Miracle-dz/UniFAR-FTUs huggingface dataset:
The knockdown of H19lncRNA reveals its regulatory role in pluripotency and tumorigenesis of human embryonic carcinoma cells

The function of imprinted H19 long non-coding RNA is still controversial. It is highly expressed in early embryogenesis and decreases after birth and re-expressed in cancer. To study the role of H19 in oncogenesis and pluripotency, we down-regulated H19 expression in vitro and in vivo in pluripotent human embryonic carcinoma (hEC) and embryonic stem (hES) cells. H19 knockdown resulted in a decrease in the expression of the pluripotency markers Oct4, Nanog, TRA-1-60 and TRA-1-81, and in the up-regulation of SSEA1; it further attenuated cell proliferation, decreased cell-matrix attachment, and up-regulated E-Cadherin expression. SCID-Beige mice transplanted with H19 down-regulated hEC cells exhibited slower kinetics of tumor formation, resulting in an increased animal survival. Tumors derived from H19 down-regulated cells showed a decrease in the expression of pluripotency markers and up-regulation of SSEA-1 and E-cadherin. Our results suggest that H19 oncogenicity in hEC cells is mediated through the regulation of the pluripotency state.
The electrolytic plating of compositionally modulated alloys and laminated metal nano-structures based on an automated computer-controlled dual-bath system

Compositionally modulated alloys (CMAs) and laminated nano-structures of metals are attracting ever-increasing enthusiasm due to their unique mechanical, electrical and, in particular, magnetic properties when compared to those of the respective bulk metals, and as evidenced by new and fascinating applications reported in the literature. Until recently, however, producing such multilayered coatings has been difficult at best, especially for larger samples of irregular configuration and in mass production. We will explain the design, objective and the use of our newly developed automated computer-controlled plating system for producing large-scale CMA coatings and laminated nano-structures of metals. Electroplating bath constituent concentrations, pH, temperature, mode of agitation, etc, as well as galvanostatic modes, e.g. direct current (d.c.) versus pulsed and/or pulse reversal currents, were optimized. Employing the automated dual-bath technique, multilayered composite materials of copper - nickel and copper - cobalt with more than 1000 alternating layers of varying dimensions, if desired, have been investigated and manufactured. The thickness of each sub-layer ranges from 25 nm to several micrometres (). Effort was also expended in the generation of CMA structures from single electroplating baths where the two metals of interest were present. The characterization results, as elucidated with scanning electron microscopy (SEM), atomic absorption spectroscopy and x-ray fluorescence and diffraction methods, and applications for such multilayered systems, in general, as well as the possibilities and limitation of the plating system are discussed.
Wi-Fi-based positioning in underground mine tunnels

The Owl Positioning System (OwlPS) was originally designed as a general-purpose Wi-Fi-based indoor positioning system. It is also a tool to compare several positioning techniques from the same input data, and was used for this purpose in previous work. In this work, OwlPS is adapted to a very specific “indoor” environment, namely underground mine tunnels, which brings its own problematics in terms of radio signal propagation and therefore impacts positioning system design. Experiment were conducted at a formerly exploited gold mine, at 70 metres under ground level, across about 400 metres of drifts. Several scenarios were defined to mimic typical use cases.
The Role and Regulatory Mechanism of 14-3-3 Sigma in Human Breast Cancer

