Miracle-dz/UniFAR-FTUs huggingface dataset:
The SET Domain Protein, Set3p, Promotes the Reliable Execution of Cytokinesis in Schizosaccharomyces pombe

In response to perturbation of the cell division machinery fission yeast cells activate regulatory networks that ensure the faithful completion of cytokinesis. For instance, when cells are treated with drugs that impede constriction of the actomyosin ring (low doses of Latrunculin A, for example) these networks ensure that cytokinesis is complete before progression into the subsequent mitosis. Here, we identify three previously uncharacterized genes, hif2, set3, and snt1, whose deletion results in hyper-sensitivity to LatA treatment and in increased rates of cytokinesis failure. Interestingly, these genes are orthologous to TBL1X, MLL5, and NCOR2, human genes that encode components of a histone deacetylase complex with a known role in cytokinesis. Through co-immunoprecipitation experiments, localization studies, and phenotypic analysis of gene deletion mutants, we provide evidence for an orthologous complex in fission yeast. Furthermore, in light of the putative role of the complex in chromatin modification, together with our results demonstrating an increase in Set3p levels upon Latrunculin A treatment, global gene expression profiles were generated. While this analysis demonstrated that the expression of cytokinesis genes was not significantly affected in set3Δ backgrounds, it did reveal defects in the ability of the mutant to regulate genes with roles in the cellular response to stress. Taken together, these findings support the existence of a conserved, multi-protein complex with a role in promoting the successful completion of cytokinesis.
Schema Theory without Expectations for GP and GAs with One-Point Crossover in the Presence of Schema Creation

This paper presents new theoretical results on GA and GP schemata which allow one to predict with a known probability whether the number of instances of a given schema at the next generation is going to be above a given threshold. Unlike previous results, the schema theory presented in this paper does not use expected values and accounts for schema creation.
Theta and alpha EEG frequency interplay in subjects with mild cognitive impairment: evidence from EEG, MRI, and SPECT brain modifications

Background: Temporo-parietal and medial temporal cortex atrophy are associated with mild cognitive impairment (MCI) due to Alzheimer disease (AD) as well as the reduction of regional cerebral blood perfusion in hippocampus. Moreover, the increase of EEG alpha3/alpha2 power ratio has been associated with MCI due to AD and with an increase in theta frequency power in a group of subjects with impaired cerebral perfusion in hippocampus. Methods: Seventy four adult subjects with MCI underwent clinical and neuropsychological evaluation, electroencephalogram (EEG) recording and high resolution 3D magnetic resonance imaging (MRI). Among the patients, a subset of 27 subjects underwent also perfusion single-photon emission computed tomography and hippocampal atrophy evaluation. Alpha3/alpha2 power ratio as well as cortical thickness was computed for each subject. Three MCI groups were detected according to increasing tertile values of alpha3/alpha2 power ratio and difference of cortical thickness among the groups estimated. Results: Higher alpha3/alpha2 power ratio group had wider cortical thinning than other groups, mapped to the Supramarginal and Precuneus bilaterally. Subjects with higher alpha3/alpha2 frequency power ratio showed a constant trend to a lower perfusion than lower alpha3/alpha2 group. Moreover, this group correlates with both a bigger hippocampal atrophy and an increase of theta frequency power. Conclusion: Higher EEG alpha3/alpha2 power ratio was associated with temporo-parietal cortical thinning, hippocampal atrophy and reduction of regional cerebral perfusion in medial temporal cortex. In this group an increase of theta frequency power was detected inMCI subjects. The combination of higher EEG alpha3/alpha2 power ratio, cortical thickness measure and regional cerebral perfusion reveals a complex interplay between EEG cerebral rhythms, structural and functional brain modifications.
The implementation of the Gofer functional programming system

The Gofer system is a functional programming environment for a small, Haskell-like language. Supporting a wide range of dierent machines, including home computers, the system is widely used, both for teaching and research. This report describes the main ideas and techniques used in the implementation of Gofer. This information will be particularly useful for work using Gofer as a platform to explore the use of new language features or primitives. It should also be of interest to those curious to see how the general techniques of functional programming language compilation are adapted to a simple, but practical, implementation.
Harmonic Analysis of oscillators through Standard Numerical Continuation Tools

In this paper, we describe a numerical continuation method that enables harmonic analysis of nonlinear periodic oscillators. This method is formulated as a boundary value problem that can be readily implemented by resorting to a standard continuation package — without modification — such as AUTO, which we used. Our technique works for any kind of oscillator, including electronic, mechanical and biochemical systems. We provide two case studies. The first study concerns itself with the autonomous electronic oscillator known as the Colpitts oscillator, and the second one with a nonlinear damped oscillator, a nonautonomous mechanical oscillator. As shown in the case studies, the proposed technique can aid both the analysis and the design of the oscillators, by following curves for which a certain constraint, related to harmonic analysis, is fulfilled.
Performance of the Hobby-Eberly Telescope and facility instruments

