Miracle-dz/UniFAR-FTUs huggingface dataset:
Alternative Designs and the Evolution of Functional Diversity

According to conventional wisdom, functional diversity is exclusively a consequence of species having evolved adaptations to fill different niches within a heterogeneous environment. This view anticipates only one optimal combination of trait values in a given environment, but it is also conceivable that alternative designs of equal fitness in the same environment might evolve. To investigate that possibility, we use a genetic algorithm to search for optimal combinations of 34 functional traits in a realistic model of tree seedling growth and survival. We show that separate lineages of seedlings evolving in identical environments result in many alternative functional designs of approximately equal fitness.
ClassMate : A System for Automated Event Extraction from Course Websites

Websites contain a huge amount of time-critical data in highly unstructured and heterogeneous form. Information Extraction systems can extract relevant entities and relationships from these sites, and identify, classify and categorize them. In this paper, we present ClassMate, a complete system for extracting key course-related events from university course websites. ClassMate pipelines web data through a Named Entity Recognition module, an windowbased event extractor, and a KMeans clusteringbased classifier.
The Role of Transcription Factors at Antisense-Expressing Gene Pairs in Yeast

Genes encoded close to one another on the chromosome are often coexpressed, by a mechanism and regulatory logic that remain poorly understood. We surveyed the yeast genome for tandem gene pairs oriented tail-to-head at which expression antisense to the upstream gene was conserved across species. The intergenic region at most such tandem pairs is a bidirectional promoter, shared by the downstream gene mRNA and the upstream antisense transcript. Genomic analyses of these intergenic loci revealed distinctive patterns of transcription factor regulation. Mutation of a given transcription factor verified its role as a regulator in trans of tandem gene pair loci, including the proximally initiating upstream antisense transcript and downstream mRNA and the distally initiating upstream mRNA. To investigate cis-regulatory activity at such a locus, we focused on the stress-induced NAD(P)H dehydratase YKL151C and its downstream neighbor, the metabolic enzyme GPM1. Previous work has implicated the region between these genes in regulation of GPM1 expression; our mutation experiments established its function in rich medium as a repressor in cis of the distally initiating YKL151C sense RNA, and an activator of the proximally initiating YKL151C antisense RNA. Wild-type expression of all three transcripts required the transcription factor Gcr2. Thus, at this locus, the intergenic region serves as a focal point of regulatory input, driving antisense expression and mediating the coordinated regulation of YKL151C and GPM1. Together, our findings implicate transcription factors in the joint control of neighboring genes specialized to opposing conditions and the antisense transcripts expressed between them.
An Observational Study of Patient Characteristics Associated with the Mode of Admission to Acute Stroke Services in North East, England

Objective Effective provision of urgent stroke care relies upon admission to hospital by emergency ambulance and may involve pre-hospital redirection. The proportion and characteristics of patients who do not arrive by emergency ambulance and their impact on service efficiency is unclear. To assist in the planning of regional stroke services we examined the volume, characteristics and prognosis of patients according to the mode of presentation to local services. Study design and setting A prospective regional database of consecutive acute stroke admissions was conducted in North East, England between 01/09/10-30/09/11. Case ascertainment and transport mode were checked against hospital coding and ambulance dispatch databases. Results Twelve acute stroke units contributed data for a mean of 10.7 months. 2792/3131 (89%) patients received a diagnosis of stroke within 24 hours of admission: 2002 arrivals by emergency ambulance; 538 by private transport or non-emergency ambulance; 252 unknown mode. Emergency ambulance patients were older (76 vs 69 years), more likely to be from institutional care (10% vs 1%) and experiencing total anterior circulation symptoms (27% vs 6%). Thrombolysis treatment was commoner following emergency admission (11% vs 4%). However patients attending without emergency ambulance had lower inpatient mortality (2% vs 18%), a lower rate of institutionalisation (1% vs 6%) and less need for daily carers (7% vs 16%). 149/155 (96%) of highly dependent patients were admitted by emergency ambulance, but none received thrombolysis. Conclusion Presentations of new stroke without emergency ambulance involvement were not unusual but were associated with a better outcome due to younger age, milder neurological impairment and lower levels of pre-stroke dependency. Most patients with a high level of pre-stroke dependency arrived by emergency ambulance but did not receive thrombolysis. It is important to be aware of easily identifiable demographic groups that differ in their potential to gain from different service configurations.
Factors affecting the atmospheric occurrence and deposition of polychlorinated biphenyls in the Southern Ocean

