Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning and sequencing of some genes responsible for porphyrin biosynthesis from the anaerobic bacterium Clostridium josui

The 6.2-kbp DNA fragment encoding the enzymes in the porphyrin synthesis pathway of a cellulolytic anaerobe, Clostridium josui, was cloned into Escherichia coli and sequenced. This fragment contained four hem genes, hemA, hemC, hemD, and hemB, in order, which were homologous to the corresponding genes from E. coli and Bacillus subtilis. A typical promoter sequence was found only upstream of hemA, suggesting that these four genes were under the control of this promoter as an operon. The hemA and hemD genes cloned from C. josui were able to complement the hemA and hemD mutations, respectively, of E. coli. The COOH-terminal region of C. josui HemA and the NH2-terminal region of C. josui HemD were homologous to E. coli CysG (Met-1 to Leu-151) and to E. coli CysG (Asp-213 to Phe-454) and Pseudomonas denitrificans CobA, respectively. Furthermore, the cloned 6.2-kbp DNA fragment complemented E. coli cysG mutants. These results suggested that both C. josui hemA and hemD encode bifunctional enzymes.
Psychophysiological responses to virtual crowds: Implications for wearable computing

Human responses to crowds were investigated with a simulation of a busy street scene using virtual reality. Both psychophysiological measures and a memory test were used to assess the influence of large crowds or individual agents who stood close to the participant while they performed a memory task. Results from most individuals revealed strong orienting responses to changes in the crowd. This was indicated by sharp increases in skin conductance and reduction in peripheral blood volume amplitude. Furthermore, cognitive function appeared to be affected. Results of the memory test appeared to be influenced by how closely virtual agents approached the participants. These findings are discussed with respect to wearable affective computing which seeks robust identifiable correlates of autonomic activity that can be used in everyday contexts.
Modeling turbulent dissipation at low and moderate Reynolds numbers

The dissipation of kinetic energy is one of the key features of turbulent flows that must be modeled accurately in order to obtain useful engineering predictions. At high Reynolds numbers the assumption of scale separation can be invoked in the modeling of the dissipation process. This paper focuses on the more difficult issue of modeling the dissipation process at moderate and low Reynolds numbers. The low and moderate Reynolds number range is very important for tuning turbulence models and for many practical engineering problems. To approach this problem, an alternative formulation to the classic dissipation scale equation is proposed. The interesting feature of this formulation, an inverse lengthscale equation, is that it captures both the high Reynolds number and low Reynolds number decay limits. A careful assessment of existing data then allows us to clearly identify the region of transition between high and low Re and propose a very simple equation system which can accurately model dissipation at any Reynolds number. The equivalent K/ϵ model is derived and the proposed model is compared with a number of other low Re dissipation modifications for the K/ϵ equation system. To complete the discussion, the issue of near-wall dissipation modeling is carefully examined and shown to be fundamentally different from the low Reynolds number limit. This is shown to be an important distinction of practical modeling importance.
Testing the formulation of Park and Dejnakarintra to calculate thunderstorm dc electric fields

Park and Dejnakarintra [1973] presented a formulation to calculate high-altitude electric fields due to electrified clouds, taking into account the presence of the ionosphere. Calculation of these fields is necessary to test the hypothesis that whistler ducts might be caused by plasma interchange of geomagnetic flux tubes driven by thundercloud electrostatic fields. To test the accuracy of the formulation, the calculated dc electric fields are compared with those measured during a thunderstorm campaign reported by Holzworth et al. [1985]. Using a conductivity profile measured during their campaign, it is shown that the formulation of Park and Dejnakarintra produces electric field predictions which are consistent with the measurements of Holzworth et al. This indicates the formulation developed by Park and Dejnakarintra is valid. The comparisons agree with measurements which show that large negative screening charges commonly exist around the top of thunderclouds, reducing the high altitude fields. These calculations indicate that the effective thunderstorm charge used in such calculations needs to be significantly reduced to account for screening charges. Such reductions lead to serious increases (up to a factor of 10) in the time required for high-altitude thunderstorm electric fields to produce whistler ducts.
Novel Trends in Clustering

