Miracle-dz/UniFAR-FTUs huggingface dataset:
Anomalous bioaccumulation of lead in the earthworm Eisenoides lonnbergi (Michaelsen)

Lead concentrations in soil organisms are usually well below those in the associated soil and tend to decrease with each higher trophic level in a food chain. Earthworms of the species Eisenoides lonnbergi provide an exception to this observation, accumulating very high concentrations of lead from acidic soils. Earthworms belonging to this species were collected from strongly to extremely acidic soils at 16 sites on a wildlife refuge in Maryland, USA. A lead concentration as high as 766 mg/kg, dry weight, was detected in depurated E. lonnbergi collected from soil containing only 17 mg/kg of lead. Concentration factors (ratio of lead concentration in earthworms to lead concentration in soil, dry wt) were highly variable at the sites, from 1.0 to 83. As suggested previously, lead absorption by earthworms is enhanced in low‐calcium soils. The anomalously high concentrations of lead found in E. lonnbergi are more closely correlated with the uptake of calcium from acidic soils than with bioaccessibility of soil lead. Environ Toxicol Chem 2018;37:914–919. Published 2017 Wiley Periodicals Inc. on behalf of SETAC. This article is a US government work and, as such, is in the public domain in the United States of America.
A churn and mobility resistant approach for DHTs

Mobile ad-hoc networks (MANETs) and distributed hash-tables (DHTs) share key characteristics in terms of self organization, decentralization, redundancy requirements, and limited infrastructure. However, node mobility and the continually changing physical topology pose a special challenge to scalability and the design of a DHT for mobile ad-hoc network. The mobile hash-table (MHT) [9] addresses this challenge by mapping a data item to a path through the environment. In contrast to existing DHTs, MHT does not to maintain routing tables and thereby can be used in networks with highly dynamic topologies. Thus, in mobile environments it stores data items with low maintenance overhead on the moving nodes and allows the MHT to scale up to several ten thousands of nodes.This paper addresses the problem of churn in mobile hash tables. Similar to Internet based peer-to-peer systems a deployed mobile hash table suffers from suddenly leaving nodes and the need to recover lost data items. We evaluate how redundancy and recovery technique used in the internet domain can be deployed in the mobile hash table. Furthermore, we show that these redundancy techniques can greatly benefit from the local broadcast properties of typical mobile ad-hoc networks.
Atomistic Simulation of Graphene-Polyurethane Nanocomposite for Use in Ballistic Applications

ii! ACKNOWLEDGEMENTS . iv! LIST OF FIGURES . vii! LIST OF TABLES . xi! 1. INTRODUCTION . 1! 1.1. Background and Motivation . 1! 1.2. Objective . 4! 1.3. Dissertation Layout . 5! 2. LITERATURE REVIEW . 8! 2.1. Polyurethane . 8! 2.2. Graphene . 11! 2.3. Overview of Graphene for Composite Filler . 16! 3. COMPUTATIONAL METHODS FOR MATERIAL SIMULATIONS . 20! 3.1. Quantum Mechanics and Density Functional Theory . 23! 3.2. Molecular Mechanics and Molecular Dynamics . 26! 3.2.1. Molecular Mechanics . 27! 3.2.2. Molecular Dynamics . 30! 4. NONELASTIC BEHAVIOR OF GRAPHENE: FIRST PRINCIPLE AND MOLECULAR MECHANICS CALCULATIONS . 38! 4.1. Motivation . 38! 4.2. Theoretical Framework . 41! 4.2.1. Equation of State . 41! 4.2.2. Nonlinear Elastic Theory . 42! 4.3. Computational Details . 48! 4.4. Results and Discussion . 50! 4.4.1. Equation of State . 50! 4.4.2. Elastic Constants: Second and Third Order . 53! 4.5. Concluding Remarks . 56!
Inhibition of TRPC1-Dependent Store-Operated Calcium Entry Improves Synaptic Stability and Motor Performance in a Mouse Model of Huntington's Disease.