Abstract. Persistent organic pollutants, such as polychlorinated biphenyls, reach the Southern Ocean atmosphere through long-range atmospheric transport. In this study we report the largest dataset available for the atmospheric occurrence of PCBs in the Southern Ocean surrounding the Antarctic Peninsula from samples obtained during three cruises in 2005, 2008 and 2009. The gas phase concentrations of total PCBs (Σ 25 PCBs) ranged from 1 to 70 pg m −3 , while the aerosol phase concentrations were significantly lower (0.04 to 0.4 pg m −3 ). The aerosol phase is enriched in the more hydrophobic congeners consistent with the model predictions of gas-particle partitioning. There is a net air-to-water diffusive flux of PCBs to the Southern Ocean, up to 100 times higher than the dry deposition flux of aerosol-bound PCBs. The air-water disequilibrium is higher for the more hydrophobic congeners consistent with the role of the biological pump removing PCBs from the water column by settling of PCBs bound to organic matter. The atmospheric half-lives of PCB 52 and 180 are of 3.8 and 1 days, respectively, as calculated from the measured atmospheric concentration and depositional fluxes. The volatilization of PCBs from Antarctic soils during the austral summer drives higher gas phase concentrations in the atmosphere over Antarctica during the warmer periods. This temperature dependence is not observed for PCBs over the adjacent Southern Ocean, probably due to the importance of long-range atmospheric transport and atmospheric deposition modulating the atmospheric occurrence of PCBs.
Corpora and Corpus-Based Morpho-Lexical Processing

The term corpus as used here refers to a collection of spoken or written texts encoded into a specific machine readable format. Corpora are used in language engineering to gather both qualitative and quantitative real language evidence. Qualitative evidence consists of examples which can be used for the construction of computational lexicons, grammars, and multi-lingual lexicons and term banks, for lexicography, etc. Quantitative information consists of statistics indicating frequent or characteristic uses of language. These statistics can also be used to guide preference-based parsers, assist in lexicography, determine translation equivalents, etc. In addition, statistics can be used to drive morphological taggers, POS taggers, alignment programs, sense taggers, etc. Common operations on corpora for the purposes of language engineering include extraction of sub-corpora; sophisticated search and retrieval, including collocation extraction, concordance generation, generation of lists of linguistic elements, etc.; and the determination of statistics such as frequency information, averages, mutual information scores, etc. We do not address corpora intended for other applications, such as stylistic studies, socio-linguistics, historical studies, information retrieval, etc., although these uses are not excluded a priori (in fact, many of the features required for these applications may be the same as those needed for language engineering). The encoding format should be standardised and homogeneous both for reasons concerning interchange and open-ended retrieval tasks [1]. Treating a restricted domain enables development of a tighter standard than that of the TEI, by providing specific encoding solutions rather than general or multiple ones, and, most importantly, by providing standards for elements particularly important in that domain (e.g., linguistic annotation). The texts are selected according to explicit criteria, according to the main purpose the corpus is supposed to serve (lexicographic tasks; terminological data extraction/acquisition; contrastive/comparative studies on parallel texts; grammar induction; machine translation; etc.). Based on several linguistic classification criteria, Sinclair defines in [1] a corpus typology (see also [2] in this volume). From that typology, we are here concerned with the special and parallel type corpora.
Language Engineering in Dialogue

