Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Secretion System of Recombinant Saccharomyces cerevisiae Using an N‐terminus Residue of Human IL‐1β as Secretion Enhancer

An N‐terminus sequence of human interleukin 1β (hIL‐1β) was used as a fusion expression partner for the production of two recombinant therapeutic proteins, human granulocyte‐colony stimulating factor (hG‐CSF) and human growth hormone (hGH), using Saccharomyces cerevisiae as a host. The expression cassette comprised the leader sequence of killer toxin of Kluyveromyces lactis, the N‐terminus 24 amino acids (Ser5‐Ala28) of mature hIL‐1β, the KEX2 dibasic endopeptidase cleavage site, and the target protein (hG‐CSF or hGH). The gene expression was controlled by the inducible UASgal/MF‐α1 promoter. With the expression vector above, both recombinant proteins were well secreted into culture medium with high secretion efficiencies, and especially, the recombinant hGH was accumulated up to around 1.3 g/L in the culture broth. This is due presumably to the significant role of fused hIL‐1β as secretion enhancer in the yeast secretory pathway. In our recent report, various immunoblotting analyses have shown that the presence of a core N‐glycosylation resident in the hIL‐1β fragment is likely to be of crucial importance in the high‐level secretion of hG‐CSF from the recombinantS. cerevisiae. When the N‐glycosylation was completely blocked with the addition of tunicamycin to the culture, the secretion of hG‐CSF and hGH was decreased to a negligible level although the other host‐derived proteins were well secreted to the culture broth regardless of the presence of tunicamycin. The N‐terminal sequencing of the purified hG‐CSF verified that the hIL‐1β fusion peptide was correctly removed by in vivo KEX2 protease upon the exit of fusion protein from Golgi complex. From the results presented in this article, it is strongly suggested that the N‐terminus fusion of the hIL‐1β peptide could be utilized as a potent secretion enhancer in the expression systems designed for the secretory production of other heterologous proteins from S. cerevisiae.
Partial error masking to reduce soft error failure rate in logic circuits

A new methodology for designing logic circuits with partial error masking is described. The key idea is to exploit the asymmetric soft error susceptibility of nodes in a logic circuit by targeting the error masking capability towards the nodes with the highest soft error susceptibility to achieve cost-effective tradeoffs between overhead and reduction in the soft error failure rate. Such techniques can be used in cost-sensitive high volume mainstream applications to satisfy soft error failure rate requirements at minimum cost. Two reduction heuristics, cluster sharing reduction and dominant value reduction, are used to reduce the soft error failure rate significantly with a fraction of the overhead required for conventional TMR.
Study of the Microbiota in Pacific White Shrimp ( Litopenaeus vannamei ) under varying O 2 Modified Atmosphere Packaging using PCR-DGGE

Occurrence and importance of spoilage related bacteria in fresh Pacific white shrimp ( Litopenaeus vannamei ) under modified atmosphere were demonstrated in the current study. Culture-independent method including PCR-DGGE (V3 region of 16S rRNA gene), displayed a fingerprint of microbial DNA extracted directly from shrimp. Four batches of raw shrimps packaged under 80% CO 2 /5% O 2 /15% N 2 , 80% CO 2 /10% O 2 /15% N 2 , 80% CO 2 /20% O 2 , as well as unsealed packages for shrimp used as the control were stored at 4 °C during 10 days of storage. Results showed that the initial dominant bacteria of shrimp were Vibrio albensis , Vibrio sp. , Photobacterium damselae , Shewanella putrefaciens , Vibrio harveyi and Vibrio parahaemolyticus . After 10 days of storage, Vibrio sp. , Shewanella sp. , Photobacterium damselae , Listonella anguillarum , Shewanella baltica , Uncultured Aeromonas sp. and Aeromonas veronii dominated in shrimps packaged in air. Modified atmosphere packaging (MAP) showed an inhibitory effect on several bacterial species such as Shewanella sp. , Listonella anguillarum , Uncultured Aeromonas sp. and Aeromonas veronii . In conclusion, this study showed the benefits of the use of culture-independent method to enhance understanding of the composition of
Anti-SIFT Images Based CAPTCHA Using Versatile Characters

