Miracle-dz/UniFAR-FTUs huggingface dataset:
Graph-based evolutionary algorithms

Evolutionary algorithms use crossover to combine information from pairs of solutions and use selection to retain the best solutions. Ideally, crossover takes distinct good features from each of the two structures involved. This process creates a conflict: progress results from crossing over structures with different features, but crossover produces new structures that are like their parents and so reduces the diversity on which it depends. As evolution continues, the algorithm searches a smaller and smaller portion of the search space. Mutation can help maintain diversity but is not a panacea for diversity loss. This paper explores evolutionary algorithms that use combinatorial graphs to limit possible crossover partners. These graphs limit the speed and manner in which information can spread giving competing solutions time to mature. This use of graphs is a computationally inexpensive method of picking a global level of tradeoff between exploration and exploitation. The results of using 26 graphs with a diverse collection of graphical properties are presented. The test problems used are: one-max, the De Jong functions, the Griewangk function in three to seven dimensions, the self-avoiding random walk problem in 9, 12, 16, 20, 25, 30, and 36 dimensions, the plus-one-recall-store (PORS) problem with n=15,16, and 17, location of length-six one-error-correcting DNA barcodes, and solving a simple differential equation semi-symbolically. The choice of combinatorial graph has a significant effect on the time-to-solution. In the cases studied, the optimal choice of graph improved solution time as much as 63-fold with typical impact being in the range of 15% to 100% variation. The graph yielding superior performance is found to be problem dependent. In general, the optimal graph diameter increases and the optimal average degree decreases with the complexity and difficulty of the fitness landscape. The use of diverse graphs as population structures for a collection of problems also permits a classification of the problems. A phylogenetic analysis of the problems using normalized time to solution on each graph groups the numerical problems as a clade together with one-max; self-avoiding walks form a clade with the semisymbolic differential equation solution; and the PORS and DNA barcode problems form a superclade with the numerical problems but are substantially distinct from them. This novel form of analysis has the potential to aid researchers choosing problems for a test suite
Geochemical characteristics of water and its suitability for drinking and irrigation use in and around Warnanagar area of Kolhapur District (Maharashtra) India

Concentrations of selected physicochemical parameters (pH, electrical conductivity, TDS, Ca 2+ , Mg 2+ , Na + , K + , Cl - + SO 4 -2 , CO 3 2- and HCO 3 - ) in surface and groundwater were studied in order to understand contamination level. For this study, water samples were collected from 22 locations representing the entire study area. Standard hydro-geochemical techniques were employed to determine the quality parameters of the water. pH and EC values of water samples show considerable changes. In most of the water samples Ca 2+ is the dominant cation followed by Mg 2+ , Na + , and K + . HCO 3 - is the major anion followed by SO 4 2- and Cl - . In general all the parameters are within prescribed limit except EC, TDS, Ca 2+ and Mg 2+ . Water types indicate that the alkaline earth metals (Ca 2+ + Ma 2+ ) exceed the alkali metals (Na + + K + ). Strong acid (Cl - + SO 4 -2 ) exceed the weak acid (CO 3 2- + HCO 3 ). Further, suitability of groundwater for irrigation was examined with different irrigation indexes. It indicates that the groundwater quality stands for EC values about 55% of the samples falls in the high salinity category and stands on a sodium percent (SP) values about 91% of the samples falls into excellent to permissible category. The RSC, SSP and KR values stand on all the water samples fall in safe for irrigation purpose. Overall, water samples from the study area shows salinity, corrosion and permeability hazards.
Expression of myostatin pro domain results in muscular transgenic mice

