Miracle-dz/UniFAR-FTUs huggingface dataset:
CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins

Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) is a widely used technique for identifying transcription factor (TF) binding events throughout an entire genome. However, ChIP-seq is limited by the availability of suitable ChIP-seq grade antibodies, and the vast majority of commercially available antibodies fail to generate usable data sets. To ameliorate these technical obstacles, we present a robust methodological approach for performing ChIP-seq through epitope tagging of endogenous TFs. We used clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-based genome editing technology to develop CRISPR epitope tagging ChIP-seq (CETCh-seq) of DNA-binding proteins. We assessed the feasibility of CETCh-seq by tagging several DNA-binding proteins spanning a wide range of endogenous expression levels in the hepatocellular carcinoma cell line HepG2. Our data exhibit strong correlations between both replicate types as well as with standard ChIP-seq approaches that use TF antibodies. Notably, we also observed minimal changes to the cellular transcriptome and to the expression of the tagged TF. To examine the robustness of our technique, we further performed CETCh-seq in the breast adenocarcinoma cell line MCF7 as well as mouse embryonic stem cells and observed similarly high correlations. Collectively, these data highlight the applicability of CETCh-seq to accurately define the genome-wide binding profiles of DNA-binding proteins, allowing for a straightforward methodology to potentially assay the complete repertoire of TFs, including the large fraction for which ChIP-quality antibodies are not available.
Osteocalcin Induces Release of Glucagon-Like Peptide-1 and Thereby Stimulates Insulin Secretion in Mice

The uncarboxylated form (ucOC), but not the γ-carboxylated form (GlaOC), of the bone-derived protein osteocalcin stimulates insulin secretion and regulates energy metabolism in insulin target tissues. Glucagon-like peptide–1 (GLP-1) is an insulin secretagogue that is released from the gut in response to food intake. We have now found that Gprc6a, a putative ucOC receptor, is expressed in epithelial cells of the mouse small intestine as well as in STC-1 enteroendocrine cells. Secretion of GLP-1 by STC-1 cells was stimulated by ucOC but not by GlaOC. The serum GLP-1 concentration in mice was increased by intraperitoneal or oral administration of ucOC, whereas GlaOC was effective in this regard only after oral application. Serum insulin levels were also increased by ucOC, and this effect was potentiated by an inhibitor of dipeptidyl peptidase IV and blocked by a GLP-1 receptor antagonist. Intravenous injection of ucOC in mice increased the serum GLP-1 concentration, and also increased the serum level of insulin. Our results suggest that ucOC acts via Gprc6a to induce GLP-1 release from the gut, and that the stimulatory effect of ucOC on insulin secretion is largely mediated by GLP-1.
Insulin‐like growth factor I stimulates oligodendrocyte development and myelination in rat brain aggregate cultures

Insulin‐like growth factor I (IGF‐I) and high concentrations of insulin have been shown to stimulate an increase in the number of oligodendrocytes that appear in developing monolayer cultures of rat brain cells (McMorris et al., Proc Natl Acad Sci USA 83:822–826, 1986; McMorris et al., Ann NY Acad Sci 605:101–109, 1990; McMorris and Dubois‐Dalcq, J Neurosci Res 21:199–209, 1988). In the present study, we investigated whether IGF‐I or insulin treatment induces a corresponding increase in the synthesis and accumulation of myelin. Aggregate cultures, established from 16‐day‐old fetal rat brains, were treated with either 100 ng/ml IGF‐I or 5,000 ng/ml insulin and analyzed for the number of oligodendrocytes, activity of 2′,3′‐cyclic nucleotide 3′‐phosphohydrolase (CNP), total amount of myelin, and synthesis rate of myelin proteins. Cultures treated with IGF‐I beginning on day 2 after explanation contained 35–80% more oligodendrocytes and had 60–160% higher CNP activity than controls when tested on day 13, 20, or 27. By day 27, treated cultures had 35–90% more myelin than controls. Similar results were observed in response to 5,000 ng/ml insulin, a concentration at which insulin binds to IGF receptors and acts as an analogue of IGF‐I. The synthesis rate of myelin proteins was measured in experiments using 5,000 mg/ml insulin. When treatment was begun at day 20 rather than day 2, cultures did not exhibit an increased number of oligodendrocytes over control during the following 4–6 days. Therefore, this paradigm was used to separate the effects of insulin‐like peptides on the number of oligodendrocytes from the effects on the synthesis rate of myelin proteins and the accumulation of myelin. Cultures treated from day 20 and controls showed no difference in either the myelin yield or the synthesis rate of myelin proteins. These data show that IGF‐I (and insulin at high concentrations) increases the amount of myelin produced in aggregate cultures; and that the increase appears to be due primarily to an increase in the number of oligodendrocytes in the cultures rather than to a direct increase in the rate of myelin protein synthesis or an increase in the amount of myelin synthesized per oligodendrocyte.
Fully Interconnected Globular Porous Biphasic Calcium Phosphate Ceramic Scaffold Facilitates Osteogenic Repair

