Miracle-dz/UniFAR-FTUs huggingface dataset:
Two AP1 sites binding JunB are essential for human papillomavirus type 18 transcription in keratinocytes

The activity and epithelial tropism of the human papillomavirus type 18 P105 early promoter, which directs the synthesis of the E6 and E7 transforming genes, are controlled by cis elements included in the viral long control region. To identify potential cellular regulators of this promoter, we mutagenized one or both of the 5'-TGACTAA-3' cis elements capable of interacting with the AP1 transcription factor, which is composed either of homodimers or heterodimers of the Jun products or of heterodimers of Jun and Fos. Mutation of both elements completely abolished P105 promoter activity in human keratinocytes. We show that either AP1 site can interact efficiently in vitro with any of the three different Jun products as heterodimers with c-Fos. However, in nuclear extracts prepared from human keratinocytes, JunB was the predominant Jun component bound to the DNA probe containing this cis element. These results implicate JunB as an important factor in human papillomavirus type 18 transcription in keratinocytes and strongly suggest a potential role of this Jun gene product in the tissue-specific transcription of the genital papillomaviruses.
T3_MM: A Markov Model Effectively Classifies Bacterial Type III Secretion Signals

Motivation Type III Secretion Systems (T3SSs) play important roles in the interaction between gram-negative bacteria and their hosts. T3SSs function by translocating a group of bacterial effector proteins into the host cytoplasm. The details of specific type III secretion process are yet to be clarified. This research focused on comparing the amino acid composition within the N-terminal 100 amino acids from type III secretion (T3S) signal sequences or non-T3S proteins, specifically whether each residue exerts a constraint on residues found in adjacent positions. We used these comparisons to set up a statistic model to quantitatively model and effectively distinguish T3S effectors. Results In this study, the amino acid composition (Aac) probability profiles conditional on its sequentially preceding position and corresponding amino acids were compared between N-terminal sequences of T3S and non-T3S proteins. The profiles are generally different. A Markov model, namely T3_MM, was consequently designed to calculate the total Aac conditional probability difference, i.e., the likelihood ratio of a sequence being a T3S or a non-T3S protein. With T3_MM, known T3S and non-T3S proteins were found to well approximate two distinct normal distributions. The model could distinguish validated T3S and non-T3S proteins with a 5-fold cross-validation sensitivity of 83.9% at a specificity of 90.3%. T3_MM was also shown to be more robust, accurate, simple, and statistically quantitative, when compared with other T3S protein prediction models. The high effectiveness of T3_MM also indicated the overall Aac difference between N-termini of T3S and non-T3S proteins, and the constraint of Aac exerted by its preceding position and corresponding Aac. Availability An R package for T3_MM is freely downloadable from: http://biocomputer.bio. cuhk.edu. hk/softwares/T3_MM. T3_MM web server: http://biocomputer.bio. cuhk.edu. hk/T3DB/T3_MM. php.
CEFAGE-UE Working Paper 2008 / 01 The Exit Decision in the European Venture Capital Market Elisabete

This article analyzes the exit decision in the European venture capital market, studying when to exit and how it interacts with the exit form. The paper emphasizes the impact of asymmetric information on the divestment decision. Our model considers the impact of characteristics of the venture capital investor, characteristics of the investment and contracting variables on the exit decision. Our results show that venture capitalists associated with nancial institutions have quicker exits, a result which is stronger for trade-sales exits. In addition, our results highlight the importance of the contracting variables on the exit decision. An unexpected but interesting result is that the presence in the board of directors leads to longer investment duration. Keywords: Asymmetric information, venture capital, trade sales, IPO, write-o¤s, exit decision, competing risks model. JEL classi cation: C24, G24, G32, G38, K22
Regional distribution and developmental expression of epidermal growth factor and transforming growth factor-alpha mRNA in mouse brain by a quantitative nuclease protection assay

