Miracle-dz/UniFAR-FTUs huggingface dataset:
Spatial scale, patchiness and population dynamics on land

The most striking difference between land and open sea is the greater structural heterogeneity of terrestrial environments. I make a distinction between two principal kinds of patches at two spatial scales, defined by the relative contributions of behaviour and demography to variation in density. At the scale of resource patches, movements of individuals among the patches influence the frequencies of ecological interaction among the mobile individuals and their offspring. Many studies have demonstrated how independently aggregated spatial distributions generally enhance stability of single-species and many-species dynamics. At the scale of habitat patches, assemblages of local populations connected by migration constitute metapopulations. I outline a range of modelling approaches to metapopulation dynamics, including spatially implicit, explicit and realistic models. I describe a novel spatially realistic approach, based on generalized incidence functions, which can be parameterized with data on the pattern of occupancy in a network of habitat patches. This approach allows one to make quantitative predictions about transient dynamics in particular metapopulations.
Exotic tree seedlings are much more competitive than natives but show underyielding when growing together

Aims Invasive species continue to be a worldwide threat to ecosystems mainly as a cause for biodiversity loss. Forest ecosystems, for example, are subject to a change in species composition due to the invasion of exotic species. s pecifying the attributes that cause the strong competitiveness of several exotic species may improve the ability to understand and effectively manage plant invasions in the future. In this study the following hypotheses were tested: (1) biomass production of below- and aboveground plant compo nents of the exotic tree species is higher than that of the natives, resulting in a higher competitiveness of the exotics; (2) the exclu sion of root competition has a positive effect on the biomass pro duction of the inferior native species; and (3) mixtures of native and exotic species yield a higher biomass production than the respective monocultures. Methods a pot experiment, containing about 2000 tree seedlings, was established. We investigated the biomass productivity and growth reactions of two native ( Quercus robur l., Carpinus betulus l.) and two exotic tree species ( Prunus serotina Ehrh., Robinia pseudoacacia l.) in different intra- and interspecific, competitive situations with and without the influence of root competition. Important Findings
Progress in Research on Cytotoxic T Lymphocyte-Associated Antigen 4 (CTLA-4) and Bladder Cancer

Cytotoxic T-lymphocyte-associated protein-4 (CTLA-4) was first discovered in 1987 and confirmed to be a protein that is mainly expressed on the surface of activated lymphocytes. CTLA-4 is expressed on the surface of T cells and binds to B7 expressed on antigen presenting cells(APCs) to potentially play a role in inhibiting lymphocyte proliferation. Inhibitors of CTLA-4 were developed to promote the anti-tumor effects of T cells and inhibit tumor growth. CTLA-4, as an immune checkpoint, has been realized as an important therapeutic target in bladder cancer. Two main CTLA-4 inhibitors are currently used: ipilimumab is a first-generation IgG1 monoclonal antibody that targets CTLA-4, and it is completely synthetic; tremelimumab, representing another class of CTLA-4 inhibitors, is a monoclonal antibody against CTLA-4 that acts similarly to ipilimumab and binds specifically to CTLA-4. The two types of CTLA-4 inhibitors were found to improve the treatment effect in patients with bladder cancer in comparison to conventional agents. To review this topic, we searched recently published related articles.
Microbial Cell Factories

Background Various genome sequencing projects are identifying many new protein sequences but it is key to attribute functions to these proteins. A huge number of proteins have been expressed in vivo to date, most of them being functionally, antigenically and immunogenically similar to their authentic counterparts. This is mainly due to the properties of cultured eukaryotic cells, which are able to carry out many types of posttranslational modifications such as addition of Nand O-linked oligosaccharides, but also palmitoylation, myristylation and phosphorylation.
Use of Plastic Wastes and Reclaimed Asphalt for Sustainable Development