Myostatin, a member of the TGF‐β family, negatively regulates skeletal muscle development. Depression of myostatin activity leads to increased muscle growth and carcass lean yield. In an attempt to down‐regulate myostatin, transgenic mice were produced with a ribozyme‐based construct or a myostatin pro domain construct. Though the expression of the ribozyme was detected, muscle development was not altered by the ribozyme transgene. However, a dramatic muscling phenotype was observed in transgenic mice carrying the myostatin pro domain gene. Expression of the pro domain transgene at 5% of β‐actin mRNA levels resulted in a 17–30% increase in body weight (P < 0.001). The carcass weight of the transgenic mice showed a 22–44% increase compared with nontransgenic littermates at 9 weeks of age (16.05 ± 0.67 vs. 11.16 ± 0.28 g in males; 9.99 ± 0.38 vs. 8.19 ± 0.19 g in females, P < 0.001). Extreme muscling was present throughout the whole carcass of transgenic mice as hind and fore limbs and trunk weights, all increased significantly (P < 0.001). Epididymal fat pad weight, an indicator of body fat, was significantly decreased in pro domain transgenic mice (P < 0.001). Analysis of muscle morphology indicated that cross‐sectional areas of fast‐glycolytic fibers (gastrocnemius) and fast‐oxidative glycolytic fibers (tibialis) were larger in pro domain transgenic mice than in their controls (P < 0.01), whereas fiber number (gastrocnemius) was not different (P > 0.05). Thus, the muscular phenotype is attributable to myofiber hypertrophy rather than hyperplasia. The results of this study suggest that the over‐expression of myostatin pro domain may provide an alternative to myostatin knockouts as a means of increasing muscle mass in other mammals. Mol. Reprod. Dev. 60: 351–361, 2001. © 2001 Wiley‐Liss, Inc.
Multiscale Model of Colorectal Cancer Using the Cellular Potts Framework

Colorectal cancer (CRC) is one of the major causes of death in the developed world and forms a canonical example of tumorigenesis. CRC arises from a string of mutations of individual cells in the colorectal crypt, making it particularly suited for multiscale multicellular modeling, where mutations of individual cells can be clearly represented and their effects readily tracked. In this paper, we present a multicellular model of the onset of colorectal cancer, utilizing the cellular Potts model (CPM). We use the model to investigate how, through the modification of their mechanical properties, mutant cells colonize the crypt. Moreover, we study the influence of mutations on the shape of cells in the crypt, suggesting possible cell- and tissue-level indicators for identifying early-stage cancerous crypts. Crucially, we discuss the effect that the motility parameters of the model (key factors in the behavior of the CPM) have on the distribution of cells within a homeostatic crypt, resulting in an optimal parameter regime that accurately reflects biological assumptions. In summary, the key results of this paper are 1) how to couple the CPM with processes occurring on other spatial scales, using the example of the crypt to motivate suitable motility parameters; 2) modeling mutant cells with the CPM; 3) and investigating how mutations influence the shape of cells in the crypt.
Expression of Angiogenesis-Related Genes Regulates Different Steps in the Process of Tumor Growth and Metastasis in Human Urothelial Cell Carcinoma of the Urinary Bladder

Objective: This study was designed to determine the relative activity of angiogenesis-related genes in the regulation of tumorigenicity and subsequent metastases of urothelial cell carcinomas (UC) of the urinary bladder. Methods: We selected the clones with the highest and lowest expression level of basic fibroblast growth factor (bFGF), vascular endothelial growth factor (VEGF)/vascular permeability factor or interleukin-8 (IL-8) in the highly tumorigenic and metastatic human UC cell line 253J B-V. Tumorigenicity and production of spontaneous lymph node metastases were evaluated 1, 2, 4, 8 and 12 weeks after orthotopic implantation of each specific expression clone into the urinary bladder of athymic nude mice. Moreover, the transitional changes in the expression of angiogenesis-related genes and neovascularization were determined in tumors and metastases. Results: At the early stage of tumor growth following orthotopic implantation, tumorigenicity and metastases were significantly increased in the clones with the highest expression of bFGF and IL-8, while they were significantly inhibited in the clones with the lowest expression of bFGF and IL-8 compared to parental 253J B-V. In the tumors, specific expression of angiogenesis-related genes and intratumor neovascularity of each clone were gradually regulated to the same level as parental 253J B-V. In metastasized tumors of the highest and lowest IL-8-expressing clones, IL-8 expression was consistently high and low, respectively. Conclusions: These findings indicate that at the early stage of tumor growth, bFGF and IL-8 expression play important roles in the regulation of angiogenesis, tumorigenicity and subsequent metastases of human bladder cancer.
Pilot assessment and survey of Syrian refugees' psychological stress and openness to referral for telepsychiatry (PASSPORT Study).

