Miracle-dz/UniFAR-FTUs huggingface dataset:
BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Mutational analyses of Cry protein block7 polypeptides that facilitate the formation of protein inclusion in Escherichia coli

4AaCter is the polypeptide from the C-terminal extension of mosquitocidal Cry4Aa toxin, and facilitates formation of protein inclusion in Escherichia coli. It has been demonstrated that the use of 4AaCter as a peptide tag results in the efficient production of heterologous protein in E. coli. It has also been demonstrated that proteins are integrated, without losing their biological activities, into the protein inclusions. Although the mechanism to form protein inclusions in E. coli is unclear, highly conserved block7 sequence in 4AaCter is thought to be one of the functional factors. In this study, to analyze the ability of block7 to form protein inclusion, synthetic genes encoding the block7 polypeptide from selected 15 Cry proteins were constructed and expressed to produce glutathione S-transferase fusions in E. coli. Unexpectedly, only three of them (Cry5Ba, Cry32Aa, and Cry48Aa) formed protein inclusion as efficiently as that of Cry4Aa (>90% efficiency). The efficiencies in forming the protein inclusion were ranging from 39% to 66% for most of the tested block7s, and almost no protein inclusion was observed in Cry47Aa block7. This suggested that the ability of block7 to form the protein inclusion may vary with the type of Cry protein or the amino acid sequences. Mutational analyses revealed that substitution of the hydrophobic amino acids in block7 significantly affected the formation of protein inclusion, suggesting some important roles of these hydrophobic amino acid residues. Present results will contribute to develop a compact peptide tag based on block7 which forms the protein inclusion efficiently.
Economic Issues in the Fisheries Sector of Tonga

There are certain characteristics of island economies that are considered hindrances to their „development‟. For example, island economies often lack the economies of scale necessary for enhanced economic development and are too remotely located from the world‟s major international financial and trading centres to fully exploit the marketing and trading opportunities that are available. However, for island economies in the South Pacific, the sea also offers great opportunities for sustained economic development. The relative abundance and accessibility of fisheries resources means that if these resources are properly managed and exploited, island economies have much potential for social and economic development. At the same time, the sea provides a significant means of basic livelihood for many rural communities in these Island countries. A major and enduring challenge is therefore to ensure that island economies in the South Pacific utilise their sea resources for social and economic development without jeopardising their communities‟ basic livelihoods. This thesis, using a combination of quantitative and qualitative methodologies, focuses on the island economy of Tonga, examining a range of economic issues in its fisheries sector both at the national level (focusing on the fisheries export) and local level (focusing on the domestic fisheries). It begins with a discussion of fish exports, including an analysis of the return to fisher-people in Tonga from fish exported to Tonga‟s major overseas fish markets. Included in the analysis of Tonga‟s fish exports are two important variables: the size of the local fish operations in Tonga, and the types of fish exported overseas. Secondly, as fish are also caught for domestic consumption, economic development issues facing Tonga‟s domestic fisheries are assessed. Only four per cent of Tongan households earn income from fishing activities. However, the overall contribution of subsistence fisheries in Tonga is estimated at more than T$12million per year. For low income earners, there is a high value associated with self-caught fish, with domestic fishing serving a critical safety net for those at the lower end of the socio-economic ladder. Even so, although fish is an important component of household diet in Tonga, an analysis of Pacific Islands New Zealand Migration Survey (PINZMS) data indicates that the consumption of fish is related to the age,
BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS A universal strategy for high-yield production of soluble and functional clostridial collagenases in E. coli

