Miracle-dz/UniFAR-FTUs huggingface dataset:
Nasty Viruses, Costly Plasmids, Population Dynamics, and the Conditions for Establishing and Maintaining CRISPR-Mediated Adaptive Immunity in Bacteria

Clustered, Regularly Interspaced Short Palindromic Repeats (CRISPR) abound in the genomes of almost all archaebacteria and nearly half the eubacteria sequenced. Through a genetic interference mechanism, bacteria with CRISPR regions carrying copies of the DNA of previously encountered phage and plasmids abort the replication of phage and plasmids with these sequences. Thus it would seem that protection against infecting phage and plasmids is the selection pressure responsible for establishing and maintaining CRISPR in bacterial populations. But is it? To address this question and provide a framework and hypotheses for the experimental study of the ecology and evolution of CRISPR, I use mathematical models of the population dynamics of CRISPR-encoding bacteria with lytic phage and conjugative plasmids. The results of the numerical (computer simulation) analysis of the properties of these models with parameters in the ranges estimated for Escherichia coli and its phage and conjugative plasmids indicate: (1) In the presence of lytic phage there are broad conditions where bacteria with CRISPR-mediated immunity will have an advantage in competition with non-CRISPR bacteria with otherwise higher Malthusian fitness. (2) These conditions for the existence of CRISPR are narrower when there is envelope resistance to the phage. (3) While there are situations where CRISPR-mediated immunity can provide bacteria an advantage in competition with higher Malthusian fitness bacteria bearing deleterious conjugative plasmids, the conditions for this to obtain are relatively narrow and the intensity of selection favoring CRISPR weak. The parameters of these models can be independently estimated, the assumption behind their construction validated, and the hypotheses generated from the analysis of their properties tested in experimental populations of bacteria with lytic phage and conjugative plasmids. I suggest protocols for estimating these parameters and outline the design of experiments to evaluate the validity of these models and test these hypotheses.
Geodesic Distance Descriptors

The Gromov-Hausdorff (GH) distance is traditionally used for measuring distances between metric spaces. It was adapted for non-rigid shape comparison and matching of isometric surfaces, and is defined as the minimal distortion of embedding one surface into the other, while the optimal correspondence can be described as the map that minimizes this distortion. Solving such a minimization is a hard combinatorial problem that requires precomputation and storing of all pairwise geodesic distances for the matched surfaces. A popular way for compact representation of functions on surfaces is by projecting them into the leading eigenfunctions of the Laplace-Beltrami Operator (LBO). When truncated, the basis of the LBO is known to be the optimal for representing functions with bounded gradient in a min-max sense. Methods such as Spectral-GMDS exploit this idea to simplify and efficiently approximate a minimization related to the GH distance by operating in the truncated spectral domain, and obtain state of the art results for matching of nearly isometric shapes. However, when considering only a specific set of functions on the surface, such as geodesic distances, an optimized basis could be considered as an even better alternative. Moreover, current simplifications of approximating the GH distance introduce errors due to low rank approximations and relaxations of the permutation matrices. Here, we define the geodesic distance basis, which is optimal for compact approximation of geodesic distances, in terms of Frobenius norm. We use the suggested basis to extract the Geodesic Distance Descriptor (GDD), which encodes the geodesic distances information as a linear combination of the basis functions. We then show how these ideas can be used to efficiently and accurately approximate the metric spaces matching problem with almost no loss of information. We incorporate recent methods for efficient approximation of the proposed basis and descriptor without actually computing and storing all geodesic distances. These observations are used to construct a very simple and efficient procedure for shape correspondence. Experimental results show that the GDD improves both accuracy and efficiency of state of the art shape matching procedures.
Branching and path-deviation of positive streamers resulting from statistical photon transport

