Miracle-dz/UniFAR-FTUs huggingface dataset:
Can the tidal quality factors of terrestrial planets and moons scale as positive powers of the tidal frequency

In geophysics and seismology, it is a common knowledge that the quality factors Q of the mantle and crust materials scale as the tidal frequency to a positive fractional power (Karato 2007, Efroimsky and Lainey 2007). In astronomy, there exists an equally common belief that such rheological models introduce discontinuities into the equations and thus are unrealistic at low frequencies. We demonstrate that, while such models indeed make the conventional expressions for the tidal torque diverge for vanishing frequencies, the emerging infinities reveal not the impossible nature of one or another rheology, but a subtle flaw in the underlying mathematical model of friction. Flawed is the common misassumption that the tidal force and torque are inversely proportional to the quality factor. In reality, they are proportional to the sine of the tidal phase lag, while the inverse quality factor is commonly identified with the tangent of the lag. The sine and tangent of the lag are close everywhere {\it{except in the vicinity of the zero frequency}}. Reinstating of this detail tames the fake infinities and rehabilitates the "impossible" scaling law (which happens to be the actual law the mantles obey). This preprint is a pilot paper. A more comprehensive treatise on tidal torques is to be published (Efroimsky and Williams 2009).
Securing broadcast against dishonest receivers

Consider a sender, Alice, who wants to transmit private messages to two receivers, Bob and Calvin, using unreliable wireless broadcast transmissions and short public feedback from Bob and Calvin. In [1], we assumed that Bob and Calvin provide honest feedback, and characterized the secure capacity region of the private messages under the requirement that Bob and Calvin do not learn each other's message. In this paper, we assume that Bob (or Calvin) may provide dishonest feedback; or even control the input message distributions, as is commonly assumed in cryptography literature. We characterize the capacity region in the case of dishonest adversaries, as well as an achievable region for the case when the adversary has complete control on the distribution of the messages. We also design polynomial time protocols for both cases, that rely on the use of coding techniques to mix and secure the private messages. As a side result, we define an extended notion of semantic security for this problem and using a similar approach to [2], we show the equivalence of different security notions.
The Role of Initiative in Tutorial Dialogue

This work is the first systematic investigation of initiative in human-human tutorial dialogue. We studied initiative management in two dialogue strategies: didactic tutoring and Socratic tutoring. We hypothesized that didactic tutoring would be mostly tutor-initiative while Socratic tutoring would be mixed-initiative, and that more student initiative would lead to more learning (i.e., task success for the tutor). Surprisingly, students had initiative more of the time in the didactic dialogues (21% of the turns) than in the Socratic dialogues (10% of the turns), and there was no direct relationship between student initiative and learning. However, Socratic dialogues were more interactive than didactic dialogues as measured by percentage of tutor utterances that were questions and percentage of words in the dialogue uttered by the student, and interactivity had a positive correlation with learning.
Phasic GABAA‐receptor activation is required to suppress epileptiform activity in the CA3 region of the immature rat hippocampus

Purpose: Despite the consistent observation that γ‐aminobutyric acid A (GABAA) receptors mediate excitatory responses at perinatal stages, the role of the GABAergic system in the generation of neonatal epileptiform activity remains controversial. Therefore, we analyzed whether tonic and phasic GABAergic transmission had differential effects on neuronal excitability during early development.
Soluble guanylyl cyclase activation promotes angiogenesis

