Miracle-dz/UniFAR-FTUs huggingface dataset:
Overproduction of Penicillin-Binding Protein 2 and Its Inactive Variants Causes Morphological Changes and Lysis in Escherichia coli

ABSTRACT Penicillin-binding protein 2 (PBP 2) has long been known to be essential for rod-shaped morphology in gram-negative bacteria, including Escherichia coli and Pseudomonas aeruginosa. In the course of earlier studies with P. aeruginosa PBP 2, we observed that E. coli was sensitive to the overexpression of its gene, pbpA. In this study, we examined E. coli overproducing both P. aeruginosa and E. coli PBP 2. Growth of cells entered a stationary phase soon after induction of gene expression, and cells began to lyse upon prolonged incubation. Concomitant with the growth retardation, cells were observed to have changed morphologically from typical rods into enlarged spheres. Inactive derivatives of the PBP 2s were engineered, involving site-specific replacement of their catalytic Ser residues with Ala in their transpeptidase module. Overproduction of these inactive PBPs resulted in identical effects. Likewise, overproduction of PBP 2 derivatives possessing only their N-terminal non-penicillin-binding module (i.e., lacking their C-terminal transpeptidase module) produced similar effects. However, E. coli overproducing engineered derivatives of PBP 2 lacking their noncleavable, N-terminal signal sequence and membrane anchor were found to grow and divide at the same rate as control cells. The morphological effects and lysis were also eliminated entirely when overproduction of PBP 2 and variants was conducted with E. coli MHD79, a strain lacking six lytic transglycosylases. A possible interaction between the N-terminal domain of PBP 2 and lytic transglycosylases in vivo through the formation of multienzyme complexes is discussed.
Hough Transformed Based Ship Segmentation Using Centerline Extraction and Feature Angles

Image segmentation is a very important step in order to accomplish automatic tasks, such as classification, being continuously demanded by our society. However, the particular case of naval images entails issues that may exacerbate the conditions for segmentation. Specifically due to water reflections the gray distribution might be very disperse throughout the image and waves produce a large amount of edges. They differ from one image to another too and thus, patterns of color or brightness are difficult to be found. Nevertheless, in this paper we take advantage of these negative characteristics by applying a Hough Transform based technique that enhances the shape of the ship. First, the ship centerline is extracted and the desired feature angles are applied based on this value. The preliminary results are further processed to obtain higher accuracy. The set of parameters is presented and discussed, as well as the non-maximal suppression step and the voting strategy employed. The results reach a higher level of detail compared to previous suggested techniques for this kind of images.
PEFAC - A Pitch Estimation Algorithm Robust to High Levels of Noise

We present PEFAC, a fundamental frequency estimation algorithm for speech that is able to identify voiced frames and estimate pitch reliably even at negative signal-to-noise ratios. The algorithm combines a normalization stage, to remove channel dependency and to attenuate strong noise components, with a harmonic summing filter applied in the log-frequency power spectral domain, the impulse response of which is chosen to sum the energy of the fundamental frequency harmonics while attenuating smoothly-varying noise components. Temporal continuity constraints are applied to the selected pitch candidates and a voiced speech probability is computed from the likelihood ratio of two classifiers, one for voiced speech and one for unvoiced speech/silence. We compare the performance of our algorithm with that of other widely used algorithms and demonstrate that it performs well in both high and low levels of additive noise.
Elevated Carbon Dioxide Alters the Structure of Soil Microbial Communities

ABSTRACT Pyrosequencing analysis of 16S rRNA genes was used to examine impacts of elevated CO2 (eCO2) on soil microbial communities from 12 replicates each from ambient CO2 (aCO2) and eCO2 settings. The results suggest that the soil microbial community composition and structure significantly altered under conditions of eCO2, which was closely associated with soil and plant properties.
Resistance Training Exercise Program for Intervention to Enhance Gait Function in Elderly Chronically Ill Patients: Multivariate Multiscale Entropy for Center of Pressure Signal Analysis