The increased cost of virgin material, declining resources and increasing plastic wastes have turned the research momentum towards sustainable and green pavements. Reclaimed Asphalt Pavement (RAP) from the construction industry and plastic wastes disposal is the main problem for Pakistan as well as other developing countries in the face of fewer funds for the construction, repair, and rehabilitation of the extensive road network. In this research, the attempt has been made to study the use of Reclaimed Asphalt Pavement and plastic wastes to counter these issues. Virgin binder was modified with three different contents (2%, 4%, and 6%) of Polyethylene Terephthalate and three contents (20%, 30%, and 40%) of Reclaimed Asphalt Pavement. Conventional properties of the modified binder were determined by penetration and softening point. At the same time, thermal stability was checked by Thermal Gravimetric Analysis, and resistance against rutting was evaluated with the help of Dynamic Shear Rheometer. It is observed that modified binder remains stable up to a temperature of 470 °C and showed improved resistance against rutting. Marshall mix properties were determined and compared to specifications of the National Highway Authority of Pakistan. Optimum Marshall stability was observed with 4% Polyethylene Terephthalate, and 30% Reclaimed Asphalt Pavement, while flow and air voids remained in limits. As per the results, utilisation of plastic wastes in asphalt pavements enhances the performance and helps to reduce the environmental pollution and landfill problems due to Reclaimed Asphalt Pavement and plastic wastes.
Comparison of carbon dioxide fluxes over three boreal black spruce forests in Canada

Although mature black spruce forests are a dominant cover type in the boreal forest of North America, it is not clear how their carbon (C) budgets vary across the continent. The installation of an eddy covariance flux tower on an Old Black Spruce (OBS) site in eastern Canada (EOBS, Québec) provided a first opportunity to compare and contrast its annual (2004) and seasonal C exchange with two other pre‐existing OBS flux sites from different climatic regions located in Saskatchewan [Southern OBS (SOBS)] and Manitoba [Northern OBS (NOBS)]. Although there was a relatively uniform seasonal pattern of net ecosystem productivity (NEP) among sites, EOBS had a lower total annual NEP than the other two sites. This was primarily because warmer soil under a thicker snowpack at EOBS appeared to increase winter C losses and low light suppressed both NEP and gross ecosystem productivity (GEP) in June. Across sites, greater total annual GEP and ecosystem respiration (R) were associated with greater mean annual air temperatures and an earlier beginning of the growing season. Also, GEP at all three sites showed a stronger relationship with air temperature in spring and early summer compared with later in the growing season, highlighting the importance of springtime conditions to the C budget of these boreal ecosystems. The three sites had different parameter estimates describing the responses of R and GEP at the half hour time scale to near surface temperature and light, respectively. On the other hand, the responses of both R and GEP to temperature at the monthly scale did not differ among sites. These results suggest that a general parameterization could be sufficient at coarse time resolutions to model the response of C exchange to environmental factors of mature black spruce forests from different climatic regions.
School of Science & Engineering Platform for Assessing and Experimenting with Complexity of Arabic Grammatical Structures Capstone Design – Spring 2015

Arabic is the fifth most spoken language in the world and the fastest growing one on the Internet. It has thus gained momentum and has seen a clear increase in the research efforts dedicated to it. However, many gaps remain in the scholarship pertaining to Arabic Natural Language Processing (ANLP). One of those gaps is related to the study of its syntactic and grammatical complexity. This capstone is an attempt at making a contribution to that that field by building a platform to assess the syntactic structures of any given text in Arabic and to determine its level of complexity. It uses a statistical approach which consists of running academic texts through the Stanford Arabic parser and storing data pertaining to those parses to draw eventual patterns and come up with metrics to characterize complexity. As a research project, this capstone consists of a theoretical component, which is thoroughly addressed in this report, and of an implementation component which is in turn divided into a Web application and a Java background process runnable through the command line.
Interactive effects of concealment, parental behaviour and predators on the survival of open passerine nests

