Miracle-dz/UniFAR-FTUs huggingface dataset:
Including the Characters of Interest During Tree Reconstruction and the Problems of Circularity and Bias in Studies of Character Evolution

Recent developments have clarified the critical importance of conducting comparative evolutionary studies in the context of phylogeny (e.g., Eldredge and Cracraft 1980; Felsenstein 1985; O'Hara 1988; Funk and Brooks 1990; Harvey et al. 1995), and this approach has been applied widely in studies of character evolution (e.g., Donoghue 1989; Brooks and McLennan 1991; Harvey and Pagel 1991; Martins and Garland 1991; Maddison and Maddison 1992; Eggleton and VaneWright 1994). Within this general phylogenetic frame of reference, a widespread belief has arisen that analyzing the evolution of particular characters in the context of phylogenetic trees based wholly or partly on those same characters is logically circular, and that independent phylogenies (i.e., ones based on data other than the characters under investigation) are needed to analyze character evolution properly (e.g., Coddington 1988; Carpenter 1989; Lauder and Liem 1989; Olmstead 1989; Sytsma 1990; Brooks and McLennan 1991; McKey 1991; Vane-Wright e al. 1992). Here I critically analyze the logic of studying character evolution in a phylogenetic context, focusing on the practice of including the characters of interest during tree reconstruction as it relates to the problem of fallacious reasoning. I develop a position implicit in several earlier articles (e.g., Maddison 1990; Harvey and Purvis 1991; Armbruster 1992, 1993; Maddison and Maddison 1992; Swofford and Maddison 1992; Deleporte 1993; de Queiroz and Wimberger 1993) in which the existence of questionable logic is recognized as being dependent on the nature of the relationship between specific premises and conclusions or, more precisely, on how the assumptions inherent in specific methods or practices bear on specific hypotheses or inferences. I argue that both including and excluding the characters of interest can lead to logical problems, which implies that, although there is a valid concern about including the characters of interest during tree reconstruction, this concern cannot be eliminated by a simple rule to always exclude those characters. Finally, I make some general recommendations intended to promote increased rigor in analyses of character evolution.
DNA Fingerprinting for Tuberculosis Control in a Metropolitan Area

textabstractTuberculosis (TB) is an infectious disease that caused 9.2 million new cases and 1.7 million deaths in the world in 2006 (1). Over one-third of the world population is infected with Mycobacterium tuberculosis, the causative organism of TB. In the Netherlands, TB was the leading cause of death in the first decades of the last century, but improved socioeconomic circumstances, infection-control measures and the introduction of effective chemotherapy have reduced TB to a relatively uncommon disease. TB mortality rates in the Netherlands declined a thousand fold in one century and incidence was the lowest ever recorded in 2006 (2). Prospects are yet less good in other parts of the world. The human immunodeficiency virus (HIV) pandemic multiplied the TB caseload in many sub-Saharan countries and drug resistance is on the increase in several countries with high rates of multidrug-resistant (MDR) strains. Recently, extensively drug-resistance (XDR) was described and XDR-TB is an emerging public health probem in a number of countries (3).
Application of Age-transformation Approaches to Mortality Projection for Japan

For projecting future mortality in ”Population Projection for Japan: 2006-2055” (NIPSSR 2007), a new ”age-shifting model”, which incorporates age-shifting as well as age-scaling of mortality, has been developed and used (Ishii 2008). These kinds of operations could be incorporated into a more general framework, i.e. an age-transformation approach. This paper serves to examine and propose a novel method for the mortality projection of Japan that is an application of the age-transformation approach.
CATCAM: Constant-time Alteration Ternary CAM with Scalable In-Memory Architecture

