Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary mapping of the SHV beta-lactamase and evidence for two separate IS26-dependent blaSHV mobilization events from the Klebsiella pneumoniae chromosome.

OBJECTIVES To determine the most likely evolutionary pathway that has led to the development of extended-spectrum SHV derivatives, and to the mobilization of blaSHV. MATERIALS AND METHODS Evolutionary mapping used a shortest-path analysis of aligned blaSHV variants, and other basic bioinformatic approaches, such as CLUSTAL W and Blast were employed. RESULTS Two main branches of the blaSHV evolutionary tree were located; both are derived from variant blaSHV-1 alleles. Identical mutations, responsible for extended-spectrum SHV substrate profiles, have been selected independently in each branch. There is evidence for a pool of non-mobile blaSHV framework sequences. Analysis of the genome sequence of Klebsiella pneumoniae confirms the chromosomal origin of blaSHV, whose mobilization has occurred at least twice, once for each of the main evolutionary branches. Both these mobilization events have been catalysed by IS26. Evolution of blaSHV to give common extended-spectrum variants is most likely to have occurred following mobilization. CONCLUSIONS These data shed new light on the evolution and mobilization of blaSHV, and these observations may be useful in predicting what might happen in future, both for blaSHV, and for other beta-lactamase genes.
Dynamic Origin–Destination Flow Estimation Using Cellular Communication System

This paper aims to develop a new approach for the estimation of dynamic origin-destination (O-D) flow using cell phones as traffic probes. The state-space model, which depends on the autoregressive dynamics of O-D flow and the time series for link volume counts, was adopted. Unlike a direct approach that uses sample O-D flows extracted from the cell-based location data as additional observations, an indirect approach is proposed wherein the assignment map in the model is derived from the passing time at observation locations and the path choice proportion. A probe phone's passing time at a certain point in a cell was approximated with its entry and exit times at cell boundaries. The average path choice proportion was also estimated using cell-based trajectories of probe phones. The simulation experiments confirmed that the approach was successfully applicable to the real-world freeway network. The results suggest that the O-D flows estimated from the present approach are promising in that the mean absolute error ratio was smaller than the case wherein only historical O-D flows are concerned. A sensitivity analysis revealed that the present approach met the requirements for an urban area encompassing a huge number of cell phone users in a microcell system.
Thermonuclease seroinhibition test for distinguishing Staphylococcus aureus from other coagulase-positive staphylococci

Since coagulase-positive staphylococci from animals are heterogeneous, another test is necessary to distinguish Staphylococcus aureus from them. Staphylococcal thermonucleases appear to be heterogeneous; antisera raised against S. aureus isolated from humans inhibit thermonuclease activity as demonstrated by the metachromatic well-agar diffusion method. The serological specificity of the thermonuclease elaborated by S. aureus of human origin was demonstrated using three antisera and 407 strains of staphylococci from diverse human and animal sources.
Episodic memory reconsolidation: Updating or source confusion?

Reactivation of apparently stable, long-term memory can render it fragile, and dependent on a re-stabilisation process referred to as “reconsolidation”. Recently we provided the first demonstration of reconsolidation effects in human episodic memory (Hupbach, Gomez, Hardt, & Nadel, 2007; Hupbach, Hardt, Gomez, & Nadel, 2008). Memory for a set of objects was modified by the presentation of a new set, if and only if participants were reminded of the first learning episode before learning the new set. The present study asks whether this effect can be interpreted as a source discrimination problem; i.e., participants have difficulties remembering which objects were presented during which session, and do not actually incorporate new objects into the reactivated memory. The present study used a recognition test and asked participants directly about the source of their memories. Participants in the no-reminder group showed very few source errors. Participants in the reminder group misattributed the source of objects from the second set as being from the first set but not vice versa, thus demonstrating updating of the original memory. This finding is informative with respect to the misinformation paradigm, and reconsolidation is discussed as a possible mechanism underlying our results and the misinformation effect.
Brainlab: A Python Toolkit to Aid in the Design, Simulation, and Analysis of Spiking Neural Networks with the NeoCortical Simulator

