Miracle-dz/UniFAR-FTUs huggingface dataset:
Microarray-based identification of tomato microRNAs and time course analysis of their response to Cucumber mosaic virus infection

A large number of plant microRNAs (miRNAs) are now documented in the miRBase, among which only 30 are for Solanum lycopersicum (tomato). Clearly, there is a far-reaching need to identify and profile the expression of miRNAs in this important crop under various physiological and pathological conditions. In this study, we used an in situ synthesized custom microarray of plant miRNAs to examine the expression and temporal presence of miRNAs in the leaves of tomato plants infected with Cucumber mosaic virus (CMV). Following computational sequence homology search and hairpin structure prediction, we identified three novel tomato miRNA precursor genes. Our results also show that, in accordance with the phenotype of the developing leaves, the tomato miRNAs are differentially expressed at different stages of plant development and that CMV infection can induce or suppress the expression of miRNAs as well as up-regulate some star miRNAs (miRNA*s) which are normally present at much lower levels. The results indicate that developmental anomalies elicited by virus infection may be caused by more complex biological processes.
Different types of tissue composition in inflammatory or reparative upper airway disorders.

BACKGROUND Composition changes of extracellular matrix (ECM) can lead to functional disorders of the upper airways (UA). The aim of this study was to systematically measure both the association patterns and the correlation degree between tissue composition parameters in UA inflammatory diseases. METHODOLOGY Nasal samples were obtained from patients with chronic rhinosinusitis with (CRS+NP), without nasal polyps (CRS), with post-operative adhesions (S) and normal nasal mucosa (NM). A reproducible semi-quantitative method, which takes epithelial and lamina propria damages into account was applied for haematoxylin and eosin, alpha-smooth muscle actin, reticulin, elastin, laminin and collagen type IV stainings. RESULTS The most severe cases of epithelial shedding have been found in a significant higher amount in CRS+NP when compared with NM. The most severe cases of inflammatory reaction were mainly found in CRS+NP. CRS+NP had significantly more severe cases of oedema than NM. Excluding elastin, networks in other ECM proteins were found modified in fibrotic fields but to a lesser extend in oedematous regions in all conditions. CONCLUSION Although non specific, oedema in the lamina propria is a key-feature of CRS+NP, while fibrosis, massively present in CRS and S, affects profoundly the distribution of ECM proteins in these areas.
Cognitive Functioning in Clinically Stable Patients with Bipolar Disorder I and II

Objectives Bipolar disorder is accompanied by cognitive impairments, which persists during euthymic phases. The purpose of the present study was to identify those neuropsychological tests that most reliably tell euthymic bipolar patients and controls apart, and to clarify the extent to which these cognitive impairments are clinically significant as judged from neuropsychological norms. Methods Patients with bipolar disorder (type I: n = 64; type II: n = 44) and controls (n = 86) were examined with a comprehensive neuropsychological test battery yielding 47 measures of executive functioning, speed, memory, and verbal skills. Multivariate analysis was used to build a model of cognitive performance with the ability to expose underlying trends in data and to reveal cognitive differences between patients and controls. Results Patients with bipolar disorder and controls were partially separated by one predictive component of cognitive performance. Additionally, the relative relevance of each cognitive measure for such separation was decided. Cognitive tests measuring set shifting, inhibition, fluency, and searching (e.g., Trail Making Test, Color-Word) had strongest discriminating ability and most reliably detected cognitive impairments in the patient group. Conclusions Both bipolar disorder type I and type II were associated with cognitive impairment that for a sizeable minority is significant in a clinical neuropsychological sense. We demonstrate a combination of neuropsychological tests that reliably detect cognitive impairment in bipolar disorder.
Traffic Sign Recognition by Color Filtering and Particle Swarm Optimization

In this paper a comprehensive approach to traffic sign detection and recognition is proposed. An RGB roadside image is acquired. Color filtering and segmentation is used to detect the boundary of traffic sign in binary mode. At the feature extraction stage, the RGB traffic sign region is cropped. The image is resized to 100x100 pixels. Finally, particle swarm optimization is used to identify the traffic sign. Experimental results show that our system can give a high recognition rate for all types of traffic signs used in Thailand: namely, prohibitory signs (red or blue), general warning signs (yellow) and construction area warning signs (amber).
INFECTIOUS DISEASES, FROM HCV TO CPE HOW SUSCEPTIBLE ARE WE?

