Miracle-dz/UniFAR-FTUs huggingface dataset:
Bison-mediated seed dispersal in a tallgrass prairie reconstruction

Bison-mediated seed dispersal may be a critical ecological process that has been eliminated in grassland ecosystems by the removal of this keystone species. In this study of epizoochory and endozoochory by bison, we installed funnel seed traps on 50, 50-m transects on the Neal Smith National Wildlife Refuge in south central Iowa, to compare the composition and density of seed species dispersed by bison with the abiotic seed rain in a tallgrass prairie reconstruction. Seed trap, dung, and shed hair samples were collected monthly from April 2011 through November 2013. Hair samples were clipped directly from bison at the end of the plant growing season during annual November round-ups. Seeds were identified and classified as native or non-native, by plant functional group, and by diaspore characteristics. A diverse mix of epizoochorus seeds, wind dispersed propagules, and seeds with smooth, rounded diaspores in bison dung, shed hair, and attached to the animals, suggests that bison are generalist dispersers of both forbs and graminoids. Bison dung contained seeds in similar proportions to those collected in seed traps. Shed bison hair contained a significantly greater proportion of both native species and grass seeds than were found in bison dung or seed trap samples. Seed compositions in shed hair and dung appeared to be influenced by the phenology
On the cost of concurrency in transactional memory

Traditional techniques for synchronization are based on \emph{locking} that provides threads with exclusive access to shared data. \emph{Coarse-grained} locking typically forces threads to access large amounts of data sequentially and, thus, does not fully exploit hardware concurrency. Program-specific \emph{fine-grained} locking or \emph{non-blocking} (\emph{i.e.}, not using locks) synchronization, on the other hand, is a dark art to most programmers and trusted to the wisdom of a few computing experts. Thus, it is appealing to seek a middle ground between these two extremes: a synchronization mechanism that relieves the programmer of the overhead of reasoning about data conflicts that may arise from concurrent operations without severely limiting the program's performance. The \emph{Transactional Memory (TM)} abstraction is proposed as such a mechanism: it intends to combine an easy-to-use programming interface with an efficient utilization of the concurrent-computing abilities provided by multicore architectures. TM allows the programmer to \emph{speculatively} execute sequences of shared-memory operations as \emph{atomic transactions} with \emph{all-or-nothing} semantics: the transaction can either \emph{commit}, in which case it appears as executed sequentially, or \emph{abort}, in which case its update operations do not take effect. Thus, the programmer can design software having only sequential semantics in mind and let TM take care, at run-time, of resolving the conflicts in concurrent executions. Intuitively, we want TMs to allow for as much \emph{concurrency} as possible: in the absence of severe data conflicts, transactions should be able to progress in parallel. But what are the inherent costs associated with providing high degrees of concurrency in TMs? This is the central question of the thesis.
M ay 2 01 8 Catering to Your Concerns : Automatic Generation of Personalised Security-Centric Descriptions for Android Apps

Android users are increasingly concerned with the privacy of their data and security of their devices. To improve the security awareness of users, recent automatic techniques produce security-centric descriptions by performing program analysis. However, the generated text does not always address users’ concerns as they are generally too technical to be understood by ordinary users. Moreover, different users have varied linguistic preferences, which do not match the text. Motivated by this challenge, we develop an innovative scheme to help users avoid malware and privacy-breaching apps by generating security descriptions that explain the privacy and security related aspects of an Android app in clear and understandable terms.We implement a prototype system, PERSCRIPTION, to generate personalised security-centric descriptions that automatically learn users’ security concerns and linguistic preferences to produce user-oriented descriptions. We evaluate our scheme through experiments and user studies. The results clearly demonstrate the improvement on readability and users’ security awareness of PERSCRIPTION’s descriptions compared to existing description generators.
Memory-Based Shallow Parsing

