Miracle-dz/UniFAR-FTUs huggingface dataset:
A Ligand-inducible Epidermal Growth Factor Receptor/Anaplastic Lymphoma Kinase Chimera Promotes Mitogenesis and Transforming Properties in 3T3 Cells*

Oncogenic rearrangements of the anaplastic lymphoma kinase (ALK) gene, encoding a receptor type tyrosine kinase, are frequently associated with anaplastic large cell lymphomas. Such rearrangements juxtapose the intracellular domain of ALK to 5′-end sequences belonging to different genes and create transforming fusion proteins. To understand how the oncogenic versions of ALK contribute to lymphomagenesis, it is important to analyze the biological effects and the biochemical properties of this receptor under controlled conditions of activation. To this aim, we constructed chimeric receptor molecules in which the extracellular domain of the ALK kinase is replaced by the extracellular, ligand-binding domain of the epidermal growth factor receptor (EGFR). Upon transfection in NIH 3T3 fibroblasts, the EGFR/ALK chimera was correctly synthesized and transported to the cell surface, where it was fully functional in forming high versus low affinity EGF-binding sites and transducing an EGF-dependent signal intracellularly. Overexpression of the EGFR/ALK chimera in NIH 3T3 was sufficient to induce the malignant phenotype; the appearance of the transformed phenotype was, however, conditionally dependent on the administration of EGF. Moreover, the EGFR/ALK chimera was significantly more active in inducing transformation and DNA synthesis than the wild type EGFR when either was expressed at similar levels in NIH 3T3 cells. Comparative analysis of the biochemical pathways implicated in the transduction of mitogenic signals did not show any increased ability of the EGFR/ALK to phosphorylate PLC-γ and MAPK compared with the EGFR. On the contrary, EGFR/ALK showed to have a consistently greater effect on phosphatidylinositol 3-kinase activity compared with the EGFR, indicating that this enzyme plays a major role in mediating the mitogenic effects of ALK in NIH 3T3 cells.
Analysis of the time-varying cortical neural connectivity in the newborn EEG: A time-frequency approach

Relationships between cortical neural recordings as a representation of functional connectivity between cortical brain regions were quantified using different time-frequency criteria. Among these, Partial Directed Coherence (PDC) and Directed Transfer Function (DTF) and their extensions have found wide acceptance. This paper aims to assess and compare the performance of these two connectivity measures that are based on time-varying multivariate AR modeling. The time-varying parameters of the AR model are estimated using an Adaptive AR modeling (AAR) approach and a short-time based stationary approach. The performance of these two approaches is compared using both simulated signal and a multichannel newborn EEG recording. The results show that the time-varying PDC outperforms the time-varying DTF measure. The results also point to the limitation of the AAR algorithm in tracking rapid parameter changes and the drawback of the short-time approach in providing high resolution time-frequency coherence functions. However, it can be demonstrated that time-varying MVAR representations of the cortical connectivity will potentially lead to better understanding of non-symmetric relations between EEG channels.
Paleoclimate of Mars as captured by the stratigraphic record in Gale Crater

A kilometers‐thick sedimentary sequence in Gale Crater exhibits stratigraphic changes in lithology that are consistent with transitions in aqueous and climatic conditions purported to be global in scale. The sequence is divided into two formations, where the Lower formation exhibits a net transition in mineralogy from clay/sulfate to sulfate/oxide assemblages and is separated from the overlying Upper formation by an erosional unconformity. Superposition and crater counts suggest strata in the Lower formation lie along the Noachian‐Hesperian time‐stratigraphic boundary, whereas beds in the Upper formation, which lack signatures indicative of clay minerals or sulfates, are thinner, more regularly spaced, and clearly younger. The observed stratigraphic trends are consistent with the rocks at Gale Crater recording a global transition from a climate favorable to clay mineral formation to one more favorable to forming sulfates and other salts.
PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM Approach

