Miracle-dz/UniFAR-FTUs huggingface dataset:
Backbone dynamics and refined solution structure of the N-terminal domain of DNA polymerase beta. Correlation with DNA binding and dRP lyase activity.

Mammalian DNA polymerase beta functions in the base excision DNA repair pathway filling in short patches (1-5 nt) in damaged DNA and removing deoxyribose 5'-phosphate from the 5'-side of damaged DNA. The backbone dynamics and the refined solution structure of the N-terminal domain of beta-Pol have been characterized in order to establish the potential contribution(s) of backbone motion to the DNA binding and deoxyribose 5'-phosphate lyase function of this domain. The N-terminal domain is formed from four helices packed as two antiparallel pairs with a 60 degrees crossing between the pairs. The RMSD of the NMR conformers (residues 13-80) is 0.37 A for the backbone heavy atoms and 0.78 A for all heavy atoms. NMR characterization of the binding site(s) for a ssDNA-5mer, ssDNA-8mer, ssDNA-9mer, and dsDNA-12mer shows a consensus surface for the binding of these various DNA oligomers, that surrounds and includes the deoxyribose 5'-phosphate lyase active site region. Connection segments between helices 1 and 2 and between helices 3 and 4 each contribute to DNA binding. Helix-3-turn-helix-4 forms a helix-hairpin-helix motif. The highly conserved hairpin sequence (LPGVG) displays a significant degree of picosecond time-scale motion within the backbone, that is possibly important for DNA binding at the phosphodiester backbone. An Omega-loop connecting helices 1 and 2 and helix-2 itself display significant exchange contributions (R(ex)) at the backbone amides due to apparent conformational type motion on a millisecond time-scale. This motion is likely important in allowing the Omega-loop and helix-2 to shift toward, and productively interact with, gapped DNA. The deoxyribose 5'-phosphate lyase catalytic residues that include K72 which forms the Schiff's base, Y39 which is postulated to promote proton transfer to the aldehyde, and K35 which assists in phosphate elimination, show highly restricted backbone motion. H34, which apparently participates in detection of the abasic site hole and assists in the opening of the hemiacetal, shows conformational exchange.
General Model for the Deployment of Time-Delay Elements in Transistorized Electronic Circuits

This paper presents a general model for the analysis of time-delay contributions due to right half plane (RHP) zeros in circuit's transfer functions. The presence of these RHP zeros is in general associated to Miller capacitances. These can be explored as a means of implementation of delay elements. A general discussion on the usage of these RHP zeros as means of designing usable delay cells is addressed, including several parasitic effects that may arise in practical implementations. The model is then verified recurring to simulation experiments.
The 5′ flanking region of the pS2 gene contains a complex enhancer region responsive to oestrogens, epidermal growth factor, a tumour promoter (TPA), the c‐Ha‐ras oncoprotein and the c‐jun protein.

Expression of the pS2 gene which is transcriptionally controlled by oestrogens in the breast cancer cell line MCF‐7 is oestrogen independent in stomach mucosa. We show here that the level of MCF‐7 cell pS2 mRNA can also be increased by the tumour promoter 12‐O‐tetradecanoylphorbol‐13‐acetate (TPA). We further demonstrate, using transient transfection assays, that the −428 to −332 5′ flanking sequence of the pS2 gene contains DNA enhancer elements responsive to oestrogens, TPA, EGF, the c‐Ha‐ras oncoprotein and the c‐jun protein.
A Map-Assisted WiFi AP Placement Algorithm Enabling Mobile Device’s Indoor Positioning

