Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural and functional characterization of an atypical activation domain in erythroid Krüppel-like factor (EKLF)

Erythroid Krüppel-like factor (EKLF) plays an important role in erythroid development by stimulating β-globin gene expression. We have examined the details by which the minimal transactivation domain (TAD) of EKLF (EKLFTAD) interacts with several transcriptional regulatory factors. We report that EKLFTAD displays homology to the p53TAD and, like the p53TAD, can be divided into two functional subdomains (EKLFTAD1 and EKLFTAD2). Based on sequence analysis, we found that EKLFTAD2 is conserved in KLF2, KLF4, KLF5, and KLF15. In addition, we demonstrate that EKLFTAD2 binds the amino-terminal PH domain of the Tfb1/p62 subunit of TFIIH (Tfb1PH/p62PH) and four domains of CREB-binding protein/p300. The solution structure of the EKLFTAD2/Tfb1PH complex indicates that EKLFTAD2 binds Tfb1PH in an extended conformation, which is in contrast to the α-helical conformation seen for p53TAD2 in complex with Tfb1PH. These studies provide detailed mechanistic information into EKLFTAD functions as well as insights into potential interactions of the TADs of other KLF proteins. In addition, they suggest that not only have acidic TADs evolved so that they bind using different conformations on a common target, but that transitioning from a disordered to a more ordered state is not a requirement for their ability to bind multiple partners.
Chilean virtual observatory

This paper presents the challenges, architecture and current status of the Chilean Virtual Observatory (ChiVO), which is a software infrastructure for accessing and processing astronomical data generated in Chile. As ChiVO is part of the International Virtual Observatory Alliance (IVOA), we strictly follow the protocols and standards that this organization produce. However, there are always open challenges due to the new observational technologies and local requirements that motivates research on every new virtual observatory, such as the complex data models and Big Data problems that the ALMA Observatory is confronting. The current ChiVO prototype includes IVOA compliant services as well as new solutions designed for ALMA data, all of them using modern software technologies.
MOLECULAR DYNAMICS STUDIES OF BIOMIMETIC MEMBRANES

We have explored the conformational dynamics of the peptide-appended pillar[5]arene (PAP) channel in lipid and block copolymer (BCP) membranes through the use of molecular dynamics (MD) simulations. The novel polymeric structures trans-1,4-polybutadiene (PB), trans-1,4-polyisoprene (PI), and poly-2-methyl-2-oxazoline (PMOXA) were created and parameterized. These structures were then used to build and simulate pure PB12PEO9, PB23 PEO16 , PI12 PEO9 , and PI23PEO16 synthetic BCP membranes. In addition, simulations of the PAP channel inserted into lipid (POPC), PB12 PEO9 , and PB23PEO16 membranes were conducted. Results of simulations containing PAP suggest that the membrane environment can affect the channel dynamics and potentially its diffusive as well as transport characteristics. Next, we began to explore the microscopic structure of block copolymer membranes using coarse-grained methods. We tested original MARTINI force-field parameters by simulating the self-assembly of a POPC lipid bilayer. We then used the MARTINI force-field to build and simulate coarse-grained models of PB12PEO9. The original MARTINI force-field was unable to show the self-assembly of PB 12PEO9 and must therefore be further optimized to observe the desired behavior.
Reduced-complexity modified per-survivor iterative timing recovery using M-algorithm for magnetic recording system

A modified per-survivor iterative timing recovery (MPS-ITR), which jointly performs timing recovery, equalization, and error-correction decoding, has been proposed in [1] to deal with the problem of timing recovery operating at low signal-to-noise ratio. Practically, this scheme exploits a split-preamble strategy in conjunction with a per-survivor soft-output Viterbi algorithm equalizer to make it more robust against severe timing jitters or cycle slips. Although the MPS-ITR outperforms other iterative timing recovery schemes [1], it still has very high complexity. In this paper, we propose a reduced-complexity MPS-ITR scheme (denoted as MPS-ITR-M) to make it more implementable in real-life applications. This is achieved by applying the M-algorithm [2] to the MPS-ITR. Numerical results indicate that at low-to-moderate complexity, the MPS-ITR-M will perform better than other schemes.
Broadband semiconductor lasers

