Miracle-dz/UniFAR-FTUs huggingface dataset:
Information transfer by leaky, heterogeneous, protein kinase signaling systems

Significance Extracellular concentrations convey information to cells about their environment. To sense these signals, cells use biomolecular networks that exhibit inevitable cell-to-cell variability and basal activity. Basal activity is widespread under physiological conditions (with phenotypic consequences), is often raised in disease, and can eradicate the transfer of information. In an experimental study of ERK signaling by single cells exhibiting heterogeneous ERK expression and basal activity, we verify our central theoretical prediction: Negative feedback substantially increases information transfer to the nucleus by preventing a near-flat average response curve and reducing sensitivity to variation in the ERK expression level. Our results reveal an important role for negative feedback mechanisms in protecting information transfer by saturable cell signaling systems from basal activity. Cells must sense extracellular signals and transfer the information contained about their environment reliably to make appropriate decisions. To perform these tasks, cells use signal transduction networks that are subject to various sources of noise. Here, we study the effects on information transfer of two particular types of noise: basal (leaky) network activity and cell-to-cell variability in the componentry of the network. Basal activity is the propensity for activation of the network output in the absence of the signal of interest. We show, using theoretical models of protein kinase signaling, that the combined effect of the two types of noise makes information transfer by such networks highly vulnerable to the loss of negative feedback. In an experimental study of ERK signaling by single cells with heterogeneous ERK expression levels, we verify our theoretical prediction: In the presence of basal network activity, negative feedback substantially increases information transfer to the nucleus by both preventing a near-flat average response curve and reducing sensitivity to variation in substrate expression levels. The interplay between basal network activity, heterogeneity in network componentry, and feedback is thus critical for the effectiveness of protein kinase signaling. Basal activity is widespread in signaling systems under physiological conditions, has phenotypic consequences, and is often raised in disease. Our results reveal an important role for negative feedback mechanisms in protecting the information transfer function of saturable, heterogeneous cell signaling systems from basal activity.
The design and analysis of distributed authentication scheme in VANET

Vehicular ad hoc networks (VANETs) have many new characteristics unlike traditional network, such as centriclessness, mobility and multi-hop transmission, which invalidate conventional key managements. The fast development and successful application of trusted computing technology provide a potential solution to achieve effective authentication and trust evaluation. According to the VANETs with hierarchy organization structure like tank group, a new authentication and trust evaluation framework is proposed based on trusted computing technology, the concepts of “trusted attribute” and “trusted grade” are introduced, and the key management architecture as well as authentication process of mobile node are explained in detail. Moreover, the real applications of the presented framework in tank fight are discussed, and the trust evaluation methods and its argumentations in the presented framework are given.
Whose firm is it anyway? Ownership effects on IPO

The conceptualization and empirical testing of firm performance in Initial Public Offerings (IPOs) continues to intrigue researchers (Daily, Certo, Dalton & Roengpitya 2003). Apart from the monetary implication, for management researchers an IPO is also seen as the first, if not the most important intentional strategic action by a public firm that changes its governance and structure, as thereafter the firm loses its ability to choose new owners in return for the large infusion of cash (Martens 2004; Nelson 2003). In this paper we test the idea that the firm’s ownership structure prior to the IPO and the post-IPO ownership structure impacts IPO performance. Following patterns found in the extent literature, we create three broad ownership classifications: Individual; Corporate; and Venture Capitalist respectively. Using signaling theory we explain why the identity of the owner and the ownership structure may be influential in determining the systematic differences in IPO performance in terms of the price differentials.
Boiling Points of Alcohols - A Comparative QSPR Study