Clostridial collagenases are foe and friend: on the one hand, these enzymes enable host infiltration and colonization by pathogenic clostridia, and on the other hand, they are valuable biotechnological tools due to their capacity to degrade various types of collagen and gelatine. However, the demand for high-grade preparations exceeds supply due to their pathogenic origin and the intricate purification of homogeneous isoforms. We present the establishment of an Escherichia coli expression system for a variety of constructs of collagenase G (ColG) and H (ColH) from Clostridium histolyticum and collagenase T (ColT) from Clostridium tetani, mimicking the isoforms in vivo. Based on a setup of five different expression strains and two expression vectors, 12 different constructs were expressed, and a flexible purification platformwas established, consisting of various orthogonal chromatography steps adaptable to the individual needs of the respective variant. This fast, cost-effective, and easy-to-establish platform enabled us to obtain at least 10 mg of highly pure mono-isoformic protein per liter of culture, ideally suited for numerous sophisticated downstream applications. This production and purification platform paves the way for systematic screenings of recombinant collagenases to enlighten the biochemical function and to identify key residues and motifs in collagenolysis.
BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Biochemical and molecular characterization of Coriolopsis rigida laccases involved in transformation of the solid waste from olive oil production

Two laccase isoenzymes were purified and characterized from the basidiomycete Coriolopsis rigida during transformation of the water-soluble fraction of “alpeorujo” (WSFA), a solid residue derived from the olive oil production containing high levels of toxic compounds. Zymogram assays of laccases secreted by the fungus growing on WSFA and WSFA supplemented with glucose showed two bands with isoelectric points of 3.3 and 3.4. The kinetic studies of the two purified isoenzymes showed similar affinity on 2,6-dimethoxyphenol and 2,2′-azinobis(3-ethylbenzthiazoline-6-sulfonic acid), used as phenolic and non-phenolic model substrate, respectively. The molecular mass of both proteins was 66 kDa with 9% N-linked carbohydrate. Physico-chemical properties of the purified laccases from media containing WSFA were similar to those obtained from medium with glucose as the main carbon source. In-vitro studies performed with the purified laccases revealed a 42% phenol reduction of WSFA, as well as changes in the molecular mass distribution. These findings indicate that these laccases are involved in the process of transformation, via polymerization by the oxidation of phenolic compounds present in WSFA. A single laccase gene, containing an open reading frame of 1,488 bp, was obtained in PCR amplifications performed with cDNA extracted from mycelia grown on WSFA. The product of the gene shares 90% identity (95% similarity) with a laccase from Trametes trogii and 89% identity (95% similarity) with a laccase from Coriolopsis gallica. This is the first report on purification and molecular characterization of laccases directly involved in the transformation of olive oil residues.
BIOTECHNOLOGICALLY RELEVANT ENZYMES AND PROTEINS Overproduction and characterization of a recombinant D-amino acid oxidase from Arthrobacter protophormiae

A screening of soil samples for D-amino acid oxidase (D-AAO) activity led to the isolation and identification of the gram-positive bacterium Arthrobacter protophormiae. After purification of the wild-type D-AAO, the gene sequence was determined and designated dao. An alignment of the deduced primary structure with eukaryotic D-AAOs and D-aspartate oxidases showed that the D-AAO from A. protophormiae contains five of six conserved regions; the C-terminal type 1 peroxisomal targeting signal that is typical for D-AAOs from eukaryotic origin is missing. The dao gene was cloned and expressed in Escherichia coli. The purified recombinant D-AAO had a specific activity of 180 U mg protein for D-methionine and was slightly inhibited in the presence of L-methionine. Mainly, basic and hydrophobic D-amino acids were oxidized by the strictly enantioselective enzyme. After a high cell density fermentation, 2.29×10 U of D-AAO were obtained from 15 l of fermentation broth.
Low glucose availability potentiates the effects of metformin on model T cell activation and exhaustion markers in vitro

