Miracle-dz/UniFAR-FTUs huggingface dataset:
Inference of a genetic network by a combined approach of cluster analysis and graphical Gaussian modeling

MOTIVATION Recent advances in DNA microarray technologies have made it possible to measure the expression levels of thousands of genes simultaneously under different conditions. The data obtained by microarray analyses are called expression profile data. One type of important information underlying the expression profile data is the 'genetic network,' that is, the regulatory network among genes. Graphical Gaussian Modeling (GGM) is a widely utilized method to infer or test relationships among a plural of variables. RESULTS In this study, we developed a method combining the cluster analysis with GGM for the inference of the genetic network from the expression profile data. The expression profile data of 2467 Saccharomyces cerevisiae genes measured under 79 different conditions (Eisen et al., PROC: Natl Acad. Sci. USA, 95, 14683-14868, 1998) were used for this study. At first, the 2467 genes were classified into 34 clusters by a cluster analysis, as a preprocessing for GGM. Then, the expression levels of the genes in each cluster were averaged for each condition. The averaged expression profile data of 34 clusters were subjected to GGM, and a partial correlation coefficient matrix was obtained as a model of the genetic network of S. cerevisiae. The accuracy of the inferred network was examined by the agreement of our results with the cumulative results of experimental studies.
[Readthrough of nonsense mutation W822X in the SCN5A gene can effectively restore expression of cardiac Na+ channels W822X].

OBJECTIVE In this study we investigated the functional restoration of nonsense mutations in the SCN5A gene. METHODS The readthrough-enhancing reagents were introduced to HEK293 cells to suppress one nonsense mutation W822X in the SCN5A gene. Patch-clamp was used to record the whole-cell current and dynamics. Western blot and immunofluorescence staining were used to certify the expression and the location of the sodium channel. RESULTS In transfected HEK293 cells, the nonsense mutation in SCN5A inhibited the expression level of full-length protein, and the sodium currents from the mutant channels were less than 3% of the wild-type level. Readthrough enhancement by decreasing translation termination efficiency with a siRNA targeting eukaryotic release factor eRF3a (a GTPase that binds eRF1), the sodium current from the mutant cDNAs was restored to as much as 30% of the wild-type. After the treatment by the readthrough-enhancing reagents, the channels from cDNA carrying W822X remained the features of wild-type phenotype, and Western blot and immunochemical staining also showed the expression of full-length channel proteins. CONCLUSION Readthrough-enhancing reagents could effectively suppress nonsense mutations in SCN5A and partially restore the function of sodium channel and the expression of full-length channels.
Study of orbitally excited B mesons and evidence for a new Bπ resonance

Using the full CDF Run II data sample, we report evidence for a new resonance, which we refer to as B(5970), found simultaneously in the B0π+ and B+π− mass distributions with a significance of 4.4 standard deviations. We further report the first study of resonances consistent with orbitally excited B+ mesons and an updated measurement of the properties of orbitally excited B0 and B0s mesons. We measure the masses and widths of all states, as well as the relative production rates of the B1, B∗2, and B(5970) states and the branching fraction of the B*0s2 state to either B*+K− and B+K−. Furthermore, we measure the production rates of the orbitally excited B0,+ states relative to the B0,+ ground state. The masses of the new B(5970) resonances are 5978±5(stat)±12(syst) MeV/c2 for the neutral state and 5961±5(stat)±12(syst) MeV/c2 for the charged state, assuming that the resonance decays into Bπ final states. The properties of the orbitally excited and the new B(5970)0,+ states are compatible with isospin symmetry.
A Wearable Fabric Computer by Planar-Fashionable Circuit Board Technique

A method to fabricate circuits on the cloth, planar fashionable circuit board (P-FCB), is proposed. And its applications such as fabric passive elements, user I/O interface, and the fabric package are introduced. The electrical and the mechanical characteristic analysis of P-FCB and the system integration methodology establishment improve the system performance and productivity. A complete wearable system is implemented by P-FCB technology for the continuous sweat monitoring and the RFID tag antenna applications.
A New Framework for Reconstruction of Images from Boundaries

The problem of reconstructing images from boundaries has been studied in the literature chiefly as one based on the information from zero crossings. In contrast, we formulate the problem within the framework of approximation theory, and we propose a representation scheme involving (i) the points arbitrarily near the boundaries and (ii) the gradient information at these points. We show that the representation scheme is complete and stable under reasonable conditions. Further, we develop an efficient reconstruction mechanism, using the concept of a regularized solution, in which we penalize a candidate solution in proportion to its departure from a model which resembles the original in shape but is simple to construct. Finally, we demonstrate the effectiveness of the cost functional with the help of experimental results, using a representation in which the number of data points is much less than the number of pixels in the original image.
Adaptive robust optimal reactive power dispatch in distribution networks

