Miracle-dz/UniFAR-FTUs huggingface dataset:
Geometric categories and o-minimal structures

The theory of subanalytic sets is an excellent tool in various analytic-geometric contexts; see, for example, Bierstone and Milman [1]. Regrettably, certain “nice” sets—like { (x, x) : x > 0 } for positive irrational r, and { (x, e−1/x) : x > 0 }—are not subanalytic (at the origin) in R. Here we make available an extension of the category of subanalytic sets that has these sets among its objects, and that behaves much like the category of subanalytic sets. The possibility of doing this emerged in 1991 when Wilkie [27] proved that the real exponential field is “model complete”, followed soon by work of Ressayre, Macintyre, Marker and the authors; see [21], [5], [7] and [19]. However, there are two obstructions to the use by geometers of this development: (i) while the proofs in these articles make essential use of model theory, many results are also stated there (efficiently, but unnecessarily) in model-theoretic terms; (ii) the results of these papers apply directly only to the cartesian spaces R, and not to arbitrary real analytic manifolds. Consequently, in order to carry out our goal we recast here some results in those papers—as well as many of their consequences—in more familiar terms, with emphasis on results of a geometric nature, and allowing arbitrary (real analytic) manifolds as ambient spaces. We thank W. Schmid and K. Vilonen for their suggestion that this would be a useful undertaking; indeed, they gave us a “wish list” (inspired by Chapters 8 and 9 of Kashiwara and Schapira [12]; see also §10 of [22]) which strongly influenced the form and content of this paper. We axiomatize in Section 1 the notion of “behaving like the category of subanalytic sets” by introducing the notion of “analytic-geometric category”. (The category Can of subanalytic sets is the “smallest” analytic-geometric category.) We also state in Section 1 a number of properties shared by all analytic-geometric categories. Proofs of the more difficult results of this nature, like the Whitney-stratifiability of sets and maps in such a category, often involve the use of charts to reduce to the case of subsets of R. For subsets of R, there already exists the theory of “o-minimal structures on the real field” (defined in Section 2); this subject is developed in detail in [4] and is an abstraction of
Chronic tuberculous epididymitis: color Doppler US findings with histopathologic correlation

AbstractBackground: The aim of this study was to determine the color Doppler features of tuberculous epididymitis and to correlate these findings with histopathologic findings. Methods: Color Doppler ultrasound (US) findings of 12 histopathologically proven tuberculous epididymitis and tuberculous epididymo-orchitis in 11 consecutive patients were retrospectively analyzed. Color Doppler US findings of tuberculous epididymitis were correlated with histopathologic findings. Results: Color Doppler US findings of tuberculous epididymitis demonstrated no blood flow in the epididymal lesions except for focal linear or spotty flow signals in the peripheral portion. These findings correlated well with pathologic findings; the central portion of the epididymal lesions demonstrated granulomas with caseation necrosis, and the peripheral portion of the epididymal lesions had several medium to small vessels. Conclusions: Color Doppler US may be helpful for differential diagnosis of tuberculous epididymitis and non–tuberculous epididymitis.
Improvement of the chemical inhibition phenotyping assay by cross-reactivity correction

Abstract Background: The fraction of an absorbed drug metabolized by the different hepatic cytochrome P450 (CYP) enzymes, relative to total hepatic CYP metabolism (fmCYP), can be estimated by measuring the inhibitory effects of presumably selective CYP inhibitors on the intrinsic metabolic clearance of a drug using human liver microsomes. However, the chemical inhibition data are often affected by cross-reactivities of the chemical inhibitors used in this assay. Methods: To overcome this drawback, the cross-reactivities exhibited by six chemical inhibitors (furafylline, montelukast, sulfaphenazole, ticlopidine, quinidine and ketoconazole) were quantified using specific CYP enzyme marker reactions. The determined cross-reactivities were used to correct the in vitro fmCYPs of nine marketed drugs. The corrected values were compared with reference data obtained by physiologically based pharmacokinetics simulation using the software SimCYP. Results: Uncorrected in vitro fmCYPs of the nine drugs showed poor linear correlation with their reference data (R2=0.443). Correction by factoring in inhibitor cross-reactivities significantly improved the correlation (R2=0.736). Conclusions: Correcting in vitro chemical inhibition results for cross-reactivities appear to offer a straightforward and easily adoptable approach to provide improved fmCYP data for a drug.
A note on Hilbert schemes of nodal curves

