Miracle-dz/UniFAR-FTUs huggingface dataset:
Vantage Feature Frames for Fine-Grained Categorization

We study fine-grained categorization, the task of distinguishing among (sub)categories of the same generic object class (e.g., birds), focusing on determining botanical species (leaves and orchids) from scanned images. The strategy is to focus attention around several vantage points, which is the approach taken by botanists, but using features dedicated to the individual categories. Our implementation of the strategy is based on {\it vantage feature frames}, a novel object representation consisting of two components: a set of coordinate systems centered at the most discriminating local viewpoints for the generic object class and a set of category-dependent features computed in these frames. The features are pooled over frames to build the classifier. Categorization then proceeds from coarse-grained (finding the frames) to fine-grained (finding the category), and hence the vantage feature frames must be both detectable and discriminating. The proposed method outperforms state-of-the art algorithms, in particular those using more distributed representations, on standard databases of leaves.
Brain Natriuretic Peptide Is Produced in Cardiac Fibroblasts and Induces Matrix Metalloproteinases

Abstract— Cardiac fibroblasts (CFs) produce extracellular matrix proteins and participate in the remodeling of the heart. It is unknown if brain natriuretic peptide (BNP) is synthesized by CFs and if BNP participates in the regulation of extracellular matrix turnover. In this study, we examined the production of BNP in adult canine CFs and the role of BNP and its signaling system on collagen synthesis and on the activation of matrix metalloproteinases (MMPs). BNP mRNA was detected in CFs, and a specific radioimmunoassay demonstrated that BNP1-32 was secreted into the media at a rate of 11.2±1.0 pg/105 cells per 48 hours (mean±SEM). The amount of BNP secretion was significantly (P <0.01) augmented by 10−7 mol/L tumor necrosis factor-&agr; in a time-dependent manner. BNP significantly (P <0.01) inhibited de novo collagen synthesis as assessed by [3H]proline incorporation, whereas zymographic MMP-2 (gelatinase) abundance was significantly (P <0.05) stimulated by BNP between 10−7 and 10−6 mol/L. In addition, protein expression of MMP-1, -2, and -3 and membranous type-1 MMP was significantly increased by 10−6 mol/L BNP. The cGMP analogue 8-bromo-cGMP (10−4 mol/L) mimicked the BNP effect, whereas inhibition of protein kinase G by KT5823 (10−6 mol/L) significantly (P <0.05) attenuated BNP-induced zymographic MMP-2 abundance. In summary, this study reports that BNP is present in cultured CFs and that BNP decreases collagen synthesis and increases MMPs via cGMP–protein kinase G signaling. These in vitro findings support a role for BNP as a regulator of myocardial structure via control of cardiac fibroblast function.
Tau, amyloid, and hypometabolism in a patient with posterior cortical atrophy

Determining the relative contribution of amyloid plaques and neurofibrillary tangles to brain dysfunction in Alzheimer disease is critical for therapeutic approaches, but until recently could only be assessed at autopsy. We report a patient with posterior cortical atrophy (visual variant of Alzheimer disease) who was studied using the novel tau tracer [18F]AV‐1451 in conjunction with [11C]Pittsburgh compound B (PIB; amyloid) and [18F]fluorodeoxyglucose (FDG) positron emission tomography. Whereas [11C]PIB bound throughout association neocortex, [18F]AV‐1451 was selectively retained in posterior brain regions that were affected clinically and showed markedly reduced [18F]FDG uptake. This provides preliminary in vivo evidence that tau is more closely linked to hypometabolism and symptomatology than amyloid. Ann Neurol 2014.
Expression of FACT in mammalian tissues suggests its role in maintaining of undifferentiated state of cells

The Facilitates Chromatin Transcription (FACT) chromatin remodeling complex, comprised of two subunits, SSRP1 and SPT16, is involved in transcription, replication and DNA repair. We recently showed that curaxins, small molecules with anti-cancer activity, target FACT and kill tumor cells in a FACT-dependent manner. We also found that FACT is overexpressed in human and mouse tumors and that tumor cells are sensitive to FACT downregulation. To clarify the clinical potential of FACT inhibition, we were interested in physiological role(s) of FACT in multicellular organisms. We analyzed SSRP1 and SPT16 expression in different cells, tissues and conditions using Immunohistochemical (IHC) staining of mouse and human tissues and analysis of publically available high-content gene expression datasets. Both approaches demonstrated coordinated expression of the two FACT subunits, which was primarily associated with the stage of cellular differentiation. Most cells of adult tissues do not have detectable protein level of FACT. High FACT expression was associated with stem or less-differentiated cells, while low FACT levels were seen in more differentiated cells. Experimental manipulation of cell differentiation and proliferation in vitro, as well as tissue staining for the Ki67 proliferation marker, showed that FACT expression is related more to differentiation than to proliferation. Thus, FACT may be part of a stem cell-like gene expression signature and play a role in maintaining cells in an undifferentiated state, which is consistent with its potential role as an anti-cancer target.
A SUMO-interacting motif activates budding yeast ubiquitin ligase Rad18 towards SUMO-modified PCNA