Summary 1. A simple model of relative effects of parental behaviour (parents present vs. absent) and nest concealment on probability of nest predation was evaluated by measuring survival of paired natural/artificial nests of four open nesting passerines over 3 years. 2. The ratio of rodent to corvid predation (i) decreased from yellowhammer (small eggs, ground/near ground nests) through blackcap (small, shrub) to song thrush and blackbird (medium sized, shrub/subcanopy); (ii) was highest in years when rodent abundance peaked ‐ this effect was clear in yellowhammer, detectable in blackcap, but not found in thrushes. An inverse relationship was found between mean annual nest survival and abundance of the major nest predator for each species. Predators differed between poorly (corvids) and well-concealed (rodents) nests in blackcap. 3. The effects on nest survival differed among species, including: positive effect of parental behaviour combined with neutral effect of concealment (thrushes); independent positive effects of behaviour and concealment (yellowhammer); neutral effect of behaviour combined with positive effect of concealment (blackcap). These patterns are consistent with hypothesis that relatively larger species with conspicuous nests (thrushes) should either engage in more vigorous nest defence or their defence is more efficient, compared with smaller species with less conspicuous nests (blackcap). 4. The positive relationship between nest concealment and survival resulted either from an effect of nest site per se (yellowhammer) or from an effect of parental behaviour (blackcap) that changed from negative (nest disclosure) to positive (nest defence) between poorly and well-concealed nests, respectively. The view that lack of a withinspecies relationship between nest concealment and survival (thrushes) results from parental behaviour compensating for predation risk associated with poor nest concealment was not supported. 5. This study demonstrated (i) multiple interactions among factors influencing the rate of nest predation, both between and within species; (ii) potential bias associated with drawing general conclusions from small-scale experiments.
Plate Bending Analysis by Two-dimensional Non-linear Partial Differential Equations

A plate bending analysis is proposed and investigated, by reducing the above structural analysis problem to the solution of a two-dimensional non-linear partial differential equation. The plate is subjected to uniformly distributed load and then the transverse displacements, the bending moments and the transverse shear forces are computed. This computational plate bending method, consists to the analysis of the load to Fourier-double series. An application of plate bending problems is finally given to the determination of the transverse displacements, the bending moments and the transverse shear forces in an orthogonal plate consisting of reinforced concrete and subjected to uniform load. Key Word and Phrases Plate Bending, Non-linear Partial Differential Equation, Structural Analysis, Transverse Displacements, Bending Moments, Transverse Shear Forces, Fourier-double Series.
Short-Time INL Testing Methodology for High-Resolution ΔΣ ADC

Abstract. This paper describes a mass production testing methodology for integral nonlinearity (INL) of a high precision ΔΣ analog-to-digital converter (ADC) in short time. We consider its INL testing by separating its analog and digital parts: ΔΣ AD modulator and digital filter. The digital filter can be tested with the scan-path method. For the AD modulator part, its nonlinear curve of the DC inputoutput characteristics can be obtained using a DC input varying with a fine step, but it takes an enormously long time; it is not practical for mass production testing. So we consider a polynomial model of the ΔΣ AD modulator input-output characteristics and estimate its coefficient values from the fundamental and harmonics power by applying a cosine input and obtaining the modulator 1-bit output power spectrum with FFT. Its INL can be estimated from the coefficients accurately when the modulator I/O characteristics is continuous. Our simulation and experimental results show that significant testing time reduction can be achieved with the proposed method.
PII: S0045-7930(00)00011-6

An accurate, fast, matrix-free implicit method has been developed to solve the three-dimensional compressible unsteady ̄ows on unstructured grids. A nonlinear system of equations as a result of a fully implicit temporal discretization is solved at each time step using a pseudo-time marching approach. A newly developed fast, matrix-free implicit method is then used to obtain the steady-state solution to the pseudo-time system. The developed method is applied to compute a variety of unsteady ̄ow problems involving moving boundaries. The numerical results obtained indicate that the use of the present implicit method leads to a signi®cant increase in performance over its explicit counterpart, while maintaining a similar memory requirement. 7 2000 Elsevier Science Ltd. All rights reserved.
Isothiocyanate induction of apoptosis in cells overexpressing Bcl-2