Falls are unpredictable accidents, and the resulting injuries can be serious in the elderly, particularly those with chronic diseases. Regular exercise is recommended to prevent and treat hypertension and other chronic diseases by reducing clinical blood pressure. The “complexity index” (CI), based on multiscale entropy (MSE) algorithm, has been applied in recent studies to show a person's adaptability to intrinsic and external perturbations and widely used measure of postural sway or stability. The multivariate multiscale entropy (MMSE) was advanced algorithm used to calculate the complexity index (CI) values of the center of pressure (COP) data. In this study, we applied the MSE & MMSE to analyze gait function of 24 elderly, chronically ill patients (44% female; 56% male; mean age, 67.56 ± 10.70 years) with either cardiovascular disease, diabetes mellitus, or osteoporosis. After a 12-week training program, postural stability measurements showed significant improvements. Our results showed beneficial effects of resistance training, which can be used to improve postural stability in the elderly and indicated that MMSE algorithms to calculate CI of the COP data were superior to the multiscale entropy (MSE) algorithm to identify the sense of balance in the elderly.
The relationship between processing speed and working memory demand in systemic lupus erythematosus: evidence from a visual n-back task.

OBJECTIVE Working memory (WM) deficits have been reported previously in systemic lupus erythematosus (SLE), but the relationship between information processing speed (PS) and WM deficits in SLE is unknown. This study examined whether or not PS slowing could account for the WM deficits observed in SLE. METHOD A visual n-back task was used to measure simple and complex PS and WM in 40 SLE patients and 36 healthy controls. Simple PS was defined as reaction time (RT) to correct responses under a very low WM load condition (0-back), while complex PS was defined as RT to correct responses under moderate and high WM load conditions (1 and 2-back). RESULTS The results showed that SLE patients performed as well as the controls at the lower WM load conditions but had fewer correct responses than controls under the highest WM load condition (2-back). SLE patients had slower RTs than controls under all conditions, but they had relatively greater RT slowing than controls under the higher WM load conditions. Further, when RT for simple PS was subtracted from complex PS, SLE patients still showed slower complex PS for the 1- and 2-back compared with controls. Both simple and complex PS slowing were related to poorer accuracy scores on the 2-back condition, only for the SLE group. CONCLUSIONS The n-back task provides a sensitive measure of PS and WM. The results suggest that PS deficits alone could not account for the WM deficits in SLE. Disease duration, disease activity, and depression did not appear to account for the observed PS and WM deficits.
STyLE-OLM: Interactive Open Learner Modelling

There is a strong argument in Artificial Intelligence in Education which advocates that computer-based learning systems need to adapt to the needs of learners if they are to provide for effective personalised instruction (Self, 1999a). Diagnosing a learner's cognitive capacity is a crucial issue in building adaptive systems. We have explored an interactive open learner modelling (IOLM) approach which conceives diagnosis as an interactive process involving both a computer system and a learner that discuss and together construct the learner model. This paper outlines the architecture of an interactive open learner modelling system and illustrates the method in a terminological domain. We discuss an evaluative study of an IOLM demonstrator - a system called STyLE-OLM. The results from the study demonstrate potential benefits of the method for improving the quality of the learner model and providing a means for fostering reflective thinking. We argue that IOLM is a fruitful approach which may be employed in intelligent learning environments both for obtaining a better model of a learner's cognitive state and engaging learners in reflective activities.
An Efficient Two-Phase  ${\rm L}^{1}$-TV Method for Restoring Blurred Images with Impulse Noise

A two-phase image restoration method based upon total variation regularization combined with an L1-data-fitting term for impulse noise removal and deblurring is proposed. In the first phase, suitable noise detectors are used for identifying image pixels contaminated by noise. Then, in the second phase, based upon the information on the location of noise-free pixels, images are deblurred and denoised simultaneously. For efficiency reasons, in the second phase a superlinearly convergent algorithm based upon Fenchel-duality and inexact semismooth Newton techniques is utilized for solving the associated variational problem. Numerical results prove the new method to be a significantly advance over several state-of-the-art techniques with respect to restoration capability and computational efficiency.
Opus: University of Bath Online Publication Store Nestedness and Τ -temperature in Ecological Networks