An appropriate scaffold, which provides structural support for transplanted cells and acts as a vehicle for the delivery of biologically active molecules, is critical for tissue engineering. We developed a fully interconnected globular porous biphasic calcium phosphate ceramic scaffold by adopting a foaming method, and evaluated its efficiency as a bone substitute and a scaffold for bone tissue engineering by in vitro and in vivo biocompatible analysis and its osteogenic healing capacity in rat tibial bone defects. They have spherical pores averaging 400um in diameter and interconnecting interpores averaging 70um in diameter with average 85% porosity. They elicited no cytotoxicity and noxious effect on cellular proliferation and osteoblastic differentiation during the cell-scaffold construct formation. Also the bone defects grafted with fully interconnected globular porous biphasic calcium phosphate ceramic blocks revealed excellent bone healing within 3 weeks. These findings suggest that the fully interconnected porous biphasic calcium phosphate scaffold formed by the foaming method can be a promising bone substitute and a scaffold for bone tissue engineering.
A Generic Program for Multistate Protein Design

Some protein design tasks cannot be modeled by the traditional single state design strategy of finding a sequence that is optimal for a single fixed backbone. Such cases require multistate design, where a single sequence is threaded onto multiple backbones (states) and evaluated for its strengths and weaknesses on each backbone. For example, to design a protein that can switch between two specific conformations, it is necessary to to find a sequence that is compatible with both backbone conformations. We present in this paper a generic implementation of multistate design that is suited for a wide range of protein design tasks and demonstrate in silico its capabilities at two design tasks: one of redesigning an obligate homodimer into an obligate heterodimer such that the new monomers would not homodimerize, and one of redesigning a promiscuous interface to bind to only a single partner and to no longer bind the rest of its partners. Both tasks contained negative design in that multistate design was asked to find sequences that would produce high energies for several of the states being modeled. Success at negative design was assessed by computationally redocking the undesired protein-pair interactions; we found that multistate design's accuracy improved as the diversity of conformations for the undesired protein-pair interactions increased. The paper concludes with a discussion of the pitfalls of negative design, which has proven considerably more challenging than positive design.
Curdlan β-1,3-Glucooligosaccharides Induce the Defense Responses against Phytophthora infestans Infection of Potato (Solanum tuberosum L. cv. McCain G1) Leaf Cells

Activation of the innate immune system before the invasion of pathogens is a promising way to improve the resistance of plant against infection while reducing the use of agricultural chemicals. Although several elicitors were used to induce the resistance of potato plant to microbial pathogen infection, the role of curdlan oligosaccharide (CurdO) has not been established. In the current study, the defense responses were investigated at biochemical and proteomic levels to elucidate the elicitation effect of CurdOs in foliar tissues of potato (Solanum tuberosum L. cv. McCain G1). The results indicate that the CurdOs exhibit activation effect on the early- and late-defense responses in potato leaves. In addition, glucopentaose was proved to be the shortest active curdlan molecule based on the accumulation of H2O2 and salicylic acid and the activities of phenylalanine amino-lyase, β-1,3-glucanase and chitinase. The 2D-PAGE analysis reveals that CurdOs activate the integrated response reactions in potato cells, as a number of proteins with various functions are up-regulated including disease/defense, metabolism, transcription, and cell structure. The pathogenesis assay shows that the ratio of lesion area of potato leaf decreased from 15.82%±5.44% to 7.79%±3.03% when the plants were treated with CurdOs 1 day before the infection of Phytophthora infestans. Furthermore, the results on potato yield and induction reactions indicate that the defense responses induced by CurdOs lasted for short period of time but disappeared gradually.
Quantitative Profiling of Immune Repertoires for Minor Lymphocyte Counts Using Unique Molecular Identifiers