Modulation of immune cell metabolism is one of promising strategies to improve cancer immunotherapies. Metformin is an anti-diabetic drug with potential anti-cancer effects, ranging from normalization of blood glucose and insulin levels, direct anti-proliferative effects on cancer cells to emerging immunomodulatory effects on anti-tumor immunity. Metformin can reduce tumor hypoxia and PD-L1 expression, as well as normalize or improve T cell function and potentiate the effect of immune checkpoint inhibitors, making it a promising adjuvant to immunotherapy of tumors with poor response such as triple negative breast cancer (TNBC). However, although the effects of metformin on cancer cells are glucose-dependent, the role of glucose in modulating its effect on T cells has not been systematically studied. We thus investigated the effect of metformin as a function of glucose level on Jurkat cell and PBMC T cell models in vitro. While low metformin concentrations had little effect on T cell function, high concentration reduced proliferation and IFN-γ secretion in both models and induced a shift in T cell populations from memory to effector subsets. The PD-1/CD69 ratio was improved by high metformin in T cells from PBMC. Low glucose and metformin synergistically reduced PD-1 and CD69 expression and IFN-γ secretion in T cells from PBMC. Low glucose level itself suppressed Jurkat cell function due to their limited metabolic plasticity, but had limited effects on T cells from PBMC apart from reduced proliferation. Conversely, high glucose did not strongly affect either T cell model. Metformin in combination with glycolysis inhibitor 2-deoxy-D-glucose (2DG) reduced PD-1 in Jurkat cells, but also strongly suppressed their function. However, low, physiologically achievable 2DG concentration itself reduced PD-1 while mostly maintaining IL-2 secretion and, interestingly, even strongly increased IFN-γ secretion regardless of glucose level. Overall, glucose metabolism can importantly influence some of the effects of metformin on T cell functionality in the tumor microenvironment. Additionally, we show that 2DG could potentially improve the anti-tumor T cell response.
Notes : Social Networks : Models , Algorithms , and Applications Lecture : April 5

1.2 Erdős-Renyi Model The above approach constitutes the sampling view of generating a random graph. Alternatively we can take a constructive view where we start with vertex set V = {1, 2, 3.n}, and selecting uniformly at random one edge from those edges not yet chosen, repeating this m times. Definition 3 G(n, p) is the random graph obtained by starting with vertex set V = {1, 2, 3.n}, letting 0 ≤ p ≤ 1, and connecting each pair vertices {i, j} by a edge with probability p This model is typically referred to as the Erdos-Renyi (ER) Random Graph Model, outlined by Erdős and Renyi in two papers from 1959 and 1960 [2, 3]. While the model bears their names, their work initially examined the properties of the G(n,m) model, only later expanding to analyze
Crime Prevention Through Environmental Design

crime. C rime Prevention through Environmental Design (CPTED) has emerged worldwide as one of the most promising and currently effective approaches to reducing opportunities for crime. Although dramatic results have been achieved in every imaginable setting— from small stores to entire residential communities—many planners, designers, and developers remain reluctant or unwilling to incorporate CPTED into their work.
An Improved Approximation Algorithm for Multiway Cut

Given an undirected graph with edge costs and a subset of k nodes called terminals, a multiway cut is a subset of edges whose removal disconnects each terminal from the rest. Multiway Cut is the problem of finding a multiway cut of minimum cost. Previously, a very simple combinatorial algorithm due to Dahlhaus, Johnson, Papadimitriou, Seymour, and Yannakakis gave a performance guarantee of 2 ( 1− 1 k ) . In this paper, we present a new linear programming relaxation for Multiway Cut and a new approximation algorithm based on it. The algorithm breaks the threshold of 2 for approximating Multiway Cut, achieving a performance ratio of at most 1.5− k . This improves the previous result for every value of k. In particular, for k = 3 we get a ratio of 7 6 < 4 3 . ∗College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0280, U.S.A. Research supported in part by NSF grant CCR-9319106. E-mail: gruia@cc.gatech. edu. †College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0280, U.S.A. Research supported in part by NSF grant CCR-9319106. E-mail: howard@cc.gatech. edu. ‡Computer Science Department, Technion — IIT, Haifa 32000, Israel. Work supported by BSF grant 96-00402, and by grants from the S. and N. Grand Research Fund, from the Smoler Research Fund, and from the Fund for the Promotion of Research at the Technion. E-mail: rabani@cs.technion. ac.il.
An Improved Approximation Algorithm for the Max-3-Section Problem