We study the Hilbert scheme and punctual Hilbert scheme of a nodal curve, and the relative Hilbert scheme of a family of curves acquiring a node. The results are then extended to flag Hilbert schemes, parametrizing chains of subschemes. We find, notably, that if the total space X of a family X/B is smooth (over an algebraically closed field k), then the relative Hilbert scheme Hilb m (X/B) is smooth over k and the flag Hilbert schemes are normal and locally complete intersection, but generally singular. The Hilbert scheme parametrizes ideal sheaves or subschemes of Projective Space or more generally, or a fixed scheme X. Perhaps the simplest case is where X is a smooth curve, for then the Hilbert scheme Hilb m (X) parametrizing length-m sub-schemes of X coincides with the symmetric product Sym m (X). Our purpose in this note is to study what is in a sense the next simplest case, where X is essentially a curve with ordinary nodes, with planar equation formally equivalent to xy = 0. Besides Hilb m (X) itself, there are (at least) 2 other types of Hilbert scheme of natural interest here: the punctual one Hilb 0 m (X), parametrizing length-m subschemes supported at a node; and the relative one Hilb m (˜ X/B), parametrizing length-m subschemes in the fibres of the family˜X/B that is the map A 2 → A 1 given by xy = t (both Hilb m (X) and Hilb m (˜ X/B) may conveniently be viewed as germs, or formal schemes, along Hilb 0 m (X). All these will be determined below. We find that Hilb 0 m (X) is a connected chain of (m − 1) nonsingular rational curves meeting transeversely; Hilb m (X) is a connected chain of (m + 1) nonsingular m-dimensional germs, whose first and last members are supported on points and each other member is supported on a component of Hilb 0 m (X), and only consecutive members intersect (and those transversely); finally, Hilb m (˜ X/B) is a smooth (m + 1)-fold. To elucidate the relations between the Hilb m for different m, with an eye to enumerative applications based on recursion on m, we will also study some flag Hilbert schemes Hilb m. , parametrizing chains of ideals whose colengths form a given sequence m. = (m 1 > m 2 > .). For some purposes, these are easier to …
Effects of l-/?-D-Arabinofuranosylcytosine on DNA Replication Intermediates Monitored by pH-Step Alkaline Elution1

The pi I-stcp alkaline elution method enables the isolation and quan tification of nascent DNA (nDNA) replication intermediates, including Okazaki fragments, short length nDNA from replicÃ3n origins, longer lengths of nascent but subgenomic length nDNA (molecular weight, 2030 x HI"), and full (or genomic) length nDNA (L. C. Erickson el al., Chromosoma, 74: 125-139, 1979). \Ve utilized this technique to study, in III -Ml cells, the effects of l-/3-l>-arabinofuranosylc)tosine (ara-C) on the formation of these replication intermediates and the kinetics of transit of radiolabel from |'H|thymidine <|'l l]il I lid) or |'l l|-:ira-( through these nDNA fragments and into full length nDNA. In the continuous presence of |3H]-ara-C (4 UM), the majority of radiolabel (>85%) remained in the nascent subgenomic fractions, with 30-50% remaining in Okazaki frag ments. These proportions did not change substantially with increasing time of exposure to |'H|-ara-C (from I to 24 h), although the total amount uf I'll|-;ir;i-< incorporated into DNA continued to increase with increas ing time of exposure. In contrast, when cells Â»ereexposed to [3H|-ara-C for 1 h, placed in drug-free medium, and studied by the pll-step method at various times thereafter, the transit of radiolabel through progressively larger nDNA intermediates and into full length nDNA was rapid and equal to that of |'ll|il I lui in cells not exposed to drug. The observed elution of | 'I l|-:ira-( in the subgenomic-length DNA fragments was not due to ara-C-induced breaks in template (parental) DNA and subsequent incorporation of |'Il|-:ira-( into the template strand, since ara-C treat ment of cells prelabeled with |"( |il I lui failed to cause substantial elution of the UC label at the various pH steps used. In studies of the effects of ara-C on |'ll|il I lui incorporation into nDNA, concentrations of 1 to 10 MMara-C inhibited total incorporation of radiolabel into DNA by >90% and incorporation into full length nDNA by >97%. In contrast, these concentrations of ara-C failed to decrease the amount of ['IIjdThd incor porated into Okazaki fragments or other non-mitochondrial low molecu lar weight nDNA, compared to control. These studies demonstrate that, in III (ill cells, ara-C causes profound inhibition of nascent chain elon gation, does not cause chain termination, and does not inhibit initiation. In fact, ara-C may stimulate initiation, leading credence to recent theories proposing cndoreduplication or reinitiation as consequences of ara-C incorporation into DNA.
Multi-topic Based Query-Oriented Summarization

