Miracle-dz/UniFAR-FTUs huggingface dataset:
Immediate-Early and Delayed Primary Response Genes Are Distinct in Function and Genomic Architecture*

The transcriptional program induced by growth factor stimulation is classically described in two stages as follows: the rapid protein synthesis-independent induction of immediate-early genes, followed by the subsequent protein synthesis-dependent induction of secondary response genes. In this study, we obtained a comprehensive view of this transcriptional program. As expected, we identified both rapid and delayed gene inductions. Surprisingly, however, a large fraction of genes induced with delayed kinetics did not require protein synthesis and therefore represented delayed primary rather than secondary response genes. Of 133 genes induced within 4 h of growth factor stimulation, 49 (37%) were immediateearly genes, 58 (44%) were delayed primary response genes, and 26 (19%) were secondary response genes. Comparison of immediateearly and delayed primary response genes revealed functional and regulatory differences. Whereas many immediate-early genes encoded transcription factors, transcriptional regulators were not prevalent among the delayed primary response genes. The lag in induction of delayed primary response compared with immediateearly mRNAs was because of delays in both transcription initiation and subsequent stages of elongation and processing. Consistent with increased abundance of RNA polymerase II at their promoters, immediate-early genes were characterized by over-representation of transcription factor binding sites and high affinity TATA boxes. Immediate-early genes also had short primary transcripts with few exons, whereas delayed primary response genes more closely resembled other genes in the genome. These findings suggest that genomic features of immediate-early genes, in contrast to the delayed primary response genes, are selected for rapid induction, consistent with their regulatory functions.
Regulation of the polarity kinases PAR-1/MARK by 14-3-3 interaction and phosphorylation

Members of the PAR-1/MARK kinase family play critical roles in polarity and cell cycle control and are regulated by 14-3-3 scaffolding proteins, as well as the LKB1 tumour suppressor kinase and atypical protein kinase C (PKC). In this study, we initially investigated the mechanism underlying the interaction of mammalian MARK3 with 14-3-3. We demonstrate that 14-3-3 binding to MARK3 is dependent on phosphorylation, and necessitates the phosphate-binding pocket of 14-3-3. We found that interaction with 14-3-3 was not mediated by the previously characterised MARK3 phosphorylation sites, which led us to identify 15 novel sites of phosphorylation. Single point mutation of these sites, as well as the previously identified LKB1-(T211) and the atypical PKC sites (T564/S619), did not disrupt 14-3-3 binding. However, a mutant in which all 17 phosphorylation sites had been converted to alanine residues (termed 17A-MARK3), was no longer able to bind 14-3-3. Wild-type MARK3 was present in both the cytoplasm and plasma membrane, whereas the 17A-MARK3 mutant was strikingly localised at the plasma membrane. We provide data indicating that the membrane localisation of MARK3 required a highly conserved C-terminal domain, which has been termed kinase-associated domain-1 (KA-1). We also show that dissociation of 14-3-3 from MARK3 did not affect catalytic activity, and that a MARK3 mutant, which could not interact with 14-3-3, was normally active. Finally, we establish that there are significant differences in the subcellular localisation of MARK isoforms, as well as in the impact that atypical PKC overexpression has on 14-3-3 binding and localisation. Collectively, these results indicate that 14-3-3 binding to MARK isoforms is mediated by multiple phosphorylation sites, and serves to anchor MARK isoforms in the cytoplasm.
Chlamydia trachomatis-induced production of interleukin-1 by human monocytes

