Miracle-dz/UniFAR-FTUs huggingface dataset:
Discrete element modeling of direct simple shear response of granular soils and model validation using laboratory tests

The direct simple shear response of spherical granular particles was modeled using discrete element modeling. The modeling approach was validated using a series of laboratory direct simple shear (DSS) element test carried out on airpluviated glass beads. The results of the model simulations were very similar to those from laboratory testing. The discrete element model also allowed the average lateral stress variations during shear loading to be computed. An overall increase in lateral stress with the progression of shearing was observed in this regard. The noted good agreement of the shear response between numerical modeling and experiments highlights the potential of discrete element modeling to effectively capture the behavior of granular materials.
Invertebrate drift patterns in a regulated river: dams, periphyton biomass or longitudinal patterns?

Macroinvertebrate drift was sampled at 15 sites along the Tongariro River, New Zealand above and below two hydroelectric dams. Sixty‐seven invertebrate taxa were collected in the drift. Trichoptera (31) were the most diverse, followed by Diptera (13), Ephemeroptera (8) and Plecoptera (8). However, chironomidae were the numerically dominant taxa in the drift throughout the river and represented over 80% of all animals collected. Of these, Orthocladiinae and Diamesinae were the most abundant. Taxonomic richness declined with distance downstream and peaked at sites with intermediate levels of periphyton biomass. The per cent of Ephemeroptera, Plecoptera and Trichoptera (EPT) was 3–4 times higher in the unregulated section of the river and declined exponentially with both distance downstream and increase in periphyton biomass, but densities were similar along the river. Of the measured environmental variables periphyton biomass was most closely linked with drift community structure. Periphyton biomass was six times higher in the lower section of the river than the upper unregulated section. The autocorrelation between periphyton biomass and distance downstream complicates the interpretation of results. However, because of the distinct differences between above and below dam sections of river in periphyton biomass and the strong link between it and invertebrate drift we suggest that the alteration of flow patterns by the hydroelectric dams and the associated shift in periphyton biomass is the most likely explanation for invertebrate drift patterns in the river. Copyright © 2009 John Wiley & Sons, Ltd.
Enabling Hierarchical Exploration for Large-Scale Multidimensional Data with Abstract Parallel Coordinates

As data collection grows more common in various domains, there is a call for adapted or newer methods of visualization to tackle magnitudes exceeding the number of available pixels on screens and challenging interactivity. Exploratory visualization of large data present two major challenges: perceptual scalability and processing scalability. The first is concerned with overcoming the fundamental limitation of screens and human perception. The second deals with efficiently processing large volumes of data to achieve responsive interactions. Multiscale visualizations are an effective technique for solving the first challenge that builds on several levels of data abstraction to provide the user with an initial overview and subsequent incremental detail. The focus of this paper is on multidimensional data, a ubiquitous form of data among large-scale data sets, and parallel coordinates, a representation largely used for this type of data. For this representation , defining abstractions and interactively generating levels is not straightforward. Building upon several previous aggregated parallel coordinates representations, we propose a unifying and thinking model for conceiving and describing multiscale parallel coordinates and their interactions. Using this formalism, we present a focus+context representation which bounds the number of visual items with a fixed resolution parameter while supporting exploration up to the item-level. Processing scala-bility is addressed by carrying out computation in a distributed manner on a remote data-intensive infrastructure. Bounding the visual items ensures perceptual scalability but also bounds the data transfer between this infrastructure and the rendering client.
Sca-1+ Cardiac Stem Cells Mediate Acute Cardioprotection via Paracrine Factor SDF-1 following Myocardial Ischemia/Reperfusion

