julilili42/papers huggingface dataset:
Universal Covers, Color Refinement, and Two-Variable Counting Logic: Lower Bounds for the Depth
2015-07-01

Given a connected graph G and its vertex x, let U(G,x) denote the universal cover of G obtained by unfolding G into a tree starting from x. Let T=T(n) be the minimum number such that, for graphs G and H with at most n vertices each, the isomorphism of U(G,x) and U(H,y) surely follows from the isomorphism of these rooted trees truncated at depth T. Motivated by applications in theory of distributed computing, Norris [Discrete Appl. Math. 1995] asks if the value of T(n) is bounded by n. We answer this question in the negative by establishing that T(n)=(2-o(1))n. Our solution uses basic tools of finite model theory such as a bisimulation version of the Immerman-Lander 2-pebble counting game. The graphs G and H we construct for each n to prove the lower bound for T(n) also show some other tight lower bounds. Both having n vertices, G and H can be distinguished in 2-variable counting logic only with quantifier depth (1-o(1))n. It follows that color refinement, the classical procedure used in isomorphism testing and other areas for computing the coarsest equitable partition of a graph, needs (1-o(1))n rounds to achieve color stabilization on each of G and H. Somewhat surprisingly, this number of rounds is not enough for color stabilization on the disjoint union of G and H, where (2-o(1))n rounds are needed.
Using fMRI to Investigate Memory in Young Children Born Small for Gestational Age
2015-07-01

This is the first fMRI study demonstrating different brain activation patterns in 4-7 year old children born SGA, suggesting that intrauterine growth restriction continues to affect neural functioning in children later-on.
An analysis of Dynamic Cortex Memory networks
2015-07-01

The recently introduced Dynamic Cortex Memory (DCM) is an extension of the Long Short Term Memory (LSTM) providing a systematic inter-gate connection infrastructure. In this paper the behavior of DCM networks is studied in more detail and their potential in the field of gradient-based sequence learning is investigated. Hereby, DCM networks are analyzed regarding particular key features of neural signal processing systems, namely, their robustness to noise and their ability of time warping. Throughout all experiments we show that DCMs converge faster and yield better results than LSTMs. Hereby, DCM networks require overall less weights than pure LSTM networks to achieve the same or even better results. Besides, a promising neurally implemented just-in-time online signal filter approach is presented, which is latency-free and still provides an accurate filtering performance much better than conventional low-pass filters. We also show that the neural networks can do explicit time warping even better than the Dynamic Time Warping (DTW) algorithm, which is a specialized method developed for this task.
HLA ligandomics identifies histone deacetylase 1 as target for ovarian cancer immunotherapy
2015-07-01

The recent approval of clincially effective immune checkpoint inhibitors illustrates the potential of cancer immunotherapy. A challenging task remains the identification of specific targets guiding immunotherapy. Facilitated by technical advances, the direct identification of physiologically relevant targets is enabled by analyzing the HLA ligandome of cancer cells. Since recent publications demonstrate the immunogenicity of ovarian cancer (OvCa), immunotherapies, including peptide-based cancer vaccines, represent a promising treatment approach. To identify vaccine peptides, we employed a combined strategy of HLA ligandomics in high-grade serous OvCa samples and immunogenicity analysis. Only few proteins were naturally presented as HLA ligands on all samples analyzed, including histone deacetylase (HDAC) 1 and 2. In vitro priming of CD8(+) T cells demonstrated that two HDAC1/2-derived HLA ligands can induce T-cell responses, capable of killing HLA-matched tumor cells. High HDAC1 expression shown by immunohistochemistry in 136 high-grade serous OvCa patients associated with significantly reduced overall survival (OS), whereas patients with high numbers of CD3(+) tumor-infiltrating lymphocytes (TILs) in the tumor epithelium and CD8(+) TILs in the tumor stroma showed improved OS. However, correlating HDAC1 expression with TILs, high levels of TILs abrogated the impact of HDAC1 on OS. This study strengthens the role of HDAC1/2 as an important tumor antigen in OvCa, demonstrating its impact on OS in a large cohort of OvCa patients. We further identified two immunogenic HDAC1-derived peptides, which frequently induce multi-functional T-cell responses in many donors, suitable for future multi-peptide vaccine trials in OvCa patients.
A spiking neuronal model learning a motor control task by reinforcement learning and structural synaptic plasticity
2015-07-01