NOTICE: this is the author's version of a work that was accepted for publication in Ecological Complexity. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was This version is made available in accordance with publisher policies. Please cite only the published version using the reference above. Abstract The τ-temperature is a measure of disorder of bipartite networks that is based on the total Manhattan distance of the adjacency matrix. Two proper­ ties of this measure are that it does not depend on permutations of lines or columns that have the same connectivity and it is completely determined by connectivities of lines and columns. The normalisation of τ is done by an uni­ form random matrix whose elements were previously sorted. τ shows no bias against uniform random matrices of several occupations, ρ, sizes, L, and shapes. The scaling of the total Manhattan distance of a random matrix is D rand ∝ L 3 ρ while the same scaling for a full nested matrix is D nest ∝ L 3 ρ 3/2. We test τ for a large set of empirical matrices to verify these scalings. The index τ cor­ relates better with the temperature of Atmar than with the N ODF index of nestedness. We conclude this work by discussing differences between nestedness indices and order/disorder indices.
Variable Step Size Technique for Adaptive Blind Decorrelation

Blind decorrelation is a related task to blind source separation (BSS) which is applicable to numerous problems. A critical challenge in adaptive blind decorrelation (ABD) is the choice of step size to achieve fast initial convergence speed and low steady state error in time-varying systems. Unfortunately, unlike some supervised training, the error factor of ABD is inaccessible in practice, and so the relation between step size and error factor can not be utilized to adjust the step size. In this paper, we first present an algorithm to restructure the error factor by adopting an auxiliary decorrelation system with some restriction, and then based on a nonlinear updating rule of step-size in the light of the error factor descending in an exponential form, we propose a novel variable step size algorithm for ABD. Simulation results indicate the good performance of our proposed method.
Recommendation for advertising messages on mobile devices

Mobile devices, especially smart phones, have been popular in recent years. With users spending much time on mobile devices, service providers deliver advertising messages to mobile device users and look forward to increasing their revenue. However, delivery of proper advertising messages is challenging since strategies of advertising in TV, SMS, or website may not be applied to the banner-based advertising on mobile devices. In this work, we study how to properly recommend advertising messages for mobile device users. We propose a novel approach which simultaneously considers several important factors: user profile, apps used, and clicking history. We apply experiments on real-world mobile log data, and the results demonstrate the effectiveness of the proposed approach.
The Xenobiotic Compound 1,4-Bis[2-(3,5-Dichloropyridyloxy)]Benzene Is an Agonist Ligand for the Nuclear Receptor CAR

ABSTRACT A wide range of xenobiotic compounds are metabolized by cytochrome P450 (CYP) enzymes, and the genes that encode these enzymes are often induced in the presence of such compounds. Here, we show that the nuclear receptor CAR can recognize response elements present in the promoters of xenobiotic-responsive CYP genes, as well as other novel sites. CAR has previously been shown to be an apparently constitutive transactivator, and this constitutive activity is inhibited by androstanes acting as inverse agonists. As expected, the ability of CAR to transactivate the CYP promoter elements is blocked by the inhibitory inverse agonists. However, CAR transactivation is increased in the presence of 1,4-bis[2-(3,5-dichloropyridyloxy)]benzene (TCPOBOP), the most potent known member of the phenobarbital-like class of CYP-inducing agents. Three independent lines of evidence demonstrate that TCPOBOP is an agonist ligand for CAR. The first is that TCPOBOP acts in a dose-dependent manner as a direct agonist to compete with the inhibitory effect of the inverse agonists. The second is that TCPOBOP acts directly to stimulate coactivator interaction with the CAR ligand binding domain, both in vitro and in vivo. The third is that mutations designed to block ligand binding block not only the inhibitory effect of the androstanes but also the stimulatory effect of TCPOBOP. Importantly, these mutations do not block the apparently constitutive transactivation by CAR, suggesting that this activity is truly ligand independent. Both its ability to target CYP genes and its activation by TCPOBOP demonstrate that CAR is a novel xenobiotic receptor that may contribute to the metabolic response to such compounds.
Improved Linear Grouping