BACKGROUND Huntington disease (HD) is a dominantly inherited neurodegenerative disorder caused by a CAG repeat expansion in the huntingtin gene. We previously discovered that mutant Huntingtin sensitizes type 1 inositol 1,4,5-trisphosphate receptor (InsP3R1) to InsP3. This causes calcium leakage from the endoplasmic reticulum (ER) and a compensatory increase in neuronal store-operated calcium (nSOC) entry. We previously demonstrated that supranormal nSOC leads to synaptic loss in striatal medium spiny neurons (MSNs) in YAC128 HD mice. OBJECTIVE We sought to identify calcium channels supporting supranormal nSOC in HD MSNs and to validate these channels as potential therapeutic targets for HD. METHODS Cortico-striatal cultures were established from wild type and YAC128 HD mice and the density of MSN spines was quantified. The expression of candidate nSOC components was suppressed by RNAi knockdown and by CRISPR/Cas9 knockout. TRPC1 knockout mice were crossed with YAC128 HD mice for evaluation of motor performance in a beamwalk assay. RESULTS RNAi-mediated knockdown of TRPC1, TRPC6, Orai1, or Orai2, but not other TRPC isoforms or Orai3, rescued the density of YAC128 MSN spines. Knockdown of stromal interaction molecule 1 (STIM1), an ER calcium sensor and nSOC activator, also rescued YAC128 MSN spines. Knockdown of the same targets suppressed supranormal nSOC in YAC128 MSN spines. These channel subunits co-immunoprecipitated with STIM1 and STIM2 in synaptosomal lysates from mouse striata. Crossing YAC128 mice with TRPC1 knockout mice improved motor performance and rescued MSN spines in vitro and in vivo, indicating that inhibition of TRPC1 may serve as a neuroprotective strategy for HD treatment. CONCLUSIONS TRPC1 channels constitute a potential therapeutic target for treatment of HD.
Surface Roughness Changes in Denture Liners in Denture Stomatitis Patients.

PURPOSE This randomized clinical trial assessed how surface roughness (Ra) in resilient liners was affected by soft tissue health conditions and time-related aspects in patients with complete dentures. METHODS Specimens of acrylic resin (control) and denture liners (silicone-based or acrylic resin-based) were inserted into the dentures of patients with and without denture stomatitis (n = 30). Ra was evaluated before denture insertion and after 7, 14, and 21 days of prosthesis wearing. Data were analyzed using three-way analysis of variance and Student-Newman-Keuls test. RESULTS Patients with stomatitis showed a higher Ra (P < .001), while all liners presented rougher surfaces after 14 days of clinical service, irrespective of the soft tissue health condition. CONCLUSION Ra of the tested denture liners was increased in patients with denture stomatitis. It is presumed that a longer wearing period will result in rougher surfaces.
Support vector machines for the classification of western handwritten capitals

In thispaper, new te hniques are presented using Support Ve tor Ma hines(SVMs) for multi- lass lassi(cid:12) ation problems. The issue of de omposing a N- lass las-si(cid:12) ation problem into a set of 2- lass lassi(cid:12) ation questions is dis ussed. In parti ular, the te hnique for normalizing the outputs of several SVMs is presented. Based on these te hniques, support ve tor lassi(cid:12)ers for the re ognition of West- ern handwritten apitals are realized. Comparisons to several other lassi(cid:12) ation methods are also presented.
QMSim: a large-scale genome simulator for livestock

SUMMARY QMSim was designed to simulate large-scale genotyping data in multiple and complex livestock pedigrees. The simulation is basically carried out in two steps. In the first step, a historical population is simulated to establish mutation-drift equilibrium, and in the second step, recent population structures are generated, which can be very complex. A wide variety of genome architectures, ranging from infinitesimal model to single-locus model, can be simulated. The program is efficient in terms of computing time and memory requirements. AVAILABILITY Executable versions of QMSim for Windows and Linux are freely available at http://www.aps. uoguelph.ca/~msargol/qmsim/.
Combinatorial therapeutic targeting of BMP2 and MEK-ERK pathways in NF1-associated malignant peripheral nerve sheath tumors