In this paper, we present a spiking neuronal model that learns to perform a motor control task. Since the long-term goal of this project is the application of such a neuronal model to study the mutual adaptation between a Brain-Computer Interface (BCI) and its user, neurobiological plausibility of the model is a key aspect. Therefore, the model was trained using reinforcement learning similar to that of the dopamine system, in which a global reward and punishment signal controlled spike-timing dependent plasticity (STDP). Based on this method, the majority of the randomly generated models were able to learn the motor control task. Although the models were only trained on two targets, they were able to reach arbitrary targets after learning. By introducing structural synaptic plasticity (SSP), which dynamically restructures the connections between neurons, the number of models that successfully learned the task could be significantly improved.
Usnea barbata CO2-supercritical extract in alkyl polyglucoside-based emulsion system: contribution of Confocal Raman imaging to the formulation development of a natural product
2015-07-01

Topical treatment of skin infections is often limited by drawbacks related to both antimicrobial agents and their vehicles. In addition, considering the growing promotion of natural therapeutic products, our objective was to develop and evaluate naturally-based emulsion system, as prospective topical formulation for skin infections-treatment. Therefore, alkyl polyglucoside surfactants were used for stabilization of a vehicle serving as potential carrier for supercritical CO2-extract of Usnea barbata, lichen with well-documented antimicrobial activity, incorporated using two protocols and three concentrations. Comprehensive physicochemical characterization suggested possible involvement of extract's particles in stabilization of the investigated system. Raman spectral imaging served as the key method in disclosing extract's particles potential to participate in the microstructure of the tested emulsion system via three mechanisms: (1) particle-particle aggregation, (2) adsorption at the oil-water interface and (3) hydrophobic particle-surfactant interactions. Stated extract-vehicle interaction proved to be correlated to the preparation procedure and extract concentration on one hand and to affect the physicochemical and biopharmaceutical features of investigated system, on the other hand. Thereafter, formulation with the best preliminary stability and liberation profile was selected for further efficiency and in vivo skin irritation potential evaluation, implying pertinent in vitro antimicrobial activity against G+ bacteria and overall satisfying preliminary safety profile.
Sufragio femenino en Chile: origen, brecha de género y estabilidad, 1935-2009
2015-07-01

Women’s suffrage was introduced in two steps in Chile: first for local elections in 1934 and later extended to all elections in 1949. This article analyzes the legislative process and the effects of women’s enfranchisement in Chile from a temporal perspective through a documentary and quantitative analysis, by means of ecological inference. Firstly, we argue that the political parties’ strategic calculations about the possible consequences of the women’s vote were fundamental for explaining the Chilean route to women’s suffrage. Secondly, we maintain that the incorporation of women into the electorate did not cause any significant electoral instability. Thirdly, our study of the gender gap shows that even though it favored right-wing and reformist-center parties for a long time, this effect has diminished considerably with the passing of time.
Effects of Cyclone Hudhud captured by a high altitude Automatic Weather Station in northwestern Nepal
2015-07-01

Between 13 October and 15 October 2014 many people were trapped by a heavy snowstorm event at Thorong La Pass (5416m amsl) on the famous Annapurna Circuit in northern Nepal, resulting 43 fatalities. In this short communication we show a climate record of an Automatic Weather Station (AWS) which is located at a similar altitude to Thorong La Pass but is 300km to the northwest along the main Himalayan ridge. Additionally, the record of the extent of the snow cover in the region was derived from Landsat 8 satellite images taken before and after the snowstorm event. During the event the AWS recorded a snow accumulation of 0.37m, while the snow cover in the study area increased from 1880km 2 on 9 October to 17 44°km 2 on 25 October. Our results, and findings from our personal communication with local people, show that the extent of the disastrous snowstorm event affected a much larger area than reported by the media, which concentrated its coverage solely on the Annapurna region.
Low ply graph drawing
2015-07-01