A solution-hybridization ribonuclease-protection assay was used to identify epidermal growth factor (EGF) mRNA in mouse brain and to compare the regional and developmental levels of EGF gene expression in the CNS with those of its structural homolog, transforming growth factor-alpha (TGF-alpha). Adult brain regions examined included brainstem, cerebellum, cerebral cortex, hippocampus, basal hypothalamus, olfactory bulb, olfactory tubercle, striatum, and thalamus. While both EGF and TGF-alpha mRNAs were detected in all regions, TGF-alpha mRNA levels were 15–170 times higher, ranging from 0.39 (cerebellum and cerebral cortex) to 2.93 (striatum) pg TGF-alpha mRNA/micrograms total cytoplasmic RNA. In contrast, EGF mRNA levels ranged from 11 to 36 fg EGF mRNA/micrograms, with the highest regional concentrations observed in olfactory bulb, basal hypothalamus, and cerebellum. In our comparison between sexes, no significant male-female differences in EGF or TGF-alpha mRNA levels were observed for any region of adult brain. However, in the pituitary gland, consisting of both endocrine and neural elements, EGF and TGF-alpha mRNA levels were significantly higher in males (234 and 215 fg/micrograms, respectively) than in females (172 and 118 fg/micrograms, respectively). An examination of growth factor gene expression in the developing CNS revealed EGF and TGF-alpha mRNAs detectable as early as embryonic day 14 (earliest time point studied). While gene expression for both peptides continued into the postnatal period, EGF and TGF-alpha mRNA levels were nearly equal to adult concentrations by postnatal day 10. Taken together, our findings provide evidence for the synthesis of EGF in brain and suggest a role for both EGF and TGF-alpha in the development and support of the mammalian CNS.
Agent Programming with Declarative Goals

A long and lasting problem in agent research has been to close the gap between agent logics and agent programming frameworks. The main reason for this problem of establishing a link between agent logics and agent programming frameworks is identified and explained by the fact that agent programming frameworks have not incorporated the concept of a `declarative goal'. Instead, such frameworks have focused mainly on plans or `goals-to-do' instead of the end goals to be realised which are also called `goals-to-be'. In this paper, a new programming language called GOAL is introduced which incorporates such declarative goals. The notion of a `commitment strategy' - one of the main theoretical insights due to agent logics, which explains the relation between beliefs and goals - is used to construct a computational semantics for GOAL. Finally, a proof theory for proving properties of GOAL agents is introduced. Thus, we offer a complete theory of agent programming in the sense that our theory provides both for a programming framework and a programming logic for such agents. An example program is proven correct by using this programming logic.
Oracle inequalities for the Lasso in the high-dimensional Aalen multiplicative intensity model

In a general counting process setting, we consider the problem of obtaining a prognostic on the survival time adjusted on covariates in high-dimension. Towards this end, we construct an estimator of the whole conditional intensity. We estimate it by the best Cox proportional hazards model given two dictionaries of functions. The first dictionary is used to construct an approximation of the logarithm of the baseline hazard function and the second to approximate the relative risk. We introduce a new data-driven weighted Lasso procedure to estimate the unknown parameters of the best Cox model approximating the intensity. We provide non-asymptotic oracle inequalities for our procedure in terms of an appropriate empirical Kullback divergence. Our results rely on an empirical Bernstein's inequality for martingales with jumps and properties of modified self-concordant functions.
Low complexity multi-layer optimization for multi-hop wireless networks

We design a low-complexity solution to multi-layer optimization in multi-hop wireless networks with throughput objectives. Considering channel sensing and power control at the physical layer, we formulate resource allocation as a non-convex throughput optimization problem that allows distributed implementation. We develop a genetic algorithm to solve this physical layer problem with local information only and then formulate a localized back-pressure algorithm to make routing, scheduling, and frequency band assignments at the link and network layers along with physical-layer considerations. We extend our multi-layer solution to cognitive radio networks with different user classes and evaluate our analytical solution via simulations. We also present hardware-in-the-loop emulation test results obtained with real radio transmissions over emulated channels and verify the performance of our distributed multilayer optimization solution for multi-hop wireless networks.
Persistent Point Feature Histograms for 3D Point Clouds