Since the read lengths of high throughput sequencing (HTS) technologies are short, de novo assembly which plays significant roles in many applications remains a great challenge. Most of the state-of-the-art approaches base on de Bruijn graph strategy and overlap-layout strategy. However, these approaches which depend on k-mers or read overlaps do not fully utilize information of single-end and paired-end reads when resolving branches, e.g. the number and positions of reads supporting each possible extension are not taken into account when resolving branches. We present PERGA (Paired-End Reads Guided Assembler), a novel sequence-reads-guided de novo assembly approach, which adopts greedy-like prediction strategy for assembling reads to contigs and scaffolds. Instead of using single-end reads to construct contig, PERGA uses paired-end reads and different read overlap size thresholds ranging from Omax to Omin to resolve the gaps and branches. Moreover, by constructing a decision model using machine learning approach based on branch features, PERGA can determine the correct extension in 99.7% of cases. When the correct extension cannot be determined, PERGA will try to extend the contigs by all feasible extensions and determine the correct extension by using look ahead technology. We evaluated PERGA on both simulated Illumina data sets and real data sets, and it constructed longer and more correct contigs and scaffolds than other state-of-the-art assemblers IDBA-UD, Velvet, ABySS, SGA and CABOG. Availability: https://github.com/hitbio/PERGA
Reflective HCI: articulating an agenda for critical practice

Reflective HCI is a style of HCI research that integrates technical practice with ongoing critical reflection. In the last thirty years, HCI researchers and practitioners have expanded their interests from aspects of cognitive ergonomics concerned with individuals using desktop computers at work to include concern for social and communal aspects of technology use and for affective and aesthetic aspects of design. This has been accompanied by the appropriation of a variety of disciplinary practices, concepts, and methodologies by HCI. In terms of the development and coherence of the discipline, it is timely to take a critical look at the assumptions, values, and traditions of each of these positions, their implications for HCI research agendas, and to try to understand the historical, cultural, and political emergence of HCI as a discipline itself. The main aim of this workshop will be to develop a systematic research agenda for reflective HCI.
Localizing interference during naming: Convergent neuroimaging and neuropsychological evidence for the function of Broca's area

To produce a word, the intended word must be selected from a competing set of other words. In other domains where competition affects the selection process, the left inferior frontal gyrus (LIFG) responds to competition among incompatible representations. The aim of this study was to test whether the LIFG is necessary for resolution of competition in word production. Using a methodological approach applying the same rigorous analytic methods to neuropsychological data as is done with neuroimaging data, we compared brain activation patterns in normal speakers (using fMRI) with the results of lesion-deficit correlations in aphasic speakers who performed the same word production task designed to elicit competition during lexical selection. The degree of activation of the LIFG in normal speakers and damage to the LIFG in aphasic speakers was associated with performance on the production task. These convergent findings provide strong support for the hypothesis that the region of cortex commonly known as Broca's area (i.e., the posterior LIFG) serves to bias competitive interactions during language production.
Effect of High Energy Ar-Ion Milling on Surface of Quenched Low-Carbon Low-Alloyed Steel

Surface preparation for electron backscatter diffraction (EBSD) measurements requires a lot of time and experience. We chose a lath martensitic iron based alloy to demonstrate the efficiency of ion polishing techniques. The average image quality (IQ) values from the EBSD measurements were assigned to be the characteristic parameter for surface goodness. The ideal ion sputtering time and the angle of incidence were determined, and the corresponding inverse pole figure (IPF) and IQ maps were compared to the mechanical polishing treatment.
Impact of human immunodeficiency virus 1 infection and inflammation on the composition and yield of cervical mononuclear cells in the female genital tract

