Miracle-dz/UniFAR-FTUs huggingface dataset:
Systematic Biology

— Phylogenies based on gene content rely on statements of primary homology to characterize gene presence or absence. These statements (hypotheses) are usually determined by techniques based on threshold similarity or distance measurements between genes. This fundamental but problematic step can be examined by evaluating each homology hypothesis by the extent to which it is corroborated by the rest of the data. Here we test the effects of varying the stringency for making primary homology statements using a range of similarity (e-value) cutoffs in 166 fully sequenced and annotated genomes spanning the tree of life. By evaluating each resulting data set with tree-based measurements of character consistency and information content, we ﬁnd a set of homology statements that optimizes overall corroborration. The resulting data set produces well-resolved and well-supported trees of life and greatly ameliorates previously noted inconsistencies such as the misclassiﬁcation of small genomes. The method presented here, which can be used to test any technique for recognizing primary homology, provides an objective framework for evaluating phylogenetic hypotheses and data sets for the tree of life. It also can serve as a technique for identifying well-corroborated sets of homologous genes for functional genomic applications. [CCM; consistency; corroboration; gene content; homology; ILD; phylogeny; presence absence; tree of life. ]
Converting among Log Scaling Methods Converting among Log Scaling Methods

ccurately measuring logs fortheir potential yield of salableproducts has challenged gener-ations of foresters. Yet sizing up irregu-lar, roughly round and tapered logs fortheir potential to yield standardizedrectangular lumber was necessary to es-timate their fair value. Log scales inNorth America were developed in the19th century, when logs tended tocome from old-growth trees of largegirth, and residues from milling themfor lumber had little value. Conse-quently, rules measured logs in termsof their lumber yield; three such rulesare still in common use. By contrast, inmuch of the rest of the world, logs aremeasured for their total cubic volume.Comparing volumes and values withthese different approaches poses a chal-lenge, and changes in the resource itselfcan affect the factors used to convertvalues.Log ScalesOf the many log scales developed,the Scribner rule remains the mostwidely used. Volumes are based on thenumber of 1-inch-thick boards, spaced
9.5 efficient digital quadrature transmitter based on IQ cell sharing

As new complex communication standards employ various modulation methods in various frequency bands, interest in the software-defined radio (SDR) transceiver to support the standards is increasing. For the flexible transceiver, a digital-intensive transmitter has many advantages and has been pursued intensively. The efficiency of the transmitter chain is strongly dependent on the PA, and switching PAs, such as Class-D and F PAs, are used due to their high efficiency. A polar transmitter is suited for the switching operation and receives a large attention. However, a CORDIC is needed for l/Q-to-Polar conversion, and it is very complex. Moreover, the polar signal has a large bandwidth compared to the l/Q signal bandwidth. On the contrary, the quadrature transmitter that does not require the CORDIC, is simple and low computing cost with low power consumption. Due to the favorable characteristics, the quadrature transmitters have been studied. [1] employs an RFDAC based on a Gilbert mixer. It operates in a current mode and the output impedance varies with the number of on-cells. Due to the impedance variation, it is difficult to have a high linearity. In [2], the input digital code is processed by delta-sigma modulation for smaller digital bits and enhanced resolution. However the modulator generates quantization noise. In [3-6], a voltage-mode transmitter is employed with a power combiner based on a switched capacitor. The output impedance is constant, determined by the total capacitance regardless of the on/off cell condition. Moreover, this architecture delivers much higher output power and efficiency than previously reported works. [4] used delta-sigma modulation with cascade PWM to improve linearity. In [5], a quadrature architecture was employed to eliminate the problems of the polar architecture. Due to the 90° phase difference of conventional digital l/Q LOs, the output power of the conventional quadrature transmitter has lower than that of polar, maximum 3dB lower when the magnitude of I and Q are equal.
Are Orthodontic Systematic Reviews Registered a Priori in PROSPERO?

