Miracle-dz/UniFAR-FTUs huggingface dataset:
A Biologically Consistent Model for Comparing Molecular Phylogenies

In the framework of the problem of combining different gene trees into a unique species phylogeny, a model for duplication/speciation/loss events along the evolutionary tree is introduced. The model is employed for embedding a phylogeny tree into another one via the so-called duplication/speciation principle requiring that the gene duplicated evolves in such a way that any of the contemporary species involved bears only one of the gene copies diverged. The number of biologically meaningful elements in the embedding result (duplications, losses, information gaps) is considered a (asymmetric) dissimilarity measure between the trees. The model duplication concept is compared with that one defined previously in terms of a mapping procedure for the trees. A graph-theoretic reformulation of the measure is derived.
Information preservation in static index pruning

We develop a new static index pruning criterion based on the notion of information preservation. This idea is motivated by the fact that model degeneration, as does static index pruning, inevitably reduces the predictive power of the resulting model. We model this loss in predictive power using conditional entropy and show that the decision in static index pruning can therefore be optimized to preserve information as much as possible. We evaluated the proposed approach on three different test corpora, and the result shows that our approach is comparable in retrieval performance to state-of-the-art methods. When efficiency is of concern, our method has some advantages over the reference methods and is therefore suggested in Web retrieval settings.
The impact of betweenness in small world networks on request for proposal coalition formation problems

The analysis of societies demonstrates the recurrent nature of small world topology in the interactions of elements in such worlds. The small world topology proves to have beneficial properties for system's performance in many cases, however there are also scenarios where the small world topology's properties negatively affect the system's outcome; thus in depth knowledge on the small world weaknesses is needed in order to develop new generations of artificial societies and new models of economic systems. In this paper, a multi-agent system based on request for proposal protocol and coalition formation organisational paradigm is used to analyse properties of small world social networks of agents. Experiments center on nodes in the network with high betweenness and in particular the distribution of agents in the population across these nodes. Results show that small world topology scenarios lose their beneficial properties when non-competitive agents are positioned as high betweeness nodes in the network.
Convergent Reinforcement Learning with Value Function Interpolation

We consider the convergence of a class of reinforcement learning algorithms combined with value function interpolation methods using the methods developed in (Littman & Szepesvari, 1996). As a special case of the obtained general results, for the first time, we prove the (almost sure) convergence of Qlearning when combined with value function interpolation in uncountable spaces.
Rainfall Patterns and U.S. Migration from Rural Mexico

In many rural regions of developing countries, natural resource dependency means changes in climate patterns hold tremendous potential to impact livelihoods. When environmentally-based livelihood options are constrained, migration can become an important adaptive strategy. Using data from the Mexican Migration Project, we model U.S. emigration from rural communities as related to community, household and climate factors. The results suggest that households subjected to very recent drought conditions are less likely to send a U.S. migrant, but in communities with drought two years prior and with strong migration histories, emigration is much more likely. In regions lacking such social networks, rainfall deficits actually reduce migration propensities, perhaps reflecting constraints in the ability to engage in migration as a coping strategy. Policy implications emphasize diversification of rural Mexican livelihoods in the face of contemporary climate change.
Comparative immunomodulatory properties of adipose‐derived mesenchymal stem cells conditioned media from BALB/c, C57BL/6, and DBA mouse strains

Adipose tissue‐derived mesenchymal stem cells (AD‐MSCs) have been shown to be capable of differentiating into multiple cell type and exert immunomodulatory effects. Since the selection of ideal stem cell is apparently crucial for the outcome of experimental stem cell therapies, therefore, in this study we compared AD‐MSCs conditioned media (CM) from BALB/c, C57BL/6, and DBA mouse strains. No significant difference was found in the morphology, cell surface markers, in vitro differentiation and proliferation potentials of AD‐MSCs isolated from C57BL/6, BALB/c, and DBA mice. The immunological assays showed some variation among the strains in the cytokines, nitric oxide (NO), and indoleamine 2,3‐dioxygenase (IDO) production and immunomodulatory effects on splenocytes functions. Our results indicated a suppression of splenocytes proliferation in the presence of AD‐MSC CM from the three inbred mouse strains. However, BALB/c CM exerted a higher suppression of splenocytes proliferation. AD‐MSCs isolated from C57BL/6 and BALB/c mice produced higher levels of TGF‐β than those from DBA mice. Furthermore, IL‐17 and IDO production was higher in AD‐MSCs isolated from BALB/c mice. Our results indicated an increased production of TGF‐β, IL‐4, IL‐10, NO, and IDO by splenocytes in response to CM from BALB/c AD‐MSCs. In conclusion, our results showed that the immunomodulatory properties of mouse AD‐MSCs is strain‐dependent and this variation should be considered during selection of appropriate stem cell source for in vivo experiments and stem cell therapy strategies. J. Cell. Biochem. 114: 955–965, 2013. © 2012 Wiley Periodicals, Inc.
Satisfiability of cross product terms is complete for real nondeterministic polytime Blum-Shub-Smale machines