Query-oriented summarization aims at extracting an informative summary from a document collection for a given query. It is very useful to help users grasp the main information related to a query. Existing work can be mainly classified into two categories: supervised method and unsupervised method. The former requires training examples, which makes the method limited to predefined domains. While the latter usually utilizes clustering algorithms to find ‘centered’ sentences as the summary. However, the method does not consider the query information, thus the summarization is general about the document collection itself. Moreover, most of existing work assumes that documents related to the query only talks about one topic. Unfortunately, statistics show that a large portion of summarization tasks talk about multiple topics. In this paper, we try to break limitations of the existing methods and study a new setup of the problem of multi-topic based query-oriented summarization. We propose using a probabilistic approach to solve this problem. More specifically, we propose two strategies to incorporate the query information into a probabilistic model. Experimental results on two different genres of data show that our proposed approach can effectively extract a multi-topic summary from a document collection and the summarization performance is better than baseline methods. The approach is quite general and can be applied to many other mining tasks, for example product opinion analysis and question answering.
Demon s tration Abs tract : U N A GI : A Protocol Te s t b ed w ith Practical Smart A ntenna s for A d hoc Net w ork s

Wireless ad hoc networks have been attracting a great deal of attention because they can be built with mobile terminals impromptu without any fixed infrastructure. A number of protocols have been proposed for wireless ad hoc networks. In particular, MAC protocols using directional antenna, which are typically referred to as directional MACs, have been proposed. They are expected to improve spatial and temporal reuse. Most studies evaluate protocols by software simulations. In those evaluations the radiation pattern of antennas and wave propagation are ideally modeled. However, those optimistic assumptions do not always apply to a real environment. One of the reasons for the heavy dependence on simulations is the unavailability of experimental hardware/software. In this paper, we develop a protocol testbed called UNAGI1/ESPAR (Ubiquitous Network testbed with an Adaptively Gain-controlled antenna for performance Improvement / ESPAR ) for wireless ad hoc networks, which enables the investigation of directional protocols in a real environment. The overview and the device list of UNAGI/ESPAR are shown in Fig. 1 and Table 1, respectively. The testbed uses the physical layer of IEEE 802.15. 4 and ESPAR (Electronically Steerable Parasitic Array Radiator) antenna developed by ATR which can electrically control the direction of transmitting/receiving beams. The testbed has a GPS receiver and GYRO sensors to obtain location and angle information, which are indispensable to different directional protocols. A debugging en-
DNA replication stress, genome instability and aging