BACKGROUND Given the scarcity of mental health resources available for refugees in areas of conflict, it is imperative to investigate interventions that would be accepted by the refugees. MATERIALS AND METHODS In this study we surveyed 354 Syrian refugees using the HADStress screening tool and asked about their openness to referral to psychiatry and telepsychiatry. RESULTS Of the surveyed sample, 41.8% had scores on HADStress that correlate to posttraumatic stress disorder. However, only 34% of the whole sample reported a perceived need to see a psychiatrist, and of those only 45% were open to telepsychiatry. CONCLUSIONS Women, those who were bilingual, and those with positive HADStress status were less likely to accept telepsychiatry; however, this finding did not reach statistical significance. This study reports a partial acceptance of Syrian refugees for telepsychiatric services despite the high prevalence of psychological stress.
Coniosporium epidermidis sp. nov., a new species from human skin

Coniosporium epidermidis sp. nov. is described from a superficial skin lesion with blackish discolouration in an 80-yr-old Chinese patient. The species produces dark, thick-walled, inflated, reluctantly liberating arthroconidia without longitudinal septa. Sequences of the ribosomal operon, as well as of the translation elongation factor 1-α support its novelty. The species is found in a lineage basal to the order Chaetothyriales, amidst relatives from rock, but also species repeatedly isolated from human skin and nails and eventually causing mild cutaneous infections. Coniosporium epidermidis is consistently found on humans, either asymptomatic or symptomatic. The species indicates a change of life style towards human pathogenicity, which is a recurrent type of ecology in derived Chaetothyriales. Superficial and cutaneous infection by melanized fungi is a new category in dermatology.
Toeplitz rectification and DOA estimation with music

The MUSIC method is widely used in the field of DoA estimation using an array of M sensors, and is known to perform well as long as the number of available samples N is much larger than M. Nevertheless, in the scenario where N is of the same order of magnitude than M, its performance degrades, essentially because the sample covariance matrix (SCM) is no more a good estimator. A classical improvement, known as "rectification", consists in forcing the SCM to have a Toeplitz structure. In this paper, we analyze this method, by considering the asymptotic regime where M, N both converge to infinity at the same rate, and by studying consistency and asymptotic normality of the related DoA estimates.
Influence of football match time–motion parameters on recovery time course of muscle damage and jump ability

ABSTRACT We analysed the time course of recovery of creatine kinase (CK) and countermovement jump (CMJ) parameters after a football match, and correlations between changes in these variables and match time–motion parameters (GPS-accelerometry) in 15 U-19 elite male players. Plasma CK and CMJ height (CMJH), average concentric force (CMJCON) and average eccentric force (CMJECC) were assessed 2 h before and 30 min, 24 h and 48 h post-match. There were substantially higher CK levels 30 min, 24 h and 48 h (ES: 0.43, 0.62, 0.40, respectively), post-match. CMJECC (ES: −0.38), CMJH (ES: −0.35) decreased 30 min post, CMJCON (ES: −0.35), CMJECC (ES: −0.35) and CMJH (ES: −1.35) decreased 24 h post, and CMJCON (ES: −0.41) and CMJH (ES: −0.53) decreased 48 h post. We found correlations between distance covered at velocities ≤21 km · h−1 and changes in CK at 24 h (r = 0.56) and at 48 h (r = 0.54) and correlations between CK and distance covered >14 km · h−1 (r = 0.50), accelerations (r = 0.48), and decelerations (r = 0.58) at 48 h. Changes in CMJCON 30 min and 24 h post (both r = −0.68) correlated with impacts >7.1·G. Decelerations >2 m · s−2 correlated with changes CMJCON (r = −0.49) at 48 h and CMJECC (r = −0.47) at 30 min. Our results suggest that match GPS-accelerometry parameters may predict muscle damage and changes in components of neuromuscular performance immediately and 24–48 h post-match.
Experimenting with recursive queries in database and logic programming systems