The clinical management of malignant peripheral nerve sheath tumors (MPNSTs) is challenging not only due to its aggressive and invasive nature, but also limited therapeutic options. Using gene expression profiling, our lab identified BMP2-SMAD1/5/8 pathway as a potential therapeutic target for treating MPNSTs. In this study, we explored the therapeutic impact of targeting BMP2-SMAD1/5/8 pathway in conjunction with RAS-MEK-ERK signaling, which is constitutively activated in MPNSTs. Our results indicated that single agent treatment with LDN-193189, a BMP2 Type I receptor inhibitor, did not affect the growth and survival of MPNST cells at biochemically relevant inhibitory concentrations. However, addition of a MEK1/2 inhibitor, selumetinib, to LDN-193189-treated cells resulted in significant inhibition of cell growth and induction of cell death. LDN-193189 at biochemically effective concentrations significantly inhibited motility and invasiveness of MPNST cells, and these effects were enhanced by the addition of selumetinib. Overall, our results advocate for a combinatorial therapeutic approach for MPNSTs that not only targets the growth and survival via inhibition of MEK1/2, but also its malignant spread by suppressing the activation of BMP2-SMAD1/5/8 pathway. Importantly, these studies were conducted in low-passage patient-derived MPNST cells, allowing for an investigation of the effects of the proposed drug treatments in a biologically-relevant context.
Ligand-activated PPARγ downregulates CXCR4 gene expression through a novel identified PPAR response element and inhibits breast cancer progression

Stromal Derived Factor-1α (SDF-1α) and its cognate receptor CXCR4 play a key role in mediating breast cancer cell invasion and metastasis. Therefore, drugs able to inhibit CXCR4 activation may add critical tools to reduce tumor progression, especially in the most aggressive form of the breast cancer disease. Peroxisome Proliferator-Activated Receptor (PPAR) γ, a member of the nuclear receptor superfamily, has been found to downregulate CXCR4 gene expression in different cancer cells, however the molecular mechanism underlying this effect is not fully understood. Here, we identified a novel PPARγ-mediated mechanism that negatively regulates CXCR4 expression in both epithelial and stromal breast cancer cells. We found that ligand-activated PPARγ downregulated CXCR4 transcriptional activity through the recruitment of the silencing mediator of retinoid and thyroid hormone receptor (SMRT) corepressor onto a newly identified PPAR response element (PPRE) within the CXCR4 promoter in breast cancer cell lines. As a consequence, the PPARγ agonist rosiglitazone (BRL) significantly inhibited cell migration and invasion and this effect was PPARγ-mediated, since it was reversed in the presence of the PPARγ antagonist GW9662. According to the ability of cancer-associated fibroblasts (CAFs), the most abundant component of breast cancer stroma, to secrete high levels of SDF-1α, BRL reduced migratory promoting activities induced by conditioned media (CM) derived from CAFs and affected CXCR4 downstream signaling pathways activated by CAF-CM. In addition, CAFs exposed to BRL showed a decreased expression of CXCR4, a reduced motility and invasion along with a phenotype characterized by an altered morphology. Collectively, our findings provide novel insights into the role of PPARγ in inhibiting breast cancer progression and further highlight the utility of PPARγ ligands for future therapies aimed at targeting both cancer and surrounding stromal cells in breast cancer patients.
REEP6 deficiency leads to retinal degeneration through disruption of ER homeostasis and protein trafficking

Abstract Retinitis pigmentosa (RP) is the most common form of inherited retinal dystrophy. We recently identified mutations in REEP6, which encodes the receptor expression enhancing protein 6, in several families with autosomal recessive RP. REEP6 is related to the REEP and Yop1p family of ER shaping proteins and potential receptor accessory proteins, but the role of REEP6 in the retina is unknown. Here we characterize the disease mechanisms associated with loss of REEP6 function using a Reep6 knockout mouse generated by CRISPR/Cas9 gene editing. In control mice REEP6 was localized to the inner segment and outer plexiform layer of rod photoreceptors. The Reep6-/- mice exhibited progressive photoreceptor degeneration from P20 onwards. Ultrastructural analyses at P20 by transmission electron microscopy and 3View serial block face scanning EM revealed an expansion of the distal ER in the Reep6-/- rods and an increase in their number of mitochondria. Electroretinograms revealed photoreceptor dysfunction preceded degeneration, suggesting potential defects in phototransduction. There was no effect on the traffic of rhodopsin, Rom1 or peripherin/rds; however, the retinal guanylate cyclases GC1 and GC2 were severely affected in the Reep6 knockout animals, with almost undetectable expression. These changes correlated with an increase in C/EBP homologous protein (CHOP) expression and the activation of caspase 12, suggesting that ER stress contributes to cell death. Collectively, these data suggest that REEP6 plays an essential role in maintaining cGMP homeostasis though facilitating the stability and/or trafficking of guanylate cyclases and maintaining ER and mitochondrial homeostasis.
Leber hereditary optic neuropathy due to a new ND1 mutation

