Miracle-dz/UniFAR-FTUs huggingface dataset:
Aquatic fate of a double‐stranded RNA in a sediment­­–water system following an over‐water application

Determining the rate of biodegradation of double‐stranded RNA (dsRNA) in the environment is an essential element of a comprehensive risk assessment of an RNA‐based agricultural product. This information is used during problem formulation to define relevant routes and durations of environmental exposure for in planta–expressed dsRNA. Although exposure to biotechnology‐derived crops expressing dsRNA traits in the aquatic environment is predicted to be minimal, little is known regarding the fate of dsRNA in these environments. To assess exposure to aquatic environments, a study was conducted to measure the rate of biodegradation of DvSnf7 dsRNA in aerobic water–sediment systems. Aquatic systems containing natural water and sediments that varied in physical and chemical characteristics were treated with dsRNA by applying DvSnf7 dsRNA directly to the water column. In the present study, DvSnf7 dsRNA dissipated rapidly from the water phase and was undetectable within 7 d as measured by QuantiGene (Affymetrix) and a sensitive insect bioassay in these diverse systems. Degradation kinetics estimated a half‐life (time to 50% dissipation [DT50]) of less than 3 d and a time to 90% dissipation of approximately 4 d. Further analysis indicated that DvSnf7 dsRNA had DT50 values of less than 6 d in both sediment‐free systems containing natural water and systems with only sediment. Taken together, the results of the present study indicate that dsRNA‐based agricultural products rapidly degrade and consequently are unlikely to persist in aquatic environments. Environ Toxicol Chem 2017;36:727–734. © 2016 SETAC
Flagellin-Deficient Legionella Mutants Evade Caspase-1- and Naip5-Mediated Macrophage Immunity

Macrophages from C57BL/6J (B6) mice restrict growth of the intracellular bacterial pathogen Legionella pneumophila. Restriction of bacterial growth requires caspase-1 and the leucine-rich repeat-containing protein Naip5 (Birc1e). We identified mutants of L. pneumophila that evade macrophage innate immunity. All mutants were deficient in expression of flagellin, the primary flagellar subunit, and failed to induce caspase-1-mediated macrophage death. Interestingly, a previously isolated flagellar mutant (fliI) that expresses, but does not assemble, flagellin did not replicate in macrophages, and induced macrophage death. Thus, flagellin itself, not flagella or motility, is required to initiate macrophage innate immunity. Immunity to Legionella did not require MyD88, an essential adaptor for toll-like receptor 5 (TLR5) signaling. Moreover, flagellin of Legionella and Salmonella induced cytotoxicity when delivered to the macrophage cytosol using Escherichia coli as a heterologous host. It thus appears that macrophages sense cytosolic flagellin via a TLR5-independent pathway that leads to rapid caspase-1-dependent cell death and provides defense against intracellular bacterial pathogens.
Physical and thermo-mechanical characterizations of resin-based dental composite reinforced with silane-modified nanoalumina filler particle

The aim of this study was to analyze the effect of adding different weight percentages of nanoalumina particles on mechanical properties of resin-based dental composite materials. The composite specimens were prepared by dispersion of different percentage weight fractions (0 wt%, 1 wt%, 2 wt% and 3 wt%) of silane-modified nanoalumina filler in a monomer system containing 50% bisphenol-A glycidyl methacrylate, 49% tri-ethylene glycol dimethacrylate, 0.2% Camphorquinone and 0.8% Ethyl 4-dimethylaminobenzoate. The filler particle before and after silane treatment was characterized using Fourier-transform infrared spectroscopy and transmission electron microscopy. The presence of C = O bond and Si–O–Si linkage between the monomer and filler was clearly indicated. Mechanical behavior of the light-cured samples was evaluated using compressive strength test, three-point flexural strength test, Vicker Micro hardness tests, dynamic mechanical analysis and simultaneous thermal analysis. The results indicated a more than 16% increase in the compressive strength in the samples containing nanoalumina filler particles. Vickers hardness of composite was increased by approximately 28% with respect to unfilled composite. The flexural modulus of composite mixed with alumina nanoparticles was increased from 1.7 to 5.1 GPa, while the values of composite were slightly decreased from 84.5 to 59.5 MPa. The dynamic mechanical analysis result revealed that the glass transition temperature was found to be increased by 30 ℃ compared to unfilled composite. It was also found that the 1 wt% nanoalumina content recorded the highest value of storage modulus. The weight loss profile and thermal stability from thermogravimetric analysis results revealed that the composite filled with 2 wt% nanoalumina content exhibited maximum thermal stability.
3D Spatially Resolved Models of the Intracellular Dynamics of the Hepatitis C Genome Replication Cycle