Neuroscience modeling experiments often involve multiple complex neural network and cell model variants, complex input stimuli and input protocols, followed by complex data analysis. Coordinating all this complexity becomes a central difficulty for the experimenter. The Python programming language, along with its extensive library packages, has emerged as a leading “glue” tool for managing all sorts of complex programmatic tasks. This paper describes a toolkit called Brainlab, written in Python, that leverages Python's strengths for the task of managing the general complexity of neuroscience modeling experiments. Brainlab was also designed to overcome the major difficulties of working with the NCS (NeoCortical Simulator) environment in particular. Brainlab is an integrated model-building, experimentation, and data analysis environment for the powerful parallel spiking neural network simulator system NCS.
Acoustic analysis of pathological voices. A voice analysis system for the screening of laryngeal diseases.

The authors propose a software system for pathological voice analysis and screening of laryngeal diseases that has the following properties: a) The analysis is totally noninvasive-the microphone is about 30 cm from the patient's mouth, and contact microphones or laryngophones are not used. b) The system is built around a low-cost personal computer (PC). The additional hardware consists of a standard sound card such as "Sound Blaster" (Creative Technology Inc., Paris, France). The card also includes a microphone. Any other analog-to-digital converter board allowing a sampling rate higher than 16 kHz, with 16 bit resolution (Sound Blaster and OROS have been already tested), and a linear phase condenser or electret microphone can be used to minimize the distortions during capture of the signal. c) The software is graphics-driven and user-friendly, therefore no special training is needed in using the system. d) The system is electrically safe since there is no electrical link between patient and PC.
Shoot Calcium and Magnesium Concentrations Differ between Subtaxa, Are Highly Heritable, and Associate with Potentially Pleiotropic Loci in Brassica oleracea1[W][OA]

Calcium (Ca) and magnesium (Mg) are the most abundant group II elements in both plants and animals. Genetic variation in shoot Ca and shoot Mg concentration (shoot Ca and Mg) in plants can be exploited to biofortify food crops and thereby increase dietary Ca and Mg intake for humans and livestock. We present a comprehensive analysis of within-species genetic variation for shoot Ca and Mg, demonstrating that shoot mineral concentration differs significantly between subtaxa (varietas). We established a structured diversity foundation set of 376 accessions to capture a high proportion of species-wide allelic diversity within domesticated Brassica oleracea, including representation of wild relatives (C genome, 1n = 9) from natural populations. These accessions and 74 modern F1 hybrid cultivars were grown in glasshouse and field environments. Shoot Ca and Mg varied 2- and 2.3-fold, respectively, and was typically not inversely correlated with shoot biomass, within most subtaxa. The closely related capitata (cabbage) and sabauda (Savoy cabbage) subtaxa consistently had the highest mean shoot Ca and Mg. Shoot Ca and Mg in glasshouse-grown plants was highly correlated with data from the field. To understand and dissect the genetic basis of variation in shoot Ca and Mg, we studied homozygous lines from a segregating B. oleracea mapping population. Shoot Ca and Mg was highly heritable (up to 40%). Quantitative trait loci (QTL) for shoot Ca and Mg were detected on chromosomes C2, C6, C7, C8, and, in particular, C9, where QTL accounted for 14% to 55% of the total genetic variance. The presence of QTL on C9 was substantiated by scoring recurrent backcross substitution lines, derived from the same parents. This also greatly increased the map resolution, with strong evidence that a 4-cM region on C9 influences shoot Ca. This region corresponds to a 0.41-Mb region on Arabidopsis (Arabidopsis thaliana) chromosome 5 that includes 106 genes. There is also evidence that pleiotropic loci on C8 and C9 affect shoot Ca and Mg. Map-based cloning of these loci will reveal how shoot-level phenotypes relate to Ca2+ and Mg2+ uptake and homeostasis at the molecular level.
Exercise training improves myocardial tolerance to in vivo ischemia-reperfusion in the rat.

