Miracle-dz/UniFAR-FTUs huggingface dataset:
D Molecular Geometry and Band Structure Modelling of Graphene and Carbon Nanotubes

Graphene, carbon nanoribbons and carbon nanotubes are allotropes of carbon that are widely used in nanotechnology research due to their remarkable properties. Electrical and mechanical properties of those allotropes vary with their molecular geometry. Theoretically, an infinite number of such geometries do exist, and it is impossible to physically prepare samples of all of them in the real world. This paper is based on developing mathematical models to describe molecular geometries of graphene and carbon nanotubes, examining their geometry dependent electronic band structures and visually representing those relations in a 3D modelling and simulation software. Paper describes equations to derive the coordinates of the atoms, algorithms to derive the orientation of the bonds of the molecular structures, implementation of those algorithms in java3D and derivation of electronic band structures. Successful results were obtained after the implementation of the algorithms which are illustrated with few screenshots at the end.
Increased Plasma P-Selectin and Decreased Thrombomodulin in Pulmonary Arterial Hypertension Were Improved by Continuous Prostacyclin Therapy

BackgroundThrombosis in situ related to endothelial cell injury may contribute to the development of pulmonary hypertension (PH). P-selectin, a leukocyte adhesion receptor present in endothelial cells and platelets, reflects endothelial injury and platelet activation, and thrombomodulin (TM), a receptor for thrombin and a major anticoagulant proteoglycan on the endothelial membrane, reflects the anticoagulant activity of the endothelium. Methods and ResultsTo assess abnormal coagulation due to endothelial injury in patients with PH, plasma levels of soluble P-selectin and TM were measured in 32 patients with primary PH (PPH), 25 with secondary pulmonary arterial hypertension (sPAH), 31 with pulmonary venous hypertension (PVH), and 17 healthy subjects (Control). These measurements were repeated after continuous infusion of prostacyclin in 15 patients with PPH and 3 with sPAH. P-selectin levels in both the sPAH and PPH groups were significantly higher than those in the Control and PVH groups (P <0.05). Plasma TM level in the PPH group was significantly lower than those in the other groups (P <0.01). After prostacyclin therapy, the lower TM level was increased and the higher P-selectin level was decreased (P <0.05). ConclusionsDecreased TM and increased P-selectin in PPH and sPAH may reflect in situ thrombosis due to endothelial injury. Prostacyclin may act not only as a vasodilator but also as an agent that improves endothelial injury and altered hemostasis in pulmonary arterial injury.
Non-alcoholic fatty liver disease, diet and gut microbiota

Non-alcoholic fatty liver disease (NAFLD) is a severe liver disease that is increasing in prevalence with the worldwide epidemic of obesity and its related insulin-resistance state. Evidence for the role of the gut microbiota in energy storage and the subsequent development of obesity and some of its related diseases is now well established. More recently, a new role of gut microbiota has emerged in NAFLD. The gut microbiota is involved in gut permeability, low-grade inflammation and immune balance, it modulates dietary choline metabolism, regulates bile acid metabolism and produces endogenous ethanol. All of these factors are molecular mechanisms by which the microbiota can induce NAFLD or its progression toward overt non-alcoholic steatohepatitis. Modification of the gut microbiota composition and/or its biochemical capacity by specific dietary or pharmacological interventions may advantageously affect host metabolism. Large-scale intervention trials, investigating the potential benefit of prebiotics and probiotics in improving cardiometabolic health in high-risk populations, are fervently awaited.
A promoter DNA demethylation landscape of human hematopoietic differentiation

Global mechanisms defining the gene expression programs specific for hematopoiesis are still not fully understood. Here, we show that promoter DNA demethylation is associated with the activation of hematopoietic-specific genes. Using genome-wide promoter methylation arrays, we identified 694 hematopoietic-specific genes repressed by promoter DNA methylation in human embryonic stem cells and whose loss of methylation in hematopoietic can be associated with gene expression. The association between promoter methylation and gene expression was studied for many hematopoietic-specific genes including CD45, CD34, CD28, CD19, the T cell receptor (TCR), the MHC class II gene HLA-DR, perforin 1 and the phosphoinositide 3-kinase (PI3K) and results indicated that DNA demethylation was not always sufficient for gene activation. Promoter demethylation occurred either early during embryonic development or later on during hematopoietic differentiation. Analysis of the genome-wide promoter methylation status of induced pluripotent stem cells (iPSCs) generated from somatic CD34+ HSPCs and differentiated derivatives from CD34+ HSPCs confirmed the role of DNA methylation in regulating the expression of genes of the hemato-immune system, and indicated that promoter methylation of these genes may be associated to stemness. Together, these data suggest that promoter DNA demethylation might play a role in the tissue/cell-specific genome-wide gene regulation within the hematopoietic compartment.
Structural basis for nucleotide exchange in heterotrimeric G proteins