Mathematical models of virus dynamics have not previously acknowledged spatial resolution at the intracellular level despite substantial arguments that favor the consideration of intracellular spatial dependence. The replication of the hepatitis C virus (HCV) viral RNA (vRNA) occurs within special replication complexes formed from membranes derived from endoplasmatic reticulum (ER). These regions, termed membranous webs, are generated primarily through specific interactions between nonstructural virus-encoded proteins (NSPs) and host cellular factors. The NSPs are responsible for the replication of the vRNA and their movement is restricted to the ER surface. Therefore, in this study we developed fully spatio-temporal resolved models of the vRNA replication cycle of HCV. Our simulations are performed upon realistic reconstructed cell structures—namely the ER surface and the membranous webs—based on data derived from immunostained cells replicating HCV vRNA. We visualized 3D simulations that reproduced dynamics resulting from interplay of the different components of our models (vRNA, NSPs, and a host factor), and we present an evaluation of the concentrations for the components within different regions of the cell. Thus far, our model is restricted to an internal portion of a hepatocyte and is qualitative more than quantitative. For a quantitative adaption to complete cells, various additional parameters will have to be determined through further in vitro cell biology experiments, which can be stimulated by the results described in the present study.
Investigating Effects of Losing Fluid on Nonlinear Structural Behavior of Rabbit ACL

This study is conducted to investigate the effects of losing fluid during extension of rabbit ACL (Anterior Cruciate Ligament) on its nonlinear behavior. The incompressible Neo-Hookean model is employed for modeling the mechanical response of ACL under the uniaxial loading. The material properties of the ligament are characterized by measuring the deformation of a continuum element regarding to two assumptions, the exact and near incompressible cases. In the near incompressible assumption, it is assumed that some fluids exit during ligament extension which influence the nonlinear structural response of the ACL. Finally, considering the nonlinearity of the ligament due to the material behavior and geometrical effect, the ligament behavior is modeled using the nonlinear FEM solution. This study provides a new insight based on the model incompressibility for the ACL of the rabbit knee. These findings help researchers to predict the patterns of injuries that occur in the ligament for different amount of losing fluid by developing the computational model to assess the nonlinear response
April 2018 Automated skeletal tissue quantification in the lower leg using peripheral quantitative computed tomography

Objective: In this paper we introduce a methodology for hard and soft tissue quantification at proximal, intermediate and distal tibia sites using peripheral quantitative computed tomography scans. Quantification of bone properties is crucial for estimating bone structure resistance to mechanical stress and adaptations to loading. Soft tissue variables can be computed to investigate muscle volume and density, muscle-bone relationship, and fat infiltration. Approach: We employed implicit active contour models and clustering techniques for automated segmentation and identification of bone, muscle and fat at 4%, 38%, and 66% tibia length. Next, we calculated densitometric, area and shape characteristics for each tissue type. We implemented our approach as a multi-platform tool denoted by TIDAQ (tissue identification and quantification) to be used by clinical researchers. Main results: We validated the proposed method against reference quantification measurements and tissue delineations obtained by semi-automated workflows. The average Deming regression slope between the tested and reference method was 1.126 for cross-sectional areas and 1.078 for mineral densities, indicating very good agreement. Our method produced high average coefficient of variation (R2) estimates: 0.935 for cross-sectional areas and 0.888 for mineral densities over all tibia sites. In addition, our tissue segmentation approach achieved an average Dice coefficient of 0.91 over soft and hard tissues, indicating very good delineation accuracy. Significance: Our methodology should allow for high throughput, accurate and reproducible automatic quantification of muscle and bone characteristics of the lower leg. This information is critical to evaluate risk of future adverse outcomes and assess the effect of medications, hormones, and behavioral interventions aimed at improving bone and muscle strength. PAPER 2018
Detection and Characterization of Reactive Oxygen and Nitrogen Species in Biological Systems by Monitoring Species-Specific Products.