TCAM (Ternary Content-Addressable Memory) is the essential component for high-speed packet classification in modern hardware switches. However, due to its relatively slow update process, recent advances in Software-Defined Network (SDN) regard them as the bottleneck to the agile deployment of network services. Rule installation in commodity switches suffers from non-deterministic delays, ranging from a few milliseconds to nearly half a second. The crux of the problem is that TCAM prioritizes rules based on physical addresses. Corresponding entries have to be reallocated according to the priority of an incoming rule, such that the insertion delay grows linearly with the number of existing rules in a TCAM.In this paper, we present Constant-time Alteration Ternary CAM (CATCAM) that can accomplish both lookup queries and update requests for packet classification in a few nanoseconds. The key to fast update is to decouple rule priorities from physical addresses. We propose a matrix-based priority encoding scheme that records the priority relation between rules and can be implemented in 8T SRAM arrays with the emerging Processing In-Memory (PIM) technique. CATCAM also comes with a hierarchical architecture to scale out, its interval-based scheduling scheme guarantees deterministic update performance in all scenarios. CATCAM is developed under full-custom design in the 28 nm process. Evaluation across benchmark workloads shows that CATCAM provides at least three orders of magnitude speedup over state-of-the-art TCAM update algorithms and offers equivalent search capability to conventional TCAM while incurring 0.3% power and 20% area overhead.
Reaction-diffusion theory of localized structures with application to vertebrate organogenesis

Biological pattern formation is addressed within the framework of Turing's (1952) chemical theory. His (linear) reaction-diffusion equations for chemical concentration have spatially inhomogeneous solutions. These stationary chemical waves are a possible mechanism for the spatial patterning of cellular differentiation in embryogenesis. Chemical mechanisms which give Turing dynamics have nonlinear rate equations. Much of the dynamics can be predicted from linear analysis, but solution is generally only possible numerically. Numerical methods for reaction-diffusion equations, especially implicit techniques, are reviewed. This work is specifically concerned with the localization of pattern. Reaction-diffusion models tend to form repeated peaks. Under some circumstances, however, patterns of localized peaks surrounded by large areas of low concentration can be formed. The requirements for this are developed and explored through comparison of two models, the Brusselator and the Gierer-Meinhardt. It is found that both can give localized pattern if the ratio of the component diffusivities is high. This leads to partly-ordered pattern, linking Turing theory with the inhibitory field theory of Wigglesworth (1940). However, the GiererMeinhardt gives less ordered pattern in two dimensions and is more susceptible to gradients in precursor concentration than the Brusselator. The different dynamics in the two models, underlying the different behaviours, are discussed.
RESECTION AND MONTE CARLO COVARIANCE FROM VANISHING POINTS FOR IMAGES OF UNKNOWN ORIGIN

Abstract. Photogrammetric analysis requires camera metadata (position, attitude, interior orientation, etc.), which is not available for all images. Modern commercial solutions for 3D reconstruction from images typically assume large amounts of purposefully-collected, highly-overlapping imagery. In this article, a system is demonstrated for recovering a 3D scene from images of unknown origin, by marking ground space axes, resecting a camera consistent with the markings, and then using the solved camera to collect 3D measurements. The capability works with close-range (vanishing points) and long-range (parallel axes) imagery. Monte Carlo analysis is used to propagate measurement uncertainty of the vanishing lines to uncertainty of exterior and interior camera parameters, which can then be used to quantify uncertainty of measurements in the 3D scene.
CaSA: End-to-end Quantitative Security Analysis of Randomly Mapped Caches

