microscopy.
Adaptive Mutations and Replacements of Virulence Traits in the Escherichia coli O104:H4 Outbreak Population

The sequencing of highly virulent Escherichia coli O104:H4 strains isolated during the outbreak of bloody diarrhea and hemolytic uremic syndrome in Europe in 2011 revealed a genome that contained a Shiga toxin encoding prophage and a plasmid encoding enteroaggregative fimbriae. Here, we present the draft genome sequence of a strain isolated in Sweden from a patient who had travelled to Tunisia in 2010 (E112/10) and was found to differ from the outbreak strains by only 38 SNPs in non-repetitive regions, 16 of which were mapped to the branch to the outbreak strain. We identified putatively adaptive mutations in genes for transporters, outer surface proteins and enzymes involved in the metabolism of carbohydrates. A comparative analysis with other historical strains showed that E112/10 contained Shiga toxin prophage genes of the same genotype as the outbreak strain, while these genes have been replaced by a different genotype in two otherwise very closely related strains isolated in the Republic of Georgia in 2009. We also present the genome sequences of two enteroaggregative E. coli strains affiliated with phylogroup A (C43/90 and C48/93) that contain the agg genes for the AAF/I-type fimbriae characteristic of the outbreak population. Interestingly, C43/90 also contained a tet/mer antibiotic resistance island that was nearly identical in sequence to that of the outbreak strain, while the corresponding island in the Georgian strains was most similar to E. coli strains of other serotypes. We conclude that the pan-genome of the outbreak population is shared with strains of the A phylogroup and that its evolutionary history is littered with gene replacement events, including most recently independent acquisitions of antibiotic resistance genes in the outbreak strains and its nearest neighbors. The results are summarized in a refined evolutionary model for the emergence of the O104:H4 outbreak population.
Dependency-based Convolutional Neural Networks for Sentence Embedding

In sentence modeling and classification, convolutional neural network approaches have recently achieved state-of-the-art results, but all such efforts process word vectors sequentially and neglect long-distance dependencies. To exploit both deep learning and linguistic structures, we propose a tree-based convolutional neural network model which exploit various long-distance relationships between words. Our model improves the sequential baselines on all three sentiment and question classification tasks, and achieves the highest published accuracy on TREC.
Complex Question Answering with ASQA at NTCIR 7 ACLIA

At NTCIR 7, we implemented the Academia Sinica Question Answering (ASQA) system for complex questions. The system uses three methods to select answer strings from a news corpus. (a) It uses syntactic patterns, which are usually used by QA systems, to retrieve more precise answer strings than those derived by traditional IR. (b) Using external knowledge, the system can find accurate answers to specific questions that the traditional IR approach can not process. (c) Entropy-based and co-occurrence-based mining methods are used to retrieve relevant answer strings for document retrieval. In the NTCIR 7 CCLQA task, ASQA achieved 0.26 in the CT-CT task and 0.20 in the CS-CS task.
Monitoring Cloud Computing by Layer, Part 2

In part I, the author briefly introduced cloud computing and a model of it that has seven layers (facility, network, hardware, OS, middleware, application, and the user). Each cloud computing deployment must have these layers, but different deployment types give control of them to different parties. Here, the author covers controls that could be implemented in the middleware, application, and user layers to monitor and audit information assurance.
Seedless fruits and the disruption of a conserved genetic pathway in angiosperm ovule development

Although the biological function of fruiting is the production and dissemination of seeds, humans have developed seedless fruits in a number of plant species to facilitate consumption. Here we describe a unique spontaneous seedless mutant (Thai seedless; Ts) of Annona squamosa (sugar apple), a member of the early-divergent magnoliid angiosperm clade. Ovules (seed precursors) of the mutant lack the outer of two normal integuments, a phenocopy of the inner no outer (ino) mutant of Arabidopsis thaliana. Cloning of the INO ortholog from A. squamosa confirmed conservation of the outer integument-specific expression pattern of this gene between the two species. All regions of the gene were detectable in wild-type A. squamosa and in other members of this genus. However, no region of the INO gene could be detected in Ts plants, indicating apparent deletion of the INO locus. These results provide a case of a candidate gene approach revealing the apparent molecular basis of a useful agronomic trait (seedless fruit) in a crop species, and indicate conservation of the role of a critical regulator of ovule development between eudicots and more ancient lineages of angiosperms. The outer integument is one synapomorphy of angiosperms separating them from other extant seed plants, and the results suggest that the evolution of this structure was contemporaneous with the derivation of INO from ancestral YABBY genes. Thus, a unique lateral structure appears to have coevolved with a novel gene family member essential for the structure's formation.
SnO2/carbon nanotube nanocomposites synthesized in supercritical fluids: highly efficient materials for use as a chemical sensor and as the anode of a lithium-ion battery