SIGNIFICANCE Since the discovery of the superoxide dismutase enzyme, the generation and fate of short-lived oxidizing, nitrosating, nitrating, and halogenating species in biological systems has been of great interest. Despite the significance of reactive oxygen species (ROS) and reactive nitrogen species (RNS) in numerous diseases and intracellular signaling, the rigorous detection of ROS and RNS has remained a challenge. Recent Advances: Chemical characterization of the reactions of selected ROS and RNS with electron paramagnetic resonance (EPR) spin traps and fluorescent probes led to the establishment of species-specific products, which can be used for specific detection of several forms of ROS and RNS in cell-free systems and in cultured cells in vitro and in animals in vivo. Profiling oxidation products from the ROS and RNS probes provides a rigorous method for detection of those species in biological systems. CRITICAL ISSUES Formation and detection of species-specific products from the probes enables accurate characterization of the oxidative environment in cells. Measurement of the total signal (fluorescence, chemiluminescence, etc.) intensity does not allow for identification of the ROS/RNS formed. It is critical to identify the products formed by using chromatographic or other rigorous techniques. Product analyses should be accompanied by monitoring of the intracellular probe level, another factor controlling the yield of the product(s) formed. FUTURE DIRECTIONS More work is required to characterize the chemical reactivity of the ROS/RNS probes, and to develop new probes/detection approaches enabling real-time, selective monitoring of the specific products formed from the probes. Antioxid. Redox Signal. 28, 1416-1432.
Applying the social relations model to self and peer evaluations

Peer evaluations of performance increasingly are being used to make organizational decisions and to provide individuals with performance related feedback. Using Kenny’s social relations model (SRM), data from 14 teams of undergraduate students who completed performance ratings of themselves and other team members were analyzed. Results indicated a significant target variance effect for the majority of performance dimensions and a significant perceiver variance effect for all performance dimensions. Results further indicated that, in general, how individuals see themselves is not congruent with how others see them, how individuals see themselves is congruent with how they see others, how individuals are seen on a particular dimension is related to how they are seen on other performance dimensions, and, how a person is seen by others does not relate to how that individual sees others. Implications, limitations, and suggestions for future research using the SRM are discussed.
The Promises and Perils of Modelling Medical Reasoning

Work by Shortliffe and Buchanan on MYCIN, key parts of which are described in the paper reprinted in this Yearbook [1], was the first detailed case study of a large medical rulebased system which handled uncertainty [2]. By publishing their insights and making the EMYCIN tool widely available to their R & D community (3], tbeMYCIN investigators promoted widespread experimentation with "expert" systems in academic and commercial settings in the early 1980's (e.g. [4-6]). This in tum led to important new insights into artificial intelligence (AI) in general and medical AI in particular [7], as well as a thriving commercial sector. Despite their drawbacks, such rule-based systems remain influential to the present day.
A higher-order theory of emotional consciousness

