Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluating The Resistome And Microbial Composition During Food Waste Feeding And Composting On A Vermont Poultry Farm

While commonly thought of as a waste product, food scraps and residuals represent an important opportunity for energy and nutrient recapture within the food system. As demands on production continue to increase, conservation of these valuable resources has become a priority area. In the wake of new legislation in Vermont, Act 148, the Universal Recycling Law, the fate of microbial species in food waste, scraps and residuals is increasingly important. The presence of antimicrobial resistance genes in all types of foods calls for an increased need to estimate risk of antibiotic resistance transfer and maintenance across all segments of food production and distribution systems, from farm to fork. Specifically, the fate of antibiotic resistance genes (ARGs) in these comingled food wastes has not been sufficiently characterized; as legislative programs increase in popularity, surveillance of these materials is pressing and should be documented to assess the risk and potential measures for mitigation and management as we approach commercial scales of implementation Previous studies have relied on a combination of targeted techniques, such as 16S rRNA sequencing and qPCR on a specific subset of ARGs; however, these may not cover the full extent of resistance or microorganisms of concern in any given sample. As sequencing technologies improve and costs continue to drop, more comprehensive tools, such as shotgun metagenomic sequencing, can be applied to these problems for both surveillance and novel gene discovery. In this study, we leveraged the increased screening power of the Illumina HiSeq and shotgun metagenomic sequencing to identify and characterize ARGs, microbial communities, and associated virulence factors of food scraps, on-farm composts, and several consumer products. Isolates were also screened for antibiotic resistance to demonstrate the functionality of ARGs identified. The resistome, microbiome, and virulence genes were characterized in all samples. Fifty unique ARGs were identified that spanned 8 major drug classes. Most frequently found were genes related to aminoglycoside, macrolide, and tetracycline resistance. Additionally, 54 distinct virulence factors and 495 bacterial species were identified. Virulence factors were present across the farm setting and mainly included gene transfer mechanisms, while bacteria clustered distinctly into site and farm, as well as separate on farm niches. The relationship between these categories was also assessed by both Pearson correlation and co-inertia analysis, with the most significant relationship being between ARGs and virulence factors (P = 0.05, RV = 0.67). While limited in this study, these patterns reinforce the finding that spread of antibiotic resistance genes may be dependent on the virulence factors present enabling transfer, rather than total microbial community composition.
Generic Tools, Specific Languages

Adapting tools to a particular domain is expensive, and the adaptation is often not very deep. To address this challenge, Generic Tools, Specific Languages shifts the focus from building and adapting tools (windows, buttons, algorithms) to building and adapting languages to a domain. The thesis applies the approach to embedded software development: mbeddr is an extensible set of integrated languages for embedded software development built with JetBrains MPS language workbench. The evaluation of mbeddr suggests that it is a productive tool for embedded software development. The evaluation of the development of mbeddr itself suggests that MPS is a suitable platform for Generic Tools, Specific Languages, and that the approach in general is worthwhile. 1.1 O V E RV I E W A N D C O N T R I B U T I O N This section provides an overview of the thesis. It starts out by describing the contribution and the research methodology. It then discusses mbeddr, the primary artifact built during the dissertation and explains its context, embedded software engineering. A discussion of the technologies used for building mbeddr – language engineering, projectional editing and JetBrains MPS – follows. The section concludes with an overview of the results. Contribution Today’s software engineering tools are hard to adapt to specific domains. A major reason is that while platforms such as Eclipse support easy extension of the tool (views, editors, buttons, menus) they do not easily support the extension of the data formats or languages that underlie a tool. The contribution of this thesis is the introduction and evaluation of a new approach to developing domain-specific software engineering tools called Generic Tools, Specific Languages. It shifts the focus from adapting the engineering tool to adapting the underlying languages to solve the problem of tool adaptation. It relies on language workbenches (the generic tool) and recent advances in language engineering, particularly, user-friendly projectional editing. The problem of tool extensibility, the Generic Tools, Specific Languages approach and the way it is evaluated is discussed in Chapter 2. The specific research questions that arise from the approach (domain-specific extensibility, language modularity and projectional editing, tool scalability, implementation efforts and the learning curve) are introduced and motivated in Section 2.6. Methodology As part of the dissertation, the Generic Tools, Specific Languages approach has been applied to embedded software engineering, resulting in a
Master ’ s Thesis 1 : Simulating the McCollough Effect in a Self – Organizing Model of the Primary Visual Cortex