Soluble guanylyl cyclase (sGC) is a cGMP-generating enzyme carrying a heme prosthetic group that functions as a nitric oxide (NO) sensor. sGC is present in most cells types, including the vascular endothelium, where its biological functions remain largely unexplored. Herein, we have investigated the role of sGC in angiogenesis and angiogenesis-related properties of endothelial cells (EC). Initially, we determined that sGC was present and enzymatically active in the chicken chorioallantoic membrane (CAM) during the days of maximal angiogenesis. In the CAM, inhibition of endogenous sGC inhibited neovascularization, whereas activation promoted neovessel formation. Using zebrafish as a model for vascular development, we did not detect any effect on vasculogenesis upon sGC blockade, but we did observe an abnormal angiogenic response involving the cranial and intersegmental vessels, as well as the posterior cardinal vein. In vitro, pharmacological activation of sGC or adenovirus-mediated sGC gene transfer promoted EC proliferation and migration, whereas sGC inhibition blocked tube-like network formation. In addition, sGC inhibition blocked the migratory response to vascular EC growth factor. Cells infected with sGC-expressing adenoviruses exhibited increased extracellular signal-regulated kinase 1/2 and p38 MAPK activation that was sensitive to sGC inhibition by 1H-[1,2,4]oxadiazolo[4,3-a]quinoxalin-1-one, suggesting that these mitogen-activated protein kinases are downstream effectors of sGC in EC. A functional role for p38 in cGMP-stimulated migration was demonstrated using SB203580 [4-(4-fluorophenyl)-2-(4-methylsulfinylphenyl)-5-(4-pyridyl)1H-imidazole]; pharmacological inhibition of p38 attenuated BAY 41-2272 [5-cyclopropyl-2-[1-(2-fluoro-benzyl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-pyrimidin-4-ylamine] and sGC overexpression-induced EC mobilization. We conclude that sGC activation promotes the expression of angiogenesis-related properties by EC and that sGC might represent a novel target to modulate neovessel formation.
Coffee consumption and prostate cancer risk and progression in the Health Professionals Follow-up Study.

BACKGROUND Coffee contains many biologically active compounds, including caffeine and phenolic acids, that have potent antioxidant activity and can affect glucose metabolism and sex hormone levels. Because of these biological activities, coffee may be associated with a reduced risk of prostate cancer. METHODS We conducted a prospective analysis of 47,911 men in the Health Professionals Follow-up Study who reported intake of regular and decaffeinated coffee in 1986 and every 4 years thereafter. From 1986 to 2006, 5035 patients with prostate cancer were identified, including 642 patients with lethal prostate cancers, defined as fatal or metastatic. We used Cox proportional hazards models to assess the association between coffee and prostate cancer, adjusting for potential confounding by smoking, obesity, and other variables. All P values were from two-sided tests. RESULTS The average intake of coffee in 1986 was 1.9 cups per day. Men who consumed six or more cups per day had a lower adjusted relative risk for overall prostate cancer compared with nondrinkers (RR = 0.82, 95% confidence interval [CI] = 0.68 to 0.98, P(trend) = . 10). The association was stronger for lethal prostate cancer (consumers of more than six cups of coffee per day: RR = 0.40, 95% CI = 0.22 to 0.75, P(trend) = . 03). Coffee consumption was not associated with the risk of nonadvanced or low-grade cancers and was only weakly inversely associated with high-grade cancer. The inverse association with lethal cancer was similar for regular and decaffeinated coffee (each one cup per day increment: RR = 0.94, 95% CI = 0.88 to 1.01, P = .08 for regular coffee and RR = 0.91, 95% CI = 0.83 to 1.00, P = .05 for decaffeinated coffee). The age-adjusted incidence rates for men who had the highest (≥6 cups per day) and lowest (no coffee) coffee consumption were 425 and 519 total prostate cancers, respectively, per 100 000 person-years and 34 and 79 lethal prostate cancers, respectively, per 100 000 person-years. CONCLUSIONS We observed a strong inverse association between coffee consumption and risk of lethal prostate cancer. The association appears to be related to non-caffeine components of coffee.
Chapter 1 Path Formation in Human Contact Networks