Emerging high-throughput sequencing methods for the analyses of complex structure of TCR and BCR repertoires give a powerful impulse to adaptive immunity studies. However, there are still essential technical obstacles for performing a truly quantitative analysis. Specifically, it remains challenging to obtain comprehensive information on the clonal composition of small lymphocyte populations, such as Ag-specific, functional, or tissue-resident cell subsets isolated by sorting, microdissection, or fine needle aspirates. In this study, we report a robust approach based on unique molecular identifiers that allows profiling Ag receptors for several hundred to thousand lymphocytes while preserving qualitative and quantitative information on clonal composition of the sample. We also describe several general features regarding the data analysis with unique molecular identifiers that are critical for accurate counting of starting molecules in high-throughput sequencing applications.
Nanostructured Materials: Processing, Properties and Applications

"Nanostructured Materials: Processing, Properties and Applications, 2nd Edition" is an extensive update to the exceptional first edition snapshot of this rapidly advancing field. Retaining the organization of the first edition, Part 1 covers the important synthesis and processing methods for the production of nanocrystalline materials. Part 2 focuses on selected properties of nanostructured materials. Potential or existing applications are described as appropriate throughout the book. The second edition has been updated throughout for the latest advances and includes two additional chapters.
Learning auditory neural representations for emotion recognition

Auditory emotion recognition has become a very important topic in recent years. However, still after the development of some architectures and frameworks, generalization is a big problem. Our model examines the capability of deep neural networks to learn specific features for different kinds of auditory emotion recognition: speech and music-based recognition. We propose the use of a cross-channel architecture to improve the generalization aspects of complex auditory recognition by the integration of previously learned knowledge of specific representation into a high-level auditory descriptor. We evaluate our models using the SAVEE dataset, the GTZAN dataset and the EmotiW corpus, and show comparable results with state-of-the-art approaches.
Improved Bloch‐Siegert based B1 mapping by reducing off‐resonance shift

An MRI method based on the Bloch‐Siegert (BS) shift phenomenon was recently proposed as a fast and precise way to map a radio frequency (RF) transmit field (B1+ field). For MRI at high field, the mapping sensitivity of this approach was limited by tissue heating associated with a BS irradiation pulse. To mitigate this, we investigated the possibility of lowering the off‐resonance frequency of this pulse since theoretical analysis indicated that the sensitivity of Bloch‐Siegert based B1+ mapping could be substantially improved when irradiating closer to resonance. Using optimized irradiation pulse shape and gradient crushers to minimize direct excitation effects, in vivo experiments on human brains at 7 T confirmed improved sensitivity with this approach. Improved sensitivity translated into an 80% reduction in B1+ estimation errors without increasing tissue heating. Published 2013. This article is a U.S. Government work and is in the public domain in the USA.
Application of Cognitive and Socio-Cultural Theories in CALL

Since it is quite difficult in traditional learning atmospheres for the learners to be exposed to the target language adequately in foreign language acquisition, CALL in which virtual environment is designed in more appropriate way has given rise. Two main paradigms, cognitive model and socio-cultural theory, have also been adopted in CALL. Moreover, rather than applying one theory, combination of these paradigms is unavoidable. However, application of this combination is challenging in practice, as these two theories have different principles. Furthermore, when it comes to online education, it turns into more challenging process. In this poster this combination is presented with the help of sample applications from Gazi University.
Morphometric Changes in the Episodic Memory Network and Tau Pathologic Features Correlate with Memory Performance in Patients with Mild Cognitive Impairment

