Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Aerobic Energy Metabolism in Podospora anserina by Two Paralogous Genes Encoding Structurally Different c-Subunits of ATP Synthase

Most of the ATP in living cells is produced by an F-type ATP synthase. This enzyme uses the energy of a transmembrane electrochemical proton gradient to synthesize ATP from ADP and inorganic phosphate. Proton movements across the membrane domain (FO) of the ATP synthase drive the rotation of a ring of 8–15 c-subunits, which induces conformational changes in the catalytic part (F1) of the enzyme that ultimately promote ATP synthesis. Two paralogous nuclear genes, called Atp9-5 and Atp9-7, encode structurally different c-subunits in the filamentous fungus Podospora anserina. We have in this study identified differences in the expression pattern for the two genes that correlate with the mitotic activity of cells in vegetative mycelia: Atp9-7 is transcriptionally active in non-proliferating (stationary) cells while Atp9-5 is expressed in the cells at the extremity (apex) of filaments that divide and are responsible for mycelium growth. When active, the Atp9-5 gene sustains a much higher rate of c-subunit synthesis than Atp9-7. We further show that the ATP9-7 and ATP9-5 proteins have antagonist effects on the longevity of P. anserina. Finally, we provide evidence that the ATP9-5 protein sustains a higher rate of mitochondrial ATP synthesis and yield in ATP molecules per electron transferred to oxygen than the c-subunit encoded by Atp9-7. These findings reveal that the c-subunit genes play a key role in the modulation of ATP synthase production and activity along the life cycle of P. anserina. Such a degree of sophistication for regulating aerobic energy metabolism has not been described before.
Where Did I(T) Put It? - A Holistic Solution to the Automatic Construction of Topic Trees for Navigation

Managing information based on hierarchical structures is prevailing, be it by storing documents physically in a file structure like MS explorer or virtually in topic trees as in many web applications. The problem is that the structure evolves over time, created individually and hence reflecting individual opinions of how information objects should be grouped. This leads to time consuming searches and error prone retrieval results since relevant documents might be stored elsewhere. Our approach aims at solving the problem by replacing or complementing the manually created navigation structures by automatically created ones. We consider existing approaches for clustering and labelling and focus on yet unrewarding aspects like having information objects in inner nodes (as it is common in folder hierarchies) and cognitively adequate labelling for textual and non-textual resources. Evaluation was done by knowledge experts based on a comparison of retrieval time for finding given documents in manually and automatic generated information structures and showed the advantage of automatically created topic trees.
Redalyc Sistema

A new species of terrestrial pitviper, Porthidium porrasi, is described from mesophytic forests of the Península de Osa and surrounding area of the Pacific versant of southwestern Costa Rica. It is most similar to P. nasutum and is characterized by a pattern of bands, persistence of the juvenile tail color in adults, and a high number of dorsal scales. Analysis of mtDNA sequences confirms its distinction from P. nasutum. The existence of this species reinforces the notion of elevated herpetofaunal endemism in southwestern Costa Rica.
Accumulating bindings

We give a Haskell implementation of Filinski’s normalisation by evaluation algorithm for the computational lambda-calculus with sums. Taking advantage of extensions to the GHC compiler, our implementation represents object language types as Haskell types and ensures that type errors are detected statically. Following Filinski, the implementation is parameterised over a residualising monad. The standard residualising monad for sums is a continuation monad. Defunctionalising the uses of the continuation monad we present the binding tree monad as an alternative.
A report on cognitive 802.11 model for NS2 simulator