The Pocket Switched Network (PSN) is a radical proposal to take advantage of short-range connectivity afforded by human face-to-face contacts, and create longer paths by having intermediate nodes ferry data on behalf of the sender. The Pocket Switched Network creates paths over time using transient social contacts. This chapter explores the achievable connectivity properties of this dynamically changing mileu, and gives a community-based heuristic to find efficient routes. We first employ empirical traces to examine the effect of the human contact process on data delivery. Contacts between a few node pairs are found to occur too frequently, leading to inadequate mixing of data, while the majority of contacts occur rarely, but are essential for global connectivity. We then examine all successful paths found by flooding and show that though delivery times vary widely, randomly sampling a small number of paths between each source and destination is sufficient to yield a delivery time distribution close to that of flooding over all paths. Thus, despite the apparent fragility implied by the reliance on rare edges, the rate at which the network can deliver data is remarkably robust to path failures. We then give a natural heuristic that finds routes by exploiting the latent social structure. Previous methods relied on building and updating routing tables to cope with dynamic network conditions. This has been shown to be cost ineffective due to the partial capture of transient network behavior. A more promising approach would be to capture the intrinsic characteristics of such networks and utilize them for routing decsions. We design and evaluate BUBBLE, a novel social-based forwarding algorithm, that utilizes the centrality and community metrics to enhance delivery performance. We empirically show that BUBBLE can efficiently identify good paths using several real mobility datasets. Nishanth Sastry Computer Laboratory, University of Cambridge, 15 JJ Thomson Avenue, Cambridge, CB3 0FD, United Kingdom. e-mail: Firstname.Lastname@cl.cam. ac.uk Pan Hui Deutsche Telekom Laboratories, Ernst-Reuter-Platz 7, 10587 Berlin, Germany. e-mail: pan.hui@telekom.de
In vitro and in vivo activity of ciprofloxacin against enterococci isolated from patients with infective endocarditis

In vitro activity of ciprofloxacin against 27 strains of enterococci was inoculum dependent. Using inocula of 10(5) to 10(6) or 10(7) to 10(8) CFU of enterococci per ml, the MICs for 50 and 90% of strains tested increased from 1 to greater than or equal to 128 micrograms of ciprofloxacin per ml with the higher inoculum compared with the lower inoculum. The MBC for 50% of strains tested increased from 2 to greater than 128 micrograms/ml and the MBC for 90% of strains tested increased from 8 to greater than 128 micrograms of ciprofloxacin per ml with the lower and higher inocula, respectively. The combination of penicillin-gentamicin was more effective in vitro than the combination of ciprofloxacin-gentamicin against the low or high inoculum of enterococci. Using two strains of enterococci, we studied the efficacy of ciprofloxacin in the treatment of enterococcal experimental endocarditis in rabbits. Ciprofloxacin used alone or combined with gentamicin was significantly less effective (P less than 0.01) than procaine penicillin alone or procaine penicillin combined with gentamicin for the treatment of enterococcal experimental endocarditis. The combination of ciprofloxacin-procaine penicillin was not a more effective therapy than procaine penicillin alone.
Positivity conditions of Lyapunov functions for systems with slope restricted nonlinearities

This paper considers absolute stability for Lur'e systems consisting of the interconnection of a linear plant with a nonlinear feedback. The nonlinearity is assumed to be both sector bounded and slope restricted. Stability of this system is determined using a Lyapunov function with a quadratic term on both the states and the nonlinearity. The main result of this paper is to relax the positivity conditions that have been imposed for such Lyapunov functions. This allows Lyapunov functions to be constructed without a positive definite quadratic matrix and whose scalars of the Lur'e term are not sign-definite. We also show that previous results can be simplified to the case of the quadratic form with Lur'e term. The benefits of considering such a Lyapunov function for stability analysis are shown both for the global case and for the local case.
Optimal Algorithms for L1-subspace Signal Processing

We describe ways to define and calculate L1-norm signal subspaces that are less sensitive to outlying data than L2-calculated subspaces. We start with the computation of the L1 maximum-projection principal component of a data matrix containing N signal samples of dimension D. We show that while the general problem is formally NP-hard in asymptotically large N, D, the case of engineering interest of fixed dimension D and asymptotically large sample size N is not. In particular, for the case where the sample size is less than the fixed dimension , we present in explicit form an optimal algorithm of computational cost 2N. For the case N ≥ D, we present an optimal algorithm of complexity O(ND). We generalize to multiple L1-max-projection components and present an explicit optimal L1 subspace calculation algorithm of complexity O(NDK-K+1) where K is the desired number of L1 principal components (subspace rank). We conclude with illustrations of L1-subspace signal processing in the fields of data dimensionality reduction, direction-of-arrival estimation, and image conditioning/restoration.
Verb Sense and Verb Subcategorization Probabilities