BACKGROUND AND PURPOSE: Mild cognitive impairment (MCI) may affect several cognitive domains, including attention and reasoning, but is often first characterized by memory deficits. The purpose of this study was to ask these 2 questions: 1) Can levels of CSF tau proteins and amyloid beta 42 peptide explain thinning of the cerebral cortex in patients with MCI? 2) How are brain morphometry, CSF biomarkers, and apolipoprotein E (APOE) allelic variation related to episodic memory function in MCI? MATERIALS AND METHODS: Hippocampal volume and cortical thickness were estimated by MR imaging and compared for patients with MCI (n = 18) and healthy controls (n = 18). In addition, regions of interest (ROIs) were selected in areas where the MCI group had atrophy and which overlapped with the episodic memory network (temporal, entorhinal, inferior parietal, precuneus/posterior cingulate, and frontal). Relationships among morphometry, CSF biomarkers, APOE, and memory were tested. The analyses were repeated with an independent sample of patients with MCI (n = 19). RESULTS: Patients with MCI and pathologic CSF values had hippocampal atrophy. However, both patients with pathologic and patients with nonpathologic CSF had a thinner cortex outside the hippocampal area. CSF pathology was related to hippocampal volume, whereas relationships with cortical thickness were found mainly in one of the samples. Morphometry correlated robustly with memory performance across MCI samples, whereas less stable results were found for tau protein. CONCLUSION: The differences in hippocampal volume between the MCI and the healthy control groups were only found in patients with pathologic CSF biomarkers, whereas differences in cortical thickness were also found for patients without such pathologic features. Morphometry in areas in the episodic memory network was robustly correlated with memory performance. It is speculated that atrophy in these areas may be associated with the memory problems seen in MCI.
Reaction Mechanism between Solid CaO and FeOx–CaO–SiO2–P2O5 Slag at 1 573 K

Solid CaO and FeOx–CaO–SiO2–P2O5 slag were reacted for 2 to 2 400 s at 1 573 K. The interface of CaO and slag were observed and analyzed by SEM/EDS. The CaO–FeO layer was formed beside solid CaO. The thickness of the CaO–FeO layer increased with time. Next to the CaO–FeO layer, 2CaO·SiO2 phase was formed in the melt and high content of FeO was included in the liquid. The activities of FeO and CaO for each phase were evaluated and reaction mechanism between solid CaO and FeOx–CaO–SiO2–P2O5 slag was discussed. The activity of FeO for 2CaO·SiO2 saturated melt is larger than that for the CaO–FeO layer, therefore, Fe2+ diffuses from slag phase to solid CaO. Then the CaO–FeO layer is formed beside solid CaO. The pass of the slag composition change accompanied by CaO dissolution are represented in the phase diagram for the FeOx–CaO–(SiO2+P2O5) pseudo ternary system.
Epitope masking of rhabdomeric rhodopsin during endocytosis-induced retinal degeneration.

PURPOSE To determine the fate of rhodopsin during endocytosis-mediated retinal degeneration. METHODS Drosophila stocks were raised in complete darkness and shifted to light for 24 h prior to dissection and fixation of retinas. 1 microm frozen sections were cut on an ultracryomicrotome, then stained with antibodies specific for rhodopsin or arrestin. Localization of photoreceptor cell-specific proteins was determined by confocal microscopy. RESULTS Flies that are in the process of undergoing endocytosis-mediated retinal degeneration exhibit an apparent loss of rhabdomeric rhodopsin at early times during the degenerative process. Using different immunological agents, genetic backgrounds, and light treatments, we have found that the binding of arrestin to rhodopsin masked the C-terminal monoclonal antibody epitope and resulted in the loss of rhodopsin immunoreactivity. The loss of immunoreactive rhabdomeric rhodopsin only occurred when rhodopsin was depleted from the plasma membrane such that it was found within the rhabdomere at stoichiometric levels with arrestin. CONCLUSIONS When rhodopsin and arrestin are found at equal levels, binding of arrestin to rhodopsin results in the masking of the antibody epitope on the C-terminus of rhodopsin. Since masking can only occur after most of the rhodopsin has been depleted from the rhabdomere, it can be concluded that during endocytosis-induced retinal degeneration, much of the rhodopsin is localized to the cell body in small puncta. These data suggest that rhodopsin is at extremely high local concentrations in the cytoplasm. The data are discussed in the context of a model for photoreceptor cell apoptosis in retinal degenerative disorders.
Electric fields in irradiated dielectrics