The branching and change in direction of propagation (path-deviation) of positive streamers in molecular gases such as air likely require a statistical process which perturbs the head of the streamer and produces an asymmetry in its space charge density. In this paper, the mechanisms for path-deviation and branching of atmospheric pressure positive streamer discharges in dry air are numerically investigated from the viewpoint of statistical photon transport and photoionization. A statistical photon transport model, based on randomly selected emitting angles and mean-free-path for absorption, was developed and embedded into a fluid-based plasma transport model. The hybrid model was applied to simulations of positive streamer coaxial discharges in dry air at atmospheric pressure. The results show that secondary streamers, often spatially isolated, are triggered by the random photoionization and interact with the thin space charge layer (SCL) of the primary streamer. This interaction may be partly responsible for path-deviation and streamer branching. The general process consists of random remote photo-electron production which initiates a back-traveling electron avalanche, collision of this secondary avalanche with the primary streamer and the subsequent perturbation to its SCL. When the SCL is deformed from a symmetric to an asymmetric shape, the streamer can experience an abrupt change in the direction of propagation. If the SCL is sufficiently perturbed and essentially broken, local maxima in the SCL can develop into new streamers, leading to streamer branching. During the propagation of positive streamers, this mechanism can take place repetitively in time and space, thus producing multi-level branching and more than two branches within one level.
RYTSI: The Rochester Institute of Technology–Yale Tip‐Tilt Speckle Imager

We have constructed a new speckle imaging system that collects a large number of speckle patterns on the detector area of a large‐format CCD. The system is called the RIT‐Yale Tip‐tilt Speckle Imager (RYTSI) because it uses two galvanometric scanning mirrors to tip and tilt each speckle pattern to a different location on the CCD chip. It therefore solves the bandwidth problem of using CCDs in speckle imaging in a unique way: the mirrors direct speckle patterns across the chip with millisecond accuracy, and the CCD is read out only when the chip is filled with patterns. The instrument was designed to accommodate a variety of detector formats, readout systems, and telescope plate scales; it was initially used at the WIYN Observatory in conjunction with an RIT (Rochester Institute of Technology) 20482 CCD. We present the design of the instrument and a sample of first results, which indicate that the instrument can be expected to recover, with high precision, both astrometric and photometric information for binary and multiple stars.
Diagnostic problem solving using swarm intelligence

Swarm intelligence can be viewed as the emergent collective intelligence of a group of agents, emphasizing direct or indirect local interactions among relatively simple agents. Swarm methods have been widely used for low-dimensional problems such as modeling collective movements in physical space (computer-generated animation, multi-robot teams, etc.), but they have been less studied in higher dimensional problems, mostly in the form of numerical optimization. In this work, we take a step toward applying these kind of systems to diagnostic problem-solving using causal networks. In our model, simple agents move in an abstract high-dimensional space, and based only on local interactions, generate a solution as a result of their collective behavior. Computational experiments show that this model can approximate the best diagnostic solutions (i.e., Bayesian optimal) in reasonably sized problems.
Modeling and Analysis of Recurrent Autoimmune Disease

Many autoimmune diseases are characterized by a pattern of recurrence and remission, in which periods of apparent self-tolerance are punctuated by intervals of recurring autoimmunity. We introduce a newly discovered class of terminally differentiated regulatory T cells, HLA-DR$^+$ T$_{{Reg}}$ cells, into an existing autoimmune disease model. Our newly developed 4-dimensional model exhibits recurrent dynamics, which are preserved in a reduced and rescaled 3-dimensional model as well. Applying dynamical systems theory, we analyze the dynamics underlying this behavior in both the 4-dimensional and 3-dimensional models and further prove that the recurrent behavior (or oscillation) arises due to a Hopf bifurcation or a persistent oscillation rather than from homoclinic orbits. Numerical simulations are conducted to verify the analytical results and identify the recurrent parameter region.
Generation of Site Specific Response Spectrum near Nuclear Power Plants : A Preliminary Case Study at Rawatbhata Station