Background Cardiac stem cells (CSCs) promote myocardial recovery following ischemia through their regenerative properties. However, little is known regarding the implication of paracrine action by CSCs in the setting of myocardial ischemia/reperfusion (I/R) injury although it is well documented that non-cardiac stem cells mediate cardioprotection via the production of paracrine protective factors. Here, we studied whether CSCs could initiate acute protection following global myocardial I/R via paracrine effect and what component from CSCs is critical to this protection. Methodology/Principal Findings A murine model of global myocardial I/R was utilized to investigate paracrine effect of Sca-1+ CSCs on cardiac function. Intracoronary delivery of CSCs or CSC conditioned medium (CSC CM) prior to ischemia significantly improved myocardial function following I/R. siRNA targeting of VEGF in CSCs did not affect CSC-preserved myocardial function in response to I/R injury. However, differentiation of CSCs to cardiomyocytes (DCSCs) abolished this protection. Through direct comparison of the protein expression profiles of CSCs and DCSCs, SDF-1 was identified as one of the dominant paracrine factors secreted by CSCs. Blockade of the SDF-1 receptor by AMD3100 or downregulated SDF-1 expression in CSCs by specific SDF-1 siRNA dramatically impaired CSC-induced improvement in cardiac function and increased myocardial damage following I/R. Of note, CSC treatment increased myocardial STAT3 activation after I/R, whereas downregulation of SDF-1 action by blockade of the SDF-1 receptor or SDF-1 siRNA transfection abolished CSC-induced STAT3 activation. In addition, inhibition of STAT3 activation attenuated CSC-mediated cardioprotection following I/R. Finally, post-ischemic infusion of CSC CM was shown to significantly protect I/R-caused myocardial dysfunction. Conclusions/Significance This study suggests that CSCs acutely improve post-ischemic myocardial function through paracrine factor SDF-1 and up-regulated myocardial STAT3 activation.
Identification and Deletion of Tft1, a Predicted Glycosyltransferase Necessary for Cell Wall β-1,3;1,4-Glucan Synthesis in Aspergillus fumigatus

Aspergillus fumigatus is an environmental mold that causes severe, often fatal invasive infections in immunocompromised patients. The search for new antifungal drug targets is critical, and the synthesis of the cell wall represents a potential area to find such a target. Embedded within the main β-1,3-glucan core of the A. fumigatus cell wall is a mixed linkage, β-D-(1,3;1,4)-glucan. The role of this molecule or how it is synthesized is unknown, though it comprises 10% of the glucans within the wall. While this is not a well-studied molecule in fungi, it has been studied in plants. Using the sequences of two plant mixed linkage glucan synthases, a single ortholog was identified in A. fumigatus (Tft1). A strain lacking this enzyme (tft1Δ) was generated along with revertant strains containing the native gene under the control of either the native or a strongly expressing promoter. Immunofluorescence staining with an antibody against β-(1,3;1,4)-glucan and biochemical quantification of this polysaccharide in the tft1Δ strain demonstrated complete loss of this molecule. Reintroduction of the gene into the knockout strain yielded reappearance in amounts that correlated with expected expression of the gene. The loss of Tft1 and mixed linkage glucan yielded no in vitro growth phenotype. However, there was a modest increase in virulence for the tft1Δ strain in a wax worm model. While the precise roles for β-(1,3;1,4)-glucan within A. fumigatus cell wall are still uncertain, it is clear that Tft1 plays a pivotal role in the biosynthesis of this cell wall polysaccharide.
Danger points, complications and medico-legal aspects in endoscopic sinus surgery

Endoscopic endonasal sinus surgery represents the overall accepted type of surgical treatment for chronic rhinosinusitis. Notwithstanding raised and still evolving quality standards, surgeons performing routine endoscopic interventions are faced with minor complications in 5% and major complications in 0.5–1%. A comprehensive review on all minor and major complications of endoscopic surgery of the paranasal sinuses and also on the anterior skull base is presented listing the actual scientific literature. The pathogenesis, signs and symptoms of each complication are reviewed and therapeutic regimens are discussed in detail relating to actual publication references. Potential medico-legal aspects are explicated and recent algorithms of avoidance are mentioned taking into account options in surgical training and education.
Price regulation of pluralistic markets subject to provider collusion