The present report was motivated by recent papers (M. Randic, M. Pompe, D. Mills and S. C. Basak, Variable Connectivity Index as a Tool for Modeling Structure-Property Relationships, Molecules 2004, 9, 1177-1193 ; G. Krenkel, E. Castro and A. A. Toropov, Improved Molecular Descriptors Based on the Optimization of Correlation Weights of Local Graph Invariants, J. Mol. Struct. (THEOCHEM) 2001, 542, 107-113), and curiosity to see whether our CROMRsel modeling procedure leads to the QSPR model comparable to their very good models. We used the CROMRsel multivariate procedure that has been designed to select the best possible model among the set of models obtained for a given number of descriptors, the criterion being the standard error of estimate. The CROMRsel procedure reproduced the Randic-Pompe-Mills-Basak structure-boiling point model and produced a two-descriptor model close to the Krenkel-Castro-Toropov model. The CROMRsel multivariate procedure is found to be competitive to the very good QSPR modeling schemes from the literature.
Almost Optimal Exploration in Multi-Armed Bandits

We study the problem of exploration in stochastic Multi-Armed Bandits. Even in the simplest setting of identifying the best arm, there remains a logarithmic multiplicative gap between the known lower and upper bounds for the number of arm pulls required for the task. This extra logarithmic factor is quite meaningful in nowadays large-scale applications. We present two novel, parameter-free algorithms for identifying the best arm, in two different settings: given a target confidence and given a target budget of arm pulls, for which we prove upper bounds whose gap from the lower bound is only doubly-logarithmic in the problem parameters. We corroborate our theoretical results with experiments demonstrating that our algorithm outperforms the state-of-the-art and scales better as the size of the problem increases.
A general necessary and sufficient optimality conditions for singular control problems

We consider a stochastic control problem where the set of strict (classical) controls is not necessarily convex and the the variable control has two components, the first being absolutely continuous and the second singular. The system is governed by a nonlinear stochastic differential equation, in which the absolutely continuous component of the control enters both the drift and the diffusion coefficients. By introducing a new approach, we establish necessary and sufficient optimality conditions for two models. The first concerns the relaxed-singular controls, who are a pair of processes whose first component is a measure-valued processes. The second is a particular case of the first and relates to strict-singular control problems. These results are given in the form of global stochastic maximum principle by using only the first order expansion and the associated adjoint equation. This improves and generalizes all the previous works on the maximum principle of controlled stochastic differential equations.
Three Mechanisms Underlie KCNQ2/3 Heteromeric Potassium M-Channel Potentiation

The non-inactivating potassium M-current exerts a strong influence on neuronal excitability. The channels responsible for this current are made up of KCNQ subunits, and mutations in most of these produce human pathologies. Notably, in terms of excitation, mutations in either KCNQ2 or KCNQ3 lead to benign neonatal familial convulsions. Although a mere reduction of 25% in KCNQ2/3 function can increase excitability to epileptogenic levels, the potentiation of these subunits has anti-epileptogenic effects. After KCNQ2/3 heteromerization, current levels can augment as much as 10-fold, and we have discovered that there are three processes underlying this potentiation. First, there is an increase in the number of channels inserted in the membrane after heteromerization of the C-terminal region. Second, the N-terminal domain from KCNQ2 exerts a negative influence on the current level. Finally, Ala 315 of KCNQ3, a residue located in the inner vestibule after the selectivity filter, plays a critical role in preventing current flow in KCNQ3 homomeric channels, whereas it is permissive in heteromers in combination with Thr at the equivalent 276 position of KCNQ2.
Workshop on Computational Personality Recognition: Shared Task

In the Workshop on Computational Personality Recognition (Shared Task), we released two datasets, varying in size and genre, annotated with gold standard personality labels. This allowed participants to evaluate features and learning techniques, and even to compare the performances of their systems for personality recognition on a common benchmark. We had 8 participants to the task. In this paper we discuss the results and compare them to previous literature.
Rats Exposed to Isoflurane In Utero during Early Gestation Are Behaviorally Abnormal as Adults

