Miracle-dz/UniFAR-FTUs huggingface dataset:
From Gene Trees to Species Trees

This paper studies various algorithmic issues in reconstructing a species tree from gene trees under the duplication and the mutation cost model. This is a fundamental problem in computational molecular biology. Our main results are as follows. A linear time algorithm is presented for computing all the losses in duplications associated with the least common ancestor mapping from a gene tree to a species tree. This answers a problem raised recently by Eulenstein, Mirkin, and Vingron [J. Comput. Bio. , 5 (1998), pp. 135--148]. The complexity of finding an optimal species tree from gene trees is studied. The problem is proved to be NP-hard for the duplication cost and for the mutation cost. Further, the concept of reconciled trees was introduced by Goodman et al. and formalized by Page for visualizing the relationship between gene and species trees. We show that constructing an optimal reconciled tree for gene trees is also NP-hard. Finally, we consider a general reconstruction problem and show it to be NP-hard even for the well-known nearest neighbor interchange distance. A new and efficiently computable metric is defined based on the duplication cost. We show that the problem of finding an optimal species tree from gene trees is NP-hard under this new metric but it can be approximated within factor 2 in polynomial time. Using this approximation result, we propose a heuristic method for finding a species tree from gene trees with uniquely labeled leaves under the duplication cost. Our experimental tests demonstrate that when the number of species is larger than 15 and gene trees are close to each other, our heuristic method is significantly better than the existing program in Page's GeneTree 1.0 that starts the search from a random tree.
Rethinking Query Processing for Energy Efficiency: Slowing Down to Win the Race

The biggest change in the TPC benchmarks in over two decades is now well underway – namely the addition of an energy efficiency metric along with traditional performance metrics. This change is fueled by the growing, real, and urgent demand for energy-efficient database processing. Database query processing engines must now consider becoming energy-aware, else they risk missing many opportunities for significant energy savings. While other recent work has focused on solely optimizing for energy efficiency, we recognize that such methods are only practical if they also consider performance requirements specified in SLAs. The focus of this paper is on the design and evaluation of a general framework for query optimization that considers both performance constraints and energy consumption as first-class optimization criteria. Our method recognizes and exploits the evolution of modern computing hardware that allows hardware components to operate in different energy and performance states. Our optimization framework considers these states and uses an energy consumption model for database query operations. We have also built a model for an actual commercial DBMS. Using our model the query optimizer can pick query plans that meet traditional performance goals (e.g., specified by SLAs), but result in lower energy consumption. Our experimental evaluations show that our system-wide energy savings can be significant and point toward greater opportunities with upcoming energy-aware technologies on the horizon.
Markets fo Heterogeneous Products: a Boundedly Rational Consumer Model

The paper is based on the acknowledgement that properties of markets stemming from features of demand are too frequently overlooked in the economic literature, and a re-balancing is necessary to properly account for theoretical and empirical phenomena. We sustain that one of the most relevant reasons for the neglect of the role of demand is the lack of an adequate representation of consumers. This claim is particu- larly relevant for evolutionary economics since its critique to the mainstream approach stopped at the representation of firms. The standard utility maximization approach to consumers? theory is even less defensible than the related assumption of producers? rationality, given the lack of competitive pressure on consumers. As a contribution to this theoretical gap, the paper presents a model for consumer based on the assumption of bounded rationality and inspired to the literature on experimental psychology. The proposed model can be applied to multi-dimensional products/services and relies on intuitive and potentially observable parameters, allow- ing for a wide range of theoretical and empirical applications. Moreover, the intrinsic structure of the model provides a clear definition of preferences, meant as ex-ante decisional criteria, distinguished from post-hoc justification of any decisional result. Though structurally simple, the proposed model is very flexible and allows for a clear exploration of the impact of specific demand features on the produced results. Several experiments show that the model can be successfully applied both to generate standard results and to implement complex configurations such as those of generated by large markets with heterogeneous products. Among the results presented, the most relevant concerns the identification of two classes of market segmentation, generated by the identical suppliers and demand? s ex- ogenous factors, but different consumers? decisional mechanisms. The results produced are observationally equivalent, but are shown to have radically different properties, and are proposed as initial elements of a taxonomy for the classification demand classes, likely to explain common properties across different markets.
Joint Mode Selection and Resource Allocation Using Evolutionary Algorithm for Device-to-Device Communication Underlaying Cellular Networks