Due to vigorous development of pattern recognition, traditional human form filling tasks would be replaced by automated processes. However, these automation processes are often misused for illegal behavior such as spam e-mail or application for website account. In order to prevent website owner from suffering the attacks of automated program, this paper proposed an innovative image-based CAPTCHA for distinguishing human and computer by embedding versatile characters in the images. The proposed method makes the characters indiscernible by automated image analysis technologies like scale-invariant feature transform while human can easily distinguish the location of the embedded characters. Our designed mechanism was capable to elude such kind of attacks. In experiments, 15 users were invited to test the system and the success rate is 86%. If wrong operations like clicking out of text boxes were excluded, the success rate reached 95%. Compare the average logging time with reCAPTCHA and HELLO CAPTCHA, the proposed method is faster than these two methods by 32 seconds and 115 seconds, respectively.
An Intelligent Fuzzy Convex Hull based Clustering Approach

mining refers to the extraction of knowledge by analyzing the data from different perspectives and accumulates them to form an useful information which could help the decision makers to take appropriate decisions. Classification and clustering has been the two broad areas in data mining. As the classification is a supervised learning approach, the clustering is an unsupervised learning approach and hence can be performed without the supervision of the domain experts. The basic concept is to group the objects in such a way so that the similar objects are closer to each. In this paper, an approach is made by fusing the concept of convex hull with fuzziness parameter. Each boundary data point is validated for the convex hull property to form a cluster. The decision value depends on the membership value of the particular point. The points satisfying the convex hull property forms a cluster. The performance
Interference alignment in MIMO cellular networks

We explore the feasibility of linear interference alignment (IA) in MIMO cellular networks. Each base station (BTS) has Nt transmit antennas, each mobile has Nr receive antennas, and a BTS transmits a single beam to each active user. We present a necessary Zero-Forcing (ZF) condition for zero interference in terms of the number of users, the number of cells, Nt and Nr. We then examine the performance of iterative (forward-backward) algorithms for jointly optimizing the transmit precoders with linear receivers. Modifications of the max-SINR and minimum leakage algorithms are presented, which are observed to converge to a ZF solution whenever the necessary conditions are satisfied. In contrast, convergence of the (original) max-SINR algorithm is problematic when the necessary conditions are satisfied with (near) equality. A more restrictive ZF condition is presented, which predicts when these convergence problems are unlikely to occur.
Underutilized resources for studying the evolution of invasive species during their introduction, establishment, and lag phases

The early phases of biological invasions are poorly understood. In particular, during the introduction, establishment, and possible lag phases, it is unclear to what extent evolution must take place for an introduced species to transition from established to expanding. In this study, we highlight three disparate data sources that can provide insights into evolutionary processes associated with invasion success: biological control organisms, horticultural introductions, and natural history collections. All three data sources potentially provide introduction dates, information about source populations, and genetic and morphological samples at different time points along the invasion trajectory that can be used to investigate preadaptation and evolution during the invasion process, including immediately after introduction and before invasive expansion. For all three data sources, we explore where the data are held, their quality, and their accessibility. We argue that these sources could find widespread use with a few additional pieces of data, such as voucher specimens collected at certain critical time points during biocontrol agent quarantine, rearing, and release and also for horticultural imports, neither of which are currently done consistently. In addition, public access to collected information must become available on centralized databases to increase its utility in ecological and evolutionary research.
Retrospective evaluation of intersubject brain registration

