Miracle-dz/UniFAR-FTUs huggingface dataset:
Medusa-1.0: a new intermediate complexity plankton ecosystem model for the global domain

Abstract. The ongoing, anthropogenically-driven changes to the global ocean are expected to have significant consequences for plankton ecosystems in the future. Because of the role that plankton play in the ocean's "biological pump", changes in abundance, distribution and productivity will likely have additional consequences for the wider carbon cycle. Just as in the terrestrial biosphere, marine ecosystems exhibit marked diversity in species and functional types of organisms. Predicting potential change in plankton ecosystems therefore requires the use of models that are suited to this diversity, but whose parameterisation also permits robust and realistic functional behaviour. In the past decade, advances in model sophistication have attempted to address diversity, but have been criticised for doing so inaccurately or ahead of a requisite understanding of underlying processes. Here we introduce MEDUSA-1.0 (Model of Ecosystem Dynamics, nutrient Utilisation, Sequestration and Acidification), a new "intermediate complexity" plankton ecosystem model that expands on traditional nutrient-phytoplankton-zooplankton-detritus (NPZD) models, and remains amenable to global-scale evaluation. MEDUSA-1.0 includes the biogeochemical cycles of nitrogen, silicon and iron, broadly structured into "small" and "large" plankton size classes, of which the "large" phytoplankton class is representative of a key phytoplankton group, the diatoms. A full description of MEDUSA-1.0's state variables, differential equations, functional forms and parameter values is included, with particular attention focused on the submodel describing the export of organic carbon from the surface to the deep ocean. MEDUSA-1.0 is used here in a multi-decadal hindcast simulation, and its biogeochemical performance evaluated at the global scale.
Distributed Asynchronous Computation of Fixed Points* 2. a Model for Distributed Asynchronous Fixed Point Algorithms

We present an algorithmic model for distribnted computation of fixed points whereby several processors participate simultaneously in the calculations while exchanging information via communication links. We place essentially no assumptions on the ordering of computation and communication between processors thereby allowing for completely uncoordinated execution. We provide a general convergence theorem for algorithms of this type, and demonstrate its applicability to several classes of problems including the calculation of fixed points of contraction and monotone mappings arising in linear and nonlinear systems of equations, optimization problems, shortest path problems, and dynamic programming.
Linearization of a ffi ne abstract categorial grammars

The abstract categorial grammar (ACG) is a grammar formalism based on linear lambda calculus. It is natural to ask how the expressive power of ACGs increases when we relax the linearity constraint on the formalism. This paper introduces the notion of affine ACGs by extending the definition of original ACGs, and presents a procedure for converting a given affine ACG into a linear ACG whose language is exactly the set of linear λ-terms generated by the original affine ACG. De Groote (2001) has introduced abstract categorial grammars (ACGs), in which both lexical entries of the grammar as well as grammatical combinations of them are represented by simply typed linear λ-terms. While the linearity constraint on grammatical combinations is thought to be reasonable, admitting non-linear λ-terms as lexical entries may allow ACGs to describe linguistic phenomena in a more natural and concise fashion. On the other hand, de Groote and Pogodalla (2003, 2004) have shown that a variety of context-free formalisms, namely, context-free grammars, linear 1 context-free tree grammars (linear CFTGs) 2 and linear context-free rewrit-1 This paper lets the term " linearity " mean non-duplication and non-deletion. Thus " linear CFTGs " means non-duplicating non-deleting CFTGs here, though usually " linear CFTGs " means non-duplicating CFTGs. 2 See also Kanazawa and Yoshinaka (2005) for complete proof of encodability of linear
Biomass estimation equations for mesquite trees in the Americas

Mesquite trees are the preferred dendroenergy sources in arid and semi-arid forests. In spite of their relative importance, regional aboveground biomass (AGB) equations for mesquite trees are scarce in the scientific literature. For that reason, the aims of this study were to: (a) harvest trees and develop regional biomass equations; (b) contrast measured data with equations developed previously; and (c) test the applicability of the fitted equation for mesquite trees in the arid and semi-arid forests of the Americas. We harvested 206 new mesquite trees from arid and semi-arid forests in northern Mexico (Coahuila, Nuevo Leon, and Tamaulipas) in addition to using two other previously compiled data sets from Mexico (N = 304) to develop a regional equation. To test the validity of this equation, for biomass equations reported for the rest of the country, as well as for North and South American mesquite trees, we contrasted AGB measurements with predictions of fitted equations. Statistical analysis revealed the need for a single, regional, semi-empirical equation as together the three data sets represented the variability of the aboveground biomass of mesquite trees across northern Mexico, as well as mesquite trees in America’s arid and semiarid regions. Due to the large quantity of mesquite trees harvested for sampling and their variability, the regional biomass equation developed encompasses all other North and South American equations, and is representative of mesquite trees throughout the arid and semi-arid forests of the Americas.
Preventing Atomicity Violations with Contracts