Human diseases caused by the intracellular bacterium Chlamydia trachomatis include genital tract infections and blinding trachoma. Chlamydial infections are characterized by chronic inflammation and scarring, and development of such complications is thought to be immunologically mediated. In this study, we show that coculture of C. trachomatis (serovar L2) with human blood monocytes induced the production of interleukin-1 (IL-1), an important mediator of inflammation, tissue remodeling, and scarring. IL-1 was produced in response to UV-inactivated elementary bodies containing from 0.1 to 50 micrograms of protein per ml, with a maximal response at 5 to 10 micrograms/ml. IL-1 activity was detected by 6 h of incubation and was maximal by 24 h. Peak levels were maintained throughout 96 h of incubation. Rabbit antibody to human IL-1(alpha + beta) effectively neutralized the thymocyte-stimulating activity of the supernatants. The apparent molecular weight of chlamydia-induced IL-1 was 16,000, as determined by gel filtration on a Bio-Gel P-60 column. Isoelectric focusing yielded two peaks of activity, with pIs of 5.5 and 6.9. Neutralization studies with antisera against human IL-1 alpha and IL-1 beta showed that the acidic and neutral peaks corresponded to IL-1 alpha and IL-1 beta, respectively, with IL-1 beta predominating. Heat-killed chlamydiae, which are not internalized by monocytes, were effective IL-1 inducers, indicating that phagocytosis was not required for IL-1 induction. Purified C. trachomatis lipopolysaccharide was also an effective IL-1 inducer, suggesting that the response to intact organisms may be largely a response to chlamydial lipopolysaccharide. Finally, purified chlamydial major outer membrane protein induced low but detectable IL-1 activity.
Simple quantification of benzodiazepine receptor binding and ligand transport using iodine-123-iomazenil and two SPECT scans.

UNLABELLED The feasibility of simplified procedures for the quantification of benzodiazepine receptor binding using [123I]iomazenil and SPECT was assessed. METHODS Six normal male volunteers were studied. Following intravenous injection of 111 MBq [123I]iomazenil, serial dynamic SPECT scanning was performed for 120 min and the concentration of lipophilic compounds in the arterial plasma was determined by chloroform extraction. Kinetic parameters were estimated by a curve-fitting procedure using the following four models: three-compartment, four-parameter (K1-k4) (3C4P), three-compartment, three-parameter (fixed K1/k2) (3C3P), three-compartment, two-parameter (fixed K1/k2 and k4) (3C2P) and two-compartment, two-parameter (K1 and k2) (2C2P). Kinetic parameters were also calculated by a table look-up procedure with 3C2P using only two SPECT data acquisitions. Parametric images were generated based on the same procedure. RESULTS In all models, the curve-fitting procedure gave similar outcomes for ligand transport (K1) and receptor density parameters (i.e., binding potential or distribution volume). The 3C4P parameters showed significant correlation between k2 and k3, while 3C3P did not show such a correlation, suggesting the stability of 3C3P. The 3C2P provided parameters essentially identical to those with the 3C3P, indicating the suitability of this model, while 2C2P gave similar distribution volume but obviously low K1. CONCLUSION Table look-up procedures based on the 3C2P model permit quantification of benzodiazepine receptor binding using [123I]iomazenil with two SPECT scans. This method may be of clinical value in the diagnosis of various diseases.
Terminology Extraction from Comparable Corpora for Latvian

This paper presents the work on terminology extraction from comparable corpora for Latvian. In the first section we introduce our work; the second section briefly describes the concept of the project and the implemented general terminology processing chain; the following two sections focus on terminology extraction workflow for Latvian and evaluation of results, respectively.
A Simple Wearable Hand Gesture Recognition Device Using iMEMS

Communicating with computer involves use of touch screens, wireless/wired mouse along with keyboards. In this paper, we propose a “Human Computer Interfacing Device” mapping Hand Gestures, most intuitive communication gesture, to communicate with computers, robots and other household electronic devices. Developments in field of communication have enabled computer commands being executed using hand gestures. This proposed novel solution achieves effective interaction with Internet giving quality feedback, intuitive control with complete mobility. Simple inertial navigation sensor like an accelerometer is utilized to get dynamic/static profile of movement to navigate the mouse or gyroscope to rotate 3-D virtual objects. Accelerometer profiles are converted into wireless interactivity. The device involves non-tactile interaction with computer screen where mouse pointer reacts to and manipulates screen content in accordance with hand gestures. The applications envisioned: interaction using gesture technology for effective communication empowering physically challenged to interact with computers including 3-D graphic interactions and simulations.
Characterization of effective capacity in antenna selection MIMO systems