Introduction Aim of this study was to assess the registration of orthodontic systematic reviews in PROSPERO. Method Seven databases were searched for orthodontic systematic reviews published in 2012-2016. After duplicate study selection and data extraction, descriptive statistics, followed by chi-square/Fisher exact tests were calculated. Finally, bivariable/multivariable regression with relative risks (RR) and 95% confidence intervals (CIs) was used. Results A total of 182 orthodontic systematic reviews were identified, 37 (20.3%) of which were registered in PROSPERO, with registration rates ranging from 4.3% in 2012 to 37.0% in 2016. Differences in review registration were found according to publication year, geographic origin, multicentre status, funding, and journal category. After controlling for confounders, each additional year was associated with increased registration probability (RR = 1.51; 95% CI = 1.19–1.93). Reviews from South America were more likely to be registered than reviews from Europe (RR = 1.49; 95% CI = 1.06–2.11). Finally, reviews published in orthodontic specialty journals were more likely to be registered than reviews in general dentistry journals (RR = 1.87; 95% CI = 1.02–3.49). Conclusions A small percentage of orthodontic systematic reviews was registered a priori, although improvement signs have been seen since the initiation of PROSPERO.
Natural language processing for resource-poor languages

Natural language processing (NLP) aims, broadly speaking, to teach computers to understand human language. This is hard as the computer must comprehend many facets of language such as semantics, syntax, pragmatics and phonology which are difficult to characterize formally, let alone encode as computer instructions. It is even harder for so-called low-resource languages where the annotated resources are very limited. There are approximately 7,000 languages in the world, but of these only a small fraction (20 languages) are considered high-resource languages. Low-resource languages are in dire need of tools and resources to overcome the resource barrier such that advances in NLP can deliver more widespread benefits. Despite the lack of annotated data, there are some unannotated data resources which might be beneficial for low-resource languages including parallel data, bilingual lexical resources or clues from related languages. However, the means for effectively incorporating these resources to improve the performance of low-resource NLP is an open research question, and the target of this thesis. Out of 7,000 languages, half of them do not have a writing system and many are falling out of use. It is estimated that by the end of this century, half of the world’s languages will be extinct. It is necessary to extend the current NLP techniques to unwritten languages to process and document the languages before they are gone forever. Transfer learning provides an important opportunity for low-resource NLP, whereby annotation is transferred from a source resource-rich language to a target resource poor-language. In this thesis, we successfully apply transfer learning for
Stability Analysis of Swarm Heterogeneous Robots with Limited Field of View

Endo T. , Maeda R. , Matsuno F. Stability Analysis of Swarm Heterogeneous Robots with Limited Field of View. Abstract. This paper presents a stability analysis of swarm robots, a group of multiple robots. In particular, we focus on robot swarms with heterogeneous abilities, in which each robot has a different sensing range and physical limitations, including maximum velocity and acceleration. In addition, each robot has a unique sensing region with a limited angle field of view. We previously proposed a decentralized navigation method for such heterogeneous swarm robots consisting of one leader and multiple followers. With the decentralized navigation method, a single leader can navigate for followers while maintaining connectivity and satisfying the physical limitations unique to each robot; i.e., each follower has a target robot and follows it without violating its physical limitations. In this paper, we focus on a stability analysis of such swarm robots. When the leader moves at a constant velocity, we mathematically prove that the shape and orientations of all robots eventually converge to the equilibrium state. For this, we must first prove that the equilibrium state exists. Then, we show the convergence of the state to its equilibrium. Finally, we carry out experiments and numerical simulations to confirm the stability analysis, i.e., the convergence of the swarm robots to the equilibrium states.
Determining the glycaemic responses of foods: conventional and emerging approaches