Clustering or finding a natural grouping of a data set is essential for knowledge discovery in many applications. This chapter provides an overview on emerging trends within the vital research area of clustering including subspace and projected clustering, correlation clustering, semi-supervised clustering, spectral clustering and parameter-free clustering. To raise the awareness of the reader for the challenges associated with clustering, the chapter first provides a general problem specification and introduces basic clustering paradigms. The requirements from concrete example applications in life sciences and the web provide the motivation for the discussion of novel approaches to clustering. Thus, this chapter is intended to appeal to all those interested in the state-of-the art in clustering including basic researchers as well as practitioners.
Assured Deletion in the Cloud: Requirements, Challenges and Future Directions

Inadvertent exposure of sensitive data is a major concern for potential cloud customers. Much focus has been on other data leakage vectors, such as side channel attacks, while issues of data disposal and assured deletion have not received enough attention to date. However, data that is not properly destroyed may lead to unintended disclosures, in turn, resulting in heavy financial penalties and reputational damage. In non-cloud contexts, issues of incomplete deletion are well understood. To the best of our knowledge, to date, there has been no systematic analysis of assured deletion challenges in public clouds. In this paper, we aim to address this gap by analysing assured deletion requirements for the cloud, identifying cloud features that pose a threat to assured deletion, and describing various assured deletion challenges. Based on this discussion, we identify future challenges for research in this area and propose an initial assured deletion architecture for cloud settings. Altogether, our work offers a systematization of requirements and challenges of assured deletion in the cloud, and a well-founded reference point for future research in developing new solutions to assured deletion.
Movement disorder profile and treatment outcomes in a one-year study of patients with schizophrenia

Background This study identified subgroups of patients with schizophrenia who differed on their movement disorder profile and compared their treatment outcomes. Methods Data from a randomized, open-label, one-year study of patients with schizophrenia who were treated with antipsychotics in usual clinical care settings were analyzed (n = 640). Five measures of movement disorder were incorporated into a single Movement Disorder Index (MDI). Subgroups that differed in their movement disorder profile over the one-year study period were compared on clinical and functional outcomes. Results Three subgroups were identified: a worsening of MDI in 15% of patients, an improvement in 33%, and no change in 53%. Compared with the other two subgroups, the MDI-worsened subgroup had poorer symptom improvement measured by the Positive and Negative Syndrome Scale (PANSS) total score (mean changes of −11.0, −18.4, and −16.8 for the patients who had a worsening of MDI, no change, and an improvement, respectively), poorer symptom improvement on the PANSS positive and anxiety/depression subscale scores, worsening on the 36-Item Short Form Health Survey (SF-36) physical component summary score, and a higher rate of hospitalization (P < 0.05). Conclusion Patients with schizophrenia who experience worsening of their MDI score appear to have poorer clinical and functional outcomes, suggesting that such worsening may be a marker of poorer prognosis.
The influence of carbon nanotubes on enzyme activity and structure: investigation of different immobilization procedures through enzyme kinetics and circular dichroism studies