Purpose 14-3-3 sigma (σ) is considered to be an important tumor suppressor and decreased expression of the same has been reported in many malignant tumors by hypermethylation at its promoter or ubiquitin-mediated proteolysis by estrogen-responsive ring finger protein (Efp). In this study, we investigated the significance of 14-3-3 σ expression in human breast cancer and its regulatory mechanism. Methods Efp was silenced using small interfering RNA (siRNA) in the MCF-7 breast cancer cell line in order to examine its influence on the level of 14-3-3 σ protein. The methylation status of the 14-3-3 σ promoter was also evaluated by methylation-specific polymerase chain reaction (PCR). The expression of Efp and 14-3-3 σ in 220 human breast carcinoma tissues was assessed by immunohistochemistry. Other clinicopathological parameters were also evaluated. Results Silencing Efp in the MCF-7 breast cancer cell line resulted in increased expression of 14-3-3 σ. The Efp-positive human breast cancers were more frequently 14-3-3 σ-negative (60.5% vs. 39.5%). Hypermethylation of 14-3-3 σ was common (64.9%) and had an inverse association with 14-3-3 σ positivity (p=0.072). Positive 14-3-3 σ expression was significantly correlated with poor prognosis: disease-free survival (p=0.008) and disease-specific survival (p=0.009). Conclusion Our data suggests that in human breast cancer, the regulation of 14-3-3 σ may involve two mechanisms: ubiquitin-mediated proteolysis by Efp and downregulation by hypermethylation. However, the inactivation of 14-3-3 σ is probably achieved mainly by hypermethylation. Interestingly, 14-3-3 σ turned out to be a very significant poor prognostic indicator, which is in contrast to its previously known function as a tumor suppressor, suggesting a different role of 14-3-3 σ in breast cancer.
Constraining nominalization: function/form competition

Abstract The present article deals with constraints on transcategorial processes such as nominalization. In particular, it addresses the issue whether one can predict the order in which verbal categories are lost and nominal categories are acquired in nominalization. It is argued that the disruption/acquisition of categories in transcategorial processes is determined by functionally based hierarchies of nominal and verbal categories, as suggested in the functional-typological literature. The hierarchy constraints in turn are shown to arise from the interaction of FuncFaith constraints forcing decategorization/recategorization and LexFaith hedging these processes. Structural factors such as morpheme order and category cumulation can also interfere with the hierarchy constraints. These structural factors can be derived from conditions on output-output correspondences (OOCs) between the morphological structure of nominalizations with that of finite verbs, on the one hand, and nonderived nouns, on the other. Thus the outcome of nominalization processes is determined by an interaction of the function-based hierarchy constraints and OOC-related structural constraints.
Bacterial Lipopolysaccharide Rapidly Inhibits Expression of C–C Chemokine Receptors in Human Monocytes

The present study was designed to investigate the effect of bacterial lipopolysaccharide (LPS) on C–C chemokine receptors (CCR) expressed in human mononuclear phagocytes. LPS caused a rapid and drastic reduction of CCR2 mRNA levels, which binds MCP-1 and -3. CCR1 and CCR5 mRNAs were also reduced, though to a lesser extent, whereas CXCR2 was unaffected. The rate of nuclear transcription of CCR2 was not affected by LPS, whereas the mRNA half life was reduced from 1.5 h to 45 min. As expected, LPS-induced inhibition of CCR2 mRNA expression was associated with a reduction of both MCP-1 binding and chemotactic responsiveness. The capacity to inhibit CCR2 expression in monocytes was shared by other microbial agents and cytokines (inactivated Streptococci, Propionibacterium acnes, and to a lesser extent, IL-1 and TNF-α). In contrast, IL-2 augmented CCR2 expression and MCP-1 itself had no effect. These results suggest that, regulation of receptor expression in addition to agonist production is likely a crucial point in the regulation of the chemokine system.
The Rodney L. White Center for Financial Research A Consumption-Based Model of the Term Structure of Interest Rates

This paper proposes a consumption-based model that can account for many features of the nominal term structure of interest rates. The driving force behind the model is a time-varying price of risk generated by external habit. Nominal bonds depend on past consumption growth through habit and on expected inflation. When calibrated to data on consumption, inflation, and the average level of bond yields, the model produces realistic volatility of bond yields and can explain key aspects of the expectations puzzle documented by Campbell and Shiller (1991) and Fama and Bliss (1987). When actual consumption and inflation data are fed into the model, the model is shown to account for many of the short and long-run fluctuations in the short-term interest rate and the yield spread. At the same time, the model captures the high equity premium and excess stock market volatility.
Simultaneous versus Sequential Accelerated Corneal Collagen Cross-Linking and Wave Front Guided PRK for Treatment of Keratoconus: Objective and Subjective Evaluation