We analyse incentives for collusive behaviour when heterogeneous providers are faced with regulated prices under two forms of yardstick competition, namely discriminatory and uniform schemes. Providers are heterogeneous in the degree to which their interests correspond to those of the regulator, with close correspondence labelled altruism. Deviation of interests may arise as a result of de-nationalisation or when private providers enter predominantly public markets. We assess how provider strategies and incentives to collude relate to provider characteristics and across different market structures. We differentiate between “pure” markets with either only self-interested providers or with only altruistic providers and “pluralistic” markets with a mix of provider type. We find that the incentive for collusion under a discriminatory scheme increases in the degree to which markets are self-interested whereas under a uniform scheme the likelihood increases in the degree of provider homogeneity. Providers’ choice of cost also depends on the yardstick scheme and market structure. In general, costs are higher under the uniform scheme, reflecting its weaker incentives. In a pluralistic market under the discriminatory scheme each provider’s choice of cost is decreasing in the degree of the other provider’s altruism, so a self-interested provider will operate at a lower cost than an altruistic provider. Under the uniform scheme providers always choose to operate at the same cost. The prospect of defection serves to moderate the chosen level of operating cost.
Social threat, social reward, and regulation of investment in romantic relationships

Regulation of romantic investment is often examined in terms of concerns over self-protection. Perceived opportunity for intimate connection has been an overlooked motivational force in investment decisions. In 4 studies, participants assessed risks of rejection and opportunity for connection from future partners (among single participants), current partners (among coupled participants), and ex-partners (all participants). Beyond rejection risks, intimacy potential of future/current partners negatively predicted pining for an ex-partner, whereas intimacy potential of ex-partners positively predicted such longing. Rewarding ex-partners garnered particularly strong investment when future/current partners were lacking in intimacy potential, suggesting the need to belong motivates pursuit of intimacy in a hydraulic fashion: When connection is lacking in one relationship, the draw of intimacy from another becomes particularly strong.
Rectal leiomyoma, a rare entity

Rectal tumors are often encountered as an incidental finding on screening colonoscopy. As per the World Health Organization, they are categorized according to their histologic appearance. These include epithelial tumors, mesenchymal tumors and lymphomas. Of interest, in our case, are mesenchymal tumors. These are sub-classified into leiomyomas and gastrointestinal stromal tumors. Our case is a 33-year old male who was diagnosed with a rectal leiomyoma. The uncommon incidence and subsequent management of a rectal leiomyoma in a male, make this case worthy for literature review.
Bayesian approaches for multiple treatment comparisons of drugs for urgency urinary incontinence are more informative than traditional frequentist statistical approaches

Objective: Bayesian statistical methods are increasingly popular as a tool for meta-analysis of clinical trial data involving both direct and indirect treatment comparisons. However, appropriate selection of prior distributions for unknown model parameters and checking of consistency assumptions required for feasible modeling remain particularly challenging. We compared Bayesian and traditional frequentist statistical methods for indirect treatment comparisons in the context of pharmacological treatments for female urinary incontinence (UI). Study Design and Setting: In a hierarchical model of eight treatments, we separately analyzed one safety and two efficacy outcomes. We produced Bayesian and frequentist treatment ranks and odds ratios across all bivariate treatment comparisons. Results: While frequentist and Bayesian analyses produced broadly comparable odds ratios of safety and efficacy, the Bayesian method’s ability to deliver the probability that any treatment is best, or among the top two such treatments, led to more meaningful clinical interpretation. In our study, Solifenacin and Trospium emerged as attractive because while neither has any significant chance of being among the least safe drugs, both have better-than-even chances of being in the top three drugs for one of the efficacy endpoints. Conclusion: Bayesian methods are more flexible and their results more clinically interpretable but require more careful development and specialized software.
Titania-based materials