Nuclear power plant is one of the largest source of producing electricity in India after thermal, hydroelectric and renewable sources of electricity. As of 2013, India has 21 nuclear reactors in operation in 6 nuclear power plants, having an installed capacity of 5780 MW and producing a total of 30, 293 GWh of electricity while six other reactors are under construction and are expected to generate an additional 6,100 MW. After 2011 Fukushima earthquake in Japan, safety of nuclear reactors has become a major concern. For assessing safety it is utmost important to have information on expected earthquake events. In case of lack of sufficient information, artificial ground motions may be generated by using geological features and faults information. This study presents simulation of near field generated ground motions of Rawatbhata nuclear power plant. For this purpose, three faults nearer to the power plant have been selected to the generate ground motions using semi-empirical approach. It is observed that as the source (M) of the earthquake increases, the amplitude of the ground motion, duration and energy content increases. Similarly, the spectral accelerations also increase due to all three active faults.
A New SU UMa-Type Dwarf Nova, QW Serpentis (= TmzV46)

We report on the results of the QW Ser campaign, which has been continued from 2000 to 2003 by the VSNET collaboration team. Four long outbursts and many short ones were caught during this period. Our intensive photometric observations revealed superhumps with a period of 0.07700(±0.00004)d during all four superoutbursts, proving the SU UMa nature of this star. The recurrence cycles of the normal outbursts and the superoutbursts were measured to be ∼ 50 days and 240(±30) days, respectively. The change rate of the superhump period was −5.8 ×10 −5 . The distance and the X-ray luminosity in the range of 0.5–2.4keV are estimated to be 380(±60)pc and logLX =3 1.0 ±0.1ergs −1 . These properties have typical values for an SU UMa-type dwarf nova with this
Vitamin D Status in Central Europe

Little published information is available regarding epidemiological data on vitamin D status in the large geographical region of Central Europe (CE). We searched the journal literature with regard to 25(OH)D concentrations among community-dwelling or healthy people living in CE. 25(OH)D concentrations varied by age, season, study sample size, and methodological approach [i.e., 25(OH)D assay used]. Concentrations of 25(OH)D in CE appeared lower than 30 ng/mL, and the magnitude of hypovitaminosis D was similar to that reported in Western Europe. While most of the studies reviewed were cross-sectional studies, a longitudinal study was also included to obtain information on seasonal variability. The longitudinal study reported wintertime 25(OH)D values close to 21–23 ng/mL for all studied age groups, with a significant increase of 25(OH)D in August reaching 42 ng/mL for those aged 0–9 years, but only 21 ng/mL for the elderly aged 80–89 years. The decrease in 25(OH)D with respect to age was attributed to decreased time spent in the sun and decreased vitamin D production efficiency. Based on the literature review on vitamin D status in the CE populations, it can be concluded that 25(OH)vitamin D levels are on average below the 30 ng/mL level.
Multi-FPGA prototyping environment: Large benchmark generation and signals routing

In multi-FPGA prototyping systems for circuit verification, serialized time-multiplexed I/O technique is used because of the limited number of I/O pins of an FPGA. The verification time depends on the number of inter-FPGA signals to share the same physical wire and be time-multiplexed. In this paper, we propose an adaptation of Pathfinder routing algorithm that minimizes the verification time of multi-FPGA systems by reducing the multiplexing ratio per physical wire. To run real experiments, we propose a large benchmark generation environment and we show that the verification system clock frequency is improved by 17% on average compared with conventional methods.
Authentication system using behavioral biometrics through keystroke dynamics

This work presents a user's authentication system for computational environments based on keystroke dynamics. The methodology proposed is low-cost, non-intrusive and can be applied in areas of monitored access software to increase the level of data security. The algorithm works by monitoring the typing of the user in real time, capturing split times in which the key was pressed and released. Five characteristics are captured in this entry: The ASCII code (American Standard Code for Information Interchange), three splits associated and a duration associated with the key, which would be the time that it remained pressed. From this data it was possible to trace metrics that were able to identify the user in question. Results obtained show a high level of accuracy.
Two-dimensional analytical modeling of fully depleted DMG SOI MOSFET and evidence for diminished SCEs

