Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of Transcription Factor Binding to Human Papillomavirus Type 16 DNA during Cellular Differentiation

ABSTRACT Human papillomaviruses (HPVs) require terminal differentiation of the host cell to produce infectious virions. The process of viral maturation involves a variety of changes in the expression/activity of host proteins that lead to high-level replication of the viral genome and expression of the late viral genes. Although the late promoter regions of HPV type 16 (HPV-16) are still not fully characterized, differentiation-dependent regulation of viral genes is thought to involve changes in the binding of host cell transcription factors to the viral promoter and regulatory regions. Currently, very little is known about specific cellular transcription factors involved in this process. We used the Panomics TransSignal protein/DNA array to identify changes in the levels of cellular transcription factors during methylcellulose-induced differentiation of W12 (20863) cells containing HPV-16. We then identified the differentially expressed transcription factors that specifically bind to HPV-16 DNA, including the known promoter and regulatory regions. We have validated the results obtained from the Panomics array by Western blot analysis. Furthermore, by chromatin immunoprecipitation assays, we have shown that many of the transcription factors identified in the above screen bind to the HPV-16 promoter/regulatory sequences in vivo and that the level of this binding is increased during differentiation. This approach identified approximately 30 transcription factors that specifically bind to HPV-16 sequences and may be involved in regulating HPV-16 transcription during differentiation. Although some of these transcription factors have previously been suggested to be involved in HPV-16 transcription, a number of them represent novel viral DNA-host protein interactions.
A Model of Add-On Pricing

This paper examines a competitive model of add-on pricing, the practice of advertising low prices for one good in hopes of selling additional products (or a higher quality product) to consumers at a high price at the point of sale. The main conclusion is that add-on pricing softens price competition between firms and results in higher equilibrium profits.
Predictors of E-Learning Satisfaction in Teaching and Learning for School Teachers: A Literature Review.

This paper develops a theoretical model of the determinants of e-learning satisfaction in teaching and learning among secondary school teachers. It is based on reviews of past studies on satisfaction in using information technology systems. Three potential groups of determinants of satisfaction among secondary school teachers were identified; user-related characteristics, organisational-related characteristics and the e-learning-system characteristics. Usage is established as a mediating variable between the three potential groups of determinants and satisfaction towards e-learning. Future research could provide a more definitive theoretical statement of e-learning satisfaction and develop an additional proposition which could be derived from a more refined theory. The research yields a theoretical framework that outlines the predictive potential of the three groups of key factors in explaining e-learning satisfaction among secondary school teachers. The factors can be considered when developing future continuous professional development courses and intervention programmes when proposing a new innovation in the curriculum.
Nerve growth factor enhances [3H]nicotine binding to a nicotinic cholinergic receptor on PC 12 cells.

Although nicotinic cholinergic agonists have functional effects on PC 12 cells, radioligand-binding sites have not been detected. We, therefore, studied PC 12 cells incubated in the presence of nerve growth factor (NGF) and determined that specific [3H]nicotine-binding sites were induced approximately 2.5-fold in the presence of NGF (50 or 100 ng/ml). Specific binding was maximal between the first (100 ng/ml NGF) and seventh (50 ng/ml NGF) days of treatment and was stable for 2 weeks with addition of NGF every 3 days. Using intact cells, average association and dissociation rates for [3H]nicotine were 0.00021 min-1 nM-1 (n = 2) and 0.048 min-1 (n = 2), respectively, at 4 C, yielding an average apparent Kd of 229 nM. At 22 C, stable equilibrium was not attained during association studies. A similar Kd value for broken cell preparations was obtained by kinetic analysis (i.e. an average association rate of 0.00042 min-1 nM-1 and dissociation rate of 0.087 min-1), yielding an average Kd value of 207 nM (n = 2) at 4 C. By saturation binding analysis of intact cells, an average Kd of 292 nM (n = 2) and a binding capacity (Bmax) of 15,118 molecules/cell were obtained. [3H]Nicotine binding was inhibited on an equimolar basis by L-(-)nicotine and N-methylcarbamylcholine. D-(+) Nicotine was 7-fold less potent, whereas alpha-bungarotoxin, mecamylamine, and atropine showed no significant inhibition. [3H]Nicotine binding was also inhibited quantitatively by mono-specific polyclonal antibodies raised against the predicted alpha 3-subunit sequence (amino acids 130-139) of the rat neuronal nicotinic cholinergic receptor. This study represents the first biochemical characterization of NGF-stimulated nicotine-binding sites on PC 12 cells and confirms previous evidence of the presence of functional nicotinic cholinergic receptors on these cells.
APPLYING TWO DIMENSIONAL KALMAN FILTERING FOR DIGITAL TERRAIN MODELLING

