Miracle-dz/UniFAR-FTUs huggingface dataset:
Control of a Wheelchair in an Indoor Environment Based on a Brain–Computer Interface and Automated Navigation

The concept of controlling a wheelchair using brain signals is promising. However, the continuous control of a wheelchair based on unstable and noisy electroencephalogram signals is unreliable and generates a significant mental burden for the user. A feasible solution is to integrate a brain-computer interface (BCI) with automated navigation techniques. This paper presents a brain-controlled intelligent wheelchair with the capability of automatic navigation. Using an autonomous navigation system, candidate destinations and waypoints are automatically generated based on the existing environment. The user selects a destination using a motor imagery (MI)-based or P300-based BCI. According to the determined destination, the navigation system plans a short and safe path and navigates the wheelchair to the destination. During the movement of the wheelchair, the user can issue a stop command with the BCI. Using our system, the mental burden of the user can be substantially alleviated. Furthermore, our system can adapt to changes in the environment. Two experiments based on MI and P300 were conducted to demonstrate the effectiveness of our system.
Subcortical Volume Loss in the Thalamus, Putamen, and Pallidum, Induced by Traumatic Brain Injury, Is Associated With Motor Performance Deficits

Background. Traumatic brain injury (TBI) has been associated with altered microstructural organization of white matter (WM) and reduced gray matter (GM). Although disrupted WM organization has been linked to poorer motor performance, the predictive value of GM atrophy for motor impairments in TBI remains unclear. Objective. Here, we investigated TBI-induced GM volumetric abnormalities and uniquely examined their relationship with bimanual motor impairments. Methods. 22 moderate to severe TBI patients (mean age = 25.9 years, standard deviation [SD] = 4.9 years; time since injury = 4.7 years, SD = 3.7 years) and 27 age- and gender-matched controls (mean age = 23.4 years; SD = 3.8 years) completed bimanual tasks and a structural magnetic resonance imaging scan. Cortical and subcortical GM volumes were extracted and compared between groups using FreeSurfer. The association between bimanual performance and GM volumetric measures was investigated using partial correlations. Results. Relative to controls, patients performed significantly poorer on the bimanual tasks and demonstrated significantly smaller total GM as well as overall and regional subcortical GM. However, the groups did not show significant differences in regional cortical GM volume. The majority of the results remained significant even after excluding TBI patients with focal lesions, suggesting that TBI-induced volume reductions were predominantly caused by diffuse injury. Importantly, atrophy of the thalamus, putamen, and pallidum correlated significantly with poorer bimanual performance within the TBI group. Conclusions. Our results reveal that GM atrophy is associated with motor impairments in TBI, providing new insights into the etiology of motor control impairments following brain trauma.
The Acetylation Motif in AMP-Forming Acyl Coenzyme A Synthetases Contains Residues Critical for Acetylation and Recognition by the Protein Acetyltransferase Pat of Rhodopseudomonas palustris

ABSTRACT The AMP-forming acyl coenzyme A (acyl-CoA) synthetases are a large class of enzymes found in both anabolic and catabolic pathways that activate fatty acids to acyl-CoA molecules. The protein acetyltransferase (Pat) from Rhodopseudomonas palustris (RpPat) inactivates AMP-forming acyl-CoA synthetases by acetylating the ε-amino group of a conserved, catalytic lysine residue. In all of the previously described RpPat substrates, this lysine residue is located within a PX4GK motif that has been proposed to be a recognition motif for RpPat. Here, we report five new substrates for RpPat, all of which are also AMP-forming acyl-CoA synthetases. This finding supports the idea that Pat enzymes may have evolved to control the activity of this family of enzymes. Notably, RpPat did not acetylate the wild-type long-chain acyl-CoA synthetase B (RpLcsB; formerly Rpa2714) enzyme of this bacterium. However, a single amino acid change two residues upstream of the acetylation site was sufficient to convert RpLcsB into an RpPat substrate. The results of mutational and functional analyses of RpLcsB and RpPimA variants led us to propose PK/RTXS/T/V/NGKX2K/R as a substrate recognition motif. The underlined positions within this motif are particularly important for acetylation by RpPat. The first residue, threonine, is located 4 amino acids upstream of the acetylation site. The second residue can be S/T/V/N and is located two positions upstream of the acetylation site. Analysis of published crystal structures suggests that the side chains of these two residues are very close to the acetylated lysine residue, indicating that they may directly interact with RpPat.
Epidural Cortical Stimulation as Adjunctive Treatment for Nonfluent Aphasia

