Miracle-dz/UniFAR-FTUs huggingface dataset:
Imaging Spatiotemporal Dynamics of Surround Inhibition in the Barrels Somatosensory Cortex

Sensory processing and its perception require that local information would also be available globally. Indeed, in the mammalian neocortex, local excitation spreads over large distances via the long-range horizontal connections in layer 2/3 and may spread over an entire cortical area if excitatory polysynaptic pathways are also activated. Therefore, a balance between local excitation and surround inhibition is required. Here we explore the spatiotemporal aspects of cortical depolarization and hyperpolarization of rats anesthetized with urethane. New voltage-sensitive dyes (VSDs) were used for high-resolution real-time visualization of the cortical responses to whisker deflections and cutaneous stimulations of the whisker pad. These advances facilitated imaging of ongoing activity and evoked responses even without signal averaging. We found that the motion of a single whisker evoked a cortical response exhibiting either one or three phases. During a triphasic response, there was first a cortical depolarization in a small cortical region the size of a single cortical barrel. Subsequently, this depolarization increased and spread laterally in an oval manner, preferentially along rows of the barrel field. During the second phase, the amplitude of the evoked response declined rapidly, presumably because of recurrent inhibition. Subsequently, the third phase exhibiting a depolarization rebound was observed and clear, and ∼16 Hz oscillations were detected. Stimulus conditions revealing a net surround hyperpolarization during the second phase were also found. By using new, improved VSD, the present findings shed new light on the spatial parameters of the intricate spatiotemporal cortical interplay of inhibition and excitation.
Accumulation of non‐erythroid αII‐spectrin and calpain‐cleaved αII‐spectrin breakdown products in cerebrospinal fluid after traumatic brain injury in rats

Although a number of increased CSF proteins have been correlated with brain damage and outcome after traumatic brain injury (TBI), a major limitation of currently tested biomarkers is a lack of specificity for defining neuropathological cascades. Identification of surrogate biomarkers that are elevated in CSF in response to brain injury and that offer insight into one or more pathological neurochemical events will provide critical information for appropriate administration of therapeutic compounds for treatment of TBI patients. Non‐erythroid αII‐spectrin is a cytoskeletal protein that is a substrate of both calpain and caspase‐3 cysteine proteases. As we have previously demonstrated, cleavage of αII‐spectrin by calpain and caspase‐3 results in accumulation of protease‐specific spectrin breakdown products (SBDPs) that can be used to monitor the magnitude and temporal duration of protease activation. However, accumulation of αII‐spectrin and αII‐SBDPs in CSF after TBI has never been examined. Following a moderate level (2.0 mm) of controlled cortical impact TBI in rodents, native αII‐spectrin protein was decreased in brain tissue and increased in CSF from 24 h to 72 h after injury. In addition, calpain‐specific SBDPs were observed to increase in both brain and CSF after injury. Increases in the calpain‐specific 145 kDa SBDP in CSF were 244%, 530% and 665% of sham‐injured control animals at 24 h, 48 h and 72 h after TBI, respectively. The caspase‐3‐specific SBDP was observed to increase in CSF in some animals but to a lesser degree. Importantly, levels of these proteins were undetectable in CSF of uninjured control rats. These results indicate that detection of αII‐spectrin and αII‐SBDPs is a powerful discriminator of outcome and protease activation after TBI. In accord with our previous studies, results also indicate that calpain may be a more important effector of cell death after moderate TBI than caspase‐3.
Coronal Microleakage in Root Canals Obturated with Lateral Compaction, Warm Vertical Compaction and Guttaflow System

