Miracle-dz/UniFAR-FTUs huggingface dataset:
N-Glycan–dependent protein folding and endoplasmic reticulum retention regulate GPI-anchor processing

Glycosylphosphatidylinositol (GPI) anchoring of proteins is a conserved posttranslational modification in the endoplasmic reticulum (ER). Soon after GPI is attached, an acyl chain on the GPI inositol is removed by post-GPI attachment to proteins 1 (PGAP1), a GPI-inositol deacylase. This is crucial for switching GPI-anchored proteins (GPI-APs) from protein folding to transport states. We performed haploid genetic screens to identify factors regulating GPI-inositol deacylation, identifying seven genes. In particular, calnexin cycle impairment caused inefficient GPI-inositol deacylation. Calnexin was specifically associated with GPI-APs, dependent on N-glycan and GPI moieties, and assisted efficient GPI-inositol deacylation by PGAP1. Under chronic ER stress caused by misfolded GPI-APs, inositol-acylated GPI-APs were exposed on the cell surface. These results indicated that N-glycans participate in quality control and temporal ER retention of GPI-APs, ensuring their correct folding and GPI processing before exiting from the ER. Once the system is disrupted by ER stress, unprocessed GPI-APs become exposed on the cell surface.
Measurement of physical and mechanical properties of beeswax

Abstract The mechanical properties of beeswax, measured as a function of temperature, using a variety of techniques, are identified and compared. The coefficient of friction of beeswax is measured and compared with that of plasticine and Nylon 6–6. It is shown that the frictional behaviour of beeswax departs from Amonton's laws and behaves instead as a classic soft, elastic polymer. Free surface energy measurements of beeswax are also reported.
Relay Selection for Heterogeneous Cellular Networks with Renewable Green Energy Sources

With the advance of the photovoltaic panel technology, the infrastructure equipment of cellular networks with solar energy sources has attracted extensive interests. It is expected that base stations (BSs) and relay stations (RSs) with renewable energy will play important roles in reducing the power consumption from electrical grids in future green cellular networks. Inspired by this technology trend, this paper considers a heterogeneous green cellular network, in which a part of RSs is powered by solar energy sources to represent the incremental deployment for the infrastructure with renewable energy in the near future. We formulate a new relay selection and power allocation problem with Mixed Integer Linear Programming to select solar-powered RSs and grid-powered RSs, such that the total grid power consumption is effectively minimized in decode-and-forward cooperative communication networks. We design an algorithm to derive the optimal solution, and also devise an efficient distributed algorithm to reduce the computational cost. The simulation results demonstrate that the algorithms can effectively reduce the total grid power consumption with different channel conditions, different deployments of RSs in a network, and different available power levels in solar-powered RSs. In addition, the problem model and the proposed algorithms can be extended to support hybrid energy sources.
Aerobic capacity explains physical functioning and participation in patients with multiple sclerosis-related fatigue.

OBJECTIVE To investigate whether aerobic capacity explains the level of self-reported physical activity, physical functioning, and participation and autonomy in daily living in persons with multiple sclerosis-related fatigue. DESIGN A cross-sectional study. PATIENTS Sixty-two participants with multiple sclerosis-related fatigue. METHODS Aerobic capacity was measured with a leg ergometer and was expressed as maximal oxygen uptake (VO2max, in ml/kg/min). Physical activity was measured with the Physical Activity Scale for Individuals with Physical Disabilities (PASIPD), physical functioning with the Short Form 36 - physical functioning (SF36-pf), and participation and autonomy in daily living with the Impact on Participation and Autonomy questionnaire (IPA). Multiple regression analyses were performed, adjusted for potential confounders (gender, age, body mass index, educational level, and employment status). RESULTS Mean maximal oxygen uptake (VO2max) was 23.9 ml/kg/min (standard deviation (SD) 6.3 ml/kg/min). There was no significant relationship between VO2max and physical activity (PASIPD): β = 0.320, 95% confidence interval (95% CI) = -0.109 to 0.749, R2 = 10.8%. Higher VO2max correlated with better physical functioning (SF36-pf): β = 1.527, 95% CI = 0.820-2.234, R2 = 25.9%, and was significantly related to IPA domains "autonomy indoors" (β = -0.043, 95% CI = -0.067 to -0.020, R2 = 20.6%), "autonomy outdoors" (β = -0.037, 95% CI = -0.062 to -0.012, R2 = 18.2%) and "social life and relationships" (β=-0.033, 95% CI = -0.060 to -0.007, R2 = 21.3%). CONCLUSION Maximum aerobic capacity was severely reduced in persons with multiple sclerosis-related fatigue. This partly explains the limited physical functioning and restrictions in participation and autonomy indoors, outdoors and in social life and relationships in these persons.
Application of Nanometer-Scale Processing Technique in High-Density Recording