The McCollough effect, an orientation–contingent color aftereffect, is a useful tool for studying the functionality of the visual system. There have been several attempts to model and understand the neural mechanisms underlying it, but none of them give a satisfactory functional explanation of the effect. Moreover, numerous experiments seem to indicate that this aftereffect involves the primary visual cortex (V1), and there have been no reported efforts to simulate it with a computational model of this cortical area. The present document constitutes the first computational study of the McCollough effect with a self–organizing map model of V1. LISSOM (Laterally Interconnected Synergetically Self–Organizing Map) is a biologically plausible, self–organizing map model of V1. Fundamental assumptions of this model are that lateral connections between cortical neurons play an important role in cortical processing, and that it self–organizes through Hebbian learning. It has already successfully accounted for important anatomical and functional features of V1, as well as for the tilt aftereffect, another visual effect. It has been recently used to model the development of color and orientation maps at the V1 level and is therefore appropriate for modeling the McCollough effect. This thesis presents a simulation of the effect with LISSOM, and the first rigorous comparison of the simulated effect with available psychophysical data on the McCollough effect. The model suggests that Hebbian learning of lateral inhibitory connections between orientation and color selective cells in V1 is the neural mechanism underlying the effect, thus lending strong support to the theory that the processing mechanisms involved in the ME are mostly located in the primary visual cortex. Moreover, the structure of the orientation and color map in V1, as well as the interactions between them, are also examined further, and it will be shown that the model accounts for both structural self–organization in color and orientation map and functional characteristics of adult vision. Thus, this thesis constitutes the first psychophysically and biologically grounded simulation of the ME, and the first to simulate complete topographic maps like those in the visual cortex. Importantly, the model was not originally developed with the ME in mind, which strongly suggests that the effect is a byproduct of the general cortical processing mechanisms in the model. The model also shows for the first time how the shortterm adaptation in the ME is related to the long-term developmental processes, providing an important link between development and adult visual function.
IRIS: A Novel Method of Direct Trust Computation for Generating Trusted Social Networks

Improving trust in social networks appears as the first step toward addressing the existing confidence and privacy concerns related to online social networks. Direct trust is used to develop different trust-based methods such as transitivity and access control, however how to compute direct trust levels is rarely discussed in the literature. To address some of the current limitations, we introduce a novel approach for generating trusted social networks and we compute trust levels between users having direct relationships. Experimental results with data extracted from FOAF files show that our work presents high accuracy.
Thalidomide radiosensitizes tumors through early changes in the tumor microenvironment.

PURPOSE The aim of this work was to study changes in the tumor microenvironment early after an antiangiogenic treatment using thalidomide (a promising angiogenesis inhibitor in a variety of cancers), with special focus on a possible "normalization" of the tumor vasculature that could be exploited to improve radiotherapy. EXPERIMENTAL DESIGN Tumor oxygenation, perfusion, permeability, interstitial fluid pressure (IFP), and radiation sensitivity were studied in an FSAII tumor model. Mice were treated by daily i.p. injection of thalidomide at a dose of 200 mg/kg. Measurements of the partial pressure of oxygen (pO(2)) were carried out using electron paramagnetic resonance oximetry. Three complementary techniques were used to assess the blood flow inside the tumor: dynamic contrast-enhanced magnetic resonance imaging, Patent Blue staining, and laser Doppler imaging. IFP was measured by a "wick-in-needle" technique. RESULTS Our results show that thalidomide induces tumor reoxygenation within 2 days. This reoxygenation is correlated with a reduction in IFP and an increase in perfusion. These changes can be attributed to extensive vascular remodeling that we observed using CD31 labeling. CONCLUSIONS In summary, the microenvironmental changes induced by thalidomide were sufficient to radiosensitize tumors. The fact that thalidomide radiosensitization was not observed in vitro, and that in vivo radiosensitization occurred in a narrow time window, lead us to believe that initial vascular normalization by thalidomide accounts for tumor radiosensitization.
Low complexity antenna grouping for energy efficiency maximization in massive MIMO systems

