Miracle-dz/UniFAR-FTUs huggingface dataset:
Interferon-Inducible CXC Chemokines Directly Contribute to Host Defense against Inhalational Anthrax in a Murine Model of Infection

Chemokines have been found to exert direct, defensin-like antimicrobial activity in vitro, suggesting that, in addition to orchestrating cellular accumulation and activation, chemokines may contribute directly to the innate host response against infection. No observations have been made, however, demonstrating direct chemokine-mediated promotion of host defense in vivo. Here, we show that the murine interferon-inducible CXC chemokines CXCL9, CXCL10, and CXCL11 each exert direct antimicrobial effects in vitro against Bacillus anthracis Sterne strain spores and bacilli including disruptions in spore germination and marked reductions in spore and bacilli viability as assessed using CFU determination and a fluorometric assay of metabolic activity. Similar chemokine-mediated antimicrobial activity was also observed against fully virulent Ames strain spores and encapsulated bacilli. Moreover, antibody-mediated neutralization of these CXC chemokines in vivo was found to significantly increase host susceptibility to pulmonary B. anthracis infection in a murine model of inhalational anthrax with disease progression characterized by systemic bacterial dissemination, toxemia, and host death. Neutralization of the shared chemokine receptor CXCR3, responsible for mediating cellular recruitment in response to CXCL9, CXCL10, and CXCL11, was not found to increase host susceptibility to inhalational anthrax. Taken together, our data demonstrate a novel, receptor-independent antimicrobial role for the interferon-inducible CXC chemokines in pulmonary innate immunity in vivo. These data also support an immunomodulatory approach for effectively treating and/or preventing pulmonary B. anthracis infection, as well as infections caused by pathogenic and potentially, multi-drug resistant bacteria including other spore-forming organisms.
Feature-Augmented Neural Networks for Patient Note De-identification

Patient notes contain a wealth of information of potentially great interest to medical investigators. However, to protect patients’ privacy, Protected Health Information (PHI) must be removed from the patient notes before they can be legally released, a process known as patient note de-identification. The main objective for a de-identification system is to have the highest possible recall. Recently, the first neural-network-based de-identification system has been proposed, yielding state-of-the-art results. Unlike other systems, it does not rely on human-engineered features, which allows it to be quickly deployed, but does not leverage knowledge from human experts or from electronic health records (EHRs). In this work, we explore a method to incorporate human-engineered features as well as features derived from EHRs to a neural-network-based de-identification system. Our results show that the addition of features, especially the EHR-derived features, further improves the state-of-the-art in patient note de-identification, including for some of the most sensitive PHI types such as patient names. Since in a real-life setting patient notes typically come with EHRs, we recommend developers of de-identification systems to leverage the information EHRs contain.
Integrating user preferences and decomposition methods for many-objective optimization

Evolutionary algorithms that rely on dominance ranking often suffer from a low selection pressure problem when dealing with many-objective problems. Decomposition and user-preference based methods can help to alleviate this problem to a great extent. In this paper, a user-preference based evolutionary multi-objective algorithm is proposed that uses decomposition methods for solving many-objective problems. Decomposition techniques that are widely used in multi-objective evolutionary optimization require a set of evenly distributed weight vectors to generate a diverse set of solutions on the Pareto-optimal front. The newly proposed algorithm, R-MEAD2, improves the scalability of its previous version, R-MEAD, which uses a simplexlattice design method for generating weight vectors. This makes the population size is dependent on the dimension size of the objective space. R-MEAD2 uses a uniform random number generator to remove the coupling between dimension and the population size. This paper shows that a uniform random number generator is simple and able to generate evenly distributed points in a high dimensional space. Our comparative study shows that R-MEAD2 outperforms the dominance-based method R-NSGA-II on many-objective problems.
Remote sensing approaches and mapping methods for monitoring soil salinity under different climate regimes