Digital Elevation Models (DEMs) have been increasingly used to model the terrain surfaces to provide the 'physical bases' for environmental studies. However, DEM is subject to systematic errors, random noise and outliers. In this paper, a newly developed two dimensional (2-D) Kalman filtering approach to generating optimal estimates of terrain variables from a noisy grid DEM is introduced, which comprises a 2-D Kalman processor, a function for outlier detection and removal, and a two-step filtering procedure. The experiment of a simulated surface indicates that after applying the developed 2-D Kalman filtering technique the outliers of a DEM can be efficiently detected and well removed. The standard deviation of random noise of the DEM can be significantly reduced by approximately 70% for elevation and about 85% for the first partial derivatives of elevation, compared with their original values. The experiment of slope calculation shows that using this approach, the effect of random noise and outliers of slope can be efficiently reduced by more than 60% in terms of standard deviation, of the results derived from Arc/Info software using the same simulated DEM data.
Holocene drought, deforestation and evergreen vegetation development in the central Mediterranean: a 5500 year record from Lago Alimini Piccolo, Apulia, southeast Italy

Pollen analysis from Lago Alimini Piccolo provides the first record of mid- and late-Holocene vegetation history of a coastal area in the easternmost region of southern Italy (Salento Peninsula). Terrestrial pollen taxa document expansions and declines of the Mediterranean forest, in relation to human activity and climate changes. Between 5200 and 4350 cal. BP a dense evergreen oak forest dominated the landscape; then a distinct opening of the forest is recorded (4350—3900 cal. BP). A new forest expansion (3900—2100 cal. BP) is characterized by an increase of Olea and evergreen shrubs, indicating a development of mediterranean climate conditions and increasing human disturbance. The Roman occupation period (2100—1500 cal. BP) shows a significant opening of the forest, expansion of halophytes and modest values of Olea. After 1500 cal. BP human impact causes a further decrease of the natural woodland in favour of an extraordinary expansion of Olea . The vegetation development at Lago Alimini Piccolo, interpreted in the light of other pollen records, provides new insights into climate evolution and evergreen vegetation development in the central Mediterranean region: (1) a temporary mid-Holocene deforestation at 4000 cal. BP, involving many Italian sites south of 43°N, was possibly caused by drought associated with an expansion or northward displacement of the North African high pressure zone; (2) the Bronze Age increase of Olea, coupled with a widespread increase of Mediterranean shrubs, suggests management of wild trees, while the beginning of intensive cultivation of olive trees is only found after the Roman time.
Good Practice in CNN Feature Transfer

The objective of this paper is the effective transfer of the Convolutional Neural Network (CNN) feature in image search and classification. Systematically, we study three facts in CNN transfer. 1) We demonstrate the advantage of using images with a properly large size as input to CNN instead of the conventionally resized one. 2) We benchmark the performance of different CNN layers improved by average/max pooling on the feature maps. Our observation suggests that the Conv5 feature yields very competitive accuracy under such pooling step. 3) We find that the simple combination of pooled features extracted across various CNN layers is effective in collecting evidences from both low and high level descriptors. Following these good practices, we are capable of improving the state of the art on a number of benchmarks to a large margin.
Programmable Self-Assembly