In this paper, we investigate antenna grouping for energy efficiency maximization in the downlink of multiuser massive MIMO systems. We construct an antenna grouping system model which partitions large-scale transmit antenna array into fixed-size groups. Beamforming is used within each group and spatial multiplexing between groups is considered. Diversity gain is then achieved by beamforming, and multiplexing gain by spatial multiplexing. System capacity and power consumption are analyzed, based on which the impact of the number of active transmit antennas per group is studied. A low complexity algorithm for finding the optimal number of active transmit antennas in each group is proposed based on binary search. Simulation results show that the proposed scheme significantly improves the energy efficiency of the system, and there exists optimal value of the number of the active transmit antennas per group in the fixed-size grouping model that maximized the energy efficiency.
Dependence on Computer Games by Adolescents

As computer game playing is a popular activity among adolescents, a questionnaire study was undertaken with 387 adolescents (12–16 years of age) to establish their “dependence” using a scale adapted from the DSM-III-R criteria for pathological gambling. Analysis indicated that one in five adolescents were currently “dependent” upon computer games. Boys played significantly more regularly than girls and were more likely to be classified as “dependent. ” The earlier children began playing computer games it appeared the more likely they were to be playing at “dependent” levels. These and other results are discussed in relation to research on other gaming dependencies.
Intrusion-tolerant middleware: the road to automatic security

The pervasive interconnection of systems throughout the world has given computer services a significant socioeconomic value that both accidental faults and malicious activity can affect. The classical approach to security has mostly consisted of trying to prevent bad things from happening-by developing systems without vulnerabilities, for example, or by detecting attacks and intrusions and deploying ad hoc countermeasures before any part of the system is damaged. Building an intrusion-tolerant system to arrive at some notion of intrusion-tolerant middleware for application support presents multiple challenges. Surprising as it might seem, intrusion tolerance isn't just another instantiation of accidental fault tolerance
Miniature Inverted-Repeat Transposable Elements of Stowaway Are Active in Potato

Miniature inverted-repeat transposable elements (MITEs) are dispersed in large numbers within the genomes of eukaryotes although almost all are thought to be inactive. Plants have two major groups of such MITEs: Tourist and Stowaway. Mobile MITEs have been reported previously in rice but no active MITEs have been found in dicotyledons. Here, we provide evidence that Stowaway MITEs can be mobilized in the potato and that one of them causes a change of tuber skin color as an obvious phenotypic variation. In an original red-skinned potato clone, the gene encoding for a flavonoid 3′,5′-hydroxylase, which is involved in purple anthocyanin synthesis, has been inactivated by the insertion of a Stowaway MITE named dTstu1 within the first exon. However, dTstu1 is absent from this gene in a purple somaclonal variant that was obtained as a regenerated plant from a protoplast culture of the red-skinned potato. The color change was attributed to reversion of flavonoid 3′,5′-hydroxylase function by removal of dTstu1 from the gene. In this purple variant another specific transposition event has occurred involving a MITE closely related to dTstu1. Instead of being fossil elements, Stowaway MITEs, therefore, still have the ability to become active under particular conditions as represented by tissue culturing.
The Economic Benefits Resulting from the First 8 Years of the Global Programme to Eliminate Lymphatic Filariasis (2000–2007)

