Miracle-dz/UniFAR-FTUs huggingface dataset:
Medicinal Chemistry : RESEARCH ; NOX1 to NOX2 Switch deactivates AMPK and induces invasive phenotype in colon cancer cells through overexpression of MMP-7

Background:Although matrix metalloproteinase(MMP)-7 expression is correlated with increased metastatic potential in human colon cancer cells, the underlying molecular mechanism of incasive phenotype remains unknown. In the current study, we investigated the regulatory effects of membrane NADPH oxidase (NOX) and AMP activated protein kinase (AMPK) on MMP-7 expression and invasive phenotype change in colon cancer cells. Methods:Production of superoxide anion was measured by lucigenin chemiluminescence assay using whole cells and protein extracts(NADPH oxidase activity), and intracellular rective oxygen species (ROS) by fluorescence microscopy using 2`,4`-dichlorofluorescein diacetate(DCF-DA). Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blotting were used to measure mRNA and protein levels, respectively. siRNA transfecition was used to assess involvement of genes in cancer invasion, which were identified by Matrigel transwell invasion assay. Luciferase reporter assay was performed to identify transcription factors linked to gene expression.Results:Under basal conditions, less invasive human colon cancer cells (HT29 and Caco-2) showed low MMP-7 expression but high NOX1 expression and AMPK phosphorylation. Treatment of HT29 and Caco-2 cells with 12-0-tetradecanoylphorbol-13-acetate (TPA) induced an invasive phenotype response along with corresponding increases basal conditions of highly invasive human colon cancer cells(SW620 and HCT116). In addition, inverse regulation between WMPK phosphorylation and NOX2 and MMP-7 expression was obserced in HT29 cells treated with different by treatment with Vit. E, DPI, apocynin, and NOX2 siRNA but not NOX1 siRNA, indicating NOX2-derived ROS production induced an invasive phenotype. TPA-induced of MMP-7 expression was suppressed by AP-1, NF-kB, and MAPK(ERK, p38, and JNK) inhibitors, whereas TPA-induced expression of NOX2 and its regulators, p47phox and p67phox, was blocked by p38 and NF-KB inhibitors. Conclusions:Molecular switch from NOX1 to NOX2 in colon cancer cells induces ROS production and subsequently enhances MMP-7 expression by deactivating AMPK, which otherwise inhibits stimulus-induced autoregulation of ROS and NOX2 gene expression.
Atomic model of the papillomavirus capsid

Papillomaviruses propagate in differentiating skin cells, and certain types are responsible for the onset of cervical cancer. We have combined image reconstructions from electron cryomicroscopy (cryoEM) of bovine papillomavirus at 9 Å resolution with coordinates from the crystal structure of small virus‐like particles of the human papillomavirus type 16 L1 protein to generate an atomic model of the virion. The overall fit of the L1 model into the cryoEM map is excellent, but residues 402–446 in the ‘C‐terminal arm’ must be rebuilt. We propose a detailed model for the structure of this arm, based on two constraints: the presence of an intermolecular disulfide bond linking residues 175 and 428, and the clear identification of a feature in the image reconstruction corresponding to an α‐helix near the C‐terminus of L1. We have confirmed the presence of the disulfide bond by mass spectrometry. Our ‘invading arm’ model shows that papilloma‐ and polyomaviruses have a conserved capsid architecture. Most of the rebuilt C‐terminal arm is exposed on the viral surface; it is likely to have a role in infection and in immunogenicity.
Brain or muscles

In complex situations such as fast locomotion across rough ground we cope with demanding movement tasks with ease. Recent investigations have shown that much of this performance may rest on carefully adjusted properties of the mechanical system and its intelligent use. The property allowing for stable performance without neuronal feedback has been termed self-stability 1 . In a first overview we attempt to explain the underlying concept and give examples from work carried out in own and affiliated laboratories which helps to understand how this concept affects our understanding of construction and function of muscle skeletal systems in highly dynamic situations.
Evolutionary Rescue in Structured Populations