Device-to-Device (D2D) has been a potential technology to improve the sum-rate of cellular networks, especially in local communication. By reusing the resource of cellular user equipment (UE), D2D can enhance the spectrum efficiency, but at the cost of introducing extra co-channel interference. In this paper, we adopt a resource reusing mechanism in which multiple D2D pairs can share multiple resource block for the sake of higher sum-rate, and then propose a joint mode selection and resource allocation method based on evolutionary algorithm (EA-MSRA-MDMR) to reduce the extra interference. Simulations show that the proposed method can achieve a higher system sum rate and fairness.  Index Terms—Device-to-Device communication, mode selection, resource allocation, evolutionary algorithm
Probabilistic Error Models for machine learning kernels implemented on stochastic nanoscale fabrics

Presented in this paper are probabilistic error models for machine learning kernels implemented on low-SNR circuit fabrics where errors arise due to voltage overscaling (VOS), process variations, or defects. Four different variants of the additive error model are proposed that describe the error probability mass function (PMF): additive over Reals Error Model with independent Bernoulli RVs (REM-i), additive over Reals Error Model with joint Bernoulli random variables (RVs) (REM-j), additive over Galois field Error Model with independent Bernoulli RVs (GEM-i), and additive over Galois field Error Model with joint Bernoulli RVs (GEM-j). Analytical expressions for the error PMF is derived. Kernel level model validation is accomplished by comparing the Jensen-Shannon divergence DJS between the modeled PMF and the PMFs obtained via HDL simulations in a commercial 45nm CMOS process of MAC units used in a 2nd order polynomial support vector machine (SVM) to classify data from the UCI machine learning repository. Results indicate that at the MAC unit level, DJS for the GEM-j models are 1-to-2-orders-of-magnitude lower (better) than the REM models for VOS and process variation errors. However, when considering errors due to defects, DJS for REM-j is between 1-to-2-orders-of-magnitude lower than the others. Performance prediction of the SVM using these models indicate that when compared with Monte Carlo with HDL generated error statistics, probability of detection pdet estimated using GEM-j is within 3% for VOS error when the error rate pη ≤ 80%, and within 5% for process variation error when supply voltage Vdd is between 0.3V and 0.7V. In addition, pdet using REM-j is within 2% for defect errors when the defect rate (the percentage of circuit nets subject to stuck-at-faults) psaf is between 10-3 and 0.2.
Brown Adipose Tissue Improves Whole-Body Glucose Homeostasis and Insulin Sensitivity in Humans

Brown adipose tissue (BAT) has attracted scientific interest as an antidiabetic tissue owing to its ability to dissipate energy as heat. Despite a plethora of data concerning the role of BAT in glucose metabolism in rodents, the role of BAT (if any) in glucose metabolism in humans remains unclear. To investigate whether BAT activation alters whole-body glucose homeostasis and insulin sensitivity in humans, we studied seven BAT-positive (BAT+) men and five BAT-negative (BAT−) men under thermoneutral conditions and after prolonged (5–8 h) cold exposure (CE). The two groups were similar in age, BMI, and adiposity. CE significantly increased resting energy expenditure, whole-body glucose disposal, plasma glucose oxidation, and insulin sensitivity in the BAT+ group only. These results demonstrate a physiologically significant role of BAT in whole-body energy expenditure, glucose homeostasis, and insulin sensitivity in humans, and support the notion that BAT may function as an antidiabetic tissue in humans.
Metabolic Syndrome and Insulin Resistance Are Associated with Chronic Kidney Disease in Nondiabetic Adults with Abdominal Obesity