In this paper, the effective capacity of a multiple-input multiple-output (MIMO) system in two different cases with receive antenna selection (RAS) and transmit antenna selection (TAS) schemes is investigated. A closed-form solution for the maximum constant arrival rate of this network with statistical delay quality of service (QoS) constraint is extracted in the quasi-static fading channel. This study is conducted in two different cases. When channel state information (CSI) is not available at the MIMO transmitter, implementation of TAS is difficult. Therefore, RAS scheme is employed and one antenna with the maximum instantaneous signal to noise ratio is chosen at the receiver. On the other hand, when CSI is available at the transmitter, TAS scheme is executed. In this case, one antenna is selected at the transmitter. Moreover, an optimal power-control policy is applied to the selected antenna and the effective capacity of the MIMO system is derived. Finally, this optimal power adaptation and the effective capacity are investigated in two asymptotic cases with the loose and strict QoS requirements. In particular, we show that in the TAS scheme with the loose QoS restriction, the effective capacity converges to the ergodic capacity. Then, an exact closed-form solution is obtained for the ergodic capacity of the channel here.
Groundwater extraction-induced land subsidence: a geodetic strain rate study in Kelantan, Malaysia

Abstract Kelantan is one of the highest groundwater-consumption states in Malaysia. The groundwater extraction provides an alternative solution for accessing a fresh water supply. However, over-exploitation of groundwater can lead to harmful geomorphological effects. We investigate the deformation rate due to land subsidence in Kelantan, Malaysia, using 17 years of GPS time-series (1999.0 – 2016.0) recorded at 11 GPS sites. Our results agree with a previous study, suggesting that northern Kelantan is subsiding at a maximum rate of 4.22 ± 0.17 mm/yr (1σ confidence level). The region also shows higher ground deformation rates than the other parts of Peninsular Malaysia (0.22 ppm/yr). In addition to the observed vertical subsidence, there is a corresponding horizontal deformation signal that manifests as strain accumulation. The dilatation strain rate shows a clear contractional pattern along the SW-NE trend of the Kelantan River, which is associated with the extensional signal in the surrounding regions.
Accurate cortical tissue classification on MRI by modeling cortical folding patterns

Accurate tissue classification is a crucial prerequisite to MRI morphometry. Automated methods based on intensity histograms constructed from the entire volume are challenged by regional intensity variations due to local radiofrequency artifacts as well as disparities in tissue composition, laminar architecture and folding patterns. Current work proposes a novel anatomy‐driven method in which parcels conforming cortical folding were regionally extracted from the brain. Each parcel is subsequently classified using nonparametric mean shift clustering. Evaluation was carried out on manually labeled images from two datasets acquired at 3.0 Tesla (n = 15) and 1.5 Tesla (n = 20). In both datasets, we observed high tissue classification accuracy of the proposed method (Dice index >97.6% at 3.0 Tesla, and >89.2% at 1.5 Tesla). Moreover, our method consistently outperformed state‐of‐the‐art classification routines available in SPM8 and FSL‐FAST, as well as a recently proposed local classifier that partitions the brain into cubes. Contour‐based analyses localized more accurate white matter–gray matter (GM) interface classification of the proposed framework compared to the other algorithms, particularly in central and occipital cortices that generally display bright GM due to their highly degree of myelination. Excellent accuracy was maintained, even in the absence of correction for intensity inhomogeneity. The presented anatomy‐driven local classification algorithm may significantly improve cortical boundary definition, with possible benefits for morphometric inference and biomarker discovery. Hum Brain Mapp 36:3563–3574, 2015. © 2015 Wiley Periodicals, Inc.
Fuzzy-integration based normalization for speaker verification

Similaritynormalizationtechniques are important for speaker veriﬁcation systems as they help to better cope with speaker variability. In the conventional normalization, the a priori probabilitiesof the cohort speakers are assumed to be equal. From this standpoint, we apply the theory of fuzzy measure and fuzzy integral to combine the likelihood values of the cohort speakers in which the assumption of equal a priori probabilities is relaxed. This approach replaces the conventional normalization term by the fuzzy integral which acts as a non-linear fusion of the similarity measures of an utterance assigned to cohort speakers. Experimental results show that the speaker veriﬁcation system using the fuzzy integral is more ﬂexible and favorable than the conventional method.
Recombination of alleles conferring specific resistance to powdery mildew at the Mla locus in barley.