Cognitive radio is a promising solution in improving spectrum utilization efficiency by allowing unlicensed users to access idle licensed spectrum opportunistically. Cognitive Radio Cognitive Network (CRCN) supports multi-interface multi-channel functions in Network Simulator 2 (NS-2). However, CRCN only supports cognitive functions to two MAC protocols that is Macng and Maccoon. Both MACs were designed along with CRCN. Existing MAC protocols such as Simple MAC and 802.11 does not support cognitive function. In this paper, modifications were made to support multi-interface multichannel function and primary user recognition in 802.11 MAC coding. Simulation was run to compare the performance of different cognitive MACs: Simple MAC, 802.11, and Macng, in smart grid communications. The performance metric used was average delay. Simulation results showed that cognitive radio outperforms non-cognitive radio. In addition, cognitive 802.11 has better delay performance than Simple MAC and Macng. This indicates that choice of cognitive MAC protocols affect the performance of smart grid communications.
New Models for Improving Supertag Disambiguation

In previous work, supertag disambiguation has been presented as a robust partial parsing technique. In this paper we present two approaches: contextual models, which exploit a variety of features in order to improve supertag performance, and class-based models, which assign sets of supertags to words in order to substantially improve accuracy with only a slight increase in ambiguity.
Fault tolerance in safety critical automotive applications: cost of agreement as a limiting factor

The high availability and safety requirements for automotive electronics are currently almost exclusively addressed by application specific engineering solutions to fault tolerance rather than by systematic approaches. Currently, systematic approaches are ruled out because of cost. The reason for this is that a systematic approach to fault tolerance requires: replication of components; and communication between replicated components to achieve agreement despite nondeterminism. While replicated components become more and more available with the connection of different control units by means of a multiplex bus, it is shown that the cost of agreement on sensor inputs will become the limiting factor for systematic approaches to fault tolerance. For that reason a new agreement algorithm is introduced which considers the problem of agreement and sensor inputs in an integrated fashion. This algorithm takes advantage of the a priori knowledge on the maximum deviation of replicated sensor inputs. Optimality of this algorithm is shown with respect to the minimum number of bits for agreement. This algorithm allows broader application of systematic fault tolerance to automotive applications. The result of this work will be used for a prototype implementation of a safety critical automotive application. <<ETX>>
Prediction of Large Alphabet Processes and Its Application to Adaptive Source Coding

The problem of predicting a sequence $x_1,x_2,. $ generated by a discrete source with unknown statistics is considered. Each letter $x_{t+1}$ is predicted using information on the word $x_1x_2. x_t$ only. In fact, this problem is a classical problem which has received much attention. Its history can be traced back to Laplace. We address the problem where each $x_i$ belongs to some large (or even infinite) alphabet. A method is presented for which the precision is greater than for known algorithms, where precision is estimated by the Kullback-Leibler divergence. The results can readily be translated to results about adaptive coding.
Widespread Epigenetic Abnormalities Suggest a Broad DNA Methylation Erasure Defect in Abnormal Human Sperm

Background Male-factor infertility is a common condition, and etiology is unknown for a high proportion of cases. Abnormal epigenetic programming of the germline is proposed as a possible mechanism compromising spermatogenesis of some men currently diagnosed with idiopathic infertility. During germ cell maturation and gametogenesis, cells of the germ line undergo extensive epigenetic reprogramming. This process involves widespread erasure of somatic-like patterns of DNA methylation followed by establishment of sex-specific patterns by de novo DNA methylation. Incomplete reprogramming of the male germ line could, in theory, result in both altered sperm DNA methylation and compromised spermatogenesis. Methodology/Principal Finding We determined concentration, motility and morphology of sperm in semen samples collected by male members of couples attending an infertility clinic. Using MethyLight and Illumina assays we measured methylation of DNA isolated from purified sperm from the same samples. Methylation at numerous sequences was elevated in DNA from poor quality sperm. Conclusions This is the first report of a broad epigenetic defect associated with abnormal semen parameters. Our results suggest that the underlying mechanism for these epigenetic changes may be improper erasure of DNA methylation during epigenetic reprogramming of the male germ line.
Calcium-Activated Potassium Channels Are Selectively Coupled to P/Q-Type Calcium Channels in Cerebellar Purkinje Neurons