Soil salinization is one of the severe land-degradation problems due to its adverse effects on land productivity. Each year several hectares of lands are degraded due to primary or secondary soil salinization, and as a result, it is becoming a major economic and environmental concern in different countries. Spatio-temporal mapping of soil salinity is therefore important to support decision-making procedures for lessening adverse effects of land degradation due to the salinization. In that sense, satellite-based technologies provide cost effective, fast, qualitative and quantitative spatial information on saline soils. The main objective of this work is to highlight the recent remote sensing (RS) data and methods to assess soil salinity that is a worldwide problem. In addition, this study indicates potential linkages between salt-affected land and the prevailing climatic conditions of the case study areas being examined. Web of Science engine is used for selecting relevant articles. "Soil salinity" is used as the main keyword for finding "articles" that are published from January 1, 2007 up to April 30, 2018. Then, 3 keywords; "remote sensing", "satellite" and "aerial" were used to filter the articles. After that, 100 case studies from 27 different countries were selected. Remote sensing based researches were further overviewed regarding to their location, spatial extent, climate regime, remotely sensed data type, mapping methods, sensing approaches together with the reason of salinity for each case study. In addition, soil salinity mapping methods were examined to present the development of different RS based methods with time. Studies are shown on the Koppen-Geiger climate classification map. Analysis of the map illustrates that 63% of the selected case study areas belong to arid and semi-arid regions. This finding corresponds to soil characteristics of arid regions that are more susceptible to salinization due to extreme temperature, high evaporation rates and low precipitation.
Mixed analog/digital receiver beamforming for 60GHz OFDM System with co-channel interference mitigation

Large antenna arrays are usually used in 60GHz for beamforming to compensate the high path loss in this band. IEEE 802.15. 3c adopted a beamforming codebook design to reduce the cost and power consumption of the large array, but which is not enough to deal with interference in a dense network. This paper proposed a mixed analog and digital receiver beamforming structure with subarray partition, which keeps the simplicity of the IEEE 802.15. 3c codebook antenna design. This structure includes 2 stages: the Analog BeamForming (ABF) stage and the Digital BeamForming (DBF) stage. In the ABF stage, the codeword of each subarray is decided as described in IEEE 802.15. 3c standard, and then the combined signal of each subarray is further optimized in the DBF stage based on Minimum Mean Square Error (MMSE) criterion. Simulation results have shown that the system performance against CCI could be significantly increased with only 1 additional Analog-Front-End (AFE) utilizing the proposed structure.
Detection in Passive MIMO Radar Networks

This paper addresses target detection in passive multiple-input multiple-output (MIMO) radar networks comprised of non-cooperative transmitters and multichannel receivers. A generalized likelihood ratio test is derived, and approximate test statistic distributions are presented for both hypotheses under common scenario conditions. Analysis and simulation results show that this detector outperforms other passive MIMO radar detectors because it exploits more correlations within the measurement data. This detector is also compared against related detectors for active MIMO radar and passive source localization sensor networks. These comparisons reveal that passive MIMO radar detection performance varies between active MIMO radar and passive source localization detection performance as a function of direct-path signal quality. Therefore, passive MIMO radar unifies active MIMO radar and passive source localization sensor networks in a common theoretical framework.
Activated cMET and IGF1R-Driven PI3K Signaling Predicts Poor Survival in Colorectal Cancers Independent of KRAS Mutational Status