The Hobby-Eberly Telescope (HET) is a revolutionary large telescope of 9.2 meter aperture, located in West Texas at McDonald Observatory. The HET operates with a fixed segmented primary and has a tracker which moves the four-mirror corrector and prime focus instrument package to track the sidereal and non-sidereal motions of objects. The HET has been taking science data for five years, but the image quality and primary mirror stability have been far from specifications. Work over the past two years has improved performance significantly, and demonstrated site-seeing limited images of 0.8 arcsec. , showing that the telescope will meet all specifications. The performance of the HET is discussed in detail. The first phase of HET instrumentation includes three facility instruments: the Low Resolution Spectrograph (LRS), the Medium Resolution Spectrograph (MRS), and High Resolution Spectrograph (HRS). The current status of the instruments is described. Upcoming near infrared capabilities for the LRS and MRS are also discussed.
Relations between evaluations of NIST tests and Lyapunov exponents of sequences generated by the logistic map over integers

We have been studying the characteristics of the sequence generated by the logistic map over integers. In this paper, we examine the relationship of the NIST statistical tests to the Lyapunov exponents of the sequence. Then, we confirm good correlations between a sign of the exponents and both p-value and proportion of the NIST statistical tests. Therefore, we prove that the exponents indicates randomness of sequences generated by the logistic map over integers.
Characterization of Random Linear Network Coding with Application to Broadcast Optimization in Intermittently Connected Networks

We address the problem of optimizing the throughput of network coded traffic in mobile networks operating in challenging environments where connectivity is intermittent and locally available memory space is limited. Random linear network coding (RLNC) is shown to be equivalent (across all possible initial conditions) to a random message selection strategy where nodes are able to exchange buffer occupancy information during contacts. This result creates the premises for a tractable analysis of RLNC packet spread, which is in turn used for enhancing its throughput under broadcast. By exploiting the similarity between channel coding and RLNC in intermittently connected networks, we show that quite surprisingly, network coding, when not used properly, is still significantly underutilizing network resources. We propose an enhanced forwarding protocol that increases considerably the throughput for practical cases, with negligible additional delay.
Transscleral diffusion of ethacrynic acid and sodium fluorescein

Purpose One of the current limitations in developing novel glaucoma drugs that target the trabecular meshwork (TM) is the induced corneal toxicity from eyedrop formulations. To avoid the corneal toxicity, an alternative approach would be to deliver TM drugs through the sclera. To this end, we quantified ex vivo diffusion coefficient of a potential TM drug, ethacrynic acid (ECA), and investigated mechanisms of ECA transport in the sclera. Methods An Ussing-type diffusion apparatus was built to measure the apparent diffusion coefficient of ECA in fresh porcine sclera at 4 °C. To understand mechanisms of ECA transport, we quantified the transscleral transport of a fluorescent tracer, sodium fluorescein (NaF), that has a similar molecular weight but is more hydrophilic compared to ECA. Furthermore, we developed a mathematical model to simulate the transport processes and used it to analyze the experimental data. The model was also used to investigate the dependence of diffusion coefficients on volume fraction of viable cells and the binding of NaF and ECA to scleral tissues. Results The diffusion coefficients of ECA and NaF in the sclera were 48.5±15.1x10-7 cm2/s (n=9) and 5.23±1.93x10-7 cm2/s (n=8), respectively. Both diffusion coefficients were insensitive to cell shrinkage caused by ECA during the diffusion experiments and cell damage caused by the storage of tissues ex vivo before the experiments. Binding of ECA to scleral tissues could not be detected. The apparent maximum binding capacity and the apparent equilibrium dissociation constant for NaF were 80±5 mM and 2.5±0.5 mM (n=3), respectively. Conclusions These data demonstrated that ECA diffusion was minimally hindered by structures in the sclera, presumably due to the lack of cells and binding sites for ECA in the sclera.
Making Design Rules: A Multi-Domain Perspective

This study analyzes the processes whereby organizations develop radical innovations in response to environmental transformations. It explores the changes in organizational structures, practices and business strategies entailed by the implementation of such innovations. From the literature on modularity, we borrow the idea that the evolutionary dynamics of artifacts and organizations are linked by design rules, i.e. a set of principles that allocate functions to components, identify the operating principle of each component and determine the interfaces among modules. Through an in-depth case study of radical innovation in tire manufacturing, we study the joint dynamics of technical and organizational change during the transition from old to new design rules. We argue that technical change and organization adaptation are linked, but that such relationship is mediated and rendered open-ended by the evolution of the underlying bodies of knowledge.
Effect of antenna separation on the capacity of BLAST in correlated channels

