Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimization of Terminal-Restriction Fragment Length Polymorphism Analysis for Complex Marine Bacterioplankton Communities and Comparison with Denaturing Gradient Gel Electrophoresis

ABSTRACT The potential of terminal-restriction fragment length polymorphism (T-RFLP) and the detection of operational taxonomic units (OTUs) by capillary electrophoresis (CE) to characterize marine bacterioplankton communities was compared with that of denaturing gradient gel electrophoresis (DGGE). A protocol has been developed to optimize the separation and detection of OTUs between 20 and 1,632 bp by using CE and laser-induced fluorescence detection. Additionally, we compared T-RFLP fingerprinting to DGGE optimized for detection of less abundant OTUs. Similar results were obtained with both fingerprinting techniques, although the T-RFLP approach and CE detection of OTUs was more sensitive, as indicated by the higher number of OTUs detected. We tested the T-RFLP fingerprinting technique on complex marine bacterial communities by using the 16S rRNA gene and 16S rRNA as templates for PCR. Samples from the Northern and Middle Adriatic Sea and from the South and North Aegean Sea were compared. Distinct clusters were identifiable for different sampling sites. Thus, this technique is useful for rapid evaluation of the biogeographical distribution and relationships of bacterioplankton communities.
Conditioning effect of transcranial magnetic stimulation evoking motor‐evoked potential on V‐wave response

The aim of this study was to examine the collision responsible for the volitional V‐wave evoked by supramaximal electrical stimulation of the motor nerve during voluntary contraction. V‐wave was conditioned by transcranial magnetic stimulation (TMS) over the motor cortex at several inter‐stimuli intervals (ISI) during weak voluntary plantar flexions (n = 10) and at rest for flexor carpi radialis muscle (FCR; n = 6). Conditioning stimulations were induced by TMS with intensity eliciting maximal motor‐evoked potential (MEPmax). ISIs used were ranging from −20 to +20 msec depending on muscles tested. The results showed that, for triceps surae muscles, conditioning TMS increased the V‐wave amplitude (~ +250%) and the associated mechanical response (~ +30%) during weak voluntary plantar flexion (10% of the maximal voluntary contraction ‐MVC) for ISIs ranging from +6 to +18 msec. Similar effect was observed at rest for the FCR with ISI ranging from +6 to +12 msec. When the level of force was increased from 10 to 50% MVC or the conditioning TMS intensity was reduced to elicit responses of 50% of MEPmax, a significant decrease in the conditioned V‐wave amplitude was observed for the triceps surae muscles, linearly correlated to the changes in MEP amplitude. The slope of this correlation, as well as the electro‐mechanical efficiency, was closed to the identity line, indicating that V‐wave impact at muscle level seems to be similar to the impact of cortical stimulation. All these results suggest that change in V‐wave amplitude is a great index to reflect changes in cortical neural drive addressed to spinal motoneurons.
Planar Graph Isomorphism is in Log-Space

Graph Isomorphism is the prime example of a computational problem with a wide difference between the best known lower and upper bounds on its complexity. There is a significant gap between extant lower and upper bounds for planar graphs as well. We bridge the gap for this natural and important special case by presenting an upper bound that matches the known log-space hardness [JKMT03]. In fact, we show the formally stronger result that planar graph canonization is in log-space. This improves the previously known upper bound of AC1 [MR91]. Our algorithm first constructs the biconnected component tree of a connected planar graph and then refines each biconnected component into a triconnected component tree. The next step is to log-space reduce the biconnected planar graph isomorphism and canonization problems to those for 3-connected planar graphs, which are known to be in log-space by [DLN08]. This is achieved by using the above decomposition, and by making significant modifications to Lindell’s algorithm for tree canonization, along with changes in the space complexity analysis. The reduction from the connected case to the biconnected case requires further new ideas, including a non-trivial case analysis and a group theoretic lemma to bound the number of automorphisms of a colored 3-connected planar graph. This lemma is crucial for the reduction to work in log-space.
Construction of a Full-length Ca2+-sensitive Adenylyl Cyclase/Aequorin Chimera*