ABSTRACT We report a proband with Leber hereditary optic neuropathy (LHON), in whom we have identified a novel homoplasmic m.3,395A>G mutation in the ND1 gene. The mutation alters a highly conserved amino acid in codon 30 which previously has been associated with LHON and leads to a severe selective complex I deficiency. By providing further evidence for pathogenicity we conclude that m.3,395A>G is pathogenic. High definition optical coherence tomography of the retina and peripapillary retinal nerve fiber layer (pRNFL) confirms recent reports that retinal ganglion cell loss precedes axonal loss in LHON and is present in the early stage of the disease. Furthermore, evaluation of two unaffected mutation carriers disclosed asymptomatic borderline ganglion cell loss and thin pRNFL in one.
Optimal training for wireless energy transfer

Wireless energy transfer (WET) is potentially a promising solution to provide convenient and reliable energy supplies for energy-constrained networks, and has drawn growing interests recently. To overcome the significant propagation loss over distance, employing multi-antennas at the energy transmitter (ET) to more efficiently direct wireless energy to desired energy receivers (ERs), termed energy beamforming, is an essential technique for WET. However, the achievable gain of energy beamforming crucially depends on the available channel state information (CSI) at the ET, which needs to be acquired practically. In this paper, we study the optimal design of one efficient channel-acquisition method for a point-to-point multiple-input multiple-output (MIMO) WET system, by exploiting the channel reciprocity based on which the ET estimates the CSI via dedicated reverse-link training from the ER. Considering the limited energy availability at the ER, the training strategy should be carefully designed so that the channel can be estimated with sufficient accuracy, and yet without consuming excessive energy at the ER. To this end, we propose to maximize the net energy at the ER, which is the total energy harvested offset by that used for channel training. The optimal training design, including the number of receive antennas to be trained, as well as the training time and power allocated, is derived. Our result shows that training helps only when the following conditions are satisfied: (i) the channel coherence time is sufficiently large; (ii) the number of antennas at the ET is large enough; and (iii) the effective signal-to-noise ratio (ESNR) is sufficiently high; otherwise, no training should be applied and isotropic energy transmission is optimal.
Analysis of Influence Factors on Wooden Biomass-pyrolysis Liquefaction

Woody biomass energy is an important part of the renewable energies;the fast pyrolysis technologies are the hotspot of studies on woody biomass energy both at home and abroad.Based on the summary of fast pyrolysis technologies of woody biomass,this paper focued on the temperature,heating rate,pressure,residence time of gas phrase,characteristics of wooden biomass,catalyst,and pyrolysis reactors in the process of pyrolysis.The paper also illustrated the factors of fast pyrolysis technique on yield of bio-oil.
Refinements on IEEE 802.11 Distributed Coordination Function Modeling Approaches

With the popularity of the IEEE 802.11 standards, many analytical saturation throughput studies for the distributed coordination function (DCF) have been reported. In this paper, we outline a number of issues and criticalities raised by previously proposed models. In particular, a careful look at backoff counter decrement rules allows us to conclude that, under saturation conditions, the slot immediately following a successful transmission can be accessed only by the station (STA) that has successfully transmitted in the previous channel access. Moreover, due to the specific acknowledgment (ACK) timeout setting adopted in the standard, the slot immediately following a collision cannot be accessed by any STA. Thus, the hypothesis of uncorrelation between consecutive channel slots and statistical homogeneity is not generally true. We propose a new backoff decrement model that retains the simplicity of traditional DCF models while being able to take into account such a correlation, and we compare the accuracy of our model with that of previously proposed approaches.
EEG-fMRI in the presurgical evaluation of temporal lobe epilepsy