This open-access article is distributed under the terms of the Creative Commons Attribution Non-Commercial License (CC BY-NC) (http:// creativecommons.org/licenses/by-nc/4.0/), which permits reuse, distribution and reproduction of the article, provided that the original work is properly cited and the reuse is restricted to noncommercial purposes. For commercial reuse, contact reprints@pulsus.com Broadband semiconductor lasers
Empirical Study on Assessment Algorithms with Confidence in Crowdsourcing

Evaluating the quality of workers is very important in crowdsourcing system and impactful methods are required in order to obtain the most appropriate quality. Previous work have introduced confidence intervals to estimate the quality of workers. However, we have found the size of the confidence interval is wide through analysis of experimental results, which leads to inaccurate worker error rates. In this paper, we propose an optimized algorithm of confidence interval to reduce the size of the confidence interval as narrow as possible and to estimate the quality of workers more precise. We verify our algorithm using the simulated data from our own crowdsourcing platform under realistic settings.
Applying Importance-Performance Analysis To IT Outsourcing: A Survey Among Financial Institutions

What is the importance of specific control and contractual mechanisms for IT outsourcing relationship quality and outsourcing success? Employing a survey among financial institutions and applying Importance-Performance Analysis (IPA) known from marketing research, we analyse the relative importance of Service Level Agreements, control and contractual mechanisms for relationship quality and outsourcing success. Results show that, consistent with prior research, IT outsourcing relationship quality is positively related to outsourcing success. Extending prior research we show that outsourcing contract quality in general is most important for relationship quality, followed by control mechanisms and the characteristics of Service Level Agreements. We contribute to theory by revealing the differential importance of specific control and contractual factors for relationship quality and outsourcing success. Furthermore, we contribute to outsourcing practice by demonstrating the importance of specific measures in an IT outsourcing context and thus deliver direction for outsourcing management.
The evidence of contaminant bacterial DNA in several commercial Taq polymerases

Bacteria identification through PCR with 16S rDNA gene universal primers was widely used in clinical, environmental and applied microbiology. In practice, it is a considerable challenge to achieve high sensitivity and a clear negative control at the same time, due to contamination of commercial Taq polymerases with trace of bacterial DNA. In this paper, besides the methods proposed so far to avoid amplification in negative controls, we propose using of 16S rDNA gene universal primer pair (27F and 1407R), which unlike other primer pairs result with a clean control. Additionally, even if the negative control checked by agarose gel is clean, it is still possible presence of detectable PCR product, and we have identified the source of DNA contamination in six commercial Taq polymerases. We tested seven commercial Taq polymerases for presence of trace contaminating DNA and only one Taq polymerase was bacterial DNA free. These data can be useful to eliminate the false positive products when mentioned polymerases are used.
Synthesis of Predictable Networks-on-Chip-Based Interconnect Architectures for Chip Multiprocessors

Today, chip multiprocessors (CMPs) that accommodate multiple processor cores on the same chip have become a reality. As the communication complexity of such multicore systems is rapidly increasing, designing an interconnect architecture with predictable behavior is essential for proper system operation. In CMPs, general-purpose processor cores are used to run software tasks of different applications and the communication between the cores cannot be precharacterized. Designing an efficient network-on-chip (NoC)-based interconnect with predictable performance is thus a challenging task. In this paper, we address the important design issue of synthesizing the most power efficient NoC interconnect for CMPs, providing guaranteed optimum throughput and predictable performance for any application to be executed on the CMP. In our synthesis approach, we use accurate delay and power models for the network components (switches and links) that are obtained from layouts of the components using industry standard tools. The synthesis approach utilizes the floorplan knowledge of the NoC to detect timing violations on the NoC links early in the design cycle. This leads to a faster design cycle and quicker design convergence across the high-level synthesis approach and the physical implementation of the design. We validate the design flow predictability of our proposed approach by performing a layout of the NoC synthesized for a 25-core CMP. Our approach maintains the regular and predictable structure of the NoC and is applicable in practice to existing NoC architectures.
The Addition of Liquid Fructose to a Western-Type Diet in LDL-R−/− Mice Induces Liver Inflammation and Fibrogenesis Markers without Disrupting Insulin Receptor Signalling after an Insulin Challenge