Hugo ter Doesty, Mark Molly, Ren e Bosy, Stan van de Burgtz and Anton Nijholty y: Department of Computer Science, University of Twente P.O. Box 217, 7500 AE Enschede, The Netherlands e-mail: fterdoest,moll,bosd,anijholtg@cs.utwente. nl z: KPN Research P.O. box 421, Leidschendam, The Netherlands e-mail: S.P.vandeBurgt@research.kpn. com Abstract The analysis of natural language in the context of keyboarddriven dialogue systems is the central issue addressed in this paper. A module that corrects typing errors, performs domain-speci c morphological analysis is developed. A parser for typed uni cation grammars has been designed and implemented in C++; for description of the lexicon and the grammar a suitable speci cation language has been developed. It is argued that typed uni cation grammars and especially the newly developed speci cation language are convenient formalisms for describing natural language use in dialogue systems. Finally we present a dialogue manager that is based on a nite state automaton; transitions in the automaton depend upon availability of information in utterances of the user. In order to keep track of the history of the dialogue, a context stack is constructed during the dialogue. The manager is implemented in Prolog.
The Effects of Multi-Level Group Identification on Intergroup Helping Behavior and Performance

We conduct an experiment to examine the effects of multi-level group identification on intergroup helping behavior. We predict and find that stronger identification with a sub-group (one’s immediate work-group) and a superordinate group (the organization in which that group is nested) – separately and interactively – increase helping behavior. We provide evidence that the relationships between stronger identification and helping behavior operate in part through increased salience of superordinate group boundaries, perceived potential benefits to one’s own group of intergroup helping, and positive affect. Collectively, our findings illustrate the importance of understanding how individuals perceive and identify with the different groups naturally present in organizations, as well as highlighting how identification can be used as an informal control to motivate important organizational behaviors like intergroup helping. Such an understanding can help firms determine the best organizational hierarchy, develop communication and control strategies to build identification at appropriate levels, and establish evaluation and compensation systems that measure and reward outcomes in a manner that accounts for these group effects.
Effect of CD logic on multiplier accumulator unit

A high performance, Low power and high speed designs are always being important in VLSI. There are different logic families exist for an efficient performance of the circuits. The Constant Delay (CD) logic style is one of the efficient logics among the digital logic family. The complicated logic expressions in the digital logic families are implemented using this high performance energy efficient logic style (Constant delay). Multiplier Accumulator Unit is the most important component in applications such as Digital Signal Processing, Field Effect Transistors, and Finite impulse response filters. A high speed and energy efficient Multiplier Accumulator unit using constant delay logic is implemented in this paper, and the performance parameters such as power, delay and power delay product (PDP) are measured. The simulation is done using HSPICE tool in both 45nm CMOS technology and 32nm CMOS technology.
Detection of Markov Random Fields on Two-Dimensional Intersymbol Interference Channels

We present a novel iterative algorithm for detection of binary Markov random fields (MRFs) corrupted by two-dimensional (2D) intersymbol interference (ISI) and additive white Gaussian noise (AWGN). We assume a first-order binary MRF as a simple model for correlated images. We assume a 2D digital storage channel, where the MRF is interleaved before being written and then read by a 2D transducer; such channels occur in recently proposed optical disk storage systems. The detection algorithm is a concatenation of two soft-input/soft-output (SISO) detectors: an iterative row-column soft-decision feedback (IRCSDF) ISI detector, and a MRF detector. The MRF detector is a SISO version of the stochastic relaxation algorithm by Geman and Geman in IEEE Trans. Pattern Anal. and Mach. Intell. , Nov. 1984. On the 2 x 2 averaging-mask ISI channel, at a bit error rate (BER) of 10^{-5}, the concatenated algorithm achieves SNR savings of between 0.5 and 2.0 dB over the IRCSDF detector alone; the savings increase as the MRFs become more correlated, or as the SNR decreases. The algorithm is also fairly robust to mismatches between the assumed and actual MRF parameters.
The tethering complex HOPS catalyzes assembly of the soluble SNARE Vam7 into fusogenic trans-SNARE complexes