SUMO-targeted ubiquitin ligases (STUbLs) recognize sumoylated proteins as substrates for ubiquitylation and have been implicated in several aspects of DNA repair and the damage response. However, few physiological STUbL substrates have been identified, and the relative importance of SUMO binding versus direct interactions with the substrate remains a matter of debate. We now present evidence that the ubiquitin ligase Rad18 from Saccharomyces cerevisiae, which monoubiquitylates the sliding clamp protein proliferating cell nuclear antigen (PCNA) in response to DNA damage, exhibits the hallmarks of a STUbL. Although not completely dependent on sumoylation, Rad18’s activity towards PCNA is strongly enhanced by the presence of SUMO on the clamp. The stimulation is brought about by a SUMO-interacting motif in Rad18, which also mediates sumoylation of Rad18 itself. Our results imply that sumoylated PCNA is the physiological ubiquitylation target of budding yeast Rad18 and suggest a new mechanism by which the transition from S phase-associated sumoylation to damage-induced ubiquitylation of PCNA is accomplished.
The essence of P2P: a reference architecture for overlay networks

The success of the P2P idea has created a huge diversity of approaches, among which overlay networks, for example, Gnutella, Kazaa, Chord, Pastry, Tapestry, P-Grid, or DKS, have received specific attention from both developers and researchers. A wide variety of algorithms, data structures, and architectures have been proposed. The terminologies and abstractions used, however, have become quite inconsistent since the P2P paradigm has attracted people from many different communities, e.g., networking, databases, distributed systems, graph theory, complexity theory, biology, etc. In this paper we propose a reference model for overlay networks which is capable of modeling different approaches in this domain in a generic manner. It is intended to allow researchers and users to assess the properties of concrete systems, to establish a common vocabulary for scientific discussion, to facilitate the qualitative comparison of the systems, and to serve as the basis for defining a standardized API to make overlay networks interoperable.
Climate Change Impacts at Department of Defense Installations

Abstract : This project is aimed at providing the U.S. Department of Defense (DoD) with a comprehensive analysis of the uncertainty associated with generating climate projections at the regional scale that can be used by stakeholders and decision makers to quantify and plan for the impacts of future climate change at specific locations. The merits and limitations of commonly used downscaling models, ranging from simple to complex, are compared, and their appropriateness for application at installation scales is evaluated. Downscaled climate projections are generated at selected DoD installations using dynamic and statistical methods with an emphasis on generating probability distributions of climate variables and their associated uncertainties. The sites selection and selection of variables and parameters for downscaling was based on a comprehensive understanding of the current and projected roles that weather and climate play in operating, maintaining, and planning DoD facilities and installations.
CHARACTERIZATION AND APPLICATION OF PHYSIOLOGICALLY BASED PHARMACOKINETIC MODELS IN RISK ASSESSMENT

The overall objectives of the IPCS are to establish the scientific basis for assessment of the risk to human health and the environment from exposure to chemicals, through international peer review processes, as a prerequisite for the promotion of chemical safety, and to provide technical assistance in strengthening national capacities for the sound management of chemicals. (Participating Organizations), following recommendations made by the 1992 UN Conference on Environment and Development to strengthen cooperation and increase coordination in the field of chemical safety. The purpose of the IOMC is to promote coordination of the policies and activities pursued by the Participating Organizations, jointly or separately, to achieve the sound management of chemicals in relation to human health and the environment. WHO Library Cataloguing-in-Publication Data Characterization and application of physiologically based pharmacokinetic models in risk assessment. e-mail: bookorders@who.int). Requests for permission to reproduce or translate WHO publications—whether for sale or for non-commercial distribution—should be addressed to WHO Press at the above address (fax: +41 22 791 4806; e-mail: permissions@who.int). The designations employed and the presentation of the material in this publication do not imply the expression of any opinion whatsoever on the part of the World Health Organization concerning the legal status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. Dotted lines on maps represent approximate border lines for which there may not yet be full agreement. The mention of specific companies or of certain manufacturers' products does not imply that they are endorsed or recommended by the World Health Organization in preference to others of a similar nature that are not mentioned. Errors and omissions excepted, the names of proprietary products are distinguished by initial capital letters. All reasonable precautions have been taken by the World Health Organization to verify the information contained in this publication. However, the published material is being distributed without warranty of any kind, either express or implied. The responsibility for the interpretation and use of the material lies with the reader. In no event shall the World Health Organization be liable for damages arising from its use.
Interactions of WASp, myosin-I, and verprolin with Arp2/3 complex during actin patch assembly in fission yeast

