Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure, Function and Regulation of Outer Membrane Proteins Involved in Drug Transport in Enterobactericeae: the OmpF/C – TolC Case

Antibiotic translocation across membranes of Gram-negative bacteria is a key step for the activity on their specific intracellular targets. Resistant bacteria control their membrane permeability as a first line of defense to protect themselves against external toxic compounds such as antibiotics and biocides. On one hand, resistance to small hydrophilic antibiotics such as ß-lactams and fluoroquinolones frequently results from the « closing » of their way in: the general outer membrane porins. On the other hand, an effective way out for a wide range of antibiotics is provided by TolC-like proteins, which are outer membrane components of multidrug efflux pumps. Accordingly, altered membrane permeability, including porin modifications and/or efflux pumps’ overexpression, is always associated to multidrug resistance (MDR) in a number of clinical isolates. Several recent studies have highlighted our current understanding of porins/TolC structures and functions in Enterobacteriaceae. Here, we review the transport of antibiotics through the OmpF/C general porins and the TolC-like channels with regards to recent data on their structure, function, assembly, regulation and contribution to bacterial resistance. Because MDR strains have evolved global strategies to identify and fight our antibiotic arsenal, it is important to constantly update our global knowledge on antibiotic transport.
A new metric for multivariate spectral estimation leading to lowest complexity spectra

A new multivariate spectral estimation technique is proposed. It is based on a constrained spectrum approximation problem, where the distance between spectra is derived from the relative entropy rate between stationary Gaussian processes. This approach may be viewed as an extension of the high-resolution estimator called THREE introduced by Byrnes, Georgiou and Lindquist in 2000. The corresponding solution features a complexity upper bound which is equal to the one featured by THREE in the scalar case thereby improving on the one so far available in the multichannel framework. The solution is computed by means of a globally convergent, matricial Newton-type algorithm. Comparative simulation indicates that this new technique outperforms PEM and N4SID in the case of short data records.
Stochastic Optimization for Large-scale Optimal Transport

Optimal transport (OT) defines a powerful framework to compare probability distributions in a geometrically faithful way. However, the practical impact of OT is still limited because of its computational burden. We propose a new class of stochastic optimization algorithms to cope with large-scale problems routinely encountered in machine learning applications. These methods are able to manipulate arbitrary distributions (either discrete or continuous) by simply requiring to be able to draw samples from them, which is the typical setup in high-dimensional learning problems. This alleviates the need to discretize these densities, while giving access to provably convergent methods that output the correct distance without discretization error. These algorithms rely on two main ideas: (a) the dual OT problem can be re-cast as the maximization of an expectation ; (b) entropic regularization of the primal OT problem results in a smooth dual optimization optimization which can be addressed with algorithms that have a provably faster convergence. We instantiate these ideas in three different setups: (i) when comparing a discrete distribution to another, we show that incremental stochastic optimization schemes can beat Sinkhorn's algorithm, the current state-of-the-art finite dimensional OT solver; (ii) when comparing a discrete distribution to a continuous density, a semi-discrete reformulation of the dual program is amenable to averaged stochastic gradient descent, leading to better performance than approximately solving the problem by discretization ; (iii) when dealing with two continuous densities, we propose a stochastic gradient descent over a reproducing kernel Hilbert space (RKHS). This is currently the only known method to solve this problem, apart from computing OT on finite samples. We backup these claims on a set of discrete, semi-discrete and continuous benchmark problems.
Tactical Scheduling for Precision Air Traffic Operations: Past Research and Current Problems

Future air transportation systems stand to benefit significantly in safety and efficiency from the predictable movement of aircraft along precisely defined paths in the airspace. Such aircraft movement, hereafter referred to as Precision Air Traffic Operations (PATO), is not widely used during periods of peak air traffic in today’s system, but is the foundation of high-capacity operations envisioned for the future. Automation and deployment of PATO, being a relatively young field of research, has not had time to establish structured theories and standardized reference literature. As a consequence, researchers interested in entering this field have difficulty applying to it classical techniques of operations research and optimal control theory. The main obstacle to such applications is the lack of access to the finer domain knowledge of air traffic operations (most importantly, knowledge of the operational constraints) needed to formulate research problems that promise deployable automation tools. Such a formulation requires the researcher to characterize and assess the research efforts and tendencies that emerged in the recent decades to address diverse problems, some outwardly similar yet essentially different. The research field of PATO has now matured to a stage where this requirement can start being met. This paper, aimed as a step in this direction, provides (a) a formulation of the general problem of defining conceptually, constructing, and using a schedule for PATO that contains specification of merging sequences and provides aircraft separation continuously in time, (b) the context necessary for understanding the formulation and its limitations, and (c) a review of prior research on future Air Traffic Operations (ATO) and, in particular, on the role of Air Traffic Control (ATC) in these operations.
PRECONDITIONING TECHNIQUES IN CHEBYSHEV COLLOCATION METHOD FOR ELLIPTIC EQUATIONS