Abstract Infectious diseases remain a leading cause of morbidity and mortality. Still, there is substantial variation in the individual outcome when humans are exposed to potentially pathogenic micro-organisms. At least, one of the factors involved in the individual susceptibility to infections, is the genetic diversity of the host‘s immune response. This article gives a concise overview of the actual knowledge on the genetic mechanisms underlying human susceptibility to infectious diseases and the methods that are used to investigate it.
Privacy-preserving mobile crowdsensing for located-based applications

Mobile crowdsensing is a new paradigm which explores the mobility and intelligence of mobile users to collect high-quality data from social events and phenomena for conducting complex sensing tasks. Nevertheless, privacy preservation and task allocation become main obstacles that need additional attention. To achieve accurate task allocation, it is inevitable to share some sensitive information of mobile users and customers, such as identities, location and points of interest. In this paper, we propose a privacy-preserving mobile crowdsensing framework (PPMC) for location-based applications to balance the tradeoff between privacy preservation and task allocation. In PPMC, we develop a matrix-based location matching mechanism for the service provider to achieve location-based task allocation without disclosing the location of mobile users and the sensing area of tasks. We also extend BBS+ signature and proxy reencryption to preserve identity privacy and data privacy for both customers and mobile users under the condition that they are honest to release and perform tasks, respectively. Finally, we discuss security properties and demonstrate the efficiency of PPMC in terms of computational and communication overhead.
Detecting and Analyzing Insecure Component Integration

Component technologies have been widely adopted for designing and engineering software applications and systems, which dynamically integrate software components to achieve desired functionalities. Engineering software in a component-based style has significant benefits, such as improved programmer productivity and software reliability. To support component integration, operating systems allow an application to dynamically load and use a component. Although developers have frequently utilized such a system-level mechanism, programming errors can lead to insecure component integration and serious security vulnerabilities. The security and reliability impact of component integration has not yet been much explored. This dissertation systematically investigates security issues in dynamic component integration and their impact on software security. On the conceptual level, we formulate two types of insecure component integration—unsafe component loading and insecure component usage—and present practical, scalable techniques to detect and analyze them. Our techniques operate directly on software binaries and do not require source code. On the practical level, we have used them to discover new vulnerabilities in popular, real-world software, and show that insecure component integration is prevalent and can be exploited by attackers to subvert important software and systems. Our research has had substantial practical impact and helped to mitigate unsafe component loadings on Microsoft Windows applications. Detecting and Analyzing Insecure Component Integration
[Human chorionic TSH-like substance (HCT-S)].

Human chorionic TSH-like substance (HCT-S : B-III-2) was extracted from the placental chorionic tissue of the normal pregnancy at term. 15 mg of purified protein was obtained from 50 kg of placental tissue. The biological activity of the purified protein was 125 mu/mg. Electrophoretic pattern of this substance suggested that this protein was fairly well purified. The thyroid gland of immature *guinea pig injecetd with this substance was hypertropied and the histological picture was obviously hyperthyroidism. As far as the immunological examinations are concerned, this substance seemed to be different from TSH of human pituitary gland, human chorionic FSH (HC-FSH) and human placental lactogen (HPL) . But it was very probable that 1 mg of HCT-S (B-III-2) was contaminated with about 40 gag of human chorionic LH (HC-LH). (See pp. 364-.376)
Influence of a temporary embryonic testis graft on the regression of Müllerian ducts in female chick embryo