Nondeterministic polynomial-time Blum-Shub-Smale Machines over the reals give rise to a discrete complexity class between NP and PSPACE. Several problems, mostly from real algebraic geometry / polynomial systems, have been shown complete (under many-one reduction by polynomial-time Turing machines) for this class. We exhibit a new one based on questions about expressions built from cross products only.
ECG signal analysis for detection of Heart Rate and Ischemic Episodes

Electrocardiogram (ECG) is generally used for diagnosis of cardiovascular abnormalities and disorders. An efficient method for analysing the ECG signal towards the detection of heart rate (HR) and ischemic episodes follows mainly five stages: pre-processing, feature extraction, heart rate detection, beat classification and ischemic episode recognition. The heart rate is calculated using the extracted features of the ECG signal. The calculated HR value can be analysed for the detection of various cardiovascular abnormalities. The ability of the method was validated on European ST-T database. The performance of ischemic episode detection shows 88.08% sensitivity (Se) and 92.42% positive predictive accuracy (PPA).
The Contemporary Significance of Schmalenbach's Concept of the Bund

This paper will look at a form of sociation known as the Bund, conceptualized by Schmalenbach in the 1920's. I shall argue that this long ignored concept, dealing with affectual form of solidarity in small groups, is of considerable relevance to contemporary issues concerning individuality and lifestyle, particularly in relation to debates surrounding their significance in modernity and postmodernity. After looking at the historical origins of the German word Bund and its usage by various groups from the Bundschuh to the Wandervogel, I shall consider its significance in the sociology of Herman Schmalenbach, particularly in relation to his critiques of Tönnies's Gemeinschaft/Gesellschaft dualism and Weber's typology of social action. A comparison of the Bund will then be made with Victor Turner's concept of communitas and Maffesoli's concept of the neo-tribe. The paper will conclude by looking at some contemporary examples of Bund-like sociations using a diverse range of examples including: the womens' peace camp at Greenham Common; soccer crews and Tom Peter's notion of the workplace based ‘self-managing team’. My central argument shall be that an understanding of the Bund is of use in explaining the significance and dynamics of all manner of elective groups and lifestyles
A Method to Investigate Software Evolutions Using Design Pattern Detection Tool

In software designing, design patterns are expected to help for implementing with clear design intention with higher quality. However, selecting appropriate patterns is not simple task, and design patterns are sometimes deployed exploratory without properly defined process. In order to clarify design patterns’ contribution to the quality and productivity, it is very important to investigate design pattern usage among the series of revisions over the time. In this paper, we propose a method to observe design pattern usage in the series of source code modifications by using a design pattern detection tool and source code management system. This method enables intuitive analysis of design pattern history that should have strong relations to the software evolutions, without any preserved design documents. We also present an analysis to revisions history of an open source software JUnit, as a preliminary experimentation of our method. In this analysis, number of design patterns in the source code are observed, and we found some patterns of significant increase/decrease of these numbers are useful to determine the type of each modification such as feature enhancement or refactoring.
Exploring Information Quality in Accounting Information Systems Adoption

Information Quality (IQ) Management plays a vital role in the process of Accounting Information Systems (AIS) adoption. IQ is emerging as a well-known business problem in modern organisations. Specifically, the level of information quality is critical for all accounting processes, and has a significant impact on business decision-making. It must be noted that modern organisations rely heavily on the use of accounting information systems for their accounting processes. There is a growing need for research to provide insights into issues and solutions related to IQ in AIS adoption. This research aims to explore ways of managing information quality and AIS adoption to investigate the relationship between the IQ issues and AIS adoption process. This study has led to the development of a framework to guide the organisations on implementing an adequate IQ management approach during the system adoption process. This research was done on 44 respondents at ten organisations within manufacturing firms in Thailand. The findings of the research’s empirical evidence suggest that IQ dimensions in AIS adoption provide assistance in all processes of decision making. This research provides empirical evidence that information quality of AIS adoption affect decision making and suggests that these variables should be considered in adopting AIS in order to improve the effectiveness of AIS.
The effect of unlabeled samples in reducing the small sample size problem and mitigating the Hughes phenomenon

