A Spectral Algorithm with Additive Clustering for the Recovery of Overlapping Communities in Networks

This paper presents a novel spectral algorithm with additive clustering designed to identify overlapping communities in networks. The algorithm is based on geometric properties of the spectrum of the expected adjacency matrix in a random graph model that we call stochastic blockmodel with overlap (SBMO). An adaptive version of the algorithm, that does not require the knowledge of the number of hidden communities, is proved to be consistent under the SBMO when the degrees in the graph are (slightly more than) logarithmic. The algorithm is shown to perform well on simulated data and on real-world graphs with known overlapping communities.Comment: Journal of Theoretical Computer Science (TCS), Elsevier, A Para\^itr

Minimising pain in farm animals: the 3S approach - ‘Suppress, Substitute, Soothe'

Recently, the French National Institute for Agricultural Research appointed an expert committee to review the issue of pain in food-producing farm animals. To minimise pain, the authors developed a ‘3S' approach accounting for ‘Suppress, Substitute and Soothe' by analogy with the ‘3Rs' approach of ‘Reduction, Refinement and Replacement' applied in the context of animal experimentation. Thus, when addressing the matter of pain, the following steps and solutions could be assessed, in the light of their feasibility (technical constraints, logistics and regulations), acceptability (societal and financial aspects) and availability. The first solution is to suppress any source of pain that brings no obvious advantage to the animals or the producers, as well as sources of pain for which potential benefits are largely exceeded by the negative effects. For instance, tail docking of cattle has recently been eliminated. Genetic selection on the basis of resistance criteria (as e.g. for lameness in cattle and poultry) or reduction of undesirable traits (e.g. boar taint in pigs) may also reduce painful conditions or procedures. The second solution is to substitute a technique causing pain by another less-painful method. For example, if dehorning cattle is unavoidable, it is preferable to perform it at a very young age, cauterising the horn bud. Animal management and constraint systems should be designed to reduce the risk for injury and bruising. Lastly, in situations where pain is known to be present, because of animal management procedures such as dehorning or castration, or because of pathology, for example lameness, systemic or local pharmacological treatments should be used to soothe pain. These treatments should take into account the duration of pain, which, in the case of some management procedures or diseases, may persist for longer periods. The administration of pain medication may require the intervention of veterinarians, but exemptions exist where breeders are allowed to use local anaesthesia (e.g. castration and dehorning in Switzerland). Extension of such exemptions, national or European legislation on pain management, or the introduction of animal welfare codes by retailers into their meat products may help further developments. In addition, veterinarians and farmers should be given the necessary tools and information to take into account animal pain in their management decision

Childhood-Onset Spinocerebellar Ataxia 3: Tongue Dystonia as an Early Manifestation

Background: Dystonia is a relatively common feature of spinocerebellar ataxia 3 (SCA3). Childhood onset of SCA3 is rare and typically associated with either relatively large, or homozygous, CAG repeat expansions. Case report: We describe a 10-year-old girl with SCA3, who presented with tongue dystonia in addition to limb dystonia and gait ataxia due to a heterozygous expansion of 84 repeats in ATXN3. Discussion: Diagnosis of the SCAs can be challenging, and even more so in children. Tongue dystonia has not previously been documented in SCA3

Data-based investigation of the effects of canopy structure and shadows on chlorophyll fluorescence in a deciduous oak forest

