Miracle-dz/UniFAR-FTUs huggingface dataset:
Derlin-1 Promotes the Efficient Degradation of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) and CFTR Folding Mutants*

A complex involving Derlin-1 and p97 mediates the retrotranslocation and endoplasmic reticulum (ER)-associated degradation of misfolded proteins in yeast and is used by certain viruses to promote host cell protein degradation (Romisch, K. (2005) Annu. Rev. Cell Dev. Biol. 21, 435-456; Lilley, B. N. , and Ploegh, H. L. (2004) Nature 429, 834-840; Ye, Y. , Shibata, Y. , Yun, C. , Ron, D. , and Rapoport, T. A. (2004) Nature 429, 841-847). We asked whether the components of this pathway are involved in the endoplasmic reticulum-associated degradation of the mammalian integral membrane protein, the cystic fibrosis transmembrane conductance regulator (CFTR), a substrate for the ubiquitin-proteasome system. We report that Derlin-1 and p97 formed complexes with CFTR in human airway epithelial cells. Derlin-1 interacted with nonubiquitylated CFTR, whereas p97 associated with ubiquitylated CFTR. Exogenous expression of Derlin-1 led to its co-localization with CFTR in the ER where it reduced wild type (WT) CFTR expression and efficiently degraded the disease-associated CFTR folding mutants, ΔF508 and G85E (>90%). Consistent with this, Derlin-1 also reduced the amount of WT or ΔF508 CFTR appearing in detergent-in-soluble aggregates. An ∼70% knockdown of endogenous Derlin-1 by RNA interference increased the steady-state levels of WT and ΔF508 CFTR by 10-15-fold, reflecting its significant role in CFTR degradation. Derlin-1 mediated the degradation of N-terminal CFTR fragments corresponding to the first transmembrane domain of CFTR, but CFTR fragments that incorporated additional domains were degraded less efficiently. These findings suggest that Derlin-1 recognizes misfolded, nonubiquitylated CFTR to initiate its dislocation and degradation early in the course of CFTR biogenesis, perhaps by detecting structural instability within the first transmembrane domain.
Automatic Maya hieroglyph retrieval using shape and context information

We propose an automatic Maya hieroglyph retrieval method integrating shape and glyph context information. Two recent local shape descriptors, Gradient Field Histogram of Orientation Gradient (GF-HOG) and Histogram of Orientation Shape Context (HOOSC), are evaluated. To encode the context information, we propose to convert each Maya glyph block into a first-order Markov chain and apply the co-occurrence of neighbouring glyphs. The retrieval results obtained based on visual matching are therefore re-ranked. Experimental results show that our method can significantly improve the glyph retrieval accuracy even with a basic co-occurrence model. Furthermore, two unique glyph datasets are contributed which can be used as novel shape benchmarks in future research.
Specification and Enforcement of Dynamic Authorization Policies Oriented by Situations

Nowadays, accessing communication networks and systems faces multitude applications with large-scale requirements dimensions. Mobility -roaming services in particular- during urgent situations exacerbate the access control issues. Dynamic authorization then is required. However, traditional access control fails to ensure policies to be dynamic. Instead, we propose to externalize the dynamic behavior management of networks and systems through situations. Situations modularize the policy into groups of rules and orient decisions. Our solution limits policy updates and hence authorization inconsistencies. The authorization system is built upon the XACML architecture coupled with a complex event- processing engine to handle the concept of situations. Situation- oriented attribute based policies are defined statically allowing static verification and validation.
DIBR 3D VIDEO WATERMARKING WITH FASTER DT-CWT QUANTIZATION