Aim. To compare objective and subjective outcome after simultaneous wave front guided (WFG) PRK and accelerated corneal cross-linking (CXL) in patients with progressive keratoconus versus sequential WFG PRK 6 months after CXL. Methods. 62 eyes with progressive keratoconus were divided into two groups; the first including 30 eyes underwent simultaneous WFG PRK with accelerated CXL. The second including 32 eyes underwent subsequent WFG PRK performed 6 months later after accelerated CXL. Visual, refractive, topographic, and aberrometric data were determined preoperatively and during 1-year follow-up period and the results compared in between the 2 studied groups. Results. All evaluated visual, refractive, and aberrometric parameters demonstrated highly significant improvement in both studied groups (all P < 0.001). A significant improvement was observed in keratometric and Q values. The improvement in all parameters was stable till the end of follow-up. Likewise, no significant difference was determined in between the 2 groups in any of recorded parameters. Subjective data revealed similarly significant improvement in both groups. Conclusions. WFG PRK and accelerated CXL is an effective and safe option to improve the vision in mild to moderate keratoconus. In one-year follow-up, there is no statistically significant difference between the simultaneous and sequential procedure.
SmartPool: Practical Decentralized Pooled Mining

Cryptocurrencies such as Bitcoin and Ethereum are operated by a handful of mining pools. Nearly 95% of Bitcoin's and 80% of Ethereum's mining power resides with less than ten and six mining pools respectively. Although miners benefit from low payout variance in pooled mining, centralized mining pools require members to trust that pool operators will remunerate them fairly. Furthermore, centralized pools pose the risk of transaction censorship from pool operators, and open up possibilities for collusion between pools for perpetrating severe attacks. In this work, we propose SMARTPOOL, a novel protocol design for a decentralized mining pool. Our protocol shows how one can leverage smart contracts, autonomous blockchain programs, to decentralize cryptocurrency mining. SMARTPOOL gives transaction selection control back to miners while yielding low-variance payouts. SMARTPOOL incurs mining fees lower than centralized mining pools and is designed to scale to a large number of miners. We implemented and deployed a robust SMARTPOOL implementation on the Ethereum and Ethereum Classic networks. To date, our deployed pools have handled a peak hashrate of 30 GHs from Ethereum miners, resulting in 105 blocks, costing miners a mere 0:6% of block rewards in transaction fees.
Privacy Preserving Record Linkage with PPJoin

Privacy-preserving record linkage (PPRL) becomes increasingly important to match and integrate records with sensitive data. PPRL not only has to preserve the anonymity of the persons or entities involved but should also be highly efficient and scalable to large datasets. We therefore investigate how to adapt PPJoin, one of the fastest approaches for regular record linkage, to PPRL resulting in a new approach called P4Join. The use of bit vectors for PPRL also allows us to devise a parallel execution of P4Join on GPUs. We evaluate the new approaches and compare their efficiency with a PPRL approach based on multibit trees.
Investigation of siRNA Nanoparticle Formation Using Mono-Cationic Detergents and Its Use in Gene Silencing in Human HeLa Cells

The focus of recent research has been on the development of siRNA vectors to achieve an innovative gene therapy. Most of the conventional vectors are siRNA nanoparticles complexed with cationic polymers and liposomes, making it difficult to release siRNA. In this study, we report on the use of MCD, a quaternary ammonium salt detergent containing a long aliphatic chain (L-chain) as an siRNA complexation agent using human HeLa cells (a model cancer cell). We prepared siRNA nanoparticles using various MCDs, and measured the diameters and zeta-potentials of the particles. The use of an MCD with a long L-chain resulted in the formation of a positively charged nanoparticle. In contrast, a negatively charged nanoparticle was formed when a MCD with a short L-chain was used. We next evaluated the gene silencing efficiency of the nanoparticles using HeLa cells expressing the luciferase protein. The results showed that the siRNA/MCD nanoparticles showed a higher gene silencing efficiency than Lipofectamine 2000. We also found that the efficiency of gene silencing is a function of the length of the alkyl chain in MCD and zeta-potential of the siRNA/MCD nanoparticles. Such information provides another viewpoint for designing siRNA vectors.
Assembly of multiple chips on flexible substrate using anisotropie conductive film for medical imaging applications