A high consumption of fat and simple sugars, especially fructose, has been related to the development of insulin resistance, but the mechanisms involved in the effects of these nutrients are not fully understood. This study investigates the effects of a Western-type diet and liquid fructose supplementation, alone and combined, on insulin signalling and inflammation in low-density lipoprotein (LDL) receptor-deficient mice (LDL-R−/−). LDL-R−/− mice were fed chow or Western diet ±15% fructose solution for 12 weeks. Plasma glucose and insulin, and the expression of genes related to inflammation in the liver and visceral white adipose tissue (vWAT), were analysed. V-akt murine thymoma viral oncogene homolog-2 (Akt) activation was measured in the liver of the mice after a single injection of saline or insulin. None of the dietary interventions caused inflammation in vWAT, whereas the Western diet induced hepatic inflammation, which was further enhanced by liquid fructose, leading also to a significant increase in fibrogenesis markers. However, there was no change in plasma glucose or insulin, or insulin-induced Akt phosphorylation. In conclusion, hepatic inflammation and fibrogenesis markers induced by a Western diet supplemented with liquid fructose in LDL-R−/− mice are not associated with a significant impairment of hepatic insulin signalling.
Fumigaclavine C improves concanavalin A‐induced liver injury in mice mainly via inhibiting TNF‐α production and lymphocyte adhesion to extracellular matrices

Fumigaclavine C, an alkaloidal metabolite, was produced by Aspergillus fumigatus (strain No. CY018). This study examined the effect of this compound on concanavalin A (Con A)‐induced liver injury in mice, a T cell‐dependent model of liver damage. Con A administration resulted in severe liver injury, T lymphocyte activation and a strong increment in spleen cell adhesion, as well as in tumour necrosis factor‐α (TNF‐α) production. Against this liver injury, the intraperitoneal administration of fumigaclavine C dose‐dependently inhibited the elevation in transaminase activity, TNF‐α production in serum and the histological changes, including inflammatory infiltration, hepatocyte necrosis and degeneration and Kupffer cell hyperplasia. In addition, this compound in‐vitro also inhibited the proliferation of spleen cells induced by Con A, and reduced their IL‐2 and TNF‐α production. Moreover, the intraperitoneal administration of fumigaclavine C inhibited the potential of spleen cells isolated from the liver‐injured mice to adhere to fibronectin, laminin and type IV collagen. These results suggest that the improvement of this T cell‐mediated liver injury by fumigaclavine C may be related to the inhibition of lymphocyte activation, proliferation and adhesion to extracellular matrices as well as the reduction in TNF‐α production.
The Continuator: Musical Interaction With Style

We propose a system, the Continuator, that bridges the gap between two classes of traditionally incompatible musical systems: (1) interactive musical systems, limited in their ability to generate stylistically consistent material, and (2) music imitation systems, which are fundamentally not interactive. Our purpose is to allow musicians to extend their technical ability with stylistically consistent, automatically learnt material. This goal requires the ability for the system to build operational representations of musical styles in a real time context. Our approach is based on a Markov model of musical styles augmented to account for musical issues such as management of rhythm, beat, harmony, and imprecision. The resulting system is able to learn and generate music in any style, either in standalone mode, as continuations of musician’s input, or as interactive improvisation back up. Lastly, the very design of the system makes possible new modes of musical collaborative playing. We describe the architecture, implementation issues and experimentations conducted with the system in several real world contexts.
Nondestructive control of a mine shaft cast iron concrete lining by active infrared thermography