Large tethering complexes play an essential role in many intracellular membrane fusion events, yet their mode of action is poorly understood. A new function of the HOPS complex is uncovered in facilitating vacuolar fusion, the specific recruitment of the soluble SNARE Vam7 for the formation of fusogenic trans-SNARE complexes.
Food Choice Architecture: An Intervention in a Secondary School and its Impact on Students’ Plant-based Food Choices

With growing evidence for the positive health outcomes associated with a plant-based diet, the study’s purpose was to examine the potential of shifting adolescents’ food choices towards plant-based foods. Using a real world setting of a school canteen, a set of small changes to the choice architecture was designed and deployed in a secondary school in Yorkshire, England. Focussing on designated food items (whole fruit, fruit salad, vegetarian daily specials, and sandwiches containing salad) the changes were implemented for six weeks. Data collected on students’ food choice (218,796 transactions) enabled students’ (980 students) selections to be examined. Students’ food choice was compared for three periods: baseline (29 weeks); intervention (six weeks); and post-intervention (three weeks). Selection of designated food items significantly increased during the intervention and post-intervention periods, compared to baseline (baseline, 1.4%; intervention 3.0%; post-intervention, 2.2%) χ2(2) = 68.1, p < 0.001. Logistic regression modelling also revealed the independent effect of the intervention, with students 2.5 times as likely (p < 0.001) to select the designated food items during the intervention period, compared to baseline. The study’s results point to the influence of choice architecture within secondary school settings, and its potential role in improving adolescents’ daily food choices.
Distributed channel aware link scheduling for CSMA based wireless networks with time-varying channels and delay sensitive applications

Distributed Channel Aware Link Scheduling for CSMA based Wireless Networks with Time-Varying Channels and Delay Sensitive Applications Bahadır ERKAN M.S. in Electrical and Electronics Engineering Supervisor: Assoc. Prof. Dr. Ezhan Karaşan August 2011 In wireless networks, interference between neighboring links is an important issue. The link scheduling algorithm controls the interference between neighboring links such that no adjacent links can be concurrently active. Distributed throughput optimum algorithms for the link scheduling problem have been proposed in the literature. However, the maximum packet delays of these distributed throughput optimum algorithms can become arbitrarily large, which significantly degrades the performances of delay sensitive applications such as “Skype”. In this thesis, we propose two distributed link scheduling algorithms: a full opportunistic algorithm and a delay based adaptive algorithm. The proposed algorithms, while maintaining throughput optimality, increase the average delay performance of the previously proposed throughput optimum scheduling algorithms by 20% under the fading radio channel. We propose a new metric “Effective Goodput”, which
Neural sliding mode control for multi-link robots

A neural sliding mode controller is presented for trajectory tracking control of multi-link robots with uncertain external disturbances and system model errors. This approach gives a new global sliding mode manifold for the second-order multi-link robots, which enable system trajectory to run on the sliding mode manifold at the initial states and eliminate the reaching phase of conventional sliding mode control. Robustness for system dynamics is guaranteed over all the response time. A radial basis function neural network (RBFNN) is employed to eliminate chattering of global sliding mode control, and enforce the sliding mode motion by its learning the upper bound of model errors and uncertain disturbances. Moreover, the stability of the controller is proven by Lyapunov function. Simulation results verify the validity of the control scheme.
Lessons of kuru research: background to recent studies with some personal reflections

The widespread exposure of the UK population to bovine spongiform encephalopathy prions, and the potential consequences for public health, led to a renewed interest in kuru, the principal example of epidemic human prion disease. Kuru research in Papua New Guinea was expanded to study the range of incubation periods possible in human prion infection, to investigate maternal and other possible natural routes of transmission, to characterize genetic susceptibility and resistance factors and to gain insights into the peripheral pathogenesis of orally acquired prion disease in humans. Although now essentially over, the kuru epidemic continues to provide important lessons.
Submergence and uplift associated with the giant 1833 Sumatran subduction earthquake: Evidence from coral microatolls