It is well known that there are micro-architectural vulnerabilities that enable an attacker to use caches to exfiltrate secrets from a victim. These vulnerabilities exploit the fact that the attacker can detect cache lines that were accessed by the victim. Therefore, architects have looked at different forms of randomization to thwart the attacker’s ability to communicate using the cache. The security analysis of those randomly mapped caches is based upon the increased difficulty for the attacker to determine the addresses that touch the same cache line that the victim has accessedIn this paper, we show that the analyses used to evaluate those schemes were incomplete in various ways. For example, they were incomplete because they only focused on one of the steps used in the exfiltration of secrets. Specifically, the step that the attacker uses to determine the set of addresses that can monitor the cache lines used by the transmitter address. Instead, we broaden the analysis of micro-architecture side channels by providing an overall view of the communication process. This allows us to identify the existence of other communication steps that can also affect the security of randomly mapped caches, but have been ignored by prior workWe design an analysis framework, CaSA, to comprehensively and quantitatively analyze the security of these randomly mapped caches. We comprehensively consider the end-to-end communication steps and study the statistical relationship between different steps. In addition, to perform quantitative analysis, we leverage the concepts from the field of telecommunications to formulate the security analysis into a statistical problem. We use CaSA to evaluate a wide range of attack strategies and cache configurations. Our result shows that the randomization mechanisms used in the state-of-the-art randomly mapped caches are insecure.
Development and Reproduction of Two Populations of Eretmocerus Species (Hymenoptera: Aphelinidae) on Bemisia tabaci (Homoptera: Aleyrodidae)

A study was conducted to determine preimaginal developmental rate, adult survival, and fertility of two populations of Eretmocerus sp. that parasitize Bemisia tabaci (Gennadius). An arrhenotokous parasitoid population was collected in Indio, Calif. , and a thelytokous parasitoid population was collected from Oahu, Hawaii. Experiments were conducted with parasitoids reared on B. tabaci hosts living on cotton, Gossypium hirsutum L. (‘Delta Pine 61’), or cucumber, Cucumis sativus L. (‘Poinsett 76’), in temperature-controlled cabinets at 20.0 and 29.0%C. Significant differences in preimaginal developmental periods were found between populations, temperatures, and plants. Adult longevity was greatest at lower temperatures. A limited preoviposition period existed. Fertilities were higher on cucumber and at 29.0%C. The sex ratio of the arrhenotokous population favored females. The intrinsic rate of natural increase (rm) for the arrhenotokous population varied from 0.0610 to 0.1149 on cotton and from 0.0856 to 0.1824 on cucumber, at 20.0 and 29.0‘C. Values for rm for the thelytokous population varied hom 0.0858 to 0.1608 on cotton and from 0.0980 to 0.2117 on cucumber, at 20.0 and 29.0%C. The results indicate that biological control of B. tabaci would probably be better obtained by Eretmocerus sp. population from Hawaii at higher temperatures.
Upregulation of mitochondrial alternative oxidase pathway protects photosynthetic apparatus against photodamage under chilling stress in Rumex K-1 leaves

This study aimed to clarify the role of mitochondrial alternative oxidase (AOX) pathway upregulation in photoprotection under chilling stress in Rumex K-1 leaves. Malate-oxaloacetate shuttleꞌs activity and AOX pathwayꞌs capacity were synchronously enhanced with light intensity increase both in control and chilling-treated leaves. Besides, the AOX pathway was upregulated more significantly when irradiated by light in chilling-treated leaves than that of control. These results suggested that excess reducing equivalents generated by photosynthesis were exported from chloroplasts and oxidized by the AOX pathway at a potentially higher rate in chilling-treated leaves than in control, which avoided the overaccumulation of excess reducing equivalents under light conditions. Also, inhibition of the AOX pathway led to more severe accumulation of hydrogen peroxide in chilling-treated leaves than that in control. Therefore, the mitochondrial AOX pathway was specifically upregulated and employed for sinking excess reducing equivalents produced by photosynthesis, which protected photosynthetic apparatus from photodamage under chilling stress in Rumex K-1 leaves.
Epigenetic information in the cell : a potential avenue for biocompatible computing