Whole testes of 13-day-old chick embryos grafted according to an original method into the extraembryonic coelom of 3-day-old recipients were next removed up to day 6. The temporary presence of a testis allowed the Mullerian ducts to retrogress, from day 8, in a high percentage of female hosts. It can be concluded that the graft secreted into the blood of the embryo enough ‘antiMullerian hormone’ to provoke regression of ducts at least 2 days after its removal and that the reaction of ducts depends on the appearance of their sensitivity to this hormone.
Osteocytes: Sensors of Mechanical Forces and Regulators of Bone Remodeling

Osteocytes make up the largest cell population in bone and are believed to be the main mechanosensory bone cells. During mechanical disuse and overuse, osteocyte viability is compromised and is found to be co-localized with increased osteoclastic bone resorption. Osteoclasts are recruited to remodel sites of apoptosis or bone microdamage; however, it is unclear whether the apoptotic or neighbouring healthy osteocytes are responsible for targeted bone remodeling. I hypothesized that apoptotic osteocytes are: (a) directly responsible for initiating bone remodeling by recruiting osteoclast precursors and directing osteoclast differentiation, and (b) indirectly responsible by signaling to nearby healthy osteocytes that, in turn, regulate osteoclastogenesis. In this in vitro study, apoptotic osteocytes were found to increase osteoclast precursor migration and osteoclast formation. Inhibition of the osteoclastogenic protein, receptor activator of nuclear factor kappa B ligand (RANKL), in conditioned medium abolished the osteoclastogenic effect of apoptotic osteocytes. Healthy osteocytes surrounded by apoptotic regions were modeled by applying apoptotic osteocyte conditioned medium to healthy
Efficient Online Relative Comparison Kernel Learning

Learning a kernel matrix from relative comparison human feedback is an important problem with applications in collaborative filtering, object retrieval, and search. For learning a kernel over a large number of objects, existing methods face significant scalability issues inhibiting the application of these methods to settings where a kernel is learned in an online and timely fashion. In this paper we propose a novel framework called Efficient online Relative comparison Kernel LEarning (ERKLE), for efficiently learning the similarity of a large set of objects in an online manner. We learn a kernel from relative comparisons via stochastic gradient descent, one query response at a time, by taking advantage of the sparse and low-rank properties of the gradient to efficiently restrict the kernel to lie in the space of positive semidefinite matrices. In addition, we derive a passive-aggressive online update for minimally satisfying new relative comparisons as to not disrupt the influence of previously obtained comparisons. Experimentally, we demonstrate a considerable improvement in speed while obtaining improved or comparable accuracy compared to current methods in the online learning setting.
Clinical course and risk factors of hepatitis C virus related liver disease in the general population: report from the Dionysos study

BACKGROUND The severity, clinical course, and risk of hepatitis C virus (HCV) related chronic liver disease are still rather poorly defined. AIMS To investigate the prevalence, risk factors, and severity of HCV related liver disease in the general population, and investigate whether infection with a specific genotype is associated with an increased risk of cirrhosis or hepatocellular carcinoma. METHODS HCV RNA determination by polymerase chain reaction (PCR) and HCV genotyping were performed in all anti-HCV positive subjects belonging to the Dionysos study (6917 subjects). Diagnosis of cirrhosis and hepatocellular carcinoma was established by liver biopsy in all cases. All the data were analysed by univariate and multivariate statistics in all the cohort. To investigate the natural history of HCV infection, anti-HCV positive subjects were followed up every six months for three years with liver function tests and ultrasonograms. RESULTS The overall prevalence of HCV RNA positivity was 2.3%. Positivity increased progressively with age, and was higher in women (ratio of men to women = 0.7). Genotypes 1b and 2a were the most frequent (42 and 24% of HCV RNA positive patients), with a prevalence of 1 and 0.6% respectively. Intravenous drug use, blood transfusions received before 1990, history of previous hepatitis among the cohabiting, and history of animal (mainly dogs) bites were significantly (p<0.05) associated with HCV infection, independently of age and sex. Multivariate analysis showed that, independently of age, sex, and alcohol intake, genotype 1b infection, with or without coinfection with other genotypes, is the major risk factor associated with the presence of cirrhosis and/or hepatocellular carcinoma. During the three years of follow up, 57 (35%) of the HCV RNA positive subjects had consistently normal alanine aminotransferase and γ-glutamyltransferase values. Two of the 22 HCV RNA positive cirrhotic patients, all drinking more than 90 g of alcohol a day, developed hepatocellular carcinoma (incidence rate = 3.0% per year). CONCLUSIONS In the general population of Northern Italy, HCV infection is widespread, but only less than 50% of the anti-HCV positive subjects, particularly those infected with genotype 1b, are associated with a more severe liver disease. Alcohol consumption greater that 30 g a day significantly aggravates the natural course of the disease.
Pain Coping Strategies for Children with Arthritis