Background Between 2000–2007, the Global Programme to Eliminate Lymphatic Filariasis (GPELF) delivered more than 1.9 billion treatments to nearly 600 million individuals via annual mass drug administration (MDA) of anti-filarial drugs (albendazole, ivermectin, diethylcarbamazine) to all at-risk for 4–6 years. Quantifying the resulting economic benefits of this significant achievement is important not only to justify the resources invested in the GPELF but also to more fully understand the Programme's overall impact on some of the poorest endemic populations. Methodology To calculate the economic benefits, the number of clinical manifestations averted was first quantified and the savings associated with this disease prevention then analyzed in the context of direct treatment costs, indirect costs of lost-labor, and costs to the health system to care for affected individuals. Multiple data sources were reviewed, including published literature and databases from the World Health Organization, International Monetary Fund, and International Labour Organization Principal Findings An estimated US$21.8 billion of direct economic benefits will be gained over the lifetime of 31.4 million individuals treated during the first 8 years of the GPELF. Of this total, over US$2.3 billion is realized by the protection of nearly 3 million newborns and other individuals from acquiring lymphatic filariasis as a result of their being born into areas freed of LF transmission. Similarly, more than 28 million individuals already infected with LF benefit from GPELF's halting the progression of their disease, which results in an associated lifetime economic benefit of approximately US$19.5 billion. In addition to these economic benefits to at-risk individuals, decreased patient services associated with reduced LF morbidity saves the health systems of endemic countries approximately US$2.2 billion. Conclusions/Significance MDA for LF offers significant economic benefits. Moreover, with favorable program implementation costs (largely a result of the sustained commitments of donated drugs from the pharmaceutical industry) it is clear that the economic rate of return of the GPELF is extremely high and that this Programme continues to prove itself an excellent investment in global health.
A mathematical model of retrieval system performance

There have been a number of major evaluations of the performance of retrieval systems against large full text and surrogate (bibliographic) databases. These evaluations have concentrated on the experimental determination of the Precision Ratio, the fraction of retrieved items that are relevant to an information request, and the Recall Ratio, the fraction of the total number of relevant items that were actually retrieved. While these measures have met with general acceptance, they have also generated much controversy. The purpose of this article is to review the results of several of the largest evaluations and to propose a simple model for the performance of such systems that may help explain the relationship between these measures and user behavior.
Measuring the indirect and direct costs of acute otitis media.

OBJECTIVES To test a method of measuring the related cost of acute otitis media (AOM) and to provide a preliminary calculation of the indirect and directs costs associated with a single, medically treated episode of AOM. DESIGN The Otitis Media Diary was used to measure indirect and direct costs associated with AOM in a prospective cohort study. Measured values included the parental time spent in otitis-specific child care and the number and type of medications used. A previously developed economic model was used to calculate the monetary costs associated with the value of caregiver time and the total opportunity cost of AOM. SETTING The pediatric clinic of Madigan Army Medical Center, Tacoma, Wash. PATIENTS A cohort of 25 children (12 with AOM and 13 controls) aged 1 to 3 years. MAIN OUTCOME MEASURES Caregiver time and medication use. RESULTS The total cost attributable to AOM in the 3-month period following diagnosis was $1330.58 (95% confidence interval, $1008.75-$1652.43), with the majority of that cost stemming from the indirect, rather than direct, costs of illness. After conservative estimates of unmeasured expenses, such as clinic visits and transportation, were accounted for, indirect costs, accrued primarily by parental time, accounted for nearly 90% (95% confidence interval, 87.1%-92.3%) of the total 3-month cost associated with AOM and its medical treatment. The cost items of the Otitis Media Diary were also highly correlated with each other and with other measures of clinical and functional health status. CONCLUSIONS Otitis Media Diary measures of parental time and medication use appear to provide a more accurate means of calculating the real social costs attributable to the AOM disease process in this cost-effectiveness analysis.
Dipyridinium 2,2′-dithiodinicotinate