In the last decade, many environmental organizations have devoted their efforts to identifying renewable biosystems, which could provide sustainable fuels and thus enhance energy security. Amidst the myriad of possibilities, some biofuels make use of different types of waste biomasses, and enzymes are often employed to hydrolyze these biomasses and produce sugars that will be subsequently converted into ethanol. In this project, we aimed to bridge nanotechnology and biofuel production: here we report on the activity and structure of the enzyme amyloglucosidase (AMG), physically adsorbed or covalently immobilized onto single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs). In fact, carbon nanotubes (CNTs) present several properties that render them ideal support systems, without the diffusion limitations displayed by porous material and with the advantage of being further functionalizable at their surface. Chemical ligation was achieved both on oxidized nanotubes (via carbodiimide chemistry), as well as on amino-functionalized nanotubes (via periodate-oxidized AMG). Results showed that AMG retained a certain percentage of its specific activity for all enzyme–carbon nanotubes complexes prepared, with the physically adsorbed samples displaying better catalytic efficiency than the covalently immobilized samples. Analysis of the enzyme’s structure through circular dichroism (CD) spectroscopy revealed significant structural changes in all samples, the degree of change being consistent with the activity profiles. This study proves that AMG interacts differently with carbon nanotubes depending on the method employed. Due to the higher activity reported by the enzyme physically adsorbed onto CNTs, these samples demonstrated a vast potential for further development. At the same time, the possibility of inducing magnetic properties into CNTs offers the opportunity to easily separate them from the original solution. Hence, substances to which they have been attached can be separated from a reaction medium, or directed by an external magnetic field to achieve efficient biofuel production. This paves the way for future design of efficient CNT–enzyme nanostructure bioreactors.
The Trouble with Weight-Dependent STDP

We fit a weight-dependent STDP rule to the classic data of Bi and Poo (1998), showing that this rule leads to slow learning in a simulation with an integrate-and-fire neuron. The slowness of learning is explained by an inequality between the range of initial weights in the data and the largest relative potentiation. We show that slow learning can be overcome with an increased learning rate, but that this approach leads to rapid forgetting in the presence of realistic levels of background spiking. Our study demonstrates that weight-dependent STDP rules, commonly used in neural simulations, have biologically unrealistic consequences. We discuss the implications of this finding for several interpretations of weight-dependent plasticity and STDP more generally, and recommend directions for further research.
Water Budget in a Tile Drained Watershed under Future Climate Change Using SWATDRAIN Model

The SWATDRAIN model was developed by incorporating the subsurface flow model, DRAINMOD, into a watershed scale surface flow model, SWAT (Soil and Water Assessment tool), to simulate the hydrology and water quality of agricultural watersheds. The model is capable of simulating hydrology under different agricultural management and climate scenarios. As an application of the SWATDRAIN model, the impact of climate change on surface/subsurface flow was evaluated in the Canagagigue Creek watershed in southern Ontario, Canada. Using the assumption that there has been no change in land cover and land management, the model was applied to simulate annual, seasonal, and monthly changes in surface and subsurface flows at the outlet of the watershed under current and future climate conditions. The climate scenario under consideration in this study for 2015–2044 was derived from CGCM2 (Canadian Global Circulation Model 2), with A2 scenario for future climatic simulation. The SWATDRAIN model’s ability to predict the impacts of future climate change scenarios in agricultural watersheds due to monthly NSE (Nash Sutcliffe Efficiency), PBIAS (Percent Bias), and RSR (Root Mean Square Error) values of 0.74, 3.67, and 0.37, respectively, for the validation phase. The results showed that general climate change effects more spring and winter hydrology than summer hydrology. The results show that the annual flow is expected to increase in future, which will lead to an increase in the sediment loads in the stream.
Channel Access Throttling for Improving WLAN QoS

The de facto QoS channel access method for the IEEE 802.11 Wireless LANs is the Enhanced Distributed Channel Access (EDCA) mechanism, which differentiates transmission treatments for data frames belonging to different traffic categories with four different levels of channel access priority. In this paper, we propose extending EDCA with Channel Access Throttling (CAT) for more flexible and efficient QoS support. By assigning different member stations different channel access parameters, CAT differentiates channel access priorities not between traffic categories but between member stations. Then by dynamically changing the channel access parameters of each member station based on a pre-computed schedule, CAT enables EDCA WLANs the benefits of scheduled access QoS. We also present evaluation results of CAT obtained from both simulations and experiments conducted using off-the-shelf WLAN hardware and open-source device driver. Our results show that CAT can proportionally partition channel capacity, significantly improve performance of multimedia applications, effectively achieve performance protection for admitted flows, and increase per cell VoIP call capacity by up to 41%.
A family of fixed-point algorithms for independent component analysis