Cervical cytobrush sampling is a relatively non‐invasive method for obtaining mucosal cells from the female genital tract. To define mucosal immune cells sampled by cervical cytobrushing and to validate this approach for local immunity studies, we investigated the impact of human immunodeficiency virus (HIV) status and inflammation on the yield and composition of cervical cytobrush specimens. Cervical cytobrush samples were obtained from 89 chronically HIV‐infected and 46 HIV‐negative women. The HIV‐infected women had significantly higher yields of CD3+, CD45+, CD19+, CD14+, Langerin+ and CD24+ cells than the uninfected women. While cytobrush‐derived T cells from uninfected women were predominantly CD4+ (4·2 CD4 : 1 CD8), CD8+ T cells were predominant in HIV‐infected women (0·6 CD4 : 1 CD8). The majority of CD4+ and CD8+ T cells from HIV‐infected and uninfected women were of the effector memory (CD45RA− CCR7− CD27−) phenotype. HIV‐infected women had significantly elevated levels of interleukin (IL)‐1β, IL‐6 and IL‐8 in cervical supernatants compared with uninfected women. We observed a significant positive correlation between T‐cell counts and IL‐1β, tumour necrosis factor (TNF)‐α and IL‐12 concentrations. Neutrophil counts correlated significantly with cervical concentrations of IL‐1β, TNF‐α, IL‐8, IL‐6 and IL‐10. Antigen‐presenting cell numbers correlated significantly with TNF‐α and IL‐12 concentrations. HIV‐infected women on antiretroviral therapy had similar levels of cervical lymphocyte infiltration and inflammation to women naïve to therapy. In conclusion, we suggest that inflammation at the cervix and HIV infection are likely to be key determinants in the absolute number of mucosal immune cells recovered by cervical cytobrushing.
Current Separations in Myxicola Giant Axons

The effect of reducing the external sodium concentration, [Na]o, on resting potential, action potential, membrane current, and transient current reversal potential in Myxicola giant axons was studied. Tris chloride was used as a substitute for NaCl. Preliminary experiments were carried out to insure that the effect of Tris substitution could be attributed entirely to the reduction in [Na]o. Both choline and tetramethylammonium chloride were found to have additional effects on the membrane. The transient current is carried largely by Na, while the delayed current seems to be independent of [Na]o. Transient current reversal potential behaves much like a pure Nernst equilibrium potential for sodium. Small deviations from this behavior are consistent with the possibility of some small nonsodium component in the transient current. An exact P Na/P K for the transient current channels could not be computed from these data, but is certainly well greater than unity and possibly quite large. The peak of the action potential varied with [Na]o as expected for a sodium action potential with some substantial potassium permeability at the time of peak. Resting membrane potential is independent of [Na]o. This finding is inconsistent with the view that the resting membrane potential is determined only by the distribution of K and Na, and P Na/P K. It is suggested that P Na /P K's obtained from resting membrane potential-potassium concentration data do not always have the physical meaning generally attributed to them.
Vegetation patterns and environmental gradients in tropical dry forests of the northern Yucatan Peninsula

Abstract Patterns of plant species composition and their relationships to soil and topographic variables were investigated in tropical dry forests across the north central Yucatan, Mexico. Seven sites were studied in the oldest accessible forests along a 200-km transect oriented northwest to southeast; an eighth site was located in a little-disturbed area located 75 km northeast of the transect. Two of the sites were on Mayan ruins. All sites were sampled using 9 - 24, 10 m × 20 m plots (n = 132) for woody stems ≥ 3.0 cm diameter breast height. The important natural forest species were Bursera simaruba, Caesalpinia gaumeri, Gymnopodium floribundum, Piscidia piscipula, and Thouinia paucidentata. The two most important woody species in ruin woodlands were Brosimum alicastrum and Croton lundellii. Forest plots (n =108) had 17 species on average, ruin plots (n = 24) nine species. Mean basal area of stems at the forest plots (20.7 m2.ha−1) was lower than in ruin plots (28.4 m2.ha−1). Detrended Correspondence Analysis generally placed plots by site along the geographic transect. Natural forest plots and sites were separated from the plots on ruin sites. The five soil and topographic variables (slope, soil depth, percent surface rock, soil pH, total soil organic matter) differed significantly among sites. Plot values were correlated with DCA axe scores. Intersite floristic variation reflects an overall west to east environmental gradient affected by climate. Nomenclature: White & Darwin (1995) and the floras and monographs used therein.
Microleakage at the cervical margin of Class II composite restorations with different intermediate layer treatments