This paper proposes a novel way of characterizing the local geometry of 3D points, using persistent feature histograms. The relationships between the neighbors of a point are analyzed and the resulted values are stored in a 16-bin histogram. The histograms are pose and point cloud density invariant and cope well with noisy datasets. We show that geometric primitives have unique signatures in this feature space, preserved even in the presence of additive noise. To extract a compact subset of points which characterizes a point cloud dataset, we perform an in-depth analysis of all point feature histograms using different distance metrics. Preliminary results show that point clouds can be roughly segmented based on the uniqueness of geometric primitives feature histograms. We validate our approach on datasets acquired from laser sensors in indoor (kitchen) environments.
Determination of heat conductivity of waste glass feed and its applicability for modeling the batch‐to‐glass conversion

The effective heat conductivity (λ) of reacting melter feed affects the heat transfer and conversion process in the cold cap, the reacting feed floating on molten glass. A heat conductivity meter was used to measure λ of samples of a cold cap retrieved from a laboratory-scale melter, loose dry powder feed samples, and samples cut from fast-dried slurry blocks. These blocks were formed to simulate the feed conditions in the cold-cap by rapidly evaporating water from feed slurry poured onto a 200°C surface. Our study indicates that the effective heat conductivity of the feed in the cold cap is significantly higher than that of loose dry powder feed, which is a result of the feed solidification during the water evaporation from the feed slurry. To assess the heat transfer at higher temperatures when feed turns into foam, we developed a theoretical model that predicts the foam heat conductivity based on morphology data from in-situ X-ray computed tomography. The implications for the mathematical modeling of the cold cap are discussed. This article is protected by copyright. All rights reserved.
Hypoxia inducible factors regulate pluripotency and proliferation in human embryonic stem cells cultured at reduced oxygen tensions

Human embryonic stem (hES) cells are routinely cultured under atmospheric, 20% oxygen tensions but are derived from embryos which reside in a 3–5% oxygen (hypoxic) environment. Maintenance of oxygen homeostasis is critical to ensure sufficient levels for oxygen-dependent processes. This study investigates the importance of specific hypoxia inducible factors (HIFs) in regulating the hypoxic responses of hES cells. We report that culture at 20% oxygen decreased hES cell proliferation and resulted in a significantly reduced expression of SOX2, NANOG and POU5F1 (OCT4) mRNA as well as POU5F1 protein compared with hypoxic conditions. HIF1A protein was not expressed at 20% oxygen and displayed only a transient, nuclear localisation at 5% oxygen. HIF2A (EPAS1) and HIF3A displayed a cytoplasmic localisation during initial hypoxic culture but translocated to the nucleus following long-term culture at 5% oxygen and were significantly upregulated compared with cells cultured at 20% oxygen. Silencing of HIF2A resulted in a significant decrease in both hES cell proliferation and POU5F1, SOX2 and NANOG protein expression while the early differentiation marker, SSEA1, was concomitantly increased. HIF3A upregulated HIF2A and prevented HIF1A expression with the knockdown of HIF3A resulting in the reappearance of HIF1A protein. In summary, these data demonstrate that a low oxygen tension is preferential for the maintenance of a highly proliferative, pluripotent population of hES cells. While HIF3A was found to regulate the expression of both HIF1A and HIF2A, it is HIF2A which regulates hES cell pluripotency as well as proliferation under hypoxic conditions.
Eurographics/siggraph Symposium on Computer Animation (2003) Learning Controls for Blend Shape Based Realistic Facial Animation

Blend shape animation is the method of choice for keyframe facial animation: a set of blend shapes (key facial expressions) are used to define a linear space of facial expressions. However, in order to capture a significant range of complexity of human expressions, blend shapes need to be segmented into smaller regions where key idiosyncracies of the face being animated are present. Performing this segmentation by hand requires skill and a lot of time. In this paper, we propose an automatic, physically-motivated segmentation that learns the controls and parameters directly from the set of blend shapes. We show the usefulness and efficiency of this technique for both, motion-capture animation and keyframing. We also provide a rendering algorithm to enhance the visual realism of a blend shape model.
Membrane adhesion and other functions for the myelin basic proteins