In barley (Hordeum vulgare L.), the Mla locus conditions reaction to the powdery mildew fungus Erysiphe graminis f.sp. hordei. Enrichment for genetic recombinants in the Mla region is possible by screening for recombination events between the flanking endosperm storage proteins hordeins C and B. Reciprocal crosses were made between the Franger (C.I. 16151) and Rupee (C.I. 16155) lines carrying the (Mla6 + Mla14) and Mla13 alleles, respectively. Recombinants were identified from F2 segregants by analyzing the extracted hordein polypeptides by sodium dodecyl sulphate - polyacrylamide gel electrophoresis. Two hundred and seventy-six recombinant gametes were identified from the 1800 seeds that were screened. Recombination of Mla alleles was analyzed by inoculating F4 recombinant lines with three isolates of E. graminis (A27, 5874, and CR3), which recognize specific Mla alleles. The linkage order established is Hor1-Mla6-Mla13-Mla14-Hor2. The genetic distances between Hor1-Mla6, Mla6-Mla13, and Mla13-Hor2, obtained using Mapmaker 3.0b F3 intercross analysis, are 3.9, 0.2, and 5.2 cM, respectively.
Motion analysis of a spherical mobile robot

SUMMARY A path planning algorithm for a spherical mobile robot rolling on a plane is presented in this paper. The robot is actuated by two internal rotors that are fixed to the shafts of two motors. These are in turn mounted on the spherical shell in mutually orthogonal directions. The system is nonholonomic due to the nonintegrable nature of the rolling constraints. Further, the system cannot be converted into a chained form, and neither is it nilpotent nor differentially flat. So existing techniques of nonholonomic path planning cannot be applied directly to the system. The approach presented here uses simple geometrical notions and provides numerically efficient and intuitive solutions. We also present the dynamic model and derive motor torques for execution of the algorithm. Along the proposed paths, we achieve dynamic decoupling of the variables making the algorithm more suitable for practical applications.
PARTICULATE MATTER SOURCE APPORTIONMENT IN COMPLEX URBAN AND INDUSTRIAL CITIES: THE CASE OF TARRAGONA, SPAIN

In the framework of UltraPAR project (Assessing the Exposure and the Health Effects of Ambient Fine and Ultrafine Particles in areas of intensive industrial activity) the outdoor air quality of 12 schools in Tarragona (Catalonia, Spain) was monitored in winter 2016–2017. High volume air samplers equipped with quartz filters were used for sampling airborne particulate matter equal or smaller than 10, 2.5, and 1 μm (known as PM10, PM2.5, and PM1 respectively). These ambient samples together with some sources samples (harbour, industrial complexes, incinerator and road traffic) were chemically, mineralogically, and isotopically characterized and it is expected to help assessing the contribution of different emission sources. Preliminary results show that the maximum PM concentrations reached 37 μg/m3 for PM1, 30 μg/m3 for PM2.5 and 54 μg/m3 for PM10 while the lead content varies in the range of 10 to 13 ng/m3. Through XRD and SEM the marine aerosol influence is confirmed in this coastal city. The carbon isotopic signatures of the different PM sizes could be a potential tracer of its origin (mineral vs combustion sources). These findings were also compared with recent and older environmental data from other studies in similar cities or specifically in this zone to explore its consistency and possible temporal variations.
Complexity-Effective Superscalar Processors

The performance tradeoff between hardware complexity and clock speed is studied. First, a generic superscalar pipeline is defined. Then the specific areas of register renaming, instruction window wakeup and selection logic, and operand bypassing are analyzed. Each is modeled and Spice simulated for feature sizes of 0.8&micro;m, 0.35&micro;m, and 0.18&micro;m. Performance results and trends are expressed in terms of issue width and window size. Our analysis indicates that window wakeup and selection logic as well as operand bypass logic are likely to be the most critical in the future.A microarchitecture that simplifies wakeup and selection logic is proposed and discussed. This implementation puts chains of dependent instructions into queues, and issues instructions from multiple queues in parallel. Simulation shows little slowdown as compared with a completely flexible issue window when performance is measured in clock cycles. Furthermore, because only instructions at queue heads need to be awakened and selected, issue logic is simplified and the clock cycle is faster --- consequently overall performance is improved. By grouping dependent instructions together, the proposed microarchitecture will help minimize performance degradation due to slow bypasses in future wide-issue machines.
Perfusion Magnetic Resonance Imaging: A Comprehensive Update on Principles and Techniques