Living organisms sense, process and produce molecular signals to regulate their activity and, thus, process information and perform computations on biological substrates. Understanding the fundamental principles of information representation and manipulation along these algorithmic bioprocesses will both advance our understanding of biology and inspire novel forms of computation. From one side of this connection, the research field of Bioinformatics uses computational tools to gain insight into the processes of life. On the other side, Biomolecular Computing attempts to utilize molecules and cellular processing machineries to operate engineered nano-scale biocomputers in live cells for in situ diagnostics, therapeutics and many other applications in biotechnology, bioengineering and biomedicine. Addressing this bifold character of information of life, this thesis contributes to the part of Computing Life by elucidating aspects of chromatin, the nucleoprotein structure of DNA in the cell. As a computation and storage layer in the cell, chromatin offers a high degree of plasticity to integrate (environmental) signals into DNA-based regulation and allows information propagation according to epigenetic principles. In this work, I present results on the complexity of chromatin modifications and reveal their impact on gene activity and related functions in the cell. I further discuss a bioinformatics pipeline I developed and that was applied for genome-wide chromatin profiling and transcriptome analysis. From the perspective of Living Computers, I address the question of information encoding by biomolecules and draw on principles of epigenetics to devise a model for an RNA interference-based equivalent of the electric flip-flop, which
Restructuring Conversations using Discourse Relations for Zero-shot Abstractive Dialogue Summarization.

Dialogue summarization is a challenging problem due to the informal and unstructured nature of conversational data. Recent advances in abstractive summarization have been focused on data-hungry neural models and adapting these models to a new domain requires the availability of domain-specific manually annotated corpus created by linguistic experts. We propose a zero-shot abstractive dialogue summarization method that uses discourse relations to provide structure to conversations, and then uses an out-of-the-box document summarization model to create final summaries. Experiments on the AMI and ICSI meeting corpus, with document summarization models like PGN and BART, shows that our method improves the ROGUE score by up to 3 points, and even performs competitively against other state-of-the-art methods.
Memoirs of the National Academy of Sciences

of the peach, pear and apple, which vary so much in their hardiness ? Every fruit grower in the Northern States knows well that certain varieties of these trees will endure the winter while others will not. This may not be due to any adaptation to cold, but it certainly does not admit of the simple explanation given by the learned author. There have certainly been variations in the hardiness of cultivated plants, and these variations have, by judicious selection, made it possible for us to extend very considerably the range of the species. -Cliarles E. Bessey.
Development of Microsatellite Markers Using Next-Generation Sequencing and Genetic Characterization in Three Natural Monument Populations of Koelreuteria paniculata (Goldenrain Tree)

This study was conducted to develop microsatellite markers in Koelreuteria paniculata using next-generation sequencing. A total of 71,114,562 reads of 20x coverage for the K. paniculata genome were generated and assembled to 141,924 contigs of a minimum of 500 bp long. One hundred seventy-nine of the 79,633 contigs containing microsatellite regions were used for primer design. Fourteen primer sets were selected as polymorphic markers by applying them to three K. paniculata populations, designated as natural monuments in Korea. Somewhat low levels of genetic diversity were observed. The grand means of the number of alleles, observed heterozygosity, and expected heterozygosity were 2.7, 0.493, and 0.407, respectively. Analysis of molecular variance indicated a high level of genetic differentiation among populations. Distinct patterns of three populations were identified in the principal coordinate analysis and Bayesian structure analysis. The probability of identity of these markers was estimated to be quite low, suggesting that these markers have the robust potential power to distinguish genetically different individuals. K. paniculata has a high economic value as an ornamental tree, and a honey tree. The novel microsatellite markers developed in this study will be useful for future breeding programs and genetic studies aimed at developing conservation plans. Additional key words: genetic diversity, genetic structure, individual identification, ornamental tree, simple sequence repeat
The Analysis of Dominance and Bidirectionality in Social Development.