Self-assembly is the phenomenon in which a collection of particles spontaneously arrange themselves into a coherent structure. Self-assembly is ubiquitous in nature. In this article we consider the task of programming active self-assembling and self-organizing systems at the level of interactions among particles in the system. To demonstrate the approach, we use it to control an experimental system called the programmable parts testbed (PPT). We also consider several illustrative examples, including polymerization, a model of a molecular ratchet, and a cooperative control scenario. In all of these systems, we provide each particle or robot with a local interaction rule book called a graph grammar.
Retirement Timing in Germany

Abstract: This article examines the timing of retirement in a household context, using longitudinal data on employment and family careers. It investigates the retirement decisions of unmarried and married elderly men and women. Since in (West) Germany, patterns of investment in alternative family and market roles over the life course are highly tendered, a separate analysis is also performed on a subsample of working spouses where both partners were employed at age fifty. The determinants of retirement decisions considered in the models are: early life course employment patterns, employment characteristics in later life, health situation, and household circumstances, including the income level. Data come from the German Socioeconomic Panel Study. An event history analysis is conducted using a piecewise constant hazard model with time-varying covariates. The analysis indicates that there are indeed important differences in retirement behavior between men and women as well as between unmarried and married individuals. The household context does matter in retirement decisions but the study discloses gender asymmetry in response to marital status and displays differences between partnerships in which both spouses are employed in late life and those that portray a traditional division of paid/unpaid labor.
Reducing Weak to Strong Bisimilarity in CCP

Concurrent constraint programming (ccp) is a well-established model for concurrency that singles out the fundamental aspects of asynchronous systems whose agents (or processes) evolve by posting and querying (partial) information in a global medium. Bisimilarity is a standard behavioural equivalence in concurrency theory. However, only recently a well-behaved notion of bisimilarity for ccp, and a ccp partition refinement algorithm for deciding the strong version of this equivalence have been proposed. Weak bisimiliarity is a central behavioural equivalence in process calculi and it is obtained from the strong case by taking into account only the actions that are observable in the system. Typically, the standard partition refinement can also be used for deciding weak bisimilarity simply by using Milner's reduction from weak to strong bisimilarity; a technique referred to as saturation. In this paper we demonstrate that, because of its involved labeled transitions, the above-mentioned saturation technique does not work for ccp. We give an alternative reduction from weak ccp bisimilarity to the strong one that allows us to use the ccp partition refinement algorithm for deciding this equivalence.
The longitudinal course of borderline psychopathology: 6-year prospective follow-up of the phenomenology of borderline personality disorder.

OBJECTIVE The syndromal and subsyndromal phenomenology of borderline personality disorder was tracked over 6 years of prospective follow-up. METHOD The psychopathology of 362 inpatients with personality disorders was assessed with the Revised Diagnostic Interview for Borderlines (DIB-R) and borderline personality disorder module of the Revised Diagnostic Interview for DSM-III-R Personality Disorders. Of these patients, 290 met DIB-R and DSM-III-R criteria for borderline personality disorder and 72 met DSM-III-R criteria for other axis II disorders (and neither criteria set for borderline personality disorder). Most of the borderline patients received multiple treatments before the index admission and during the study. Over 94% of the total surviving subjects were reassessed at 2, 4, and 6 years by interviewers blind to previously collected information. RESULTS Of the subjects with borderline personality disorder, 34.5% met the criteria for remission at 2 years, 49.4% at 4 years, 68.6% at 6 years, and 73.5% over the entire follow-up. Only 5.9% of those with remissions experienced recurrences. None of the comparison subjects with other axis II disorders developed borderline personality disorder during follow-up. The patients with borderline personality disorder had declining rates of 24 symptom patterns but remained symptomatically distinct from the comparison subjects. Impulsive symptoms resolved the most quickly, affective symptoms were the most chronic, and cognitive and interpersonal symptoms were intermediate. CONCLUSIONS These results suggest that symptomatic improvement is both common and stable, even among the most disturbed borderline patients, and that the symptomatic prognosis for most, but not all, severely ill borderline patients is better than previously recognized.
Calpain I Induces Cleavage and Release of Apoptosis-inducing Factor from Isolated Mitochondria*