When one approximates elliptic equations by the spectral collocation method on the Chebyshev-Gauss-Lobatto (CGL) grid, the resulting coefficient matrix is dense and ill-conditioned. It is known that a good preconditioner, in the sense that the preconditioned system becomes well conditioned, can be constructed with finite difference on the CGL grid. However, there is a lack of an efficient solver for this preconditioner in multi-dimension. A modified preconditioner based on the approximate inverse technique is constructed in this paper. The computational cost of each iteration in solving the preconditioned system is O(lNxNy logNx), where Nx, Ny are the grid sizes in each direction and l is a small integer. Numerical examples are given to demonstrate the efficiency of the proposed preconditioner.
Staphylococcus aureus triggered reactive arthritis.

OBJECTIVES--To report two patients who developed reactive arthritis in association with Staphylococcus aureus infection. METHODS--A review of the case notes of two patients. RESULTS--Two adult female patients have developed sterile arthritis in association with Staph aureus infection. The first patient has had two episodes of arthritis; the first followed olecranon bursitis, the second followed infection of a central venous catheter used for dialysis. The second patient developed sterile arthritis while being treated for pyomyositis. Both patients had a self limited arthritis and were HLA-B27 negative. CONCLUSION--Reactive arthritis may rarely follow Staph aureus infection. HLA-B27 negativity may be associated with a self limited arthritis in these cases.
The therapeutic expression of anger: Emotionally expressive writing and exposure

s for articles published between 1985 and March 1993 found 7,355 articles referencing anxiety and 15,369 referencing depression, compared to 704 referencing anger (Digiuseppe, Tafrate, & Eckhardt, 1994). Another search of Index Medicus, using the same procedures and publication time period, found 8,850 publications referencing anxiety, 8,352 referencing depression, and 744 referencing anger (Digiuseppe, Tafrate, & Eckhardt, 1994). Inspired by these reports similar searches were conducted on 06/15/2011 using Psych Info. Using a keyword search for articles published between 2000 and 2011, the following results were found: “Anxiety Treatment” resulted in 205 identified articles; “Depression Treatment” found 907 publications ; “Anger Treatment” resulted in 39 references. The searches produced a total of 1,152 articles of which 78.80% were about the treatment of depression, 17.81% were about the treatment of anxiety, and only 3.39% were about the treatment of anger. The same search was conducted again except this time the broader key words of “anxiety”, “depression”, and “anger” were used. The search resulted in the following article counts: 66,177 for “Anxiety”; 82,889 for “Depression”; and 9,931 for Anger. Thus, the searches produced a total of 158,997 published studies of which 52.13% were about depression, 41.62% were about anxiety, and only 6.25% were about anger. Based on these publication numbers it appears that anger is indeed an understudied emotion. Taken together, it seems clear that like depression and anxiety, anger is a commonly experienced emotion that at times is highly adaptive and part of the normal human experience. Also, just like depression and anxiety, when experienced too frequently, too intensely, or inappropriately, anger can have a wide variety of negative consequences and significantly disrupt important behavior, impair functioning, and
An Adaptive Feature Extraction Method for Motor-Imagery BCI Systems

Recently, the research on Brain-Computer Interface (BCI) technology has achieved great progress, and the BCI system based on Motor Imagery (MI) has been intensively studied in many labs. The essential part of signal processing in BCI is how to extract the MI features in electroencephalographic (EEG) and recognize the MI task accurately. One challenge lies in that EEG signals are non-stationary, whose features vary with time. The traditional methods often don’t perform well in BCI, because it does not capture the change of EEG automatically. In this paper, an improved adaptive common spatial patterns (ACSP) method is proposed to adapt to the change of EEG. We test our method for adaptive feature extraction with data from BCI motor imagery experiment, and the efficacy is evaluated by the feature classification accuracy with a support vector machine (SVM) classifier. The results show the effectiveness of the improved adaptive algorithm.
Visibility restoration of lake crater hazy image based on dark channel prior