To realize ultrahigh density recording in high precision using polycarbonate as a recording media, the nanometer-scale mechanical processing properties of polycarbonate and fluorocarbon plasma-treated polycarbonate were investigated using atomic force microscopy (AFM). The surface free energy of the polycarbonate specimen can be reduced by fluorocarbon plasma-treatment, resulting in processing force being reduced. Thus, nanometer-scale precise processing of polycarbonate can be realized. Lines and spaces with intervals minimized to 60 nm were performed on the fluorocarbon plasma-treated polycarbonate. Viscoelastic properties of the fluorinated polycarbonate were evaluated using AFM in force modulation mode. Fluorocarbon plasma treatment can reduce friction force of a polycarbonate sample and improve its wear resistance. Therefore, the friction durability corresponding to the reliability of data reproduction was markedly improved.
High Performance System Framework for Parallel in-Silico Biological Simulations

The parallel implementation of methods and algorithms for analysis of biological data using high-performance computing is essential for accelerating the research and reduce the investment. The paper presents a high-performance framework for carrying out scientific experiments in the area of bioinformatics, on the basis of parallel computer simulations on a heterogeneous compact computer cluster. Several of the most popular and widely used methods and algorithms using for simulations intended for high performance platforms in order to increase the efficiency of the computations have been implemented. Important role is building up a database consisting of a reference genetic biological data, advanced software tools for in-silico simulations for the purposes of molecular biology, and web portal enabling secure access to the services. Web portal provides as services access and extraction of biological data and execution of various parallel program implementations based on algorithms for comparative analysis of biological data. The proposed framework is verified experimentally for the case study of investigation the influenza virus variability.
An Improved Energy Detector for Mobile Cognitive Users Over Generalized Fading Channels

A cooperative cognitive radio network (CRN) with improved energy detection-based spectrum sensing is analyzed in various fading scenarios. Generalized multipath (Nakagami-<inline-formula> <tex-math notation="LaTeX">$m$ </tex-math></inline-formula>) fading and enriched multipath (Nakagami-<inline-formula> <tex-math notation="LaTeX">$q$ </tex-math></inline-formula>) fading models are considered along with two other general fading distributions, i.e., <inline-formula> <tex-math notation="LaTeX">$\kappa$ </tex-math></inline-formula>-<inline-formula> <tex-math notation="LaTeX">$\mu$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$\eta$ </tex-math></inline-formula>-<inline-formula> <tex-math notation="LaTeX">$\mu$ </tex-math></inline-formula> distributions. For spectrum sensing, instead of conventional power 2-based detection method, the arbitrary power <inline-formula> <tex-math notation="LaTeX">$p$ </tex-math></inline-formula>-based improved energy detector is used. The impact of the cognitive user mobility on the performance of the improved energy detector is investigated. Specifically, the statistics for the received signal are derived over various fading environments. The performance of the considered CRN system is evaluated in terms of probability of false alarm, probability of missed detection, and receiver operating characteristics (ROC) curves. Moreover, the area under the ROC curve is also obtained. Simulation results are provided to corroborate the theoretical results derived in this paper.
Performance evaluation of acoustic scene classification using DNN-GMM and frame-concatenated acoustic features