Tooth-colored posterior restorations are now chosen as the first choice of caries treatment by many patients. Most popular tooth-colored restoration is the direct composite. The current composites have been improved, demonstrating proper wear resistance for the posterior regions. When all margins of composite restorations are located in enamel, satisfactory esthetics and longevity have been reported in small restorations. But in larger restorations where cervical margins are located in dentin, long-term success is more difficult to attain. Despite significant improvements in adhesive dentin bonding, polymerization shrinkage continues to rupture the Microleakage at the cervical margin of Class II composite restorations with different intermediate layer treatments
A multiple tuning method for PID controllers using constrained particle swarm optimization

The design of PID controllers can be considered as a constrained nonlinear optimization problem. This paper proposes a novel multiple tuning method for PID controllers based on the constrained particle swarm optimization algorithm. The design objective is to achieve the near-optimal performance subject to constraints in the time and frequency domain. Different optimization indexes and constraints can be selected to satisfy the multiple requirements of the processes. The proposed PID tuning method is tested on various kinds of processes with improved performance over the classic ZN tuning and other methods.
Coding and signal space diversity for a class of fading and impulsive noise channels

The transmission over the Gaussian mixture noise channel with perfect channel state information at the receiver side is considered. Lower and upper bounds on the achievable pairwise error probability (PEP) are derived for finite and infinite codeword lengths. It is shown that diversity codes, i.e., unitary transforms, can be applied to achieve a diversity gain. A large class of diversity codes is determined for which-if the codeword length is increased-the PEP between any two codewords approaches either zero or the lower bound on the PEP.
CHARACTERIZATION OF THE NONLINEAR VISCOELASTIC CONSTITUTIVE PROPERTIES OF MILD CHEDDAR CHEESE FROM INDENTATION TESTS

A methodology to convert the indentation force–displacement response into the stress–strain properties of nonlinear viscoelastic materials was evaluated. Mild cheddar cheese was used as the test material, and indentation tests were performed using two spherical indenters of different sizes. The indentation tests were performed at different speeds, and the corresponding force–displacement responses were fitted with an analytical solution to obtain the time-dependent constants and the instantaneous force–displacement response. An inverse analysis based on the finite element method was performed to obtain the strain-dependent constants from the instantaneous force–displacement response. The predictions of the viscoelastic stress–strain properties from the indentation tests were compared to independent measurements through uniaxial compression tests, and a reasonable agreement was obtained.
Chemical silver plating on polyester/cotton blended fabric

Chemical plating is a metallizing process that can impart unique properties to textile fabrics. It has great potential for use in textile production, especially in the functional and decorative aspects. The present study examined the feasibility of applying chemical silver plating to a polyester/cotton blended fabric (T/C fabric) as well as investigating the properties of the silver-plated T/C fabric. It was found that chemical silver plating helped to produce T/C fabric with a novel appearance and to improve its performance. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 100: 4383–4387, 2006
Evidence for a Role of srGAP3 in the Positioning of Commissural Axons within the Ventrolateral Funiculus of the Mouse Spinal Cord

Slit-Robo signaling guides commissural axons away from the floor-plate of the spinal cord and into the longitudinal axis after crossing the midline. In this study we have evaluated the role of the Slit-Robo GTPase activating protein 3 (srGAP3) in commissural axon guidance using a knockout (KO) mouse model. Co-immunoprecipitation experiments confirmed that srGAP3 interacts with the Slit receptors Robo1 and Robo2 and immunohistochemistry studies showed that srGAP3 co-localises with Robo1 in the ventral and lateral funiculus and with Robo2 in the lateral funiculus. Stalling axons have been reported in the floor-plate of Slit and Robo mutant spinal cords but our axon tracing experiments revealed no dorsal commissural axon stalling in the floor plate of the srGAP3 KO mouse. Interestingly we observed a significant thickening of the ventral funiculus and a thinning of the lateral funiculus in the srGAP3 KO spinal cord, which has also recently been reported in the Robo2 KO. However, axons in the enlarged ventral funiculus of the srGAP3 KO are Robo1 positive but do not express Robo2, indicating that the thickening of the ventral funiculus in the srGAP3 KO is not a Robo2 mediated effect. We suggest a role for srGAP3 in the lateral positioning of post crossing axons within the ventrolateral funiculus.
OPTIMAL TRAJECTORY PLANNING AND LQR CONTROL FOR A QUADROTOR UAV