Objective Drug-resistant temporal lobe epilepsy (TLE) often requires thorough investigation to define the epileptogenic zone for surgical treatment. We used simultaneous interictal scalp EEG-fMRI to evaluate its value for predicting long-term postsurgical outcome. Methods 30 patients undergoing presurgical evaluation and proceeding to temporal lobe (TL) resection were studied. Interictal epileptiform discharges (IEDs) were identified on intra-MRI EEG and used to build a model of haemodynamic changes. In addition, topographic electroencephalographic correlation maps were calculated between the average IED during video-EEG and intra-MRI EEG, and used as a condition. This allowed the analysis of all data irrespective of the presence of IED on intra-MRI EEG. Mean follow-up after surgery was 46 months. International League Against Epilepsy (ILAE) outcomes 1 and 2 were considered good, and 3–6 poor, surgical outcome. Haemodynamic maps were classified according to the presence (Concordant) or absence (Discordant) of Blood Oxygen Level-Dependent (BOLD) change in the TL overlapping with the surgical resection. Results The proportion of patients with good surgical outcome was significantly higher (13/16; 81%) in the Concordant than in the Discordant group (3/14; 21%) (χ2 test, Yates correction, p=0.003) and multivariate analysis showed that Concordant BOLD maps were independently related to good surgical outcome (p=0.007). Sensitivity and specificity of EEG-fMRI results to identify patients with good surgical outcome were 81% and 79%, respectively, and positive and negative predictive values were 81% and 79%, respectively. Interpretation The presence of significant BOLD changes in the area of resection on interictal EEG-fMRI in patients with TLE retrospectively confirmed the epileptogenic zone. Surgical resection including regions of haemodynamic changes in the TL may lead to better postoperative outcome.
Progress in developing Poisson-Boltzmann equation solvers

Abstract This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nanoobjects, the last one referring to objects that do not have biological function themselves but nowadays are frequently used in biophysical and medical approaches in conjunction with bio-macromolecules. The problem of modeling macromolecular electrostatics is reviewed from two different angles: as a mathematical task provided the specific definition of the system to be modeled and as a physical problem aiming to better capture the phenomena occurring in the real experiments. In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies in molecular motors, mitochondria complex, photosynthetic machinery and systems involving large nanoobjects.
Asymptotic detection of incipient faults in the case of nonlinear heteroscedasticity and the calibration of measurement systems

The sensor calibration is an important issue in the theory and practice of measurements. The calibration consists of comparing the output of the instrument or sensor under test against the output of an instrument of known accuracy when the same input is applied to both instruments. The goal of the sensor calibration is twofold: first, it is necessary to detect (and to remove) systematic biases in the sensor outputs; second it is necessary to adjust the model of random sensor error in order to get an optimal estimation of the measured parameters. This second task is especially important if the sensor outputs are processed by using the least-squares (LS) filter or the Kalman filter. The paper is devoted to the sensor calibration by using the sensor bias detection and the parameter estimation in the nonlinear model of the sensor heteroscedasticity. The heteroscedasticity occurs in regression when the measurement noise variance is non-constant. Both method, the bias detection test, and the sensor noise estimator, are based on a linear quasi-maximum likelihood estimator.
Research of low-power pulsed laser welding of stainless steel with activating fluxes

To improve the welding efficiency and reduce cost,the possibility of the penetration improvement on the welding joints by low-power pulsed laser with activating fluxes was studied.Based on the research of low-power pulsed laser welding of SUS304 stainless steel with five activating fluxes(TiO_2,SiO_2,Cr_2O_3,CaF_2,NaF),the effect of the fluxes on the penetration of joints,as well as the mechanism of penetration improvement,was studied,and the relevant data was received.The results show that the penetration can be changed with all the activating fluxes,among which TiO_2 and SiO_2 can deepen the penetration by 38.290% and 17.175% respectively.Meanwhile the depth/width ratios are improved in different degrees by Cr_2O_3,TiO_2 and SiO_2,however the fluoride has little effect on this ratio.The existence of activating fluxes not only improves the absorption rate of laser power,but also changes the convection of the welding pool,which makes the microstructures within the welding vary.The result is helpful for the further application of the activating fluxes in the laser technique.
A Solution-Processed Transparent NiO Hole-Extraction Layer for High-Performance Inverted Perovskite Solar Cells.

A highly transparent NiO layer was prepared by a solution processing method with nickel(II) 2-ethylhexanoate in non-polar solvent and utilized as HTM in perovskite solar cells. Excellent optical transmittance and the matched energy level lead to the enhanced power conversion efficiency (PCE, 18.15 %) than that of conventional sol-gel-processed NiO-based device (12.98 %).