We present memory-based learning approaches to shallow parsing and apply these to five tasks: base noun phrase identification, arbitrary base phrase recognition, clause detection, noun phrase parsing and full parsing. We use feature selection techniques and system combination methods for improving the performance of the memory-based learner. Our approach is evaluated on standard data sets and the results are compared with that of other systems. This reveals that our approach works well for base phrase identification while its application towards recognizing embedded structures leaves some room for improvement.
THE ROUNDING OF THE PHASE TRANSITION FOR DISORDERED PINNING WITH STRETCHED EXPONENTIAL TAILS 1

The presence of frozen-in or quenched disorder in a system can often modify the nature of its phase transition. A particular instance of this phenomenon is the so-called rounding effect: it has been shown in many cases that the free energy curve of the disordered system at its critical point is smoother than that of the homogeneous one. In particular some disordered systems do not allow ﬁrst-order transitions. We study this phenomenon for the pinning of a renewal with stretched-exponential tails on a defect line (the distribution K of the renewal increments satisﬁes K(n) ∼ c K exp ( − n ζ ) , ζ ∈ ( 0 , 1 ) ) which has a ﬁrst order transition when disorder is not present. We show that the critical behavior of the disordered system depends on the value of ζ : when ζ > 1 / 2 the transition remains of ﬁrst order, whereas the free energy diagram is smoothed for ζ ≤ 1 / 2. Furthermore we show that the rounding effect is getting stronger when ζ diminishes.
Compressive Phase Retrieval via Generalized Approximate Message Passing

In phase retrieval, the goal is to recover a signal x ∈ CN from the magnitudes of linear measurements Ax ∈ CM. While recent theory has established that M ≈ 4N intensity measurements are necessary and sufficient to recover generic x, there is great interest in reducing the number of measurements through the exploitation of sparse \mbi x, which is known as compressive phase retrieval. In this work, we detail a novel, probabilistic approach to compressive phase retrieval based on the generalized approximate message passing (GAMP) algorithm. We then present a numerical study of the proposed PR-GAMP algorithm, demonstrating its excellent phase-transition behavior, robustness to noise, and runtime. Our experiments suggest that approximately M ≥ 2 Klog2(N/K) intensity measurements suffice to recover K-sparse Bernoulli-Gaussian signals for \mbi A with i.i. d Gaussian entries and K ≪ N. Meanwhile, when recovering a 6678-sparse 65536-pixel grayscale image from 32768 randomly masked and blurred Fourier intensity measurements at 30 dB measurement SNR, PR-GAMP achieved an output SNR of no less than 28 dB in all of 100 random trials, with a median runtime of only 7.3 seconds. Compared to the recently proposed CPRL, sparse-Fienup, and GESPAR algorithms, our experiments suggest that PR-GAMP has a superior phase transition and orders-of-magnitude faster runtimes as the sparsity and problem dimensions increase.
Analysis of regularized LS reconstruction and random matrix ensembles in compressed sensing

Performance of regularized least-squares estimation in noisy compressed sensing is studied in the limit when the problem dimensions grow large. The sensing matrix is sampled from the rotationally invariant ensemble that encloses as special cases the standard IID and row-orthogonal constructions. The analysis is carried out using the replica method in conjunction with some novel matrix integration results. The numerical experiments show that for noisy compressed sensing, the standard IID ensemble is a suboptimal choice for the measurement matrix. Orthogonal constructions provide a superior performance in all considered scenarios and are easier to implement in practice.
Exploiting Opportunistic Multiuser Detection in Decentralized Multiuser MIMO Systems