Objective. To present information on pain management strategies for children with juvenile idiopathic arthritis (JIA). Methods. The second author developed a manual to present pain management strategies to children. The use of the manual was pilot-tested with a group of children with JIA. Telephone interviews were used to gather information on implementation of pain management strategies. Results. Children were able to implement the pain management strategies. Children reported a reduction in daily pain experiences related to JIA when using the pain management strategies. Conclusions. The pain management strategies were successful as an adjunctive intervention for short-term pain management. Pain symptoms related to JIA can severely limit children's participation in daily activities. Further study on how children use pain management strategies to improve their involvement in daily activities will provide useful clinical information.
An Improved Spectral Graph Partitioning 28 P ST fK Algorithm for Mapping Parallel Computations

Efficient use of a distributed memory parallel computer requires that the computational load be balanced across processors in a way that minimizes interprocessor communication. We present a new domain mapping algorithm that extends recent work in which ideas from spectral graph theory have been applied to this problem. Our generalization of spectral graph bisection involves a novel use of multiple eigenvectors to allow for division of a computation into four or eight parts at each stage of a recursive decomposition. The resulting method is suitable for scientific computations like irregular finite elements or differences performed on hypercube or mesh architecture machines. Experimental results confirm that the new method provides better decompositions arrived at more economically and robustly than with previous spectral methods. We have also improved upon the known spectral lower bound for graph bisection. This work was supported by the Applied Mathematical Sciences program, U.S. Department of Energy, Office of Energy Research, and was performed at Sandia National Laboratories, operated for the U.S. Department of Energy under contract No. DE-AC04-76DPO0789.
A Key Management Scheme for Secure Communications of Advanced Metering Infrastructure in Smart Grid

Advanced metering infrastructure (AMI) is an important component of the smart grid. The cyber security should be considered prior to the AMI system applications. To ensure confidentiality and integrality, a key management scheme (KMS) for a large amount of smart meters (SMs) and devices is required, which is not a properly solved problem until now. Compared with other systems, there are three specific features of AMI that should be carefully considered, including hybrid transmission modes of messages, storage and computation constraints of SMs, and unfixed participators in demand response (DR) projects. In order to deal with security requirements and considering the distinctive features, a novel KMS is proposed. First, the key management framework of an AMI system is constructed based on the key graph. Furthermore, three different key management processes are designed to deal with the hybrid transmission modes, including key management for unicast, broadcast, and multicast modes. Relatively simple cryptographic algorithms are chosen for key generation and refreshing policies due to the storage and computation constraints of SMs. Specific key refreshing policies are designed since the participators in a certain DR project are not fixed. Finally, the security and performance of the KMS are analyzed. According to the results, the proposed scheme is a possible solution for AMI systems.
Thiolated Lysine‐Leucine Peptides Self‐Assemble into Biosilica Nucleation Pits on Gold Surfaces