In this paper, we study the use of unlabeled sam- ples in reducing the problem of small training sample size that can severely affect the recognition rate of classifiers when the dimensionality of the multispectral data is high. We show that by using additional unlabeled samples that are available at no extra cost, the performance may be improved, and therefore the Hughes phenomenon can be mitigated. Furthermore, by ex- periments, we show that by using additional unlabeled samples more representative estimates can be obtained. We also pro- pose a semiparametric method for incorporating the training (Le., labeled) and unlabeled samples simultaneously into the parameter estimation process.
Methodological Modifications in a Longitudinal Qualitative Research Design

This article explores methodological shifts in longitudinal qualitative research and illustrates how researchers can maintain methodological continuity while staying open to necessary modifications. We describe methodological modifications and changes that occurred during our longitudinal research process. These change processes were initiated due to general advances in the field of qualitative research methodology, personal research experiences gained during the research process, and preliminary analysis findings. The change processes complicated our methodological decision making and simultaneously refined study purposes and analytical intentions. The investigation of change over time, time in context, and time and texture also play a significant role in our examples and reflections in this article. We argue that careful analysis and accounting of methodological continuity, modification, and changes can strengthen the trustworthiness of longitudinal studies, an important goal considering the methodological complexity often associated with longitudinal qualitative research.
Understanding the Spreading Patterns of Mobile Phone Viruses

Viruses and Mobile Phones While traditional cellphones have been relatively immune to viruses, smartphones (like Palm, Blackberry, iPhone, and many Nokia brands) that can share programs and data with each other could potentially be vulnerable to virus epidemics. Why then haven't we experienced any major mobile virus outbreak so far? Wang et al. (p. 1071; published online 2 April; see the Perspective by Havlin) believe that the answer is related to the spreading patterns possible in the current mobile phone systems. They studied the anonymized billing record of a mobile phone company, representing the calling patterns and the coordinates of the closest mobile phone tower each time a group of 6.2 million mobile phone subscribers used their phone. While a Bluetooth virus could reach all susceptible users given sufficient time, its spread, limited by human mobility, was relatively slow. In contrast, MMS viruses would have an explosive spreading pattern, but could only reach the group of individuals that know each other and carry the same phone. Thus, no major virus outbreak is likely until one operating system encompasses a larger fraction of the total smartphone market. Current mobile phone usage prevents major mobile virus outbreaks, but conditions could arise leading to a phone epidemic. We modeled the mobility of mobile phone users in order to study the fundamental spreading patterns that characterize a mobile virus outbreak. We find that although Bluetooth viruses can reach all susceptible handsets with time, they spread slowly because of human mobility, offering ample opportunities to deploy antiviral software. In contrast, viruses using multimedia messaging services could infect all users in hours, but currently a phase transition on the underlying call graph limits them to only a small fraction of the susceptible users. These results explain the lack of a major mobile virus breakout so far and predict that once a mobile operating system’s market share reaches the phase transition point, viruses will pose a serious threat to mobile communications.
Hierarchically nanostructured materials for sustainable environmental applications

This review presents a comprehensive overview of the hierarchical nanostructured materials with either geometry or composition complexity in environmental applications. The hierarchical nanostructures offer advantages of high surface area, synergistic interactions, and multiple functionalities toward water remediation, biosensing, environmental gas sensing and monitoring as well as catalytic gas treatment. Recent advances in synthetic strategies for various hierarchical morphologies such as hollow spheres and urchin-shaped architectures have been reviewed. In addition to the chemical synthesis, the physical mechanisms associated with the materials design and device fabrication have been discussed for each specific application. The development and application of hierarchical complex perovskite oxide nanostructures have also been introduced in photocatalytic water remediation, gas sensing, and catalytic converter. Hierarchical nanostructures will open up many possibilities for materials design and device fabrication in environmental chemistry and technology.
A Rare Case of Hypopharyngeal Screw Migration after Spine Stabilization with Plating