We previously proposed a method of acoustic scene classification using a deep neural network-Gaussian mixture model (DNN-GMM) and frame-concatenated acoustic features. It was submitted to the Detection and Classification of Acoustic Scenes and Events (DCASE) 2016 Challenge and was ranked eighth among 49 algorithms. In the proposed method, acoustic features in temporally distant frames were concatenated to capture their temporal relationship. The experimental results indicated that the classification accuracy is improved by increasing the number of concatenated frames. On the other hand, the frame concatenation interval, which is the interval with which the frames used for frame concatenation are selected, is another important parameter. In our previous method, the frame concatenation interval was fixed to 100 ms. In this paper, we optimize the number of concatenated frames and the frame concatenation interval for the previously proposed method. As a result, it was confirmed that the classification accuracy of the method was improved by 2.61% in comparison with the result submitted to the DCASE 2016.
A Method for the Production of Randomly Oriented Fiber Reinforced Thermoplastic Composites and Their Mechanical Properties

A unique method for the production of well mixed reinforced fiber/thermoplastic fiber mats for compression molding or stampable sheet molding was developed. In this method, bundles of continuous or discontinuous fibers are supplied to the apparatus, which is called “fiber separating/flying machine”, and the fibers are mixed homogeneously after separation and cutting of the fiber bundles. Various reinforcement mixed mats using carbon fiber (CF), glass fiber (GF), aramid fiber (KF) and thermoplastic matrix polyamide fiber (PA 6) were prepared by this method. Operating conditions of the machine for the preparation of the uniformly mixed mats, their properties and also compression molding conditions were investigated. Various mechanical properties of these composites were measured, and the influence of content of reinforcement fibers, their properties and orientation on the mechanical properties were discussed. The tensile properties of CF reinforced PA 6 composites did not increase monotonically with increasing fiber content, but rather decreased when flller content exceeded 20%, which seems to be due to a change in the fiber orientation.KF reinforced PA 6 composites showed the highest impact strength and fractaure toughness of the materials investigated in this study, and it was found that KF is able to improve the fracture properties of CF and GF reinforced composites.
Surface-treated polypropylene fiber for reinforced repair mortar cementitious composites

The effects of surface treatment of polypropylene (PP) fiber on the mechanical and microstructure of fiber-reinforced cementitious (FRC) composites are investigated. Surface treatment of the PP fiber was performed with 3-aminopropyltrimethoxy silane (APS) and methyltriethoxy silane (MTES) in order to improve interaction between PP fiber and matrix. The effects of APS and MTES on the surface of PP fiber are studied by scanning electron microscopy, energy dispersive spectrometer, and Fourier transform infrared spectroscopy. The experiment results indicated that the treatment of PP fiber with APS and MTES can effectively increase the adhesion between fiber and matrix, and an improvement in the flexure and compressive strength of the cementitious composites was found in the samples containing treated PP fiber compared to the samples containing untreated PP fiber. The optimized mechanical properties could be obtained using 1.0% APS (by weight) and 1.0% MTES (by weight)-treated PP fiber at studied conditions, respectively.
A Quantitative Theory for Supersolidus Liquid Phase Sintering

AbstractA theory is presented for supersolidus liquid phase sintering. It is assumed that densification is by a viscous flow process involving the formation of liquid films along the interfaces in polycrystalline, prealloyed particles. The rigidity of the particle is determined by the percolation threshold where structural integrity is lost and the particle fragments into a viscous solid–liquid mixture. The overall process is modelled with dimensionless parameters that involve temperature and time, as well as various microstructural parameters including grain size, particle size, and liquid film thickness. The results illustrate the interplay of the parameters and lead to suggestions for optimal practice. PM/0553
Glycodelin is a potential novel follow-up biomarker for malignant pleural mesothelioma

Malignant pleural mesothelioma (MPM) is a rare and aggressive tumor with a short survival time arising from the mesothelial cells of the pleura. Soluble mesothelin-related peptide (SMRP), osteopontin or EFEMP1 (Fibulin-3) are well described biomarkers for malignant mesothelioma with moderate sensitivity and specificity. In this study, we characterized the expression of glycodelin, a marker for risk pregnancy, in MPM by RNA and protein analyses and investigated its potential as a MPM biomarker. We were able to detect glycodelin in the serum of MPM patients. Compared to benign lung diseases, the serum levels were significant increased. Patients with high glycodelin serum levels revealed a worse overall survival. The glycodelin serum levels correlated with the tumor response to treatment. A comparison of SMRP and glycodelin serum measurement in a large patient cohort demonstrated that the detection of both soluble factors can increase the reliable diagnostic of MPM. Glycodelin was highly expressed in MPM tumors. Analyses of a tissue micro array indicated that the immunomodulatory form glycodelin A was expressed in MPM and correlated with the survival of the patients. Altogether, glycodelin seems to be a new potential biomarker for the aggressive malignant pleural mesothelioma.
Cytoplasmic Dynein and Dynactin Are Required for the Transport of Microtubules into the Axon

