Miracle-dz/UniFAR-FTUs huggingface dataset:
Absence of the Min System Does Not Cause Major Cell Division Defects in Agrobacterium tumefaciens

In A. tumefaciens, the essential FtsZ protein is located at the growth pole before shifting to the mid-cell right before division. Loss of FtsZ causes a halt in cell separation and lysis of cells. To understand how FtsZ polymerization is regulated to properly localize the FtsZ ring at the mid-cell, we have conducted a systematic characterization of the Min system in A. tumefaciens. Our findings indicate that the Min system is not required for cell survival. Yet, we find that the deletion of either minE or minCDE results in a broad cell size distribution, including an increase in the proportion of short and long cells. We observe that the site of constriction is misplaced in the minE or minCDE deletion strains allowing for short cells to arise from sites of constriction near the cell poles. Remarkably, the short cells are viable and contain DNA. In order to observe chromosome replication and segregation in these strains, YFP-ParB is used as a proxy to track the origin of replication as cells elongate and divide. In the absence of the Min proteins, duplication and segregation of the origin of replication is frequently delayed. Taken together, our data suggest that the Min system contributes to the proper regulation of FtsZ placement and subsequent cell division. Furthermore, the failure to precisely place FtsZ rings at mid-cell in the min mutants impacts other cell cycle features including chromosome segregation.
CluB: a cluster based framework for mitigating distributed denial of service attacks

Distributed Denial of Service (DDoS) attacks are threats not only for the direct targets but also for the core of the network. They are also hard to detect in advance, hence methods to deal with them need to be proactive. By building on earlier work and improving on distribution of control aspects, we propose a Cluster Based framework, which is called CluB, to mitigate DDoS attacks; the method balances the effectiveness-overhead trade-off by addressing the issue of granularity of control in the network. CluB can collaborate with different routing policies in the network, including contemporary datagram options. We estimate the effectiveness of the framework and also study a set of factors for tuning the granularity of control.
Supermarket and Grocery Store–Based Interventions to Promote Healthful Food Choices and Eating Practices: A Systematic Review

Introduction Increasingly high rates of obesity have heightened interest among researchers and practitioners in identifying evidence-based interventions to increase access to healthful foods and beverages. Because most food purchasing decisions are made in food stores, such settings are optimal for interventions aimed at influencing these decisions. The objective of this review was to synthesize the evidence on supermarket and grocery store interventions to promote healthful food choices. Methods We searched PubMed through July 2012 to identify original research articles evaluating supermarket and grocery store interventions that promoted healthful food choices. We categorized each intervention by type of intervention strategy and extracted and summarized data on each intervention. We developed a scoring system for evaluating each intervention and assigned points for study design, effectiveness, reach, and availability of evidence. We averaged points for each intervention category and compared the strength of the evidence for each category. Results We identified 58 articles and characterized 33 interventions. We found 7 strategies used alone or in combination. The most frequently used strategy was the combination of point-of-purchase and promotion and advertising (15 interventions); evidence for this category was scored as sufficient. On average, of 3 points possible, the intervention categories scored 2.6 for study design, 1.1 for effectiveness, 0.3 for reach, and 2 for availability of evidence. Three categories showed sufficient evidence; 4 showed insufficient evidence; none showed strong evidence. Conclusion More rigorous testing of interventions aimed at improving food and beverage choices in food stores, including their effect on diet and health outcomes, is needed.
Neuromodulation for depression: Insights gained from neuroimaging and computational models

NEUROMODULATION FOR DEPRESSION: INSIGHTS GAINED FROM NEUROIMAGING AND COMPUTATIONAL MODELS Yagna Pathak, B.S., M.Eng. Marquette University, 2014 Major depressive disorder (MDD) is a public health concern worldwide, affecting a sixth of the American population. Neuromodulation therapies have been employed to treat severe cases of treatment resistant depression. These procedures attempt to modulate activity in cortical regions that represent nodes in brain circuits believed to be involved in MDD. One challenge in neuromodulation trials has been the difficulty in quantifying outcome variability. We sought to understand the effects of neuromodulation therapies and their sources of variability while adding an objective perspective to assess clinical improvement in neuropsychiatric disorders such as depression. The goal of my dissertation was to investigate the neuronal circuitry of MDD patients who were treated using neuromodulation. Our primary measures were behavior scores and results from functional neuroimaging. The specific aims of this study were to answer three fundamental questions: 1) What is the role of stimulation parameters in patient response to chronic epidural cortical stimulation (EpCS) for MDD? 2) What functional changes result from repetitive transcranial magnetic stimulation (rTMS) for MDD? 3) How does stimulation of different targets in the depressive circuit affect antidepressive response? Our results suggest that combining neuroimaging with computational tools can increase the predictive power to determine who is likely to respond to a specific neuromodulation treatment course. We demonstrated the significance of stimulation parameters (location, polarity, duration) and the engagement of crucial nodes of the depressive circuit in order to achieve a sustained clinical improvement. Additionally, we showed that it is possible to affect deeper brain regions by targeting superficial areas that are easier to access with noninvasive modalities. The approaches highlighted in this dissertation can provide valuable insights about patients evaluated for neuromodulation for depression.
Pathogenesis of murine gammaherpesvirus infection in mice deficient in CD4 and CD8 T cells