The dianion of the title salt, 2C5H6N+·C12H6N2O4S2 2−, lies on a special position of 2 site symmetry that relates one thionicotinate part to the other, and the dihedral angle between the niotinate planes is 89.2 (2)°. The pyridinium cations are hydrogen bonded to the carboxylate group by way of N—H⋯O links.
A Note on the Onsager Model of Nematic Phase Transitions

We study Onsager's free energy functional for nematic liquid crystals with an orientation parameter on a unit circle. For a class of interaction potentials we obtain explicit expressions for all critical points, analyze their stability, and construct the corresponding bifurcation diagram. We also derive asymptotic expansions of the equilibrium density of orientations near the critical and zero temperatures.
Proving Properties of Typed A-Terms Using Realizability , Covers , and Sheaves MS-CIS-94-60 LOGIC & COMPUTATION 89

The main purpose of this paper is to take apart the reducibility method in order to understand how its pieces fit together, and in particular, to recast the conditions on candidates of reducibility as sheaf conditions. there has been a feeling among experts on this subject that it should be possible to present the reducibility method using more semantic means, and that a deeper understanding would then be gained. This paper gives mathematical substance to this feeling, by presenting a generalization of the reducibility method based on a semantic notion of realizability which uses the notion of a cover algebra (as in abstract sheaf theory). A key technical ingredient is the introduction a new class of semantic structures equipped with preorders, called preapplicative structures. These structures need not be extensional. In this framework, a general realizability theorem can be shown. Kleene's recursive realizability and a variant of Kreisel's modified realizability both fit into this framework. We are then able to prove a meta-theorem which shows that if a property of realizers satisfies some simple conditions, then it holds for the semantic interpretations of all terms. Applying this theorem to the special case of the term model, yields a general theorem for proving properties of typed λterms, in particular, strong normalization and confluence. This approach clarifies the reducibility method by showing that the closure conditions on candidates of reducibility can be viewed as sheaf conditions. the above approach is applied to the simply-typed λ-calculus (with types →, ×, +, and ⊥) , and to the second-order (polymorphic λ-calculus (with types → and ∀2), for which it yields a new theorem. Comments University of Pennsylvania Department of Computer and Information Science Technical Report No. MSCIS-94-60. This technical report is available at ScholarlyCommons: http://repository.upenn. edu/cis_reports/866 Proving Properties of Typed A-Terms Using Realizability, Covers, and Sheaves MS-CIS-94-60 LOGIC & COMPUTATION 89
Modelling of the concentration—effect relationship of THC on central nervous system parameters and heart rate — insight into its mechanisms of action and a tool for clinical research and development of cannabinoids

Pharmacokinetics after pulmonary administration of δ-9-tetrahydrocannabinol (THC) and its major metabolites 11-OH-THC and 11-nor-9-COOH-THC was quantified. Additionally, the relationship between THC and its effects on heart rate, body sway and several visual analogue scales was investigated using pharmacokinetic—pharmacodynamic (PK-PD) modelling. This provided insights useful for the research and development of novel cannabinoids and the physiology and pharmacology of cannabinoid systems. First, the PK-PD model gave information reflecting various aspects of cannabinoid systems. The delay between THC concentration and effect was quantified in equilibration half-lives of 7.68 min for heart rate and from 39.2 to 84.8 min for the CNS responses. This suggests that the effect of THC on the different responses could be due to different sites of action or different physiological mechanisms. Differences in the shape of the concentration—effect relationship could indicate various underlying mechanisms. Second, the PK-PD model can be used for prediction of THC concentration and effect profiles. It is illustrated how this can be used to optimise studies with entirely different trial designs. Third, many new cannabinoid agonists and antagonists are in development. PK-PD models for THC can be used as a reference for new agonists or as tools to quantitate the pharmacological properties of cannabinoid antagonists.