Previous work from our laboratory suggested that microtubules are released from the neuronal centrosome and then transported into the axon (Ahmad, F.J., and P.W. Baas. 1995. J. Cell Sci. 108: 2761–2769). In these studies, cultured sympathetic neurons were treated with nocodazole to depolymerize most of their microtubule polymer, rinsed free of the drug for a few minutes to permit a burst of microtubule assembly from the centrosome, and then exposed to nanomolar levels of vinblastine to suppress further microtubule assembly from occurring. Over time, the microtubules appeared first near the centrosome, then dispersed throughout the cytoplasm, and finally concentrated beneath the periphery of the cell body and within developing axons. In the present study, we microinjected fluorescent tubulin into the neurons at the time of the vinblastine treatment. Fluorescent tubulin was not detected in the microtubules over the time frame of the experiment, confirming that the redistribution of microtubules observed with the experimental regime reflects microtubule transport rather than microtubule assembly. To determine whether cytoplasmic dynein is the motor protein that drives this transport, we experimentally increased the levels of the dynamitin subunit of dynactin within the neurons. Dynactin, a complex of proteins that mediates the interaction of cytoplasmic dynein and its cargo, dissociates under these conditions, resulting in a cessation of all functions of the motor tested to date (Echeverri, C.J., B.M. Paschal, K.T. Vaughan, and R.B. Vallee. 1996. J. Cell Biol. 132: 617–633). In the presence of excess dynamitin, the microtubules did not show the outward progression but instead remained near the centrosome or dispersed throughout the cytoplasm. On the basis of these results, we conclude that cytoplasmic dynein and dynactin are essential for the transport of microtubules from the centrosome into the axon.
Interval graph mining

Frequent subgraph mining is a difficult data mining problem aiming to find the exact set of frequent subgraphs into a database of graphs. Current subgraph mining approaches make use of the canonical encoding which is one of the key operations. It is well known that canonical encodings have an exponential time complexity. Consequently, mining all frequent patterns for large and dense graphs is computationally expensive. In this paper, we propose an interval approach to handle canonicity, leading to two encodings, lower and upper encodings, with a polynomial time complexity, allowing to tightly enclose the exact set of frequent subgraphs. These two encodings lead to an interval graph mining algorithm where two minings are launched in parallel, a lower mining (resp. upper mining) using the lower (resp. upper) encoding. The interval graph mining approach has been implemented within the state of the art Gaston miner. Experiments performed on synthetic and real graph databases coming from stock market and biological datasets show that our interval graph mining is effective on dense graphs.
Associations of serum 25-hydroxycholecalciferol and parathyroid hormone with serum lipids differ by sex and vitamin D status

Abstract Objective Although emerging evidence indicates an association between vitamin D and serum lipids, the data are still inconsistent. The purpose of the present study was to investigate whether 25-hydroxycholecalciferol (25-hydroxyvitamin D3; 25(OH)D3) or intact parathyroid hormone (iPTH) was independently related to serum lipids in elderly women and men. Design Cross-sectional study. Fasting serum levels of 25(OH)D3, iPTH, TAG, total cholesterol (TC), HDL cholesterol (HDL-C) and LDL cholesterol (LDL-C) were assessed. Body composition was measured by bioelectrical impedance analysis. Lifestyle factors, such as nutrient intake, time spent outdoors, physical activity, smoking, supplement intake and medication, were assessed by questionnaires. Multiple regression analyses were performed to examine associations of 25(OH)D3 and iPTH with serum lipids. Setting Giessen, Germany. Subjects One hundred and ninety-three well-functioning German elderly aged 66–96 years. Results After adjusting for age, body fat, physical activity, smoking, alcohol intake, lipid-modifying drugs and either iPTH or 25(OH)D3, 25(OH)D3 was a predictor of TAG (standardised coefficient beta (β)=–0·180), HDL-C (β=0·197), LDL-C:HDL-C (β=−0·298) and TC:HDL-C (β=−0·302) in women, whereas iPTH was a predictor of HDL-C (β=−0·297) in men. In sub-analysis, associations between 25(OH)D3 and TC (β=−0·252), HDL-C (β=0·230), LDL-C (β=−0·324), LDL-C:HDL-C (β=−0·412) and TC:HDL-C (β=−0·380) were found in women with 25(OH)D3 concentrations above or equal the median vitamin D status (62·3 nmol/l), but not in women with lower 25(OH)D3 concentrations. Conclusions In the elderly, associations of 25(OH)D3 and iPTH with serum lipids may differ by sex and may require a vitamin D status above 62 nmol/l.
Variability in ACL Tunnel Placement