The study is devoted to the mathematical modeling of the thermophysical experiment related to diagnostics of the space under cast-iron tubbings of a shaft lining by the optical lock-in thermography. The defect detection is carried out by analyzing of phase characteristics of temperature oscillations on the tubbing surface. To compute the phase characteristics, the digital lock-in correlation method is used. For mathematical processing of the noisy data, the mathematical algorithm has been developed. An effectiveness of the proposed approach has been illustrated by the results of the numerical experiments.
Nuclear Export of African Swine Fever Virus p37 Protein Occurs through Two Distinct Pathways and Is Mediated by Three Independent Signals

ABSTRACT Nucleocytoplasmic shuttling activity of the African swine fever virus p37 protein, a major structural protein of this highly complex virus, has been recently reported. The systematic characterization of the nuclear export ability of this protein constituted the major purpose of the present study. We report that both the N- and C-terminal regions of p37 protein are actively exported from the nucleus to the cytoplasm of yeast and mammalian cells. Moreover, experiments using leptomycin B and small interfering RNAs targeting the CRM1 receptor have demonstrated that the export of p37 protein is mediated by both the CRM1-dependent and CRM1-independent nuclear export pathways. Two signals responsible for the CRM1-mediated nuclear export of p37 protein were identified at the N terminus of the protein, and an additional signal was identified at the C-terminal region, which mediates the CRM1-independent nuclear export. Interestingly, site-directed mutagenesis revealed that hydrophobic amino acids are critical to the function of these three nuclear export signals. Overall, our results demonstrate that two distinct pathways contribute to the strong nuclear export of full-length p37 protein, which is mediated by three independent nuclear export signals. The existence of overlapping nuclear export mechanisms, together with our observation that p37 protein is localized in the nucleus at early stages of infection and exclusively in the cytoplasm at later stages, suggests that the nuclear transport ability of this protein may be critical to the African swine fever virus replication cycle.
3D FDM production and mechanical behavior of polymeric sandwich specimens embedding classical and honeycomb cores

Abstract Desktop 3D FDM (Fused Deposition Modelling) printers are usually employed for the production of nonstructural objects. In recent years, the present authors tried to use this technology also to produce structural elements employed in the construction of small UAVs (Unmanned Aerial Vehicles). Mechanical stresses are not excessive for small multirotor UAVs. Therefore, the FDM technique combined with polymers, such as the ABS (Acrylonitrile Butadiene Styrene) and the PLA(Poly Lactic Acid), can be successfully employed to produce structural components. The present new work is devoted to the production and preliminary structural analysis of sandwich configurations. These new lamination schemes could lead to an important weight reduction without significant decreases of mechanical properties. Therefore, it could be possible, for the designed application (e.g., a multifunctional small UAV produced via FDM), to have stiffener and lighter structures easy to be manufactured with a low-cost 3D printer. The new sandwich specimens here proposed are PLA sandwich specimens embedding a PLA honeycomb core produced by means of the same extruder, multilayered specimens with ABS external layers and an internal homogeneous PLA core using different extruders for the two materials, sandwich specimens with external ABS skins and an internal PLA honeycomb core using different extruders for the two materials, and sandwich specimens where two different extruders have been employed for PLA material used for skins and for the internal honeycomb core. For all the proposed configurations, a detailed description of the production activity is given.Moreover, several preliminary results about three-point bending tests, different mechanical behaviors and relative delamination problems for each sandwich configuration will be discussed in depth.
A programmable voltage reference optimized for power management applications