Cerebellar Purkinje neurons fire spontaneously in the absence of synaptic transmission. P/Q-type voltage-gated calcium channels and calcium-activated potassium channels are required for normal spontaneous activity. Blocking P/Q-type calcium channels paradoxically mimics the effects of blocking calcium-activated potassium channels. Thus, an important function of the P/Q-type calcium channels is to provide calcium for activation of calcium-activated potassium channels. Purkinje neurons express several classes of voltage-gated calcium channels, and the P/Q- and T-type channels make comparable contributions to total calcium entry after an action potential. Here we demonstrate that calcium-activated potassium channels are activated exclusively by calcium entering through P/Q-type voltage-gated calcium channels. This selective coupling is maintained even when calcium flux through voltage-gated channels is increased by increasing the extracellular calcium concentration. Small decreases in P/Q current density are likely to alter spontaneous activity of Purkinje neurons via decreased recruitment of calcium-activated potassium channels. In both human and murine animal models, mutations that decrease P/Q current density in Purkinje neurons also cause cerebellar ataxia. Alterations in the spontaneous activity of Purkinje neurons may be an important contributing factor to the ataxia in these subjects.
Natural speaker-independent Arabic speech recognition system based on Hidden Markov Models using Sphinx tools

This paper reports the design, implementation, and evaluation of a research work for developing a high performance natural speaker-independent Arabic continuous speech recognition system. It aims to explore the usefulness and success of a newly developed speech corpus, which is phonetically rich and balanced, presenting a competitive approach towards the development of an Arabic ASR system as compared to the state-of-the-art Arabic ASR researches. The developed Arabic AS R mainly used the Carnegie Mellon University (CMU) Sphinx tools together with the Cambridge HTK tools. To extract features from speech signals, Mel-Frequency Cepstral Coefficients (MFCC) technique was applied producing a set of feature vectors. Subsequently, the system uses five-state Hidden Markov Models (HMM) with three emitting states for tri-phone acoustic modeling. The emission probability distribution of the states was best using continuous density 16 Gaussian mixture distributions. The state distributions were tied to 500 senons. The language model contains uni-grams, bi-grams, and tri-grams. The system was trained on 7.0 hours of phonetically rich and balanced Arabic speech corpus and tested on another one hour. For similar speakers but different sentences, the system obtained a word recognition accuracy of 92.67% and 93.88% and a Word Error Rate (WER) of 11.27% and 10.07% with and without diacritical marks respectively. For different speakers but similar sentences, the system obtained a word recognition accuracy of 95.92% and 96.29% and a Word Error Rate (WER) of 5.78% and 5.45% with and without diacritical marks respectively. Whereas different speakers and different sentences, the system obtained a word recognition accuracy of 89.08% and 90.23% and a Word Error Rate (WER) of 15.59% and 14.44% with and without diacritical marks respectively.
Learning Robust Representations for Data Analytics

Learning compact representations from high-dimensional and large-scale data plays an essential role in many real-world applications. However, many existing methods show limited performance when data are contaminated with severe noise. To address this challenge, we have proposed several effective methods to extract robust data representations, such as balanced graphs, discriminative subspaces, and robust dictionaries. In addition, several topics are provided as future work.
Quantitative architecture usability assessment with scenarios

In this paper, we propose a quantitative scenario-based method for dealing with the quality attributes for future software systems before any architecture implementation effort is actually done. The exploration of the possible design variants for a future system is done using so-called user scenarios. The method supports the software architects in developing future systems that meet their specific quality requirements. The method was validated in an industrial case study focusing on the usability aspects.
A Hypergraph Model for Computing Page Reputation on Web Collections

In this work we propose a representation of the web as a directed hypergraph, instead of a graph, where links can connect not only pairs of pages, but also pairs of disjoint sets of pages. In our model, the web hypergraph is derived from the web graph by dividing the set of pages into non-overlapping blocks and using the links between pages of distinct blocks to create hyperarcs. Each hyperarc connects a block of pages to a single page and is created with the goal of providing more reliable information for link analysis methods. We used the hypergraph structure to compute the reputation of web pages by experimenting hypergraph versions of two previously proposed link analysis methods, Pagerank and Indegree. We present experiments which indicate the hypergraph versions of Pagerank and Indegree produce better results when compared to their original graph versions.
A General Characterization of Sync Word for Asynchronous Communication