Environmental change, if severe, can drive a population extinct unless the population succeeds in adapting to the new conditions. How likely is a population to win the race between population decline and adaptive evolution? Assuming that environmental degradation progresses across a habitat, we analyze the impact of several ecological factors on the probability of evolutionary rescue. Specifically, we study the influence of population structure and density-dependent competition as well as the speed and severity of environmental change. We also determine the relative contribution of standing genetic variation and new mutations to evolutionary rescue. To describe population structure, we use a generalized island model, where islands are affected by environmental deterioration one after the other. Our analysis is based on the mathematical theory of time-inhomogeneous branching processes and complemented by computer simulations. We find that in the interplay of various, partially antagonistic effects, the probability of evolutionary rescue can show nontrivial and unexpected dependence on ecological characteristics. In particular, we generally observe a nonmonotonic dependence on the migration rate between islands. Counterintuitively, under some circumstances, evolutionary rescue can occur more readily in the face of harsher environmental shifts, because of the reduced competition experienced by mutant individuals. Similarly, rescue sometimes occurs more readily when the entire habitat degrades rapidly, rather than progressively over time, particularly when migration is high and competition strong.
Face classification via sparse approximations

2D face classification problem is very difficult because of the illumination, pose, expression and occlusion factor. The sparse Representation based classification (SRC) provides a significant amount of robustness against to illumination changes and noise. In this study, sparse approximation is used on face recognition and applied to “Extended Yale Face B” database. Results of sparse approximation classification are compared with Fisher Linear Discriminator.
Computational Intelligence and Machine Learning in Bioinformatics 1

It is worth noting that a well-known machine learning algorithm (namely, the perceptron, inspired to the behaviour of a neuronal cell [5]), has just been applied to bioinformatics in the eighties to distinguish translation initiation sites in prokaryotic organisms [6], and starting from this early application, a growing number of computational intelligence and machine learning methods has been applied and often developed to deal with a wide range of bioinformatics problems in genomics, proteomics, gene expression analysis, biological evolution, systems biology, and other relevant bioinformatics domains.
Cognitive Reserve in Dementia: Implications for Cognitive Training

Cognitive reserve (CR) is a potential mechanism to cope with brain damage. The aim of this study was to evaluate the effect of CR on a cognitive training (CT) in a group of patients with dementia. Eighty six participants with mild to moderate dementia were identified by their level of CR quantified by the CR Index questionnaire (CRIq) and underwent a cycle of CT. A global measure of cognition mini mental state examination (MMSE) was obtained before (T0) and after (T1) the training. Multiple linear regression analyses highlighted CR as a significant factor able to predict changes in cognitive performance after the CT. In particular, patients with lower CR benefited from a CT program more than those with high CR. These data show that CR can modulate the outcome of a CT program and that it should be considered as a predictive factor of neuropsychological rehabilitation training efficacy in people with dementia.
A cutting plane method based on redundant rows for improving fractional distance

In this paper, an idea of the cutting plane method is employed to improve the fractional distance of a given binary parity check matrix. The fractional distance is the minimum weight (with respect to lscr1-distance) of vertices of the fundamental polytope. The cutting polytope is defined based on redundant rows of the parity check matrix and it plays a key role to eliminate unnecessary fractional vertices in the fundamental polytope. We propose a greedy algorithm and its efficient implementation for improving the fractional distance based on the cutting plane method.
Thermal fluctuations of immature SOD1 lead to separate folding and misfolding pathways