Flip-chip interconnection technology based on anisotropic conductive film (ACF) has been selected to assemble multiple chips (i.e. ASICs - Application-Specific Integrated Circuits) on a flexible substrate in an electro-acoustic module. The chips are relatively large with a high number of I/O pins distributed over its area (on the order of 100 mm2). In this work, the processes of bonding one single chip, two chips simultaneously and four chips simultaneously to a substrate using ACF were characterized and compared. The results show similar effect of bond force on electrical resistance of ACF interconnects for bonded samples with one single chip, two chips and four chips. High bond yield values (more than 99 %) are obtained for all groups of samples bonded with a normalized bond force varying from 50 N/chip to 500 N/chip. In general, higher bond force, hence higher bond pressure, provides better ACF interconnects in terms of lower electrical resistance and higher bond yield. This work has demonstrated the feasibility of bonding multiple chips, each of which has a relatively large area with a high number of I/O pins, to a flexible substrate using ACF.
Validation of an immunoassay for soluble Klotho protein: decreased levels in diabetes and increased levels in chronic kidney disease.

The Klotho gene has been identified as an aging suppressor gene that encodes a transmembrane protein, which is expressed primarily in renal tubules. There are 2 forms of Klotho, membrane and secreted. However, there is a paucity of data on levels of soluble Klotho in diseases like diabetes and kidney disease. We validated an enzyme-linked immunosorbent assay for Klotho and quantitated Klotho levels separately in patients with diabetes and also in patients with chronic kidney disease (CKD). The Klotho assay showed good precision and was linear down to 19 ng/mL. There were no significant effects on Klotho levels with the addition of common interferents such as ascorbate, triglycerides, or hemolysis; only bilirubin (250 mg/L) significantly reduced Klotho levels (P < .05). There was a significant reduction in Klotho levels in samples with glycated hemoglobin (HbA(1c)) levels of 6.5% or more compared with control samples (HbA(1c) < 6.5%; P < . 001). We also documented significantly higher levels of Klotho with CKD. Thus, we validated an assay for Klotho and made the novel observation that levels are decreased in diabetes and increased in CKD.
A Limiting Solution for the Dependence of Film Thickness on Velocity in EHL Contacts with Very Thin Films

In recent years there have been substantial improvements in the capabilities of numerical modeling of elastohydrodynamic lubricant (EHL) films and it is now possible to analyze a very wide range of conditions rather than needing to rely on extrapolation using classical film thickness regression equations such as those of Dowson and Higginson. However, a new controversy has arisen concerning the film thickness-velocity dependence in EHL contacts at very low speeds and high loads, with some predictions showing a film thickness much less than that predicted by the classical equations. The present article applies the well-established limiting analysis, first presented by Grubin-Ertel, to the inlet of the EHL contact. It is shown that when the load is high and the speed is low (and the pressure gradient is very high in the inlet) an accurate resolution of the inlet pressure rise is critical for the determination of the film thickness. Discretization errors of this type might be responsible for discrepancies between the classical equations and some recently published numerical predictions.
Electroacoustic Absorber Using Disturbance-Observer-Type Velocity Estimator

An electroacoustic absorber (EA) using the direct impedance control (DIC) technique for broadband noise reduction requires a pair of pressure and velocity sensors. Due in part to the need for an array-type EA for acoustically large spaces, its installation cost increases. To overcome this problem, an EA using a disturbance-observer-type velocity estimator instead of a velocity sensor is proposed in this paper. To verify the feasibility of the proposed EA system, its specific acoustic admittance and noise absorbing performance are investigated and compared with those of an EA using a velocity sensor. The experimental results show that the proposed EA system performs sufficiently well for the frequency range of interest (20-500 Hz). Since the frequency range of interest may differ depending on the users' needs, it is more effective to adjust the noise absorbing performance of the EA. Therefore, it is also suggested to modify the original Q-filter by adding a lag compensator in the disturbance-observer-type velocity estimator. The stability issues of the proposed EA systems are addressed. The proposed EA system with the modified Q-filter can be expanded to an array system for practical acoustic noise control problems such as room acoustic modal control and vehicle interior noise control.
Quantify customer perception using natural language reviews