As the base station is usually placed above local clutter, the angular spectrum incident on the base is narrow, inducing correlation among base antenna signals, which reduces the capacity of a multiple transmit and receive antenna systems. In this work the general expression for link capacity is derived, when there is correlation among receive antennas and among transmit antennas. It is found that an antenna separation of 4 wavelengths between nearest neighbors in a linear base array of dually polarized antennas allows one to achieve 80% of the capacity attainable in the uncorrelated antenna case.
On the apparent attenuation in the spatial coherence estimated from seismic arrays

Several recent studies have used the coherence of seismic noise between stations to retrieve the phase slowness and attenuation. However, there is considerable debate on the feasibility of attenuation retrieval, its interpretation, and its dependence on the noise directionality and has been the subject of several analytical and numerical studies. In this article, we perform a detailed analysis of the various factors that play a role in the estimation of spatial coherence and attenuation from seismic arrays using data from the Southern California Seismic Network. For instance, certain common preprocessing steps such as averaging neighboring frequencies to improve the estimate are sufficient to introduce attenuation‐like effects. The presence of first‐mode surface Rayleigh wave and P waves in addition to the fundamental mode in Southern California (at frequencies 0.05–0.2 Hz) suggests that the underlying spatial coherence is better modeled as a linear combination of the above wave types. Although this describes the observed coherence better than a simple zeroth‐order Bessel function, the resulting phase cancelations due to the multiple seismic waves can be misconstrued as attenuation if not taken into consideration. Using simulations, we show that due to the slowness inhomogeneity, azimuthally averaging the coherence is not equivalent to homogenizing the medium and instead introduces apparent attenuation in the coherence due to interference. Trying to fit an exponential decay model to this apparent attenuation results in an attenuation coefficient which is similar to previously published results.
Atmospheric Chemistry and Physics Measuring the Antarctic Ozone Hole with the New Ozone Mapping and Profiler Suite (omps)

The new Ozone Mapping and Profiler Suite (OMPS), which launched on the Suomi National Polar-orbiting Partnership satellite in October 2011, gives a detailed view of the development of the Antarctic ozone hole and extends the long series of satellite ozone measurements that go back to the early 1970s. OMPS includes two modules – nadir and limb – to measure profile and total ozone concentrations. The new limb module is designed to measure the vertical profile of ozone between the lowermost stratosphere and the mesosphere. The OMPS observations over Antarctica show excellent agreement with the measurements obtained from independent satellite and ground-based instruments. This validation demonstrates that OMPS data can ably extend the ozone time series over Antarctica in the future. The OMPS observations are used to monitor and characterize the evolution of the 2012 Antarctic ozone hole. While large ozone losses were observed in September 2012, a strong ozone rebound occurred in October and Novem-ber 2012. This ozone rebound is characterized by rapid increases of ozone at mid-stratospheric levels and a splitting of the ozone hole in early November. The 2012 Antarctic ozone hole was the second smallest on record since 1988.
Expectation-based Comprehension: Modeling the Interaction of World Knowledge and Linguistic Experience

ABSTRACT The processing difficulty of each word we encounter in a sentence is affected by both our prior linguistic experience and our general knowledge about the world. Computational models of incremental language processing have, however, been limited in accounting for the influence of world knowledge. We develop an incremental model of language comprehension that constructs—on a word-by-word basis—rich, probabilistic situation model representations. To quantify linguistic processing effort, we adopt Surprisal Theory, which asserts that the processing difficulty incurred by a word is inversely proportional to its expectancy (Hale, 2001; Levy, 2008). In contrast with typical language model implementations of surprisal, the proposed model instantiates a novel comprehension-centric metric of surprisal that reflects the likelihood of the unfolding utterance meaning as established after processing each word. Simulations are presented that demonstrate that linguistic experience and world knowledge are integrated in the model at the level of interpretation and combine in determining online expectations.
Circulating adhesion molecules and arterial stiffness

Summary Aim VCAM-1 and ICAM-1 are two important members of the immunoglobulin gene superfamily of adhesion molecules, and their potential role as biomarkers of diagnosis, severity and prognosis of cardiovascular disease has been investigated in a number of clinical studies. The aim of the present study was to determine the relationship between circulating ICAM-1 and VCAM-1 levels and aortic stiffness in patients referred for echocardiographic examination. Methods Aortic distensibility was determined by echocardiography using systolic and diastolic aortic diameters in 63 consecutive patients referred for echocardiography. Venous samples were collected in the morning after a 12-hour overnight fast, and serum concentrations of ICAM-1 and VCAM-1 were measured using commercial enzyme immunoassay kits. Results Data of a total of 63 participants (mean age 55.6 ± 10.5 years, 31 male) were included in the study. Circulating levels of adhesion molecules were VCAM-1: 12.604 ± 3.904 ng/ml and ICAM-1: 45.417 ± 31.429 ng/ml. We were unable to demonstrate any correlation between indices of aortic stiffness and VCAM-1 and ICAM-1 levels. Conclusion The role of soluble adhesion molecules in cardiovascular disease has not been fully established and clinical studies show inconsistent results. Our results indicate that levels of circulating adhesion molecules cannot be used as markers of aortic stiffness in patients.
360-degree Quantified Self