The myelin basic proteins are a set of peripheral membrane polypeptides which play an essential role in myelination. Their most well‐documented property is the unique ability to ‘seal’ the cytoplasmic aspects of the myelin membrane, but this is probably not the only function for these highly charged molecules. Despite extensive homology, the individual myelin basic proteins (MBPs) exhibit different expression patterns and biochemical properties, and so it is now believed that the various isoforms are not functionally equivalent in myelinating cells. We now think that while the major MBPs are intracellular adhesion molecules, some of the quantitatively less abundant isoforms that are expressed very early in development may have regulatory effects on the myelination program.
Strong and Provably Secure Database Access Control

Existing SQL access control mechanisms are extremely limited. Attackers can leak information and escalate their privileges using advanced database features such as views, triggers, and integrity constraints. This is not merely a problem of vendors lagging behind the state-of-the-art. The theoretical foundations for database security lack adequate security definitions and a realistic attacker model, both of which are needed to evaluate the security of modern databases. We address these issues and present a provably secure access control mechanism that prevents attacks that defeat popular SQL database systems.
The effect of animation on comprehension and interest

Although animations are believed to be effective in learning and teaching, several studies have failed to confirm this. Nevertheless, animations might be more attractive and motivating. Fourth and sixth grade students learned the operation of a bicycle pump from graphics that were: (i) presented simultaneously; (ii) presented successively; (iii) self-paced, or (iv) animated. The presentation mode affected evaluation of perceived comprehensibility, interestingness,enjoymentandmotivation,butnotcomprehensiontestscore.Fourthgraderswhowere lowinneedforcognitionratedtheanimationsasmoreenjoyableandmotivating,whereassixth graders rated self-paced graphics as more interesting and motivating. The evaluations of sixth graders correspond to results of many studies on learning. Animations are not more effective than equivalent static graphics in learning, and they are not seen as more motivating by sixth graders.
Accumulate–Repeat–Accumulate Codes: Capacity-Achieving Ensembles of Systematic Codes for the Erasure Channel With Bounded Complexity

This paper introduces ensembles of systematic accumulate-repeat-accumulate (ARA) codes which asymptotically achieve capacity on the binary erasure channel (BEC) with bounded complexity, per information bit, of encoding and decoding. It also introduces symmetry properties which play a central role in the construction of new capacity-achieving ensembles for the BEC. The results here improve on the tradeoff between performance and complexity provided by previous constructions of capacity-achieving code ensembles defined on graphs. The superiority of ARA codes with moderate to large block length is exemplified by computer simulations which compare their performance with those of previously reported capacity-achieving ensembles of low-density parity-check (LDPC) and irregular repeat-accumulate (IRA) codes. ARA codes also have the advantage of being systematic.
Biochemical activities of the ParA partition protein of the P1 plasmid

The unit‐copy P1 plasmid depends for stability on a plasmld‐encoded partition region called par, consisting of the parA and parB genes and the parS site. ParA is absolutely required for partition, but its partition‐critical role is not known. Purified ParA protein is shown to possess an ATPase activity in vitro which is specifically stimulated by purified ParB protein and by DNA. ParA is responsible for regulation of expression of parA and parB, and purified ParA has an ATP‐dependent, site‐specific DNA binding activity which recognizes a sequence that overlaps the parA promoter. The rote of the ATP‐dependence of the binding activity, as well as other possible functions of the ATPase activity in partition, is discussed.
MELAS syndrome: correlation between clinical features and molecular genetic analysis