Genome instability is a fundamentally important component of aging in all eukaryotes. How age-related genome instability occurs remains unclear. The free radical theory of aging posits oxidative damage to DNA and other cellular constituents as a primary determinant of aging. More recent versions of this theory predict that mitochondria are a major source of reactive oxygen species (ROS) that cause oxidative damage. Although substantial support for the free radical theory exists, the results of some tests of this theory have been contradictory or inconclusive. Enhanced growth signaling also has been implicated in aging. Many efforts to understand the effects of growth signaling on aging have focused on inhibition of oxidative stress responses that impact oxidative damage. However, recent experiments in the model organism Saccharomyces cerevisiae (budding yeast) and in higher eukaryotes suggest that growth signaling also impacts aging and/or age-related diseases—including cancer and neurodegeneration—by inducing DNA replication stress, which causes DNA damage. Replication stress, which has not been broadly considered as a factor in aging, may be enhanced by ROS that signal growth. In this article, we review evidence that points to DNA replication stress and replication stress-induced genome instability as important factors in aging.
Meta-heurística aplicada ao planejamento de atividades de lotes de vagões em terminais ferroviários

Railroad is very important for the Brazilian economy, especially in the transport of grains and ores. One area of study for railway operation is concerning rail yards and terminals, and a railway terminal is a yard specialized in products loading and unloading. In these terminals, railway wagons spend half of their service lives and carry out several activities, usually made by sets of wagons called lots. An activity in the terminal may have a predecessor, i.e., it requires the conclusion of another activity to start. In addition, it can be executed in more than one mode (Multi-mode), demanding different resources, which are expensive and scarce, therefore, shared. As delays in operation can generate fines, the goal is to minimize the total time that batches of wagons remain in the terminals (staying time), considering the limitation of terminal resources. The operation at terminals has other characteristics that increase its complexity, such as: setup time between specific activities; variation of resource availability over time (scheduled maintenance); and the blocking characteristic, which keeps a resource occupied by the lot even after the activity's end, due to the movement constraint of the batch imposed by rails and / or other facilities. Only one work was found in the literature considering the characteristics of the problem. It proposed a mathematical model based on the Resource Constrained Project Scheduling Problem (RCPSP). However, the model takes a long time to resolve instances, making it impractical for the dynamic of a rail terminal operation. Thus, a meta-heuristic based on the Ant Colony Optimization meta-heuristic (ACO) was developed in this research for the scheduling of activities of wagons' batches in rail terminals, aiming to minimize the staying time of the lots in the terminal and to do it with a processing time consistent with response time of the railway operation. Although there are many meta-heuristics in the literature addressing the RCPSP, including ACO, none were found, considering all the characteristics of the problem, neither addressing the concept of resource blocking with multiple resources per activity. The meta-heuristic generated results that were equal to or close to optimal, and for larger instances, it got results better than the mathematical model found in the literature. In addition, it took less than 2 minutes to do it, an operationally acceptable processing time, and far below the model execution time, which for the largest instances ran for more than 20 hours.
Hierarchical Taxonomy Aware Network Embedding

Network embedding learns the low-dimensional representations for vertices, while preserving the inter-vertex similarity reflected by the network structure. The neighborhood structure of a vertex is usually closely related with an underlying hierarchical taxonomy---the vertices are associated with successively broader categories that can be organized hierarchically. The categories of different levels reflects similarity of different granularity. The hierarchy of the taxonomy therefore requires that the learned representations support multiple levels of granularity. Moreover, the hierarchical taxonomy enables the information to flow between vertices via their common categories, and thus provides an effective mechanism for alleviating data scarcity. However, incorporating the hierarchical taxonomy into network embedding poses a great challenge (since the taxonomy is generally unknown), and it is neglected by the existing approaches. In this paper, we propose NetHiex, a NETwork embedding model that captures the latent HIErarchical taXonomy. In our model, a vertex representation consists of multiple components that are associated with categories of different granularity. The representations of both the vertices and the categories are co-regularized. We employ the nested Chinese restaurant process to guide the search of the most plausible hierarchical taxonomy. The network structure is then recovered from the latent representations via a Bernoulli distribution. The whole model is unified within a nonparametric probabilistic framework. A scalable expectation-maximization algorithm is derived for optimization. Empirical results demonstrate that NetHiex achieves significant performance gain over the state-of-arts.
Microbial based therapy of cancer: A new twist to an age old practice