Abstract A low-glycaemic diet is crucial for those with diabetes and cardiovascular diseases. Information on the glycaemic index (GI) of different ingredients can help in designing novel food products for such target groups. This is because of the intricate dependency of material source, composition, food structure and processing conditions, among other factors, on the glycaemic responses. Different approaches have been used to predict the GI of foods, and certain discrepancies exist because of factors such as inter-individual variation among human subjects. Besides other aspects, it is important to understand the mechanism of food digestion because an approach to predict GI must essentially mimic the complex processes in the human gastrointestinal tract. The focus of this work is to review the advances in various approaches for predicting the glycaemic responses to foods. This has been carried out by detailing conventional approaches, their merits and limitations, and the need to focus on emerging approaches. Given that no single approach can be generalised to all applications, the review emphasises the scope of deriving insights for improvements in methodologies. Reviewing the conventional and emerging approaches for the determination of GI in foods, this detailed work is intended to serve as a state-of-the-art resource for nutritionists who work on developing low-GI foods.
A Hitting Set Relaxation for $k$-Server and an Extension to Time-Windows

We study the <tex>$k$</tex>-server problem with time-windows. In this problem, each request <tex>$i$</tex> arrives at some point <tex>$v_{i}$</tex> of an <tex>$n$</tex>-point metric space at time <tex>$b_{i}$</tex> and comes with a deadline <tex>$e_{i}$</tex>. One of the <tex>$k$</tex> servers must be moved to <tex>$v_{i}$</tex> at some time in the interval [<tex>$b_{i}, e_{i}$</tex>] to satisfy this request. We give an online algorithm for this problem with a competitive ratio of <tex>$\text{poly}\log(n, \Delta)$</tex>, where <tex>$\Delta$</tex> is the aspect ratio of the metric space. Prior to our work, the best competitive ratio known for this problem was <tex>$O(k\ \text{poly}\log(n))$</tex> given by Azar et al. (STOC 2017). Our algorithm is based on a new covering linear program relaxation for <tex>$k$</tex>-server on HSTs. This LP naturally corresponds to the min-cost flow formulation of <tex>$k$</tex>-server, and easily extends to the case of time-windows. We give an online algorithm for obtaining a feasible fractional solution for this LP, and a primal dual analysis framework for accounting the cost of the solution. Together, they yield a new <tex>$k$</tex>-server algorithm with poly-logarithmic competitive ratio, and extend to the time-windows case as well. Our principal technical contribution lies in thinking of the covering LP as yielding a truncated covering LP at each internal node of the tree, which allows us to keep account of server movements across subtrees. We hope that this LP relaxation and the algorithm/analysis will be a useful tool for addressing <tex>$k$</tex>-server and related problems.
Towards a dynamic pragmatics

2 Enduring Commitments and Loose Talk: Empirical and Conceptual Issues 3 2.1 Loose Talk: An introduction. 3 2.2 A Surprising Commitment: A New Observation about Loose Talk. 4 2.3 The Enduring Commitments of Loose Talk: Theoretical Consequences . 5 2.4 Commitments and Two Kinds of Conventions in Language Use . 7 2.5 The Pragmatics of Loose Talk . 11 2.6 Krifka’s approximate interpretation of number terms and related issues: Some open questions 14
Spectroscopy of galaxies in distant clusters. III. The population of Cl 0024+1654

We present the results of a spectroscopic study of 38 objects in the field of the very rich, concentrated cluster Cl 0024+1654 at a redshift of z = 0.391. All of the red galaxies and 14 of the 22 blue objects are found to be cluster members. The spectra of the blue cluster members are very similar to those of low-redshift spirals, suggesting that these distant galaxies are also undergoing protracted periods of star formnation. These data support Butcher and Oemler's suggestion that this cluster provides evidence for evolution of the blue population of clusters, to the extent that no low-redshift, concentrated cluster is known to have such a large population of blue galaxies. Three of the blue cluster members have spectra typical of active galactic nuclei, which lends support to the proposal of Dressler and Gunn that such activity was much more common only 4--5 x 10/sup 9/ yr ago. On the other hand, no '' starburst'' galaxies like those in the 3C 295 cluster have been found. We describe a technique for finding emission-line galaxies at a known redshift by imaging through a narrow-band filter centered on redshifted (OII) lambda3727 and demonstrate that this procedure detects (OII) emissionmore » at a level consistent with our spectroscopic measurements. With this technique, we have found other examples of blue galaxies with (OII) emission, and the strongest of these was confirmed to be an AGN by subsequent spectroscopic measurement. This method is extremely efficient because it covers the entire field at once and will be particularly valuable for work on higher redshift clusters where even multislit spectroscopy is difficult at the present time. « less
Assimilation of soil moisture data with the ensemble Kalman filter for the intermediate scale soil moisture predictions in the Netherlands