This paper studies the design of decentralized multiuser (MU) multi-antenna/multiple-input-multiple-output (MIMO) systems for wireless spectrum sharing over a fixed frequency band, in which users independently update their transmit covariance matrices for individual transmit-rate maximization in an iterative manner. This design problem was usually investigated in the literature by assuming that each user treats the co-channel interference from all the other users as additional noise at the receiver and, accordingly, the conventional single-user decoder (SUD) is applied. This paper considers a more advanced decoder design approach for decentralized MU-MIMO systems, in which each user opportunistically cancels the co-channel interference from certain subset of coexisting users when their signals are jointly decodable with the desired signal at the receiver. The new decoding scheme is thus termed opportunistic multiuser detection (OMD). This paper derives the optimal transmit covariance matrix for users' iterative maximization of individual transmit rates with the proposed OMD at the receiver, and evaluates the achievable throughput gains for decentralized MU-MIMO systems against the conventional SUD. Promising applications of the OMD for achieving maximum interference mitigation gains in spectrum sharing based wireless systems such as cognitive radio networks and cellular networks are demonstrated.
The deductive database system [Lscr ][Dscr ][Lscr ]++

This paper describes the [Lscr ][Dscr ][Lscr ]++ system and the research advances that have enabled its design and development. We begin by discussing the new nonmonotonic and nondeterministic constructs that extend the functionality of the [Lscr ][Dscr ][Lscr ]++ language, while preserving its model-theoretic and fixpoint semantics. Then, we describe the execution model and the open architecture designed to support these new constructs and to facilitate the integration with existing DBMSs and applications. Finally, we describe the lessons learned by using [Lscr ][Dscr ][Lscr ]++ on various tested applications, such as middleware and datamining.
Coding for Classical-Quantum Channels With Rate Limited Side Information at the Encoder: Information-Spectrum Approach

We study the hybrid classical-quantum version of the channel coding problem for the famous Gel’fand–Pinsker channel. In the classical setting for this channel the conditional distribution of the channel output given the channel input is a function of a random parameter called the channel state. We study this problem when a rate limited version of the channel state is available at the encoder for the classical-quantum Gel’fand–Pinsker channel. We establish the capacity region for this problem in the information-spectrum setting. The capacity region is quantified in terms of spectral-sup classical mutual information rate and spectral-inf quantum mutual information rate.
An integrated tool for microarray data clustering and cluster validity assessment

In this paper we present a data mining system, which allows the application of different clustering and cluster validity algorithms for DNA microarray data. This tool may improve the quality of the data analysis results, and may support the prediction of the number of relevant clusters in the microarray datasets. This systematic evaluation approach may significantly aid genome expression analyses for knowledge discovery applications. The developed software system may be effectively used for clustering and validating not only DNA microarray expression analysis applications but also other biomedical and physical data with no limitations. The program is freely available for non-profit use on request at http://www.cs. tcd.ie/Nadia.Bolshakova/Machaon.html
Compressive Imaging Using Approximate Message Passing and a Markov-Tree Prior

We propose a novel algorithm for compressive imaging that exploits both the sparsity and persistence across scales found in the 2D wavelet transform coefficients of natural images. Like other recent works, we model wavelet structure using a hidden Markov tree (HMT) but, unlike other works, ours is based on loopy belief propagation (LBP). For LBP, we adopt a recently proposed “turbo” message passing schedule that alternates between exploitation of HMT structure and exploitation of compressive-measurement structure. For the latter, we leverage Donoho, Maleki, and Montanari's recently proposed approximate message passing (AMP) algorithm. Experiments with a large image database suggest that, relative to existing schemes, our turbo LBP approach yields state-of-the-art reconstruction performance with substantial reduction in complexity.
CUNY Academic Works CUNY Academic Works

: Over the years a range of positive algorithmic results have been obtained for learning various classes of monotone Boolean functions from uniformly distributed random examples. Prior to our work, however, the only negative result for learning monotone functions in this model has been an information-theoretic lower bound showing that certain super-polynomial-size monotone circuits cannot be learned to accuracy 1 / 2 + ω ( log n / √ n ) (Blum, Burch, and Langford, FOCS’98 ). This is in contrast with the situation for non-monotone functions, where a wide range of cryptographic hardness results establish that various “simple” classes of polynomial-size circuits are not learnable by polynomial-time algorithms. In this paper we establish cryptographic hardness results for learning various “simple” classes of monotone circuits, thus giving a computational analogue of the information-∗
Relating stability of individual dynamical networks to change in psychopathology

