Miracle-dz/UniFAR-FTUs huggingface dataset:
International Journal of General Systems

Codon usage bias reveals the silent molecular evolution pattern. Previous research showed the codon usage bias was associated with many biological processes, such as protein expression level, genetic coding error minimization, mRNA stability, codon context, tRNA richness, CpG suppression, DNA methylation, and tissue or organ speciﬁcity. In this paper we reviewed major methods of codon usage bias measurement. Since most of existing methods are only suitable for the comparison of codon usage bias within a single genome, we introduced a new informatics index, referred to as synonymous codon usage order (SCUO), to measure synonymous codon usage bias within and across genomes. In this method, Shannon informational theory was applied to describe the SCUO of each gene using a value ranging from 0 to 1, with larger values associated with greater codon usage bias. We compared our method with the codon adaptation index (CAI) method for measuring codon bias in Escherichia coli and Sacharomyces cerevisiae . We also studied the correlation between SCUO and CAI, and the relation of SCUO with gene length, gene function, and GC composition. In addition, we explored the correlation between SCUO and mRNA abundance in S. cerevisiae using SAGE expression data. The software package codonO is freely available at http://digbio.missouri. edu/ , wanx/cu/codonO/.
Correlation of the serum cell division cycle 42 with CD4+ T cell subsets and in-hospital mortality in Stanford type B aortic dissection patients

Objective Cell division cycle 42 (CDC42) regulates CD4+ T-cell differentiation and participates in vascular stiffness and atherosclerosis and is involved in the progression of Stanford type B aortic dissection (TBAD). This study aimed to explore the correlation between serum CDC42 level and CD4+ T cell subsets and in-hospital mortality in TBAD patients. Methods Serum CDC42 and peripheral blood T-helper (Th) 1, Th2, and Th17 cells were detected in 127 TBAD patients by enzyme-linked immunosorbent assay and flow cytometry, respectively. Serum CDC42 was also quantified in 30 healthy controls. Results Serum CDC42 was decreased in TBAD patients vs. healthy controls (median [interquartile range (IQR)]: 418.0 (228.0–761.0) pg/ml vs. 992.0 (716.3–1,445.8) pg/ml, P < 0.001). In TBAD patients, serum CDC42 was negatively correlated with Th17 cells (P = 0.001), but not Th1 (P = 0.130) or Th2 cells (P = 0.098). Seven (5.5%) patients experienced in-hospital mortality. Serum CDC42 was reduced in patients who experienced in-hospital mortality vs. those who did not (median (IQR): 191.0 (145.0–345.0) pg/ml vs. 451.5 (298.3–766.8) pg/ml, P = 0.006). By receiver operating characteristic analysis, serum CDC42 showed a good ability for estimating in-hospital mortality [area under curve = 0.809, 95% confidence interval (CI) = 0.662–0.956]. By the multivariate logistic regression analysis, elevated serum CDC42 [odd ratio (OR) = 0.994, 95% CI = 0.998–1.000, P = 0.043] was independently correlated with lower risk of in-hospital mortality, while higher age (OR = 1.157, 95% CI = 1.017–1.316, P = 0.027) was an independent factor for increased risk of in-hospital mortality. Conclusion Serum CDC42 negatively associates with Th17 cells and is independently correlated with decreased in-hospital mortality risk in TBAD patients.
Creek`s Aquaculture Techniques in Rangamati Hill Tracts of Bangladesh