Wearable devices with a wide range of sensors have contributed to the rise of the Quantified Self movement, where individuals log everything ranging from the number of steps they have taken, to their heart rate, to their sleeping patterns. Sensors do not, however, typically sense the social and ambient environment of the users, such as general life style attributes or information about their social network. This means that the users themselves, and the medical practitioners, privy to the wearable sensor data, only have a narrow view of the individual, limited mainly to certain aspects of their physical condition. In this paper we describe a number of use cases for how social media can be used to complement the check-up data and those from sensors to gain a more holistic view on individuals' health, a perspective we call the 360° Quantified Self. Health-related information can be obtained from sources as diverse as food photo sharing, location check-ins, or profile pictures. Additionally, information from a person's ego network can shed light on the social dimension of wellbeing which is widely acknowledged to be of utmost importance, even though they are currently rarely used for medical diagnosis. We articulate a long-term vision describing the desirable list of technical advances and variety of data to achieve an integrated system encompassing Electronic Health Records (EHR), data from wearable devices, alongside information derived from social media data.
Comparison of haplotype-based tests for detecting gene-environment interactions with rare variants

Dissecting the genetic mechanism underlying a complex disease hinges on discovering gene-environment interactions (GXE). However, detecting GXE is a challenging problem especially when the genetic variants under study are rare. Haplotype-based tests have several advantages over the so-called collapsing tests for detecting rare variants as highlighted in recent literature. Thus, it is of practical interest to compare haplotype-based tests for detecting GXE including the recent ones developed specifically for rare haplotypes. We compare the following methods: haplo.glm, hapassoc, HapReg, Bayesian hierarchical generalized linear model (BhGLM) and logistic Bayesian LASSO (LBL). We simulate data under different types of association scenarios and levels of gene-environment dependence. We find that when the type I error rates are controlled to be the same for all methods, LBL is the most powerful method for detecting GXE. We applied the methods to a lung cancer data set, in particular, in region 15q25.1 as it has been suggested in the literature that it interacts with smoking to affect the lung cancer susceptibility and that it is associated with smoking behavior. LBL and BhGLM were able to detect a rare haplotype-smoking interaction in this region. We also analyzed the sequence data from the Dallas Heart Study, a population-based multi-ethnic study. Specifically, we considered haplotype blocks in the gene ANGPTL4 for association with trait serum triglyceride and used ethnicity as a covariate. Only LBL found interactions of haplotypes with race (Hispanic). Thus, in general, LBL seems to be the best method for detecting GXE among the ones we studied here. Nonetheless, it requires the most computation time.
Multi-borders classification

The number of possible methods of generalizing binary classification to multi-class classification increases exponentially with the number of class labels. Often, the best method of doing so will be highly problem dependent. Here we present classification software in which the partitioning of multi-class classification problems into binary classification problems is specified using a recursive control language.
Screening Rules for Overlapping Group Lasso

Recently, to solve large-scale lasso and group lasso problems, screening rules have been developed, the goal of which is to reduce the problem size by efficiently discarding zero coefficients using simple rules independently of the others. However, screening for overlapping group lasso remains an open challenge because the overlaps between groups make it infeasible to test each group independently. In this paper, we develop screening rules for overlapping group lasso. To address the challenge arising from groups with overlaps, we take into account overlapping groups only if they are inclusive of the group being tested, and then we derive screening rules, adopting the dual polytope projection approach. This strategy allows us to screen each group independently of each other. In our experiments, we demonstrate the efficiency of our screening rules on various datasets.
Network Working Group a Session Initiation Protocol (sip) Event Notification Extension for Collections Draft-ietf-simple-event-list-00

Internet-Drafts are working documents of the Internet Engineering Task Force (IETF), its areas, and its working groups. Note that other groups may also distribute working documents as Internet-Drafts. Internet-Drafts are draft documents valid for a maximum of six months and may be updated, replaced, or obsoleted by other documents at any time. It is inappropriate to use Internet-Drafts as reference material or to cite them other than as "work in progress. " Abstract This document presents an extension to the Session Initiation Protocol (SIP)-Specific Event Notification mechanism for subscribing to a homogenous collection of event packages. Instead of the subscriber sending a SUBSCRIBE for each resource individually, the subscriber can subscribe to an entire collection, and then receive notifications when the state of any of the resources in the collection changes.