A two-dimensional (2-D) analytical model for the surface potential variation along the channel in fully depleted dual-material gate silicon-on-insulator MOSFETs is developed to investigate the short-channel effects (SCEs). Our model includes the effects of the source/drain and body doping concentrations, the lengths of the gate metals and their work functions, applied drain and substrate biases, the thickness of the gate and buried oxide and also the silicon thin film. We demonstrate that the surface potential in the channel region exhibits a step function that ensures the screening of the drain potential variation by the gate near the drain resulting in suppressed SCEs like the hot-carrier effect and drain-induced barrier-lowering (DIBL). The model is extended to find an expression for the threshold voltage in the submicrometer regime, which predicts a desirable "rollup" in the threshold voltage with decreasing channel lengths. The accuracy of the results obtained using our analytical model is verified using 2-D numerical simulations.
Relaxation Projections and the Method of Moments

Theory in spatial ecology has to steer a narrow and challenging course between the Scylla of oversimplification and the Charybdis of intractability. Until about 15 years ago, most of theoretical ecology was based on the mean-field paradigm, thus targeting well-mixed ecological systems. Although the underlying assumption of spatial homogeneity is violated for many, if not most, ecological populations and communities in the field, mean-field approaches appeared to be the only way forward. They even took center stage in certain areas, as in epidemiological systems (Bailey 1975; Anderson and May 1991), today recognized as typical examples of ecological processes for which space matters. It was only with the advent and ready availability of modern computer technology that explorations into critical effects of spatial heterogeneities became feasible (Levin 1974, 1976; Weiner and Conte 1981; Weiner 1982; Pacala and Silander 1985; Holsinger and Roughgarden 1985; Pacala 1986; Hogeweg 1988). Today, computer screens and journals abound with images of spatially extended simulations that have convincingly demonstrated that many predictions of classical ecological theory are inappropriate in the presence of spatially structured habitats or short-range ecological interactions. Despite their value as counterexamples to mean-field predictions and their usefulness in exploring the emergence of macroscopic effects resulting from microscopic ecological mechanisms, simulation studies often remain inconclusive. Are the reported phenomena robust under changed ecological parameters? Where, among the noisy dynamics of individual-based and stochastic models, is the ecological signal? How many (usually timeconsuming) spatial simulations have to be run before reliable conclusions can be drawn? These questions remind us that only part of our ecological understanding is based on description: on top of this, we look for mechanistic explanations and for reliable generalizations from observations.
Preterm Delivery Disrupts the Developmental Program of the Cerebellum

A rapid growth in human cerebellar development occurs in the third trimester, which is impeded by preterm delivery. The goal of this study was to characterize the impact of preterm delivery on the developmental program of the human cerebellum. Still born infants, which meant that all development up to that age had taken place in-utero, were age paired with preterm delivery infants, who had survived in an ex-utero environment, which meant that their development had also taken place outside the uterus. The two groups were assessed on quantitative measures that included molecular markers of granule neuron, purkinje neuron and bergmann glia differentiation, as well as the expression of the sonic hedgehog signaling pathway, that is important for cerebellar growth. We report that premature birth and development in an ex-utero environment leads to a significant decrease in the thickness and an increase in the packing density of the cells within the external granular layer and the inner granular layer well, as a reduction in the density of bergmann glial fibres. In addition, this also leads to a reduced expression of sonic hedgehog in the purkinje layer. We conclude that the developmental program of the cerebellum is specifically modified by events that follow preterm delivery.
Modeling I/O Interference in Data Intensive Map-Reduce Applications

Map-Reduce is a popular framework for very large-scale data mining and processing. Recently, some works have attempted to model the behavior of Map-Reduce, but these existing models ignore the non-linearity of disk I/O performance under contention, which is a critical aspect of estimating the performance of data intensive applications. Understanding I/O interference between tasks running on the same node is critical in optimizing task scheduling for improved resource utilization. In this paper, we present a model to estimate the I/O behavior of Map-Reduce applications that can be used to achieve these goals.
Cardiac function in mild primary hyperparathyroidism and the outcome after parathyroidectomy