Aims: we investigate whether insulin resistance is associated with an increased prevalence for chronic kidney disease irrespective of the concurrent presence of metabolic syndrome. Methods: 1638 patients with abdominal obesity were selected. Metabolic syndrome and abdominal obesity were defined according to the International Diabetes Federation criteria. Insulin resistance was defined by Homeostasis Model Assessment Index >P75. Chronic kidney disease was defined by the presence of a low estimated glomerular filtration rate (Results: metabolic syndrome was present in 1030 (62.9%) patients and insulin resistance in 787 (48%). Conversely 61% of those with metabolic syndrome were insulin resistant and 79% of those with insulin resistance had metabolic syndrome. Chronic kidney disease was present in 18%. In multivariate analysis, chronic kidney disease was increased in subjects with insulin resistance (odds ratio [OR] = 1.350; CI 95%: 1.021 - 1.785; p = 0.035) and in those with metabolic syndrome (OR = 1.417; CI 95%: 1.045 - 1.922; p = 0.025). Conclusions: Metabolic syndrome and insulin resistance were significant and independently associated with chronic kidney disease in nondiabetic adults with abdominal obesity.
A general collaborative filtering framework based on matrix bordered block diagonal forms

Recommender systems based on Collaborative Filtering (CF) techniques have achieved great success in e-commerce, social networks and various other applications on the Web. However, problems such as data sparsity and scalability are still important issues to be investigated in CF algorithms. In this paper, we present a novel CF framework that is based on Bordered Block Diagonal Form (BBDF) matrices attempting to meet the challenges of data sparsity and scalability. In this framework, general and special interests of users are distinguished, which helps to improve prediction accuracy in collaborative filtering tasks. Experimental results on four real-world datasets show that the proposed framework helps many traditional CF algorithms to make more accurate rating predictions. Moreover, by leveraging smaller and denser submatrices to make predictions, this framework contributes to the scalability of recommender systems.
A Daoist Perspective of Normative Media Practice: Profile Interview: Shelton Gunaratne, Minnesota State University Moorhead

Humanocentric theory of communication? Eastern cosmological notion of yin-yang, Daoism and media responsibility? How is Eastern philosophy relevant to continual efforts in the academe to lift the standards of journalism? These questions are tackled in The Dao of the Press: A Humanocentric Theory, Cresskill, NJ: Hampton Press, 2005. Eric Loo spoke with author and media academic Shelton Gunaratne at the Association of Education in Journalism and Mass Communication annual convention in Toronto in August 2004.
Living on the Margins

Summary A handful of scholars have acknowledged that, along side the traditional homeless, there are now older people who become homeless for the first time in old age. Few researchers, however, have systematically compared the recent older homeless with the chronic or traditional homeless. In the research presented here, we compare recent older homeless with long-term older homeless adults in Toronto according to their health and wealth, their housing history, and their use of health and social services. Findings indicate that people who become homeless for the first time at older ages have needs that are different from the lifetime elderly homeless and require different approaches to intervention.
Connexin hemichannels in the lens

The normal function and survival of cells in the avascular lens is facilitated by intercellular communication through an extensive network of gap junctions formed predominantly by three connexins (Cx43, Cx46, and Cx50). In expression systems, these connexins can all induce hemichannel currents, but other lens proteins (e.g., pannexin1) can also induce similar currents. Hemichannel currents have been detected in isolated lens fiber cells. These hemichannels may make significant contributions to normal lens physiology and pathophysiology. Studies of some connexin mutants linked to congenital cataracts have implicated hemichannels with aberrant voltage-dependent gating or modulation by divalent cations in disease pathogenesis. Hemichannels may also contribute to age- and disease-related cataracts.
CompreX: XML compression applied to the airborne Internet

As the airborne Internet emerges from pure conceptualization to actual implementation, the physical limitations of the airborne environment will become a significant issue. While land-based network applications benefit from nearly unlimited bandwidth, near-zero transmission latencies and potentially unlimited computational power, airborne resources are limited in all three of these areas. In order to move the development of the airborne Internet forward so that it will become a viable reality, solutions to these limitations must be explored and developed. This paper presents an approach being developed by Architecture Technology Corporation to provide an approach to XML compression, collectively called "CompreX", that would be suitable for implementation in the airborne Internet environment. CompreX follows a three-pronged approach to compressing XML communications, which include an XML-tuned compression algorithm, an XML binary encoder and a process called inter-document redundancy compression. This paper presents the results of preliminary research and testing in each of these three areas
Effect of high doses of a sustained-release bovine somatotropin on antibody formation in dairy cows.