INTRODUCTION Root canal obturation seals the root canal system to prevent re-entry and/or growth of microorganisms. The provision of an appropriate restoration to coronally seal the access cavity affects the success of endodontic treatment. The purpose of this study was to evaluate the coronal microbial leakage in root canals that were either filled by lateral compaction, GuttaFlow or warm vertical compaction. MATERIALS AND METHODS In this ex vivo study, 80 single-rooted human extracted teeth were randomly divided into three experimental groups (n=20) and two positive and negative control groups (n=10). The teeth in experimental groups were obturated with cold lateral compaction, GuttaFlow system or warm vertical compaction techniques. After sterilization of the whole system with gamma-ray, saliva leakage was tested using a split-chamber model. Specimens were monitored every 24 hours for 30 days. The data were analyzed using log-rank and Kaplan-Meier survival analysis tests. RESULTS There were no significant differences in impeding saliva leakage between the three experimental groups (P>0.05). CONCLUSION Under the conditions of this ex vivo study, it can be concluded that the sealing ability of cold lateral compaction, warm vertical compaction and GuttaFlow system was comparable.
Open Access Research Article Genome-wide in Silico Screen for Ccch-type Zinc Finger Proteins of Trypanosoma Brucei, Trypanosoma Cruzi and Leishmania Major

Background: CCCH type zinc finger proteins are RNA binding proteins with regulatory functions at all stages of mRNA metabolism. The best-characterized member, tritetraproline (TTP), binds to AU rich elements in 3' UTRs of unstable mRNAs, mediating their degradation. In kinetoplastids, CCCH type zinc finger proteins have been identified as being involved in the regulation of the life cycle and possibly the cell cycle. To date, no systematic listing of CCCH proteins in kinetoplastids is available. Results: We have identified the complete set of CCCH type zinc finger proteins in the available genomes of the kinetoplastid protozoa Trypanosoma brucei, Trypanosoma cruzi and Leishmania major. One fifths (20%) of all CCCH motifs fall into non-conventional classes and many had not been previously identified. One third of all CCCH proteins have more than one CCCH motif, suggesting multivalent RNA binding. One third have additional recognizable domains. The vast majority are unique to Kinetoplastida or to a subgroup within. Two exceptions are of interest: the putative orthologue of the mRNA nuclear export factor Mex67 and a 3'-5' exoribonuclease restricted to Leishmania species. CCCH motifs are absent from these proteins in other organisms and might be unique, novel features of the Kinetoplastida homologues. Of the others, several have a predicted, and in one case experimentally confirmed, connection to the ubiquitination pathways, for instance a HECT-type E3 ubiquitin ligase. The total number of kinetoplastid CCCH proteins is similar to the number in higher eukaryotes but lower than in yeast. A comparison of the genomic loci between the Trypanosomatidae homologues provides insight into both the evolution of the CCCH proteins as well as the CCCH motifs. Conclusion: This study provides the first systematic listing of the Kinetoplastida CCCH proteins. The number of CCCH proteins with more then one CCCH motif is larger than previously estimated, due to the identification of non-conventional CCCH motifs. Experimental approaches are now necessary to examine the functions of the many unique CCCH proteins as well as the function of the putative Mex67 and the Leishmania 3'-5' exoribonuclease. Background Pathogenic kinetoplastid protozoa, such as the widely studied 'Tritryps' Trypanosoma cruzi (Tc), Leishmania major (Lm) and Trypanosoma brucei (Tb), have complex biphasic life cycles and consequently require changes in gene expression in response to extrinsic and intrinsic signals. For instance, at least 5% of all Tb genes are developmentally regulated at the mRNA level between any two of the experimentally tractable life cycle stages …
Spectrophotometry of Sextans A and B: Chemical Abundances of H II Regions and Planetary Nebulae