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease involving cytotoxic conformations of Cu, Zn superoxide dismutase (SOD1). A major challenge in understanding ALS disease pathology has been the identification and atomic-level characterization of these conformers. Here, we use a combination of NMR methods to detect four distinct sparsely populated and transiently formed thermally accessible conformers in equilibrium with the native state of immature SOD1 (apoSOD12SH). Structural models of two of these establish that they possess features present in the mature dimeric protein. In contrast, the other two are non-native oligomers in which the native dimer interface and the electrostatic loop mediate the formation of aberrant intermolecular interactions. Our results show that apoSOD12SH has a rugged free energy landscape that codes for distinct kinetic pathways leading to either maturation or non-native association and provide a starting point for a detailed atomic-level understanding of the mechanisms of SOD1 oligomerization. DOI: http://dx.doi. org/10.7554/eLife.07296. 001
‘Shit shows’ or ‘like-minded schools’: charter schools and the neoliberal logic of Teach For America

Abstract Over the past three decades, two neoliberal educational reform efforts have emerged in tandem – the charter school movement and Teach For America (TFA). This paper critically examines the relationship between these entities through the lens of TFA corps members placed in charter schools, and explores two types of schools described by interviewees, namely, ‘shit shows,’ and ‘like-minded schools. ’ Grounded in corps members’ teaching experiences, this paper argues that even at its best, the close partnership between TFA and charters can create a mutually reinforcing educational subculture that is isolated from broader educational discourses and practices. At its worst, this partnership can result in the ill-advised ‘propping up’ of under-funded, mismanaged, ill-equipped charters that might otherwise struggle to find adequate staffing and, consequently, close. This paper suggests that these two tendencies – toward corps members’ insularity and poor placement – have the potential to conflict with the charter movement’s and TFA’s stated purposes of improving the quality of schooling for disadvantaged and marginalized students.
Probabilistic Non-negative Inconsistent-resolution Matrices Factorization

In this paper, we tackle with the problem of analyzing datasets with different resolution such as a pair of user's individual data and user group's data, for example "userA visited shopA 5 times" and "users whose attributes are men purchased itemA 80 times in total". In order to establish a basic approach to this problem, we focus on the simplified scenario and propose a new probabilistic model called probabilistic non-negative inconsistent-resolution matrices factorization (pNimf). pNimf is rigorously derived from the data generative process using latent high-resolution data which underlie low-resolution data. We conduct experiments on real purchase log data and confirm that the proposed model provides superior performance, and that the performance improves as the number of low-resolution data increases. These results imply that our way of modeling using latent high-resolution data can become the basic approach to the problem of analyzing dataset with different resolution.
The Paradoxical Role of Similarity in Creative Reasoning

In this paper we present a semantic similarity metric that wholly relies on the hierarchical structure of WordNet which makes it amenable as a means of evaluating creativity when considering creative recategorizations of concepts in an Ontology (Veale, 2004). Many creative discoveries are only acknowledged long after their conception due to changes in the evaluation criteria (Bento and Cardoso, 2004), therefore evaluation plays a critical role in creative reasoning systems. We evaluate the similarity function and report a correlation value of 0.84 between human and machine similarity judgments on the dataset of (Miller and Charles, 1991), which is suggestively close to the upper-bound of 0.88 postulated by (Resnik, 1999). We then use the similarity metric as basis for evaluating some examples of creative categorizations. An extension of the metric is also suggested as a means of assessing analogical similarity by looking for analogical cues
On Quasivarieties of Groups and Equations Over Groups

A proof is given that the quasivariety of groups generated by finite and torsion‐free groups does not contain the class of periodic groups. This result is related to (and inspired by) the solvability of equations over groups. The proof uses the Feit–Thompson theorem on the solvability of finite groups of odd order as well as Kostrikin–Zelmanov results on the restricted Burnside problem, and applies technical details of a recent construction of weakly finitely presented periodic groups. 2000 Mathematics Subject Classification 20E06, 20F05, 20F06, 20F50 (primary).
Defining and Analyzing P2P Applications with a Data-Dependency Formalism