It is increasing popular to integrate distributed generation (DG) into distribution systems, the traditional optimal reactive power dispatch approach is no longer able to cope with it. The robust optimization (RO) theory is introduced to deal with the uncertainty of large-scale DGs. Adaptive robust optimal reactive power dispatch (AR-OPRD) is proposed to reduce the conservation of RO. An adaptive function is constructed to derive the relationship between the optimal reactive power output and active power output of an arbitrary DG. A new cutting plane algorithm is introduced to solve AR-ORPD mathematical model efficiently. In this paper, examples have been used to demonstrate the validity and effectiveness of the method.
A Comparative Molecular Dynamics Study of Thermophilic and Mesophilic Ribonuclease HI Enzymes

Abstract We studied a pair of homologous thermophilic and mesophilic ribonuclease HI enzymes by molecular dynamics simulations. Each protein was subjected to three 5 ns simulations in explicit water at both 310 K and 340 K. The thermophilic enzyme showed larger overall positional fluctuations at both temperatures, while only the mesophilic enzyme at the higher temperature showed significant instability. When the temperature is changed, the relative flexibility of different local segments on the two proteins changed differently. Principal component analysis showed that the simulations of the two proteins explored largely overlapping regions in the conformational space. However, at 340 K, the collective structure variations of the thermophilic protein are different from those of the mesophilic protein. Our results, although not in accordance with the view that hyperthermostability of proteins may originate from their conformational rigidity, are consistent with several recent experimental and simulation studies which showed that thermophilic proteins may be conformationally more flexible than their mesophilic counterparts. The decorrelation between conformational rigidity and hyperthermostability may be attributed to the temperature dependence and long range nature of electrostatic interactions that play more important roles in the structural stability of thermophilic proteins.
Information theoretic clustering used for two items loan management system

Clustering is an effective machine learning method for classification and decision making. This paper builds a system model for loan management and incorporates the information clustering algorithm into this system. This clustering algorithm describes the cluster memberships with a non-parametric mutual information estimate between cluster assignment and data distribution. It can improve the classification accuracy and efficiency.
Gene Expression Profiles Associated with Pediatric Relapsed AML

Development of relapse remains a problem for further improvements in the survival of pediatric AML patients. While virtually all patients show a good response to initial treatment, more patients respond poorly when treated at relapse. The cellular characteristics of leukemic blast cells that allow survival of initial treatment, relapse development and subsequent resistance to salvage treatment remain largely elusive. Therefore, we studied if leukemic blasts at relapse biologically resemble their initial diagnosis counterparts. We performed microarray gene expression profiling on paired initial and relapse samples of 23 pediatric AML patients. In 11 out of 23 patients, gene expression profiles of initial and corresponding relapse samples end up in different clusters in unsupervised analysis, indicating altered gene expression profiles. In addition, shifts in type I/II mutational status were found in 5 of these 11 patients, while shifts were found in 3 of the remaining 12 patients. Although differentially expressed genes varied between patients, they were commonly related to hematopoietic differentiation, encompassed genes involved in chromatin remodeling and showed associations with similar transcription factors. The top five were CEBPA, GFI1, SATB1, KLF2 and TBP. In conclusion, the leukemic blasts at relapse are biologically different from their diagnosis counterparts. These differences may be exploited for further development of novel treatment strategies.
Cognitive Decline and Literacy Among Ethnically Diverse Elders

Researchers on genetic and environmental influences on risk for Alzheimer’s disease must be prepared for the growing ethnic and racial diversity of our participants. Within the investigation, years of education has typically served as a proxy for cognitive reserve, which may be one factor in influencing risk of cognitive decline among aging people. However, among ethnic minorities, years of education is a poor reflection of the value of educational experience and native ability. This study was conducted among 1002 ethnically diverse English-speaking residents of Northern Manhattan who were cognitively and functionally normal at a baseline evaluation. We found that literacy level was a better predictor of decline in memory, executive function, and language skills than was years of education. The results of this study suggest that in an ethnically diverse cohort, literacy level should be considered as a mediator of the interactions of biological and environmental factors on cognitive decline.
Design Maintenance in Process Eco-Systems

This paper addresses the problem of managing business process changes at the design level within a complex business process repository. We argue that a formal process eco-systems view can provide a particular useful solution to the problem in which their inter-process relationships can be properly described. Our intent is to build a modular infrastructure to support change management in process eco-systems by leveraging a change propagation approach that would maintain the inter-process relationships. This permits us to propagate the changes, made on a particular process, to the rest of the processes for maintaining the relationship equilibrium of such eco-system. Our experimental evaluation suggests that the propagation of change can be efficiently achieved, which suggests that the real source of complexity stems from the redesign of individual models.
The relationship between exposure to alcohol advertising in stores, owning alcohol promotional items, and adolescent alcohol use.

