Miracle-dz/UniFAR-FTUs huggingface dataset:
Confinement-Induced Glassy Dynamics in a Model for Chromosome Organization.

Recent experiments showing scaling of the intrachromosomal contact probability, P(s)∼s(-1) with the genomic distance s, are interpreted to mean a self-similar fractal-like chromosome organization. However, scaling of P(s) varies across organisms, requiring an explanation. We illustrate dynamical arrest in a highly confined space as a discriminating marker for genome organization, by modeling chromosomes inside a nucleus as a homopolymer confined to a sphere of varying sizes. Brownian dynamics simulations show that the chain dynamics slows down as the polymer volume fraction (ϕ) inside the confinement approaches a critical value ϕ(c). The universal value of ϕ(c)(∞)≈0.44 for a sufficiently long polymer (N≫1) allows us to discuss genome dynamics using ϕ as the sole parameter. Our study shows that the onset of glassy dynamics is the reason for the segregated chromosome organization in humans (N≈3×10(9), ϕ≳ϕ(c)(∞)), whereas chromosomes of budding yeast (N≈10(8), ϕ
A new attack on the KMOVcryptosystem

Abstract. In this paper, we analyze the security of the KMOV publickey cryptosystem. KMOV is based on elliptic curves over the ring Z n where n = pq is the product of two large unknown primes of equal bit-size. We consider KMOV with a public key (n,e) where the exponent esatisﬁes an equation ex−(p+1)(q+1)y = z,with unknown parameters x,y, z. Using Diophantine approximations and lattice reduction techniques,we show that KMOV is insecure when x, y, z are suitably small. 1. IntroductionIn 1991, Koyama, Maurer, Okamoto and Vanstone [7] introduced a newpublic key cryptosystem based on elliptic curves, called KMOV. The KMOVcryptosystemis basedon elliptic curvesoverthe ringZ n wheren = pq isanRSAmodulus, that is, the product of two large unknown primes of equal bit-size.Introduced in 1978 by Rivest, Shamir and Adleman, RSA [9] is one of the mostpopular cryptosystems in research as well as in commercial domain (see [2], [5]). The RSA public key is denoted by (n,e) where n = pq is an RSA modulus ande is an integer satisfying gcd(e,(p−1)(q −1)) = 1. The corresponding privateexponent d is an integer satisfying ed ≡ 1 (mod (p − 1)(q − 1)). Then, thereexists some integer k such that(1) ed−k(p−1)(q −1) = 1.Similarly, the KMOV public key is denoted by (n,e) where n = pq and e isan integer satisfying gcd(e,(p + 1)(q + 1)) = 1. The corresponding privateexponent d is an integer satisfying ed ≡ 1 (mod (p + 1)(q + 1)) which can bereformulated as an equation(2) ed−k(p+1)(q +1) = 1.The security of RSA and KMOV is mainly based on the diﬃculty of factoringthe RSA modulus n. To speed up the encryption or decryption one may tryto use small public or secret decryption exponent. Many important papers
BEST of KAUST at TREC 2011: Building Effective Search in Twitter

In our first-ever appearance at TREC, we explore initial ideas on building an effective search tool over tweet stream as a participation in this year’s microblog track. Among those ideas are tweet expansion with short representation of terms that frequently co-occur with hashtags and URLs, and re-ranking based on statistics that estimate user popularity (using replies and mentions), tweet popularity, URL popularity and user topic authority (using simple user profiles). Initial results show that re-ranking improves the effectiveness while expansion sometimes harms it. Overall, the system built for the task is indeed a great resource for further extensions and experiments.
Using Machine Learning in Trace-driven Energy-Aware Simulations of High-Throughput Computing Systems

When performing a trace-driven simulation of a High Throughput Computing system we are limited to the knowledge which should be available to the system at the current point within the simulation. However, the trace-log contains information we would not be privy to during the simulation. Through the use of Machine Learning we can extract the latent patterns within the trace-log allowing us to accurately predict characteristics of tasks based only on the information we would know. These characteristics will allow us to make better decisions within simulations allowing us to derive better policies for saving energy. We demonstrate that we can accurately predict (up-to 99% accuracy), using oversampling and deep learning, those tasks which will complete while at the same time provide accurate predictions for the task execution time and memory footprint using Random Forest Regression.
Do robotic and non-robotic arm movement training drive motor recovery after stroke by a common neural mechanism? experimental evidence and a computational model