The clinical manifestations and mitochondrial DNA (mtDNA) mutations in a Taiwanese family with a female proband exhibiting mitochondrial myopathy, encephalopathy, lactic acidosis and stroke‐like episodes syndrome are reported. Clinically, the proband had a stroke‐like episode with right hemiparesis, hemianopsia and mental dysfunction as well as short stature, hearing impairments, and elevated lactate levels. Brain magnetic resonance images showed multiple increased signal intensities over the left frontal, parietal and temporal areas. There were no ragged‐red fibers, but paracrystalline inclusion bodies were shown in the muscle biopsies under electron microscopic examination. A deficiency of NADH‐CoQ reductase was also found in biochemical studies of the muscles. The family survey revealed no abnormal findings except for headache and episodic vomiting in her mother. The molecular analysis of mtDNA disclosed a mutation from A to G at the nucleotide pair 3243 of the mitochondrial transfer RNALeu gene in the blood, hair follicles and/or muscle of the maternal relatives. A characteristic finding of the MELAS family is variation of percentage of mutated mtDNA in various tissues and individuals. However, a higher proportion of mutated mtDNA was noted in the proband than that in the asymptomatic or oligosymptomatic family members. From the data, the variable clinical phenotypes in this MELAS family can be explained at least partly, by the different proportions of mutant mtDNA in the target tissues of the profound and maternal relatives.
Joint Infrared Target Recognition and Segmentation Using a Shape Manifold-Aware Level Set

We propose new techniques for joint recognition, segmentation and pose estimation of infrared (IR) targets. The problem is formulated in a probabilistic level set framework where a shape constrained generative model is used to provide a multi-class and multi-view shape prior and where the shape model involves a couplet of view and identity manifolds (CVIM). A level set energy function is then iteratively optimized under the shape constraints provided by the CVIM. Since both the view and identity variables are expressed explicitly in the objective function, this approach naturally accomplishes recognition, segmentation and pose estimation as joint products of the optimization process. For realistic target chips, we solve the resulting multi-modal optimization problem by adopting a particle swarm optimization (PSO) algorithm and then improve the computational efficiency by implementing a gradient-boosted PSO (GB-PSO). Evaluation was performed using the Military Sensing Information Analysis Center (SENSIAC) ATR database, and experimental results show that both of the PSO algorithms reduce the cost of shape matching during CVIM-based shape inference. Particularly, GB-PSO outperforms other recent ATR algorithms, which require intensive shape matching, either explicitly (with pre-segmentation) or implicitly (without pre-segmentation).
Overweight and obesity weakly predict the development of periodontal infection.

AIM The aim of this study was to investigate the association between body weight and periodontal infection in a longitudinal setting. MATERIAL AND METHODS This study was based on a subpopulation of the Health 2000 Survey that included dentate, non-diabetic subjects aged 30-59 years, who had never smoked and who had participated in the Follow-Up Study on Finnish Adults' Oral Health approximately 4 years later (n=396). The number of new teeth with deepened (4 mm deep or deeper) periodontal pockets in the follow-up examination was used as the outcome variable. Body weight was measured using body mass index, categorized into three categories: <25.0 (normal weight), 25.0-29.9 (overweight) and 30.0 or more (obesity). Incidence rate ratios were estimated using Poisson's regression models. RESULTS Body weight was weakly, but not statistically significantly, associated with the number of new teeth with deepened periodontal pockets among subjects who were periodontally healthy in the baseline examinations, whereas only a minuscule association was found among subjects who had periodontal infection at baseline. CONCLUSIONS The results of this follow-up study do not provide evidence that overweight and obesity can be considered significant risk factors in the pathogenesis of periodontal infection.
World Journal of Surgical Oncology Open Access Metastatic Sweat Gland Adenocarcinoma: a Clinico-pathological Dilemma

Background: Sweat gland adenocarcinoma is a rare malignancy with high metastatic potential seen more commonly in later years of life. Scalp is the most common site of occurrence and it usually spreads to lymph nodes. Liver, lung and bones are the distant sites of metastasis with fatal results. The differentiation between apocrine and eccrine metastatic sweat gland carcinoma is often difficult. The criteria's are inadequate to be of any practical utility.