Background:Preclinical evidence suggests that commonly used anesthetic agents induce long-lasting neurobehavioral changes when administered early in life, but there has been virtually no attention to the neurodevelopmental consequences for the fetus of maternal anesthesia. This study tested the hypothesis that fetal rats exposed to isoflurane during maternal anesthesia on gestational day 14, which corresponds to the second trimester in humans, would be behaviorally abnormal as adults. Methods:Timed, pregnant rats were randomly assigned on gestational day 14 to receive 1.4% isoflurane in 100% oxygen (n = 3) or 100% oxygen (n = 2) for 4 h. Beginning at 8 weeks of age, male offspring (N = 12–14 in control and anesthesia groups, respectively) were evaluated for spontaneous locomotor activity, hippocampal-dependent learning and memory (i.e., spontaneous alternations, novel object recognition, and radial arm maze), and anxiety (elevated plus maze). Results:Isoflurane anesthesia was physiologically well tolerated by the dams. Adult rats exposed prenatally to isoflurane were not different than controls on spontaneous locomotor activity, spontaneous alternations, or object recognition memory, but made more open arm entries on the elevated plus maze and took longer and made more errors of omission on the radial arm maze. Conclusions:Rats exposed to isoflurane in utero at a time that corresponds to the second trimester in humans have impaired spatial memory acquisition and reduced anxiety, compared with controls. This suggests the fetal brain may be adversely affected by maternal anesthesia, and raises the possibility that vulnerability to deleterious neurodevelopmental effects of isoflurane begins much earlier in life than previously recognized.
Large Magnetic Anisotropy of a Single Atomic Spin Embedded in a Surface Molecular Network

Magnetic anisotropy allows magnets to maintain their direction of magnetization over time. Using a scanning tunneling microscope to observe spin excitations, we determined the orientation and strength of the anisotropies of individual iron and manganese atoms on a thin layer of copper nitride. The relative intensities of the inelastic tunneling processes are consistent with dipolar interactions, as seen for inelastic neutron scattering. First-principles calculations indicate that the magnetic atoms become incorporated into a polar covalent surface molecular network in the copper nitride. These structures, which provide atom-by-atom accessibility via local probes, have the potential for engineering anisotropies large enough to produce stable magnetization at low temperatures for a single atomic spin.
Mental health inequalities in Wales, UK: Multi–level investigation of the effect of area deprivation

Background Geographical variation in the prevalence of common mental disorders has not been explained adequately. Aims To investigate whether regional mental health differences in Wales would persist after having taken into account the characteristics of individuals and regional social deprivation. Method Data from the 1998 Welsh Health Survey were used. Common mental disorders were assessed with the mental health index included in the Short-Form 36 health survey (SF–36). The data were analysed using a multi–level linear regression model. Results Of the total variance in the mental health index, 1.47% occurred at regional level (95% CI 0.56–2.38). Adjustment for individual characteristics did not explain the between-region variation. A higher area deprivation score was associated with a higher score on the mental health index. Conclusions Mental health differences in Wales are partly explained by the level of regional social deprivation.
Parametric Shape-from-Shading by Radial Basis Functions

We present a new method of shape from shading by using radial basis functions to parameterize the object depth. The radial basis functions are deformed by adjusting their centers, widths, and weights such that the intensity errors are minimized. The initial centers and widths are arranged hierarchically to speed up convergence and to stabilize the solution. Although the smoothness constraint is used, it can be eventually dropped out without causing instabilities in the solution. An important feature of our parametric shape-from-shading method is that it offers a unified framework for integration of multiple sensory information. We show that knowledge about surface depth and/or surface normals anywhere in the image can be easily incorporated into the shape from shading process. It is further demonstrated that even qualitative knowledge can be used in shape from shading to improve 3D reconstruction. Experimental comparisons of our method with several existing ones are made by using both synthetic and real images. Results show that our solution is more accurate than the others.
Early closure of temporary ileostomy—the EASY trial: protocol for a randomised controlled trial