We present the results of high-quality long-slit spectroscopy of planetary nebulae (PNe) and H II regions in the two dwarf irregular (dIrr) galaxies Sextans A and B, which belong to a small group of galaxies just outside the Local Group. The observations were obtained with the New Technology Telescope ESO Multi-Mode Instrument. In Sextans A we obtained the element abundances in its only known PN and in three H II regions with the classical Te method. The oxygen abundances in these three H II regions of Sextans A are all consistent within the individual rms uncertainties, with an average 12 + log(O/H) = 7.54 ± 0.06. The oxygen abundance of the PN in Sextans A is, however, significantly higher: 12 + log(O/H) = 8.02 ± 0.05. This PN is even more enriched in nitrogen and helium, suggesting a classification as a PN of type I. The PN abundances of S and Ar, which are presumably unaffected by nucleosynthesis in the progenitor star, are well below those in the H II regions, indicating lower metallicity at the epoch of the PN progenitor formation (∼1.5 Gyr ago, according to our estimates based on the PN parameters). In Sextans B we obtained spectra of one PN and six H II regions. Element abundances with the Te method could be derived for the PN and three of the H II regions. For two of these H II regions, which have a separation of only ∼70 pc in projection, the oxygen abundances do not differ within the rms uncertainties, with a mean of 12 + log(O/H) = 7.53 ± 0.05. The third H II region, which is about 0.6 kpc northeast of the first two, is twice as metal-rich, with 12 + log(O/H) = 7.84 ± 0.05. This suggests considerable inhomogeneity in the present-day metallicity distribution in Sextans B. Whether this implies a general chemical inhomogeneity among populations of comparable age in Sextans B, and thus a metallicity spread at a given age, or whether we happen to see the short-lived effects of freshly ejected nucleosynthesis products prior to their dispersal and mixing with the ambient interstellar medium will require further study. For the PN we measured an O/H ratio of 12 + log(O/H) = 7.47 ± 0.16, consistent with that of the low-metallicity H II regions. We discuss the new metallicity data for the H II regions and PNe in the context of the published star formation histories and published abundances of the two dIrr galaxies. Both dIrrs show generally similar star formation histories in the sense of continuous star formation with amplitude variations but differ in their detailed enrichment timescales and star formation rates as a function of time. If we combine the photometrically derived estimates for the mean metallicity of the old red giant branch population in both dIrrs with the present-day metallicity of the H II regions, both dIrrs have experienced chemical enrichment by at least 0.8 dex (lower limit) throughout their history.
Design and evaluation of Pokespace: A bimanual haptic interaction technique

This thesis presents a new approach to haptic interaction technique design in which haptic feedback is displayed with a device held in the non-dominant hand, while the dominant hand controls a standard mouse. I believe that this approach has the potential to increase the fluency of everyday human-computer interaction by enabling a more effective division of tasks between the haptic and visual modalities. These ideas are expounded in a set of principles intended to guide the design of such techniques. I also present Pokespace, a novel interaction technique which follows those principles. Finally, I describe a series of three user studies intended to investigate and evaluate both the design principles and Pokespace. The results of the studies, though not unanimously positive, confirmed that Pokespace has the potential to support interaction without visual attention, and suggested several improvements to both the interaction technique and the underlying principles.
Social Network Analysis Inspired Content Placement with QoS in Cloud Based Content Delivery Networks

Content Placement (CP) problem in Cloud based Content Delivery Networks (CCDNs) leverage resource elasticity to build cost effective CDNs that guarantee QoS. In this paper, we present our novel CP model, which optimally places content on surrogates in the cloud, to achieve (a) minimum cost of leasing storage and bandwidth resources for data coming into and going out of the cloud zones and regions, (b) guarantee Service Level Agreement (SLA), and (c) minimize degree of QoS violations. The CP problem is NP Hard, hence we design a unique push based heuristic, called Weighted Social Network Analysis (W SNA) for CCDN providers. W-SNA is based on Betweeness Centrality (BC) from SNA and prioritizes surrogates based on their relationship to the other vertices in the network graph. To achieve our unique objectives, we further prioritize surrogates based on weights derived from storage cost and content requests. We compare our heuristic to current state of the art Greedy Site (GS) and purely Social Network Analysis (SNA) heuristics, which are relevant to our work. We show that W-SNA outperforms GS and SNA in minimizing cost and QoS. Moreover, W-SNA guarantees SLA but also minimizes the degree of QoS violations. To the best of our knowledge, this is the first model and heuristic of its kind, which is timely and gives a fundamental pre allocation scheme for future online and dynamic resource provision for CCDNs.
Two-Photon Holographic Stimulation of ReaChR