The probabili stic relation between verbs and their arguments plays an important role in psychological theories of human language processing. For example, Ford, Bresnan and Kaplan (1982) proposed that verbs li ke position have two lexical forms: a more preferred form that subcategorizes for three arguments (SUBJ, OBJ, PCOMP) and a less preferred form that subcategorizes for two arguments (SUBJ, OBJ). Many recent psychological experiments suggest that humans use these kinds of verb-argument preferences as an essential part of the process of sentence interpretation. (Cli fton et al. 1984, Ferreira & McClure 1997, Garnsey et al. 1997, MacDonald 1994, Mitchell & Holmes 1985, Boland et al. 1990, Trueswell et al. 1993). It is not completely understood how these preferences are realized, but one possible model proposes that each lexical entry for a verb expresses a conditional probability for each potential subcategorization frame (Jurafsky 1996, Narayanan and Jurafsky 1998).
Evolutionary dynamics in set structured populations

Evolutionary dynamics are strongly affected by population structure. The outcome of an evolutionary process in a well-mixed population can be very different from that in a structured population. We introduce a powerful method to study dynamical population structure: evolutionary set theory. The individuals of a population are distributed over sets. Individuals interact with others who are in the same set. Any 2 individuals can have several sets in common. Some sets can be empty, whereas others have many members. Interactions occur in terms of an evolutionary game. The payoff of the game is interpreted as fitness. Both the strategy and the set memberships change under evolutionary updating. Therefore, the population structure itself is a consequence of evolutionary dynamics. We construct a general mathematical approach for studying any evolutionary game in set structured populations. As a particular example, we study the evolution of cooperation and derive precise conditions for cooperators to be selected over defectors.
Tails of the City: Caudal Autotomy in the Tropical Lizard, Anolis cristatellus, in Urban and Natural Areas of Puerto Rico

Abstract Urbanization creates drastic changes in habitat and presents considerable challenges and new sources of predation to urban-dwelling herpetofauna. Research on lizards has documented increased rates of mortality in urban areas due to generalist predators such as raccoons, feral cats, and domestic animals. Caudal autotomy (self-amputation of the tail) is a defense mechanism used to escape predation in a wide range and large number of lizard species. The tail is autotomized to evade capture, and in most species with autotomy, the tail is regenerated partially or completely. Caudal autotomy can be used as an indirect measure of predation environment; however, few prior studies have used lizard caudal autotomy to measure the predation environment of urban areas. We compared caudal autotomy rates in the Puerto Rican crested anole, Anolis cristatellus, between urban and natural sites in four Puerto Rican municipalities. Across all municipalities, we found the frequency of caudal autotomy and regeneration to be consistently, significantly higher in urban than in natural areas. Our findings suggest that differences exist in the predation regime experienced by lizards in urban and natural habitats across the island of Puerto Rico. At this time, however, we are not able to identify the specific nature of the difference in predation regime between sites. The difference in autotomy rate that we found may be driven by higher predation pressure in urban areas, differences in the predator assemblage between sites, or simply lower predator efficiency in urban habitats.
ICGA-PSO-ELM Approach for Accurate Multiclass Cancer Classification Resulting in Reduced Gene Sets in Which Genes Encoding Secreted Proteins Are Highly Represented

A combination of Integer-Coded Genetic Algorithm (ICGA) and Particle Swarm Optimization (PSO), coupled with the neural-network-based Extreme Learning Machine (ELM), is used for gene selection and cancer classification. ICGA is used with PSO-ELM to select an optimal set of genes, which is then used to build a classifier to develop an algorithm (ICGA_PSO_ELM) that can handle sparse data and sample imbalance. We evaluate the performance of ICGA-PSO-ELM and compare our results with existing methods in the literature. An investigation into the functions of the selected genes, using a systems biology approach, revealed that many of the identified genes are involved in cell signaling and proliferation. An analysis of these gene sets shows a larger representation of genes that encode secreted proteins than found in randomly selected gene sets. Secreted proteins constitute a major means by which cells interact with their surroundings. Mounting biological evidence has identified the tumor microenvironment as a critical factor that determines tumor survival and growth. Thus, the genes identified by this study that encode secreted proteins might provide important insights to the nature of the critical biological features in the microenvironment of each tumor type that allow these cells to thrive and proliferate.
Vocal copying of individually distinctive signature whistles in bottlenose dolphins