The oncogenic protein Bcl-2 is overexpressed in many cancers and prevents cells from undergoing apoptosis in response to traditional chemotherapeutic agents. Recent research has focussed on the development of novel agents that can disrupt the function of Bcl-2 and trigger apoptosis in cancer cells. The isothiocyanates are a class of naturally-occurring phytochemical with potential for development as both chemopreventive and chemotherapeutic agents. This thesis investigated the ability of the isothiocyanates to induce apoptosis in cells that overexpressed Bcl-2. Initially, phenethyl isothiocyanate was shown to be cytotoxic to the Jurkat Tlymphoma cell line with an LD50 of 7.4 μM. Bcl-2 expression had little protective effect, and even greater than 50-fold overexpression only increased the LD50 to 15.1 μM. Morphological and biochemical assays indicated that death still occurred by apoptosis despite overexpression of Bcl-2. A variety of other isothiocyanates were also screened for cytotoxic activity. While the isothiocyanate moiety was crucial for induction of apoptosis, the chemistry of the side chain attached to the isothiocyanate moiety also profoundly influenced the ability of an isothiocyanate to kill Bcl-2 overexpressing cells. The aromatic isothiocyanates were generally far more cytotoxic than aliphatic isothiocyanates. However, within the aromatic isothiocyanates tested in this study the length of the carbon linker group, between the phenyl ring and the isothiocyanate moiety, also influenced cytotoxic activity. Phenethyl isothiocyanate was identified as the most promising compound when targeting cells that overexpressed Bcl-2. Given that minor structural alterations significantly altered cytotoxic activity it is hypothesised that specific interactions with cellular targets may mediate induction of apoptosis by the isothiocyanates. Finally, using a sensitive proteomic technique to label oxidised thiol proteins a preliminary investigation of the targets of the isothiocyanates was performed. A number of thiol proteins were selectively modified following exposure to phenethyl isothiocyanate. One thiol protein that consistently changed was identified as mitochondrial peroxiredoxin-3. Changes to the oxidation state of peroxiredoxin-3 occurred well before activation of apoptosis and may play a role in mediating induction of apoptosis in cells that overexpress Bcl-2. The results of this thesis have provided a platform to permit further investigation of the chemotherapeutic potential of the isothiocyanates and investigation of the mechanisms that allow the isothiocyanates to induce apoptosis in cells that overexpress the oncogene Bcl-2. In the future, the identification of primary targets of the isothiocyanates may aid the design and testing of novel anticancer drugs, and it will also provide novel insight into the regulation of apoptosis.
Clonal dissemination of Staphylococcus aureus isolates causing nosocomial infections, Tehran, Iran

Objective(s): In the current research, the prevalence of Staphylococcus aureus clones and genes encoding antimicrobial resistance and toxins were examined among 120 S. aureus strains from nosocomial infections in tehran, Iran. Materials and Methods: Antimicrobial susceptibility was examined, based on disk diffusion and PCR method to identify resistance and toxin-encoding genes. Based on the polymorphisms in SCCmec, agr, spa, and MLST, the isolates were typed. Results: Among 120 S. aureus isolates, 85 (70.8%) were methicilin resistant S. aureus (MRSA), and 35 (29.2%) were methicilin sensetive S. aureus (MSSA). The tested isolates contained resistance genes, including ant(4΄)-Ia (90%), aac(6΄)-Ie/aph(2˝) (80%), aph(3΄)-IIIa (30%), erm(A) (26.7%), erm(B) (10.8%), erm(C) (11.7%), msr(A) (40.8%), msr(B) (14.2%), tet(M) (45.8%), and mupA (8.3%). The MRSA strains were clustered into six different clones. The most common genotypes included ST239-SCCmec III/t037 (23.3%), ST239-SCCmec III/t388 (22.5%), ST22-SCCmec IV/t790 (8.3%), ST15-SCCmec IV/t084 (7.5%), ST585-SCCmec III/t713 (5%), and ST239-SCCmec III/t924 (4.2%), respectively. ST182/t196 (8.3%) and ST123/t171 (5%) belonged exclusively to MSSA strains. Overall, 10 (66.7%) and 5 (33.3%) out of 15 isolates with pvl genes were attributed to clones ST22-SCCmec IV/t790 and ST15-SCCmec IV/t084, respectively. ST22-SCCmec IV/t790, ST239-SCCmec III/t037, and ST15-SCCmec IV/t084, were related to high-level mupirocin-resistant phenotypes. Conclusion: The genetic diversity of S. aureus was confirmed in our hospitals, and ST239-SCCmec III/t037 showed a relatively high prevalence in our study. It seems that assessment of resistance and virulence genes in different S. aureus molecular types is necessary for proper antibiotic consumption.
Nonparametric Methods Lecture 5