Objective Primary hyperparathyroidism (PHPT) is associated with cardiovascular morbidity. The extent of cardiovascular abnormalities in patients with mild-asymptomatic disease is unclear. Using sensitive echocardiographic methods, we compared cardiac structure and function in patients with mild PHPT and in healthy controls, and evaluated the changes after parathyroidectomy (PTX). Methods In a prospective case–control design, we studied 51 PHPT patients without any cardiovascular risk factors/diseases and 51 healthy matched controls. Cardiac structure, and systolic and diastolic function were evaluated by echocardiography and Doppler tissue imaging (DTI). Blood pressure (BP) and heart rate were measured. Results We observed no differences in systolic or diastolic function or in cardiac morphology between the PHPT patients and the age-matched healthy controls. The regional peak systolic myocardial velocities (S′) measured with DTI decreased at all sites (P<0.05) after PTX (tricuspid annulus 14.23±1.85 to 13.48±1.79, septal 8.48±0.96 to 7.97±0.85, and lateral 9.61±2.05 to 8.87±1.63 cm/s, part of the mitral annulus). At baseline, systolic BP was higher in patients compared to controls (127.6±17.1 vs 119.6±12.6 mmHg, P<0.05). After PTX, both systolic (127.6±17.1 vs 124.6±16.6 mmHg, P<0.05) and diastolic (80.3±9.6 vs 78.4±8.6 mmHg, P<0.05) BP decreased. Conclusions Our results indicate that patients with PHPT without cardiovascular risk factors have a normal global systolic and diastolic function and cardiac morphology. BP and the systolic velocities were marginally reduced after PTX, but reflected the values of the control group. Our findings warrant further investigation of the clinical and prognostic significance of these possibly disease-related inotropic effects.
Pair Analysis of Field Galaxies from the Red-Sequence Cluster Survey

We study the evolution of the number of close companions of similar luminosities per galaxy (Nc) by choosing a volume-limited subset of the photometric redshift catalog from the Red-Sequence Cluster Survey (RCS-1). The sample contains over 157,000 objects with a moderate redshift range of 0.25 ⩽ z⩽ 0.8 and MRc ⩽ − 20. This is the largest sample used for pair evolution analysis, providing data over nine redshift bins with about 17,500 galaxies in each. After applying incompleteness and projection corrections, Nc shows a clear evolution with redshift. The Nc value for the whole sample grows with redshift as (1 + z)m, where m = 2.83 ± 0.33 in good agreement with N-body simulations in a ΛCDM cosmology. We also separate the sample into two different absolute magnitude bins: -25 ⩽ MRc ⩽ − 21 and -21 < MRc ⩽ − 20, and find that the brighter the absolute magnitude, the smaller the m-value. Furthermore, we study the evolution of the pair fraction for different projected separation bins and different luminosities. We find that the m-value becomes smaller for larger separation, and the pair fraction for the fainter luminosity bin has stronger evolution. We derive the major merger remnant fraction frem = 0.06, which implies that about 6% of galaxies with -25 ⩽ MRc ⩽ − 20 have undergone major mergers since z = 0.8.
Closed-Form Error Analysis of Dual-Hop Relaying Systems over Nakagami-m Fading Channels

In this paper we investigate the end-to-end performance of dual-hop relaying systems over non identical-Nakagami-m fading channels. Our analysis considers channel state information (CSI-) assisted relays that just amplify and retransmit the information signal also known as "non-regenerative" relays. New closed-form expressions for the average bit error probability (ABEP) are derived. The proposed expressions apply to general operating scenarios with distinct Nakagami-m fading parameters and average signal to noise ratios (SNRs) between the hops. When the fading parameter is an odd multiple of one half, the ABEP is expressed in terms of hypergeometric functions. When m takes any real non integer value, the obtained results involve the fourth Appell's hypergeometric function. For an arbitrary fading parameter, an analysis of such a scheme is performed using the well known moment-based approach.