Background Oncogenic mutational analysis provides predictive guidance for therapeutics such as anti-EGFR antibodies, but it is successful only for a subset of colorectal cancer (CRC) patients. Method A comprehensive molecular profiling of 120 CRC patients, including 116 primary, 15 liver metastasis, and 1 peritoneal seeding tissue samples was performed to identify the relationship between v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) WT and mutant CRC tumors and clinical outcomes. This included determination of the protein activation patterns of human epidermal receptor 1 (HER1), HER2, HER3, c-MET, insulin-like growth factor 1 receptor (IGF1R), phosphatidylinositide 3-kinase (PI3K), Src homology 2 domain containing (Shc), protein kinase B (AKT), and extracellular signal-regulated kinase (ERK) kinases using multiplexed collaborative enzyme enhanced reactive (CEER) immunoassay. Results KRAS WT and mutated CRCs were not different with respect to the expression of the various signaling molecules. Poor prognosis in terms of early relapse (<2 years) and shorter disease-free survival (DFS) correlated with enhanced activation of PI3K signaling relative to the HER kinase pathway signaling, but not with the KRAS mutational status. KRAS WT CRCs were identified as a mixed prognosis population depending on their level of PI3K signaling. KRAS WT CRCs with high HER1/c-MET index ratio demonstrated a better DFS post-surgery. c-MET and IGF1R activities relative to HER axis activity were considerably higher in early relapse CRCs, suggesting a role for these alternative receptor tyrosine kinases (RTKs) in driving high PI3K signaling. Conclusions The presented data subclassified CRCs based on their activated signaling pathways and identify a role for c-MET and IGF1R-driven PI3K signaling in CRCs, which is superior to KRAS mutational tests alone. The results from this study can be utilized to identify aggressive CRCs, explain failure of currently approved therapeutics in specific CRC subsets, and, most importantly, generate hypotheses for pathway-guided therapeutic strategies that can be tested clinically.
Micro-Policies: Formally Verified, Tag-Based Security Monitors

Recent advances in hardware design have demonstrated mechanisms allowing a wide range of low-level security policies (or micro-policies) to be expressed using rules on metadata tags. We propose a methodology for defining and reasoning about such tag-based reference monitors in terms of a high-level "symbolic machine" and we use this methodology to define and formally verify micro-policies for dynamic sealing, compartmentalization, control-flow integrity, and memory safety, in addition, we show how to use the tagging mechanism to protect its own integrity. For each micro-policy, we prove by refinement that the symbolic machine instantiated with the policy's rules embodies a high-level specification characterizing a useful security property. Last, we show how the symbolic machine itself can be implemented in terms of a hardware rule cache and a software controller.
Remark on “Algorithm 474: Bivariate Interpolation and Smooth Surface Fitting Based on Local Procedures [E2]”

Subroutine S F C F I T contains a violation of the Fortran Standard [1] similar to that observed [2] in a previous contribution by the same author [3]. Section 7.1. 2.8 states that the initial value of a DO statement must be less than or equal to the valu~ represented by the terminal parameter. When L X or L Y are input as 2, DO statements labeled 10, 30, 60, and 80 violate this rule. Error conditions of
Inference of message sequence charts

Software designers draw Message Sequence Charts for early modeling of the individual behaviors they expect from the concurrent system under design. Can they be sure that precisely the behaviors they have described are realizable by some implementation of the components of the concurrent system? If so, can one automatically synthesize concurrent state machines realizing the given MSCs? If, on the other hand, other unspecified and possibly unwanted scenarios are "implied" by their MSCs, can the software designer be automatically warned and provided the implied MSCs? In this paper we provide a framework in which all these questions are answered positively. We first describe the formal framework within which one can derive implied MSCs, and we then provide polynomial-time algorithms for implication, realizability, and synthesis. In particular, we describe a novel algorithm for checking deadlock-free (safe) realizability.
A novel one-to-many and many-to-one asymmetric encryption model and its algorithms

Traditional asymmetric encryption algorithms involve only two parties: one party is a sender encrypter and the other a receiver decrypter, in which each party has two different keys: a private key and a public key. However, if applied in some multiparty-oriented environments, there may be a serious problem that each party needs to store and manage many keys, which is not only an overload but also a potential safety hazard. In this paper, we built a new secure communication model for private client-server networks, in which each party only needs to store a private key, but it can still implement two-way secure communications with two properties of "one-to-many encryption" i.e., if the server encrypts a plaintext, all clients can decrypt the ciphertext by using their respective private keys and "many-to-one encryption" i.e., if each client encrypts a plaintext by using his or her private key, only the server can decrypt the ciphertext. Furthermore, by introducing the basic theories for solving linear equations and ElGamal cryptographic algorithms, we designed the corresponding encryption and decryption algorithms in detail. The analysis results show that our algorithms are secure and efficient, and there are many good potential applications in military and electronic commerce fields. Copyright © 2015 John Wiley & Sons, Ltd.
An efficient projection for l1, ∞ regularization