Experimental studies examining the effects of regular exercise on cardiac responses to ischemia and reperfusion (I/R) are limited. Therefore, these experiments examined the effects of endurance exercise training on myocardial biochemical and physiological responses during in vivo I/R. Female Sprague-Dawley rats (4 mo old) were randomly assigned to either a sedentary control group or to an exercise training group. After a 10-wk endurance exercise training program, animals were anesthetized and mechanically ventilated, and the chest was opened by thoracotomy. Coronary occlusion was achieved by a ligature around the left coronary artery; occlusion was maintained for 20 min, followed by a 10-min period of reperfusion. Compared with untrained, exercise-trained animals maintained higher ( P < 0.05) peak systolic blood pressure throughout I/R. Training resulted in a significant ( P < 0.05) increase in ventricular nonprotein thiols, heat shock protein (HSP) 72, and the activities of superoxide dismutase (SOD), phosphofructokinase (PFK), and lactate dehydrogenase. Furthermore, compared with untrained controls, left ventricles from trained animals exhibited lower levels ( P < 0.05) of lipid peroxidation after I/R. These data demonstrate that endurance exercise training improves myocardial contractile performance and reduces lipid peroxidation during I/R in the rat in vivo. It appears likely that the improvement in the myocardial responses to I/R was related to training-induced increases in nonprotein thiols, HSP72, and the activities of SOD and PFK in the myocardium.
Interleukin-1-induced long-lasting changes in hypothalamic corticotropin-releasing hormone (CRH)--neurons and hyperresponsiveness of the hypothalamus-pituitary-adrenal axis

Hypothalamic CRH neurons that control ACTH secretion from the pituitary gland have secretory terminals in the external zone of the median eminence (ZEME). These neurons can coproduce vasopressin (AVP), a neuropeptide that potentiates the ACTH releasing effects of CRH. Recently, we found increased AVP production in adult rats weeks after single exposure to a stressor, which may play a role in event-induced stress disorders. Here, we describe the long-term changes in the HPA axis of adult male rats following a single exposure to a stressor, the cytokine interleukin-1 beta (IL-1 beta). The effects on storage and release of AVP and CRH were established by quantitative immunocytochemistry, the effects on ACTH and corticosterone responses by radioimmunoassay. Single administration of IL-1 beta (5 micrograms/kg i.p.) induces a delayed (at least 4 d) and a long-lasting (at least 3 weeks) increase of vasopressin (AVP) stores in CRH terminals of the ZEME without affecting the CRH stores, and a marked increase of the fraction of CRH terminals that costore AVP. Eleven days after IL-1 beta administration, a second IL-1 beta challenge causes a marked depletion of the AVP stores in the ZEME within 2 hr, which is not seen in rats treated with vehicle 11 d earlier. This is accompanied by twofold higher ACTH and corticosterone responses, as compared to those in vehicle pretreated rats. IL-1 beta-pretreated rats also showed increased ACTH and corticosterone responses to electric footshocks. We conclude that transient activation of the HPA axis by a single administration of IL-1 beta induces a delayed and long-lasting hyperproduction, hyperstorage, and hypersecretion of AVP from hypothalamic CRH neurons that results in hyperresponsiveness of the HPA axis to subsequent stimuli.
An Intelligent Maximum Power Point Tracker Using Peak Current Control

The perturbation and observation (P&O) maximum power point tracking (MPPT) algorithms are commonly used in photovoltaic (PV) systems due to their easy implementation and ability to track the maximum power point (MPP) of the solar array under widely varying atmospheric conditions viz. solar irradiation, panel temperature etc. P&O algorithm based on peak current control and the use of instantaneous sampled values to calculate the next perturbation direction have the potential for faster transients and smaller oscillations around the MPP. The use of fixed variation of the reference current results in a compromise sub-optimum solution. This paper discusses a fuzzy logic based P&O MPPT with peak current control with variable variation of the reference current for improved transient as well as steady-state performance. Simulation results show a 15 % gain in the transient response and decrease of the power loss in the steady state. Besides, both the P&O scheme with fixed variation for the reference current and the intelligent MPPT algorithm were able to identify the global MPP in a partially shaded PV module, however the performance of the intelligent MPPT algorithm was better
Olfactory Bulb Short Axon Cell Release of GABA and Dopamine Produces a Temporally Biphasic Inhibition–Excitation Response in External Tufted Cells