We study a problem of sequential frame synchronization for a frame transmitted uniformly in $A$ slots. For a discrete memoryless channel (DMC), Venkat Chandar et al showed that the frame length $N$ must scale with $A$ as $e^{N \alpha(Q)} > A$ for the frame synchronization error to go to zero (asymptotically with $A$). Here, $Q$ denotes the transition probabilities of the DMC and $\alpha(Q)$, defined as the synchronization threshold, characterizes the scaling needed of $N$ for asymptotic error free frame synchronization. We show that the asynchronous communication framework permits a natural tradeoff between the sync frame length $N$ and the channel (usually parameterised by the input). For an AWGN channel, we study this tradeoff between the sync frame length $N$ and the input symbol power $P$ and characterise the scaling needed of the sync frame energy $E = N P$ for optimal frame synchronisation.
A MULTI-BUNCH, THREE-DIMENSIONAL, STRONG-STRONG BEAM-BEAM SIMULATION CODE FOR PARALLEL COMPUTERS

For simulating the strong-strong beam-beam effect, using Particle-In-Cell codes has become one of the methods of choice. While the two-dimensional problem is readily treatable using PC-class machines, the three-dimensional problem, i.e., a problem encompassing hourglass and phase-averaging effects, requires the use of parallel processors. In this paper, we introduce a strong-strong code NIMZOVICH 1 , which was specifically designed for parallel processors and which is optimally used for many bunches and parasitic crossings. We describe the parallelization scheme and give some benchmarking results.
Information Cascades in Email Forwarding Networks CS 224 W Project Report Group

Recent information diffusion research has often focused on social networking sites like Facebook and Twitter, such as the analysis of reposting or hashtags as trends go “viral. ” Partially due to its more private nature, email has been less popular of late. However, email’s near universal adoption as a means of online communication, its prevalence in commercial and academic environments, and the well-established use of forwarding to spread information make information diffusion in email networks — and specifically the mechanics of forwarding behavior — a relevant and important area to explore. This research could provide insight about, for instance, whether introducing an email to a specific part of the network would make it more likely to spread through the rest of the network, with implications for emergency response (spreading important information), political campaigning (spreading a candidate’s message), and computer security (spreading a potentially malicious file or URL).
Concurrent trastuzumab with adjuvant radiotherapy in HER2-positive breast cancer patients: acute toxicity analyses from the French multicentric study.

BACKGROUND Trastuzumab (T) combined with chemotherapy has been recently shown to improve outcome in HER2-positive breast cancer (BC). The aim of this study was to evaluate the toxic effects of concurrent radiation therapy (RT) and T administration in the adjuvant setting. PATIENTS AND METHODS Data of 146 patients with stages II-III HER2-positive BC were recorded. Median age was 46 years. In all, 32 (23%) and 114 (77%) patients received a weekly and a 3-week T schedule, respectively. A median dose of 50 Gy was delivered after surgery. Internal mammary chain (IMC) was irradiated in 103 (71%) patients. RESULTS Grade >2 dermatitis and esophagitis were noted in 51% and 12%, respectively. According to the Common Toxicity Criteria v3.0 scale and HERA (HERceptin Adjuvant) trial criteria, respectively, 10% and 6% of the patients had a grade >/=2 of left ventricular ejection fraction (LVEF) decrease after RT. Multivariate analyses revealed two independent prognostic factors: weekly T administration (for LVEF decrease) and menopausal status (for dermatitis). Higher level of T cumulative dose (>1600 mg) was only borderline of statistical significance for acute esophagitis toxicity. CONCLUSION We showed that weekly concurrent T and RT are feasible in daily clinical practice with, however, a decrease of LVEF. Cardiac volume sparing and patient selections for IMC irradiation are highly recommended. Longer follow-up is warranted to evaluate late toxic effects.
SurroundSense : Localizing Mobile Phones Using Ambient Light , Sound , Color , and Motion

