Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Adenine Methylation Is Required to Replicate Both Vibrio cholerae Chromosomes Once per Cell Cycle

DNA adenine methylation is widely used to control many DNA transactions, including replication. In Escherichia coli, methylation serves to silence newly synthesized (hemimethylated) sister origins. SeqA, a protein that binds to hemimethylated DNA, mediates the silencing, and this is necessary to restrict replication to once per cell cycle. The methylation, however, is not essential for replication initiation per se but appeared so when the origins (oriI and oriII) of the two Vibrio cholerae chromosomes were used to drive plasmid replication in E. coli. Here we show that, as in the case of E. coli, methylation is not essential for oriI when it drives chromosomal replication and is needed for once-per-cell-cycle replication in a SeqA-dependent fashion. We found that oriII also needs SeqA for once-per-cell-cycle replication and, additionally, full methylation for efficient initiator binding. The requirement for initiator binding might suffice to make methylation an essential function in V. cholerae. The structure of oriII suggests that it originated from a plasmid, but unlike plasmids, oriII makes use of methylation for once-per-cell-cycle replication, the norm for chromosomal but not plasmid replication.
Role of serotonin and norepinephrine systems in functional recovery after stroke

Stroke is a leading cause of permanent disability worldwide. Physiotherapy facilitates motor recovery after stroke but recovery is often incomplete, highlighting the need to develop other methods (e.g. utilizing more intensive rehabilitation or combining rehabilitation with drug therapy) to augment existing therapies. Depression is a common occurrence after stroke and consequently a large population of stroke patients are treated with antidepressants. Most antidepressants act to facilitate actions of serotonin, norepinephrine, or both. Despite the prevalence of antidepressant use, little is known about how these drugs might affect the recovery of motor function in these patients. The involvement of serotonin and norepinephrine in motor recovery after focal ischemia in the rat was the focus of this thesis. Serotonin selective reuptake inhibitors are often the antidepressants of choice in the stroke population. In the first experiment a chronic dose of fluoxetine (a serotonin specific reuptake inhibitor) was combined with rehabilitation to determine if it facilitated motor recovery. No effect of the drug was found suggesting that facilitating the serotonin system has little or no effect on motor recovery. In the second experiment norepinephrine was depleted using N-(2-chloroethyl)-Nethyl- 2-bromobenzylamine, a neurotoxin specific for terminals of norepinephrine cells of the locus coeruleus. Depleting norepinephrine terminals improved recovery in animals exposed to enriched rehabilitation as well as standard housed animals. This suggests that norepinephrine plays a role in recovery of function but that role may be more complicated than previously thought. The final experiment compared four different endothelin-1 models of focal ischemia, including the models used in the previous experiments (experiment 1: focal ischemia of the cortex and striatum by localized injection or experiment 2: by injection adjacent to the middle cerebral artery). While all four models produced similar behavioural deficits the model that targeted the middle cerebral artery (the most commonly used model) yielded the lowest success rate (as determined by survival and ability to produce a forelimb reaching deficit). The more successful model combining cortical and striatal injections of endothelin-1 was further characterized using magnetic resonance imaging and found to have blood flow dynamics similar to clinical stroke. The results of this thesis help to clarify previous findings regarding the antidepressant, fluoxetine and recovery of function. In addition, the current findings further explore the role of norepinephrine in stroke recovery with indications for future research. Finally, I introduce a new endothelin-1 model of focal ischemia that is a more consistent and clinically relevant alternative to existing models.
The role of unique personal representations in understanding and responding to the emotions of others