This thesis discusses the applicability of assimilation of artificial SMAP data into a quasi steady state hydrological model to improve soil moisture estimates. The model used for this research was SIMGRO and since no real SMAP data were available at the time of the research, artificial SMAP data were used. The ensemble Kalman filter was used to assimilate the data. To test the method a case study was performed in the North-East of the Netherlands. It was found that this is a feasible method for improving soil moisture estimates. Even if a quasi steady state model is used. However, for practical application more research is necessary and it is very important to use a correctly validated and calibrated model. The systematic errors of the model should be as small as possible. A fully dynamic model could improve the results. Furthermore it was found that due to the difference in scale between the model (1 x 1 km) and the SMAP data (3 x 3 km) the effect of the Kalman filter is not as large on the finer grid as on the coarser observation grid. This effect might increase when a even finer grid is used. Due to the generic nature of the method it can be applied to more locations in the Netherlands, where it can potentially help improving soil moisture estimates in real time forecasting systems.
The Advantages of Incorporating Historical Geographic Information Systems (H-GIS) into Modern Coastal Management Planning

As the terrestrial and marine effects of climate change continue to intensify, the value of natural habitats as a form of protection against a variety of ecological issues is becoming clear. Coastal wetlands, for example, provide protection against incoming storm surges and extreme weather, serve to improve water quality through the sequestration of various pollutants, and offer serious potential as a new source of biofuel. Unfortunately, many of the areas that have been affected by coastal habitat loss still suffer from the same problems that caused those ecosystems to change in the first place. Cities continue to release effluence into estuaries; hydrological engineering projects continue to redirect waterways that change flow and sediment patterns; and increasing populations in coastal areas all assert significant pressures on intertidal ecosystems. This ongoing changing of the landscape-and the length of time that anthropogenic factors have been influencing these habitats-has made modern-day environmental planning and management important yet complicated pursuits. As a result, planners and managers must constantly look for new tools to better understand their environment. Incorporating historically derived environmental data into geographic information systems (GIS) can enhance the quality of ecological models, which subsequently offers environmental planners and managers with a more robust understanding of the ecosystems encompassed within their project areas.
Environmental Pest Management: Challenges for Agronomists, Ecologists, Economists and Policymakers

For thousands of years, farmers have protected their crops by combating one pest at a time, using one control method (Lewis et al. 1997), with very little consideration of the surrounding environment. Over the years, new control methods, tactics and technologies have been adopted. These include employment of resistant crop genotypes; pest‐ retarding cultivation practices such as tillage, crop rotation, timing of planting and harvest and sanitation; chemical pesticides, including new chemistries, formulations and delivery tools; biological control agents; sterile insect techniques (SIT); transgenic crops; and now transgenic pests through gene‐drive mechanisms. Such pest‐centric approaches have remained the dominant dogma throughout the evolution of mainstream plant protection. Some 55 years ago, a promising attempt was made to adopt a system‐wide view of pest management. In its early form, Integrated Pest Management (IPM) was intended to provide a more holistic approach to pest management (van den Bosch and Stern 1962) than that offered by the supervised control commonplace at the time (Figure 18.1a). During the following decades, some pest management programmes were developed in the spirit of IPM. However, these also tended to target a specific pest or pest group in a particular crop. IPM thus remained focused on pest populations even when area‐wide approaches were adopted. Interactions between pest control measures and human and ecological environments have not been incorporated in pest management programmes. Perhaps as a result, we have failed to reduce yield losses to pests and to produce more food in sustainable and environmentally compatible ways. It has been estimated that global crop losses to arthropods, diseases and weeds increased from 34.9% in 1965 (Cramer 1967) to 42.1% in 1988–1990 (Oerke et al. 1994) despite continuous intensification of pest control efforts. In light of this, it is imperative that we renew our efforts to develop and implement pest management schemes that are effective, economically viable, sustainable and safe to humans and the environment. Towards this end, chapters in the present volume review the state of our understanding of pest population management and discuss Environmental Pest Management: The Need for Long‐term Governmental Commitment
3D-The Five-Minute Rule 30 Years Later and Its Impact on the Storage Hierarchy