Significance Although emotions, or feelings, are the most significant events in our lives, there has been relatively little contact between theories of emotion and emerging theories of consciousness in cognitive science. In this paper we challenge the conventional view, which argues that emotions are innately programmed in subcortical circuits, and propose instead that emotions are higher-order states instantiated in cortical circuits. What differs in emotional and nonemotional experiences, we argue, is not that one originates subcortically and the other cortically, but instead the kinds of inputs processed by the cortical network. We offer modifications of higher-order theory, a leading theory of consciousness, to allow higher-order theory to account for self-awareness, and then extend this model to account for conscious emotional experiences. Emotional states of consciousness, or what are typically called emotional feelings, are traditionally viewed as being innately programmed in subcortical areas of the brain, and are often treated as different from cognitive states of consciousness, such as those related to the perception of external stimuli. We argue that conscious experiences, regardless of their content, arise from one system in the brain. In this view, what differs in emotional and nonemotional states are the kinds of inputs that are processed by a general cortical network of cognition, a network essential for conscious experiences. Although subcortical circuits are not directly responsible for conscious feelings, they provide nonconscious inputs that coalesce with other kinds of neural signals in the cognitive assembly of conscious emotional experiences. In building the case for this proposal, we defend a modified version of what is known as the higher-order theory of consciousness.
Experimental validation of a subject-specific maximum endurance time model

Abstract This study aimed at experimentally validating a subject-specific maximum endurance time (MET) model. Thirty health participants (15 males and 15 females; Age: mean = 21.5 years, SD = 1.6 years) volunteered to conduct an isometric elbow flexion task until exhaustion. The endurance times of each participant were measured under relative exertion levels ranging from 30% MVC (Maximum Voluntary Contraction) to 70% MVC at 10% intervals. Assessment of the model showed that the intensity–endurance time relationship for each studied individual could be well fitted by the subject-specific MET model (R2 > 0.89). The fatigue rates identified from the model fitting were normally distributed (Mean = 0.96 min−1, SD = 0.29 min−1). In addition, the fatigue rates of the male group were significantly higher than the female group. The subject-specific MET model can be used to predict the MET for individual workers, and further support physical task design, based on the fatigability data of a targeted worker population. Practitioner Summary: Ergonomists have extensively used MET models in physical fatigue assessment and physical task design. A subject-specific MET model could be used to predict the MET at individual levels, and also to support work design for a target worker population, based on the fatigability data distribution obtained from sampled workers.
How Does Sampling Methodology Influence Molecular Detection and Isolation Success in Influenza A Virus Field Studies?

ABSTRACT Wild waterfowl are important reservoir hosts for influenza A virus (IAV) and a potential source of spillover infections in other hosts, including poultry and swine. The emergence of highly pathogenic avian influenza (HPAI) viruses, such as H5N1 and H5N8, and subsequent spread along migratory flyways prompted the initiation of several programs in Europe, North America, and Africa to monitor circulation of HPAI and low-pathogenicity precursor viruses (low-pathogenicity avian influenza [LPAI] viruses). Given the costs of maintaining such programs, it is essential to establish best practice for field methodologies to provide robust data for epidemiological interpretation. Here, we use long-term surveillance data from a single site to evaluate the influence of a number of parameters on virus detection and isolation of LPAI viruses. A total of 26,586 samples (oropharyngeal, fecal, and cloacal) collected from wild mallards were screened by real-time PCR, and positive samples were subjected to isolation in embryonated chicken eggs. The LPAI virus detection rate was influenced by the sample type: cloacal/fecal samples showed a consistently higher detection rate and lower cycle threshold (Ct ) value than oropharyngeal samples. Molecular detection was more sensitive than isolation, and virus isolation success was proportional to the number of RNA copies in the sample. Interestingly, for a given Ct value, the isolation success was lower in samples from adult birds than in those from juveniles. Comparing the results of specific real-time reverse transcriptase (RRT)-PCRs and of isolation, it was clear that coinfections were common in the investigated birds. The effects of sample type and detection methods warrant some caution in interpretation of the surveillance data.
Setting the rules: Private power, political underpinnings, and legitimacy in global monetary and financial governance