One hypothesis flowing from the network theory of psychopathology is that symptom network structure is associated with psychopathology severity and in turn, one may expect that individual network structure changes with the level of psychopathology severity. However, this expectation has rarely been addressed directly. This study aims to examine (1) the stability of individual contemporaneous symptom networks over a one-year period and (2) whether network stability is associated with a change in psychopathology. We used daily diary data of n = 66 individuals, located along the psychosis severity continuum, from two separate 90-day periods, one year apart (t = 180). Based on the newly developed Individual Network Invariance Test (INIT) to assess symptom-network stability, participants were divided into two groups with stable and unstable networks and we tested whether these groups differed in their absolute change in psychopathology severity. The majority of the sample (n = 51, 77.3%) showed a stable network over time while most individuals showed a decrease in psychopathological severity. We found no significant association between a change in psychopathology severity and individual network stability. Our results call for further critical evaluation of the association between networks and psychopathology to optimize the implementation of clinical applications based on current methods.
Estimate of lysine nutritional requirements for Japanese quail breeders

Background Japanese quail breeders are the basis for genetic improvement and multiplication for commercial layers, however, there have been no known studies on the optimal lysine level for these birds. Thus, study the egg output response to the lysine (Lys) supply using different e-functions and evaluate the that best fit, have allowed the partition the lysine requirements for maintenance, both weight and egg output maximum. Methods The objectives of this study were to identify the responses to various Lys levels, identify the functions related to these responses and determine the ideal Lys intake amount for Japanese quail breeders. A completely randomized design of seven treatments with seven replicated was used. Treatments consisted of diet supplementation by Lys in concentrations of 16.8, 11.8, 8.4, 6.7, 5.0, 3.4, and 1.7 g/kg. Six exponential models were adjusted. Results The level of Lys was found to affect bird responses (P < 0.001). The birds responded to the levels provided, allowing for the creation of a lysine response curve. A monomolecular function with four parameters was balanced against the statistics of adjustment and selection of models. It was possible to estimate the level of lysine required for maintenance as 133 ± 2 mg/kg BW0.67, and based an average of 41% efficiency, 22 mg Lys produced 1 g of egg output (EO). The daily intake calculated by the monomolecular factorial model was 284 mg Lys for a bird with 0.170 kg body weight and production of 10 g EO/day. The four-parameter monomolecular function proposed in this study is adequate for interpreting the animal response and calculating lysine intake for breeders.
Pharmacophore mapping approach to find anti-cancer phytochemicals with metformin-like activities against transforming growth factor (TGF)-beta receptor I kinase: An in silico study

The most frequently prescribed first-line treatment for type II diabetes mellitus is metformin. Recent reports asserted that this diabetes medication can also shield users from cancer. Metformin induces cell cycle arrest in cancer cells. However, the exact mechanism by which this occurs in the cancer system is yet to be elucidated. Here, we investigated the impact of metformin on cell cycle arrest in cancer cells utilizing transforming growth factor (TGF)-beta pathway. TGF-ß pathway has significant effect on cell progression and growth. In order to gain an insight on the underlying molecular mechanism of metformin’s effect on TGF beta receptor 1 kinase, molecular docking was performed. Metformin was predicted to interact with transforming growth factor (TGF)-beta receptor I kinase based on molecular docking and molecular dynamics simulations. Furthermore, pharmacophore was generated for metformin-TGF-ßR1 complex to hunt for novel compounds having similar pharmacophore as metformin with enhanced anti-cancer potentials. Virtual screening with 29,000 natural compounds from NPASS database was conducted separately for the generated pharmacophores in Ligandscout® software. Pharmacophore mapping showed 60 lead compounds for metformin-TGF-ßR1 complex. Molecular docking, molecular dynamics simulation for 100 ns and ADMET analysis were performed on these compounds. Compounds with CID 72473, 10316977 and 45140078 showed promising binding affinities and formed stable complexes during dynamics simulation with aforementioned protein and thus have potentiality to be developed into anti-cancer medicaments.
Sediment partitioning, continental slopes and base‐of‐slope systems