An existing model for quantitatively predicting electric field build-up in dielectrics is used to demonstrate the importance of material parameters. Results indicate that electron irradiation will produce 10 to the 6th power V/cm in important materials. Parameters which can alter this build-up are discussed. Comparison to known irradiation induced dielectric charging experiments is discussed.
Restoration of Hyperspectral Astronomical Data with Spectrally Varying Blur

In this paper we present a method for hyper-spectral image restoration for integral field spectrographs (IFS) data. We specifically address two topics: (i) the design of a fast approximation of spectrally varying operators and (ii) the comparison between two kind of regularization functions: quadratic and spatial sparsity functions. We illustrate this method with simulations coming from the Multi Unit Spectroscopic Explorer (MUSE) instrument. It shows the clear increase of the spatial resolution provided by our method as well as its denoising capability.
Evaluation of Antimicrobial Durability and Anti-Biofilm Effects in Urinary Catheters Against Enterococcus faecalis Clinical Isolates and Reference Strains

Background: Enterococcus faecalis, Escherichia coli, Staphylococcus epidermidis, Pseudomonas aeruginosa and Candida albicans biofilms are major causes of catheter-associated urinary tract infections. Antimicrobial-coated or impregnated urinary catheters are seen as a possible way to prevent these infections. Aims: To determine the biofilm-forming ability of 89 E. faecalis isolates from urinary tract infections and to compare several urinary catheters for antimicrobial durability and the inhibitory effects on biofilm formation of different laboratory strains and clinical isolates of E. faecalis. Study Design: In vitro experimental study. Methods: The biofilm forming ability of E. faecalis isolates was determined by the crystal violet staining and plate counting methods. For comparison of urinary catheters, biofilms of 45 E. faecalis isolates from the catheter samples of hospitalized patients and five laboratory strains of E. coli ATCC25922, S. epidermidis ATCC35984, P. aeruginosa ATCC27853, E. faecalis ATCC29212 and C. albicans ATCC90028 were formed on the catheters in 24-well tissue culture plates. Scanning electron microscopy analysis was performed to observe biofilms. Results: All 89 E. faecalis isolates were found to be biofilm positive. Nitrofurazone-impregnated catheters significantly reduced the cell counts of E. faecalis isolates and completely inhibited the formation of P. aeruginosa and S. epidermidis biofilms compared with the others. Regarding reduction of biofilm cell counts, a hydrophilic-coated catheter was more effective against P. aeruginosa, whereas a silver-coated catheter was found to be more effective against S. epidermidis. The nitrofurazone-impregnated catheter had the best antimicrobial durability. Conclusion: Urine isolates of E. faecalis had considerable ability with respect to biofilm formation. The nitrofurazone-impregnated catheter was the most effective against all tested bacteria; however, the effect of a hydrophilic or silver-coated catheter depends on the species present in it.
Limits of Preprocessing

We present a first theoretical analysis of the power of polynomial-time preprocessing for important combinatorial problems from various areas in AI. We consider problems from Constraint Satisfaction, Global Constraints, Satisfiability, Nonmonotonic and Bayesian Reasoning. We show that, subject to a complexity theoretic assumption, none of the considered problems can be reduced by polynomial-time preprocessing to a problem kernel whose size is polynomial in a structural problem parameter of the input, such as induced width or backdoor size. Our results provide a firm theoretical boundary for the performance of polynomial-time preprocessing algorithms for the considered problems.
Packet Switching in Radio Channels: Part III - Polling and (Dynamic) Split-Channel Reservation Multiple Access

Here we continue the analytic study of packet switching in radio channels which we reported upon m our two previous papers [1], [2] Again we consider a population of terminals communicating with a central station over a packet-switched radio channel. The allocation of bandwidth among the contending terminals can be fixed [e.g., time-division multiple access (TDMA) or frequency-division multiple access (FDMA)], random [e.g., ALOHA or carrier sense multiple access (CSMA)] or centrally controlled (e.g., polling or reservation). In this paper we show that with a large population of bursty users, (as expected) random access is superior to both fixed assignment and polling. We also introduce and analyze a dynamic reservation technique which we call split-channel reservation multiple access (SRMA) which is interesting in that it is both simple and efficient over a large range of system parameters.