We consider the problem of characterizing graphs with low ply number and algorithms for creating layouts of graphs with low ply number. Informally, the ply number of a straight-line drawing of a graph is defined as the maximum number of overlapping disks, where each disk is associated with a vertex and has a radius that is half the length of the longest edge incident to that vertex. We show that internally triangulated biconnected planar graphs that admit a drawing with ply number 1 can be recognized in O(n log n) time, while the problem is in general NP-hard. We also show several classes of graphs that have 1-ply drawings. We then show that binary trees, stars, and caterpillars have 2-ply drawings, while general trees have (h+1)-ply drawings, where h is the height of the tree. Finally we discuss some generalizations of the notion of a ply number.
A practical approach for 1/4-SHPEDs
2015-07-01

Avoiding crossings for reducing visual clutter is one of the main objectives in the area of graph drawing. Apart from work on geometric solutions to this problem, there are radical approaches originating from information visualization in which edges are drawn just partially. Theory on this approach is already established in several directions and 1/4-SHPED arose as standard. A 1/4-SHPED (Symmetric Homogeneous Partial Edge Drawing) is a drawing model in which vertices are drawn as points and edges as two pieces (= stubs) of a straight-line segment, each incident to a vertex, without any crossing stubs, and with stub size 1/4 of the total edge length. If crossings are permitted in a 1/4-SHPED, we call it 1/4-nSHPED (n = nearly). 1/4-nSHPEDs and 1/4-SHPEDs help the reader inferring adjacent vertices by approximating the distance due to four times the stub length. Symmetry of stubs helps to verify adjacency. We describe a force-directed algorithm that aims at producing a 1/4-SHPED. The algorithm is finally evaluated with several classes of graphs.
Conclusions from an object-delivery robotic competition: SICK robot day 2014
2015-07-01

Contrary to controlled experiments in a laboratory, robotics competitions pose a real challenge to an intelligent autonomous system. To allow a good performance, robotic systems have to be very robust to unforeseen circumstances in a highly constrained time frame. In this paper we present the design, implementation and performance of the robotic system we developed for participation in the SICK robot day 2014, with which we achieved very good results, placing second, with the same maximum score as the first. The task of this competition was to alternately fetch and deliver objects in a simplified warehouse scenario. Participating robots had to be able to carry out different tasks, such as detecting filling and delivery stations, receiving and analysing bar-code labelled objects as well as navigating in an arena among three other robots.
Science gateways - leveraging modeling and simulations in HPC infrastructures via increased usability
2015-07-01

Modeling and simulations, which necessitate HPC infrastructures, are often based on complex scientific theories and involve interdisciplinary research teams. IT specialists support with the efficient access to HPC infrastructures. They design, implement and configure the simulations and models reflecting the sophisticated theoretical models and approaches developed and applied by domain researchers. Roles in such interdisciplinary teams may overlap dependent on the knowledge and experience with computational resources and/or the research domain. Bioinformaticians, for example, are in general trained to act as IT specialists, while having also a good knowledge about biology and chemistry to support the user community competently. Domain researchers are mainly not IT specialists and the requirement to employ HPC infrastructures via command line often forms a huge hurdle for them. Thus, there is the need to increase the usability of simulations and models on HPC infrastructures for the uptake by the user community. Science gateways form a solution, which offer a graphical user interface tailored to a specific research domain with a single point of entry for job and data management hiding the underlying infrastructure. In the last 10 years quite a few web development frameworks, science gateway frameworks and APIs with different foci and strengths have evolved to support the developers of science gateways in implementing an intuitive solution for a target research domain. The selection of a suitable technology for a specific use case is essential and helps reducing the effort in implementing the science gateway by re-using existing software or frameworks. Thus, a solution for a user community can be provided more efficiently. This paper goes into detail for science gateway concepts as well as information resources, gives examples for successful technologies and proposes criteria for choosing a technology for a use case.
Appendiceal diverticulitis shortly after a performed laparoscopic sigma resection
2015-07-01