Although numerous methods to register brains of different individuals have been proposed, no work has been done, as far as we know, to evaluate and objectively compare the performances of different nonrigid (or elastic) registration methods on the same database of subjects. In this paper, we propose an evaluation framework, based on global and local measures of the relevance of the registration. We have chosen to focus more particularly on the matching of cortical areas, since intersubject registration methods are dedicated to anatomical and functional normalization, and also because other groups have shown the relevance of such registration methods for deep brain structures. Experiments were conducted using 6 methods on a database of 18 subjects. The global measures used show that the quality of the registration is directly related to the transformation's degrees of freedom. More surprisingly, local measures based on the matching of cortical sulci did not show significant differences between rigid and non rigid methods.
A smoothed finite element method for analysis of anisotropic large deformation of passive rabbit ventricles in diastole

The smoothed FEM (S‐FEM) is firstly extended to explore the behavior of 3D anisotropic large deformation of rabbit ventricles during the passive filling process in diastole. Because of the incompressibility of myocardium, a special method called selective face‐based/node‐based S‐FEM using four‐node tetrahedral elements (FS/NS‐FEM‐TET4) is adopted in order to avoid volumetric locking. To validate the proposed algorithms of FS/NS‐FEM‐TET4, the 3D Lame problem is implemented. The performance contest results show that our FS/NS‐FEM‐TET4 is accurate, volumetric locking‐free and insensitive to mesh distortion than standard linear FEM because of absence of isoparametric mapping. Actually, the efficiency of FS/NS‐FEM‐TET4 is comparable with higher‐order FEM, such as 10‐node tetrahedral elements. The proposed method for Holzapfel myocardium hyperelastic strain energy is also validated by simple shear tests through the comparison outcomes reported in available references. Finally, the FS/NS‐FEM‐TET4 is applied in the example of the passive filling of MRI‐based rabbit ventricles with fiber architecture derived from rule‐based algorithm to demonstrate its efficiency. Hence, we conclude that FS/NS‐FEM‐TET4 is a promising alternative other than FEM in passive cardiac mechanics. Copyright © 2015 John Wiley & Sons, Ltd.
MaRVIN: A platform for large-scale analysis of Semantic Web data

Web Science requires efficient techniques for analysing large datasets. Many Semantic Web problems are difficult to solve through common divide-and-conquer strategies, since they are hard to partition. We present MaRVIN, a parallel and distributed platform for processing large amounts of RDF data, on a network of loosely-coupled peers. We present our divide-conquer-swap strategy and show that this model converges towards completeness. We evaluate performance, scalability, load balancing and efficiency of our system.
PLOG: Easily Create Digital Picture Stories Through Cell Phone Cameras

With a cell phone camera a person can take pictures and imme diately transmit them to larger repositories using telecommunication channels. This provides the potential for anywhere, anytime picture sharing and story telling. It can also increase awareness among peers within a social network. But while we enjoy telli ng stories around this informal content, the necessary act of downloading, organizing and then presenting the digital media is tedious and can discourage frequent use. We present PLOG, an application that stresses ease-of-use story telling through cell pho ne photography. The user simply takes pictures and performs simple click -and-send uploads using their phone. From a local machine, PLOG automatically downloads the images; time clusters the pictures together and then presents them as story vignettes. These vignettes can be viewed different ways and at home, shared with friends or posted in public places. We describe the implementation of PLOG and di scuss issues related to this light -weight method of story telling and awareness.
A multivariate analysis approach to the integration of proteomic and gene expression data

In order to understand even the simplest cellular processes, we need to integrate proteomic, gene expression and other biomolecular data. To date, most computational approaches aimed at integrating proteomics and gene expression data use direct gene/protein correlation measures. However, due to post‐transcriptional and translational regulations, the correspondence between the expression of a gene and its protein is complicated. We apply a multivariate statistical method, co‐inertia analysis (CIA), to visualise gene and proteomic expression data stemming from the same biological samples. Principal components analysis or correspondence analysis can be used for data exploration on single datasets. CIA is then used to explore the relationships between two or more datasets. We further explore the data by projecting gene ontology (GO) information onto these plots to describe the cellular processes in action. We apply these techniques to gene expression and protein abundance data from studies of the human malarial parasite life cycle and the NCI‐60 cancer cell lines. In each case, we visualise gene expression, protein abundance and GO classes in the same low dimensional projections and identify GO classes that are likely to be of biological importance.
Fixable or fate? Perceptions of the biology of depression.