Background. There is increasing interest in the application of cortical stimulation (CS) as an adjuvant strategy in aphasia rehabilitation. Epidural CS, although more invasive than other methods, can provide high-frequency ipsilesional stimulation with greater spatial specificity. Objective. We review methods and results of a phase 1 study of epidural CS in combination with rehabilitation therapy in aphasia and provide new objective and self-report data collected between 6 and 21 months after the end of treatment. Methods. Eight stroke survivors with nonfluent aphasia received intensive language therapy, 3 hours a day, for 6 weeks. Four participants also underwent surgical implantation of an epidural stimulation device that was activated only during therapy sessions. Behavioral data were collected before treatment, at the end of treatment, and at 6 and 12 weeks after the end of treatment. Of the 8 participants, 7 also participated in the longer-term follow-up visit. Results. Changes in objective scores from baseline were larger in investigational participants than controls at all assessments, including the longer-term follow-up visit. Satisfaction ratings and ratings of overall improvement by investigational participants and their companions were more varied than those of the controls, but all indicated that they would recommend the investigational treatment to others with aphasia. Conclusions. Improvements were generally maintained for at least 12 weeks posttreatment and possibly as long as 21 months posttreatment. Epidural CS is a potentially safe, feasible adjunctive intervention for persons with chronic nonfluent aphasia that spares the ventral premotor cortex and warrants further investigation.
Bicarbonate Administration Is Potentially Harmful in Patients with Moderate Acidosis

I was surprised to read in the article by Waters et al. (1) that the iatrogenic acidosis after normal saline administration was treated with bicarbonate dosed using an arterial blood base deficit measurement. Substantial research indicates bicarbonate administration is not efficacious and is potentially harmful in patients with a moderate acidosis (2–7). Prospective awareness that patients receiving large amounts of normal saline likely will become acidotic is the norm. Thus, I wonder if the choice to treat with bicarbonate came from a review board perception that to allow the study to continue, the acidosis had to be treated in some way, effective or ineffective. Clinically, I doubt that many would choose to employ a technique of rescue-bicarbonate at a base deficit level of 5 mEq/L, and I wonder how that number was determined given the concern for intracellular acidosis, hypernatremia, and other adverse effects ascribed to bicarbonate therapy.
Improving the Robustness of Myoelectric Pattern Recognition for Upper Limb Prostheses by Covariate Shift Adaptation

Fundamental changes over time of surface EMG signal characteristics are a challenge for myocontrol algorithms controlling prosthetic devices. These changes are generally caused by electrode shifts after donning and doffing, sweating, additional weight or varying arm positions, which results in a change of the signal distribution - a scenario often referred to as covariate shift. A substantial decrease in classification accuracy due to these factors hinders the possibility to directly translate EMG signals into accurate myoelectric control patterns outside laboratory conditions. To overcome this limitation, we propose the use of supervised adaptation methods. The approach is based on adapting a trained classifier using a small calibration set only, which incorporates the relevant aspects of the nonstationarities, but requires only less than 1 min of data recording. The method was tested first through an offline analysis on signals acquired across 5 days from seven able-bodied individuals and four amputees. Moreover, we also conducted a three day online experiment on eight able-bodied individuals and one amputee, assessing user performance and user-ratings of the controllability. Across different testing days, both offline and online performance improved significantly when shrinking the training model parameters by a given estimator towards the calibration set parameters. In the offline data analysis, the classification accuracy remained above 92% over five days with the proposed approach, whereas it decreased to 75% without adaptation. Similarly, in the online study, with the proposed approach the performance increased by 25% compared to a test without adaptation. These results indicate that the proposed methodology can contribute to improve robustness of myoelectric pattern recognition methods in daily life applications.
Skilled Reach Performance Correlates With Corpus Callosum Structural Integrity in Individuals With Mild Motor Impairment After Stroke: A Preliminary Investigation