Optogenetics provides a unique approach to remotely manipulate brain activity with light. Reaching the degree of spatiotemporal control necessary to dissect the role of individual cells in neuronal networks, some of which reside deep in the brain, requires joint progress in opsin engineering and light sculpting methods. Here we investigate for the first time two-photon stimulation of the red-shifted opsin ReaChR. We use two-photon (2P) holographic illumination to control the activation of individually chosen neurons expressing ReaChR in acute brain slices. We demonstrated reliable action potential generation in ReaChR-expressing neurons and studied holographic 2P-evoked spiking performances depending on illumination power and pulse width using an amplified laser and a standard femtosecond Ti:Sapphire oscillator laser. These findings provide detailed knowledge of ReaChR's behavior under 2P illumination paving the way for achieving in depth remote control of multiple cells with high spatiotemporal resolution deep within scattering tissue.
A visualization tool for exploring multi-scale network traffic anomalies

Visualization is an intuitive and powerful way of understanding the evolution of huge amounts of network traffic in terms of characterizing network anomalies. We propose an interactive tool to display, explore, and understand network traffic focusing on anomalies. It displays traffic on different temporal and spatial (address and port) scales and lets users navigate network data by using a simple interface. Different graphical representations are used to highlight anomalies quickly, and textual packet information about corresponding plotted points are provided. The proposed tool provides good support for understanding traffic behavior and for evaluating the effectiveness of anomaly detection method. The tool directly reads dump files and uses no intermediate database in daily operations. This paper demonstrates several examples emphasizing specific patterns for various anomalies.
AN EXPLANATION OF INTERGENERATIONAL EDUCATIONAL MOBILITY USING THE CORRELATED MARE MODEL: A DANISH TEST CASE

We examine Danish student participation in upper secondary and university education in 1985 and 2005 using a generalization of the famous Mare educational transition model. Factors not related to the observed characteristics of the household in which the respondent was raised have become more important relative to observable family background variables for upper secondary school success than they were a generation ago. This conclusion is based a new mobility index which we have developed to measure the relative dependence of respondent educational success on family background variables which in turn resolves a paradox in our empirical results. The conclusion is also con…rmed by the application of the conventional methods that are usually used to measure mobility.
Semi-Global Stability Analysis of Observer-Based Extremum-Seeking for Hammerstein Plants

This paper considers semi-global stability of an observer-based extremum-seeking (ES) scheme acting on a Hammerstein plant. Unlike previous semi-global analyses, no restriction is placed on the speed of the ES dynamics relative to the plant dynamics. For any set of frequencies of a probing sinusoidal “dither,” it is shown how the plant output can be made to converge to an arbitrarily small neighborhood of its minimum from an arbitrarily large set of initial conditions. Furthermore, in the absence of noise, it is shown how increasing the dither frequency can allow arbitrarily fast convergence of the plant input to a small neighborhood of its optimum. Practical application of the results requires no a priori knowledge of the plant nonlinearity; however, in order to design the ES scheme to operate over a wide range of dither frequencies, some knowledge of the plant dynamics is required. Simulation examples are used to demonstrate these results and to highlight practical considerations when using a high-frequency dither.
Weakly Hard Real-Time Systems

In a hard real-time system, it is assumed that no deadline is missed, whereas, in a soft or firm real-time system, deadlines can be missed, although this usually happens in a nonpredictable way. However, most hard real-time systems could miss some deadlines provided that it happens in a known and predictable way. Also, adding predictability on the pattern of missed deadlines for soft and firm real-time systems is desirable, for instance, to guarantee levels of quality of service. We introduce the concept of weakly hard real-time systems to model real-time systems that can tolerate a clearly specified degree of missed deadlines. For this purpose, we define four temporal constraints based on determining a maximum number of deadlines that can be missed during a window of time (a given number of invocations). This paper provides the theoretical analysis of the properties and relationships of these constraints. It also shows the exact conditions under which a constraint is harder to satisfy than another constraint. Finally, results on fixed priority scheduling and response-time schedulability tests for a wide range of process models are presented.
Qualitative Crosstalk Analysis of Wnt and Notch Signaling in Mammalian Skin