The use of bacteria in the regression of tumors has long been known. Various approaches for using bacteria in cancer therapy include the use of bacteria as sensitizing agents for chemotherapy, as delivery agents for cancer drugs and as agents for gene therapy. The tumor regression stimulated by infecting microorganisms has been attributed to activation of the immune system of the host. However, recent studies indicate that when tumor-harboring mice with defective immune systems are infected with certain microorganisms, the regression of the tumor is still observed, suggesting that there are other host factors contributing to the microbial associated regression of tumors. Since the use of live or attenuated bacteria for tumor regression has associated toxic effects, studies are in progress to identify a pure microbial metabolite or any component of the microbial cell that might have anti-cancer activity. It has now been demonstrated that a redox protein from Pseudomonas aeruginosa, a cupredoxin, can enter into human cancer cells and trigger the apoptotic cell death. In vivo, this cupredoxin can lead to the regression of tumor growth in immunodeficient mice harboring xenografted melanomas and breast cancer tumors without inducing significant toxic effects, suggesting that it has potential anti-cancer activity. This bacterial protein interacts with p53 and modulates mammalian cellular activity. Hence, it could potentially be used as an anti-cancer agent for solid tumors and has translational value in tumor-targeted or in combinational-biochemotherapy strategies for cancer treatments. Here, we focus on diverse approaches to cancer biotherapy, including bacteriolytic and bacterially-derived anti-cancer agents with an emphasis on their mechanism of action and therapeutic potential.
Auxin-independent depletion of degron-tagged proteins by TIR1

(https://www.micropublication.org/media/2020/01/Screen-Shot-2020-01-11-at-5.29.58-PM.png) Figure 1: A. Example side-by-side micrograph of FLAG::degron::ERFA-3 and degron::ERFA-3;TIR1 adult animals. Expression tagged with mRuby was visualized by fluorescence microscopy. The shorter and thicker appearance of the TIR1 expressing s characteristic of the dumpy phenotype. B. Western blot of ERFA-3 protein levels in FLAG::degron::ERFA-3 and FLAG::degron::E TIR1 mixed-stage animals cultured at 15°C. C. Western blot of ALG-1 protein levels in N2 and FLAG::degron::ALG-1; TIR1 L4 animals cultured at 20°C.
Comparative ecology of seed size and dispersal

Seed mass is correlated with a number of other plant traits, including dispersal mode, growth form and specific leaf area. Specific leaf area is the main determinant of potential relative growth rate and an indicator of the site quality to which a species is adapted. The relationships with dispersal mode and growth form have consistent form in five datasets from three continents, and each account for about 20-30% of variation in log seed mass. Thus, there is also very substantial variation within growth form and dispersal categories. Much, but not all, of the 20-30% is associated with shifted family composition between growth forms or dispersal modes. Experiments have shown that seedlings of larger-seeded species are better able to survive hazards including deep shade, drought, physical damage and the presence of competing vegetation. If there is a common mechanism under these different hazards, it seemingly must be a `reserve effect', whereby during deployment and early growth larger-seeded species hold a bigger percentage of seed reserves uncommitted to seedling structure and available to support respiration or repair damage. A reserve effect has not yet been demonstrated directly. It remains possible that different mechanisms operate under different hazards. Under a reserve effect, advantages of larger seed size should be temporary, and temporary advantage has indeed been observed with regard to seedling survival under dense shade. Although larger seed mass confers benefits on seedlings, larger seeds must necessarily be produced in smaller numbers per unit of resource allocated. Seed mass is presumed to have evolved as a compromise between these counterposed pressures. Yet there has proved to be surprisingly little difference in average seed mass between very different vegetation regions, at least in temperate climates. Rather, there is startlingly wide variation in seed mass among species growing interspersed with each other. Recent applications of game theory may be capable of accounting for this wide variation between coexisting species, but at present these models are driven by competition among seedling species (as opposed to between seedlings and adults). It remains unclear whether competition among seedlings is a decisive influence on species composition in most of the world's vegetation types.