Eighty-two lactating Holstein cows received either one, three, or five concurrent, intramuscular injections of a unit dose (.6 g) of zinc methionyl bST (some-tribove) or five doses of the vehicle. Injections were administered at 14-d intervals from 60 d postpartum until the end of lactation or necropsy. Thirty-eight cows continued on the same treatment for a 2nd yr. Blood bST antibodies developed within the first 7 wk of treatment, and the number of cows with anti-bST binding generally declined with time. Thirteen out of 59 cows receiving bST developed binding activity > 25% (positives) during the 1st yr. At the . 6-g dose level, no binding was detected after wk 15. Seven of the 13 positive cows were among the group randomly selected to continue on study during yr 2. In the 2nd yr, only 2 out of 24 bST-treated cows were positive. Binding activity was associated with the IgG fraction in serum. Binding capacities of antibodies ranged from . 625 to 3.04 mg of bST/L, and affinities ranged from 1.14 x 10(8) to 3.14 x 10(8) L/mol. Cows considered to be clinically positive had performance similar to those of their herdmates having binding < 25%. No evidence of a pathologic effect of antibodies existed in treated cows, their calves, or fetuses. The presence of anti-bST antibodies did not affect milk production of the cow or growth of the calves conceived during bST treatment.
When do creditors with heterogeneous beliefs agree to run?

This paper explores, in a multiperiod setting, the funding liquidity of a borrower that finances its operations through short-term debt. The short-term debt is provided by a continuum of creditors with heterogeneous beliefs about the prospects of the borrower. In each period, creditors observe the borrower’s fundamentals and decide on the amount they invest in its short-term debt. We formalize this problem as a coordination game, and we show that there exists a unique reasonable Nash equilibrium. We show that the borrower is able to refinance if and only if the liquid net worth is above an illiquidity barrier, and we explicitly find this barrier in terms of the distribution of capital and beliefs across creditors.
Induction of Candida albicans Drug Resistance Genes by Hybrid Zinc Cluster Transcription Factors

ABSTRACT The pathogenic yeast Candida albicans can develop resistance to azole antifungal drugs by overexpressing ERG11, which encodes the drug target, or the multidrug efflux pumps MDR1 and CDR1/CDR2. The constitutive upregulation of these genes is usually caused by gain-of-function mutations in the zinc cluster transcription factors Upc2, Mrr1, and Tac1, respectively. These transcription factors are also required for the induction of their target genes in drug-susceptible strains in the presence of specific stimuli. By swapping the DNA-binding domains of Mrr1, Tac1, and Upc2 we investigated if the hybrid transcription factors could activate their new target genes in response to the same signals. When Tac1 was targeted to the MDR1 and ERG11 promoters, the expression of these genes became inducible by fluphenazine. Similarly, MDR1 and CDR2 were strongly upregulated by fluconazole when Upc2 was fused to the DNA-binding domains of Mrr1 and Tac1, respectively. In contrast, Mrr1 was unable to promote gene expression in response to benomyl when it was targeted to the CDR2 and ERG11 promoters instead of the MDR1 promoter. These results suggest that Tac1 and Upc2 themselves are activated by the inducers fluphenazine and fluconazole, respectively, whereas benomyl does not activate Mrr1 itself but a coregulatory factor that is present at the promoters of Mrr1 target genes. Strains in which the expression levels of Mrr1 and Tac1 target genes were controlled by Upc2 exhibited increased fluconazole resistance, demonstrating that the ability to efficiently upregulate the expression of efflux pumps in the presence of the drug results in enhanced intrinsic fluconazole resistance.
Mammal invaders on islands: impact, control and control impact