In recent years the <i>l</i><sub>1</sub>, <sub>∞</sub> norm has been proposed for joint regularization. In essence, this type of regularization aims at extending the <i>l</i><sub>1</sub> framework for learning sparse models to a setting where the goal is to learn a set of jointly sparse models. In this paper we derive a simple and effective projected gradient method for optimization of <i>l</i><sub>1</sub>, <sub>∞</sub> regularized problems. The main challenge in developing such a method resides on being able to compute efficient projections to the <i>l</i><sub>1</sub>, <sub>∞</sub> ball. We present an algorithm that works in <i>O</i>(<i>n</i> log <i>n</i>) time and <i>O</i>(<i>n</i>) memory where <i>n</i> is the number of parameters. We test our algorithm in a multi-task image annotation problem. Our results show that <i>l</i><sub>1</sub>, <sub>∞</sub> leads to better performance than both <i>l</i><sub>2</sub> and <i>l</i><sub>1</sub> regularization and that it is is effective in discovering jointly sparse solutions.
Power Allocation Strategies for Distributed Space-Time Codes in Two-Way Relay Networks

We study a two-way relay network (TWRN), where distributed space-time codes are constructed across multiple relay terminals in an amplify-and-forward mode. Each relay transmits a scaled linear combination of its received symbols and their conjugates, with the scaling factor chosen based on automatic gain control. We consider equal power allocation (EPA) across the relays, as well as the optimal power allocation (OPA) strategy given access to instantaneous channel state information (CSI). For EPA, we derive an upper bound on the pairwise-error-probability (PEP), from which we prove that full diversity is achieved in TWRNs. This result is in contrast to one-way relay networks, in which case a maximum diversity order of only unity can be obtained. When instantaneous CSI is available at the relays, we show that the OPA which minimizes the conditional PEP of the worse link can be cast as a generalized linear fractional program, which can be solved efficiently using the Dinkelback-type procedure. We also prove that, if the sum-power of the relay terminals is constrained, then the OPA will activate at most two relays.
Atp6v0d2 Is an Essential Component of the Osteoclast‐Specific Proton Pump That Mediates Extracellular Acidification in Bone Resorption

Bone resorption relies on the extracellular acidification function of vacuolar (V‐) ATPase proton pump(s) present in the plasma membrane of osteoclasts. The exact configuration of osteoclast‐specific V‐ATPases remains largely unknown. In this study, we found that Atp6v0d2 (d2), an isoform of the d subunit in the V‐ATPase, showed 5‐fold higher expression than that of Atp6v0d1 (d1) in mature osteoclasts, indicating a potential function in osteoclastic bone resorption. When d2 was depleted at an early stage of RANKL‐induced osteoclast differentiation in vitro, formation of multinucleated cells was severely impaired. However, depletion of d2 at a late differentiation stage did not affect osteoclast fusion but did abolish the activity of extracellular acidification and bone resorption of mature osteoclasts. We also showed the association of the two tagged‐proteins d2 and a3 when co‐expressed in mammalian cells with a co‐immunoprecipitation assay. Moreover, glutathione‐S‐transferase (GST) pull‐down assay showed the direct interaction of d2 with the N terminus of Atp6v0a3 (a3), which is the functionally identified osteoclast‐specific component of V‐ATPase. Therefore, our results show the dual function of d2 as a regulator of cell fusion in osteoclast differentiation and as an essential component of the osteoclast‐specific proton pump that mediates extracellular acidification in bone resorption.
Fast and Complete Conflict Detection for Packet Classifiers