Background. Recovery of arm function after stroke is often incomplete. An improved understanding of brain structure–motor behavior relationships is needed for the development of novel and targeted rehabilitation interventions. Objective. To examine the relationship between skilled reach performance and the integrity of two putative white matter motor pathways, corticospinal tract and corpus callosum, after stroke. Methods. Eleven individuals with chronic stroke (poststroke duration, mean 62.5 ± 42.4 months) and mild motor impairment (upper extremity Fugl-Meyer score, mean 54.2 ± 7.6) reached to six targets presented at three distances and two directions. Fractional anisotropy (FA) obtained from diffusion tensor imaging was used to determine the structural integrity of the corticospinal tract and the corpus callosum. Results. Overall reach performance was decreased in the paretic arm compared with the nonparetic arm. While FA was decreased in the ipsilesional corticospinal tract, FA in the corticospinal tract did not correlate with variability in reach performance between individuals. Instead, FA in the premotor section of the corpus callosum correlated with reach performance; individuals with higher FA in premotor corpus callosum tended to reach faster with both the paretic and nonparetic arms. Conclusions. The structural connections between the two premotor and supplemental cortices that traverse the premotor corpus callosum may play an important role in supporting motor control and could become a target for interventions aimed at improved arm function in this population.
Partial scan by use of empirical testability

The objective of the partial scan method proposed is to obtain maximum fault coverage for the number of scan elements selected. Empirical testability difference (ETD), a measure of the potential improvement in the overall testability of the circuit, is used to successively select storage elements for scan. ETD is calculated by using testability measures based on empirical evaluation of the circuit with the actual test sequence generator. In addition, ETD focuses on the hard-to-detect faults rather than all faults once such faults are known. The method has been extensively tested with ten of the sequential circuits given by F. Brglez et al. (1989) using the FASTEST provided by T. Kelsey and K. Saluja (1989). The results of these tests indicate that ETD yields on average either 27% of the number of uncovered faults for the same number of scan elements or 21% fewer scan elements for the same fault coverage compared to the other methods studied. <<ETX>>
Local and Extensive Neuroplasticity in Carpal Tunnel Syndrome: A Resting-State fMRI Study

Carpal tunnel syndrome (CTS) is a most common peripheral nerve entrapment neuropathy characterized by sensorimotor deficits in median nerve innervated digits. Block-design task-related functional magnetic resonance imaging (fMRI) studies have been used to investigate CTS-related neuroplasticity in the primary somatosensory cortices. However, considering the persistence of digital paresthesia syndrome caused by median nerve entrapment, spontaneous neuronal activity might provide a better understanding of CTS-related neuroplasticity, which remains unexplored. The present study aimed to investigate both local and extensive spontaneous neuronal activities with resting-state fMRI. A total of 28 bilateral CTS patients and 24 normal controls were recruited, and metrics, including amplitude of low-frequency fluctuation (ALFF) and voxel-wise functional connectivity (FC), were used to explore synaptic activity at different spatial scales. Correlations with clinical measures were further investigated by linear regression. Decreased amplitudes of low-frequency fluctuation were observed in the bilateral primary sensory cortex (SI) and secondary sensory cortex (SII) in CTS patients (AlphaSim corrected P < .05). This was found to be negatively related to the sensory thresholds of corresponding median nerve innervated fingers. In the voxel-wise FC analysis, with predefined seed regions of interest in the bilateral SI and primary motor cortex, we observed decreased interhemispheric and increased intrahemispheric FC. Additionally, both interhemispheric and intrahemispheric FC were found to be significantly correlated with the mean ALFF.
Connections of the Cerebral Cortex