The invasion of ecosystems by exotic species is currently viewed as one of the most important sources of biodiversity loss. The largest part of this loss occurs on islands, where indigenous species have often evolved in the absence of strong competition, herbivory, parasitism or predation. As a result, introduced species thrive in those optimal insular ecosystems affecting their plant food, competitors or animal prey. As islands are characterised by a high rate of endemism, the impacted populations often correspond to local subspecies or even unique species. One of the most important taxa concerning biological invasions on islands is mammals. A small number of mammal species is responsible for most of the damage to invaded insular ecosystems: rats, cats, goats, rabbits, pigs and a few others. The effect of alien invasive species may be simple or very complex, especially since a large array of invasive species, mammals and others, can be present simultaneously and interact among themselves as well as with the indigenous species. In most cases, introduced species generally have a strong impact and they often are responsible for the impoverishment of the local flora and fauna. The best response to these effects is almost always to control the alien population, either by regularly reducing their numbers, or better still, by eradicating the population as a whole from the island. Several types of methods are currently used: physical (trapping, shooting), chemical (poisoning) and biological (e.g. directed use of diseases). Each has its own set of advantages and disadvantages, depending on the mammal species targeted. The best strategy is almost always to combine several methods. Whatever the strategy used, its long‐term success is critically dependent on solid support from several different areas, including financial support, staff commitment, and public support, to name only a few. In many cases, the elimination of the alien invasive species is followed by a rapid and often spectacular recovery of the impacted local populations. However, in other cases, the removal of the alien is not sufficient for the damaged ecosystem to revert to its former state, and complementary actions, such as species re‐introduction, are required. A third situation may be widespread: the sudden removal of the alien species may generate a further disequilibrium, resulting in further or greater damage to the ecosystem. Given the numerous and complex population interactions among island species, it is difficult to predict the outcome of the removal of key species, such as a top predator. This justifies careful pre‐control study and preparation prior to initiating the eradication of an alien species, in order to avoid an ecological catastrophe. In addition, long‐term monitoring of the post‐eradication ecosystem is crucial to assess success and prevent reinvasion.
Role of the Human T-Cell Leukemia Virus Type 1 PTAP Motif in Gag Targeting and Particle Release

ABSTRACT Human T-cell leukemia virus type 1 (HTLV-1) Gag is targeted to the plasma membrane for particle assembly and release. How HTLV-1 Gag targeting occurs is not well understood. The PPPY and PTAP motifs were previously shown to be involved in HTLV-1 particle release with PTAP playing a more subtle role in virus budding. These L domains function through the interaction with host cellular proteins normally involved in multivesicular body (MVB) morphogenesis. The plasma membrane pathway rather than the MVB pathway was found to be the primary pathway for HTLV-1 particle release in HeLa cells. Intriguingly, disruption of the PTAP motif led to a defect in the targeting of Gag from the plasma membrane to CD63-positive MVBs. Particles or particle buds were observed to be associated with MVBs by electron microscopy, implying that Gag targeting to the MVB resulted in particle budding. Blocking clathrin-dependent endocytosis was found not to influence localization of the HTLV-1 Gag PTAP mutant, indicating that Gag did not reach the MVBs through clathrin-dependent endocytosis. Our observations imply that the interaction between Gag and TSG101 is not required for Gag targeting to the MVB. Overexpression of dynamitin p50 increased particle release, suggesting that there was an increase in the intracellular transport of MVBs to the cell periphery by the utilization of the dynein-dynactin motor complex. Intriguingly, virus particle release with this mutant was reduced by 20-fold compared to that of wild type in HeLa cells, which is in marked contrast to the less-than-twofold defect observed for particle production of the HTLV-1 Gag PTAP mutant from 293T cells. These results indicate that the role of the PTAP motif in L domain function is cell type dependent.