How a receptor transmits a signal G protein–coupled receptors (GPCRs) transmit diverse external signals into the cell. When activated by an outside stimulus, they bind to a G protein inside the cell and accelerate exchange of a bound guanosine diphosphate (GDP) nucleotide for guanosine triphosphate, which initiates intercellular signaling. Dror et al. used atomic-level molecular dynamics simulations to show how GPCRs enhance GDP release. The G protein is dynamic and frequently adopts a conformation that exposes GDP even without the receptor bound. GPCR binding to this conformation favors an additional structural rearrangement that favors GDP release. The authors confirmed these predictions experimentally using double electron-electron resonance spectroscopy. Science, this issue p. 1361 Atomic-level simulations show how G protein–coupled receptors trigger G protein signaling. G protein–coupled receptors (GPCRs) relay diverse extracellular signals into cells by catalyzing nucleotide release from heterotrimeric G proteins, but the mechanism underlying this quintessential molecular signaling event has remained unclear. Here we use atomic-level simulations to elucidate the nucleotide-release mechanism. We find that the G protein α subunit Ras and helical domains—previously observed to separate widely upon receptor binding to expose the nucleotide-binding site—separate spontaneously and frequently even in the absence of a receptor. Domain separation is necessary but not sufficient for rapid nucleotide release. Rather, receptors catalyze nucleotide release by favoring an internal structural rearrangement of the Ras domain that weakens its nucleotide affinity. We use double electron-electron resonance spectroscopy and protein engineering to confirm predictions of our computationally determined mechanism.
Image appearance modeling and high-dynamic-range image rendering

Recently, the field of color appearance modeling has been extended further into the spatial and temporal domains through efforts known as image appearance modeling. Image appearance models have applications in rendering and visualization of image data, cross-media image and video reproduction, and image quality specification. This presentation provides an overview of one such model, iCAM, illustrates several examples of its application, and reviews a psychophysical experiment aimed at evaluating iCAM and other algorithms for tone mapping of high-dynamic-range (HDR) images. Initial psychophysical results for HDR image rendering indicates that the Durand and Dorsey [2002] algorithm produces the most preferred results in a general sense. A full technical report on this work can be found at <www.cis. rit.edu/mcsl/research/reports.html>. Example iCAM code and further references can be found at <www.cis. rit.edu/mcsl/iCAM>.
TLR4 and Insulin Resistance

Chronic inflammation is a key feature of insulin resistance and obesity. Toll-Like Receptor 4 (TLR4), involved in modulating innate immunity, is an important mediator of insulin resistance and its comorbidities. TLR4 contributes to the development of insulin resistance and inflammation through its activation by elevated exogenous ligands (e.g., dietary fatty acids and enteric lipopolysaccharide) and endogenous ligands (e.g., free fatty acids) which are elevated in obese states. TLR4, expressed in insulin target tissues, activates proinflammatory kinases JNK, IKK, and p38 that impair insulin signal transduction directly through inhibitory phosphorylation of insulin receptor substrate (IRS) on serine residues. TLR4 activation also leads to increased transcription of pro-inflammatory genes, resulting in elevation of cytokine, chemokine, reactive oxygen species, and eicosanoid levels that promote further insulin-desensitization within the target cell itself and in other cells via paracrine and systemic effects. Increased understanding of cell type-specific TLR4-mediated effects on insulin action present the opportunity and challenge of developing related therapeutic approaches for improving insulin sensitivity while preserving innate immunity.
Robust Decision Making under Strategic Uncertainty in Multiagent Environments

We introduce the notion of strategic uncertainty for boundedly rational, non-myopic agents as an analog to the equilibrium selection problem in classical game theory. We then motivate the need for and feasibility of addressing strategic uncertainty and present an algorithm that produces decisions that are robust to it. Finally, we show how agents' rationality levels and planning horizons alter the robustness of their decisions.
Ecological Experiments with Model Systems

Some of the classic experiments in ecology have involved real organisms interacting in the laboratory, that is, model systems. Ecologists are increasingly using model systems to investigate problems of global environmental change and questions about the assembly, persistence, and stability of complex communities. Model laboratory systems are a halfway house between mathematical models and the full complexity of the field, and they yield powerful insights into the dynamics of populations and ecosystems.
Detecting and Filtering Non-responsive Traffic in AQM Queues without Packet Header Examination