Data from satellite, aircraft, drone, and ground-based measurements have already shown that canopy-scale sun-induced chlorophyll fluorescence (SIF) is tightly related to photosynthesis, which is linked to vegetation carbon assimilation. However, our ability to effectively use those findings are hindered by confounding factors, including canopy structure, fluctuations in solar radiation, and sun–canopy geometry that highly affect the SIF signal. Thus, disentangling these factors has become paramount in order to use SIF for monitoring vegetation functioning at the canopy scale and beyond. Active chlorophyll fluorescence measurements (FyieldLIF), which directly measures the apparent fluorescence yield, have been widely used to detect physiological variation of the vegetation at the leaf scale. Recently, the measurement of FyieldLIF has become feasible at the canopy scale, opening up new opportunities to decouple structural, biophysical, and physiological components of SIF at the canopy scale. In this study, based on top-of-canopy measurements above a mature deciduous forest, reflectance (R), SIF, SIF normalized by incoming photosynthetically active radiation (SIFy), FyieldLIF, and the ratio between SIFy and FyieldLIF (named Φk) were used to investigate the effects of canopy structure and shadows on the diurnal and seasonal dynamics of SIF. Further, random forest (RF) models were also used to not only predict FyieldLIF and Φk, but also provide an interpretation framework by considering additional variables, including the R in the blue, red, green, red-edge, and near-infrared bands; SIF; SIFy; and solar zenith angle (SZA) and solar azimuth angle (SAA). Results revealed that the SIF signal is highly affected by the canopy structure and sun–canopy geometry effects compared to FyieldLIF. This was evidenced by the weak correlations obtained between SIFy and FyieldLIF at the diurnal timescale. Furthermore, the daily mean SIF‾y captured the seasonal dynamics of daily mean F‾yieldLIF and explained 58 % of its variability. The findings also revealed that reflectance in the near-infrared (R-NIR) and the NIRv (the product of R-NIR and normalized difference vegetation index (NDVI)) are good proxies of Φk at the diurnal timescale, while their correlations with Φk decrease at the seasonal timescale. With FyieldLIF and Φk as outputs and the abovementioned variables as predictors, this study also showed that the RF models can explain between 86 % and 90 % of FyieldLIF, as well as 60 % and 70 % of Φk variations under clear-sky conditions. In addition, the predictor importance estimates for FyieldLIF RF models revealed that R at 410, 665, 740, and 830 nm; SIF; SIFy; SZA; and SAA emerged as the most useful and influential factors for predicting FyieldLIF, while R at 410, 665, 705, and 740 nm; SZA; and SAA are crucial for predicting Φk. This study highlighted the complexity of interpreting diurnal and seasonal dynamics of SIF in forest canopies. These dynamics are highly dependent on the complex interactions between the structure of the canopy, the vegetation biochemical properties, the illumination angles (SZA and SAA), and the light conditions (ratio of diffuse to direct solar radiation). However, such measurements are necessary to better separate the variability in SIF attributable to radiation and measurement conditions from the subtler variability attributable to plant physiological processes.</p

Mukaiyama addition of (trimethylsilyl) acetonitrile to dimethyl acetals mediated by trimethylsilyl trifluoromethanesulfonate

(Trimethylsilyl) acetonitrile reacts smoothly with dimethyl acetals in the presence of stoichiometric trimethylsilyl trifluoromethanesulfonate (TMSOTf) to yield β-methoxynitriles. The ideal substrates for this reaction are acetals derived from aromatic aldehydes. Elimination to the corresponding α,β-unsaturated nitriles is observed as the major product in the case of electron-rich acetals. A mechanistic hypothesis that includes isomerization of the silylnitrile to a nucleophilic N-silyl ketene imine is presented

Asymptotic Expansions for Stationary Distributions of Perturbed Semi-Markov Processes

New algorithms for computing of asymptotic expansions for stationary distributions of nonlinearly perturbed semi-Markov processes are presented. The algorithms are based on special techniques of sequential phase space reduction, which can be applied to processes with asymptotically coupled and uncoupled finite phase spaces.Comment: 83 page