Developing peer-to-peer (P2P) applications became increasingly important in software development. Nowadays, a large number of organizations from many different sectors and sizes depend more and more on collaboration between actors to perform their tasks. These P2P applications usually have a recursive behavior that many modeling approaches cannot describe and analyze (e.g., finite-state approaches). In this paper, we present a formal approach that combines component-based development with well-understood methods and techniques from the field of Attribute Grammars and Data-Flow Analysis in order to specify the behavior of P2P applications, and then construct an abstract representation (i.e., Data-Dependency Graph) to perform analyzes on it.
Understanding Urban Mobility via Taxi Trip Clustering

Clustering of a large amount of taxi GPS mobility data helps to understand the spatio-temporal dynamics for the applications of urban planning and transportation. In this paper we cluster the origin-destination pairs of the passenger taxi rides to provide useful insight into the city mobility patterns, urban hot-spots, road network usage and general patterns of the crowd movement within the city of Singapore. We perform experiments on a large scale Singapore taxi dataset consisting of more than 10 million passenger origin-destination GPS points. We use the clusi VAT sampling scheme to obtain the sample trips which return coarse clusters describing the major crowd movement and reduce the data points that are not captured by the coarse clusters and may bring in noises during fine-grained clustering. After the sampling step we use the well known density based clustering algorithm DBSCAN to find cluster structure in the sampled data points and later extend it to the rest of the dataset using nearest prototype rule. We report 24 trip clusters from the dataset which are compact enough to draw meaningful conclusions about the city mobility patterns and the number of trips in each cluster is large enough to be representative of the general traffic movement.
Coming to Terms with the Concept of Moving Species Threatened by Climate Change – A Systematic Review of the Terminology and Definitions

Intentional moving of species threatened by climate change is actively being discussed as a conservation approach. The debate, empirical studies, and policy development, however, are impeded by an inconsistent articulation of the idea. The discrepancy is demonstrated by the varying use of terms, such as assisted migration, assisted colonisation, or managed relocation, and their multiple definitions. Since this conservation approach is novel, and may for instance lead to legislative changes, it is important to aim for terminological consistency. The objective of this study is to analyse the suitability of terms and definitions used when discussing the moving of organisms as a response to climate change. An extensive literature search and review of the material (868 scientific publications) was conducted for finding hitherto used terms (N = 40) and definitions (N = 75), and these were analysed for their suitability. Based on the findings, it is argued that an appropriate term for a conservation approach relating to aiding the movement of organisms harmed by climate change is assisted migration defined as follows: Assisted migration means safeguarding biological diversity through the translocation of representatives of a species or population harmed by climate change to an area outside the indigenous range of that unit where it would be predicted to move as climate changes, were it not for anthropogenic dispersal barriers or lack of time. The differences between assisted migration and other conservation translocations are also discussed. A wide adoption of the clear and distinctive term and definition provided would allow more focused research on the topic and enable consistent implementation as practitioners could have the same understanding of the concept.
Jaw Displacement and Metrical Structure in Japanese: The Effect of Pitch Accent, Foot Structure, and Phrasal Stress

Natural languages organize their utterances into smaller rhythmical units; i.e. the observation which is often referred to as “metrical organization”. The specific phonetic realizations of metrical organizations differ from one language to another. For example, English makes use of strong-weak rhythmic alternations by way of stress (e.g. Liberman and Prince 1977, Prince 1983 et seq.), whereas Japanese primarily makes use of pitch accent 1). The acoustic correlates of English stress include, for example, increased duration and larger intensity (e.g. Fry 1955, 1958, Plag et al. 2011), whereas Japanese pitch accent is primarily realized as changes in F0 (Beckman 1986, Poser 1984, Sugito 1998, Weitzman 1970). The phonology of cross-linguistic patterns of metrical organization is now well understood largely owing to the development of Metrical Phonology (e.g. Liberman and Prince 1977, Gordon 2011, Hayes 1995). How English stress is realized acoustically is also well understood (e.g. Fry 1955, 1958, Gordon 2011, 2014, Plag et al. 2011). Less well studied, however, are articulatory correlates of metrical structure in natural languages. Several recent works based on EMA (ElectroMagnetic Articulograph) show that jaw displacement may reflect metrical organization of utterances in English (Erickson et al. 2012, 2014a, b, Menezes and Erickson 2013, see also de Jong 1995, Kelso et al. 1985, Vatikiotis-Bateson and Kelso 1993): the magnitude of metrical prominence correlates well with the magnitude of jaw displacement. Building on this research program, this paper explores a yet even less studied area of research; that is, how Japanese metrical structure is reflected in jaw displacement patterns. We specifically investigate how three aspects of Japanese metrical features—pitch accent, foot structure, and phrasal stress—manifest themselves in jaw displacement patterns.
Picking Some News about the Retroviral Vector World from the 9th Symposium of the European Society of Gene Therapy