Abstract This article considers the problem of reasoning on massive amounts of (possibly distributed) data. Presently, existing proposals show some limitations: (i) the quantity of data that can be handled contemporarily is limited, because reasoning is generally carried out in main-memory; (ii) the interaction with external (and independent) Database Management Systems is not trivial and, in several cases, not allowed at all; and (iii) the efficiency of present implementations is still not sufficient for their utilization in complex reasoning tasks involving massive amounts of data. This article provides a contribution in this setting; it presents a new system, called DLVDB, which aims to solve these problems. Moreover, it reports the results of a thorough experimental analysis we have carried out for comparing our system with several state-of-the-art systems (both logic and databases) on some classical deductive problems; the other tested systems are LDL++, XSB, Smodels, and three top-level commercial Database Management Systems. DLVDB significantly outperforms even the commercial database systems on recursive queries.
Hydroquinone: Environmental Pollution, Toxicity, and Microbial Answers

Hydroquinone is a major benzene metabolite, which is a well-known haematotoxic and carcinogenic agent associated with malignancy in occupational environments. Human exposure to hydroquinone can occur by dietary, occupational, and environmental sources. In the environment, hydroquinone showed increased toxicity for aquatic organisms, being less harmful for bacteria and fungi. Recent pieces of evidence showed that hydroquinone is able to enhance carcinogenic risk by generating DNA damage and also to compromise the general immune responses which may contribute to the impaired triggering of the host immune reaction. Hydroquinone bioremediation from natural and contaminated sources can be achieved by the use of a diverse group of microorganisms, ranging from bacteria to fungi, which harbor very complex enzymatic systems able to metabolize hydroquinone either under aerobic or anaerobic conditions. Due to the recent research development on hydroquinone, this review underscores not only the mechanisms of hydroquinone biotransformation and the role of microorganisms and their enzymes in this process, but also its toxicity.
Maternal Transfer and Protective Role of the Alternative Complement Components in Zebrafish Danio rerio

Embryos of most fish develop externally and are exposed to an aquatic environment full of potential pathogens, whereas they have little or only limited ability to mount an efficient and protective response. How fish embryos survive pathogenic attacks remains poorly defined. Here we demonstrate that the maternal immunization of female zebrafish with formalin-killed Aeromonas hydrophila causes a significant increase in C3 and Bf contents in the mother, a corresponding rise in the offspring, and induces a remarkable increase in the hemolytic activities in both the mother and offspring. In addition, the embryos derived from the immunized mother are significantly more tolerant to A. hydrophila challenge than those from the unimmunized fish, and blocking C3 and Bf activities by injection of the antibodies against C3 and Bf into the embryos render them more susceptible to A. hydrophila. These results clearly show that the protection of zebrafish embryos against A. hydrophila can be achieved by the maternally-transferred immunity of the complement system operating via the alternative pathway. This appears to be the first report providing in vivo evidences for the protective role of the alternative complement components in the early embryos of zebrafish, paving the way for insights into the in vivo function of other maternally-transferred factors in fish.
Heterologous Stop Codon Readthrough of Metazoan Readthrough Candidates in Yeast

Recent analysis of genomic signatures in mammals, flies, and worms indicates that functional translational stop codon readthrough is considerably more abundant in metazoa than previously recognized, but this analysis provides only limited clues about the function or mechanism of readthrough. If an mRNA known to be read through in one species is also read through in another, perhaps these questions can be studied in a simpler setting. With this end in mind, we have investigated whether some of the readthrough genes in human, fly, and worm also exhibit readthrough when expressed in S. cerevisiae. We found that readthrough was highest in a gene with a post-stop hexamer known to trigger readthrough, while other metazoan readthrough genes exhibit borderline readthrough in S. cerevisiae.
Outlier-Robust Greedy Pursuit Algorithms in $\ell _{p}$ -Space for Sparse Approximation

Greedy pursuit, which includes matching pursuit (MP) and orthogonal matching pursuit (OMP), is an efficient approach for sparse approximation. However, conventional greedy pursuit algorithms designed for inner product space are not robust against outliers. In this paper, we devise a new definition of correlation in lp-space with p > 0, called lp-correlation, and introduce the concept of orthogonality in lp-space. Based on the lp-correlation and lp-orthogonality, which are generalizations of the absolute inner product and orthogonality of inner product space, respectively, we develop three greedy pursuit algorithms, namely, lp-MP, lp-OMP, and weak lp-MP, for robust sparse approximation in the presence of outliers. The convergence of the three algorithms is proved. In particular, the lp-norm of the residual of each algorithm decays exponentially. It is revealed that the exponential decay factor in the worst case is related to the minimal lp-correlation of the residual and the dictionary. Numerical examples on sparse signal recovery and harmonic retrieval in impulsive noise demonstrate that the lp-greedy pursuit algorithms with are more outlier-resistant than their counterparts in inner product space.
Co-expression of Argonaute2 Enhances Short Hairpin RNA-induced RNA Interference in Xenopus CNS Neurons In Vivo