A growing number of mobile computing applications is centered around the user’s location. The notion of location is broad, ranging from physical coordinates (latitude/longitude) to logical locations (like Starbucks). While extensive research has been performed in physical localization, there has been far fewer attempts in recognizing logical places. This paper argues that the increasing number of sensors on mobile phones presents new opportunities. We postulate that ambient light, sound, and color in a place convey a photoacoustic signature that can be sensed by in-built cameras and microphones in mobile phones. In-built accelerometers may also be useful in inferring broad classes of user-movements, often induced by the nature of the place. By combining these optical, acoustic, and motion attributes, it may be feasible to construct an identifying fingerprint for logical localization. Hence, users in adjacent shops can be separated logically, even though their physical positions are extremely close. The implications may be valuable as more services begin to interact with the end-user based on the user’s surroundings or situation. This paper proposes SurroundSense, a mobile phone based system that attempts logical localization using ambient light, color, sound, and user activity. Evaluation results from 75 stores in Durham show that SurroundSense is an promising step towards a rich research direction.
A covalently bound photoisomerizable agonist. Comparison with reversibly bound agonists at electrophorus electroplaques

After disulphide bonds are reduced with dithiothreitol, trans-3- (α-bromomethyl)-3’-[α- (trimethylammonium)methyl]azobenzene (trans-QBr) alkylates a sulfhydryl group on receptors. The membrane conductance induced by this “tethered agonist” shares many properties with that induced by reversible agonists. Equilibrium conductance increases as the membrane potential is made more negative; the voltage sensitivity resembles that seen with 50 [mu]M carbachol. Voltage- jump relaxations follow an exponential time-course; the rate constants are about twice as large as those seen with 50 μM carbachol and have the same voltage and temperature sensitivity. With reversible agonists, the rate of channel opening increases with the frequency of agonist-receptor collisions: with tethered trans-Qbr, this rate depends only on intramolecular events. In comparison to the conductance induced by reversible agonists, the QBr-induced conductance is at least 10-fold less sensitive to competitive blockade by tubocurarine and roughly as sensitive to “open-channel blockade” bu QX-222. Light-flash experiments with tethered QBr resemble those with the reversible photoisomerizable agonist, 3,3’,bis-[α-(trimethylammonium)methyl]azobenzene (Bis-Q): the conductance is increased by cis {arrow} trans photoisomerizations and decreased by trans {arrow} cis photoisomerizations. As with Bis-Q, ligh-flash relaxations have the same rate constant as voltage-jump relaxations. Receptors with tethered trans isomer. By comparing the agonist-induced conductance with the cis/tans ratio, we conclude that each channel’s activation is determined by the configuration of a single tethered QBr molecule. The QBr-induced conductance shows slow decreases (time constant, several hundred milliseconds), which can be partially reversed by flashes. The similarities suggest that the same rate-limiting step governs the opening and closing of channels for both reversible and tethered agonists. Therefore, this step is probably not the initial encounter between agonist and receptor molecules.
Contribution to new numerical integration in dynamics

The problem of time integration in the dynamics of building structures is primarily a mathematical problem of the accuracy of the numerical integration of the acceleration time course. All existing methods are trying more or less successfully to master this problem. The best known and most widely used is the Newmark method, which by its very nature is only a trapezoidal rule applied to both acceleration and speed. The most effective method of numerical integration of repeated integrals was introduced mathematically [1], namely the modification of numerical integration methods of the Gaussian type for use on repeated integrals. In this work is introduced their simple use in problem solution of mechanics and dynamics of structures and consequently comparison of the results with the traditional Newmark Direct Time Integration method is presented.