The Qualitative networks framework allows to construct discrete executable models of biological systems. An efficient symbolic algorithm can be used to verify that all stable states of such a model are consistent with a set of requirements derived from the laboratory experimental data. Here we consider the crosstalk between the Notch and Wnt pathways that play a key role in the regulation of cell proliferation and differentiation. We extend the analysis of our model of interaction between these pathways in mammalian skin. By further constraining the requirements from the model, we formulate a hypothesis that the ligand Jagged, which is part of the Notch pathway, is a downstream target of Wnt signaling. This prediction has been recently validated experimentally by Estrach et al. ? Current address: Computer Science Department, Stanford University, Stanford, CA 94305. E-mail: marc.schaub@a3.epfl. ch ? Current address: Microsoft Research, Cambridge CB3 0FB, UK.
Localisation of prostaglandin F 2 , and E 2 binding sites in the human eye

Prostaglandin F2a reduces intraocular pressure possibly by increasing uveoscleral outflow. To further understand the mechanism of its action binding sites for prostaglandin F2a and, for comparison, prostaglandin E2 were localised in sections of human cadaveric eyes using an in vitro ligand-binding technique and autoradiography. Specific binding sites for both prostaglandin F2a and E2 were co-localised at a high level in the areas ofthe ciliary muscles and iris sphincter muscles, and at a lower level in the iris epithelium and the retina. The results suggest that prostaglandin F2a and also prostaglandin E2, could modulate uveoscleral outflow by binding to their receptors located on the ciliary muscles and inducing their relaxation. in vitro ligand binding technique and auto-
The design of the lower body of the compliant humanoid robot “cCub”

The “iCub ”is a robotic platform that was developed by the RobotCub [1] consortium to provide the cognition research community with an open “child-like ”humanoid platform for understanding and development of cognitive systems [1]. In this paper we present the mechanical realization of the lower body developed for the “cCub ”humanoid robot, a derivative of the original “iCub”, which has passive compliance in the major joints of the legs. It is hypothesized that this will give to the robot high versatility to cope with unpredictable disturbance ranging from small uneven terrain variations to unexpected collisions or even accidental falls. As part of the AMARSI European project, the passive compliance of this newly developed robot will be exploited for safer interaction, energy efficient and more aggressive damage-safe learning. The passive compliant actuation module used is a compact unit based on the series elastic actuator principle (SEA). In addition to the passive compliance the “cCub ”design includes other significant updates over the original prototype such as full joint state sensing including joint torque sensing and improved range of motion and torque capabilities. In this paper, the new leg mechanisms of the “cCub ”robot are introduced.
Dipping Technique for Ureteroileal Anastomosis in Orthotopic Ileal Neobladder: 20-Year Experience in 670 Patients—No Stenosis with Preservation of the Upper Tract

Objectives. Many techniques were described for ureteroileal anastomosis in orthotopic bladder substitution, ranging from nonrefluxing to refluxing techniques, all aiming at preservation of the upper tract. We describe our technique of dipping the ureter into the ileal pouch, which is simple and had no complications. Patients and Methods. Our technique implies dipping the ureter in the lateral side of the pouch, in right and left corners, with two rows of four sutures fixing the seromuscular layer of the ureter to the seromuscular layer of the ileal pouch. The procedure was applied in both normal ureteric calibre and dilated ureter. Total number of procedures done was 1,340 ureters in 670 patients after radical cystectomy for invasive carcinoma of the bladder of urothelial and nonurothelial cancer. Results. Followup of patients every six months and onward did not show stenosis in the ureteroileal anastomotic site. Filling of the ureter with contrast dye on ascending pouchogram was observed in patients who had considerably dilated ureters at the time of cystectomy. Normal ureter did not show clinical reflux but radiological filling of the ureter when the intravesical pressure exceeded the leak point pressure. Time to perform the dipping technique was 5–7 minutes for each site. Conclusion. Dipping technique for ureteroileal anastomosis in orthotopic ileal neobladder avoids the incidence of stenosis, preserves the upper tract, is a fast procedure, stands the evaluation in long-term followup, and was practiced successfully for twenty years.