THE DESIGN OF data management systems has always been influenced by the storage hardware landscape. In the 1980s, database engines used a two-tier storage hierarchy consisting of dynamic random access memory (DRAM) and hard disk drives (HDD). Given the disparity in cost between HDD and DRAM, it was important to determine when it made economic sense to cache data in DRAM as opposed to leaving it on the HDD. In 1987, Jim Gray and Gianfranco Putzolu established the five-minute rule that gave a precise answer to this question: “1KB records referenced every five minutes should be memory resident. ”9 They arrived at this value by using the then-current price-performance characteristics of DRAM and HDD shown in Table 1 for computing the break-even interval at which the cost of holding 1KB of data in DRAM matches the cost of I/O to fetch it from HDD. Today, enterprise database engines use a three-tier storage hierarchy as depicted in Figure 1. DRAM or NAND flash solid state device (SSD)-based performance tier is used for hosting data accessed by latency-critical transaction processing and real-time analytics applications. The HDD-based capacity tier hosts data accessed by latency-insensitive batch analytics applications. The archival tier is not used for online query processing, but for storing data that is only accessed rarely during regulatory compliance audits or disaster recovery. This tier is primarily based on tape and is extremely crucial as a longterm data repository for several application domains like physics, banking, security, and law enforcement. In this article, we revisit the fiveminute rule three decades after its inception. We recomputed break-even intervals for each tier of the modern, multi-tiered storage hierarchy and use guidelines provided by the five-minute rule to identify impending changes in the design of data management engines for emerging storage hardware. We summarize our findings here: ˲ HDD is tape. The gap between DRAM and HDD is increasing as the five-minute rule valid for the DRAM– HDD case in 1987 is now a four-hour rule. This implies the HDD-based capacity tier is losing relevance for not just performance sensitive applications, but for all applications with a non-sequential data access pattern. ˲ Non-volatile memory is DRAM. The gap between DRAM and SSD is shrinking. The original five-minute rule is now valid for the DRAM–SSD case, and the break-even interval is less than a minute for newer non-volatile memory (NVM) devices like 3DThe FiveMinute Rule 30 Years Later and Its Impact on the Storage Hierarchy DOI:10.1145/3318163
Synthesis of the yeast cell wall and its regulation.

PERSPECTIVES AND SUMMARY . 764 YEAST CELL WALL . 765 Chemistry 765 Structure . 767 CELL WALL AND SEPTUM FORMATION DURING THE YEAST CELL CyCLE 770 CELLULAR ASPECTS OF CELL WALL BIOSyNTHESIS 771 Initiation of Cell Wall Synthesis at Bud Emergence . 771 Cell Wall Synthesis During Bud Enlargement . 773 Regulation of synthesis 773 Localization of synthesis 773 Insertion of new cell wall 774 Function of cdc genes 774 Septum Formation. 775 Relationship to other cell cycle events 775 Chitin synthesis . 776 Cell Wall Synthesis after Cytokinesis . 776 Remarks 777
Image and Information

A well-known old adage says that {\em "A picture is worth a thousand words! "} (attributed to the Chinese philosopher Confucius ca 500 years BC). But more precisely, what do we mean by information in images? And how can it be retrieved effectively by machines? We briefly highlight these puzzling questions in this column. But first of all, let us start by defining more precisely what is meant by an "Image. "