Software developers are expected to protect concurrent accesses to shared regions of memory with some mutual exclusion primitive that ensures atomicity properties to a sequence of program statements. This approach prevents data races but may fail to provide all necessary correctness properties.The composition of correlated atomic operations without further synchronization may cause atomicity violations. Atomic violations may be avoided by grouping the correlated atomic regions in a single larger atomic scope. Concurrent programs are particularly prone to atomicity violations when they use services provided by third party packages or modules, since the programmer may fail to identify which services are correlated. In this paper we propose to use contracts for concurrency, where the developer of a module writes a set of contract terms that specify which methods are correlated and must be executed in the same atomic scope. These contracts are then used to verify the correctness of the main program with respect to the usage of the module(s). If a contract is well defined and complete, and the main program respects it, then the program is safe from atomicity violations with respect to that module. We also propose a static analysis based methodology to verify contracts for concurrency that we applied to some real-world software packages. The bug we found in Tomcat 6.0 was immediately acknowledged and corrected by its development team.
Prioritizing spatial accuracy in high-resolution fMRI data using multivariate feature weight mapping

Although ultra-high-field fMRI at field strengths of 7T or above provides substantial gains in BOLD contrast-to-noise ratio, when very high-resolution fMRI is required such gains are inevitably reduced. The improvement in sensitivity provided by multivariate analysis techniques, as compared with univariate methods, then becomes especially welcome. Information mapping approaches are commonly used, such as the searchlight technique, which take into account the spatially distributed patterns of activation in order to predict stimulus conditions. However, the popular searchlight decoding technique, in particular, has been found to be prone to spatial inaccuracies. For instance, the spatial extent of informative areas is generally exaggerated, and their spatial configuration is distorted. We propose the combination of a non-parametric and permutation-based statistical framework with linear classifiers. We term this new combined method Feature Weight Mapping (FWM). The main goal of the proposed method is to map the specific contribution of each voxel to the classification decision while including a correction for the multiple comparisons problem. Next, we compare this new method to the searchlight approach using a simulation and ultra-high-field 7T experimental data. We found that the searchlight method led to spatial inaccuracies that are especially noticeable in high-resolution fMRI data. In contrast, FWM was more spatially precise, revealing both informative anatomical structures as well as the direction by which voxels contribute to the classification. By maximizing the spatial accuracy of ultra-high-field fMRI results, global multivariate methods provide a substantial improvement for characterizing structure-function relationships.
Complex dynamics on a Monopoly Market with Discrete Choices and Network Externality

In this paper, we explore the effects of the introduction of localised externalities through interaction structures upon local and global properties of the simplest market model: the discrete choice model with a single homogeneous product and a single seller (monopoly). Following Kirman, the resulting market is viewed as a complex interactive system. We use an ACE (Agent based Computational Economics) approach to investigate the market mechanisms and underline in what way the knowledge of generic properties of complex adaptive system dynamics can enhance our perception of the market mechanism in the numerous cases where individual decisions are inter-related. Résumé Dans ce papier, nous explorons les effets de l’introduction d’externalités transmises par des structures d’interactions sur les propriétés locales et globales du plus simple modèle de marché : choix discret, produit homogène, monopole. A la suite de Kirman, le marché ainsi décrit peut être considéré comme un système complexe interactif. Nous utilisons une approche multi-agents (ACE) pour explorer les mécanismes de marché et monter de quelle manière les propriétés génériques des systèmes complexes adaptatifs peuvent améliorer notre perception des phénomènes de marchés lorsque les choix des agents sont interdépendants. 10e Rencontre Internationale ACSEG (Approches Connexionnistes en Sciences Economiques et de Gestion) Université de Nantes, 20 et 21 novembre 2003
A Generic Authorship Verification Scheme Based on Equal Error Rates

We present a generic authorship verification scheme for the PAN-2015 identification task. Our scheme uses a two-step training phase on the training corpora. The first phase learns individual feature category parameters as well as decision thresholds based on equal error rates. The second phase builds feature category ensembles which are used for majority vote decisions because ensem- bles can outperform single feature categories. All feature categories used in our method are very simple to gain multiple advantages: Our method is entirely in- dependent of any external linguistic resources (even word lists), and hence it can easily applied to many languages. Moreover, the classification is very fast due to simple features. Additionally, we make use of parallelization. The evaluation of our scheme on a 40% split (which we did not use for training) of the official PAN- 2015 training corpus led to an average corpus accuracy of 68.12%; in detail 60% for the Dutch, 67.5% for the English, 60% for the Greek and 85% for the Spanish subcorpus. The overall computation runtime was approximately 27 seconds.
On some examples of group actions and group extensions