Objective The objective is to evaluate efficiency based on data on morbidity and mortality, health-related quality of life and healthcare-related costs after early reversal of temporary ileostomy after rectal resection for cancer compared with the standard procedure (late reversal). Background Reversal of a temporary ileostomy is generally associated with a low morbidity and mortality. However, ostomy reversal may cause complications requiring reoperation with subsequent major complications, in ranges from 0% to 7–9% and minor complications varying from 4–5% to 30%. Based on studies exploring and describing the time of closure in previous studies which are mostly of low quality, a recent review concluded that closing a temporary stoma within 2 weeks did not seem to be associated with an increase in morbidity and mortality. Design and methods Early closure of temporary ileostomy (EASY), a randomised controlled trial, is a prospective randomised controlled multicentre study which is performed within the framework of the Scandinavian Surgical Outcomes Research Group (http://www.ssorg.net/) and plans to include 200 patients from Danish and Swedish hospitals. The primary end-point of the study is the frequency of complications 0–12 months after surgery (the stoma creation operation). The secondary end-points of the study are (1) comparison of the total costs of the two groups at 6 and 12 months after surgery (stoma creation); (2) comparison of health-related quality of life in the two groups evaluated with the 36-item short-form and European Organization for Research and Treatment of Cancer Quality of Life Questionnaire-CR29/CR30 at 3, 6 and 12 months after surgery (stoma creation); and (3) comparison of disease-specific quality of life in the two groups at 3, 6 and 12 months after surgery (stoma creation). Discussion The aim of the EASY trial is to evaluate the efficiency of early reversal of temporary ileostomy after surgery for rectal cancer versus late reversal. The EASY trial is expected to have a huge impact on patient safety as well as an improvement in patient-reported outcome. Clinical trials identifier NCT01287637.
A sex-adjusted and age-adjusted genome screen for nested alcohol dependence diagnoses

Alcohol dependence is a complex disorder with a substantial genetic contribution to susceptibility. The Collaborative Study on the Genetics of Alcoholism is a multi-site study whose purpose is to detect, localize, and characterize genes contributing to this susceptibility. Previous linkage analyses of the trait of alcohol dependence in Collaborative Study on the Genetics of Alcoholism have used affected sib-pair methods with a dichotomous phenotype definition. In contrast, the analysis in this paper uses a sex-adjusted and age-adjusted multiple threshold liability model. The use of such a model, in that it includes unaffected as well as as affected subjects and in that it utilizes the differential severity of a diagnosis scale, should heuristically be more powerful than a straight affected sib-pair analysis. Three regions of interest are found on chromosome 1 (lod 5.17), chromosome 4 (lod 3.46), and chromosome 8 (lod 4.31). The region on chromosome 1 near the marker D1S532 is in the region previously reported as linked to alcohol dependence and correlated phenotypes in this dataset. The region on chromosome 4 near the alcohol dehydrogenase gene cluster has been reported to be linked to alcohol dependence in other studies, as well as to the alcohol consumption phenotype ‘Maximum Number of Drinks in a 24-Hour Period’ in this dataset. The region on chromosome 8 near the marker D8S1988 is homologous to a section of rat chromosome 5 to which an alcohol consumption phenotype has been linked.
A Novel Synthetic Smoothened Antagonist Transiently Inhibits Pancreatic Adenocarcinoma Xenografts in a Mouse Model

Background Hedgehog (Hh) signaling is over-activated in several solid tumors where it plays a central role in cell growth, stroma recruitment and tumor progression. In the Hh signaling pathway, the Smoothened (SMO) receptor comprises a primary drug target with experimental small molecule SMO antagonists currently being evaluated in clinical trials. Principal Findings Using Shh-Light II (Shh-L2) and alkaline phosphatase (AP) based screening formats on a “focused diversity” library we identified a novel small molecule inhibitor of the Hh pathway, MS-0022 (2-bromo-N-(4-(8-methylimidazo[1,2-a]pyridin-2-yl)phenyl)benzamide). MS-0022 showed effective Hh signaling pathway inhibition at the level of SMO in the low nM range, and Hh pathway inhibition downstream of Suppressor of fused (SUFU) in the low µM range. MS-0022 reduced growth in the tumor cell lines PANC-1, SUIT-2, PC-3 and FEMX in vitro. MS-0022 treatment led to a transient delay of tumor growth that correlated with a reduction of stromal Gli1 levels in SUIT-2 xenografts in vivo. Significance We document the in vitro and in vivo efficacy and bioavailability of a novel small molecule SMO antagonist, MS-0022. Although MS-0022 primarily interferes with Hh signaling at the level of SMO, it also has a downstream inhibitory effect and leads to a stronger reduction of growth in several tumor cell lines when compared to related SMO antagonists.
Forensic Analysis of Instant Messenger Applications on Android Devices