Deciphering the role slope topography plays in partitioning sediment on siliciclastic continental slope and base‐of‐slope systems helps our understanding of slope depositional processes in significant ways: (1) by validation of large‐scale depositional process models for continental margins, (2) by validation of numerical basin‐scale stratigraphic forward models used to test and deploy source‐to‐sink (S2S) concepts and (3) by creating models for setting reservoir presence and quality expectations in frontier areas poorly constrained by wells and seismic. A global database consisting of >700 km of drilled stratigraphy provide empirical rock data lacking from most S2S studies. Analysis of calibrated seismic stratigraphic units characterised using the contextual framework laid out in this paper show that both gross depositional environments (GDEs) and sand content occur across slope profiles in systematic ways. The challenge in using these observations to quantify reservoir risk and uncertainty lies with relating the observations to depositional processes that can be used to characterise frontier basins that lack calibration. Depositional process‐based understanding encoded in 3D stratigraphic forward models (SFM) can simulate both lithologies and GDEs providing broad predictions for exploration at the scale of an entire basin or slope system. Stratigraphic forward models allow the integration of S2S understanding and provide a framework for testing sediment‐partitioning hypotheses in frontier settings. Valid S2S models must balance sediment yield from the source catchments with sinks, and be consistent with basin specific observations. The proportions of GDEs across the slope provide additional validation criteria to ensure the models are plausible.
ASSESSING CARRYING CAPACITY OF PABBI HILLS KHARIAN RANG E

A survey was conducted to assess the carrying capacity of the Pabbi Hills Kharian Range during the month of May, 2005. A total of 374.27 kg ha-1 dry matter was assessed using standard techniques. The livestock being raised in these areas were cattle and goats only. Average weight of a cow and a goat was estimated to be 300 and 25 kg, respectively. The annual requirement of dry matter per animal unit was estimated to be 2190 kg, which can be met through grazing of 12 ha / AU/ year carrying capacity. Key worlds: Animal unit, Carrying capacity, Forage, Mesquite.
The effects of Fe, Mg, and Pt-doping on the improvement of Ni stabilized on Al2O3-CeO3 catalysts for methane dry reforming

Herein, the promotional effects of Mg, Fe, and Pt on Ni-based catalysts supported on Al2O3-CeO2 (Ni/Al2O3-CeO2) were investigated in the dry reforming of methane (DRM) reaction. The interaction of a suitable amount of MgO and FeO with Ce2O3 stabilized in the catalysts was demonstrated by the temperature-programmed desorption of CO2 (CO2-TPD). Ce2O3 has a high basicity for adsorbing CO2, generating a monoclinic Ce2O2CO3 species in the DRM reaction. Surface oxygen ions were also produced by adding MgO and FeO, as demonstrated by the temperature-programmed reduction of H2 (H2-TPR). Monoclinic Ce2O2CO3 and surface oxygen may both be used to oxidize and remove the carbon that was deposited, maintaining the high activity and stability of the metal Ni and Pt catalysts. The high dispersion and synergistic interactions between the platinum and oxide phases, which are associated with the decrease in reduction temperature and the rise in the number of basic sites, are responsible for the increased activity of Pt with M–Ni/Al2O3-CeO2 catalysts. The co-doped Ni/Al2O3-CeO2 catalysts with Mg and Fe significantly enhanced the activity (more than 80% methane and 84% CO2 conversion), the selectivity toward syngas (∼90%), and maintained the H2/CO ratio at about 0.97 at 700 °C.