We consider the Max-$3$-Section problem, where we are given an undirected graph $ G=(V,E)$ equipped with non-negative edge weights $w :E\rightarrow \mathbb{R}_+$ and the goal is to find a partition of $V$ into three equisized parts while maximizing the total weight of edges crossing between different parts. Max-$3$-Section is closely related to other well-studied graph partitioning problems, e.g., Max-$k$-Cut, Max-$3$-Cut, and Max-Bisection. We present a polynomial time algorithm achieving an approximation of $ 0.795$, that improves upon the previous best known approximation of $ 0.673$. The requirement of multiple parts that have equal sizes renders Max-$3$-Section much harder to cope with compared to, e.g., Max-Bisection. We show a new algorithm that combines the existing approach of Lassere hierarchy along with a random cut strategy that suffices to give our result.
4 Concluding Remarks

We do not know the integrality ratio for the relaxation we propose. It is possible that a better rounding procedure can be discovered. Here are the worst examples of which we are aware. For k = 3, the following example (which also appeared in 7]) satisses all the new constraints and shows that the integrality ratio is at least 16 15. Consider the graph G = (V; E). V = fS f1; 2; 3gj 1 jSj 2g, where f1g; f2g; f3g are the terminals. E = ffS; Tgj S 6 = T; jS \ Tj = 1g. The edges fS; Tg with S or T of size 1 (between a terminal and a nonterminal) have cost 2, and the edges with jSj = jTj = 2 (between two nonterminals) have cost 1. It is not hard to see that the optimum multiway cut has cost 8 (by enumerating over all distinct assignments of the nonterminals to terminals). On the other hand, assigning length 1 2 to all the edges is a feasible (optimal) solution to the relaxation (i.e., place nonterminal fi; jg midway between terminals fig and fjg in the 2-simplex). This solution has value 7:5. Thus, the ratio of the integral optimum to the fractional optimum for this example is at least 16 15. The example can be generalized to k = 4. The graph has vertex set V = fS f1; 2; 3; 4gj 1 jSj 2g, where f1g; f2g; f3g; f4g are the terminals. The edge set is deened as in the previous example: E = ffS; Tgj S 6 = T; jS \ Tj = 1g. The 12 edges fS; Tg such that jSj = 1 or jTj = 1 (between a terminal and a nonterminal) have cost 3, and the 12 edges fS; Tg such that jSj = jTj = 2 (between two nonterminals) have cost 1. By exhaustive search, one can verify that the optimum multiway cut has cost 26. There is a feasible fractional solution in which all edges have length 1 2. Its cost is 24, so the integrality ratio in this case is at least 13 12. 8 Now suppose that i j and that by the time i is processed, neither u nor v has been assigned to a vertex. For uv to be cut, we must have 2 I L (I R n I L). The crux of the …
Sub-Pixel Dispersion Model for Coded Aperture Snapshot Spectral Imaging

Coded aperture snapshot spectral imaging (CASSI) aims to reconstruct three-dimensional spatial-spectral images from a single snapshot measurement. Traditional CASSI systems model the imaging process as a sum of binary spatial modulation and ideal stair-stepping spectral shifts of the scene pixels. However, the actual optical reality does not match the current imaging model as the dispersion in the system is continuous. Certain spectral bands are shifted to align the sensor pixels perfectly, while others are pixel-misaligned and projected into two adjacent pixels. Existing imaging models have ignored the pixel-misaligned spectral bands, resulting in the limitations of the reconstruction quality and spectral band number. In this paper, we present a sub-pixel dispersion model that accounts for the continuous dispersion in the CASSI system. We discretize the scene spectrum with dense sampling and express the spectral shifts in the sub-pixel level to consider both the pixel-aligned and pixel-misaligned spectral bands, thus accurately modeling the CASSI imaging process towards actual optical reality. We integrate the proposed model into two mainstream reconstruction algorithms, including the traditional handcrafted prior and deep image prior. The proposed precise model makes the reconstruction targets of these algorithms closer to the optical reality, which increases the reconstruction accuracy and spectral bands. Both simulations and experiments with actual systems demonstrate the effectiveness of the proposed model.
Robust reference tracking control subject to time-varying delay with future reference anticipation