Emotional expressions like sadness and crying are thought to signal need and adaptively motivate others to help. Such clear displays often do elicit empathy and prosocial behavior, but can also elicit personal distress, aggression, and even horror. The perception-action model (PAM) assumes that such varying responses reflect individuals’ differing internal representations for affective states and situations derived from prior experience in life, family, and culture. This assumption was tested across two studies by predicting the prosocial response to sad (distraught) versus more positive (resilient) female targets through the strength of individual associations between females and sadness. Participant associations were measured with two different methods: a modified Implicit Associations Test (IAT) that measured female-sadness and male-anger associations (Chapter 2) and a priming task that measured associations between gender and sadness as well as gender role stereotypes (Chapter 3). Across studies, participants with stronger female-sadness associations offered more help to distraught over resilient females, an effect that was specific to the affective associations and not due to more general stereotyping. People appear to behave more prosocially towards those who express emotion in ways they believe are normative, but these beliefs differ across individuals, with profound implications for interpersonal exchanges.
Explaining the Determinants of First Phase HIV Decay Dynamics through the Effects of Stage-dependent Drug Action

A recent investigation of the effect of different antiretroviral drug classes on first phase dynamics of HIV RNA plasma virus levels has indicated that drugs acting at stages closer to viral production, such as the integrase inhibitor raltegravir, can produce a steeper first phase decay slope that may not be due to drug efficacy. Moreover it was found that for most drug classes the first phase transitions from a faster (phase IA) to a slightly slower decay region (phase IB) before the start of the usual second phase. Neither of these effects has been explained to date. We use a mathematical model that incorporates the different stages of the HIV viral life cycle in CD4+ T cells: viral entry, reverse transcription, integration, and viral production, to investigate the intracellular HIV mechanisms responsible for these complex plasma virus decay dynamics. We find differences in the phase IA slope across drug classes arise from a higher death rate of cells when they enter the productively infected stage post-integration, with a half-life of approximately 8 hours in this stage, whereas cells in earlier stages of the infection cycle have half-lives similar to uninfected cells. This implies any immune clearance is predominantly limited to the productive infection stage. We also show that the slowing of phase IA to phase IB at day 2 to 4 of monotherapy, depending on drug class, is a result of new rounds of infection. The level at which this slowing occurs is a better indicator of drug efficacy than the slope of the initial decay.
The “Reading the Mind in the Eyes” test: Systematic review of psychometric properties and a validation study in Italy

Introduction. The “Reading the Mind in the Eyes” test (henceforth, Eyes test) is a simple but advanced Theory of Mind test, and it is widely used across different cultures. This study assessed the reliability and construct (convergent and discriminant) validity of the Eyes test in Italy. Methods. A sample of 18- to 32-year-old undergraduate students of both sexes (N=200, males=46%) were invited to fill in the Italian version of the Eyes test, the Empathy Quotient (EQ), the Toronto Alexithymia Scale (TAS), and the Marlowe-Crowne Social Desirability Scale (SDS). Results. Internal consistency (Cronbach's alpha) was . 605. Confirmatory factor analysis provided evidence for a unidimensional model, with maximal weighted internal consistency reliability=. 719. Test–retest reliability for the Eyes test, as measured by intraclass correlation coefficient, was . 833 (95% confidence interval=.745 to .902). Females scored significantly higher than males on both the Eyes test and the EQ, replicating earlier work. Those participants who scored lower than 30 on the EQ (n=10) also scored lower on the Eyes test than those who did not (p<.05). Eyes test scores were not related to social desirability. Conclusions. This study confirms the validity of the Eyes test. Both internal consistency and test–retest stability were good for the Italian version of the Eyes test.
Attitudes of coaches towards doping.