The translocation of apoptosis-inducing factor (AIF) from mitochondria to the nucleus has been implicated in the mechanism of glutamate excitotoxicity in cortical neurons and has been observed in vivo following acute rodent brain injuries. However, the mechanism and time course of AIF redistribution to the nucleus is highly controversial. Because elevated intracellular calcium is one of the most ubiquitous features of neuronal cell death, this study tested the hypothesis that cleavage of AIF by the calcium-activated protease calpain mediates its release from mitochondria. Both precursor and mature forms of recombinant AIF were cleaved near the amino terminus by calpain I in vitro. Mitochondrial outer membrane permeabilization by truncated Bid induced cytochrome c release from isolated liver or brain mitochondria but only induced AIF release in the presence of active calpain. Enzymatic inhibition of calpain by calpeptin precluded AIF release, demonstrating that proteolytic activity was required for release. Calpeptin and the mitochondrial permeability transition pore antagonist cyclosporin A also inhibited calcium-induced AIF release from mouse liver mitochondria, implicating the involvement of an endogenous mitochondrial calpain in release of AIF during permeability transition. Cleavage of AIF directly decreased its association with pure lipid vesicles of mitochondrial inner membrane composition. Taken together, these results define a novel mechanism of AIF release involving calpain processing and identify a potential molecular checkpoint for cytoprotective interventions.
Poster : Towards a Model for Analysing Anti-Phishing Authentication Ceremonies

Phishing uses both social engineering and technical means to carry out attacks. Therefore, human factors incorrect human trust decisions play an important role in phishing. Many online authentication techniques place a disproportional burden on human abilities. Assumptions made about human-protocol behaviour are often flawed. In our approach we use the concept of a ceremony to analyse and improve the anti-phishing security of web authentication. A ceremony [4] is an extension of the concept of network protocol that includes user interface, human-to-human communication and transfers of physical objects that carry data. It is one way of extending the reach of current methods for analysing protocols to include humans. A secure ceremony is secure against both normal and social engineering attacks, such as phishing. The complexity of defining a ceremony comes with modelling a human node and the major effort yet to be accomplished in the field of ceremony design and analysis is the modelling of the memory and processing performed by human nodes [4], [1]. In this paper we present our recent and on-going work on researching human communication processing in antiphishing authentication ceremonies. We propose a new Human Factors in Anti-Phishing Authentication Ceremonies (APAC) framework and outline how to apply the framework to model human node behaviour. By applying our model, it will be possible to identify design principles for minimising human node interaction errors in anti-phishing authentication ceremonies.
On the origin, evolution and phylogeny of giraffes Giraffa camelopardalis

The origin, phylogeny, and evolution of modem giraffes (Giraffa camelopardalis) is obscure. We review here the literature and conclude that the proximate ancestors of modern giraffes probably evolved in southern central Europe about 8 million years ago (Mya). These ancestors appear to have arisen from the gelocid ancestral assemblage of 20–25 Mya via the family Palaeomerycidae. From the palaeomerycids arose the Antilocaprinae (Pronghorns) via the subfamily Dromomerycinae, and two subfamilies of giraffids, the Climacoceratidae and Canthumerycidae. The terminal genus of the Climacoceratid line was the now extinct massive giraffid Sivatherium sp. The Canthumerycids gave rise to the okapi and giraffes via the intermediate forms of Giraffokeryx, Palaeotragus sp. (of which the okapi is the extant form), Samotherium sp. and Bohlinia sp. All of which are extinct. Stimulated by climate change, progeny of Bohlinia entered China and north India, evolved into typical Giraffa species and became extinct there about 4 Mya. Similarly, following their preferred habitat, African Giraffa entered Africa via Ethiopia about 7 Mya. Here, seemingly unaffected by the climate changes occurring to the east and causing extinction of its Asian counterparts, Giraffa radiated into several sequential and coeval species culminating with the evolution of G. camelopardalis in East Africa from where it dispersed to its modern range. Fossils of G. camelopardalis appear about 1 Mya in East Africa. The underlying stimulus for Giraffa evolution seems to have been the vegetation change that began about 8 Mya, from the prevalent forest (C3) biome to a savannah/woodland/shrub (C4) biome. Giraffa's success as a genus is attributed to its great height and unique coat markings. Its height is a consequence of elongation of all seven cervical vertebrae and of the lower more than the upper limb bones. Advantages conferred by its height include protection from predation, increased vigilance, and in males sexual dominance and access to nutrients. Its coat colourings are highly hereditable and provide protection from predation by camouflage, especially in the young. As giraffe are unable to sweat and pant, the patches may also act as thermal windows and may have an important thermoregulatory function.
Filtered spectra arising from permutative categories