Evidence for coexpression of two or more classic neurotransmitters in neurons has increased, but less is known about cotransmission. Ventral tegmental area (VTA) neurons corelease dopamine (DA), the excitatory transmitter glutamate, and the inhibitory transmitter GABA onto target cells in the striatum. Olfactory bulb (OB) short axon cells (SACs) form interglomerular connections and coexpress markers for DA and GABA. Using an optogenetic approach, we provide evidence that mouse OB SACs release both GABA and DA onto external tufted cells (ETCs) in other glomeruli. Optical activation of channelrhodopsin specifically expressed in DAergic SACs produced a GABAA receptor-mediated monosynaptic inhibitory response, followed by DA–D1-like receptor-mediated excitatory response in ETCs. The GABAA receptor-mediated hyperpolarization activates Ih current in ETCs; synaptically released DA increases Ih, which enhances postinhibitory rebound spiking. Thus, the opposing actions of synaptically released GABA and DA are functionally integrated by Ih to generate an inhibition-to-excitation “switch” in ETCs. Consistent with the established role of Ih in ETC burst firing, we show that endogenous DA release increases ETC spontaneous bursting frequency. ETCs transmit sensory signals to mitral/tufted output neurons and drive intraglomerular inhibition to shape glomerulus output to downstream olfactory networks. GABA and DA cotransmission from SACs to ETCs may play a key role in regulating output coding across the glomerular array.
Graph-based Semi-Supervised Model for Joint Chinese Word Segmentation and Part-of-Speech Tagging

This paper introduces a graph-based semisupervised joint model of Chinese word segmentation and part-of-speech tagging. The proposed approach is based on a graph-based label propagation technique. One constructs a nearest-neighbor similarity graph over all trigrams of labeled and unlabeled data for propagating syntactic information, i.e., label distributions. The derived label distributions are regarded as virtual evidences to regularize the learning of linear conditional random fields (CRFs) on unlabeled data. An inductive character-based joint model is obtained eventually. Empirical results on Chinese tree bank (CTB-7) and Microsoft Research corpora (MSR) reveal that the proposed model can yield better results than the supervised baselines and other competitive semi-supervised CRFs in this task.
Pallidotomy suppresses beta power in the subthalamic nucleus of Parkinson’s disease patients

Parkinsonian patients, who have had a unilateral pallidotomy, may require bilateral deep brain stimulation of the subthalamic nucleus (STN), due to disease progression. The current model of the basal ganglia circuitry does not predict a direct effect of pallidotomy on the neuronal activity of the ipsilateral STN. To date, only three studies have investigated the effect of pallidotomy on overall activity of the STN or neuronal firing rate, but not on the spectral content of the neuronal oscillatory activity. Moreover, none of these studies attempted to differentiate the effects on the dorsal (sensory‐motor) and ventral (associative‐limbic) parts of the STN. We studied the effect of pallidotomy on spectral power in six frequency bands in the STN ipsilateral and contralateral to pallidotomy from seven patients and in 60 control nuclei of patients without prior functional neurosurgery, and investigated whether this effect is different on the dorsal and ventral STN. The data show that pallidotomy suppresses beta power (13–30 Hz) in the ipsilateral STN. This effect tends predominantly to be present in the dorsal part of the STN. In addition, spectral power in the frequency range 3–30 Hz is significantly higher in the dorsal part than in the ventral part. The effect of pallidotomy on STN neural activity is difficult to explain with the current model of basal ganglia circuitry and should be envisaged in the context of complex modulatory interactions in the basal ganglia.
Endothelin and vascular function in liver disease