It is well-known that finite groups which can act freely on a sphere must be rather special. To be precise we know that their abelian subgroups are cyclic (see [CE], Theorem XII.11.6) and conversely that any group satisfying this condition acts freely on a finite complex with the homotopy type of a sphere (a result due to Swan [Sw]). How does this extend to other groups? The first fact to keep in mind is that any finite group will act freely on some product of equidimensional spheres (see [O]). Hence it makes sense to determine the minimal number n such that G acts freely on a finite complex X ' (S) for some m. In this paper we address this problem for finite 2-groups; in this context the following interesting question has been raised (see [ACPW], Benson’s problem list):
Secure & Lightweight Distance-Bounding

Distance-bounding is a practical solution aiming to prevent relay attacks. The main challenge when designing such protocols is maintaining their inexpensive cryptographic nature, whilst being able to protect against as many, if not all, of the classical threats posed in their context. Moreover, in distancebounding, some subtle security shortcomings related to the PRF (pseudorandom function) assumption and ingenious attack techniques based on observing verifiers’ outputs have recently been put forward. Also, the recent terrorist-fraud by Hancke somehow recalls once more the need to account for noisy communications in the security analysis of distance-bounding. In this paper, we attempt to incorporate the lessons taught by these new developments in our distance-bounding protocol design. The result is a new class of protocols, with increasing levels of security, accommodating the latest advances3; at the same time, we preserve the lightweight nature of the design throughout the whole class.
A Study On The Prevalence Of Minor Physical Anomalies In Schizophrenia And Bipolar Disorder And Their First Degree Relatives: A Comparative Study

Introduction: Minor physical anomalies (MPAs) comprise a range of subtle, clinically and cosmetically insignificant errors in the development of morphological structures found in the eyes, ears, mouth, head, hands and feet. Minor physical anomalies (MPAs) may bear major informational value for diagnostic, prognostic, and epidemiological purposes. Methodology: This study was conducted at Ranchi Institute Of Neuro-Psychiatry and Allied Sciences (RINPAS), Ranchi. The purpose of study was to compare the prevalence of Minor Physical Anomalies (MPAs) in schizophrenia, bipolar affective disorder (currently manic), their first-degree relatives and normal community control. Cross sectional research design was used in the present study, and the sample was selected using the non-probability purposive sampling technique. Results: There were no significant differences found in marital status, ethnicity, religion and domicile among the five groups. A significant difference was found in employment, treatment history, past history, and family history of respondent. Conclusion: Although MPAs are by no means specific to schizophrenia, they appear to be more prevalent among patients with schizophrenia compared to patients with other psychotic patients and their FDR. Moreover, MPAs of craniofacial region were more frequent in FDR of both schizophrenia and bipolar patients compared to respective psychotic patients and normal community controls.
Missing Data Interpolation With Gausssian Pyramids

I describe a technique for interpolation of missing data in which local operators of many scales but identical shape serve as basis functions. A data structure known as the Gaussian pyramid is developed to represent image information at different scales. This data structure in essence consists of a series of lowpass filtered versions of the original image stacked up one on top of the other forming a pyramid like structure. I first show how to generate a set of reduced images which stack up to form the Gaussian pyramid structure and then show how we can use this Gaussian pyramid structure to fill in missing data. Several examples of filling in missing data with this algorithm are shown and in most cases the results are comparable with those estimated using a prediction filter approach.
Multigene family of ribosomal DNA in Drosophila melanogaster reveals contrasting patterns of homogenization for IGS and ITS spacer regions. A possible mechanism to resolve this paradox.

The multigene family of rDNA in Drosophila reveals high levels of within-species homogeneity and between-species diversity. This pattern of mutation distribution is known as concerted evolution and is considered to be due to a variety of genomic mechanisms of turnover (e.g., unequal crossing over and gene conversion) that underpin the process of molecular drive. The dynamics of spread of mutant repeats through a gene family, and ultimately through a sexual population, depends on the differences in rates of turnover within and between chromosomes. Our extensive molecular analysis of the intergenic spacer (IGS) and internal transcribed spacer (ITS) spacer regions within repetitive rDNA units, drawn from the same individuals in 10 natural populations of Drosophila melanogaster collected along a latitudinal cline on the east coast of Australia, indicates a relatively fast rate of X-Y and X-X interchromosomal exchanges of IGS length variants in agreement with a multilineage model of homogenization. In contrast, an X chromosome-restricted 24-bp deletion in the ITS spacers is indicative of the absence of X-Y chromosome exchanges for this region that is part of the same repetitive rDNA units. Hence, a single lineage model of homogenization, coupled to drift and/or selection, seems to be responsible for ITS concerted evolution. A single-stranded exchange mechanism is proposed to resolve this paradox, based on the role of the IGS region in meiotic pairing between X and Y chromosomes in D. melanogaster.
Minimally Supervised Domain-Adaptive Parse Reranking for Relation Extraction