An experiment was conducted in nine suitable (average .10±2 ha) creeks of Rangamati hill tracts Bangladesh viz . , of Langadu, Naniarchar and Sadar Upazila for evaluating growth, survival and production performance of Indian major carps ( Labeo rohita, Catla catla, Cirrhinus mrigala ) in a completely randomized design into three different treatments with three replications for a period of one year. Stocking density, growth, survival was checked periodically and total yield calculated from stocking and harvesting data. A significant spatial variation in specific growth rate (SGR) and yields was found despite uniform stocking densities, attributable to variation in environmental parameters. Among the results rohu was found to have comparatively higher SGR of 1.51±0.55 in Naniarchar where as langadu creek was reported with higher SGR of 1.46±0.94, 1.57±0.41 and 1.46 ±. 64 for rohu catla, and mrigal. Rangamati sadar Upazilla creek was found to be conducive to Catla with a SGR of 1.55±. 78. In general, higher gross and net productions were reported from Original Research Article Sadar Upazilla, Langadu and Naniarchar creeks, suggestive of its suitability for developing creeks aquaculture technology. However research findings will help the community of Chittagong hill tracts by giving appropriate technology for sustainable fish production in creeks.
A Multi-decadal Rock Magnetic Record of Monsoonal Variations During the Past 3,700 Years from a Tropical Indian Tank

We have explored the potentia1 of using magnetic susceptibility( χ if ) as a proxy for past rainfall variations in a tropical region, and also the potentia1 of tank-bed sediments from Southern India as a paleoarchive The 3,700-year rock magnetic record from Thimmannanayakanakere (14°12 N, 76°24 E), a smaH tank near Chitradurga town, Karnataka, exhibits considerable fluctudtions in χ if Discountlng the possibilitestres of magnetite from biogenic and anthropogenic sources and of dissolutio of magnetic minerals, the χ if signal must be related principally to rainfall in the tank-catchment There is a good correlation of χ if with instrumental rainfall data (r = 0 65 for Peninsular India, r = 0 45 for Chitradurga Stationa)n d histoncally recorded rainfall events Presuming that χ if variations are produced mainly by rainfall variations and that there was no signtficant human impact in the catchment and no slumping or bioturbatio of sediments we have reconstructed the paleorainfall profile for thc last 3,700 years for Chitradurga region The profile is chronologically constrained by two I4c dates Several events of drought and high rainfall, and onset of aridity are corretatable with similar events documented in speleothems from chfferent parts of india, a tree-ring from western India and lake sediments from Rajasthan We have thus shown that χ if 1s a proxy for rainfall in tropical regions and that tank-bed sediments from tropical lndia are an important archive of paleorainfall/paleoclimate data.
The Influence of Physical Education Over A Semester on the Psycho-Physical Development in Elementary School Students

Study purpose. The aim of this study was to determine the impact of the physical education program over a semester on physical fitness, sport-specific skills (football and basketball) and the quality of life in elementary school students (7th and 8th grade). Materials and methods. 128 students (64 boys and 64 girls) from three elementary schools, aged 13‒14, participated in the study. A battery of five diagnostic tests was used to assess physical fitness: Modified Agility “T” test, Illinois Agility Run Test, 10x5 Shuttle Run Test, Standing Balance Test and 2-Minute Step in Place Test. Training polygons with elements of sports were used to assess football and basketball skills. Determining the level of quality of life was carried out with a pediatric quality of life questionnaire (Pediatric Quality of Life Inventory TM – PedsQL). Results. The study found statistically significant improvements in the results of most physical fitness tests in all team sports on training polygons, as well as in the level of quality of life for both boys and girls in both grades. Conclusion. It can be concluded that the physical education program was well organized and implemented and thus had a positive effect on improving the psycho-physical status of students.
Working Papers Department of Economics University of Vienna

This paper studies the driving forces behind the considerable expansion of the underground economy during the late 1990s. I propose a novel explanation for this phenomenon: the sharp increase in market competition worldwide, which reduces prices and profits and drives firms into the shadow economy. Empirical evidence from a panel covering 42 countries from 1995 to 2000 shows that increased competition is indeed correlated with an expansion of the underground economy. The effect is weaker in high-income, high-tax, low-corruption countries that provide public services which make it worthwhile for firms to operate in the official economy despite growing competitive pressure.
Improving force resultant model for anchors in clays from large deformation finite element analysis