This project focuses on the multi-label classiﬁcation of product (BeerAdvocate dataset) and service (Yelp restaurants) reviews. We found Recurrent Neural Networks (RNN) with Long Short Term Memory (LSTM) and Convolutional Neural Networks (CNN) to be the most suitable Neural Network architecture for unstructured natural language content like reviews. We achieved validation accuracies of 56-58% with LSTM and CNN, against best-performing baselines 55% (from Support Vector Machines) and 47% (from the Random Forest approach). This is in line with similar best in class performance by neural networks in the RNN [5],[6] and CNN [13],[14] families. The typical skew towards higher scores in reviews has been removed, and equal numbers of reviews corresponding to each label were considered. While our architecture works far superiorly on binary classiﬁcation tasks (82% accuracy), we have focused on 5-label classiﬁcation since that is more representative of the actual application we target (predicting quantiﬁed summary of reviews).
PcG-Mediated Higher-Order Chromatin Structures Modulate Replication Programs at the Drosophila BX-C

Polycomb group proteins (PcG) exert conserved epigenetic functions that convey maintenance of repressed transcriptional states, via post-translational histone modifications and high order structure formation. During S-phase, in order to preserve cell identity, in addition to DNA information, PcG-chromatin-mediated epigenetic signatures need to be duplicated requiring a tight coordination between PcG proteins and replication programs. However, the interconnection between replication timing control and PcG functions remains unknown. Using Drosophila embryonic cell lines, we find that, while presence of specific PcG complexes and underlying transcription state are not the sole determinants of cellular replication timing, PcG-mediated higher-order structures appear to dictate the timing of replication and maintenance of the silenced state. Using published datasets we show that PRC1, PRC2, and PhoRC complexes differently correlate with replication timing of their targets. In the fully repressed BX-C, loss of function experiments revealed a synergistic role for PcG proteins in the maintenance of replication programs through the mediation of higher-order structures. Accordingly, replication timing analysis performed on two Drosophila cell lines differing for BX-C gene expression states, PcG distribution, and chromatin domain conformation revealed a cell-type-specific replication program that mirrors lineage-specific BX-C higher-order structures. Our work suggests that PcG complexes, by regulating higher-order chromatin structure at their target sites, contribute to the definition and the maintenance of genomic structural domains where genes showing the same epigenetic state replicate at the same time.
Identification of a Conserved RNA Replication Element (cre) within the 3Dpol-Coding Sequence of Hepatoviruses

ABSTRACT Internally located, cis-acting RNA replication elements (cre) have been identified within the genomes of viruses representing each of the major picornavirus genera (Enterovirus, Rhinovirus, Aphthovirus, and Cardiovirus) except Hepatovirus. Previous efforts to identify a stem-loop structure with cre function in hepatitis A virus (HAV), the type species of this genus, by phylogenetic analyses or thermodynamic predictions have not succeeded. However, a region of markedly suppressed synonymous codon variability was identified in alignments of HAV sequences near the 5′ end of the 3Dpol-coding sequence of HAV, consistent with noncoding constraints imposed by an underlying RNA secondary structure. Subsequent MFOLD predictions identified a 110-nucleotide (nt) complex stem-loop in this region with a typical AAACA/G cre motif in its top loop. A potentially homologous RNA structure was identified in this region of the avian encephalitis virus genome, despite little nucleotide sequence relatedness between it and HAV. Mutations that disrupted secondary RNA structure or the AAACA/G motif, without altering the amino acid sequence of 3Dpol, ablated replication of a subgenomic HAV replicon in transfected human hepatoma cells. Replication competence could be rescued by reinsertion of the native 110-nt stem-loop structure (but not an abbreviated 45-nt stem-loop) upstream of the HAV coding sequence in the replicon. These results suggest that this stem-loop is functionally similar to cre elements of other picornaviruses and likely involved in templating VPg uridylylation as in other picornaviruses, despite its significantly larger size and lower free folding energy.