The endothelins are a group of three related peptides with two receptor subtypes, ETA and ETB. Following the discovery of endothelin 1 as a potent vasoconstrictor, there has been intense interest in the role of endothelin on vascular function in liver disease. Speculation on the role of endothelin in the pathogenesis of acute renal failure, including hepatorenal syndrome, has also been speculated.
Neuronal Mechanisms of Respiratory Pattern Generation Are Evolutionary Conserved

A brainstem region, the paratrigeminal respiratory group (pTRG), has been suggested to play a crucial role in the respiratory rhythm generation in lampreys. However, a detailed characterization of the pTRG region is lacking. The present study performed on isolated brainstem preparations of adult lampreys provides a more precise localization of the pTRG region with regard to both connectivity and neurochemical markers. pTRG neurons projecting to the vagal motoneuronal pool were identified in a restricted area of the rostral rhombencephalon at the level of the isthmic Müller cell I1 close to sulcus limitans of His. Unilateral microinjections of lidocaine, muscimol, or glutamate antagonists into the pTRG inhibited completely the bilateral respiratory activity. In contrast, microinjections of glutamate agonists enhanced the respiratory activity, suggesting that this region is critical for the respiratory pattern generation. The retrogradely labeled pTRG neurons are glutamatergic and surrounded by terminals with intense substance P immunoreactivity. Cholinergic neurons were seen close to, and intermingled with, pTRG neurons. In addition, α-bungarotoxin binding sites (indicating nicotinic receptors) were found throughout the pTRG area and particularly on the soma of these neurons. During apnea, induced by blockade of ionotropic glutamate receptors within the same region, microinjections of 1 μm substance P or 1 mm nicotine into the pTRG restored rhythmic respiratory activity. The results emphasize the close similarities between the pTRG and the mammalian pre-Bötzinger complex as a crucial site for respiratory rhythmogenesis. We conclude that some basic features of the excitatory neurons proposed to generate respiratory rhythms are conserved throughout evolution.
The effect of a brief mindfulness induction on processing of emotional images: an ERP study

The ability to effectively direct one’s attention is an important aspect of regulating emotions and a component of mindfulness. Mindfulness practices have been established as effective interventions for mental and physical illness; however, the underlying neural mechanisms of mindfulness and how they relate to emotional processing have not been explored in depth. The current study used a within-subjects repeated measures design to examine if focused breathing, a brief mindfulness induction, could modulate event-related potentials (ERPs) during emotional image processing relative to a control condition. We related ERP measures of processing positive, negative, and neutral images (the P300 and late positive potential – LPP) to state and trait mindfulness measures. Overall, the brief mindfulness induction condition did not influence ERPs reflecting emotional processing; however, in the brief mindfulness induction condition, those participants who reported feeling more decentered (a subscale of the Toronto Mindfulness Scale) after viewing the images had reduced P300 responses to negative versus neutral images.
Slant path radiative transfer for the assimilation of sounder radiances

ABSTRACT This paper reports on the influence of taking the slanted satellite viewing geometry better into account in the simulation and assimilation of sounding radiances. The traditional approach is to use a vertical profile extracted at the geo-location information provided with the data. The present work instead investigates using a slanted profile, extracted from model fields along the instrument’s line of sight. Taking the viewing geometry better into account leads to significant improvements in the simulation of brightness temperatures from model fields compared to the traditional approach. This is particularly noticeable for larger zenith angles, for channels that peak in the upper troposphere or higher and have relatively low noise, and for high and mid-latitudes. The finding also suggests that the model fields capture useful information on horizontal gradients, at least on the relevant spatial scales. The improved simulations of the sounder radiances lead to significant reductions in the size of the analysis increments at mid and high latitudes and particularly in the stratosphere during the assimilation. The system shows a statistically improved self-consistency out to the day-3 forecast range.