Independent Component Analysis (ICA) is a statistical signal processing technique whose main applications are blind source separation, blind deconvolution, and feature extraction. Estimation of ICA is usually performed by optimizing a 'contrast' function based on higher-order cumulants. In this paper, it is shown how almost any error function can be used to construct a contrast function to perform the ICA estimation. In particular, this means that one can use contrast functions that are robust against outliers. As a practical method for nding the relevant extrema of such contrast functions, a xed-point iteration scheme is then introduced. The resulting algorithms are quite simple and converge fast and reliably. These algorithms also enable estimation of the independent components one-by-one, using a simple de ation scheme.
Soil chemical surveying: A path to a deeper understanding of prehistoric sites and societies in Sweden

A large number of contract archaeological investigations have been conducted in Sweden over the last 10–15 years. In this article, the applicability of soil chemical surveying in connection with contract archaeology is discussed, focusing on soil sampling, soil magnetic susceptibility, and phosphate analysis. Results from case studies from an area of the west coast of southern Sweden are presented. The investigated sites cover periods ranging from the Bronze Age to the Late Iron Age/Medieval time (3500–1000 B.P.). Results show that the chemical loading of prehistoric settlements varies considerably both quantitatively and spatially depending on different socioeconomic strategies and behavior. © 2007 Wiley Periodicals, Inc.
Automated segmentation of the prostate in 3D MR images using a probabilistic atlas and a spatially constrained deformable model.

PURPOSE The authors present a fully automatic algorithm for the segmentation of the prostate in three-dimensional magnetic resonance (MR) images. METHODS The approach requires the use of an anatomical atlas which is built by computing transformation fields mapping a set of manually segmented images to a common reference. These transformation fields are then applied to the manually segmented structures of the training set in order to get a probabilistic map on the atlas. The segmentation is then realized through a two stage procedure. In the first stage, the processed image is registered to the probabilistic atlas. Subsequently, a probabilistic segmentation is obtained by mapping the probabilistic map of the atlas to the patient's anatomy. In the second stage, a deformable surface evolves toward the prostate boundaries by merging information coming from the probabilistic segmentation, an image feature model and a statistical shape model. During the evolution of the surface, the probabilistic segmentation allows the introduction of a spatial constraint that prevents the deformable surface from leaking in an unlikely configuration. RESULTS The proposed method is evaluated on 36 exams that were manually segmented by a single expert. A median Dice similarity coefficient of 0.86 and an average surface error of 2.41 mm are achieved. CONCLUSIONS By merging prior knowledge, the presented method achieves a robust and completely automatic segmentation of the prostate in MR images. Results show that the use of a spatial constraint is useful to increase the robustness of the deformable model comparatively to a deformable surface that is only driven by an image appearance model.
Efficient HEVC decoder for heterogeneous CPU with GPU systems

The High Efficiency Video Coding (HEVC) standard provides higher compression efficiency than other video coding standards but at the cost of increased computational load, which makes it hard to achieve real-time encoding/decoding of high-resolution, high-quality video sequences. In this paper, we investigate how Graphics Processing Units (GPUs) can be employed to accelerate HEVC decoding. GPUs are known to provide massive processing capability for throughput computing kernels, but the HEVC entropy decoding kernel cannot be executed efficiently on GPUs. We therefore propose a complete HEVC decoding solution for heterogeneous CPU+GPU systems, in which the entropy decoder is executed on the CPU and the remaining kernels on the GPU. Furthermore, the decoder is pipelined such that the CPU and the GPU can decode different frames in parallel. The proposed CPU+GPU decoder achieves an average frame rate of 150 frames per second for Ultra HD 4K video sequences when four CPU cores are used with an NVIDIA GeForce Titan X GPU.
Analysis of glacier facies using satellite techniques