Publisher Summary Titania-based materials are easily formed on titanium metal and its alloys by chemical and thermal treatments. Metals can be used under high load conditions, because of their high fracture toughness, but they do not bond to living bone and are usually fixed to the surrounding bone by a mechanical interlocking with the bone via a roughened surface or by filling polymethylmethacrylate bone cement into a gap between a metallic implant and the bone. Fixation using these methods is not stable for long periods, and sometimes autogenous bone is transplanted around metallic implants for fixation. However, harvesting of the autogenous bone involves excessive invasion and sometimes leads to complications. In view of these facts, it would be desirable for metallic implants to exhibit bone-bonding capability. To provide a bone-bonding capability to a metallic material, a coating of calcium phosphate on a metallic implant using a plasma-spray technique has been developed and used clinically. However, in this method, calcium phosphate is only coated on the surfaces exposed to the plasma and the coated layer is relatively thick; hence, a uniform bioactive layer cannot be formed on complex shapes. In contrast to this, thin, uniform titania-based coatings can be formed on all surfaces, even on complex shapes using solution and thermal treatments of the metal. This chapter describes the formation of titania-based materials on metals, the properties of these titania-based materials, and the mechanism of apatite formation on these titania-based materials.
Understanding homogeneous nucleation in solidification of aluminum by molecular dynamics simulations

Homogeneous nucleation from aluminum (Al) melt was investigated by million-atom molecular dynamics simulations utilizing the second nearest neighbor modified embedded atom method potentials. The natural spontaneous homogenous nucleation from the Al melt was produced without any influence of pressure, free surface effects and impurities. Initially isothermal crystal nucleation from undercooled melt was studied at different constant temperatures, and later superheated Al melt was quenched with different cooling rates. The crystal structure of nuclei, critical nucleus size, critical temperature for homogenous nucleation, induction time, and nucleation rate were determined. The quenching simulations clearly revealed three temperature regimes: sub-critical nucleation, super-critical nucleation, and solid-state grain growth regimes. The main crystalline phase was identified as face-centered cubic, but a hexagonal close-packed (hcp) and an amorphous solid phase were also detected. The hcp phase was created due to the formation of stacking faults during solidification of Al melt. By slowing down the cooling rate, the volume fraction of hcp and amorphous phases decreased. After the box was completely solid, grain growth was simulated and the grain growth exponent was determined for different annealing temperatures.
A review of the role of five kinds of alternatives to in- feed antibiotics in broiler production

In view of severe restriction of total ban on the use of antibiotics as growth promoters and therapeutic agents in poultry industry, the search for alternatives to replace antibiotics has gained increasing interest in animal nutrition. Gut micro flora appears to be the target for IFAs and alternatives to exert health benefits and some growth-promoting effects. Subsequent to banning of use of antibiotics as growth promoter sin poultry nutrition, numerous studies turned to finding of alternative solutions, that is, other natural substances, which would have positive effect on chicken growth and feed conversion. Today, several groups of these additives are in use and most often probiotics, prebiotics, synbiotic, acidifiers and phytobiotics additives. Considering that each of the stated groups has its own specificities, the objective of this work was to present main mechanism of their action and to present their effect on production results in fattening of broiler chickens through review of research published in this field.
Depression, Stress, and Quality of Life in Persons with Chronic Kidney Disease: The Heart and Soul Study

Background: The effect of mild chronic kidney disease (CKD) on depression, stress, quality of life (QOL), and health status is not well understood. We compared these outcomes in subjects with and without CKD. Methods: We performed a cross-sectional study of 967 outpatients enrolled in the Heart and Soul Study. CKD was defined as a measured creatinine clearance <60 ml/min. Outcome measures included depressive symptoms measured using the Patient Health Questionnaire (PHQ), stress measured using the Perceived Stress Scale (PSS), and QOL and overall health rated as excellent, very good, good, fair, or poor. Results: The prevalence of depressive symptoms (17 vs. 19%, p = 0.4) or perceived stress (11 vs. 16%, p = 0.09) did not vary significantly by CKD. The prevalence of fair or poor QOL was not significantly different in subjects with CKD, compared with those without CKD (24 vs. 23%, p = 0.65). Age-adjusted analyses revealed a significant association of CKD with QOL (p = 0.003), however, this association no longer reached statistical significance after adjustment for confounders (p = 0.06). Subjects with CKD were more likely to report poor or fair overall health than subjects without CKD (42 vs. 34%, p = 0.03). After multivariate adjustment, CKD remained significantly associated with worse overall health (OR = 1.65, 95% CI 1.21–2.24, p = 0.001), and modestly associated with QOL (OR = 1.31, 95% CI 0.99–1.75, p = 0.06), but had no association with depression (p = 0.48) or stress (p = 0.24). Conclusion: In this study of persons with coronary artery disease, subjects with CKD had reduced overall health and modestly reduced QOL; however, mental health was similar in those with and without CKD. These findings suggest that self- assessed overall health may decline at earlier stages of renal dysfunction than mental health outcomes or QOL.
The Guanine Nucleotide Exchange Factor RIC8 Regulates Conidial Germination through Gα Proteins in Neurospora crassa