Ca2+-sensitive adenylyl cyclases are key integrators of Ca2+ and cAMP signaling. To selectively probe dynamic changes in [Ca2+] i at the plasma membrane where adenylyl cyclases reside, a full-length, Ca2+-inhibitable type VI adenylyl cyclase/aequorin chimera has been constructed by a two-stage polymerase chain reaction method. The expressed adenylyl cyclase/aequorin chimera was appropriately localized to the plasma membrane, as judged by biochemical fractionation and functional analysis. The chimera retained full adenylyl cyclase activity and sensitivity to inhibition by physiological [Ca2+] i elevation. The aequorin portion of the chimeric construct was also capable of measuring changes in [Ca2+] both in vitro and in vivo. When the plasma membrane-tagged aequorin and cytosolic aequorin were compared in their measurement of [Ca2+] i , they showed contrasting sensitivities depending on whether the [Ca2+] i originated from internal stores or capacitative entry. This is the first full-length enzyme-aequorin chimera that retains the full biological properties of both aequorin and a Ca2+-sensitive adenylyl cyclase. This novel chimeric Ca2+ sensor provides the unique ability to directly report the dynamics of [Ca2+] i that regulates this Ca2+-sensitive enzyme under a variety of physiological conditions. Since this chimera is localized to the plasma membrane, it can also be used to assess local changes in [Ca2+] i at the plasma membrane as distinct from global changes in [Ca2+] i within the cytosol.
Explicit, Minimum-Delay Space-Time Codes Achieving The Diversity-Multiplexing Gain Tradeo

In the recent landmark paper of Zheng and Tse it is shown that there exists a fundamental tradeoff between diversity gain and multiplexing gain, referred to as the DiversityMultiplexing gain(D-MG) tradeoff. The present paper presents the first explicit construction of space-time (ST) codes for arbitrary number of transmit antennas that achieve the D-MG tradeoff. It is shown here that ST codes with non-vanishing determinant (NVD) constructed from cyclicdivision-algebras (CDA), are optimal under the D-MG tradeoff for any number nt, nr of transmit and receive antennas and with minimum delay T = nt. The full result shows optimality of a wider class of constructions. CDA-based ST codes with NVD have previously been constructed for restricted values of nt. A unified construction of D-MG optimal CDA-based ST codes with NVD is given here, for any number nt of transmit antennas. The results also establish that for any nt, nr, the D-MG tradeoff at T = nt is the same as that forT ≥ nt + nr − 1. In addition, we also show that the CDA based ST constructions achieve the optimal D-MG tradeoff of a wider class of channels.
Life-Cycle Impacts of Inland Northwest and Northeast/North Central Forest Resources

Determining the life-cycle inventory (LCI) and impact of forest harvest, regeneration, and growth is necessary in conducting a life-cycle assessment of wood products. This publication provides quantitative assessments of the economic and environmental impacts of forest management activities covering portions of the Inland Northwest (INW), including Montana, Idaho, and eastern Washington, and of the Northeastern and North Central (NE/NC) forests from Minnesota to Maine and south as far as Missouri, West Virginia, and Pennsylvania. The management scenarios provide the inputs needed to develop an LCI on all the inputs and outputs for wood products as impacted by forest treatments and the harvesting of logs in the region. Productive timberlands were grouped according to forest type, productivity, management intensity, and ownership into three broad forest types in the west: cold, dry, and moist; and four in the east: spruce/fir, northern hardwoods, oak/hickory, and aspen/birch. Spruce/fir represented the feedstock to softwood lumber and a composite of northern hardwoods and oak/hickory the feedstock to hardwood lumber. Simulations used the US Forest Service Forest Vegetation Simulator to estimate standing and harvested biomass and log volumes passed on as resources to the manufacturing segments for lumber, plywood, or oriented strandboard. The combinations of ownership, management intensity, and forest type were stratified and averaged to produce a single estimate of yield and the corresponding harvesting impacts. Both historic harvest rates and increased management intensity scenarios were simulated for each region. In the INW, the shift to the higher intensity scenario increased the average production of merchantable volume at harvest to 249 - 399 m 3 /ha when averaged across the forested land in each ownership class. For the NE/NC region, the production of merchantable volume averaged 263 m 3 /ha for softwood and 328 m 3 /ha for hardwood forests with an insignificant volume response from shifting land into more intensive management. Average growth varied widely for INW forest categories from a low on federal land for the base case of 0.7 - 6.7 m 3 /haha·yr for moist state and private land under the intensive management alternative. Current condition estimates of softwood log and bark carbon exported for mill processing in the INW and NE/NC regions were 751 and 988 kg/ha·yr, respectively.
ESTIMATION OF INUNDATED AREAS DURING THE 2011 FLOODS IN THE CHAO PHRAYA RIVER BASIN USING SAR AND OPTICAL SATELLITE IMAGERY