Different dose-matched, upper extremity rehabilitation training techniques, including robotic and non-robotic techniques, can result in similar improvement in movement ability after stroke, suggesting they may elicit a common drive for recovery. Here we report experimental results that support the hypothesis of a common drive, and develop a computational model of a putative neural mechanism for the common drive. We compared weekly motor control recovery during robotic and unassisted movement training techniques after chronic stroke (n = 27), as assessed with quantitative measures of strength, speed, and coordination. The results showed that recovery in both groups followed an exponential time course with a time constant of about 4–5 weeks. Despite the greater range and speed of movement practiced by the robot group, motor recovery was very similar between the groups. The premise of the computational model is that improvements in motor control are caused by improvements in the ability to activate spared portions of the damaged corticospinal system, as learned by a biologically plausible search algorithm. Robot-assisted and unassisted training would in theory equally drive this search process.
Examination of Blood‐Brain Barrier Transferrin Receptor by Confocal Fluorescent Microscopy of Unfixed Isolated Rat Brain Capillaries

Abstract: Isolated rat brain capillaries were analyzed by confocal microscopy. Fluorescent immunoliposomes bearing the OX26 anti‐transferrin receptor monoclonal antibody were synthesized and incubated with freshly isolated unfixed microvessels to visualize binding to luminal and abluminal membranes of the endothelium. Intactness of the endothelial structure was demonstrated by computer‐aided reconstruction of a series of consecutive optical sections. These results indicate that analysis of unfixed brain capillaries by confocal microscopy offers the possibility of assigning the presence of membrane receptors to either the luminal or the basolateral plasma membrane domain.
On Non Commutative G 2 structure

Using an algebraic orbifold method, we present non-commutative aspects of G2 structure of seven dimensional real manifolds. We first develop and solve the non commutativity parameter constraint equations defining G2 manifold algebras. We show that there are eight possible solutions for this extended structure, one of which corresponds to the commutative case. Then we obtain a matrix representation solving such algebras using combinatorial arguments. An application to matrix model of M-theory is discussed. adil.belhaj@uam.es gdelmoral@delta.ft. uam.es
Protection of Baculovirus-Vectors against Complement-Mediated Inactivation by Recombinant Soluble Complement Receptor Type 1

Abstract Baculovirus-based vectors are efficient means for gene transfer into hepatocytes in vitro. However, gene transfer in vivo is hampered by inactivation of baculovirus by the complement system. In this study, we demonstrate protection of baculovirus vectors against complement-mediated inactivation through recombinant soluble complement receptor type 1 (sCR1). Blocking of only the alternative complement pathway by a mutant of sCR1 did not result in baculovirus survival in human serum. The data suggest the use of sCR1 as a potent drug to facilitate baculovirus-mediated gene transfer into hepatocytes in vivo.
When does lower bitrate give higher quality in modern video services?

Due to the difficulties on approximating the human perception with algorithms, increasing the users Quality of Experience (QoE) in modern video services is a challenging task. But more than that, prior to estimating QoE, it is important to know how different types of network impairments actually affect the video quality. This paper takes a closer look at the relation between the network quality of service (QoS) and the video QoE degradation. Using a sophisticated network emulation environment, we benchmark a range of video types and video quality levels under controlled network conditions. Our analysis shows that, along with a number of expected situations come also some counterintuitive QoS-to-QoE conditions. We discuss ways in which a better understanding of the mutual influence between networks and video streams could lead to more efficient utilization of the Internet.
Preconditioning-induced protection of photoreceptors requires activation of the signal-transducing receptor gp130 in photoreceptors