modern day Smartphone's have built in apps like "WhatsApp & Viber" which allow users to exchange instant messages, share videos, audio's and images via Smartphone's instead of relying on their desktop Computers or laptop thereby increasing the portability and convenience for a layman smart phone user. An Instant Messenger (IM) can serve as a very useful yet very dangerous platform for the victim and the suspect to communicate. The increased use of Instant messengers on Android phones has turned to be the goldmine for mobile and computer forensic experts. Traces and Evidence left by applications can be held on Android phones and retrieving those potential evidences with right forensic technique is strongly required. This paper focuses on conducting forensic data analysis of 2 widely used IMs applications on Android phones: WhatsApp and Viber. 5 Android phones were analyzed covering 3 different versions of Android OS: Froyo (2.2), GingerBread (2.3.x) and Ice- Cream Sandwich (4.0.x). The tests and analysis were performed with the aim of determining what data and information can be found on the device's internal memory for instant messengers e.g. chat messaging logs and history, send & received image or video files, etc. Determining the location of data found from FileSystem Extraction of the device was also determined. The experiments and results show that heavy amount of potential evidences and valuable data can be found on Android phones by forensic investigators.
UvA-DARE ( Digital Academic Repository ) Identifying Persons at Risk for PTSD After Trauma with TSQ in The Netherlands

In The Netherlands about 80% of the population experience a traumatic event while about 14% develop post traumatic stress disorder (PTSD). Considering this high prevalence the prevention or early treatment of posttraumatic stress is important from a health as well as costbenefit perspective. The aim of this study was to examine whether we could identify subjects at risk of developing PTSD. We included 100 Dutch victims of different civil traumas that contacted the Victim Support Foundation. The trauma screening questionnaire (TSQ), was used as a screening tool. The results show that a cut-off score of 7 on the TSQ correctly identified most subjects with PTSD. We found a moderate positive correlation between PTSD and the severity of complaints. We also found a significant relationship between the TSQ and depression symptoms. This study indicates that the Dutch version of the TSQ is a useful instrument for identifying future cases of PTSD.
Investigation of the Saturation Pulse Artifact in Non-Enhanced MR Angiography of the Lower Extremity Arteries at 7 Tesla

When performing non-enhanced time-of-flight MR angiography of the lower extremity arteries at 7 T with cardiac triggering, the acquisition time is a crucial consideration. Therefore, in previous studies, saturation RF pulses were applied only every second TR. In the axial source images a slight artifact with an appearance similar to aliasing could be observed. The purpose of this study was to investigate the origin of this artifact. The reason for the artifact is supposed to be related to the two effective TRs during acquisition caused by the sparsely applied saturation RF pulse. Several sequence variants were simulated and implemented within the sequence source code to examine this hypothesis. An adaptation of the excitation flip angles for each TR as well as a correction factor for the k-space data was calculated. Additionally, a different ordering of the k-space data during acquisition was implemented as well as the combination of the latter with the k-space correction factor. The observations from the simulations were verified using both a static and a flow phantom and, finally, in a healthy volunteer using the same measurement setup as in previous volunteer and patient studies. Of all implemented techniques, only the reordering of the k-space was capable of suppressing the artifact almost completely at the cost of creating a ringing artifact. The phantom measurements showed the same results as the simulations and could thus confirm the hypothesis regarding the origin of the artifact. This was additionally verified in the healthy volunteer. The origin of the artifact could be confirmed to be the periodic signal variation caused by two effective TRs during acquisition.