In 2011, massive flooding and inundation in the Chao Phraya River basin, in Thailand, caused serious damage to various activities for a prolonged period of time. Although snapshot images of the inundated area are available, detailed information including temporal changes of the inundated areas and the relationship with meteorological and hydrological conditions are not well documented, particularly for the middle and upper sections of the basin. Therefore, we conducted an analysis using two types of satellite data, HJ-1A and Envisat, to better understand behavior of the large-scale inundation occurred in 2011, focusing on the middle section of the Chao Phraya River basin. In the analysis, water surface in selected domains was extracted using the NDWI value calculated from HJ-1A data. The threshold value of the Envisat ASAR image was then adjusted so that the inundated area estimated from Envisat gives the closest possible match with that estimated from HJ-1A. Finally, the inundated area was estimated for the whole study domain based on the same threshold value from the Envisat data. Results indicated that the inundated area began to extend along the Yom and Nan rivers in early August and continued to spread down to the Nakhon Sawan city area until October. A significant increase in inundated areas occurred between Sep. 2 and Sep. 13, during which higher rainfall intensity was observed. Even after the water level in rivers receded below the bank-full elevation, large areas were left inundated along rivers, particularly over low-lying marsh and paddy fields. In addition, several areas located far from rivers were also inundated, which was likely a consequence of water ponding in paddy fields.
Towards Minimizing Disappointment in Repeated Games

We consider the problem of learning in repeated games against arbitrary associates. Specifically, we study the ability of expert algorithms to quickly learn effective strategies in repeated games, towards the ultimate goal of learning near-optimal behavior against any arbitrary associate within only a handful of interactions. Our contribution is three-fold. First, we advocate a new metric, called disappointment, for evaluating expert algorithms in repeated games. Unlike minimizing traditional notions of regret, minimizing disappointment in repeated games is equivalent to maximizing payoffs. Unfortunately, eliminating disappointment is impossible to guarantee in general. However, it is possible for an expert algorithm to quickly achieve low disappointment against many known classes of algorithms in many games. Second, we show that popular existing expert algorithms often fail to achieve low disappointment against a variety of associates, particularly in early rounds of the game. Finally, we describe a new meta-algorithm that can be applied to existing expert algorithms to substantially reduce disappointment in many two-player repeated games when associates follow various static, reinforcement learning, and expert algorithms.
Health-Related Social Control and Risk Perceptions in Emerging Adults

Health behaviors decline during emerging adulthood, and social network members may attempt to influence or regulate emerging adults’ health behaviors using various health-related social control strategies. A paucity of research examines social control in emerging adults or moderators of the social control process. This study examined health risk perceptions as a moderator of the relationship between social control and affective and behavioral responses to control in 275 emerging adults. Moderated mediation analyses indicated that for those individuals with higher perceived severity of developing future health conditions, the links between positive control, more positive emotions, and more behavior change became weaker but the links between negative control, fewer positive emotions, and less behavior change became stronger. Understanding emerging adults’ health risk perceptions may be beneficial in health promotion for this at-risk developmental group.
DEFENDER: Detecting and Forecasting Epidemics Using Novel Data-Analytics for Enhanced Response