SnO2/multi-walled carbon nanotube (MWCNT) nanocomposites were prepared via oxidation of SnCl2 in a supercritical CO2–methanol mixture containing MWCNTs. The as-prepared nanocomposites were characterized by means of x-ray diffraction, x-ray photoelectron spectroscopy, and transmission electron microscopy. It was indicated that SnO2 nanoparticles with size of 3–5 nm were uniformly and tightly decorated on the MWCNTs. The chemiluminescence characteristic to H2S and electrochemical performance of the as-prepared SnO2/MWCNT composites were investigated. The SnO2/MWCNT composites exhibited extremely high efficiency for detecting H2S, and also displayed good electrochemical performance as the anode material in a lithium-ion battery.
Nanographene device fabrication using atomic force microscope

A report is presented on the local anodic oxidation of graphene film prepared by chemical vapour deposition using contact mode atomic force microscopy. Raman spectroscopy was used to check the uniformity and thickness of large area graphene film. Various kinds of patterns such as lines, ribbons and further, more complex structures, such as hexagons, two-terminal bar-like devices, were written by varying the tip voltage from -6 to -12 V and the tip speed from 60 to 200 nm/s. It was found that one can easily write any kind of patterns by just manipulating the tip voltage and tip speed instead of concentrating on other factors such as controlled humidity conditions, applied force on the tip and tip current. Also, it is confirmed that with an increase in tip voltage and by slowing the tip movement during lithography, one can write very narrow and sharp patterns which are important factors for the fabrication of graphene-based electronic devices.
Work–family boundary management styles in organizations

We develop a cross-level model and typology of work–family (W–F) boundary management styles in organizations. A boundary management style is the general approach an individual uses to demarcate boundaries and attend to work and family roles. We argue that variation in W–F boundary management styles (integrator, separator, alternating) is a function of individual boundary-crossing preferences (flexibility, permeability, symmetry, direction); the centrality and configuration of work–family role identities; as well as the organizational work–family climate for customization. The model assumes that an individual’s perceived control to enact a boundary style that aligns with boundary-crossing preferences and identities has direct effects on individual perceptions of work–family conflict and also moderates the level of work–family conflict of boundary management styles experienced across organizational contexts. We offer propositions relevant to future research and practice.
Understanding the impact of socialbot attacks in online social networks

Online social networks (OSN) like Twitter or Facebook are popular and powerful since they allow reaching millions of users online. They are also a popular target for socialbot attacks. Without a deep understanding of the impact of such attacks, the potential of online social networks as an instrument for facilitating discourse or democratic processes is in jeopardy. In this extended abstract we present insights from a live lab experiment in which social bots aimed at manipulating the social graph of an online social network, in our case Twitter. We explored the link creation behavior between targeted human users and our results suggest that socialbots may indeed have the ability to shape and influence the social graph in online social networks. However, our results also show that external factors may play an important role in the creation of social links in OSNs.
An approach to measuring kernel energy in software applications

The large widespread of mobile devices and the increasing demand for high performance has made energy an important constraint in computer's technology. In this paper, we propose a simple software methodology that can be adapted by researchers to estimate the energy cost of kernels. Kernels are operations that can be implemented in hardware and are executed frequently in algorithms. This energy estimation helps in exploiting opportunities for energy optimizations in various algorithms. As a case study, we apply our methodology on back propagation (BP) algorithm and we estimate the energy cost of its kernels on two different architectures using: a) Simulation tools for the RISC architecture b) Physical measurement of the current and voltage using special boards for the CISC architecture. Our experiments show that the produced energy costs using our method have 5.14% error with respect to the costs of these kernels in real codes, which proves the high accuracy of our methodology. The results also show that different architectures exhibit different energy consumption when executing the same kernel which proves that alternative kernel implementations have impact on energy saving. Based on the estimated energy costs of the kernels, we further propose an energy optimization technique by using lookup tables (LUT). The proposed technique targets the exponential kernel because of its high energy consumption and replaces it with a LUT. The experimental results show a significant reduction of 99.97% in the energy consumed by the exponential kernel.
The fabrication process of microfluidic devices integrating microcoils for trapping magnetic nano particles for biological applications

In this study, a concept of microfluidic chip with embedded planar coils is designed and fabricated for the aim of trapping effectively functionalized magnetic nanobeads and immobilizing antibody (IgG type). The planar coils as a heart of microfluidic chip is designed with criterion parameters which are optimized from simulation parameters of the maximum magnetic field, low power consumption and high power efficiency by FE method. The characterization of microcoils such as effectively nanobeads (300 nm) at low temperature (<37oC) is performed and confirmed. The channel network in PDMS material is designed for matching with entire process (including mixing and trapping beads) in microfluidic chip. A process of PDMS’s surface modification is also carried out in the assemble step of chip in order to limit the non-specific adsorption of many bio substances on PDMS surface. The microfluidic chip assemble is performed by using some developed techniques of reversible packaging PDMS microfluidic chip (such as stamping technique, using non-adhesive layer, oxygen plasma combining with solvent treatment). These packaging methods are important to reused microchip (specially the bottom substrate) in many times. The immobilization of antibody IgG-type is performed inside microfluidic chip following the standard protocol of bead-based ELISA in micro test tube. The result showed that IgG antibodies are well grafted on the surface of carboxyl-beads (comparing to result of standard protocol); these grafted antibodies are confirmed by coupling them with labeled second antibody (Fab-FITC conjugation).