BACKGROUND Coaches are usually held to be among the main actors of doping prevention campaigns. The aim of this study was to document certain attitudes of professional coaches faced with doping, and to evaluate how they confronted it on an everyday basis. METHODS EXPERIMENTAL DESIGN prospective study by self-reporting questionnaire. SETTING AND PARTICIPANTS the questionnaire was mailed to the last 800 graduated coaches (1994-1997) in the Lorraine region, Eastern France. The 260 responding coaches comprised 77 women and 183 men, the average age being 30.8 +/- 8.0 years (mean +/- standard deviation). RESULTS 10.3% of coaches consider that an athlete may use doping with no health hazard with the help of a physician, and 30.0% that an athlete who declines doping has little chance of succeeding. 5.8% had used doping drugs in the last twelve months (1 to 6 times). 13.5% of coaches mention that athletes (1 to 5 per coach on average) told them they had been prompted to use doping drugs during the previous 12 months. 80.7% consider that the current methods of preventing doping in sport are ineffective, and 98.1% of them consider that they have a role to play within this context, but 80.3% consider themselves badly trained in the prevention of doping. Only 10.4% have organized a doping prevention action during the last 12 months. CONCLUSIONS In this study, professional coaches do not seem to be efficient in the prevention of doping. Further education and training for coaches on doping is advisable.
Security evaluation of application-specific integrated circuits and field programmable gate arrays against setup time violation attacks

Fault attacks are real threats against hardware implementations of robust cryptographic algorithms such as advanced encryption standard (AES). The authors present an active non-invasive attack to inject faults during the execution of the algorithm and describe setup time violation attacks by under-powering and overclocking an application-specific integrated circuit. Then a security evaluation is presented against setup time violation attacks of several AES architectures on two field programmable gate arrays (FPGA) brands, namely Altera Stratix and Xilinx Virtex5. The authors notice that the architecture of the substitution box greatly impacts the faults statistics. These statistics are furthermore different depending on the FPGA vendor, and also notice that it is more difficult to inject single fault in the most recent technology. Also, the use-cases show how difficult it is to predict the most vulnerable resource in an FPGA. Finally, a low-cost countermeasure against this kind of attack is presented.
Job Related Tension, Interactional Justice and Job Involvement among Workers of Dangote Cement Company Gboko

The study assessed job related tension, interactional justice and job involvement among workers of Dangote Cement Company Gboko in Benue State, Nigeria. 173 (94 males and 79 females) workers participated in the study. Their ages ranged from 20-55 years with the mean age of 32.80 years. Job-related Tension Scale was used to assess workers job related tension. Interactional Justice Sub-scale was used to measure respondents' perceptions of interactional justice. Job involvement was measured using Job Involvement Scale. Results showed that job related tension has significant influence on job involvement. Interactional justice has no significant influence on job involvement. Results further show that job related tension and interactional justice have interactive effect on job involvement. It is therefore recommended that industries wanting to improve workers job involvement should consider multi-factorial approach of reducing job related tension and increasing interactional justice.
Velocity statistics from spectral line data: effects of density–velocity correlations, magnetic field and shear

In a previous work, Lazarian and Pogosyan suggested a technique to extract velocity and density statistics, of interstellar turbulence, by means of analysing statistics of spectral line data cubes. In this paper, we test that technique by studying the effect of correlation between velocity and density fields, providing a systematic analysis of the uncertainties arising from the numerics, and exploring the effect of a linear shear. We make use of both compressible magnetohydrodynamics simulations and synthetic data to emulate spectroscopic observations and to test the technique. With the same synthetic spectroscopic data, we have also studied anisotropies of the two point statistics and related those anisotropies with the magnetic field direction. This presents a new technique for magnetic field studies. The results show that the velocity and density spectral indices measured are consistent with the analytical predictions. We have identified the dominant source of error with the limited number of data points along a given line of sight. We decrease this type of noise by increasing the number of points and by introducing Gaussian smoothing. We argue that in real observations the number of emitting elements is essentially infinite and that the source of noise vanishes.
Language Independent Named Entity Identification using Wikipedia