In recent years social and news media have increasingly been used to explain patterns in disease activity and progression. Social media data, principally from the Twitter network, has been shown to correlate well with official disease case counts. This fact has been exploited to provide advance warning of outbreak detection, forecasting of disease levels and the ability to predict the likelihood of individuals developing symptoms. In this paper we introduce DEFENDER, a software system that integrates data from social and news media and incorporates algorithms for outbreak detection, situational awareness and forecasting. As part of this system we have developed a technique for creating a location network for any country or region based purely on Twitter data. We also present a disease nowcasting (forecasting the current but still unknown level) approach which leverages counts from multiple symptoms, which was found to improve the nowcasting accuracy by 37 percent over a model that used only previous case data. Finally we attempt to forecast future levels of symptom activity based on observed user movement on Twitter, finding a moderate gain of 5 percent over a time series forecasting model.
Hoarding and Frugality Tendencies and their Impact on Consumer Behaviors

ABSTRACT Frugality and hoarding represent underresearched consumer behaviors with far-reaching consumption implications. This study explores the extent to which personality and cultural antecedents of consumers' frugal and hoarding behavioral tendencies overlap. It further explores the extent to which frugality and hoarding affect impulsive and compulsive buying behaviors. A structural equation model technique was used. The results show negative, significant relationships between frugality and both impulsive and compulsive consumer behaviors, as well as positive and significant relationships between hoarding and both impulsive and compulsive consumer behavior. It further provides implications for marketing management and marketing policy.
Measuring the Effectiveness of Wikipedia Articles: How Does Open Content Succeed?

Since 2001 Wikipedia has grown up to one of the most important sources of knowledge worldwide. The voluntarily and independent nature of the project has made it a very unique case of Information Systems with various elements which could affect the way each article is developed. In this paper by referring to the DeLone& McLean model of Information Systems success and considering the body of research in the field, the measures for evaluating the effectiveness of wiki articles have been identified. Then using a sample of 804 articles in Wikipedia and Structural Equation Model (SEM) method the model has been validated. The findings indicate that in the context of Wikipedia open content, system quality and information quality could be merged together and after this simplification, they can affect use and user satisfaction in open content platforms such as Wikipedia.
Image Classification from Generalized Image Distance Features: Application to Detection of Interstitial Disease in Chest Radiographs

One of the most important tasks in medical image analysis is to detect the absence or presence of disease in an image, without having precise delineations of pathology available for training. A novel method is proposed to solve such a classification task, based on a generalized representation of an image derived from local per-pixel features. From this representation, differences between images can be computed, and these can be used to classify the image requiring knowledge of only global image labels for training. It is shown how to construct multiple representations of one image to get multiple classification opinions and combine them to smooth over errors of individual classifiers. The performance of the method is evaluated on the detection of interstitial lung disease on standard chest radiographs. The best result is obtained for the combining classification scheme yielding an area under the ROC curve of 0.955
Self-similar Magnetocentrifugal Disk Winds with Cylindrical Asymptotics