Retinal degenerations are a class of neurodegenerative disorders that ultimately lead to blindness due to the death of retinal photoreceptors. In most cases, death is the result of long-term exposure to environmental, inflammatory, and genetic insults. In age-related macular degeneration, significant vision loss may take up to 70–80 years to develop. The protracted time to develop blindness suggests that retinal neurons have an endogenous mechanism for protection from chronic injury. Previous studies have shown that endogenous protective mechanisms can be induced by preconditioning animals with sublethal bright cyclic light. Such preconditioning can protect photoreceptors from a subsequent damaging insult and is thought to be accomplished through induced expression of protective factors. Some of the factors shown to be associated with protection bind and activate the signal transducing receptor gp130. To determine whether stress-induced endogenous protection of photoreceptors requires gp130, we generated conditional gp130 knockout (KO) mice with the Cre/lox system and used light-preconditioning to induce neuroprotection in these mice. Functional and morphological analyses demonstrated that the retina-specific gp130 KO impaired preconditioning-induced endogenous protection. Photoreceptor-specific gp130 KO mice had reduced protection, although the Müller cell KO mice did not, thus gp130-induced protection was restricted to photoreceptors. Using an animal model of retinitis pigmentosa, we found that the photoreceptor-specific gp130 KO increased sensitivity to genetically induced photoreceptor cell death, demonstrating that gp130 activation in photoreceptors had a general protective role independent of whether stress was caused by light or genetic mutations.
LPS Structure and PhoQ Activity Are Important for Salmonella Typhimurium Virulence in the Gallleria mellonella Infection Model

The larvae of the wax moth, Galleria mellonella , have been used experimentally to host a range of bacterial and fungal pathogens. In this study we evaluated the suitability of G . mellonella as an alternative animal model of Salmonella infection. Using a range of inoculum doses we established that the LD50 of Salmonella Typhimurium strain NCTC 12023 was 3.6 × 103 bacteria per larva. Further, a set of isogenic mutant strains depleted of known virulence factors was tested to identify determinants essential for S . Typhimurium pathogenesis. Mutants depleted of one or both of the type III secretion systems encoded by Salmonella Pathogenicity Islands 1 and 2 showed no virulence defect. In contrast, we observed reduced pathogenic potential of a phoQ mutant indicating an important role for the PhoPQ two-component signal transduction system. Lipopolysaccharide (LPS) structure was also shown to influence Salmonella virulence in G . mellonella . A waaL (rfaL) mutant, which lacks the entire O-antigen (OAg), was virtually avirulent, while a wzz ST/wzz fepE double mutant expressing only a very short OAg was highly attenuated for virulence. Furthermore, shortly after infection both LPS mutant strains showed decreased replication when compared to the wild type in a flow cytometry-based competitive index assay. In this study we successfully established a G . mellonella model of S . Typhimurium infection. By identifying PhoQ and LPS OAg length as key determinants of virulence in the wax moth larvae we proved that there is an overlap between this and other animal model systems, thus confirming that the G . mellonella infection model is suitable for assessing aspects of Salmonella virulence function.
Primary biliary cirrhosis: incidence and predictive factors of cirrhosis development in ursodiol-treated patients.

BACKGROUND & AIMS Ursodeoxycholic acid (UDCA) slows the progression of primary biliary cirrhosis (PBC). However, some UDCA-treated patients escape and progress toward cirrhosis and end-stage disease. This study aimed to assess the incidence of cirrhosis in UDCA-treated patients with PBC and to determine the predictive factors of cirrhosis development under this treatment. METHODS A Markov model was used to describe the progression toward cirrhosis in 183 UDCA-treated patients with PBC. A total of 254 pairs of liver biopsy specimens collected during 655 patient-years were studied. RESULTS The incidence of cirrhosis after 5 years of UDCA treatment was 4%, 12%, and 59% among patients followed-up from stages I, II, and III, respectively. At 10 years, the incidence was 17%, 27%, and 76%, respectively. The median time for developing cirrhosis from stages I, II, and III was 25 years, 20 years, and 4 years, respectively. The independent predictive factors of cirrhosis development were serum bilirubin greater than 17 mumol/L, serum albumin less than 38 g/L, and moderate to severe lymphocytic piecemeal necrosis. CONCLUSIONS This study provides new data about the time course of PBC under UDCA and constitutes a rationale for the design and evaluation of clinical trials aimed to assess the efficacy of drugs associated with UDCA.
Optimal Stabilization Using Lyapunov Measures