Vocal learning is relatively common in birds but less so in mammals. Sexual selection and individual or group recognition have been identified as major forces in its evolution. While important in the development of vocal displays, vocal learning also allows signal copying in social interactions. Such copying can function in addressing or labelling selected conspecifics. Most examples of addressing in non-humans come from bird song, where matching occurs in an aggressive context. However, in other animals, addressing with learned signals is very much an affiliative signal. We studied the function of vocal copying in a mammal that shows vocal learning as well as complex cognitive and social behaviour, the bottlenose dolphin (Tursiops truncatus). Copying occurred almost exclusively between close associates such as mother–calf pairs and male alliances during separation and was not followed by aggression. All copies were clearly recognizable as such because copiers consistently modified some acoustic parameters of a signal when copying it. We found no evidence for the use of copying in aggression or deception. This use of vocal copying is similar to its use in human language, where the maintenance of social bonds appears to be more important than the immediate defence of resources.
Efficient Strategy to Generate a Vectored Duck Enteritis Virus Delivering Envelope of Duck Tembusu Virus

Duck Tembusu virus (DTMUV) is a recently emerging pathogenic flavivirus that has resulted in a huge economic loss in the duck industry. However, no vaccine is currently available to control this pathogen. Consequently, a practical strategy to construct a vaccine against this pathogen should be determined. In this study, duck enteritis virus (DEV) was examined as a candidate vaccine vector to deliver the envelope (E) of DTMUV. A modified mini-F vector was inserted into the SORF3 and US2 gene junctions of the attenuated DEV vaccine strain C-KCE genome to generate an infectious bacterial artificial chromosome (BAC) of C-KCE (vBAC-C-KCE). The envelope (E) gene of DTMUV was inserted into the C-KCE genome through the mating-assisted genetically integrated cloning (MAGIC) strategy, resulting in the recombinant vector, pBAC-C-KCE-E. A bivalent vaccine C-KCE-E was generated by eliminating the BAC backbone. Immunofluorescence and western blot analysis results indicated that the E proteins were vigorously expressed in C-KCE-E-infected chicken embryo fibroblasts (CEFs). Duck experiments demonstrated that the insertion of the E gene did not alter the protective efficacy of C-KCE. Moreover, C-KCE-E-immunized ducks induced neutralization antibodies against DTMUV. These results demonstrated, for the first time, that recombinant C-KCE-E can serve as a potential bivalent vaccine against DEV and DTMUV.
On the role of NOS1 ex1f‐VNTR in ADHD—allelic, subgroup, and meta‐analysis

Attention deficit/ hyperactivity disorder (ADHD) is a heritable neurodevelopmental disorder featuring complex genetics with common and rare variants contributing to disease risk. In a high proportion of cases, ADHD does not remit during adolescence but persists into adulthood. Several studies suggest that NOS1, encoding nitric oxide synthase I, producing the gaseous neurotransmitter NO, is a candidate gene for (adult) ADHD. We here extended our analysis by increasing the original sample, adding two further samples from Norway and Spain, and conducted subgroup and co‐morbidity analysis. Our previous finding held true in the extended sample, and also meta‐analysis demonstrated an association of NOS1 ex1f‐VNTR short alleles with adult ADHD (aADHD). Association was restricted to females, as was the case in the discovery sample. Subgroup analysis on the single allele level suggested that the 21‐repeat allele caused the association. Regarding subgroups, we found that NOS1 was associated with the hyperactive/impulsive ADHD subtype, but not to pure inattention. In terms of comorbidity, major depression, anxiety disorders, cluster C personality disorders and migraine were associated with short repeats, in particular the 21‐repeat allele. Also, short allele carriers had significantly lower IQ. Finally, we again demonstrated an influence of the repeat on gene expression in human post‐mortem brain samples. These data validate the role of NOS‐I in hyperactive/impulsive phenotypes and call for further studies into the neurobiological underpinnings of this association. © 2015 Wiley Periodicals, Inc.