Volcanic degassing is often happened on top of Mt Kelud. One of the indicator of its activity is the changing of the lake color. An observation has been conducted for years to watch the condition of the lake using a CCTV camera, the volcanology officer. Since it is located on top of the mountain, weather condition always change from clear, cloudy, or hazy. Obviously, the vision of the camera is limited or even blocked by the haze or fog. In this paper, we use a haze removal technique based on dark channel prior. The problem comes up because the airlight hard to estimate on non-sky area. By comparing different size of the patches, we found that, in our case, for smaller patch the airlight closes to its maximum limit. This airlight almost equals to sky region. For image improvement, we use guided image filter to maintain image quality after transmission map estimation. According to FADE (Fog Aware Density Evaluator) the fog density estimated to be 0.6333 and SSIM (Structural Similarity) 0.9977.
Multiuser bi-directional communications in cooperative relay networks

In this paper, we extend the concept of the one-directional multiuser peer-to-peer amplify-and-forward relaying scheme to that of a bi-directional two-phase relaying scheme. The relay weights are chosen to maximize the minimal received quality-of-service of all the users under constraints on the individual and the total power at the relays. The computation of the relay weights is accomplished by approximately solving a non-convex optimization problem using a sequential convex programming algorithm of low complexity. In our simulations, the proposed bi-directional relaying scheme outper-formed the one-directional multiuser peer-to-peer scheme.
The Effects of Caffeine and Exercise on Implicit and Explicit Memory Performance in Younger Adults: an Investigation of Physiological Arousal

Memory performance is best during an individual’s optimal time-of-day, when physiological arousal is naturally highest, and decreases significantly during their non-optimal time of day when arousal declines. Previous research suggests that the time-of-day at which a memory task is completed may contribute to age related disparities in memory performance. Ryan et al. (2002) found that this deficit could be eliminated in older adults by administering caffeine during their non-optimal time-of-day, the late afternoon. However, there are no benefits of caffeine if administered during an individual’s optimal time of day. It remains unclear whether the same patterns of effects of caffeine would be seen in younger adults. Experiment 1 examined whether caffeine enhanced memory in the early morning. Thirty minutes after consuming a cup of coffee (caffeinated or decaffeinated), participants completed implicit and explicit versions of a word stem completion task. Young adults who consumed caffeinated coffee demonstrated significant improvements in explicit memory, but not implicit memory. Experiment 2 examined the effect of caffeine in younger adults during their optimal time of day, where results show that caffeine had no effect on memory performance. This suggests that that caffeine serves a compensatory role, aiding time-of-day deficits. Finally, experiment 3 examined whether exercise would also ameliorate time-of-day deficits. Young adults completed 15 minutes of either cardiovascular exercise or gentle stretching. Heart rates were taken throughout the experiment to measure physiological arousal. While exercise clearly increased physiological arousal, exercise had no effect on either explicit or implicit memory. Taken together, these results suggest a unique mechanism for caffeine-induced arousal that compensates for time-of-day memory deficits.
Synthetic nucleases for genome engineering in plants: prospects for a bright future.

By inducing double-strand breaks (DSB), it is possible to initiate DNA recombination. For a long time, it was not possible to use DSB induction for efficient genome engineering due to the lack of a means to target DSBs to specific sites. This limitation was overcome by development of modified meganucleases and synthetic DNA-binding domains. Domains derived from zinc-finger transcription factors or transcription activator-like effectors may be designed to recognize almost any DNA sequence. By fusing these domains to the endonuclease domains of a class II restriction enzyme, an active endonuclease dimer may be formed that introduces a site-specific DSB. Recent studies demonstrate that gene knockouts via non-homologous end joining or gene modification via homologous recombination are becoming routine in many plant species. By creating a single genomic DSB, complete knockout of a gene, sequence-specific integration of foreign DNA or subtle modification of individual amino acids in a specific protein domain may be achieved. The induction of two or more DSBs allows complex genomic rearrangements such as deletions, inversions or the exchange of chromosome arms. The potential for controlled genome engineering in plants is tremendous. The recently discovered RNA-based CRISPR/Cas system, a new tool to induce multiple DSBs, and sophisticated technical applications, such as the in planta gene targeting system, are further steps in this development. At present, the focus remains on engineering of single genes; in the future, engineering of whole genomes will become an option.
Relational Self-Construal Moderates Relationship between Relational Success and Self-Esteem