Abstract This paper presents an improved plasticity force-resultant model for anchors deeply embedded in clays, developed from large deformation finite element analyses. The current available force-resultant models for anchors are mainly developed from small strain finite element analysis while experimental approach has not been used due to technical challenges. The advantage of large deformation finite element analysis is that it provides much more data points to fit the yield surface than small strain finite element analysis, in addition to avoiding excess mesh distortion problems. Furthermore, the flow rule or normality can be effectively checked in the large deformation finite element analysis and further used to improve the fitting quality. After validated against retrospective simulations, the better performance of the developed plasticity force-resultant model is demonstrated by comparing with available experimental observations from centrifuge test.
Investigation of Guayule's Agronomic Performance and Agro-processing in South Africa

ii DECLARATION . iv ACKNOWLEDGEMENTS . v DEDICATION . vii LIST OF FIGURES . viii LIST OF TABLES . xii ABBREVIATIONS . xiii Chapter 1: Literature Review . 1 1.
Contractivity of Distributed Optimization and Nash Seeking Dynamics

In this letter, we study distributed optimization and Nash equilibrium-seeking dynamics from a contraction theoretic perspective. Our first result is a novel bound on the logarithmic norm of saddle matrices. Second, for distributed gradient flows based upon incidence and Laplacian constraints over arbitrary topologies, we establish strong contractivity over an appropriate invariant vector subspace. Third, we give sufficient conditions for strong contractivity in pseudogradient and best response games with complete information, show the equivalence of these conditions, and consider the special case of aggregative games.
Complementarity and Nondegeneracy in Semide(cid:12)nite Programming (cid:3)

Primal and dual nondegeneracy conditions are de(cid:12)ned for semidefinite programming. Given the existence of primal and dual solutions, it is shown that primal nondegeneracy implies a unique dual solution and that dual nondegeneracy implies a unique primal solution. The converses hold if strict complementarity is assumed. Primal and dual nondegeneracy assumptions do not imply strict complementarity, as they do in LP. The primal and dual nondegeneracy assumptions imply a range of possible ranks for primal and dual solutions X and Z. This is in contrast with LP where nondegeneracy assumptions exactly determine the number of variables which are zero. It is shown that primal and dual nondegeneracy and strict complementarity all hold generically. Numerical experiments suggest probability distributions for the ranks of X and Z which are consistent with the nondegeneracy conditions.
Challenges and Prospects of E-learning at the National Open University of Nigeria

This descriptive survey using a questionnaire investigated the challenges and prospects of e-learning at the National Open University of Nigeria (NOUN). The sample for the study consisted of 250 students randomly selected from five faculties at NOUN’s Akure Study Centre, with 50 students randomly selected from each faculty. The questionnaire was validated by experts in computer science education, educational technology and tests and measurement. Findings revealed that challenges included lack of enough computers, shortage of Internet facilities, students’ lack of access to elearning facilities and tools, high cost of software and erratic power supply (a major challenge), while prospects included promoting distance learning, extending the frontiers of knowledge, eradicating eilliteracy, and making education more effective. Recommendations were, among others, that an enabling environment for e-learning should be ensured, assurance of a constant power supply, education stakeholders should ensure procurement of requisite information and communication technology (ICT) equipment and make it available for students’ use, with maintenance and upgrading as the need arises. Finally, the study revealed that the e-learning influences students’ ICT competence.
Advance in Bioaerosol Removal Technologies; A Review