AIM This paper describes adolescents' exposure to alcohol advertising in stores and to alcohol-branded promotional items and their association with self-reported drinking. METHODS A cross-sectional survey was administered in non-tracked required courses to sixth, seventh, and eighth graders (n = 2125) in three California middle schools. Logistic regressions compared the odds of ever (vs. never) drinking and current (vs. ever) drinking after controlling for psychosocial and other risk factors for adolescent alcohol use. RESULTS Two-thirds of middle school students reported at least weekly visits to liquor, convenience, or small grocery stores where alcohol advertising is widespread. Such exposure was associated with higher odds of ever drinking, but was not associated with current drinking. One-fifth of students reported owning at least one alcohol promotional item. These students were three times more likely to have ever tried drinking and 1.5 times more likely to report current drinking than students without such items. CONCLUSIONS This study provides clear evidence of an association of adolescent drinking with weekly exposure to alcohol advertising in stores and with ownership of alcohol promotional items. Given their potential influence on adolescent drinking behaviour, retail ads, and promotional items for alcohol deserve further study.
AUTOMATED SPEECH SYNTHESIZER AND CONVERTER IN CUE SYMBOL GENERATION FOR HEARING IMPARDS

For the interaction of normally speaking personals with hearing impards the communication gap leads to a non-interactive medium for the two communicator. To develop a communication approach in this paper we propose a medium for the conversion of speech signal to visual cue symbols by automatically synthesizing the given speech signal and mapping to cue symbols for visual representation. The developed system is focused with the objective of reducing the communication gap between normal people and vocally disabled. Humans know each other by conveying their ideas, thoughts, and experiences to the people around them. There are numerous ways to achieve this and the best one among the rest is the gift of "Speech". Through speech everyone can very convincingly transfer their thoughts and Understand each other. It will be injustice if we ignore those who are deprived of this invaluable gift. The only means of communication available to the vocally disabled is the use of "Sign Language". Using sign language they are limited to their own world. This limitation prevents them from interacting with the outer world to share their feelings, creative ideas and Potentials. Very few people who are not themselves deaf ever learn to Sign language. These limitation increases the isolation of deaf and dumb people from the common society. Technology is one way to remove this hindrance and benefit these people. Several researchers have explored these possibilities and have successfully achieved finger spelling recognition with high levels of accuracy. But progress in the recognition of sign language, as a whole has various limitations in today's applications.
The Bacterial Two-Hybrid System Uncovers the Involvement of Acetylation in Regulating of Lrp Activity in Salmonella Typhimurium

N𝜀-lysine acetylation is an abundant and important Post-translational modification in bacteria. We used the bacterial two-hybrid system to screen the genome library of the Salmonella Typhimurium to identify potential proteins involved in acetyltransferase Pat – or deacetylase CobB-mediated acetylation. Then, the in vitro (de)acetylation assays were used to validate the potential targets, such as STM14_1074, NrdF, RhaR. Lrp, a leucine-responsive regulatory protein and global regulator, was shown to interact with Pat. We further demonstrate that Lrp could be acetylated by Pat and deacetylated by NAD+-dependent CobB in vitro. Specifically, the conserved lysine residue 36 (K36) in helix-turn-helix (HTH) DNA-binding domain of Lrp was acetylated. Acetylation of K36 impaired the function of Lrp through altering the affinity with the target promoter. The mutation of K36 in chromosome mimicking acetylation enhanced the transcriptional level of itself and attenuated the mRNA levels of Lrp-regulated genes including fimA, which was confirmed by yeast agglutination assay. These findings demonstrate that the acetylation regulates the DNA-binding activity of Lrp, suggesting that acetylation modification of transcription factors is a conserved regulatory manner to modulate gene expression in bacteria and eukaryotes.
BEM CİNSİYET ROLÜ ENVANTERİNİN GEÇERLİK VE GÜVENİRLİK ÇALIŞMASI

This study explores the validity and reliability of the masculinity and femininity measures of Bem Sex-Role Inventory. In order to determine the validity and reliability of this inventory, we worked with 100 subjects consisting of the students of the Faculty of Languages and History-Geography, Ankara University, and the results are evaluated.
Population differentiation of the African cyprinid Barbus neumayeri across dissolved oxygen regimes