Murine gammaherpesvirus is a natural pathogen of wild mice. The virus infects alveolar cells and spleen cells during the primary infection and establishes a latent/persistent infection in B lymphocytes. Little is known about the immunological response to gammaherpesviruses during a primary infection. To address this issue, we investigated the pathogenesis of murine herpesvirus 68 (MHV-68) infection in mice deficient in CD4 or CD8 T-cell populations. Infection of the lung and spleen were greatly exacerbated in CD8-deficient mice, reflected by elevated virus titers in the lung and an increase in the number of infected splenocytes located around germinal centers. This finding contrasts with clearance of virus from the lung and spleen by day 12 postinfection in CD4-depleted animals. These data clearly indicate a major role for CD8 T cells in recovery from an acute MHV-68 infection. Whereas CD4 T cells fail to influence the course of infection in the lung, they do contribute to lymphoproliferation seen in the spleen (splenomegaly) during the primary infection. The significance of these results are discussed in relation to the immune response to other herpesviruses, in particular Epstein-Barr virus, with which MHV-68 shares similar molecular and biological properties.
Epidemiology of Tuberculosis in a High HIV Prevalence Population Provided with Enhanced Diagnosis of Symptomatic Disease

Background Directly observed treatment short course (DOTS), the global control strategy aimed at controlling tuberculosis (TB) transmission through prompt diagnosis of symptomatic smear-positive disease, has failed to prevent rising tuberculosis incidence rates in Africa brought about by the HIV epidemic. However, rising incidence does not necessarily imply failure to control tuberculosis transmission, which is primarily driven by prevalent infectious disease. We investigated the epidemiology of prevalent and incident TB in a high HIV prevalence population provided with enhanced primary health care. Methods and Findings Twenty-two businesses in Harare, Zimbabwe, were provided with free smear- and culture-based investigation of TB symptoms through occupational clinics. Anonymised HIV tests were requested from all employees. After 2 y of follow-up for incident TB, a culture-based survey for undiagnosed prevalent TB was conducted. A total of 6,440 of 7,478 eligible employees participated. HIV prevalence was 19%. For HIV-positive and -negative participants, the incidence of culture-positive tuberculosis was 25.3 and 1.3 per 1,000 person-years, respectively (adjusted incidence rate ratio = 18.8; 95% confidence interval [CI] = 10.3 to 34.5: population attributable fraction = 78%), and point prevalence after 2 y was 5.7 and 2.6 per 1,000 population (adjusted odds ratio = 1.7; 95% CI = 0.5 to 6.8: population attributable fraction = 14%). Most patients with prevalent culture-positive TB had subclinical disease when first detected. Conclusions Strategies based on prompt investigation of TB symptoms, such as DOTS, may be an effective way of controlling prevalent TB in high HIV prevalence populations. This may translate into effective control of TB transmission despite high TB incidence rates and a period of subclinical infectiousness in some patients.
Aliasing-Free Wideband Beamforming Using Sparse Signal Representation

Sparse signal representation (SSR) is considered to be an appealing alternative to classical beamforming for direction-of-arrival (DOA) estimation. For wideband signals, the SSR-based approach constructs steering matrices, referred to as dictionaries in this paper, corresponding to different frequency components of the target signal. However, the SSR-based approach is subject to ambiguity resulting from not only spatial aliasing, just like in classical beamforming, but also from the over-completeness of the dictionary, which is typical to SSR. We show that the ambiguity caused by the over-completeness of the dictionary can be alleviated by using multiple measurement vectors. In addition, by considering the uniform linear array (ULA) structure, we argue that if the target signal contains at least two frequencies, whose absolute difference phrased in wavelengths is larger than twice the array spacing, the spatial aliasing corresponding to these frequencies will be completely distinct. These properties enable us to adapt the existing ℓ1 algorithms to extract the target DOAs without ambiguity.
Indole, a Signaling Molecule Produced by the Gut Microbiota, Negatively Impacts Emotional Behaviors in Rats