The 9th symposium of the European Society of Gene Therapy (ESGT) organized by Murat Tuncer (President of the Meeting), Bernd Gansbacher (President of the ESGT), and Meral Ozguc (Secretary of the Meeting) took place in Antalya, South Turkey, on 2–4 November 2001. Although the international political context made difficult the coming of some researchers, this symposium has drawn an interesting picture of the works in progress in Europe and in the Mediterranean area.
Estimation of Spatially Correlated Random Fields in Heterogeneous Wireless Sensor Networks

We develop new algorithms for spatial field reconstruction, exceedance level estimation and classification in heterogeneous (mixed analog & digital sensors) Wireless Sensor Networks (WSNs). We consider spatial physical phenomena which are observed by a heterogeneous WSN, meaning that it consists partially of sparsely deployed high-quality sensors and partially of low-quality sensors. The high-quality sensors transmit their (continuous) noisy observations to the Fusion Centre (FC), while the low-quality sensors first perform a simple thresholding operation and then transmit their binary values over imperfect wireless channels to the FC. The resulting observations are mixed continuous and discrete (1-bit decisions) observations, and are combined in the FC to solve the inference problems. We first formulate the problem of spatial field reconstruction, exceedance level estimation and classification in such heterogeneous networks. We show that the resulting posterior predictive distribution, which is key in fusing such disparate observations, involves intractable integrals. To overcome this problem, we develop an algorithm that is based on a multivariate series expansion approach resulting in a Saddle-point type approximation. We then present comprehensive study of the performance gain that can be obtained by augmenting the high-quality sensors with low-quality sensors using real data of insurance storm surge database known as the Extreme Wind Storms Catalogue.
Current Research on Restoring Ridgetop Pine Communities With Stand Replacement Fire

Ridgetop pine communities of the Southern Appalachian Mountains historically have been maintained by lightning- and human-caused fires. With fire suppression for several decades, characteristic stands are entering later seral stages. They typically have an overstory of Table Mountain (Pinus pungens)and/or pitch pine (P. rigida), a midstory of chestnut oak (Quercus prinus), scarlet oak (Q. coccinea), and blackgum (Nyssa sylvatica), and a shrub layer of dense mountain laurel (Kalmia latifolia). Previous research suggests that restoration of these communities can be accomplished with the high-intensity fires that open the forest canopy and expose mineral soil. Three recent studies examined plant-community response to high-intensity prescribed fires. A series of corollary studies help to explain some of the results of these field studies. High and medium-high intensity fires provided adequate sunlight for pines seedlings, whereas medium-low and low intensity fires did not. Post-burn duff was deep and did not vary by fire intensity. We observed sufficient seedling densities to restore pine-dominated stands after all but the highest intensity fires. Many seedlings survived the first growing season as their roots penetrated duff to reach mineral soil. Hardwood rootstocks resprouted on sites treated with all fire intensities and may outcompete pine seedlings for available resources. High-intensity fires may have reduced mycorrhizal abundance and moisture availability for new germinants. Fires of lower intensity than previously recommended or multiple fires of very low-intensity may best provide conditions for pine regeneration, but additional research is needed.