Anterior cervical spine fusion and stabilization with plating are well-established surgical procedures for the treatment of myelopathy, cervical spine traumas, and spinal infectious diseases. Various complications have been described in the literature, more frequently, intraoperative bleeding, peri- or postoperative hypopharyngeal, and/or esophageal ruptures with mediastinal deep infection and loosening and extrusion of the screws from the plating. Screw migration has also been observed as a complication of the procedure, either early in the postoperative period or delayed, even after many years. In some instances, the esophageal perforation can recover spontaneously with absence of complications, even if a case of plate failure and graft migration with lethal sudden airways obstruction has been reported. We describe a case of hypopharyngeal screw migration after cervical spine stabilization with plating never described before in the literature.
A situational analysis of the use of sign language in the education of the Deaf in Zambia: A case of Magwero and St Joseph's schools for the Deaf

Abstract This article presents a situational analysis of the use of sign language in the education of the Deaf in Zambia. It reports on research findings on the levels of training for teachers of the Deaf; challenges that teachers and pupils have to contend with; views of stakeholders on how sign language is used and ought to be used in the education of the Deaf; as well as their views on the significance of sign language in the education of the Deaf.
A TSV noise-aware 3-D placer

In this work, a three-dimensional partitioning-based force-directed placer is developed to minimize coupling noise between through silicon vias (TSVs) in three-dimensional integrated circuits. TSV decoupling force is introduced and determined by the TSV coupling noise to separate TSVs with strong coupling noise. The experimental results indicate that TSV coupling noise can be effectively reduced by 36.3% on average with only 6.0% wirelength overhead. Besides, the developed 3-D placer shows great performance in wirelength that is competitive to a state-of-the-art 3-D placer.
An electron-microscopic study of centrioles in differentiating motor neuroblasts.

Mature neurons with centrioles were first described at the end of the nineteenth century and have been observed in many animals (see Cajal, 1911; Ariens Kappers, Huber & Crosby, 1936). As mitosis rarely, if ever, occurs after morphological differentiation of the neuroblast begins, the function of the centrioles in nerve cells posed a problem which has yet to be resolved. Held (1909) described centrosomes in differentiating neuroblasts as being associated with the ‘fibrillogenous zone’, which suggests a role for the centriole in the differentiation of neurofibrils. Recently, electron-microscopic observations have refocused attention on the possibility of morphological and functional association between the centrioles of nerve cells and the fibrillar elements, especially neurotubules, which appear to be similar in fine structure to microtubules of other types of cells and to spindle tubules of the mitotic apparatus.
Nonhuman anthropoid primate femoral neck trabecular architecture and its relationship to locomotor mode

Functional analyses of human and nonhuman anthropoid primate femoral neck structure have largely ignored the trabecular bone. We tested hypotheses regarding differences in the relative distribution and structural anisotropy of trabecular bone in the femoral neck of quadrupedal and climbing/suspensory anthropoids. We used high‐resolution X‐ray computed tomography to analyze quantitatively the femoral neck trabecular structure of Ateles geoffroyi, Symphalangus syndactylus, Alouatta seniculus, Colobus guereza, Macaca fascicularis, and Papio cynocephalus (n = 46). We analyzed a size‐scaled superior and inferior volume of interest (VOI) in the femoral neck. The ratio of the superior to inferior VOI bone volume fraction indicated that the distribution of trabecular bone was inferiorly skewed in most (but not all) quadrupeds and evenly distributed the climbing/suspensory species, but interspecific comparisons indicated that all taxa overlapped in these measurements. Degree of anisotropy values were generally higher in the inferior VOI of all species and the results for the two climbing/suspensory taxa, A. geoffroyi (1.71 ± 0.30) and S. syndactylus (1.55 ± 0.04), were similar to the results for the quadrupedal anthropoids, C. guereza (male = 1.64 ± 0.13; female = 1.68 ± 0.07) and P. cynocephalus (1.47 ± 0.13). These results suggest strong trabecular architecture similarity across body sizes, anthropoid phylogenetic backgrounds, and locomotor mode. This structural similarity might be explained by greater similarity in anthropoid hip joint loading mechanics than previously considered. It is likely that our current models of anthropoid hip joint mechanics are overly simplistic. Anat Rec, 2007. © 2007 Wiley‐Liss, Inc.
Cognition in Organizational Analysis: Who's Minding the Store?

Research on cognition in organizations has focused primarily on managers and how they think while performing a variety of managerial tasks. This approach limits our understanding of cognition at the collective level and the interactive effects across levels of analysis. We propose a framework of cognition — based on structure, process, and style — which can be applied to the individual, group and organizational levels of analysis. By mapping the territory, we observe certain well-travelled routes, while other terrain remains relatively unexplored. This map also identifies theoretical and methodological road blocks which suggest a number of future research directions.