Gut microbiota produces a wide and diverse array of metabolites that are an integral part of the host metabolome. The emergence of the gut microbiome-brain axis concept has prompted investigations on the role of gut microbiota dysbioses in the pathophysiology of brain diseases. Specifically, the search for microbe-related metabolomic signatures in human patients and animal models of psychiatric disorders has pointed out the importance of the microbial metabolism of aromatic amino acids. Here, we investigated the effect of indole on brain and behavior in rats. Indole is produced by gut microbiota from tryptophan, through the tryptophanase enzyme encoded by the tnaA gene. First, we mimicked an acute and high overproduction of indole by injecting this compound in the cecum of conventional rats. This treatment led to a dramatic decrease of motor activity. The neurodepressant oxidized derivatives of indole, oxindole and isatin, accumulated in the brain. In addition, increase in eye blinking frequency and in c-Fos protein expression in the dorsal vagal complex denoted a vagus nerve activation. Second, we mimicked a chronic and moderate overproduction of indole by colonizing germ-free rats with the indole-producing bacterial species Escherichia coli. We compared emotional behaviors of these rats with those of germ-free rats colonized with a genetically-engineered counterpart strain unable to produce indole. Rats overproducing indole displayed higher helplessness in the tail suspension test, and enhanced anxiety-like behavior in the novelty, elevated plus maze and open-field tests. Vagus nerve activation was suggested by an increase in eye blinking frequency. However, unlike the conventional rats dosed with a high amount of indole, the motor activity was not altered and neither oxindole nor isatin could be detected in the brain. Further studies are required for a comprehensive understanding of the mechanisms supporting indole effects on emotional behaviors. As our findings suggest that people whose gut microbiota is highly prone to produce indole could be more likely to develop anxiety and mood disorders, we addressed the issue of the inter-individual variability of indole producing potential in humans. An in silico investigation of metagenomic data focused on the tnaA gene products definitively proved this inter-individual variability.
Updating a Systematic Review about Selection of Software Requirements Elicitation Techniques

Quality of software producis is closely related to the elicitation requirement process. Several studies point out that elicitation techniques achieve different results when applied in different contexts. This paper presents some recommendations about the situations in which elicitation techniques are useful. Recommendations are based on a previous systematic review, which was updated and expanded with 13 new empirical studies and more than 60 new empirical results. The aggregation process generated 5 new evidences and modified 4 existing ones. In the previous review, it was found that interviews were one of the most adequate techniques in most situations. The new evidence supports the same conclusion
Interventions for reducing the use of seclusion in psychiatric facilities

Background The authors of a recent systematic review concluded that the use of non-pharmacological containment methods, excluding restraint and seclusion, was not supported by evidence. Their focus on randomised, controlled trials, however, does not reflect the research that has been, or could be, conducted. Aims To find empirically supported interventions that allow reduction in the use of seclusion in psychiatric facilities. Method We reviewed English-language, peer-reviewed literature on interventions that allow reduction in the use of seclusion. Results Staff typically used multiple interventions, including state-level support, state policy and regulation changes, leadership, examinations of the practice contexts, staff integration, treatment plan improvement, increased staff to patient ratios, monitoring seclusion episodes, psychiatric emergency response teams, staff education, monitoring of patients, pharmacological interventions, treating patients as active participants in seclusion reduction interventions, changing the therapeutic environment, changing the facility environment, adopting a facility focus, and improving staff safety and welfare. Conclusions Reducing seclusion rates is challenging and generally requires staff to implement several interventions.
Designing Cyber Insurance Policies: The Role of Pre-Screening and Security Interdependence

Cyber insurance is a viable method for cyber risk transfer. However, it has been shown that depending on the features of the underlying environment, it may or may not improve the state of network security. In this paper, we consider a single profit-maximizing insurer (principal) with voluntarily participating insureds/clients (agents). We are particularly interested in two distinct features of cybersecurity and their impact on the contract design problem. The first is the interdependent nature of cybersecurity, whereby one entity’s state of security depends not only on its own investment and effort, but also the efforts of others’ in the same eco-system (i.e., externalities). The second is the fact that recent advances in Internet measurement combined with machine learning techniques now allow us to perform accurate quantitative assessments of security posture at a firm level. This can be used as a tool to perform an initial security audit, or pre-screening, of a prospective client to better enable premium discrimination and the design of customized policies. We show that security interdependency leads to a “profit opportunity” for the insurer, created by the inefficient effort levels exerted by interdependent agents who do not account for the risk externalities when insurance is not available; this is in addition to risk transfer that an insurer typically profits from. Security pre-screening then allows the insurer to take advantage of this additional profit opportunity by designing the appropriate contracts which incentivize agents to increase their effort levels, allowing the insurer to “sell commitment” to interdependent agents, in addition to insuring their risks. We identify conditions under which this type of contract leads to not only increased profit for the principal, but also an improved state of network security.
Design and tensile properties of a bcc Ti-rich high-entropy alloy with transformation-induced plasticity