As the 3D content market is growing up rapidly, copyright issues on the 3D content naturally have come into play. Among the various 3D coding techniques, depth-imagebased rendering (DIBR) has been studied by numerous researchers due to its coding efficiency and 2D compatibility. However, conventional watermarking scheme for 2D content cannot be directly applied to the DIBR content because DIBR process is considered as a new type of attack in terms of watermarking design. In this paper, we propose a watermarking scheme for DIBR 3D videos with an improved version of DT-CWT magnitude quantization. In order for efficient watermark embedding and extraction on DIBR 3D videos, all frames are grouped. Then, the watermark is embedded repeatedly and periodically so that extraction performance is enhanced. Furthermore, the quantization process is improved to a faster version by checking sum of magnitude and setting a start point of quantization order optimally. The simulation results show that the embedded watermark is stably extracted from center views and virtual views. Moreover, when the watermarked virtual views are distorted or processed by compression, scaling, median filtering and noise addition, the embedded watermark is extracted with low BERs.
Single-walled carbon-nanotube forest immunosensor for amplified detection of cancer biomarkers

Prostate specific antigen (PSA) is a major biomarker used clinically in the detection of prostate cancer. Current commercial immunoassays for detection of this biomarker rely on spectroscopic absorbance and electro-chemiluminescence which are able to detect as low as 0.03 ng/mL of PSA within 100muL of serum. In this paper, a novel amplified electrochemical technique for detection of prostate specific antigen is described. This electrochemical approach is a highly sensitive method that can have detection limit of 0.004 ng/mL in only 10 mL of serum, a mass detection limit 75 times lower than current commercial techniques. This highly sensitive, low cost and fast detection method not only allows for detection of cancer biomarkers in serum, but also in tissue and cells. Moreover, immunoassay arrays based on this methodology will be highly promising for application in large-scale clinical screening and point-of-care diagnostics. Characterization of the anti-PSA amplification tag in this amplification system using TEM, AFM, SEM, and CE is also described
Human pose estimation using structural support vector machines

This paper addresses the issue of 2D human upper-body pose estimation under cluttered environments using a discriminative structured framework. Most previous approaches focus on solving such a problem using generative models. However, a generative model has two drawbacks: a) not suitable for real-time application due to its slow inference algorithm and b) prone to over fitting given limited training data. In this work, we propose to use structured discriminative regression models for 2D human upper-body pose estimation in a model-free manner to overcome the aforementioned drawbacks. In contrast to a standard discriminative regression model, a structured regression model for human pose estimation can not only learn the relevance between image features and the presentation of human pose but also catch the inner relationship between each output. Our experimental results demonstrate the benefits brought by using structured discriminative models to articulated human pose estimation problem on cluttered images from the benchmarking Buffy the Vampire Slayer dataset and the highly challenging images from PASCAL VOC 2007 and 2008 Challenge datasets.
Network Effects and Land Redistribution: A Natural Experiment in Zimbabwe

The paper investigates whether positive network effects may have existed between large-scale commercial farmers and small-scale communal farmers prior to the recent land redistribution in Zimbabwe. A difference-in-difference approach is used where measurement is carried out using several data sources including farm level, geographic and survey information for cotton farmers in Mashonaland Central. It tests whether the removal of large-scale farmers has resulted in a decline in productivity for those small-scale farmers close to redistributed land as compared to those located at greater distances from large-scale/commercial farms. A significant negative productivity effect is found in addition to a country-wide negative redistribution effect. The latter is most likely due to wider economic and political instability over the last 10 years.
Experimental Results of a New Method on Lessening The Grating Lobes' Effects in Phased Arrays

To design a phased array antenna, different criteria should be considered. Nulls must be placed toward the interferes' directions and the main beam should be focused on the desired user. To accomplish these conditions, several methods can be used. What is important in this paper is how additional roots can be added into AF1 polynomial to help main beam steering and reduce the grating lobes effects
Static magnetic fields enhanced the potency of cisplatin on k562 cells.