Not often a book summarizing two decades of study is nevertheless only the author's sixth formal pub lication on the subject. Such is the case withConnections of the Cerebral Cortex. The first and largest section is devoted to cortico-subcortical and associational connections, traced by serial chartings of Marchi degenerations from nearly 200 experimental lesions in the monkey. The material in this chapter alone could easily have been disseminated over a score of separate journal publications. To have it all available in one volume is a convenience for which the author deserves commendation. Successive chapters discuss the anatomy of the thalamus and thalamocortical radiation, and compare findings in the monkey with the author's earlier studies on the rat. The book concludes with an annotated atlas in which the experimental findings are applied to the human brain. Cytoarchitectonic studies have led the author to introduce several modifications of Brodmann's plan of
GigA and GigB are Master Regulators of Antibiotic Resistance, Stress Responses, and Virulence in Acinetobacter baumannii

ABSTRACT A critical component of bacterial pathogenesis is the ability of an invading organism to sense and adapt to the harsh environment imposed by the host's immune system. This is especially important for opportunistic pathogens, such as Acinetobacter baumannii, a nutritionally versatile environmental organism that has recently gained attention as a life-threatening human pathogen. The emergence of A. baumannii is closely linked to antibiotic resistance, and many contemporary isolates are multidrug resistant (MDR). Unlike many other MDR pathogens, the molecular mechanisms underlying A. baumannii pathogenesis remain largely unknown. We report here the characterization of two recently identified virulence determinants, GigA and GigB, which comprise a signal transduction pathway required for surviving environmental stresses, causing infection and antibiotic resistance. Through transcriptome analysis, we show that GigA and GigB coordinately regulate the expression of many genes and are required for generating an appropriate transcriptional response during antibiotic exposure. Genetic and biochemical data demonstrate a direct link between GigA and GigB and the nitrogen phosphotransferase system (PTSNtr), establishing a novel connection between a novel stress response module and a well-conserved metabolic-sensing pathway. Based on the results presented here, we propose that GigA and GigB are master regulators of a global stress response in A. baumannii, and coupling this pathway with the PTSNtr allows A. baumannii to integrate cellular metabolic status with external environmental cues. IMPORTANCE Opportunistic pathogens, including Acinetobacter baumannii, encounter many harsh environments during the infection cycle, including antibiotic exposure and the hostile environment within a host. While the development of antibiotic resistance in A. baumannii has been well studied, how this organism senses and responds to environmental cues remain largely unknown. Herein, we investigate two previously identified virulence determinants, GigA and GigB, and report that they are required for in vitro stress resistance, likely comprising upstream elements of a global stress response pathway. Additional experiments identify a connection between GigA/GigB and a widely conserved metabolic-sensing pathway, the nitrogen phosphotransferase system. We propose that coordination of these two pathways allows A. baumannii to respond appropriately to changing environmental conditions, including those encountered during infection.
EEG-Based Strategies to Detect Motor Imagery for Control and Rehabilitation

Advances in brain–computer interface (BCI) technology have facilitated the detection of Motor Imagery (MI) from electroencephalography (EEG). First, we present three strategies of using BCI to detect MI from EEG: operant conditioning that employed a fixed model, machine learning that employed a subject-specific model computed from calibration, and adaptive strategy that continuously compute the subject-specific model. Second, we review prevailing works that employed the operant conditioning and machine learning strategies. Third, we present our past work on six stroke patients who underwent a BCI rehabilitation clinical trial with averaged accuracies of 79.8% during calibration and 69.5% across 18 online feedback sessions. Finally, we perform an offline study in this paper on our work employing the adaptive strategy. The results yielded significant improvements of 12% (p < 0.001) and 9% (p < 0.001) using all the data and using limited preceding data respectively in the feedback accuracies. The results showed an increase in the amount of training data yielded improvements. Nevertheless, results of using limited preceding data showed a larger part of the improvement was due to the adaptive strategy and changing subject-specific models did not deteriorate the accuracies. Hence the adaptive strategy is effective in addressing the non-stationarity between calibration and feedback sessions.
A Plasmid-Borne System To Assess the Excision and Integration of Staphylococcal Cassette Chromosome mec Mediated by CcrA and CcrB