The giant Sumatran subduction earthquake of 1833 appears as a large emergence event in fossil coral microatolls on the reefs of Sumatra's outer-arc ridge. Stratigraphic analysis of these and living microatolls nearby allow us to estimate that 1833 emergence increased trenchward from about 1 to 2 m. This pattern and magnitude of uplift are consistent with about 13 m of slip on the subduction interface and suggest a magnitude (Mw) of 8.8-9.2 for the earthquake. The fossil microatolls also record rapid submergence in the decades prior to the earthquake, with rates increasing trenchward from 5 to 11 mm/yr. Living microatolls show similar rates and a similar pattern. The fossil microatolls also record at least two less extensive emergence events in the decades prior to 1833. These observations show that coral microatolls can be useful paleoseismic and paleogeodetic instruments in convergent tectonic environments.
Anchor Side Chains of Short Peptide Fragments Trigger Ligand-Exchange of Class II MHC Molecules

Class II MHC molecules display peptides on the cell surface for the surveillance by CD4+ T cells. To ensure that these ligands accurately reflect the content of the intracellular MHC loading compartment, a complex processing pathway has evolved that delivers only stable peptide/MHC complexes to the surface. As additional safeguard, MHC molecules quickly acquire a ‘non-receptive’ state once they have lost their ligand. Here we show now that amino acid side chains of short peptides can bypass these safety mechanisms by triggering the reversible ligand-exchange. The catalytic activity of dipeptides such as Tyr-Arg was stereo-specific and could be enhanced by modifications addressing the conserved H-bond network near the P1 pocket of the MHC molecule. It affected both antigen-loading and ligand-release and strictly correlated with reported anchor preferences of P1, the specific target site for the catalytic side chain of the dipeptide. The effect was evident also in CD4+ T cell assays, where the allele-selective influence of the dipeptides translated into increased sensitivities of the antigen-specific immune response. Molecular dynamic calculations support the hypothesis that occupation of P1 prevents the ‘closure’ of the empty peptide binding site into the non-receptive state. During antigen-processing and -presentation P1 may therefore function as important “sensor” for peptide-load. While it regulates maturation and trafficking of the complex, on the cell surface, short protein fragments present in blood or lymph could utilize this mechanism to alter the ligand composition on antigen presenting cells in a catalytic way.
Variance Based Algorithm for Grouped-Subcarrier Allocation in OFDMA Wireless Systems

In this paper, a reduced complexity algorithm is proposed for grouped-subcarriers and power allocation in the downlink of OFDMA packet access wireless systems. The available subcarriers for data communication are grouped into partitions (groups) where each group is defined as a subchannel. The scheduler located at the base station allocates subchannels to users based on the variance of subchannel gains. The proposed algorithm for group allocation is a two-step algorithm that allocates groups to users based on the descending order of their variances to resolve the conflicting selection problem, followed by a step of fairness proportionality enhancement. To reduce the feedback burden and the complexity of the power allocation algorithm, each user feeds back the CSI on each group if the variance of gains of subcarriers inside it is less than a predefined threshold. To Show the performance of the proposed scheme, a selection of simulation results is presented.
A new sampling technique and SVM classification for feature selection in high-dimensional Imbalanced dataset

Feature selection in high-dimensional Imbalanced dataset (where one class highly outnumbers the other class) is an exigent task in data mining. Feature selection refers to selecting a subset of features from the original dataset. This paper focus on two problems i) Balancing the dataset ii) extracting the features. A new technique called Evolutionary sampling technique [EST] is developed to balance the dataset and Support Vector Machine [SVM] classification is used to calculate the accuracy and also to overcome the over fitting problem while sampling the dataset. The techniques are evaluated on a micro array dataset.