Diverticulosis of the vermiform appendix is rare and usually asymptomatic or associated with mild, chronic or intermittent abdominal pain. A 52-year-old patient was admitted to our department due to lower abdominal pain. Assuming the second episode of diverticulitis of the sigmoid, a computed tomography (CT) was performed, and complicated sigmoid diverticulitis and an accentuated appendix without inflammatory signs were diagnosed. Laparoscopic sigmoid resection was performed with an intraoperative macroscopic inconspicuous appendix. Two months later, right-sided abdominal pain returned. CT scan showed increasing signs of thickened appendix. Because of a gallbladder polyp, a combined laparoscopic appendectomy and cholecystectomy with one additional laparoscopic access was performed. Pathology detected a small diverticulum of the appendix and a small tubular adenoma with low-grade intraepithelial neoplasia in the gallbladder. Although diverticulitis of the appendix is very rare, it should be considered in patients with right lower abdominal pain, and appendectomy should be performed even in macroscopic unsuspicious cases.
Holocaust Cartoons as Ideographs
2015-07-01

The Holocaust cartoon competition of 2006 in Iran as an instance of social controversy has the potential to raise social and political arguments over various international and global issues. Through using McGee’s theory of ideograph and Edwards and Winkler’s theory of representative form, I identify the ideographs used in these cartoons and argue that the Holocaust cartoons function ideographically to portray Jews, Judaism, Palestine, Israel, Zionism, and the Holocaust. I explain how these controversial images function as representative characters and representative anecdotes and create different ideological interpretations of the Holocaust and associated issues, such as Israel–Palestine conflicts and Western freedom of speech. I argue that the cartoons suggest a connection between Nazism and Zionism, or the Nazi and Israeli regimes, by juxtaposing various elements and situations. I explain that the cartoons anecdotally refer to the Holocaust and represent it as myth or hoax used by Jews/Zionists to justify creation of the nation of Israel.
A fast dense stereo matching algorithm with an application to 3D occupancy mapping using quadrocopters
2015-07-01

We propose a fast algorithm for computing stereo correspondences and correcting the mismatches. The correspondences are computed using stereo block matching and refined with a depth-aware method. We compute 16 disparities at the same time using SSE instructions. We evaluated our method on the Middlebury benchmark and obtained promosing results for practical realtime applications. The use of SSE instructions allows us to reduce the time needed to process the Tsukuba stereo pair to 8 milliseconds (125 fps) on a Core i5 CPU with 2×3.3 GHz. Our disparity refinement method has corrected 40% of the wrong matches with an additional computational time of 5.2% (0.41ms). The algorithm has been used to build 3D occupancy grid maps from stereo images. We used the datasets provided by the EuRoC Robotic Challenge. The reconstruction was accurate enough to perform realtime safe navigation.
Subtle Impact of Akt1 and Akt3 on Exploratory Behavior in Gene Targeted Mice
2015-07-01

Abstract. The present study explored the impact of Akt1 and Akt3 on behavior. Akt1 (akt1 -/- ) and Akt3 (akt3 -/- ) knockout mice were compared to wild type (wt) mice. The akt1 -/- mice, akt3 -/- mice, and wt mice were similar in most parameters of the open-field test. However, the distance traveled in the center area was slightly but significantly less in akt3 -/- mice than in wt mice. In the light/dark transition test akt1 -/- mice had significantly lower values than wt mice and akt3 -/- mice for distance traveled, number of rearings, rearing time in the light area, as well as time spent and distance traveled in the entrance area. They were significantly different from akt3 -/- mice in the distance traveled, visits, number of rearings, rearing time in the light area, as well as time spent, distance traveled, number of rearings, and rearing time in the entrance area. In the O-maze the time spent, and the visits to open arms, as well as the number of protected and unprotected headdips were significantly less in akt1 -/- mice than in wt mice, whereas the time spent in closed arms was significantly more in akt1 -/- mice than in wt mice. Protected and unprotected headdips were significantly less in akt3 -/- mice than in wt mice. In closed area, akt3 -/- mice traveled a significantly larger distance at larger average speed than akt1 -/- mice. No differences were observed between akt1 -/- mice, akt3 -/- mice and wt-type mice in the time of floating during the forced swimming test. In conclusion, akt1 -/- mice and less so akt3 -/ mice display subtle changes in behavior.
Phosphoinositide-Dependent Protein Kinase 1 (PDK1)
2015-07-01