Abstract The different snow and ice types on a glacier may be subdivided according to the glacier-facies concept. The surficial expression of some facies may be detected at the end of the balance year by the use of visible and near-infrared image data from the Landsat multispectral scanner (MSS) and thematic mapper (TM) sensors. Ice and snow can be distinguished by reflectivity differences in individual or ratioed TM bands on Brúarjökull, an outlet glacier on the northern margin of the Vatnajökull ice cap, Iceland. The Landsat scene shows the upper limit of wet snow on 24 August 1986. Landsat-derived reflectance is lowest for exposed ice and increases markedly at the transient snow line. Above the slush zone is a gradual increase in near-infrared reflectance as a result of decreasing grain-size of the snow, which characterizes drier snow. Landsat data are useful in measuring the areal extent of the ice facies, the slush zone within the wet-snow facies, the snow facies (combined wet-snow, percolation and dry-snow facies), and the respective positions of the transient snow line and the slush limit. In addition, fresh snowfall and/or airborne contaminants, such as soot and tcphra, can limit the utility of Landsat data for delineation of the glacier facies in some cases.
A Dynamically Optimized Fluctuation Smoothing Rule for Scheduling Jobs in a Wafer Fabrication Factory

This paper presents a dynamically optimized fluctuation smoothing rule to improve the performance of scheduling jobs in a wafer fabrication factory. The rule has been modified from the four-factor bi-criteria nonlinear fluctuation smoothing 4f-biNFS rule, by dynamically adjusting factors. Some properties of the dynamically optimized fluctuation smoothing rule were also discussed theoretically. In addition, production simulation was also applied to generate some test data for evaluating the effectiveness of the proposed methodology. According to the experimental results, the proposed methodology was better than some existing approaches to reduce the average cycle time and cycle time standard deviation. The results also showed that it was possible to improve the performance of one without sacrificing the other performance metrics.
Recent Results Obtained from Continuous Monitoring of Crustal Deformation

Recent work carried out in Japan to investigate crustal deformation related to earthquakes is summarized. (1) In regard to short-term anomalous strains and tilts before the occurrence of earthquakes, several authors have reported cases in which an anomalous change was detected by only one component of tiltmeters or extensometers. Other reports have involved some uncertainties with respect to meteorological disturbances and stabilities of instruments. Consequently, we have not yet obtained reliable evidence of earthquake precursors, which should be observed simultaneously with more than two instruments or at more than two observation sites after environmental and instrumental noise is carefully eliminated from the original data. (2) Attempts to search for earthquake precursors by means of monitoring the temporal variations of tidal strains at Mikawa and Amagase are also reported. Anomalous variations in tidal strain amplitudes were found at Mikawa 3 or 4 months before a moderate earthquake (M=5.7) occurred on March 14, 1983. Such anomalous variations were not found at Amagase. (3) Co-seismic strain- and tilt-steps observed at many observatories in Japan are discussed. Some observed co-seismic steps have extremely large amplitudes compared with theoretical amplitudes which were calculated using dislocation fault models. This discrepancy may mainly be due to instability of instruments. (4) Observational studies on migration of crustal deformation carried out in tectonically active regions, such as Izu Peninsula and Tohoku district, are discussed together with numerical experiments to simulate strain migration using a two-dimensional finite element technique.
Locally non-rigid registration for mobile HDR photography

Image registration for stack-based HDR photography is challenging. If not properly accounted for, camera motion and scene changes result in artifacts in the composite image. Unfortunately, existing methods to address this problem are either accurate, but too slow for mobile devices, or fast, but prone to failing. We propose a method that fills this void: our approach is extremely fast - under 700ms on a commercial tablet for a pair of 5MP images - and prevents the artifacts that arise from insufficient registration quality.