We construct a two-parameter family of models for self-collimated, magnetized outflows from accretion disks. As in previous magnetocentrifugal wind solutions, a flow at zero initial poloidal speed leaves the surface of a disk in Kepler rotation about a central star, and it is accelerated and redirected toward the pole by rotating, helical magnetic fields that thread the disk. At large distances from the disk, the flow streamlines asymptote to wrap around the surfaces of nested cylinders, with velocity v and magnetic field B directed in the axial (ẑ) and toroidal (φ̂) directions. In the asymptotic regime, the velocity secularly decreases with cylindrical radius R from the inside to the outside of the flow because successive streamlines originate in the circumstellar disk in successively shallower portions of the stellar potential. In contrast to previous disk wind modeling, we have explicitly implemented the cylindrical asymptotic boundary condition to examine the consequences for flow dynamics. The present solutions are developed within the context of r-self-similar flows, such that v, the density ρ, and B scale with spherical radius r as v ∝ r-1/2, ρ ∝ r-q, and B ∝ r-(1+q)/2; q must be smaller than unity in order to achieve cylindrical collimation. We self-consistently obtain the shapes of magnetic field lines and the θ-dependence of all flow quantities. The solutions are characterized by q together with the ratios RA/R1 and R0/R1, where for a given streamline, R0 is the radius of its footpoint in the disk, RA is the cylindrical radius where the flow makes an Alfvén transition, and R1 is its final asymptotic cylindrical radius. For given q and R0/R1, RA/R1 must be found as an eigenvalue such that the Alfvén transition is made smoothly. In the solutions we have found, the asymptotic poloidal speed vz on any streamline is typically just a few tenths of the Kepler speed ΩR0 at the corresponding disk footpoint, while the asymptotic rotation speed vφ may be a few tenths to several tenths of ΩR0. The asymptotic toroidal Alfvén speed vA,φ = Bφ/(4πρ)1/2 is, however, a few times ΩR0; thus the outflows remain magnetically dominated, never making a fast-MHD transition. We discuss the implications of these models for interpretations of observed optical jets and molecular outflows from young stellar systems, and we suggest that the difficulty of achieving strong collimation in vector velocity simultaneously with a final speed comparable to ΩR0 argues against isolated jets and in favor of models with broader winds.
Ubiquitous Memory Introspection (Preliminary Manuscript)

AbstractModern memory systems play a critical role in the performance of applications, but a detailed un-derstanding of the application beha vior in the memory system is not trivial to attain. It requires timeconsuming simulations of the memory hierarchy using long traces, and often using detailed modeling.It is increasingly possible to access hardw are performance counters to measure events in the memorysystem, but the measurements remain coarse grained, better suited for performance summaries than pro-viding instruction level feedback. The availability of a low cost, online, and accurate methodology forderi ving ne-grained memory beha vior proles can pro ve extremely useful for runtime analysis andoptimization of programs.This paper presents a ne w methodology for Ubiquitous Memory Introspection (UMI). It is an onlineand lightweight mini-simulation methodology that focuses on simulating short memory access tracesrecorded from frequently executed code regions. The simulations are fast and can pro vide proling re-sults at varying granularities, do wn to that of a single instruction or address. UMI naturally complementsruntime optimizations techniques and enables ne w opportunities for memory specic optimizations.In this paper , we present a prototype implementation of a runtime system implementing UMI. Theprototype is readily deplo yed on commodity processors, requires no user interv ention, and can operatewith stripped binaries and legac y softw are. The prototype operates with an average runtime overhead of20% but this slo wdo wn is only 6% slo wer than a state of the art binary instrumentation tool. W e used32 benchmarks, including the full suite of SPEC2000 benchmarks, for our evaluation. W e sho w thatthe mini-simulation results accurately reect the cache performance of tw o existing memory systems, anIntel Pentium 4 and an AMD Athlon MP (K7) processor . W e also demonstrate that low level prolinginformation from the online simulation can serv e to identify high-miss rate load instructions with a 77%rate of accurac y compared to full ofine simulations that required days to complete. The online prolingresults are used at runtime to implement a simple softw are prefetching strate gy that achie ves a speedupgreater than 60% in the best case.
Clutter spatial-temporal characteristics for forward-looking missile-borne diving radar

A multi-channel forward-looking missile-borne radar diving model is proposed in this paper with a formulation characterizing the relationship of clutter angle-Doppler response. The difference between the horizontal and diving platform is that an additional Doppler frequency is induced by the diving velocity. We show that the diving Doppler frequency leads to the clutter spectrum serious varying across range which increases the non-homogeneity of the training data and degrades the performance of the space-time adaptive processing (STAP). We numerically characterize the spatial-temporal clutter spectrum of forward-looking missile-borne diving array radar and discuss the influence of additional Doppler frequency caused by the diving velocity component.