PURPOSE This study investigates whether 8.8 mT static magnetic fields (SMFs) can enhance the killing potency of cisplatin (DDP) on human leukemic cells (K562). METHODS The cell proliferation, cell cycle distribution, DNA damage, and the change in cell surface ultrastructure after K562 cells were exposed to 8.8 mT SMFs with or without DDP were analyzed. RESULTS The results show that SMFs enhanced the killing effect of DDP on K562 cells, reducing the efficient killing concentration of DDP on K562 cells from 20 to 10 microg/mL. Atomic force microscope observation showed that the cell surface ultrastructure was altered. The results of fluorescence-activated cell sorting analysis indicated that K562 cells treated with SMF plus DDP were arrested at the S phase. The SMF exposure induced DNA to become thicker than controls, and breakage of DNA occurred in the DDP group; however, DNA breakage was increased in the SMF + DDP group. CONCLUSIONS The results show that SMFs enhanced the anticancer effect of DDP on K562 cells. The mechanism correlated with the DNA damage model. This study also shows the potentiality of SMFs as an adjunctive treatment method for chemotherapy.
Editorial – Synthetic Biology: Engineering Complexity and Refactoring Cell Capabilities

Synthetic Biology is now in its second decade and many goals have been achieved toward the rational design of biological systems. This Research Topic features and reviews some of the latest progress in Synthetic Biology with a focus on research at the intersection between rational design and natural complexity with a potential outcome to concrete biotechnological applications. Kelwick et al. (2014) summarize the great expansion in the genetic toolkit and DNA assembly techniques that are currently available for synthetic biologists. These tools will advance the implementation of new functions and the production of useful metabolites in living cells in a controlled fashion. Using engineering formality, Synthetic Biology aims to identify biological design principles that can be used for practical applications. As one of the results, metabolic engineering is now becoming feasible to introduce novel functions and properties into an increasing number of microbial hosts. Examples come from Yu et al. (2014) and Heider et al. (2014) that describe the production of fatty-acid-derived chemicals and astaxanthin in microbes, respectively. Furthermore, bacteria can be engineered for the conversion of waste into renewable products, as Nieves et al. (2015) demonstrate with the bioconversion of lignocellulose.
Elevated levels of the antimicrobial peptide LL‐37 in hidradenitis suppurativa are associated with a Th1/Th17 immune response

Hidradenitis suppurativa (HS) is an inflammatory skin disease with poorly understood immunopathogenic mechanisms. LL‐37 is an antimicrobial peptide, which is transcribed from the CAMP (cathelicidin antimicrobial peptide) gene. Previous reports showed upregulated levels of CAMP and LL‐37 in HS lesions, and therefore, the aim of this study was to compare levels of LL‐37 in HS to other inflammatory skin diseases and to establish immunomodulatory functions of LL‐37 in HS. We confirm an upregulation of the LL‐37 peptide in lesional HS skin with comparable levels as in psoriasis patients and are able to positively correlate the presence of LL‐37 in HS with the presence of T cells, macrophages, neutrophils, IFN‐γ, IL‐17, IL‐23, TNF‐α, IL‐32 and IL‐1β. Mechanistically, LL‐37 boosts the proliferation of unspecifically activated CD4+ T cells via an increased calcium signalling independent of antigen‐presenting cells. Targeting LL‐37 may therefore represent a new therapeutic option for the treatment of this recalcitrant disease, but it has to be kept in mind that LL‐37 also has an antimicrobial function.
Catching Idlers with Ease: A Lightweight Wait-State Profiler for MPI Programs

Load imbalance usually introduces wait states into the execution of parallel programs. Being able to identify and quantify wait states is therefore essential for the diagnosis and remediation of this phenomenon. An established method of detecting wait states is to generate event traces and compare relevant timestamps across process boundaries. However, large trace volumes usually prevent the analysis of longer execution periods. In this paper, we present an extremely lightweight wait-state profiler which does not rely on traces that can be used to estimate wait states in MPI codes with arbitrarily long runtimes. The profiler combines scalability with portability and low overhead.
Primal-dual RNC approximation algorithms for (multi)-set (multi)-cover and covering integer programs

We build on the classical greedy sequential set cover algorithm, in the spirit of the primal-dual schema, to obtain simple parallel approximation algorithms for the set cover problem and its generalizations. Our algorithms use randomization, and our randomized voting lemmas may be of independent interest. Fast parallel approximation algorithms were known before for set cover, though not for any of its generalizations. <<ETX>>
Sequence variation in G-protein-coupled receptors: analysis of single nucleotide polymorphisms