Numerical solutions for the optimal feedback stabilization of discrete time dynamical systems is the focus of this technical note. Set-theoretic notion of almost everywhere stability introduced by the Lyapunov measure, weaker than conventional Lyapunov function-based stabilization methods, is used for optimal stabilization. The linear Perron-Frobenius transfer operator is used to pose the optimal stabilization problem as an infinite dimensional linear program. Set-oriented numerical methods are used to obtain the finite dimensional approximation of the linear program. We provide conditions for the existence of stabilizing feedback controls and show the optimal stabilizing feedback control can be obtained as a solution of a finite dimensional linear program. The approach is demonstrated on stabilization of period two orbit in a controlled standard map.
Distributed Geometric-Programming-Based Power Control in Cellular Cognitive Radio Networks

Power control is critical for wireless communications that allow spectrum sharing among secondary users and primary users. In this paper, we derive an optimal distributed power control strategy aiming at the total capacity maximization of secondary network with interference constraints to primary users. Due to the nonconvexity of system utility, geometric programming is introduced to transform nonconvex optimization problems into convex optimization problems. Furthermore, system utility is usually coupled which means each utility depends not only on its local variables but also on the variables of other utilities. We introduce auxiliary variables and extra equality constraints to transfer the coupling in utility to coupling in constraints. The solution of the proposed power control strategy is shown to be globally optimal and leads to excellent performance.
A Semi-Digital Delay Locked Loop with Unlimited Phase Shift Capability and 0 . 08-400 MHz

Delay locked loops are an attractive alternative to VCO based phase locked loops due to their simpler design and inherent stability [1]-[3]. The primary disadvantage of conventional DLLs is their limited phase range, which limits their application to mesochronous environments. This dual DLL architecture combines several techniques to achieve unlimited phase shift, low jitter and large operating range. The desired delay is generated by phase interpolation [2], but the use of tighter spaced 30° edges results in lower noise sensitivity. Owing to its digital control [4] but avoiding the use of a VCO, the DLL can operate with just periodic calibration. Finally, by utilizing self-biasing [3] it achieves large operating range and low jitter.
The pituitary gland and age-dependent regulation of body composition.

CONTEXT The prevalence of obesity is increased in hypopituitarism. In the general population, body mass index (BMI) and waist circumference increase with advancing age. It remains uncertain whether age-related changes in pituitary function contribute to the changes in body composition associated with advancing years. OBJECTIVE Our objective was to study the relationship between pituitary function, body composition, and age in a large cohort of patients with hypopituitarism and a matched reference population. DESIGN, SETTING, AND PARTICIPANTS A total of 3632 GH-deficient adults with hypopituitarism, adequately replaced with all pituitary hormones except for GH, from the prospective KIMS database (Pfizer International Metabolic Database) were included in present analysis. A random sample of the general population (3427 subjects) was used as reference. Patients and controls were grouped by gender in five age cohorts of 10 yr from 28 yr onward. MAIN OUTCOME MEASURES Differences in BMI and waist circumference were evaluated. RESULTS Patients had a significantly higher BMI and waist circumference than controls, with larger differences at younger age. With advancing age, an increase in BMI and waist circumference was seen in controls but was virtually absent in the patients with adult-onset GH deficiency and hypopituitarism. CONCLUSION Patients with hypopituitarism have more excess body fat than age-matched controls, especially in the youngest age groups. The normal increase in fat mass with advancing age is not seen in adult-onset GH-deficient hypopituitarism, suggesting a potential role for the normal pituitary gland as an age-dependent regulator of body composition in adult life.
Regularity Measure and Influence Weight for Analysis and Visualization of Consumer's Attitude