Linear grouping is a technique where linear relationship information is gathered for a set of rigid points. This information is used to accelerate vertex transformation, vertex clipping, texture transformation, etc. The linear grouping technique is an optimization problem, originally implemented in a best-first branch-and-bound search. In this paper, we introduce several new extensions and improvements to linear grouping. In particular, the search algorithm is greatly improved.
Pre-immunization with an Intramuscular Injection of AAV9-Human Erythropoietin Vectors Reduces the Vector-Mediated Transduction following Re-Administration in Rat Brain

We have recently demonstrated that adeno-associated virus serotype 9 (AAV9)-mediated human erythropoietin (hEPO) gene delivery into the brain protects dopaminergic (DA) neurons in the substantia nigra in a rat model of Parkinson's disease. In the present study, we examined whether pre-exposure to AAV9-hEPO vectors with an intramuscular or intrastriatal injection would reduce AAV9-mediated hEPO transduction in rat brain. We first characterized transgene expression and immune responses against AAV9-hEPO vectors in rat striatum at 4 days, 3 weeks and 6 months, and with doses ranging from 1011 to 1013 viral genomes. To sensitize immune system, rats received an injection of AAV9-hEPO into either the muscle or the left striatum, and then sequentially an injection of AAV9-hEPO into the right striatum 3 weeks later. We observed that transgene expression exhibited in a time course and dose dependent manner, and inflammatory and immune responses displayed in a time course manner. Intramuscular, but not intrastriatal injections of AAV9-hEPO resulted in reduced levels of hEPO transduction and increased levels of the major histocompatibility complex (MHC) class I and class II antigen expression in the striatum following AAV9-hEPO re-administration. There were infiltration of the cluster of differentiation 4 (CD4)-and CD8-lymphacytes, and accumulation of activated microglial cells and astrocytes in the virally injected striatum. In addition, the sera from the rats with intramuscular injections of AAV9-hEPO contained greater levels of antibodies against both AAV9 capsid protein and hEPO protein than the other treatment groups. hEPO gene expression was negatively correlated with the levels of circulating antibodies against AAV9 capsid protein. Intramuscular and intrastriatal re-administration of AAV9-hEPO led to increased numbers of red blood cells in peripheral blood. Our results suggest that pre-immunization with an intramuscular injection can lead to the reduction of transgene expression in the striatal re-administration.
On Becoming a Psychoanalyst in Japan

ABSTRACT This special issue introduces psychoanalysis in Japan, its history, thoughts, and development, through the autobiographies of some Japanese psychoanalysts. I graduated relatively recently from a training course in psychoanalysis at the Japan Institute of Psychoanalysis and was certified as a psychoanalyst by the Japan Psychoanalytic Society (JPS). If I am to write about why I aimed to become a psychoanalyst in Japan and how I became one, not only my personal history but also the influences of Japanese culture and Japanese therapeutic culture will undoubtedly be important. In this article, by relating my life history, I trace the path I followed for becoming a psychoanalyst and explore the broader implications of my experience. The paper “An Autobiographical Study” by Freud (1925) is a famous autobiographical psychoanalytic essay, and a more recent paper “Learning from Life―Becoming a Psychoanalyst” by Casement (2006) is also well known. To publicize an autobiography, a psychoanalyst always includes the possibility of self-disclosure. Because I am still practicing psychoanalysis regularly, I hesitate slightly to write this article. However, writing an autobiography is also, in part, a process of self-analysis after becoming a psychoanalyst, and can be considered a part of a psychoanalyst’s interminable training (Okada, 2012).
p75 Neurotrophin Receptor Expression Defines a Population of BDNF-Responsive Neurogenic Precursor Cells