We assessed the disease-causing potential of single nucleotide polymorphisms (SNPs) based on a simple set of sequence-based features. We focused on SNPs from the dbSNP database in G-protein-coupled receptors (GPCRs), a large class of important transmembrane (TM) proteins. Apart from the location of the SNP in the protein, we evaluated the predictive power of three major classes of features to differentiate between disease-causing mutations and neutral changes: (i) properties derived from amino-acid scales, such as volume and hydrophobicity; (ii) position-specific phylogenetic features reflecting evolutionary conservation, such as normalized site entropy, residue frequency and SIFT score; and (iii) substitution-matrix scores, such as those derived from the BLOSUM62, GRANTHAM and PHAT matrices. We validated our approach using a control dataset consisting of known disease-causing mutations and neutral variations. Logistic regression analyses indicated that position-specific phylogenetic features that describe the conservation of an amino acid at a specific site are the best discriminators of disease mutations versus neutral variations, and integration of all our features improves discrimination power. Overall, we identify 115 SNPs in GPCRs from dbSNP that are likely to be associated with disease and thus are good candidates for genotyping in association studies.
Long‐term depression in vivo: Effects of sex, stress, diet, and prenatal ethanol exposure

Long‐term depression (LTD) of synaptic efficacy has proven a difficult phenomenon to examine in vivo, despite the ease with which it is induced in a variety of in vitro preparations. Prior exposure to an acute stressful episode does however seem to enhance the capacity of the hippocampus to exhibit LTD in vivo in male animals. In the present experiments, we examined the capacity for low‐frequency stimuli (low‐frequency stimulation (LFS)) to induce LTD in juvenile male and female animals following an acute stress episode. Interestingly, prior exposure to stress was only required for the induction of LTD in male animals, while both control and stressed female animals exhibited equivalent LTD. In animals that were exposed to ethanol in utero, a similar requirement for prior exposure to stress to elicit LTD was found for male, but not female animals. This prenatal ethanol exposure did not in itself alter the capacity for LTD induction in either sex; however, in utero food restriction did enhance LTD induction in both male and female animals, irrespective of whether they were exposed to stress just prior to being administered LFS. These results indicate that in utero dietary restriction more drastically affects CA1 LTD than in utero ethanol exposure. In addition, female animals seem to exhibit LTD in vivo in the absence of stress much more easily than their male counterparts. © 2008 Wiley‐Liss, Inc.
Asymptotic spectral efficiency regions of two-user MC-CDMA systems in frequency-selective Rayleigh fading

In this paper we derive asymptotic performance measures for multiuser receivers in the uplink of multi-carrier (MC) CDMA communication systems with multiple signatures per user. We examine spectral efficiency regions of multi-signature CDMA, for both the optimal and optimal-linear receivers. We also derive an approximate expression for the asymptotic average signal to interference and noise ratio at the output of the optimal-linear multiuser receiver in the case of two users. Simulation studies demonstrate that the asymptotic results closely predict performance of practical finite systems.
A stochastic optimal control solution to the energy management of a microgrid with storage and renewables

The presence of renewable energy generators in a microgrid calls for the usage of storage units so as to smooth the variability in energy production. This work addresses the optimal management of a battery in a microgrid including a wind turbine facility. A Markov chain model is employed to predict the wind power production and the optimal management of the energy storage element is formulated as a stochastic optimal control problem. An approximate dynamic programming approach resting on system abstraction is then proposed for control policy design. Some numerical examples show the effectiveness of the approach.
Use of Repetitive DNA Sequences and the PCR To DifferentiateEscherichia coli Isolates from Human and Animal Sources