Population level response to hypoxia has become an issue of global significance because of increased frequency and intensity of hypoxic events worldwide, and the potential for global warming to exacerbate hypoxic stress. In this study, we sequenced two nuclear intronic regions and a single mitochondrial region across seven populations of the African cyprinid, Barbus neumayeri from two river drainages in Uganda: the Rwembaita Swamp-Njuguta River System and the Dura River. We then examined two indices of population structure, GST and Jost's D, to detect links between oxygen availability and genetic variation and to determine if population genetic structure was associated with (i) dissolved oxygen regime (hypoxia or normoxia), (ii) geographical distance, or (iii) a combination of dissolved oxygen regime and geographical distance. Our results indicate that over a large scale (between drainages), geographical distance significantly affects the genetic structure of populations. However, within a single drainage, dissolved oxygen regime plays a key role in determining the genetic structure of populations. Within the Rwembaita-Njuguta system, gene flow was high between locations of similar oxygen regimes, but low between areas characterized by divergent oxygen regimes. Interestingly, GST analyses appear to yield less realistic measures of population structure than Jost's D, suggesting that caution must be taken when interpreting and comparing the results from different studies. These results support the idea that aquatic dissolved oxygen can act as a selective force limiting gene flow among populations of aquatic species and therefore should be considered when implementing conservation plans and assessing environmental impact of human activities.
A GPS-Free Wireless Mesh Network Localization Approach

Wireless Mesh Networks (WMN) is a new type of wireless access network that combines the advantages of Wireless Local Area Networks (WLAN) with those of Mobile Ad hoc networks (MANET). The localization of mobile nodes in WMN has not been paid much attention as of yet in comparison with that of WLAN and MANET. As an essential component of user mobility support, localization in WMN should be more accurate in order to meet the need of mobile users in WMN. In this paper, we propose a Ring Overlapping based Localization algorithm (ROL) that is based on Subtle Partial Range Aware (SPRA) distance measurement method. The experiments show that our new algorithms receive better results than existing methods and can reduce localization error within 3 meters in buildings.
Gastrointestinal tract morphological alteration by unpleasant physical treatment and modulating role of Lactobacillus in broilers

1. An experiment was conducted to determine the effects of supposedly unpleasant physical treatment on broiler performance, small intestinal development and ameliorating role of probiotics. 2. The following treatments were applied from day one: (1) chicks exposed to normal human contact fed basal diet (control); (2) chicks were exposed to unpleasant physical treatment and fed basal diet (UPT-BD); and (3) chicks were exposed to unpleasant physical treatment and fed basal diet supplemented with Lactobacillus (UPT-BDL). Chicks were exposed to UPT from days 1 to 21. Different segments of gastrointestinal tract were sampled at 14, 28, 35 and 42 d of age. 3. Broilers of UPT-BD had lower feed consumption compared with control group at 7 d of age. Overall, UPT-BDL birds showed higher body weight gain (BWG) and better feed conversion ratio (FCR) over the course of the experiment. 4. Birds of UPT-BD had lower concentrations of lactic, propionic and butyric acids in the caecum as compared with other groups at 14 d of age. Acetic acid concentration was profoundly decreased in both UPT groups compared to the control. 5. Duodenal villus height of UPT-BD broilers showed a slight reduction compared to the control and UPT-BDL birds at 14 d of age. Afterwards until day 42, UPT-BDL birds showed the highest villus height among treatments in different parts of the small intestine. 6. The results suggested that, even though UPT did not have significant inhibitory effects on the development of the small intestine and broiler performance, it negatively affected bacterial metabolic end products in the caecum, which could be ameliorated by the addition of Lactobacillus.
Positioning of an inchworm type actuator with five degrees of freedom

We previously proposed many micro actuators consisted of piezoelectric elements (piezo) and electromagnets. These micro actuators realized small displacement in unlimited working area by the principle of an inchworm. One of these micro actuators is a self-propelled Stewart platform. It moves in the three linear and rotational directions. However, the tilt angle of the stage was very small. In this paper, we proposed the actuator with five degrees of freedom consisted of six piezos and six electromagnets. Its structure is similar to a cyclohexane structure. The actuator proposed can be operated two modes. One is a stage motion mode, and the other is a self-propelled motion mode. In the stage motion mode, three bottom electromagnets are excited and the stage moves by the principle of an inchworm. In the self-propelled motion mode, three top electromagnets are excited and the actuator moves by the principle of an inchworm. Step displacement both in the self-propelled motion mode and in the stage motion mode is described. Moving speed and positioning are also discussed.
Random-shapelet: An algorithm for fast shapelet discovery

Time series shapelets proposes an approach to extract subsequences most suitable to discriminate time series belonging to distinct classes. Computational complexity is the major issue with shapelets: the time required to identify interesting subsequences can be intractable for large cases. In fact, it is required to evaluate all the subsequences of all the time series of the training dataset. In the literature, improvements have been proposed to accelerate the process, but few provide a solution that dramatically reduces the time required to find a solution. We propose a random-based approach that reduces the time necessary to find a solution, in our experimentation until 3 orders of magnitude compared to the original method. Based on extensive experimentations on several data sets from the literature, we show that even with a few time available, random-shapelet algorithm is able to find very competitive shapelets.