RNA interference (RNAi) is an evolutionarily conserved mechanism for sequence-specific gene silencing. Recent advances in our understanding of RNAi machinery make it possible to reduce protein expression by introducing short hairpin RNA (shRNA) into cells of many systems, however, the efficacy of RNAi-mediated protein knockdown can be quite variable, especially in intact animals, and this limits its application. We built adaptable molecular tools, pSilencer (pSi) and pReporter (pRe) constructs, to evaluate the impact of different promoters, shRNA structures and overexpression of Ago2, the key enzyme in the RNA-induced silencing complex, on the efficiency of RNAi. The magnitude of RNAi knockdown was evaluated in cultured cells and intact animals by comparing fluorescence intensity levels of GFP, the RNAi target, relative to mCherry, which was not targeted. Co-expression of human Ago2 with shRNA significantly enhanced efficiency of GFP knockdown in cell lines and in neurons of intact Xenopus tadpoles. Human H1- and U6-promotors alone or the U6-promotor with an enhancer element were equally effective at driving GFP knockdown. shRNA derived from the microRNA-30 design (shRNAmir30) enhanced the efficiency of GFP knockdown. Expressing pSi containing Ago2 with shRNA increased knockdown efficiency of an endogenous neuronal protein, the GluR2 subunit of the AMPA receptor, functionally accessed by recording AMPA receptor-mediated spontaneous synaptic currents in Xenopus CNS neurons. Our data suggest that co-expression of Ago2 and shRNA is a simple method to enhance RNAi in intact animals. While morpholino antisense knockdown is effective in Xenopus and Zebrafish, a principle advantage of the RNAi method is the possibility of spatial and temporal control of protein knockdown by use of cell type specific and regulatable pol II promoters to drive shRNA and Ago2. This should extend the application of RNAi to study gene function of intact brain circuits.
Minimizing Internal Speedup for Performance Guaranteed Switches With Optical Fabrics

We consider traffic scheduling in an N times N packet switch with an optical switch fabric, where the fabric requires a reconfiguration overhead to change its switch configurations. To provide 100% throughput with bounded packet delay, a speedup in the switch fabric is necessary to compensate for both the reconfiguration overhead and the inefficiency of the scheduling algorithm. In order to reduce the implementation cost of the switch, we aim at minimizing the required speedup for a given packet delay bound. Conventional Birkhoff-von Neumann traffic matrix decomposition requires N2 - 2N + 2 configurations in the schedule, which lead to a very large packet delay bound. The existing DOUBLE algorithm requires a fixed number of only 2N configurations, but it cannot adjust its schedule according to different switch parameters. In this paper, we first design a generic approach to decompose a traffic matrix into an arbitrary number of Ns (N2 - 2N + 2 > NS > N) configurations. Then, by taking the reconfiguration overhead into account, we formulate a speedup function. Minimizing the speedup function results in an efficient scheduling algorithm ADAPT. We further observe that the algorithmic efficiency of ADAPT can be improved by better utilizing the switch bandwidth. This leads to a more efficient algorithm SRF (scheduling residue first). ADAPT and SRF can automatically adjust the number of configurations in a schedule according to different switch parameters. We show that both algorithms outperform the existing DOUBLE algorithm.
Model checking probabilistic pushdown automata

We consider the model checking problem for probabilistic pushdown automata (pPDA) and properties expressible in various probabilistic logics. We start with properties that can be formulated as instances of a generalized random walk problem. We prove that both qualitative and quantitative model checking for this class of properties and pPDA is decidable. Then, we show that model checking for the qualitative fragment of the logic PCTL and pPDA is also decidable. Moreover, we develop an error-tolerant model checking algorithm for general PCTL and the subclass of stateless pPDA. Finally, we consider the class of properties definable by deterministic Buchi automata, and show that both qualitative and quantitative model checking for pPDA is decidable.