Bioaerosols are air pollutants that affect human health in various routes. They are characteristically diverse; such as bacteria, viruses and fungi, that everyone has different characteristics and effects, various solutions and technologies are studied or applied for their removal and inactivation. Regarding to lack of specific and integrated publications about the different air quality guidelines for bioaerosols and the methods and technologies, attending to approach the standards, purpose of this study was set on the development of the issue. The importance of presence of bioaerosols in breathing air and related standards and guidelines, also controlling technologies such as filtration, ultraviolet (UV) radiation, photo catalyst, temperature and electrostatic precipitators were surveyed in this study by using the scientific literature.Given the results, UV irradiation and photocatalytic methods are ineffective for allergens. In this way, filtration is unable for inactivation of the bioaerosols, then there is the threat that they can aerosolize again. Hence, these technologies individually cannot provide the air quality standards which have established for sensitive conditions such as operation rooms. Regarding the discussions, application of the methods that include collection and inactivation of the bioaerosols simultaneously, such as electrostatic precipitators, could be more effective in the likewise environments.
Recursive Compositional Models for Vision : Description and Review of Recent Work Long (

This paper describes and reviews a class of hierarchical probabilistic models of images and objects. Visual structures are represented in a hierarchical form where complex structures are composed of more elementary structures following a design principle of recursive composition. Probabilities are defined over these structures which exploit properties of the hierarchy—e.g. long range spatial relationships can be represented by local potentials at the upper levels of the hierarchy. The compositional nature of this representation enables efficient learning and inference algorithms. In particular, parts can be shared between different object models. Overall the architecture of Recursive Compositional Models (RCMs) provides a balance between statistical and computational complexity. The goal of this paper is to describe the basic ideas and common themes of RCMs, to illustrate their success on a range of vision tasks, and to gives pointers to the literature. In particular, we show that RCMs generally give state of the art results when applied to a range of different vision tasks and evaluated on the leading benchmarked datasets.
Cerberus: The Power of Choices in Datacenter Topology Design

CHEN GRINER, School of Electrical and Computer Engineering, Ben Gurion University of the Negev, Israel JOHANNES ZERWAS, Technical University of Munich, Germany ANDREAS BLENK, Technical University of Munich, Germany MANYA GHOBADI, Computer Science and Artificial Intelligence Laboratory, MIT, USA STEFAN SCHMID, Faculty of Computer Science, University of Vienna, Austria CHEN AVIN, School of Electrical and Computer Engineering, Ben Gurion University of the Negev, Israel
Excursions of Interhemispheric Field‐Aligned Currents in Africa

The interhemispheric field‐aligned currents (IHFACs) are the most evident currents connecting the solar quiet (Sq) current systems in the Northern and Southern Hemispheres. Understanding these coupling currents has practical importance for space weather forecast of the magnetosphere‐ionosphere interactions and their potential impacts on low‐orbiting spacecraft. In this paper, we have examined digital magnetic records from September 2008 to August 2009 at nine Magnetic Data Acquisition System (MAGDAS) stations in order to uniquely determine the variability of IHFACs in terms of their excursions in the African sector. By excursions, we mean the direction in which the IHFACs are moving as a function of local time or latitude. Different from theoretical prediction, we found prominent positive IHFACs around dusk in February and March equinox. A novel feature of this study is the semidiurnal variation control of the coupling between the Northern and Southern Hemispheres. In addition, we found terdiurnal variation in September with their associated strong diurnal variations from October through December. Quite unexpectedly, in January, a significant latitudinal depletion in the intensities of IHFACs was observed from dawn to dusk, compared to any other months under investigation, accompanied with a marked reduction of the prominent diurnal variations at the magnetic equator (Addis Ababa, AAB). The fact that the excursions of IHFACs in January experience an unusual retardation with respect to their intensities points to a relation with the effects of sudden stratospheric warming.
Improving abstract interpretations by combining domains

In this paper we consider static analyses based on abstract interpretation of logic programs over combined domains. It is known that analyses over combined domains potentially provide more information than obtainable by performing the independent abstract interpretations. However, the construction of a combined analysis often requires redefining the basic operations for the combined domain. We demonstrate for logic programs that in practice it is possible to obtain precision in a combined analysis without redefining the basic operations. We also propose a way of performing the combination which can be more precise than the straightforward application of the classical “reduced product” approach, while keeping the original components of the basic operations. The advantage of the approach is that proofs of correctness for the new domains are not required and implementations can be reused. We illustrate our results by showing that a combined sharing analysis—constructed from “old” proposals—compares well with other “new” proposals suggested in recent literature both from the point of view of efficiency and accuracy.
RandomMix: A mixed sample data augmentation method with multiple mixed modes