As research into UAVs accelerates into the 21st ce n ury, alternatives to fixed wing vehicles such as the quadrotor are causing interest. Th e quadrotor is a small agile vehicle which could be suitable for search and rescue, surve illance and remote inspection. For autonomous operation a control system that incorporate s both trajectory planning and trajectory following is required. Trajectory planning can be posed as a constrained optimization problem typically within the control space an d with some constraints being placed in the output space. However, differential flatness e nables the optimization to occur within the output space and therefore simplifies the problem . A parameterization of the output is required to reduce the problem to a finite dimension al problem, this can be done using any number of techniques. Trajectory following can be achieved using linear multivariable control techniques such as LQR control.
Monitoring and Analysis of Respiratory Patterns Using Microwave Doppler Radar

Noncontact detection characteristic of Doppler radar provides an unobtrusive means of respiration detection and monitoring. This avoids additional preparations, such as physical sensor attachment or special clothing, which can be useful for certain healthcare applications. Furthermore, robustness of Doppler radar against environmental factors, such as light, ambient temperature, interference from other signals occupying the same bandwidth, fading effects, reduce environmental constraints and strengthens the possibility of employing Doppler radar in long-term respiration detection, and monitoring applications such as sleep studies. This paper presents an evaluation in the of use of microwave Doppler radar for capturing different dynamics of breathing patterns in addition to the respiration rate. Although finding the respiration rate is essential, identifying abnormal breathing patterns in real-time could be used to gain further insights into respiratory disorders and refine diagnostic procedures. Several known breathing disorders were professionally role played and captured in a real-time laboratory environment using a noncontact Doppler radar to evaluate the feasibility of this noncontact form of measurement in capturing breathing patterns under different conditions associated with certain breathing disorders. In addition to that, inhalation and exhalation flow patterns under different breathing scenarios were investigated to further support the feasibility of Doppler radar to accurately estimate the tidal volume. The results obtained for both experiments were compared with the gold standard measurement schemes, such as respiration belt and spirometry readings, yielding significant correlations with the Doppler radar-based information. In summary, Doppler radar is highlighted as an alternative approach not only for determining respiration rates, but also for identifying breathing patterns and tidal volumes as a preferred nonwearable alternative to the conventional contact sensing methods.
Towards Business Integration as a Service 2.0 (BIaaS 2.0)

Cloud Computing Business Framework (CCBF) is a framework for designing and implementation of Could Computing solutions. This proposal focuses on how CCBF can help to address linkage in Cloud Computing implementations. This leads to the development of Business Integration as a Service 1.0 (BIaaS 1.0) allowing different services, roles and functionalities to work together in a linkage-oriented framework where the outcome of one service can be input to another, without the need to translate between domains or languages. BIaaS 2.0 aims to allow automation, enhanced security, advanced risk modelling and improved collaboration between processes in BIaaS 1.0. The benefits from adopting BIaaS 1.0 and developing BIaaS 2.0 are illustrated using a case study from the University of Southampton and several collaborators including IBM US. BIaaS 2.0 can work with mainstream technologies such as scientific workflows, and the proposal and demonstration of BIaaS 2.0 will be aimed to certainly benefit industry and academia.
Serine proteases: structure and mechanism of catalysis.

PERSPECTIVES AND SUMMARY . 331 THE REACTION SEQUENCE AND INTERMEDIATES . 333 TRANSITION-STATE STABILIZATION . 338 STRUCTURAL FEATURES PARTICIPATING IN CATALYSIS . 341 Polypeptide Binding on the Acyl-Group Side 342 Side-Chain Specificity Sites 344 Polypeptide Binding on the Leaving-Group Side 346 Tetrahedral Binding and the Oxyanion Binding Site 348 The Reactive Serine and the Charge Relay System . 351