This paper addresses the challenges of controlling systems over a network, considering the detrimental effects of network-induced delays and dynamic model uncertainties. To tackle these issues, a method is proposed that combines a stability criterion for systems with time-varying delays and model uncertainties with a predictive controller for linear systems, incorporating future references. The main objective is to ensure a given tolerance to network induced time-varying delays while accounting for model uncertainties and future references. The main motivation of the method is illustrated through simulations of an omnidirectional robot controlled remotely over a wireless network. The obtained results provide valuable insights into tuning the parameters of the unconstrained predictive controller in order to illustrate the usefulness of the proposed method in the presence of time-varying delays.
Discrimination of Earthquakes and Underwater Explosions Using Neural Networks

We report on the implementation of an automatic system able to discriminate between explosion-generated artificial seismic events and local earthquakes in the Phlegraean Fields (Italy). The explosions are fired weekly at the sea bottom (tens of meters below sea level) by fishermen in Pozzuoli bay; earthquakes are volcano-tectonic quakes with depths shallower than 4 km. The discrimination system is based on an artificial neural network and is composed of two modules. The first is devoted to the extraction of the seismogram signatures and the second to the classification of the seismic events into two classes. For the features extraction (preprocessing stage), instead of the conventional Fourier spectral analysis, we use a Linear Prediction Coding (LPC) algorithm. This approach compresses the data from 256 samples to only 7 parameters and can extract robust features for the spectrogram representation. The classification is performed using a supervised neural algorithm based on a Multilayer Neural Network (MLP) architecture. We applied the method to a set of 30 seismic events recorded by the stations of the local seismic network, 15 of which were generated by the fishermen's explosions and 15 were volcano-tectonic earthquakes. We dealt with a total of 280 records from different stations, 121 relating to explosions and 159 to earthquakes. Data were divided in a training set containing 120 traces for earthquakes and 90 for explosions, and a test set containing 70 traces corresponding to 39 records for earthquakes and 31 records for explosions. On the test set the neural net gave a classification performance of 92%, indicating a good ability of the net to generalize. Manuscript received 10 January 2002.
Potential Toxicity and Mechanisms of T-2 and HT-2 Individually or in Combination on the Intestinal Barrier Function of Porcine Small Intestinal Epithelial Cells

Under natural conditions, T-2 toxin can be easily metabolized to HT-2 toxin by deacetylation, and T-2 and HT-2 are usually co-contaminated in grain and feed at a high detected rate. Our previous information indicated that T-2 toxin could injure the function of the intestinal barrier, but the combined toxicity and mechanism of T-2 and HT-2 on the intestinal cells of porcines are still unknown. Therefore, we aimed to explore T-2 and HT-2 individually and combined on cellular viability, cell membrane integrity, the expression of tight junction-related proteins, and the generation of inflammatory factors in porcine intestinal epithelial cells (IPEC-J2). The results showed that T-2 and HT-2, individually or in combination, could induce a decrease in cell viability, an increase in LDH release and IL-1, IL-6, and TNF-α generation, and a decrease in the anti-inflammatory factor IL-10. Based on the analysis of immunofluorescence staining, real-time PCR, and western blotting, the tight junction protein expressions of Claudin-1, Occludin, and ZO-1 were significantly decreased in the T-2 and HT-2 individual or combination treated groups compared with the control. Furthermore, all the parameter changes in the T-2 + HT-2 combination group were much more serious than those in the individual dose groups. These results suggest that T-2 and HT-2, individually and in combination, could induce an intestinal function injury related to an inflammatory response and damage to the intestinal barrier function in porcine intestinal epithelial cells. Additionally, T-2 and HT-2 in combination showed a synergistic toxic effect, which will provide a theoretical basis to assess the risk of T-2 + HT-2 co-contamination in porcine feed.