Recognition of Named Entities (NEs) is a difficult process in Indian languages like Hindi, Telugu, etc., where sufficient gazetteers and annotated corpora are not available compared to English language. This paper details a novel clustering and co-occurrence based approach to map English NEs with their equivalent representations from different languages recognized in a language-independent way. We have substituted the required language specific resources by the richly structured multilingual content of Wikipedia. The approach includes clustering of highly similar Wikipedia articles. Then the NEs in an English article are mapped with other language terms in interlinked articles based on co-occurrence frequencies. The cluster information and the term co-occurrences are considered in extracting the NEs from non-English languages. Hence, the English Wikipedia is used to bootstrap the NEs for other languages. Through this approach, we have availed the structured, semi-structured and multilingual content of the Wikipedia to a massive extent. Experimental results suggest that the proposed approach yields promising results in rates of precision and recall.
Delays in activity-based neural networks

In this paper, we study the effect of two distinct discrete delays on the dynamics of a Wilson–Cowan neural network. This activity-based model describes the dynamics of synaptically interacting excitatory and inhibitory neuronal populations. We discuss the interpretation of the delays in the language of neurobiology and show how they can contribute to the generation of network rhythms. First, we focus on the use of linear stability theory to show how to destabilize a fixed point, leading to the onset of oscillatory behaviour. Next, we show for the choice of a Heaviside nonlinearity for the firing rate that such emergent oscillations can be either synchronous or anti-synchronous, depending on whether inhibition or excitation dominates the network architecture. To probe the behaviour of smooth (sigmoidal) nonlinear firing rates, we use a mixture of numerical bifurcation analysis and direct simulations, and uncover parameter windows that support chaotic behaviour. Finally, we comment on the role of delays in the generation of bursting oscillations, and discuss natural extensions of the work in this paper.
Spinophilin acts as a tumor suppressor by regulating Rb phosphorylation

The scaffold protein Spinophilin (SPN) is a regulatory subunit of phosphatase1a located at 17q21.33. This region is frequently associated with microsatellite instability and LOH containing a relatively high density of known tumor suppressor genes, including BRCA1. Several linkage studies have suggested the existence of an unknown tumor suppressor gene distal to BRCA1. Spn may be this gene, but the mechanism through which this gene makes its contribution to cancer has not been described. In this study, we aimed to determine how loss of Spn may contribute to tumorigenesis. We explored the contribution of SPN to PP1a-mediated Rb regulation. We found that the loss of Spn downregulated PPP1CA and PP1a activity, resulting in a high level of phosphorylated Rb and increased ARF and p53 activity. However, in the absence of p53, reduced levels of SPN enhanced the tumorigenic potential of the cells. Furthermore, the ectopic expression of SPN in human tumor cells greatly reduced cell growth. Taken together, our results demonstrate that the loss of Spn induces a proliferative response by increasing Rb phosphorylation, which, in turn, activates p53, thereby neutralizing the proliferative response. We suggest that Spn may be the tumor suppressor gene located at 17q21.33 acting through Rb regulation.
Use of AI Techniques for Residential Fire Detection in Wireless Sensor Networks

Early residential fire detection is important for prompt extinguishing and reducing damages and life losses. To detect fire, one or a combination of sensors and a detection algorithm are needed. The sensors might be part of a wireless sensor network (WSN) or work independently. The previous research in the area of fire detection using WSN has paid little or no attention to investigate the optimal set of sensors as well as use of learning mechanisms and Artificial Intelligence (AI) techniques. They have only made some assumptions on what might be considered as appropriate sensor or an arbitrary AI technique has been used. By closing the gap between traditional fire detection techniques and modern wireless sensor network capabilities, in this paper we present a guideline on choosing the most optimal sensor combinations for accurate residential fire detection. Additionally, applicability of a feed forward neural network (FFNN) and Naive Bayes Classifier is investigated and results in terms of detection rate and computational complexity are analyzed.
Soft-Switch DC-DC Converter with a High Conversion Ratio for an Electrical Bicycle