Abstract. Phosphatidylinositol-3-kinase (PI3K) signaling influences susceptibility to virus infections, anoxia, obstetric complications, and cancer; which are changed in patients with schizophrenia and their first degree relatives. Therefore PI3K signaling might have impact on the pathophysiology of schizophrenia. PI3K signaling crucially involves phosphoinositide-dependent protein kinase (PDK1). Increased anxiety behavior is observed in PDK1 hypomorphic mice. Here we show enhanced prevalence of schizophrenia in carriers of the PDK1 CC genotype in human beings. Moreover, decreased parietal P300 amplitude, which is a well-studied schizophrenic endophenotype, was observed in PDK1 CC carriers. Glutamate and glutamine concentrations are increased in the frontal lobe of PDK1 dysmorphic mice and human CC individuals. Our results demonstrate that the PDK1 CC genotype is associated with increased risk to develop schizophrenia, a typical endophenotype profile observed in the disease and modified neurotransmitter concentrations in brain regions associated with the disease.
Improving accuracy of source level timing simulation for GPUs using a probabilistic resource model
2015-07-01

After their success in the high performance and desktop market, Graphic Processing Units (GPUs), that can be used for general purpose computing are introduced for embedded systems on a chip (SOCs). Due to some advanced architectural features, like massive simultaneous multithreading, static performance analysis and high-level timing simulation are difficult to apply to code running on these systems. This paper extends a method for performance simulation of GPUs. The method uses automated performance annotations in the application's OpenCL C source code, and an extended performance model for derivation of a kernels runtime from metrics produced by the execution of annotated kernels. The final results are then generated using a probabilistic resource conflict model. The model reaches an accuracy of 90% on most test cases and delivers a higher average accuracy than previous methods.
Synthesis of Glycoconjugated Phthalonitriles for New Phthalocyanine-Based Photosensitizers
2015-07-01

GRAPHICAL ABSTRACTExcellent photophysical and photochemical properties completed by magnificent take-up rates in malignant tissues attracted a great deal of interest to the application of glycosylated and glycoconjugated phthalocyanines in photodynamic therapy. In this study we describe the concise synthesis and full characterization of 16 differently 3,6-bisglycoconjugated phthalonitriles 3, 5, 6, 8, and 48–59, which are precursors for a new generation of photosensitizers, namely, nonperipheral glycoconjugated phthalocyanines. The first example for the synthesis of a nonperipheral glycoconjugated zinc phthalocyanine 60 from phthalonitrile 48 is also presented in this work.
Sloginsky drawings of graphs
2015-07-01

In this paper we combine the recently introduced slanted orthogonal (for short: slog) model with the traditional Kandinsky approach into the new Sloginsky model. The slog model introduces diagonal segments into orthogonal drawings and restricts crossings exclusively to these diagonal segments. Additionally, the traditional 90° bends of orthogonal drawings are replaced by so called half-bends. While the slog model is restricted to graphs of maximum vertex degree four, the Kandinsky model allows arbitrary vertex degree. By combining the two approaches we can profit from the advantages of both models, namely arbitrary vertex degree and increased readability. Since we seek drawings of non-planar graphs, we adopt the topology-shape-metrics (TSM) approach. Motivated by a recent complexity result that shows that the problem of minimizing the total number of bends is NP-hard even for plane graphs [1], we give an ILP formulation that results in Sloginsky drawings that are optimal in terms of the total number of bends. We also perform experiments and discuss properties of the new model.