Background: Multicenter and multisurgeon cohort studies on anterior cruciate ligament (ACL) reconstruction are becoming more common. Minimal information exists on intersurgeon and intrasurgeon variability in ACL tunnel placement. Purpose/Hypothesis: The purpose of this study was to analyze intersurgeon and intrasurgeon variability in ACL tunnel placement in a series of The Multicenter Orthopaedic Outcomes Network (MOON) ACL reconstruction patients and in a clinical cohort of ACL reconstruction patients. The hypothesis was that there would be minimal variability between surgeons in ACL tunnel placement. Study Design: Cross-sectional study; Level of evidence, 3. Methods: Seventy-eight patients who underwent ACL reconstruction by 8 surgeons had postoperative imaging with computed tomography, and ACL tunnel location and angulation were analyzed using 3-dimensional surface processing and measurement. Intersurgeon and intrasurgeon variability in ACL tunnel placement was analyzed. Results: For intersurgeon variability, the range in mean ACL femoral tunnel depth between surgeons was 22%. For femoral tunnel height, there was a 19% range. Tibial tunnel location from anterior to posterior on the plateau had a 16% range in mean results. There was only a small range of 4% for mean tibial tunnel location from the medial to lateral dimension. For intrasurgeon variability, femoral tunnel depth demonstrated the largest ranges, and tibial tunnel location from medial to lateral on the plateau demonstrated the least variability. Overall, surgeons were relatively consistent within their own cases. Using applied measurement criteria, 85% of femoral tunnels and 90% of tibial tunnels fell within applied literature-based guidelines. Ninety-one percent of the axes of the femoral tunnels fell within the boundaries of the femoral footprint. Conclusion: The data demonstrate that surgeons performing ACL reconstructions are relatively consistent between each other. There is, however, variability of average tunnel placement up to 22% of mean condylar depth, likely reflecting the difference in individual surgeons’ preferred tunnel locations. Individual surgeons are relatively consistent in their cases of ACL tunnels.
Optimal Power Allocation for Cognitive Radios with Multiple Status Changes in Primary User Traffic

The effects of a primary user's (PU) multiple random arrivals and departures on the throughput of the sensing-based spectrum sharing cognitive radio networks are investigated in this paper. We give a comprehensive study on the probability that the PU change its state n times during the whole frame time, and propose a new model to describe the PU traffic. Based on this proposed model, an optimal power allocation strategy with four-level is presented, to maximize the achievable throughput of the SU. Simulation results show that the throughput of the SU can be improved considerably by our scheme.
Weakly Supervised Image Classification with Coarse and Fine Labels

We consider image classification in a weakly supervised scenario where the training data are annotated at different levels of abstractions. A subset of the training data are annotated with coarse labels (e.g. wolf, dog), while the rest of the training data are annotated with fine labels (e.g. breeds of wolves and dogs). Each coarse label corresponds to a superclass of several fine labels. Our goal is to learn a model that can classify a new image into one of the fine classes. We investigate how the coarsely labeled data can help improve the fine label classification. Since it is usually much easier to collect data with coarse labels than those with fine labels, the problem setup considered in this paper can benefit a wide range of real-world applications. We propose a model based on convolutional neural networks (CNNs) to address this problem. We demonstrate the effectiveness of the proposed model on several benchmark datasets. Our model significantly outperforms the naive approach that discards the extra coarsely labeled data.