Figure-ground discrimination is an important problem in computer vision. Previous work usually assumes that the color distribution of the figure can be described by a low dimensional parametric model such as a mixture of Gaussians. However, such approach has difficulty selecting the number of mixture components and is sensitive to the initialization of the model parameters. In this paper, we employ non-parametric kernel estimation for color distributions of both the figure and background. We derive an iterative Sampling-Expectation (SE) algorithm for estimating the color distribution and segmentation. There are several advantages of kernel-density estimation. First, it enables automatic selection of weights of different cues based on the bandwidth calculation from the image itself. Second, it does not require model parameter initialization and estimation. The experimental results on images of cluttered scenes demonstrate the effectiveness of the proposed algorithm.
Designing an Engaging Robotic Teaching Assistant for Adults Using the Engagement Profile

We report on an exploratory study conducted at a graduate school in Sweden with a humanoid robot, Baxter. First, we describe a list of potentially useful capabilities for a robot teaching assistant derived from brainstorming and interviews with faculty members, teachers, and students. These selected capabilities consist of reading, greeting, alerting, remote operation, clarification, and motion. Second, we present feedback on how the robot's capabilities, demonstrated in part with the Wizard of Oz approach, were perceived, and iteratively adapted over the course of several lectures, using the \EP tool. Third, we discuss observations and findings regarding the capabilities and the development process. Our findings suggest that using a social robot as a teaching assistant is promising using the chosen capabilities. We find that personalizing the capabilities and the role of embodiment are important topics to be considered in future work.
Intellectual Property Rights

Communicated concepts of property ownership, including intellectual property, depend on cultural values and norms. In many parts of the world, conceptual private ownership lacks definitive regulations that apply in the Western world. This lack of cultural parallelism reflects and engenders significant problems in an age where growing technological advances spread ideas and devices across cultural boundaries bringing philosophical, financial, and other practical concerns that create questions about the role of local norms in governing international transference of innovations. Intellectual property rights (IPRs) are the focus of enormous contemporary international diplomatic efforts to the business of innovative technology and the artistic arena of music, literature, and art. This article briefly outlines the historical development of Western IPRs, illustrates many problems from a non-ethnocentric study of the topic.
The relationship between water content and frost tolerance in shoots of hardwood seedlings

La relation entre la tolerance au gel et le contenu en eau des tiges de semis d'essences feuillues a ete etudiee lors de deux experiences d'endurcissement au froid. Dans la premiere (experience 1), des semis de bouleau jaune (Betula alleghaniensis Britton) âges de 3 mois ont ete soumis, en cabinets de croissance, a des temperatures decroissantes sous des conditions de jours courts (JC, 8 h) ou de jours longs (JL, 16 h). Dans la deuxieme (experience 2), des semis de chene rouge (Quercus rubra L.), de chene a gros fruits (Quercus macrocarpa Michx.) et de bouleau jaune ont ete endurcis sous des conditions naturelles dans un tunnel de production. La tolerance au gel a ete determinee par des tests de congelation effectues sur des semis entiers (experience 1) ou sur la partie apicale (5 cm) de la tige principale (experience 2) et les dommages ont ete evalues visuellement. Le contenu en eau de la partie apicale (5 cm) de la tige a ete exprime par le rapport masse seche sur masse fraiche (MS/MF). La tolerance au gel et le rapport MS/MF ont augmente dans les deux experiences. Dans la premiere experience, les semis exposes aux JC se sont davantage endurcis (JC, -19,2°C ; JL, -15,7°C) et ont montre apres 60 jours un rapport MS/MF plus eleve que ceux qui avaient ete exposes aux JL. Dans la deuxieme experience, le chene a gros fruit, le bouleau jaune et le chene rouge ont atteint, le 2 novembre, un endurcissement de -26,7, -25,1 et -20,4°C, respectivement. Les trois essences ont atteint un rapport MS/MF de 50 % a la meme date. Pour les deux experiences, des valeurs de MS/MF plus elevees que 45 % correspondent a une tolerance au gel egale ou inferieure a -10°C.