Modelling the time-varying cell capacity in LTE networks

In wireless orthogonal frequency-division multiple access (OFDMA) based networks like Long Term Evolution (LTE) or Worldwide Interoperability for Microwave Access (WiMAX) a technique called adaptive modulation and coding (AMC) is applied. With AMC, different modulation and coding schemes (MCSs) are used to serve different users in order to maximise the throughput and range. The used MCS depends on the quality of the radio link between the base station and the user. Data is sent towards users with a good radio link with a high MCS in order to utilise the radio resources more efficiently while a low MCS is used for users with a bad radio link. Using AMC however has an impact on the cell capacity as the quality of a radio link varies when users move around; this can even lead to situations where the cell capacity drops to a point where there are too little radio resources to serve all users. AMC and the resulting varying cell capacity notably has an influence on admission control (AC). AC is the algorithm that decides whether new sessions are allowed to a cell or not and bases its decisions on, amongst others, the cell capacity. The analytical model that is developed in this paper models a cell with varying capacity caused by user mobility using a continuous -time Markov chain (CTMC). The cell is divided into multiple zones, each corresponding to the area in which data is sent towards users using a certain MCS and transitions of users between these zones are considered. The accuracy of the analytical model is verified by comparing the results obtained with it to results obtained from simulations that model the user mobility more realistically. This comparison shows that the analytical model models the varying cell capacity very accurately; only under extreme conditions differences between the results are noticed. The developed analytical and simulation models are then used to investigate the effects of a varying cell capacity on AC. Also, an optimisation algorithm that adapts the parameter of the AC algorithm which determines the amount of resources that are reserved in order to mitigate the effects of the varying cell capacity is studied using the models. Updating the parameter of the AC algorithm is done by reacting to certain triggers that indicate good or bad performance and adapt the parameters of the AC algorithm accordingly. Results show that using this optimisation algorithm improves the quality of service (QoS) that is experienced by the users.This work was partially supported by the Spanish Government through project TIN2010-21378-C02-02 and contract BES-2007-15030.Sas, B.; Bernal Mor, E.; Spaey, K.; Pla, V.; Blondia, C.; Martínez Bauset, J. (2014). Modelling the time-varying cell capacity in LTE networks. 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Admission control in the downlink of WCDMA/UMTS. In LNCS: Vol. 3427. Mobile and wireless systems (pp. 136–151).Garcia, D., Martinez, J., & Pla, V. (2005). Admission control policies in multiservice cellular networks: optimum configuration and sensitivity. In G. Kotsis, & O. Spaniol (Eds.), Lecture notes in computer science: Vol. 3427. Wireless systems and mobility in next generation Internet (pp. 121–135).Guo, J., Liu, F., & Zhu, Z. (2007). Estimate the call duration distribution parameters in GSM system based on K-L divergence method. In International conference on wireless communications, networking and mobile computing (pp. 2988–2991), Shanghai, China, September 2007.Hossain, M., Hassan, M., & Sirisena, H. R. (2004). Adaptive resource management in mobile wireless networks using feedback control theory. Telecommunications Systems, 24(3–4), 401–415.Jeong, S.S., Han, J.A., & Jeon, W.S. (2005). Adaptive connection admission control scheme for high data rate mobile networks. 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(2001). Call admission control for capacity-varying networks. Telecommunications Systems, 16(1–2), 15–40.SOCRATES. www.fp7-socrates.eu .Spaey, K., Sas, B., & Blondia, C. (2010). Self-optimising call admission control for LTE downlink. In COST 2100 TD(10)10056, Joint Workshop COST 2100 SWG 3.1 & FP7-ICT-SOCRATES, Athens, Greece.Spilling, A. G., Nix, A. R., Beach, M. A., & Harrold, T. J. (2000). Self-organisation in future mobile communications. Electronics & Communication Engineering Journal, 3, 133

A Queueing Theoretic Approach to Decoupling Inventory

This paper investigates the performance of different hybrid push-pull systems with a decoupling inventory at the semi-finished products and reordering thresholds. Raw materials are ‘pushed’ into the semi-finished product inventory and customers ‘pull’ products by placing orders. Furthermore, production of semi-finished products starts when the inventory goes below a certain level, referred to as the threshold value and stops when the inventory attains stock capacity. As performance of the decoupling stock is critical to the overall cost and performance of manufacturing systems, this paper introduces a Markovian model for hybrid push-pull systems. In particular, we focus on a queueing model with two buffers, thereby accounting for both the decoupling stock as well as for possible backlog of orders. By means of numerical examples, we assess the impact of different reordering policies, irregular order arrivals, the set-up time distribution and the order processing time distribution on the performance of hybrid push-pull systems

Engineered artificial antigen presenting cells facilitate direct and efficient expansion of tumor infiltrating lymphocytes

<p>Abstract</p> <p>Background</p> <p>Development of a standardized platform for the rapid expansion of tumor-infiltrating lymphocytes (TILs) with anti-tumor function from patients with limited TIL numbers or tumor tissues challenges their clinical application.</p> <p>Methods</p> <p>To facilitate adoptive immunotherapy, we applied genetically-engineered K562 cell-based artificial antigen presenting cells (aAPCs) for the direct and rapid expansion of TILs isolated from primary cancer specimens.</p> <p>Results</p> <p>TILs outgrown in IL-2 undergo rapid, CD28-independent expansion in response to aAPC stimulation that requires provision of exogenous IL-2 cytokine support. aAPCs induce numerical expansion of TILs that is statistically similar to an established rapid expansion method at a 100-fold lower feeder cell to TIL ratio, and greater than those achievable using anti-CD3/CD28 activation beads or extended IL-2 culture. aAPC-expanded TILs undergo numerical expansion of tumor antigen-specific cells, remain amenable to secondary aAPC-based expansion, and have low CD4/CD8 ratios and FOXP3+ CD4+ cell frequencies. TILs can also be expanded directly from fresh enzyme-digested tumor specimens when pulsed with aAPCs. These "young" TILs are tumor-reactive, positively skewed in CD8+ lymphocyte composition, CD28 and CD27 expression, and contain fewer FOXP3+ T cells compared to parallel IL-2 cultures.</p> <p>Conclusion</p> <p>Genetically-enhanced aAPCs represent a standardized, "off-the-shelf" platform for the direct ex vivo expansion of TILs of suitable number, phenotype and function for use in adoptive immunotherapy.</p