Location information and positioning technology are important to some Internet of Things (IoT) applications. The accuracy of indoor positioning using WiFi can be substantially enhanced by appropriate access point (AP) placement strategies, i.e., in a given indoor environment to deploy the WiFi APs at the locations where the mobile devices can work out their location more precisely. The plan of AP placement needs to be generated automatically by algorithms, especially for large-scale indoor environment. This paper presents an indoor map system that provides coordinate system and graphic representation. The detailed map information such as walls can be explicitly expressed and used to assist the AP placement algorithm. In this paper, AP placement is formulated into an optimization problem in which the sum of Euclidean distance of fingerprints among all the reference points (RPs) is maximized. The fingerprint at RP is predicted by an indoor radio propagation model which takes the attenuation of walls into consideration with the assistance of our indoor map. The optimization problem is solved by particle swarm optimization (PSO) and evaluated by k-nearest neighbors positioning algorithm in a real-world environment. The experimental results show that our map-assisted AP placement can provide higher positioning accuracy.
A questionnaire based study of subjective sleep quality: The psychometric evaluation of the Hungarian version of the Groningen Sleep Quality Scale

Jelen tanulmanyban bemutatjuk a Groningen Alvasminőseg Skala (Groningen Sleep Quality Scale) magyar verziojanak 201 szemely adatain nyugvo pszichometriai jellemzőit. A skalat ket fuggetlen mintan — 123 egyetemista es 78 pszichiatriai beteg altal kitoltott kerdőiv alapjan — vizsgaltuk meg. A Groningen Alvasminőseg Skala belső reliabilitasa mindket minta eseteben kifejezetten jonak bizonyult, a Cronbach alfa erteke mindket esetben meghaladta a 0,85-os erteket. A skala validitas vizsgalatat 4 kulonboző kerdőiv — a WHO jollet kerdőiv roviditett valtozata (WBI-5), a Beck Depresszio Kerdőiv roviditett valtozata (BDI-R), a Szubjektiv Testi Tunet Skala (PHQ-15) es a Vonasszorongas kerdőiv (STAI-T) segitsegevel vegeztuk el. A negy kerdőiv adatai es az egyes kerdőivek alvasminősegre vonatkozo tetelei mindket mintan szignifikans es kozepesen erős korrelaciot mutattak a Groningen Alvasminőseg Skalan nyert eredmenyekkel. A skala binaris logisztikus regresszio analizise alapjan a WHO-5, a PHQ-15 es (tendenciaszinten) a.
Improvement in the Production of L-Lysine by Overexpression of Aspartokinase (ASK) in C. glutamicum ATCC 21799

Purpose : To clone Corynebacterium glutamicum ATCC21799 aspartokinase gene (EC 2.7.2.4) using shuttle expression vector pEKEx2 in order to increase lysine production. Methods : C. glutamicum DNA was extracted and used for amplification of aspartokinase gene (ask) by cloning into an E. coli/C. glutamicum shuttle expression vector, pEKEx2. Initially, the recombinant vector transformed into E. coli DH5a and then into C. glutamicum. Results : Electrophoresis of recombinant protein by SDS-PAGE showed that the molecular weight of the recombinant protein was 42 KD. The induction of recombinant vector by IPTG had an inhibitory effect on cell growth due to over-expression of the cloned gene. The results of lysine assay by Chinard method showed that lysine production increased about two-fold, compared with the parent strain, as a result of increased copy numbers of lysC gene in recombinant strain. Conclusion : A two-fold increase in lysine production was observed by cloning of the ASK gene in C. glutamicum rather than in E. coli, due to the presence of lysine exporter channel which facilitates lysine extraction. Keywords : LysC gene, Corynebacterium glutamicum, L- lysine, Cloning, Aspartokinase, E. coli
Graph-based robust localization and mapping for autonomous mobile robotic navigation