ABSTRACT The rep-PCR DNA fingerprint technique, which uses repetitive intergenic DNA sequences, was investigated as a way to differentiate between human and animal sources of fecal pollution. BOX and REP primers were used to generate DNA fingerprints from Escherichia coli strains isolated from human and animal sources (geese, ducks, cows, pigs, chickens, and sheep). Our initial studies revealed that the DNA fingerprints obtained with the BOX primer were more effective for grouping E. coli strains than the DNA fingerprints obtained with REP primers. The BOX primer DNA fingerprints of 154 E. coli isolates were analyzed by using the Jaccard band-matching algorithm. Jackknife analysis of the resulting similarity coefficients revealed that 100% of the chicken and cow isolates and between 78 and 90% of the human, goose, duck, pig, and sheep isolates were assigned to the correct source groups. A dendrogram constructed by using Jaccard similarity coefficients almost completely separated the human isolates from the nonhuman isolates. Multivariate analysis of variance, a form of discriminant analysis, successfully differentiated the isolates and placed them in the appropriate source groups. Taken together, our results indicate that rep-PCR performed with the BOX A1R primer may be a useful and effective tool for rapidly determining sources of fecal pollution.
User Priority Based Adaptive Subcarrier-and-Bit Allocation Algorithm for OFDM System

In this paper, a simple subcarrier-and-bit allocation algorithm is proposed to solve the minimization problem of the outage rate by giving different priority to each user. Herein, outage rate is defined as the proportion of a number of total users to a number of some users who do not satisfy the data rate requirement. A proposed algorithm takes three steps of grouping and ordering, initial allocation and refinement. Numerical results show that the proposed algorithm can dramatically reduce the outage rate and eventually improve the total throughput as a number of users increases.
Improvisational Storytelling Agents

The problem of improvisational story generation involves one or more agents collaborating in order to create a story without any advance notice of topic. We present a pipeline for an artificial agent that is capable of improvisational storytelling while collaborating with a human agent. Starting with story corpora, we “eventify” sentences, which creates a simplified and abstracted representation. The rest of the pipeline–the agent’s response–is broken into three parts: generating successive events (event-to-event), translating of events back into natural language (event-to-sentence), and plugging the specifics of the story back into the generated sentences (slot filling). We discuss techniques for each of these sub-problems.
Alpha and Beta Diversity in Central European Beech Forests

Recently, the beech forests of southern Central Europe (including large parts of the Illyrian region) have been syntaxonomically revised, using a TURBOVEG database containing more than 5800 relevés, mainly from Austria, Switzerland, Germany, the Czech Republic, Hungary, Slovenia and Croatia. The same TURBOVEG database was used to calculate patterns of alpha and beta diversity within beech forests. A strong correlation between local species richness and soil pH was found. Beta diversity is related with area and the number of associations therein.
Center for Molecular Medicine meeting on Wnt Signaling in Development and Disease

Introduction Wnt signalling is implicated in numerous aspects of development, cell biology and physiology. this meeting brought together several leading scientists in the Wnt signalling field, who discussed their latest research in this rapidly growing discipline. the expanding number of diseases that are the consequence of mutations in components of the Wnt signalling pathway also attracted researchers with a more clinical interest. Many new insights were presented into
Macromodelling oscillators using Krylov-subspace methods

We present an efficient method for automatically extracting unified amplitude/phase macromodels of arbitrary oscillators from their SPICE-level circuit descriptions. Such comprehensive oscillator macromodels are necessary for accuracy when speeding up simulation of higher-level circuits/systems, such as PLLs, in which oscillators are embedded. Standard MOR techniques for linear time invariant (LTI) and varying (LTV) systems are not applicable to oscillators on account of their fundamentally nonlinear phase behavior. By employing a cancellation technique to deflate out the phase component, we restore the validity and efficacy of Krylov-subspace-based LTV MOR techniques for macromodelling oscillator amplitude responses. The nonlinear phase response is re-incorporated into the macromodel after the amplitude components have been reduced. The resulting unified macromodels predict oscillator waveforms, in the presence of any kind of input or interference, at far lower computational cost than full SPICE-level simulation, and with far greater accuracy compared to existing macromodels. We demonstrate the proposed techniques on LC and ring oscillators, obtaining speedups of 30-120times with no appreciable loss of accuracy, even for small circuits