Yeast actin patches are dynamic structures that form at the sites of cell growth and are thought to play a role in endocytosis. We used biochemical analysis and live cell imaging to investigate actin patch assembly in fission yeast Schizosaccharomyces pombe. Patch assembly proceeds via two parallel pathways: one dependent on WASp Wsp1p and verprolin Vrp1p converges with another dependent on class 1 myosin Myo1p to activate the actin-related protein 2/3 (Arp2/3) complex. Wsp1p activates Arp2/3 complex via a conventional mechanism, resulting in branched filaments. Myo1p is a weaker Arp2/3 complex activator that makes unstable branches and is enhanced by verprolin. During patch assembly in vivo, Wsp1p and Vrp1p arrive first independent of Myo1p. Arp2/3 complex associates with nascent activator patches over 6–9 s while remaining stationary. After reaching a maximum concentration, Arp2/3 complex patches move centripetally as activator proteins dissociate. Genetic dependencies of patch formation suggest that patch formation involves cross talk between Myo1p and Wsp1p/Vrp1p pathways.
Visual Interactions Conform to Pattern Decorrelation in Multiple Cortical Areas

Neural responses to visual stimuli are strongest in the classical receptive field, but they are also modulated by stimuli in a much wider region. In the primary visual cortex, physiological data and models suggest that such contextual modulation is mediated by recurrent interactions between cortical areas. Outside the primary visual cortex, imaging data has shown qualitatively similar interactions. However, whether the mechanisms underlying these effects are similar in different areas has remained unclear. Here, we found that the blood oxygenation level dependent (BOLD) signal spreads over considerable cortical distances in the primary visual cortex, further than the classical receptive field. This indicates that the synaptic activity induced by a given stimulus occurs in a surprisingly extensive network. Correspondingly, we found suppressive and facilitative interactions far from the maximum retinotopic response. Next, we characterized the relationship between contextual modulation and correlation between two spatial activation patterns. Regardless of the functional area or retinotopic eccentricity, higher correlation between the center and surround response patterns was associated with stronger suppressive interaction. In individual voxels, suppressive interaction was predominant when the center and surround stimuli produced BOLD signals with the same sign. Facilitative interaction dominated in the voxels with opposite BOLD signal signs. Our data was in unison with recently published cortical decorrelation model, and was validated against alternative models, separately in different eccentricities and functional areas. Our study provides evidence that spatial interactions among neural populations involve decorrelation of macroscopic neural activation patterns, and suggests that the basic design of the cerebral cortex houses a robust decorrelation mechanism for afferent synaptic input.
Trial Design for Testing and Evaluation of Metal Detectors Used in Humanitarian Landmine Clearance

In spite of many efforts directed to new technologies, the metal detector is still the main detection tool used in humanitarian landmine clearance. The most de- tailed proposal for a standard for testing metal detectors is the CEN Workshop Agreement 14747:2003. Since 2003 a series of tests has been executed with the pur- pose of optimisation and more detailed specification of the testing procedures. The main purpose of the test procedures is the identification of the most appropriate de- vice for certain conditions of application. The reliability of a detection system is influenced by the intrinsic physical capability of the method, the application factor and the human factor. The physical capabilities and some influences of application conditions can be evaluated in laboratory meas- urements, but the influence of the human factor and other environmental influences can be derived correctly from blind tests only, since they are conducted under field conditions. This paper discusses the design of the experiment for testing and evaluation of metal detectors based on the experiences gained from several field tests performed from 2003 to 2005. These tests evaluated the latest models of four metal detector manu- facturers. Both pulse induction and continuous wave detectors were tested. Also the shapes of their coils are different: most of the detectors use a single coil, but some use the "double-D" configuration. Some of the detectors are static mode detectors, some dynamic mode ones. They all have some data processing to compensate the soil background effects. The influences of soil, target type and its depth, as well as the human operator influ- ence are evaluated with the application of an appropriate design of experiment. A full factorial design was applied to the maximum detection height measurements and a fractional factorial design to the blind tests, also called reliability tests. The results of both tests are discussed in this paper. The performance indicators of the blind tests are the probability of detection (POD) and the false alarm rate (FAR). The methods for the design of experiment and data evaluation for multiple parameter in- fluences are applicable also in other areas of non-destructive testing.
Extra-Precise Iterative Refinement for Overdetermined Least Squares Problems