Simultaneous Localization and Mapping (SLAM) means to estimate the positions and orientations of the mobile robot and to construct the model of the environment, essential and critical for autonomous navigation and widely used in a large range of application fields, the research goal is to design, implement and validate graph-based robust SLAM algorithm in indoor office-like dynamic scenarios. On the local level, scan matching is executed to estimate the local-relative-roto-translation value: first, pre-processing is performed to filter out the parts corresponding to the moving objects in the raw LIDAR data; second, conditioned-hough-transform-and-linear-regression-based line-segment detection is accomplished to detect the line features from the rest of LIDAR data; third, matching by fitting point to line is applied to estimate the roto-translation value. On the global level, the topological graph is constructed with the previously estimated motion constraints and batch optimization is achieved by a linear solution to estimate the global robot trajectory. Meanwhile, for the local line-feature maps which includes information about the static environment, they are transformed to the global frame based on the robot-pose information and integrated to construct the global-line-feature map. The experiments have verified the effectiveness of this hierarchical algorithm: locally, even when there is much rotation error in the input odometry data, the two sets of laser scan data can still be well matched; globally, the linear solution method can lead to much accurate and efficient results; and the line-feature-based mapping is effective to preserve the key geometrical characteristics of the environment.
Infant holding side biases displayed by fathers in maternity hospitals

Women and mothers prefer to hold infants and young children on the left side of their bodies. However, previous data reported in the literature for men and fathers have yielded inconclusive results in this regard. The aim of the present study was to (1) look for a left‐side holding bias in 94 new fathers studied in 3 maternity hospitals, and (2) investigate any recorded bias in relation to a number of variables (e.g. handedness and hemisphere specialisation in the perception of facial emotions) and the varying effects of the latter on populations of mothers and unselected participants. The results showed that a significant percentage (65%) of fathers preferred to hold their newborn infants on the left side. This holding bias in fathers was governed by neither the couple’s number of children, nor handedness, nor hemispheric specialisation in emotion perception.
A Novel Cervical Spinal Cord Window Preparation Allows for Two-Photon Imaging of T-Cell Interactions with the Cervical Spinal Cord Microvasculature during Experimental Autoimmune Encephalomyelitis

T-cell migration across the blood–brain barrier (BBB) is a crucial step in the pathogenesis of experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS). Two-photon intravital microscopy (2P-IVM) has been established as a powerful tool to study cell–cell interactions in inflammatory EAE lesions in living animals. In EAE, central nervous system inflammation is strongly pronounced in the spinal cord, an organ in which 2P-IVM imaging is technically very challenging and has been limited to the lumbar spinal cord. Here, we describe a novel spinal cord window preparation allowing to use 2P-IVM to image immune cell interactions with the cervical spinal cord microvascular endothelium during EAE. We describe differences in the angioarchitecture of the cervical spinal cord versus the lumbar spinal cord, which will entail different hemodynamic parameters in these different vascular beds. Using T cells as an example, we demonstrate the suitability of this novel methodology in imaging the post-arrest multistep T-cell extravasation across the cervical spinal cord microvessels. The novel methodology includes an outlook to the analysis of the cellular pathway of T-cell diapedesis across the BBB by establishing visualization of endothelial junctions in this vascular bed.
The wrong end of the stick: language-impaired children's understanding of non-literal language

The comprehension of non-literal language was investigated in 18 children with specific language impairment (SLI), including a subgroup identified by clinicians as having semantic-pragmatic difficulties, match ed with a normally developing control group. No difference in group mean scores was found between the SLI children and the control group; however, differences in the relationship between receptive language level and non-literal comprehension performance were found. The subgroup identified as having semantic-pragmatic difficulties performed no worse than the other SLI children and the control children. Implications are discussed for the diagnosis and treatment of semantic-pragmatic dis order.
Spatiotemporal regulation of Rho1 and Cdc42 activity during Candida albicans filamentous growth