Abstract Given a special Γ-category 𝒞 satisfying some mild hypotheses, we construct a sequence of spectra interpolating between the spectrum associated to 𝒞 and the Eilenberg-Mac Lane spectrum Hℤ. Examples of categories to which our construction applies are: the category of finite sets, the category of finite-dimensional vector spaces, and the category of finitely-generated free modules over a reasonable ring. In the case of finite sets, our construction recovers the filtration of Hℤ by symmetric powers of the sphere spectrum. In the case of finite-dimensional complex vector spaces, we obtain an apparently new sequence of spectra, {Am }, that interpolate between bu and . We think of Am as a “bu-analogue” of Sp m (S) and describe far-reaching formal similarities between the two sequences of spectra. For instance, in both cases the mth subquotient is contractible unless m is a power of a prime, and in vk -periodic homotopy the filtration has only k + 2 non-trivial terms. There is an intriguing relationship between the bu-analogues of symmetric powers and Weiss's orthogonal calculus, parallel to the not yet completely understood relationship between the symmetric powers of spheres and the Goodwillie calculus of homotopy functors. We conjecture that the sequence {Am }, when rewritten in a suitable chain complex form, gives rise to a minimal projective resolution of the connected cover of bu. This conjecture is the bu-analogue of a theorem of Kuhn and Priddy about the symmetric power filtration. The calculus of functors provides substantial supporting evidence for the conjecture.
Generalisation for neural networks through data sampling and training procedures, with applications to streamflow predictions

Abstract. Since the 1990s, neural networks have been applied to many studies in hydrology and water resources. Extensive reviews on neural network modelling have identified the major issues affecting modelling performance; one of the most important is generalisation, which refers to building models that can infer the behaviour of the system under study for conditions represented not only in the data employed for training and testing but also for those conditions not present in the data sets but inherent to the system. This work compares five generalisation approaches: stop training, Bayesian regularisation, stacking, bagging and boosting. All have been tested with neural networks in various scientific domains; stop training and stacking having been applied regularly in hydrology and water resources for some years, while Bayesian regularisation, bagging and boosting have been less common. The comparison is applied to streamflow modelling with multi-layer perceptron neural networks and the Levenberg-Marquardt algorithm as training procedure. Six catchments, with diverse hydrological behaviours, are employed as test cases to draw general conclusions and guidelines on the use of the generalisation techniques for practitioners in hydrology and water resources. All generalisation approaches provide improved performance compared with standard neural networks without generalisation. Stacking, bagging and boosting, which affect the construction of training sets, provide the best improvement from standard models, compared with stop-training and Bayesian regularisation, which regulate the training algorithm. Stacking performs better than the others although the benefit in performance is slight compared with bagging and boosting; furthermore, it is not consistent from one catchment to another. For a good combination of improvement and stability in modelling performance, the joint use of stop training or Bayesian regularisation with either bagging or boosting is recommended. Keywords: neural networks, generalisation, stacking, bagging, boosting, stop-training, Bayesian regularisation, streamflow modelling