OBJECTIVE Previous research has shown that biological (e.g., genetic, biochemical) accounts of depression--currently in ascendancy--are linked to the general public's pessimism about the syndrome's prognosis. This research examined for the first time whether people with depressive symptoms would associate biological accounts of depression with pessimism about their own prognoses and whether a psychoeducation intervention portraying the biology of depression as malleable could decrease prognostic pessimism among symptomatic individuals. METHOD In 3 studies, participants were recruited online and assessed for depression symptoms. Those with significant depressive symptomatology (a Beck Depression Inventory-II score of at least 16) rated their endorsement of biochemical and genetic causal attributions for their symptoms and indicated expected length of symptom duration. An audiovisual intervention emphasizing the malleability of gene effects and neurochemistry was developed, and its effects on symptomatic individuals' prognostic pessimism, feelings of agency, guilt, and general hopelessness were measured. RESULTS Biochemical and genetic causal attributions for depression were significantly associated with prognostic pessimism among symptomatic individuals. The malleability intervention significantly reduced prognostic pessimism, increased feelings of agency, and decreased general hopelessness. CONCLUSIONS Biochemical and genetic attributions for depression are related to prognostic pessimism among individuals with depressive symptoms, and not just among the general public. However, emphasizing the malleability of gene effects and brain chemistry in depression can foster more optimism about depression-related beliefs.
Draft Genome Sequence of a Diazotrophic, Plant Growth–Promoting Rhizobacterium of the Pseudomonas syringae Complex

ABSTRACT We report here the draft genome sequence of Pseudomonas syringae GR12-2, a nitrogen-fixing, plant growth–promoting bacterium, isolated from the rhizosphere of an Arctic grass. The 6.6-Mbp genome contains 5,676 protein-coding genes, including a nitrogen-fixation island similar to that in P. stutzeri.
Bioinformatic, Biochemical, and Immunological Mining of MHC Class I Restricted T Cell Epitopes for a Marburg Nucleoprotein Microparticle Vaccine

The Marburg virus (MARV), the virus responsible for Marburg hemorrhagic fever (MHF), is considered a top-priority pathogen for vaccine development. Recent outbreaks in Equatorial Africa have highlighted the urgency of MARV because of its high fatality rate and historical concerns about potential weaponization. Currently, there are no licensed vaccines for MARV. Existing vaccine candidates rely on attenuated recombinant vesicular stomatitis virus carrying MARV glycoprotein (VSVΔG) or the chimpanzee replication-defective adenovirus 3 vector ChAd3-MARV. Although these platforms provide significant protection in animal models, they face challenges because of their limited thermal stability and the need for cold storage during deployment in resource-poor areas. An alternative approach involves using adjuvanted poly (lactic-co-glycolic acid) (PLGA) microparticles loaded with synthetic peptides representing MHC class I—restricted T cell epitopes. This vaccine platform has demonstrated effectiveness in protecting against SARS-CoV-2 and EBoV disease in animal models and has the advantage of not requiring cold storage and remaining stable at room temperature for over six months. This report outlines the design, manufacturing, and in vivo immunogenicity testing of PLGA microparticle human vaccines designed to prevent Marburg hemorrhagic fever.
PARP 1 promotes nucleotide excision repair through DDB 2 stabilization and recruitment of ALC 1

The Rockefeller University Press $30.00 J. Cell Biol. Vol. 199 No. 2 235–249 www.jcb. org/cgi/doi/10.1083/jcb.201112132 JCB 235 A. Pines and M.G. Vrouwe contributed equally to this paper. Correspondence to Leon Mullenders: l.mullenders@lumc.nl; or Alex Pines: a.pines@lumc.nl Abbreviations used in this paper: 6-4PP, 6-4 pyrimidine pyrimidone photoproduct; AraC, cytosine--arabinofuranoside; CPD, cyclobutane pyrimidine dimer; FLIP, fluorescence loss in photobleaching; HU, hydroxyurea; LC, liquid chromatography; MS, mass spectrometry; NER, nucleotide excision repair; NHF, normal human fibroblast; PAR, poly(ADP-ribose); PARG, PAR glycohydrolase; PARPi, PARP inhibition; shRNA, short hairpin RNA; ssDNA, single-stranded DNA; XP, xeroderma pigmentosum. Introduction
Tumor front grading in prediction of survival and lymph node metastases in patients with laryngeal carcinoma.