Nanostructured silica architectures have led to many applications in electronic and optical devices, and catalysis. Recently, bioinspired approaches based on peptide‐assisted silica fabrication have attracted great attention because of low production cost and mild, sustainable fabrication methods. Herein it is demonstrated that biomimetic peptides can also exert control over silica mineralization when bounded to inorganic surfaces. The amphiphilic α‐helical peptide LKα14 (Ac‐LKKLLKLLKKLLKLC‐OH) is used, which is based on leucine and lysine and has been a model system for surface studies and mineralization in solution for several years. LKα14 has been anchored to gold surfaces via terminal cysteine groups as linkers. Using X‐ray photoelectron spectroscopy, vibrational sum frequency generation spectroscopy, scanning force microscopy, and molecular dynamic simulations, it is found that LKα14 peptides assemble into laterally ordered structures with ≈5 nm wide cavities which serve as effective nucleating sites for silica nanoparticles.
Assembling of Parallel Programs for Large Scale Numerical Modeling

The main ideas of the Assembly Technology (AT) in its application to parallel implementation of large scale realistic numerical models on a rectangular mesh are considered and demonstrated by the parallelization (fragmentation) of the Particle-In-Cell method (PIC) application to solution of the problem of energy exchange in plasma cloud. The implementation of the numerical models with the assembly technology is based on the construction of a fragmented parallel program. Assembling of a numerical simulation program under AT provides automatically different useful dynamic properties of the target program including dynamic load balance on the basis of the fragments migration from overloaded into underloaded processor elements of a multicomputer. Parallel program assembling approach also can be considered as combination and adaptation for parallel programming of the well known modular programming and domain decomposition techniques and supported by the system software for fragmented programs assembling
Experimental Analysis of Concurrent Packet Transmissions in Low-Power Wireless Networks

We undertake a systematic experimental study of the effects of concurrent packet transmissions in low-power wireless networks. Our measurements, conducted with Mica2 motes equipped with CC1000 radios, confirm that guaranteeing successful packet reception with high probability in the presence of concurrent transmissions requires that the signal-to-interference-plus-noise-ratio (SINR) exceed a critical threshold. However, groups of radios show a wide gray region of about 6 dB. We find that this occurs because the SINR threshold can vary significantly depending on the measured signal power and radio hardware. We find that it is harder to estimate the level of interference in the presence of multiple interferers. We also find that the measured SINR threshold generally increases with the number of interferers. Our study offers a better understanding of concurrent transmissions and suggests richer interference models and useful guidelines to improve the design and analysis of wireless network protocols.
Early Postoperative Infection Following Open Reduction Internal Fixation Repair of Closed Malleolar Fractures

Background: Early postoperative infection (EPI) following hardware placement in patients with malleolar fractures is a serious complication. Identifying factors that place patients at risk for early infection may help target interventions to prevent infections. Methods: Data for the study included all adult patients who underwent operative management for closed malleolar fracture from 2006 to 2013 in the National Surgical Quality Improvement Program database. Characteristics of patients with and without EPI were compared using univariate tests. Logistic regression was used to perform a multivariable analysis of risk factors for EPI while controlling for covariates. Length of stay was analyzed using a generalized linear model. Results: The analysis sample included 7054 patients, of whom 116 developed EPI. Patients with EPI were slightly older on average, more likely to have diabetes, and had higher anesthesia class. Multivariable analysis identified several risk factors for EPI, including diabetes (odds ratio [OR] = 2.6; 95% CI = 1.5-4.5; P < .0001), American Society of Anaesthesiology (ASA) class 3+ (OR = 2.3; 95% CI = 1.03-5.0; P = .04), unclean surgery (OR = 2.4; 95% CI = 1.3-4.2; P < .0001), and inpatient location (OR 1.7, 1.1-2.7; P = .01). After controlling for other factors, EPI was not significantly associated with a longer hospital stay (0.2 days, P = .55). Conclusion: In the 30 days after hardware placement for malleolar fracture, infection occurs with increased frequency in older patients, diabetics, those with higher anesthesia class, and in the setting of unclean surgery and inpatient operative location. Patients with the identified risk factors should be followed closely for development of infection. Levels of Evidence: Level III: Retrospective cohort study