A 3-bits programmable, low drift, high PSRR and high precision voltage reference, optimized for Power Management (PM) applications, is presented. The topology is based on a high-performance bandgap voltage reference that presents a PSRR of up to 80 dB, which is required in PM applications, because they employ mixed-signal circuits, where high frequency switching noise is present. The proposed approach was successfully verified in a standard 0.35 μm CMOS process. The experimental results confirmed that, for power supply between 3.0 and 3.3 V, and temperatures in −20°C to 80°C range, the programmable output voltage VREF exhibits a worst case precision of ±3%.
Micropatterned Elastic Gold‐Nanowire/Polyacrylamide Composite Hydrogels for Wearable Pressure Sensors

Elastic hydrogels have recently attracted remarkable attention because of their unique mechanical and stimulus‐responsive properties. In this work, a novel elastic supramolecular hydrogel for wearable pressure sensors is developed by photocrosslinking polyacrylamide (PAAm) through covalent bonds and hydrogen bonds as well as ionic bonds in the presence of poly(acrylic acid) and Ca2+. Gold nanowires (Au NWs) are homogeneously mingled with the PAAm hydrogel to attain a conductive composite hydrogel. Using an in‐house optical maskless exposure technology, printable piezoresistive pressure sensors are quickly fabricated by directly patterning the composite hydrogel into microribs on flexible electrodes. The pressure sensors with microrib structures exhibit a bimodal contact mode between Au NWs, which provides a new pathway to engineer the sensor's sensitivity and operation range. In the experiments, the pressure sensor with optimized microrib structures shows not only ultrahigh sensitivity (i.e., 3.71 kPa−1 in the pressure range of 0–2.8 kPa) but also low detection limit (i.e., 0.2 Pa) and long‐term stability. A flexible hand‐shape electrode device and an arterial pulse monitoring sensor are demonstrated to reveal the potentials of such a pressure sensor on wearable device applications.
APD: the Antimicrobial Peptide Database

An antimicrobial peptide database (APD) has been established based on an extensive literature search. It contains detailed information for 525 peptides (498 antibacterial, 155 antifungal, 28 antiviral and 18 antitumor). APD provides interactive interfaces for peptide query, prediction and design. It also provides statistical data for a select group of or all the peptides in the database. Peptide information can be searched using keywords such as peptide name, ID, length, net charge, hydrophobic percentage, key residue, unique sequence motif, structure and activity. APD is a useful tool for studying the structure-function relationship of antimicrobial peptides. The database can be accessed via a web-based browser at the URL: http://aps.unmc. edu/AP/main.html.
Design and modeling of a new variable stiffness robot joint

Safety constraints are a major aspect for human robots interaction. A new variable stiffness robot joint (VSR-joint) is proposed for operating safely. The proposed concept allows for the development of an actuation unit with a wide range of stiffness and a fast stiffness regulation response. The design of VSR-joint is compact and integrated highly and the operating is simply. The mechanics, the principle of operation and the model of the VSR-joint are proposed. The principle of operation of VSR-joint is based on a lever arm mechanism with a continuously regulated pivot point. The VSR-Joint features a highly dynamic stiffness adjustment along with a mechanically programmable system behavior. This allows an easy adaption to a big variety of tasks. Preliminary results are presented to demonstrate the fast stiffness regulation response and the wide range of stiffness achieved by the proposed VSR-Joint design.
Comparative mycobacterial genomics as a tool for drug target and antigen discovery

Genomics and the associated downstream technologies are generating vast data sets that provide new opportunities for understanding and combating both infectious and genetic diseases in humans. The genomic approach has been applied to tuberculosis, a major cause of transmissible morbidity and mortality, with notable success. Complete genome sequences are now available for three members of the Mycobacterium tuberculosis complex and the related intracellular pathogen M. leprae. Many of the predictions generated in silico by genomics have been validated through functional analysis, including studies of the transcriptome and proteome, and led to the identification of essential genes. Knowledge of the latter defines potential targets for new and existing drugs and their specificity can be assessed by comparative genomics with the host or other pathogens. Genomics is also furthering tuberculosis vaccine development by pinpointing potentially antigenic proteins as well as providing better diagnostic tools to detect infection.