Transportation plays a big part in our society and to keep our environment sustainable, an environmental solution is needed. Unlike the car which accounts for a substantial percentage of worldwide greenhouse gas emissions, the electrical bicycle provides a healthy environmental-friendly alternative. The proposed electrical bicycle uses a universal series motor which has a low cost and weight but needs a high supply voltage. Standard batteries have a 24 V supply voltage which is far too low for universal series motor so a DC-DC converter with a high conversion ratio is needed. This paper proposes a soft-switch DC-DC converter with a high conversion ratio with an efficiency of 92%.
Neighborhood formation and anomaly detection in bipartite graphs

Many real applications can be modeled using bipartite graphs, such as users vs. files in a P2P system, traders vs. stocks in a financial trading system, conferences vs. authors in a scientific publication network, and so on. We introduce two operations on bipartite graphs: 1) identifying similar nodes (Neighborhood formation), and 2) finding abnormal nodes (Anomaly detection). And we propose algorithms to compute the neighborhood for each node using random walk with restarts and graph partitioning; we also propose algorithms to identify abnormal nodes, using neighborhood information. We evaluate the quality of neighborhoods based on semantics of the datasets, and we also measure the performance of the anomaly detection algorithm with manually injected anomalies. Both effectiveness and efficiency of the methods are confirmed by experiments on several real datasets.
Sonographic Findings for the Common Extensor Tendon of the Elbow in the General Population

Objective. To describe structural characteristics and sonographic alterations of the common extensor tendon (CET). Methods. In 240 patients, we determined the body mass index; sonographic CET thickness, morphologic characteristics, and alterations; and color Doppler measurements of the epicondylar artery width and peak systolic velocity. Age, sex, epicondylalgia history, activities (work, sports, and hobbies), and dominant and nondominant elbows were noted. Results. The CET was thicker in the dominant elbow (4.77 versus 4.61 mm [P = .023]), male patients (dominant, 5.09 versus 4.46 mm [P < .001]; nondominant, 5.00 versus 4.21 mm [P < .001]), patients involved in risk activities (dominant, 5.21 versus 4.70 mm [P < .001]; nondominant, 5.12 versus 4.53 mm [P < .001]), and those with a history of epicondylalgia (right, 5.27 versus 4.70 mm [P < .001]; left, 4.86 versus 4.60 mm [P = .316]). Thickness correlated weakly with age (dominant, r = 0.284; nondominant, r = 0.215) and moderately with weight (dominant, r = 0.492; nondominant, r = 0.502). The mean epicondylar artery diameter was 1.35 mm (SD, 0.96 mm); mean peak velocity, 13.01 cm/s (SD, 4.90 cm/s). Morphologic abnormalities were found in 79.5% of patients with a history of epicondylalgia; 7.7% with no history had abnormalities; and 55.9% with abnormalities but no history were older than 55 years. Bone spurs (49.2% versus 16.4% [P < .001]), tendon calcifications (21.5% versus 3.9% [P < .001]), and bone cortex abnormalities (12.3% versus 1.7% [P < .001]) were found more often in non‐normal elbows; 79.4% of bone spurs in normal elbows occurred in patients older than 55 years. Conclusions. Mild sonographic alterations in the CET and bone spurs should be considered with caution when assessing epicondylar pain, especially in patients older than 55 years and those with a history of epicondylalgia.
Wave propagation in gravitational systems: Completeness of quasinormal modes.

The dynamics of relativistic stars and black holes are often studied in terms of the quasinormal modes (QNM’s) of the Klein-Gordon (KG) equation with different effective potentials V (x). In this paper we present a systematic study of the relation between the structure of the QNM’s of the KG equation and the form of V (x). In particular, we determine the requirements on V (x) in order for the QNM’s to form complete sets, and discuss in what sense they form complete sets. Among other implications, this study opens up the possibility of using QNM expansions to analyse the behavior of waves in relativistic systems, even for systems whose QNM’s do not form a complete set. For such systems, we show that a complete set of QNM’s can often be obtained by introducing an infinitesimal change in the effective potential.