Although our understanding of adult neurogenesis has increased dramatically over the last decade, confusion still exists regarding both the identity of the stem cell responsible for neuron production and the mechanisms that regulate its activity. Here we show, using flow cytometry, that a small population of cells (0.3%) within the stem cell niche of the rat subventricular zone (SVZ) expresses the p75 neurotrophin receptor (p75NTR) and that these cells are responsible for neuron production in both newborn and adult animals. In the adult, the p75NTR-positive population contains all of the neurosphere-producing precursor cells, whereas in the newborn many of the precursor cells are p75NTR negative. However, at both ages, only the neurospheres derived from p75NTR-positive cells are neurogenic. We also show that neuron production from p75NTR-positive but not p75NTR-negative precursors is greatly enhanced after treatment with brain-derived neurotrophic factor (BDNF) or nerve growth factor. This effect appears to be mediated specifically by p75NTR, because precursor cells from p75NTR-deficient mice show a 70% reduction in their neurogenic potential in vitro and fail to respond to BDNF treatment. Furthermore, adult p75NTR-deficient mice have significantly reduced numbers of PSA-NCAM (polysialylated neural cell adhesion molecule)-positive SVZ neuroblasts in vivo and a lower olfactory bulb weight. Thus, p75NTR defines a discrete population of highly proliferative SVZ precursor cells that are able to respond to neurotrophin activation by increasing neuroblast generation, making this pathway the most likely mechanism for the increased neurogenesis that accompanies raised BDNF levels in a variety of disease and behavioral situations.
Altered distribution of mitochondria impairs calcium homeostasis in rat hippocampal neurons in culture

The specificity of Ca2+ signals is conferred in part by limiting changes in cytosolic Ca2+ to subcellular domains. Mitochondria play a major role in regulating Ca2+ in neurons and may participate in its spatial localization. We examined the effects of changes in the distribution of mitochondria on NMDA‐induced Ca2+ increases. Hippocampal cultures were treated with the microtubule‐destabilizing agent vinblastine, which caused the mitochondria to aggregate and migrate towards one side of the neuron. This treatment did not appear to decrease the energy status of mitochondria, as indicated by a normal membrane potential and pH gradient across the inner membrane. Moreover, electron microscopy showed that vinblastine treatment altered the distribution but not the ultrastructure of mitochondria. NMDA (200 µm, 1 min) evoked a greater increase in cytosolic Ca2+ in vinblastine‐treated cells than in untreated cells. This increase did not result from impaired Ca2+ efflux, enhanced Ca2+ influx, opening of the mitochondrial permeability transition pore or altered function of endoplasmic reticulum Ca2+ stores. Ca2+ uptake into mitochondria was reduced by 53% in vinblastine‐treated cells, as reported by mitochondrially targeted aequorin. Thus, the distribution of mitochondria maintained by microtubules is critical for buffering Ca2+ influx. A subset of mitochondria close to a Ca2+ source may preferentially regulate Ca2+ microdomains, set the threshold for Ca2+‐induced toxicity and participate in local ATP production.
Trilaminar Multiway Reconstruction Tree for Efficient Large Scale Structure from Motion

Accuracy and efficiency are two key problems in large scale incremental Structure from Motion (SfM). In this paper, we propose a unified framework to divide the image set into clusters suitable for reconstruction as well as find multiple reliable and stable starting points. Image partitioning performs in two steps. First, some small image groups are selected at places with high image density, and then all the images are clustered according to their optimal reconstruction paths to these image groups. This promises that the scene is always reconstructed from dense places to sparse areas, which can reduce error accumulation when images have weak overlap. To enable faster speed, images outside the selected group in each cluster are further divided to achieve a greater degree of parallelism. Experiments show that our method achieves significant speedup, higher accuracy and better completeness.