GOTTMAN, JoHN M. , and RINGLAND, JAMES T. The Analysis of Dominance and Bidirectionality in Social Development. CHILD DEVELOPMENT, 1981, 52, 393-412. This paper is a reexamination of 2 concepts that have played a role in the direct observation of social interaction and the study of social development, namely, the concepts of dominance and bidirectionality. This paper argues that a reconceptualization based on the sequential character of social interaction would add much theoretical clarity to these 2 concepts. In this paper the sequential nature of social interaction is addressed by applying time-series analysis to redefine (as a function of social context) the concept of dominance as asymmetry in predictability in the behavior of 2 interacting individuals. The potential benefits of this redefinition are then discussed in the context of literature on children's social behavior with their peers. Bidirectionality in social interaction, defined as symmetrical predictability in behavior, is then discussed in the context of parent-infant interaction. A serious methodological problem is then raised, namely, the problem of autocorrelation in each person's behavior in making inferences about cross-correlation between people. Mathematical models and corresponding statistical procedures are presented to solve this problem. Procedures are discussed that address the concepts of cyclicity within a person and synchronicity between people who are interacting and that assess asymmetry and symmetry (i.e., dominance and bidirectionality) in social interaction. Previously published data on mother-infant play is then reexamined to illustrate the practical use of this approach. These techniques are, however, completely general for inferring relationships between 2 variables that change with time and thus may provide a foundation for the study of other developmental problems.
Information and Efficiency: Another Viewpoint

THE importance of bringing economic analysis to bear on the problems of efficient economic organization hardly requires comment, but there is a need to review the manner in which the notion of efficiency is used in these problems. The concept of efficiency has been abused frequently because of the particular approach used by many analysts. My aim is to examine the mistakes and the vagueness associated with this approach. I shall focus attention on the problem of efficiently allocating resources to the production of information because in this case the issues stand out clearly. Since Kenneth J. Arrow's paper "Economic Welfare and the Allocation of Resources for Invention"' has been most influential in establishing the dominant viewpoint about this subject, my commentary necessarily is a critique of Arrow's analysis. The view that now pervades much public policy economics implicitly presents the relevant choice as between an ideal norm and an existing "imperfect" institutional arrangement. This nirvana approach differs considerably from a comparative institution approach in which the relevant choice is between alternative real institutional arrangements. In practice, those who adopt the nirvana viewpoint seek to discover discrepancies between the ideal and the real and if discrepancies are found, they deduce that the real is inefficient. Users of the comparative institution approach attempt to assess which alternative real institutional arrangement seems best able to cope with the economic problem; practitioners of this approach may use an ideal norm to provide standards from which divergences are assessed for all practical alternatives of interest and select as efficient that alternative which seems most likely to minimize the divergence.2
COVIDLies: Detecting COVID-19 Misinformation on Social Media

The ongoing pandemic has heightened the need for developing tools to ﬂag COVID-19-related misinformation on the internet, specifically on social media such as Twitter. However, due to novel language and the rapid change of information, existing misinformation detection datasets are not effective for evaluating systems designed to detect misin-formation on this topic. Misinformation detection can be divided into two sub-tasks: (i) retrieval of misconceptions relevant to posts being checked for veracity, and (ii) stance detection to identify whether the posts Agree , Dis-agree , or express No Stance towards the retrieved misconceptions. To facilitate research on this task, we release C OVID L IES 1 , a dataset of 6761 expert-annotated tweets to evaluate the performance of misinformation detection systems on 86 different pieces of COVID-19 related misinformation. We evaluate existing NLP systems on this dataset, providing initial benchmarks and identifying key challenges for future models to improve upon.
Evaluation of Bacoside A Content in Different Accessions and Various Organs of Bacopa monnieri (L.) Wettst

Bacoside A, a secondary metabolite in Bacopa monnieri, is used in the treatment of neuropharmacological disorders. Three phenotypic characters and bacoside A maker were assessed in 22 accessions of B. monnieri collected from Karnataka, India. Bacoside was highest (18.36 mg.g-1 DW) in accession collected from Belgaum (accession number Bm2) and lowest (3.53 mg.g-1 DW) in accession collected from Dharwad (accession number Bm7). Analysis of bacoside A in various parts of B. monnieri revealed variability and was highest in stolons (9.54 mg.g-1 DW) and lowest in leaves (1.91 mg.g-1 DW).