ABSTRACT A new bcc Ti-rich high-entropy alloy (HEA) of composition Ti35Zr27.5Hf27. 5Nb5Ta5 was designed using the ‘d-electron alloy design’ approach. The tensile behavior displays a marked transformation-induced plasticity effect resulting in a high normalized work-hardening rate of 0.103 without loss of ductility when compared to the reference composition Ti20Zr20Hf20Nb20Ta20. In this paper, a detailed microstructural analysis was performed to understand the deformation process, revealing architectural-type microstructures and a high volume fraction (65%) of internally twinned stress-induced martensite α″ after mechanical testing. This study opens the way to mechanical properties optimization and enhancement of titanium-based HEAs by combining multiple alloying designs. IMPACT STATEMENT For the first time, proof is given that transformation-induced plasticity was triggered in a bcc refractory high-entropy alloy, leading to a twofold increase in the normalized work-hardening rate. GRAPHICAL ABSTRACT
Lexical Cohesion: Some Implications of an Empirical Study

Lexical cohesion refers to the perceived unity of text achieved by the author’s usage of words with related meanings[1]. Data from an experiment with 22 readers aimed at eliciting lexical cohesive patterns they see in 10 texts [2, 3] is used to shed light on a number of theoretical and applied aspects of the phenomenon: which items in the text carry the cohesive load; what are the appropriate data structures to represent cohesive texture; what are the relations employed in cohesive structures.
That went over my head: Constraints on the visual vocabulary of comics

“Upfixes” are graphic representations originating in the visual vocabulary used in comics where objects float above a character’s head, such as lightbulbs to mean inspiration. We posited that these graphic signs use an abstract schema stored in memory. This schema constrains upfixes to their position above the head and requires them to “agree” with the expression of their associated face. We asked participants to rate and interpret upfix-face pairs where the upfix was either above the head or beside the head, and/or agreed or disagreed with the face. Our stimuli also contrasted conventional and novel upfixes. Overall, both position and agreement impacted the rating and interpretations of both conventional and unconventional upfixes, and such understanding is modulated by experience reading comics. These findings support that these graphic signs extend beyond memorized individual items, and use a learned abstract schema stored in long-term memory, governed by particular constraints.
Adaptive Spatio-Temporal Filtering for Movement Related Potentials in EEG-Based Brain–Computer Interfaces

Movement related potentials (MRPs) are used as features in many brain-computer interfaces (BCIs) based on electroencephalogram (EEG). MRP feature extraction is challenging since EEG is noisy and varies between subjects. Previous studies used spatial and spatio-temporal filtering methods to deal with these problems. However, they did not optimize temporal information or may have been susceptible to overfitting when training data are limited and the feature space is of high dimension. Furthermore, most of these studies manually select data windows and low-pass frequencies. We propose an adaptive spatio-temporal (AST) filtering method to model MRPs more accurately in lower dimensional space. AST automatically optimizes all parameters by employing a Gaussian kernel to construct a low-pass time-frequency filter and a linear ridge regression (LRR) algorithm to compute a spatial filter. Optimal parameters are simultaneously sought by minimizing leave-one-out cross-validation error through gradient descent. Using four BCI datasets from 12 individuals, we compare the performances of AST filter to two popular methods: the discriminant spatial pattern filter and regularized spatio-temporal filter. The results demonstrate that our AST filter can make more accurate predictions and is computationally feasible.
Pedagogical Frameworks and Technologies for Online Network Laboratory Instruction - Research Issues in Matching Technology to Pedagogical Processes

We investigate the technological issues involved in designing an electronic learning system that adapts pedagogical approaches and best practice instructional strategies to model, design and implement a blended virtual learning space. We discuss technology issues that are challenging in the design and implementation of a modular integrated web environment (IWE) used to deliver online network laboratory learning. We show that the IWE must incorporate an online laboratory tutorial system for guided practice to elicit performance from the learner. Also, the learning space must be designed to match the quality of service (QoS) requirements to the interaction taking place in the learning space and the characteristics of the delivery media must be matched to learning process. This approach promotes good student interaction & infrastructure management.