We present the algorithm, error bounds, and numerical results for extra-precise iterative refinement applied to overdetermined linear least squares (LLS) problems. We apply our linear system refinement algorithm to Björck’s augmented linear system formulation of an LLS problem. Our algorithm reduces the forward normwise and componentwise errors to <i>O</i>(<i>ϵ</i><sub>w</sub>), where <i>ϵ</i><sub>w</sub> is the working precision, unless the system is too ill conditioned. In contrast to linear systems, we provide two separate error bounds for the solution <i>x</i> and the residual <i>r</i>. The refinement algorithm requires only limited use of extra precision and adds only <i>O</i>(<i>mn</i>) work to the <i>O</i>(<i>mn</i><sup>2</sup>) cost of QR factorization for problems of size <i>m</i>-by-<i>n</i>. The extra precision calculation is facilitated by the new extended-precision BLAS standard in a portable way, and the refinement algorithm will be included in a future release of LAPACK and can be extended to the other types of least squares problems.
Distributed Averaging Using Periodic Gossiping

The distributed averaging problem is a consensus problem whose objective is to devise a protocol which will enable all the members of a group of autonomous agents to compute the average of the initial values of their individual consensus variables in a distributed manner. Periodic gossiping is a deterministic method for solving the distributed averaging problem by stipulating that each pair of agents which are allowed to gossip, do so repeatedly in accordance with a prespecified periodic schedule. Agent pairs which are allowed to gossip correspond to edges on a given connected, undirected graph. In general, the rate at which the agents' consensus variables converge to the desired average value depends on the order in which the gossips occur over a period. The main contributions of this paper are first to characterize the classes of periodic gossip sequences which have the same convergence rate and second to prove that if the graph of allowable gossips is a tree with each edge restricted to gossiping once per period, the convergence rate is quite surprisingly, fixed and invariant over all possible periodic gossip sequences the graph allows. To arrive at these results, a new and unusual graph theoretic concept, namely the transfer function of a node of an undirected graph, is used. Among all the trees with the same number of edges, optimal tree structures, which yield the fastest convergence rate, can then be sought.
Association between Statin Use and Cancer: Data Mining of a Spontaneous Reporting Database and a Claims Database

Purpose: In recent years, the potential risk of cancer associated with statin use has been a focus of much interest. However, it remains uncertain whether statin therapy is associated with cancer risk. To examine the association between statin use and the risk of cancer, we conducted data mining using the US Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) and a large organized database of claims constructed by a database vendor (The Japan Medical Data Center Co., Ltd, Tokyo, Japan [JMDC]). Methods: Relevant reports in the FAERS, which included data from the first quarter of 2004 through the end of 2012, were identified and analyzed. The reporting odds ratio (ROR) was used to detect spontaneous report signals and was calculated using the case/non-case method. Additionally, signals were detected via the information component (IC) using the IC025 metric. Furthermore, event sequence symmetry analysis (ESSA) was applied to identify the risk of cancer following treatment with statins over the period January 2005 to July 2013. Results: In the FAERS database analyses, significant signals for colorectal cancer and pancreatic cancer were found for statins as a class. In the ESSA, significant associations between statin use and colorectal cancer and pancreatic cancer were found, with adjusted sequence ratios (95% confidence intervals) of 1.20 (1.08-1.34) and 1.31 (1.13-1.53), respectively, at an interval of 48 months. Conclusions: Multi-methodological approaches using different algorithms and databases suggest that statin use is associated with an increased risk for colorectal cancer and pancreatic cancer.
Metamorphic Testing and Its Applications

An “oracle” in software testing is a procedure by which testers can decide whether the output of the program under testing is correct. In some situations, however, the oracle is no t available or too difficult to apply. This is known as the “oracle problem”. In other situations, the oracle is often the human tester who checks the testing result manually. The manual prediction and verification of program output greatl y decreases the efficiency and increases the cost of testing. A metamorphic testing method has been proposed to test programs without the involvement of an oracle. It employs properties of the target function, known as metamorphic relations, to generate follow-up test cases and verify the outputs auto∗ c 2004 Software Engineering Association, Japan. This material is presented to ensure timely dissemination of scholarly and technical work. Personal use of this material is permitted. Copyright and all r ights therein are retained by authors or by other copyright holders. All persons copying this information are expected to adhere to the terms and constraints invoked by each author’s copyright. In most cases, these works ma y not be reposted without the explicit permission of the copyright holder. Permission to reprint/republish this material for advertising or promot ional purposes or for creating new collective works for resale or redistribut ion to servers or lists, or to reuse anyrcopyrighted component of this work in other works must be obtained from the Software Engineers Association, Japan. † This research is supported in part by a discovery grant of the Aus
Hemodynamic Consequences of Auto-PEEP

Auto–positive end-expiratory pressure (PEEP) is a common but frequently unrecognized problem in critically ill patients. It has important physiologic consequences and can cause shock and cardiac arrest. Treatment consists of relieving expiratory airflow obstruction and reducing minute ventilation delivered by positive pressure ventilation. Sedation and fluid management are important adjunctive therapies. This analytic review discusses the prevalence, pathophysiology, and hemodynamic consequences of auto-PEEP and an approach to its treatment.