This study examined the role of the relational self-construal, the degree to which people incorporate close relationships into their self-concept, in the Sociometer Theory, which claims that self-esteem is the output from relational acceptance or rejection. I hypothesized that (a) the relational self-construal will moderate the relationship between loneliness and self-esteem, and (b) the relational self-construal will moderate the relationship between the quality of relationships and self-esteem. A total of 183 undergraduates completed a series of online questionnaires. I found a significant negative correlation between loneliness and self-esteem. I also found that for women, but not men, the relational self-construal moderates the relationship between the quality of relationships and self-esteem. So, for high relational women, the quality of relationships is positively related to self-esteem, whereas for low relational women, there is no relationship between the quality of relationships and self-esteem. This study demonstrated the importance of the relational self-construal for relational theories such as the Sociometer theory. This study also suggested that gender differences play a role in the relationship between the quality of relationships, relational self-construal, and self-esteem. RELATIONAL SELF-CONSTRUAL 4 Relational Self-Construal Moderates Relationship between Relational Success and Self-Esteem The need to belong is a central human motivation (Baumeister & Leary, 1995). People have a profound drive to form intimate interpersonal relationships, and positive outcomes result when people develop these relationships. Social relationships have also been consistently linked with health benefits (House, Landis, & Umberson, 1988). Past research on the need to belong shows how fundamental and powerful relationships can be; however, the self-concept has a role in relationships, too. The current research examines the benefits of relationships in general, and particular focus is given to specific, close relationships. The purpose of this study is to explore the importance of the self-concept for relational success and self-worth. This analysis incorporates individual differences, which provides depth and variety to the relational literature.
Nerve Regeneration Restores Supraspinal Control of Bladder Function after Complete Spinal Cord Injury

A life-threatening disability after complete spinal cord injury is urinary dysfunction, which is attributable to lack of regeneration of supraspinal pathways that control the bladder. Although numerous strategies have been proposed that can promote the regrowth of severed axons in the adult CNS, at present, the approaches by which this can be accomplished after complete cord transection are quite limited. In the present study, we modified a classic peripheral nerve grafting technique with the use of chondroitinase to facilitate the regeneration of axons across and beyond an extensive thoracic spinal cord transection lesion in adult rats. The novel combination treatment allows for remarkably lengthy regeneration of certain subtypes of brainstem and propriospinal axons across the injury site and is followed by markedly improved urinary function. Our studies provide evidence that an enhanced nerve grafting strategy represents a potential regenerative treatment after severe spinal cord injury.
Comparing Differences in Presence during Social Interaction in Augmented Reality versus Virtual Reality Environments: An Exploratory Study

In augmented reality (AR) environments, users experience the physical environment and other users directly along with mediated virtual objects embedded in the environment. In immersive virtual reality (VR), users experience of a visual environment (and sometimes other senses) is completely mediated. The representation of user’s body in virtual environments granted us a new research territory in dualistic interaction between the mind and body: how do the virtual body and user’s mind interact one another, and eventually affect user’s behaviors to the environment? An experiment was conducted to explore potential effect of users and interactant’s body to sense of presence in VR and AR environments. Results from the study suggest that the absence of representations of the user’s body in VR environment may lessen sense of spatial presence comparing with AR environment
THE WEAK CONVERGENCE ANALYSIS OF TAU-LEAPING METHODS: REVISITED

There are two scalings for the convergence analysis of tau-leaping methods in the literature. We try to resolve this debate in the paper. We point out the shortcomings of both scalings. We systematically develop the weak Ito-Taylor expansion based on the infinitesimal generator of the chemical kinetic system and generalize the rooted tree theory for ODEs and SDEs driven by Brownian motion to rooted directed graph theory for the jump processes. We formulate the local truncation error analysis based on the large volume scaling. We find that even in this framework the midpoint tau-leaping does not improve the weak local order for the covariance compared with the explicit tau-leaping. We propose a procedure to explain the numerical order behavior by abandoning the dependence on the volume constant V from the leading error term. The numerical examples validate our arguments. We also give a general global weak convergence analysis for the explicit tau-leaping type methods in the large volume scaling.
A retrospective study of 109 dogs with mandibular fractures

Summary Objective: To determine patient factors and fracture morphology of dogs presented with mandibular fractures to a small animal referral centre in South Africa. Methods: Patient data on age, sex, breed and aetiology of dogs with mandibular fractures were recorded. The fractures were classified according to the anatomical location, displacement, fracture type, fracture line direction, periodontal pathology, and whether there were teeth in the fracture line or not by evaluation of preoperative radiographs. Clinical observations indicated whether these fractures were open or closed. Results: In total, 109 dogs with 135 mandibular fractures were included in the study. Small breed dogs and dogs less than eight months of age predominated (102/109). Dog fights were the most common aetiology in this study (68/109). The molar region was the most commonly affected region (56/135). Evaluation of the radiographs revealed that transverse (73/135), relatively unstable (116/135), and displaced (112/135) fractures were the most common. The majority of fractures involved teeth in the fracture line (100/135), with the first molar frequently involved (54/135). The majority of fractures were open (104/135). Clinical significance: The results obtained from this study may be used to guide patient and fracture morphology selection in biomechanical studies of mandibular fracture repair techniques. Screening of this patient population may inspire the search for new treatment options for mandibular fracture repair in South Africa.