The paper demonstrates how the generic parser of a minimally supervised information extraction framework can be adapted to a given task and domain for relation extraction (RE). For the experiments a generic deep-linguistic parser was employed that works with a largely hand-crafted head-driven phrase structure grammar (HPSG) for English. The output of this parser is a list of n best parses selected and ranked by a MaxEnt parse-ranking component, which had been trained on a more or less generic HPSG treebank. It will be shown how the estimated confidence of RE rules learned from the n best parses can be exploited for parse reranking. The acquired reranking model improves the performance of RE in both training and test phases with the new first parses. The obtained significant boost of recall does not come from an overall gain in parsing performance but from an application-driven selection of parses that are best suited for the RE task. Since the readings best suited for successful rule extraction and instance extraction are often not the readings favored by a regular parser evaluation, generic parsing accuracy actually decreases. The novel method for task-specific parse reranking does not require any annotated data beyond the semantic seed, which is needed anyway for the RE task.
Psychometric Validation of the Dutch Version of the Desire Thinking Questionnaire (DTQ-D)

Abstract. Desire thinking refers to verbal and imaginal elaboration of a desired target. It predicts escalations in craving intensity and subsequent alcohol use. This article aimed to determine the psychometric properties of the Dutch version of the Desire Thinking Questionnaire (DTQ-D). In Study 1, a confirmatory factor analysis provided support for the original two-factor solution, achieved with adequate internal consistency. The DTQ-D demonstrated partial invariance over time. In Study 2, convergent validity with measures of craving was demonstrated. Discriminant validity with measures of severity of alcohol use and perseverative thinking was satisfactory. Concurrent validity was established by comparing three distinctive groups of alcohol users with increasing levels of drinking: a normative and an out- and in-patient sample. The normative group scored significantly lower on the DTQ-D than the clinical groups. Within the normative sample a low and higher at-risk drinking group could be distinguished. Overall, the DTQ-D possesses reasonable psychometric properties for use with alcohol-drinking samples. However, additional psychometric evaluation in larger clinical samples as well as in other addictions is warranted.
Oscillation May Play a Role in Time Domain Central Auditory Processing

To study how sound intensity altered the temporal response pattern of a unit, we recorded from 92 single neurons in the inferior colliculus (IC) of the little brown bat and investigated their firing patterns in response to brief tone pulses (2 msec duration) at the characteristic frequency of the unit over a wide dynamic range (10-90 dB sound pressure level). We found two unusual response characteristics at high sound levels in approximately one-third of the IC neurons investigated. For 16 IC neurons (17%), an increase in sound level not only elicited a shorter response latency and an increase in spike count but also transformed the firing pattern of the unit from phasic to periodic; this pattern was more pronounced at higher sound levels. The firing periodicity was unit specific, ranging from 1.3 to 6.7 msec. Twenty-seven IC neurons (29%) exhibited a longer response latency at higher sound levels compared with lower sound levels [i.e., paradoxical latency shift (PLS)]. The majority of this population showed a one or more quantum increase in latency when sound level was elevated. The quantum shift was also unit specific, ranging from 1.2 to 8.2 msec. We further investigated the firing patterns of 14 IC neurons showing PLS before, during, and after iontophoretic application of bicuculline. For 12 of these neurons, drug application abolished the PLS and transformed the firing patterns of the unit at high sound levels from phasic into sustained periodic discharges. Our results suggest that neural oscillation in combination with ordinary inhibition may be responsible for the creation of PLSs shown previously to be important for temporal information processing.
Co-experience: user experience as interaction

User experience is becoming a key term in the world of interactive product design. The term itself lacks proper theoretical definition and is used in many different, even contradictory, ways. This paper reviews various existing approaches to understanding user experience and describes three main approaches and their differences. A missing perspective is noted in all three: their focus is on only the individual having the experience and neglects the kinds of experiences that are created together with others. To address this, a new elaboration called co-experience is presented. It builds on an existing approach but borrows from symbolic interactionism to create a more inclusive interactionist framework for thinking about user experiences. Data from a study on mobile multimedia messaging are used to illustrate and discuss the framework.