ABSTRACT Resistance to methicillin and other β-lactam antibiotics in staphylococci is due to mecA, which is carried on a genomic island, staphylococcal cassette chromosome mec (SCCmec). The chromosomal excision and integration of SCCmec are mediated by the site-specific recombinase CcrAB or CcrC, encoded within this element. A plasmid-borne system was constructed to assess the activities of CcrA and CcrB in the excision and integration of SCCmec in Escherichia coli and Staphylococcus aureus. The excision frequency in E. coli mediated by CcrAB from methicillin-resistant S. aureus (MRSA) strain N315 was only 9.2%, while the integration frequency was 31.4%. In S. aureus the excision and integration frequencies were 11.0% and 18.7%, respectively. Truncated mutants identified the N-terminal domain of either CcrB or CcrA to be necessary for both integration and excision, while the C-terminal domain was important for recombination efficiency. Site-directed mutagenesis of the N-terminal domain identified S11 and R79 of CcrA and S16, R89, T149, and R151 of CcrB to be residues essential for catalytic activities, and the critical location of these residues was consistent with a model of the tertiary structure of the N terminus of CcrA and CcrB. Furthermore, CcrAB and CcrC, cloned from a panel of 6 methicillin-resistant S. aureus strains and 2 methicillin-resistant Staphylococcus epidermidis strains carrying SCCmec types II, IV, and V, also catalyzed integration at rates 1.3 to 10 times higher than the rates at which they catalyzed excision, similar to the results from N315. The tendency of SCCmec integration to be favored over excision may explain the low spontaneous excision frequency seen among MRSA strains. IMPORTANCE Spontaneous excision of the genomic island (SCCmec) that encodes resistance to beta-lactam antibiotics (methicillin resistance) in staphylococci would convert a methicillin-resistant strain to a methicillin-susceptible strain, improving therapy of difficult-to-treat infections. This study characterizes a model system by which the relative frequencies of excision and integration can be compared. Using a plasmid-based model for excision and integration mediated by the recombinases CcrA and CcrB, integration occurred at a higher frequency than excision, consistent with the low baseline excision frequency seen in most strains. This model system can now be used to study conditions and drugs that may raise the SCCmec excision frequency and generate strains that are beta-lactam susceptible.
EscA Is a Crucial Component of the Type III Secretion System of Enteropathogenic Escherichia coli

ABSTRACT The virulence of many Gram-negative pathogens is associated with type III secretion systems (T3SSs), which deliver virulence effector proteins into the cytoplasm of host cells. Components of enteropathogenic Escherichia coli (EPEC) T3SS are encoded within the locus of enterocyte effacement (LEE). While most LEE-encoded T3SS proteins in EPEC have assigned names and functions, a few of them remain poorly characterized. Here, we studied a small LEE-encoded protein, Orf15, that shows no homology to other T3SS/flagellar proteins and is only present in attaching and effacing pathogens, including enterohemorrhagic E. coli and Citrobacter rodentium. Our findings demonstrated that it is essential for type III secretion (T3S) and that it is localized to the periplasm and associated with the inner membrane. Membrane association was driven by the N-terminal 19 amino acid residues, which were also shown to be essential for T3S. Consistent with its localization, Orf15 was found to interact with the EPEC T3SS outer membrane ring component, EscC, which was previously shown to be embedded within the outer membrane and protruding into the periplasmic space. Interestingly, we found that the predicted coiled-coil structure of Orf15 is critical for the protein's function. Overall, our findings suggest that Orf15 is a structural protein that contributes to the structural integrity of the T3S complex, and therefore we propose to rename it EscA.