Packet classification filters are used to classify packets based on header fields. A filter conflict occurs when two or more filters overlap, causing an ambiguity in packet classification. These conflicts may cause quality-of-service failures, security vulnerabilities, or routing errors in network services, e.g., differentiated services and firewalls. There are two types of conflicts, i.e., overlapping and subset. While the subset conflict problem can be solved by reordering filters, overlapping conflicts are resolved by inserting resolve filters. None of the existing algorithms detects both types of conflicts for multidimensional filters with arbitrary-range fields. To fill the research gap, we present a series of algorithms based on a previous algorithm that reports all overlapping filters without identifying overlapping conflicts. We improve the previous algorithm to extract overlapping conflicts by modifying either data structures or operations. To further reduce the cost of conflict detection, we define new data structures to process range fields with their boundary addresses. The algorithm based on new bit vectors can detect partial overlaps between multidimensional filters with arbitrary ranges. Our experimental results show that the new algorithm is two times faster than the algorithms based on the original data structures in detecting both types of conflicts.
The role of dietary selenium in bovine mammary gland health and immune function

Abstract Mastitis is not only a major cause of economic losses to the dairy industry but also a major problem in ensuring the quality and safety of the milk, associated with high somatic cell counts and residues of antibiotics used for treatment. One innovative approach to protection against mastitis is to stimulate the animal's natural defense mechanisms. Technological advances in immunological research have increased our ability to exploit the immunity of the bovine mammary gland during periods of high susceptibility to disease. The trace element selenium affects the innate and the adaptive immune responses of the mammary gland through cellular and humoral activities. Substantial research has been carried out on the effect of selenium (Se) on the immune function of the mammary gland and subsequent improvement in bovine udder health and mastitis control. Levels higher than current recommendations and Se-yeast can potentially be used to enhance our capacity to modulate the physiological mechanisms of the bovine mammary gland to respond to infection. This article provides an overview of the most recent research in this field.
A Thermodynamical Approach for Evaluating Energy Consumption of the Forward Osmosis Process Using Various Draw Solutes

The forward-osmosis (FO) processes have received much attention in past years as an energy saving desalination process. A typical FO process should inclu de a draw solute recovery step which contributes to the main operation costs of the process. Therefore, investigating the energy consumption is very important for the development and employment of the forward osmosis process. In this work, NH3-CO2, Na2SO4, propylene glycol mono-butyl ether, and dipropylamine were selected as draw solutes. The FO processes of different draw solute recovery approaches were simulated by Aspen PlusTM with a customized FO unit model. The electrolyte Non-Random Two-Liquid (Electrolyte-NRTL) and Universal Quasi Chemical (UNIQUAC) models were employed to calculate the thermodynamic properties of the feed and draw solutions. The simulation results indicated that the FO performance decreased under high feed concentration, while the energy consumption was improved at high draw solution concentration. The FO process using Na2SO4 showed the lowest energy consumption, followed by NH3-CO2, and dipropylamine. The propylene glycol mono-butyl ether process exhibited the highest energy consumption due to its low solubility in water. Finally, in order to compare the equivalent work of the FO processes, the thermal energy requirements were converted to electrical work.
Advanced Imaging of Cardiac Sarcoidosis

Sarcoidosis is a systemic granulomatous disease of unknown etiology. Cardiac involvement may occur, leading to an adverse outcome. Although early treatment to improve morbidity and mortality is desirable, sensitive and accurate detection of cardiac sarcoidosis remains a challenge. Accordingly, interest in the use of advanced imaging such as cardiac MR and PET with 18F-FDG is increasing in order to refine the clinical workup. Although the field is still facing challenges and uncertainties, this article presents a summary of clinical background and the current state of diagnostic modalities and treatment of cardiac sarcoidosis.