Recently, analysis of massive purchase histories is thought to be effective for marketing science. For successful sales strategies and advertisements, understanding of consumer's attitude (motivation toward purchasing) is important. However, marketers could obtain merely static attitude for the limited consumers using subjective questionnaires. We focus on purchase rhythm (regularity) as one approach to automatically extracting dynamic attitude transition. We propose "regular behavior measure" which quantifies how well each purchase corresponds to the user's own daily habits. It considers non-periodic habits as well as periodic habits using multiple probabilistic models, we consider purchase probability and the number of purchased dates simultaneously. We also define "influence weight" to quantify whether each item is purchased on a fixed day of the week (DoW) or year-month (YM) using Normalized Mutual Information. We analyze actual purchase data to show the effectiveness of our visualization that considers consumer's regularity transitions.
Inheritance in Hierarchical Relational Structures

A brief survey is conducted of the inheritance principle - the conveyance of properties between components within a hierarchical relational structure. The standard form of inheritance is considered, using the subset (is-a) relation and highlighted as an example of downward inheritance. Downward inheritance is extended to specialisation of actions, and cases are presented in which the rule fails.An alternative and less well-known form of inheritance is introduced - upward inheritance. Several examples in which upward inheritance is valid and others in which it is not valid are given, in a treatment highlighting the analogy with downward inheritance. The validity of the rule, in those case in which it operates, is underlined, to distinguish it from induction.A brief account is given of the search for the underlying reasons for the validity of inheritance rules and these are then given. The solution turns out to be due to a hidden or implicit quantifier within the relations that are used. The semantical nature of the problem and of its solution are stressed, emphasising the impossibility of a purely syntactic analysis and solution to the problem. Various points of interest arising from the analysis are listed and discussed.
Parsing the Motion of Single Molecules: A Novel Algorithm for Deconvoluting the Dynamics of Individual Receptors at the Cell Surface

To truly understand signal transduction, we will ultimately need to understand the dynamics and kinetics of individual proteins as they perform their functions in a single cell. Groundbreaking advances in single-molecule biophysics now allow us to follow the motion of many individual proteins on the cell surface with the use of fluorescent probes, such as quantum dots. However, discriminating the directed movement of single molecules from their natural Brownian motion remains a challenge. A recent paper provides a powerful statistical approach for distinguishing periods of directed motion of individual γ-aminobutyric acid (GABA) receptors from periods during which they undergo Brownian motion. This new methodology should help single-molecule researchers determine the dynamics of individual proteins participating in signaling cascades.
Identifying the Span of the Effective Stimulus in Reading. Final Report.

A computer-based Eye-Novement Controlled Display System was developed for the study of perceptual processes in reading. Stu:les were conducted to identify the region from which skilled readers pick up various types of visual information during a fixation while reading. The results indicated that the subjects acquired word length pattern information at least 12 to 15 character positions to the right of the fixation point, and that this information primarily influenced saccade lengths. Specific letter and word shape information was acquired no further than 12 or 13 character positions to the right of the fixation point. It appeared that words were given a semantic interpretation only if they began no more than 5 or 6 character positions to the right of the fixation point. The perceptual span was found to be asymmetric, with the subjects acquiring information no further than 4 character positions to the left of the fixation point, and perhaps less. (Author/RB)
Is Denoising Dead?

Image denoising has been a well studied problem in the field of image processing. Yet researchers continue to focus attention on it to better the current state-of-the-art. Recently proposed methods take different approaches to the problem and yet their denoising performances are comparable. A pertinent question then to ask is whether there is a theoretical limit to denoising performance and, more importantly, are we there yet? As camera manufacturers continue to pack increasing numbers of pixels per unit area, an increase in noise sensitivity manifests itself in the form of a noisier image. We study the performance bounds for the image denoising problem. Our work in this paper estimates a lower bound on the mean squared error of the denoised result and compares the performance of current state-of-the-art denoising methods with this bound. We show that despite the phenomenal recent progress in the quality of denoising algorithms, some room for improvement still remains for a wide class of general images, and at certain signal-to-noise levels. Therefore, image denoising is not dead - yet.