Data augmentation is a very practical technique that can be used to improve the generalization ability of neural networks and prevent overﬁtting. Recently, mixed sample data augmentation has received a lot of attention and achieved great success. In order to enhance the performance of mixed sample data augmentation, a series of recent works are devoted to obtaining and analyzing the salient regions of the image, and using the saliency area to guide the image mixing. However, obtaining the salient information of an image requires a lot of extra calculations. Different from improving performance through saliency analysis, our proposed method RandomMix mainly increases the diversity of the mixed sample to enhance the generalization ability and performance of neural networks. Moreover, RandomMix can improve the robustness of the model, does not require too much additional calculation, and is easy to insert into the training pipeline. Finally, experiments on the CIFAR-10/100, Tiny-ImageNet, ImageNet, and Google Speech Commands datasets demonstrate that RandomMix achieves better performance than other state-of-the-art mixed sample data augmentation meth-ods.
DISTRIBUTIONAL CLUSTERING OF WORDS FOR TEXT CATEGORIZATION RESEARCH THESIS SUBMITTED IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE IN COMPUTER SCIENCE RON BEKKERMAN

We study an approach to text categorization that combines distributional clustering of words and a Support Vector Machine (SVM) classifier. The word-cluster representation is computed using the recently introduced Information Bottleneck method, which generates a compact and efficient representation of documents. When combined with the classification power of the SVM, this method yields high performance in text categorization. We compare this technique with SVM-based categorization using the simple minded bag-of-words (BOW) representation. The comparison is performed over three known datasets. On one of these datasets (the 20 Newsgroups) the method that is based on word clusters significantly outperforms the word-based representation in terms of categorization accuracy or representation efficiency. On the two other sets (Reuters-21578 and WebKB) the word-based representation slightly outperforms the word-cluster representation. We investigate the potential reasons for this behavior.
Complex Near‐Surface Rheology Inferred From the Response of Greater Tokyo to Strong Ground Motions

Strong ground motion can induce dynamic strains large enough for the Earth's subsurface to respond nonlinearly and to cause permanent, or plastic, damage. The 2011 Mw 9.0 Tohoku‐Oki earthquake, Japan, generated exceptional and well‐recorded ground motions in the greater Tokyo area. We use continuous records from 234 stations of the dense MeSO‐net seismic network to monitor the temporal evolution of the material properties of the shallow subsurface (upper ∼100 m). We apply the single‐station cross‐correlation method to reconstruct the near‐surface reflectivity response through time. We find that the strong ground motions from the mainshock caused large perturbations in the near‐surface structure, with significant drops in seismic velocities up to 11%. For most sites, we observe a logarithmic and complete recovery of the seismic wave speed, suggesting a relaxation process that can be explained by a viscoelastic rheology. Some sites exhibit an instantaneous and permanent change, which suggests a plastic rheology. Finally, dense seismic measurements allow for statistical inference between seismic velocity drops, recovery time scales, and permanent perturbations and ground motion strength and site conditions. This study highlights the potential for seismic interferometry to assess near‐surface rheology with dense seismic arrays.
@ CMU

The amount of labeled training data required for image interpretation tasks is a major drawback of current methods. How can we use the gigantic collection of unlabeled images available on the web to aid these tasks? In this paper, we present a simple approach based on the notion of patch-based context to extract useful priors for regions within a query image from a large collection of (6 million) unlabeled images. This contextual prior over image classes acts as a non-redundant complimentary source of knowledge that helps in disambiguating the confusions within the predictions of local region-level features. We demonstrate our approach on the challenging tasks of region classiﬁcation and surface-layout estimation.