PURPOSE Despite innumerous both therapeutic and histopathologic studies that have been performed no morphologic markers are currently available in order to predict the outcome in patients with laryngeal cancer. According to the recent reports nowadays tumor front grading (TFG) is one of the most reliable methods of estimation of the progress of the changes in the peripheral part of tumor and it seems to be one of the technics, which is able to assess the dynamics of the tumor growth quite precisely. In this sudy it was presented direct relation between morphological features of tumor front and survival. MATERIAL AND METHODS The authors have analysed 120 cases of patients who were operated on the laryngeal squamous cell carcinoma in ENT Department Medical University of Lódź between 1995-2000. Features of the morphologic tumor front grading was performed on H&E-stained sections in the peripheral parts of a tumor. Dependence on tumor grade G, tumor size T, lymph node metastases and survival were analysed. RESULTS Our study showed that feature such as TFG is very useful in prediction of survival in patients with laryngeal squamous cell carcinoma in comparison to the histological differentiation degree. The statistical analysis showed no significant correlation between TFG score and tumor size T, nodal status N and G feature. CONCLUSIONS The presented study emphasizes that TFG might influence decisions regarding therapeutic management and could eventually lead to more appropriate and individualized therapy. It is necessary to extend the traditional histopathological diagnosis by TFG, which assesses the dynamics of the malignant process and it seems to be a good prognostic method in prediction of survival of patients with squamous cell carcinoma.
An estrogen-inducible protein binds specifically to a sequence in the 3' untranslated region of estrogen-stabilized vitellogenin mRNA

The 3' untranslated region (3'-UTR) has been implicated in the estrogen stabilization of hepatic Xenopus laevis vitellogenin mRNA. We used RNA gel mobility shift assays to demonstrate that Xenopus liver contains a factor which binds with very high specificity to a segment of the 3'-UTR of vitellogenin B1 and B2 mRNAs. We detected a single high-affinity binding site in the vitellogenin mRNA 3'-UTR and localized the binding site to a 27-nucleotide region. Since binding was abolished by proteinase K digestion, at least a component of the factor is a protein. Following estrogen administration, binding was induced approximately four- to fivefold in extracts from liver polysomes. The hepatic vitellogenin mRNA-binding protein was found in both polysomes and cytosol. Since the protein was also estrogen inducible in cytosol, this represents a genuine induction, not simply recruitment of the cytosolic protein into polysomes. UV cross-linking studies with the 27-nucleotide recognition sequence revealed bands corresponding to bound proteins with apparent molecular weights of 71,000 and 141,000. This appears to be the first example of steroid hormone-inducible proteins binding to an mRNA 3'-UTR. Its induction by estrogen and its sequence-specific binding to a region of vitellogenin mRNA important in estrogen-mediated stabilization suggest that the protein may play a role in the regulation of mRNA stability.
Optimized GPU Acceleration Algorithm of Convolutional Neural Networks for Target Detection

Target detection is a hard real-time task for video and image processing. This task has recently been accomplished through the feedforward process of convolutional neural net-works (CNN), which is usually accelerated by general-purpose graphic units (GPUs). However, there is a challenge for this task. The running speed remains to be improved. In this paper, we present an efficient image combination algorithm to accelerate the feedforward process of CNN. We run our experiments on a GTX980 card. Compared with that of cuDNNv3(a standard Nvidia deep learning library), a high speedup of 6.97x is obtained in the detection task.