Perfusion is a fundamental biological function that refers to the delivery of oxygen and nutrients to tissue by means of blood flow. Perfusion MRI is sensitive to microvasculature and has been applied in a wide variety of clinical applications, including the classification of tumors, identification of stroke regions, and characterization of other diseases. Perfusion MRI techniques are classified with or without using an exogenous contrast agent. Bolus methods, with injections of a contrast agent, provide better sensitivity with higher spatial resolution, and are therefore more widely used in clinical applications. However, arterial spin-labeling methods provide a unique opportunity to measure cerebral blood flow without requiring an exogenous contrast agent and have better accuracy for quantification. Importantly, MRI-based perfusion measurements are minimally invasive overall, and do not use any radiation and radioisotopes. In this review, we describe the principles and techniques of perfusion MRI. This review summarizes comprehensive updated knowledge on the physical principles and techniques of perfusion MRI.
Feasible wrench space and its estimation for isometric haptic interaction

Standard approaches to mapping force to displacement or force to velocity with multi-DoF isometric haptic devices typically ignore the directional variability in a user's feasible wrench. We demonstrate that such a directionally-uniform mapping tends to either over-sensitize the interaction in some directions or under-utilize the user's operational range. To increase the effective use of the user's operational range it is necessary to model that range across all directions; for high-dimensional devices that measure wrenches (i.e, forces and torques) the space of directions is non-trivial to model by sampling. We present an approach that uses in-depth measurement of the feasible wrench space of a small number of users to extract a generic model for a given device interaction context; the generic model can then be automatically fitted to other users through a small number of measurements. In a user study comparing our method against the standard directionally-uniform assumption we show that our method generates a significantly better estimation of a user's output range, while requiring only a few measurements.
Using association rules to discover search engines related queries

We present a method for automatic generate suggestions of related queries submitted to Web search engines. The method extracts information from the log of past submitted queries to search engines using algorithms for mining association rules. Experimental results were performed on a log containing more than 2.3 million queries submitted to a commercial searching engine giving correct suggestions in 90.5% of the top 5 suggestions presented for common queries extracted from a real log.
Adapt cases: extending use cases for adaptive systems

Adaptivity is prevalent in today's software. Mobile devices self-adapt to available network connections, washing machines adapt to the amount of laundry, etc. Current approaches for engineering such systems facilitate the specification of adaptivity in the analysis and the technical design. However, the modeling of platform independent models for adaptivity in the logical design phase remains rather neglected causing a gap between the analysis and the technical design phase. To overcome this situation, we propose an approach called Adapt Cases. Adapt Cases allow the explicit modeling of adaptivity with domain-specific means, enabling adaptivity to gather attention early in the software engineering process. Since our approach is based on the concept of use cases it is easy adoptable in new and even running projects that use the UML as a specification language, and additionally, can be easily incorporated into model-based development environments.
A Policy-Based Decision Making Approach for Orchestrating Autonomic Elements

Autonomic systems encompass elements, components, and sometimes smaller autonomic sub-systems. Composition, integration and orchestration at different levels of such autonomic systems are significant issues in the interoperability of their constituent elements. This research focuses on orchestration as an important process of interoperability in an abstract autonomic system model. Policy-based management has potential to play an important role in orchestrating constituent components of autonomic systems/elements, and also to fill the gap between business and IT objectives. This research applies policy-based orchestration using crisp and fuzzy policies to reach the business goals of the system, and to obey the constraints defined by the service level agreement (SLA). First, a simulated model has been used in MATLAB/Simulink environment, and then the system is implemented by Agent Building and Learning Environment (ABLE) in Java