The role of private market agents in global monetary and financial governance has increased as globalization has proceeded. This shift in both markets and patterns of governance has often been encouraged by states themselves in pursuit of liberalization policies. Much of the literature views these developments in a positive light, yet there are other aspects of these developments that also merit attention. This article supports its central propositions with two cases of emerging global financial governance processes: the Basel II capital adequacy standards for international banking supervision and the International Organization of Securities Commissions-based transnational regulatory processes underpinning the functioning of cross-border securities markets. Based on the case findings, the article argues first that private sector self-regulation and/or public-private partnership in governance processes can leave public authorities vulnerable to dependence on the information and expertise provided by private agents in a fast-moving market environment. Policy in the vital domain of financial regulation has been increasingly aligned to private sector preferences to a degree that should raise fears of bureaucratic capture. Second, the article contends that the overall outcome in terms of global financial system efficiency and stability has been mixed, bringing a range of important benefits but also instability and crisis for many societies to a degree that has led to challenges to global governance itself. The case material indicates that the input, output and accountability phases of legitimacy in global monetary and financial governance are highly problematic, and much of the problem relates to the way in which private market agents are integrated into the decision-making process. Third, the article posits that a better consideration of these three ‘phases’ of legitimacy and their interrelationships is likely to enhance the political underpinnings and legitimacy of global financial and monetary order.
Complement Dependence of Murine Costimulatory Blockade‐Resistant Cellular Cardiac Allograft Rejection

Building on studies showing that ischemia–reperfusion‐(I/R)‐injury is complement dependent, we tested links among complement activation, transplantation‐associated I/R injury, and murine cardiac allograft rejection. We transplanted BALB/c hearts subjected to 8‐h cold ischemic storage (CIS) into cytotoxic T‐lymphocyte associated protein 4 (CTLA4)Ig‐treated wild‐type (WT) or c3−/− B6 recipients. Whereas allografts subjected to 8‐h CIS rejected in WT recipients with a median survival time (MST) of 37 days, identically treated hearts survived >60 days in c3−/− mice (p < 0.05, n = 4–6/group). Mechanistic studies showed recipient C3 deficiency prevented induction of intragraft and serum chemokines/cytokines and blunted the priming, expansion, and graft infiltration of interferon‐γ–producing, donor‐reactive T cells. MST of hearts subjected to 8‐h CIS was >60 days in mannose binding lectin (mbl1−/−mbl2−/−) recipients and 42 days in factor B (cfb−/−) recipients (n = 4–6/group, p < 0.05, mbl1−/−mbl2−/− vs. cfb−/−), implicating the MBL (not alternative) pathway. To pharmacologically target MBL‐initiated complement activation, we transplanted BALB/c hearts subjected to 8‐h CIS into CTLA4Ig‐treated WT B6 recipients with or without C1 inhibitor (C1‐INH). Remarkably, peritransplantation administration of C1‐INH prolonged graft survival (MST >60 days, p < 0.05 vs. controls, n = 6) and prevented CI‐induced increases in donor‐reactive, IFNγ‐producing spleen cells (p < 0.05). These new findings link donor I/R injury to T cell–mediated rejection through MBL‐initiated, complement activation and support testing C1‐INH administration to prevent CTLA4Ig‐resistant rejection of deceased donor allografts in human transplant patients.
Definitions of women's sexual dysfunction reconsidered: Advocating expansion and revision

In light of various shortcomings of the traditional nosology of women's sexual disorders for both clinical practice and research, an international multi-disciplinary group has reviewed the evidence for traditional assumptions about women's sexual response. It is apparent that fullfillment of sexual desire is an uncommon reason/incentive for sexual activity for many women and, in fact, sexual desire is frequently experienced only after sexual stimuli have elicited subjective sexual arousal. The latter is often poorly correlated with genital vasocongestion. Complaints of lack of subjective arousal despite apparently normal genital vasocongestion are common. Based on the review of existing evidence-based research, many modifications to the definitions of women's sexual dysfunctions are recommended. There is a new definition of sexual interest/desire disorder, sexual arousal disorders are separated into genital and subjective subtypes and the recently recognized condition of persistent sexual arousal is included. The definition of dyspareunia reflects the possibility of the pain precluding intercourse. The anticipation and fear of pain characteristic of vaginismus is noted while the assumed muscular spasm is omitted given the lack of evidence. Finally, a recommendation is made that all diagnoses be accompanied by descriptors relating to associated contextual factors and to the degree of distress.