Heterotrimeric G protein signaling is essential for normal hyphal growth in the filamentous fungus Neurospora crassa. We have previously demonstrated that the non-receptor guanine nucleotide exchange factor RIC8 acts upstream of the Gα proteins GNA-1 and GNA-3 to regulate hyphal extension. Here we demonstrate that regulation of hyphal extension results at least in part, from an important role in control of asexual spore (conidia) germination. Loss of GNA-3 leads to a drastic reduction in conidial germination, which is exacerbated in the absence of GNA-1. Mutation of RIC8 leads to a reduction in germination similar to that in the Δgna-1, Δgna-3 double mutant, suggesting that RIC8 regulates conidial germination through both GNA-1 and GNA-3. Support for a more significant role for GNA-3 is indicated by the observation that expression of a GTPase-deficient, constitutively active gna-3 allele in the Δric8 mutant leads to a significant increase in conidial germination. Localization of the three Gα proteins during conidial germination was probed through analysis of cells expressing fluorescently tagged proteins. Functional TagRFP fusions of each of the three Gα subunits were constructed through insertion of TagRFP in a conserved loop region of the Gα subunits. The results demonstrated that GNA-1 localizes to the plasma membrane and vacuoles, and also to septa throughout conidial germination. GNA-2 and GNA-3 localize to both the plasma membrane and vacuoles during early germination, but are then found in intracellular vacuoles later during hyphal outgrowth.
Considering Agency and Data Granularity in the Design of Visualization Tools

Previous research has identified trade-offs when it comes to designing visualization tools. While constructive "bottom-up' tools promote a hands-on, user-driven design process that enables a deep understanding and control of the visual mapping, automated tools are more efficient and allow people to rapidly explore complex alternative designs, often at the cost of transparency. We investigate how to design visualization tools that support a user-driven, transparent design process while enabling efficiency and automation, through a series of design workshops that looked at how both visualization experts and novices approach this problem. Participants produced a variety of solutions that range from example-based approaches expanding constructive visualization to solutions in which the visualization tool infers solutions on behalf of the designer, e.g., based on data attributes. On a higher level, these findings highlight agency and granularity as dimensions that can guide the design of visualization tools in this space.
Oxidative stress in operating room personnel: occupational exposure to anesthetic gases

Health professionals exposed to anesthetic gases are at higher risk of reproductive, neurological, hematological, immunological, hepatic and renal system diseases. We investigated if oxidative stress induced by chronic exposure to anesthetic gases has any association with this matter. Plasma lipid peroxidation, total antioxidant capacity and total thiol molecule levels were measured in 66 operating room staff in comparison with 66 controls. The exposed group had a significantly higher level of lipid peroxidation with decreased thiol groups compared to control subjects. Total antioxidant capacity of the body was no different among exposed and not exposed subjects. Increased lipid peroxidation in the blood of exposed subjects warns that oxygen free radicals have increased in the body and thus might attack cells, which, in the longterm, results in multi-organ damage. The remaining blood total antioxidant capacity at normal values is promising and means that other non-thiol antioxidants, such as uric acid, transferrin, ceruloplasmin, albumin, and vitamin antioxidants, such as a-tocopherol and ascorbic acid, have been stimulated to maintain the total anti-oxidant power of the body at normal state.