Rho G‐proteins are critical for polarized growth, yet little is known about the dynamics of their activation during fungal filamentous growth. We first investigated the roles of Rho1 and Rho2 during Candida albicans filamentous growth. Our results show that Rho1 is required for invasive filamentous growth and that Rho2 is not functionally redundant with Rho1. Using fluorescent reporters, we examined the dynamics of the active form of Rho1 and Cdc42 during initiation and maintenance of hyphal growth. Quantitative analyses indicated that the distribution, but not the level, of these active G‐proteins is altered during initial polarization upon germ tube emergence. A comparison of the dynamics of these active G‐proteins during budding and hyphal growth indicates that a higher concentration of active Cdc42 was recruited to the germ tube tip than to the bud tip. During hyphal elongation, active Cdc42 remained tightly restricted to the hyphal tip, whereas active Rho1 was broadly associated with the apex and subsequently recruited to the cell division site. Furthermore, our data suggest that phosphoinositide‐bis‐phosphates are critical to stabilize active Rho1 at the growth site. Together, our results point towards different regulation of Cdc42 and Rho1 activity during initiation and maintenance of filamentous growth.
Intelligent agents: a way to reduce the gap between applications and networks

Network management (NM) has been in some way an activity apart from any other carried on the networks. Monitoring networks and systems resources independently from how users and applications are using them, has proven to be an inadequate approach since in most of the situations it's impossible to trace the relationship between network or systems faults and the applications affected by them. Furthermore, the degradation of network and systems resources can be considered as a fault from an application point of view, and there aren't any form to be aware of this degradation/fault, since applications requirements are not known to the network management system (NMS), and even when it happens the network can apparently still be viewed as functioning. Currently, the management efforts are used mostly to diagnose the origin of the faults, or to notify the systems administrators of the presence of a fault which in our opinion could be perceived by the network manager at very late stage. In this article we propose a way to bring the management closer to application and user requirements. The approach relies on spreading intelligent agents through network segments or domains, these agents being the management front-ends responsible to: collect QoS requirements concerning application operation over the network monitor required resources, perform when possible corrective actions, or at least provide management staff with powerful data so that they can take the corrective actions faster than before. We expect to benefit from being aware of how network and systems are used to develop a proactive management in real time, without the burden of classical approaches.
Multi-dimensionality of Idea Framing in Group Work in Academic Settings

This paper reports on the findings of a study which investigated the group interaction patterns of overseas Malaysian students on a British undergraduate programme. It discusses the different ways ideas are framed and developed in group interaction tasks; and the linguistic manifestations (lexical and syntactic features) of these different types of idea framing, which seem to mediate the process of generating and framing ideas. This paper first briefly discusses the theoretical issues underlying the study. Then the findings and categories of idea framing which arise from the analysis of group interaction data are discussed. Finally, it draws attention to the various types of analysis which might be undertaken to give a richer picture of the way knowledge is constructed and ideas are framed in group interaction tasks.
Emotion-focused therapy of depression

ABSTRACT A review of emotion-focused therapy (EFT) of depression including a discussion of its evidence base is provided. EFT aims within an affectively attuned empathic relationship to access and transform habitual maladaptive emotional schematic memories that are seen as the source of the depression. These memories often involve feelings of the shame of worthlessness, anxious insecurity and the sadness of abandonment. Through the therapeutic process, adaptive emotions are accessed to transform maladaptive emotions and to organize the person for adaptive responses. This process of changing emotion with emotion is aided by the use of specific therapeutic techniques that help stimulate arousal of emotion and its processing.
Jitter analysis of ring oscillator in a PLL

This paper proposes a nonlinear approach and a linear approach to predict a ring oscillator's phase noise and timing jitter due to device noise. Both approaches show that a ring oscillator's phase noise power spectral density is proportional to (/spl omega//sub 0///spl Delta//spl omega/)/sup 2/. In addition, estimation of the timing jitter caused by supply or substrate noise is also provided in the paper.
Optogenetic Interrogation of Dopaminergic Modulation of the Multiple Phases of Reward-Seeking Behavior

Phasic activation of dopaminergic neurons is associated with reward-predicting cues and supports learning during behavioral adaptation. While noncontingent activation of dopaminergic neurons in the ventral tegmental are (VTA) is sufficient for passive behavioral conditioning, it remains unknown whether the phasic dopaminergic signal is truly reinforcing. In this study, we first targeted the expression of channelrhodopsin-2 to dopaminergic neurons of the VTA and optimized optogenetically evoked dopamine transients. Second, we showed that phasic activation of dopaminergic neurons in freely moving mice causally enhances positive reinforcing actions in a food-seeking operant task. Interestingly, such effect was not found in the absence of food reward. We further found that phasic activation of dopaminergic neurons is sufficient to reactivate previously extinguished food-seeking behavior in the absence of external cues. This was also confirmed using a single-session reversal paradigm. Collectively, these data suggest that activation of dopaminergic neurons facilitates the development of positive reinforcement during reward-seeking and behavioral flexibility.
Automatic clustering of grid nodes

In a grid-computing environment, resource selection and scheduling depend on the network topology connecting the computation nodes. This paper presents a method to hierarchically group compute nodes distributed across the Internet into logical clusters, and determine the relative location of the clusters. At inter-domain level, distance from landmarks (a small group of distributed reference nodes) is the basis for converting the location of nodes inside a complex network structure onto a simple geometric space. The position of compute nodes in this geometric space is the basis for partitioning nodes into clusters. For compute nodes within an administrative domain, minimum RTT is used as the metric to partition nodes into clusters. This approach leads to an efficient, scalable and portable method of clustering grid nodes and building a distance map among clusters. We demonstrate the system for automatic clustering by applying it to computation nodes distributed across five universities in Texas.
A multi-agent control framework for co-adaptation in brain-computer interfaces

In a closed-loop brain-computer interface (BCI), adaptive decoders are used to learn parameters suited to decoding the user's neural response. Feedback to the user provides information which permits the neural tuning to also adapt. We present an approach to model this process of co-adaptation between the encoding model of the neural signal and the decoding algorithm as a multi-agent formulation of the linear quadratic Gaussian (LQG) control problem. In simulation we characterize how decoding performance improves as the neural encoding and adaptive decoder optimize, qualitatively resembling experimentally demonstrated closed-loop improvement. We then propose a novel, modified decoder update rule which is aware of the fact that the encoder is also changing and show it can improve simulated co-adaptation dynamics. Our modeling approach offers promise for gaining insights into co-adaptation as well as improving user learning of BCI control in practical settings.
Differential skeletal preservation at Windover Pond: causes and consequences.

In this paper, we evaluate the causes of differential skeletal preservation in the Windover Pond skeletal series (8BR246). We collected data on sex and age for approximately 110 individuals, and calculated a preservation score for each individual based on the presence of 80 skeletal landmarks. Our research questions evaluated the relationship between bone preservation and individual age and sex, and between the presence of preserved brain material and skeletal preservation, and the effects of burial location on bone preservation. The results indicate variability in average preservation for the sample (micro = 0.53, SD = 0.22) with an apparent lack of sex-specific (P = 0.79) or age-specific (P = 0.37) differences in preservation. The relationship between brain and skeletal preservation (P = 0.15) was not significant. The horizontal distribution of burials was not significantly correlated with skeletal preservation (north: r = -0.10, P = 0.93; east: r = 0.09, P = 0.45); however, vertical depth was a significant predictor of preservation (r = -0.31, P = 0.005), indicating that skeletal preservation decreased as burials were located closer to the ground surface. The observed variability in preservation scores may be related to the partial drying and resubmergence of the uppermost burials for the last few millennia. Comparison of Windover element-specific survival rates with previous analyses based on terrestrial samples (Galloway et al. [1997] Forensic taphonomy, Boca Raton: CRC Press; Waldron [1987] Death, decay and reconstruction, Manchester: Manchester University Press; Willey et al. [1997] Am J Phys Anthropol 104:513-528) affirms the relationship between element weight or density and bone survival. The unique taphonomic context of our study sample effected little change in bone deterioration processes.