In the current Internet, long-term TCP flows and bursty shortterm flows both exist. The mix between the aggregated longterm TCP traffic (responsive traffic) and the bursty traffic (non-responsive traffic) has great impact on the performance of Active Queue Management (AQM) algorithms in routers. We introduce a new solution to differentiate between responsive and unresponsive traffic in AQM queues without identifying individual flows through packet headers. The proposed solution is based on statistic measurement on the incoming traffic rate and the AQM packet loss rate. We show the design of our scheme and illustrate the effectiveness through simulation results.
TCP implementations and false time out detection in OBS networks

This paper compares Reno, new-Reno and selective acknowledgements (SACK), the three most common TCP implementations today in (future) optical burst switched (OBS) networks. In general, SACK, which considers multiple triple duplicated ACKed (TD) losses in one round, is found to perform best in OBS networks, while new-Reno, which improves Reno in packet switched networks by fast retransmission in responding to partial ACKs, may however perform worse than Reno. All three TCP implementations react to a time out (TO) loss in the same way (i.e., using slow start). In OBS networks, where a burst may contain all packets from one round, and a burst loss occurs mainly due to contention instead of buffer overflow, such a TO event may no longer imply heavy congestion, or in other words, it may he a false TO or FTO. Such FTOs, which may he common in OBS networks especially for fast TCP flows, can significantly degrade the performance of all existing TCP implementations. Accordingly, we also propose a new TCP implementation called burst TCP (BTCP) which can detect FTOs and react properly, and as a result, improve over the existing TCP implementations significantly.
Functional Effects of Two Voltage-Gated Sodium Channel Mutations That Cause Generalized Epilepsy with Febrile Seizures Plus Type 2

Two mutations that cause generalized epilepsy with febrile seizures plus (GEFS+) have been identified previously in theSCN1A gene encoding the α subunit of the Nav1.1 voltage-gated sodium channel (Escayg et al., 2000). Both mutations change conserved residues in putative voltage-sensing S4 segments, T875M in domain II and R1648H in domain IV. Each mutation was cloned into the orthologous rat channel rNav1.1, and the properties of the mutant channels were determined in the absence and presence of the β1 subunit in Xenopus oocytes. Neither mutation significantly altered the voltage dependence of either activation or inactivation in the presence of the β1 subunit. The most prominent effect of the T875M mutation was to enhance slow inactivation in the presence of β1, with small effects on the kinetics of recovery from inactivation and use-dependent activity of the channel in both the presence and absence of the β1 subunit. The most prominent effects of the R1648H mutation were to accelerate recovery from inactivation and decrease the use dependence of channel activity with and without the β1 subunit. The DIV mutation would cause a phenotype of sodium channel hyperexcitability, whereas the DII mutation would cause a phenotype of sodium channel hypoexcitability, suggesting that either an increase or decrease in sodium channel activity can result in seizures.
Application of Vegetative Buffer Strips Under Natural Rainfall to Conserve Soil and Water

Abstract Soil erosion is one of the most serious environmental issues in the world. The use of vegetative buffer strips is an effective strategy to reduce surface water pollutions as well as soil erosion. The present research has been conducted with aim to study the efficiency of buffer strips in runoff volume and sediment control using experimental plots. In this regard, twelve experimental plots with the dimensions of 1 m × 10 m were provided, and runoff samples were collected monthly to measure runoff volume and sediment. Vetiver grass and tall fescue were used as the plant species of the studied vegetative buffer strips. It was found that, vegetative buffer strips reduced the runoff volume up to 97% and sediment concentration up to 96%. Vetiver grass showed a high efficiency in runoff and sediment control; but, the maximum efficiency is achieved when this species is used along with a plant similar to the tall fescue in terms of density and uniformity. Also, periodic cutting the plants and cleaning the buffer strips can be considered as effective strategies to prevent vegetative buffer strips acting as the source of sediment.
On the Euclidean Minimum Spanning Tree Problem

Given a weighted graph G (V, E), a minimum spanning tree for G can be obtained in linear time using a randomized algorithm or nearly linear time using a deterministic algorithm. Given n points in the plane, we can construct a graph with these points as nodes and an edge between every pair of nodes. The weight on any edge is the Euclidean distance between the two points. Finding a minimum spanning tree for this graph is known as the Euclidean minimum spanning tree problem (EMSTP). The minimum spanning tree algorithms alluded to before will run in time O(n2) (or nearly O(n2)) on this graph. In this note we point out that it is possible to devise simple algorithms for EMSTP in k-dimensions (for any constant k) whose expected run time is O(n), under the assumption that the points are uniformly distributed in the space of interest.
Cannabis use, cognitive performance and mood in a sample of workers

There are well documented acute and chronic effects of cannabis use on mental functioning. However, less is known about any effects on cognition within the context of work and everyday life. The aim of the study was to examine any association between cannabis use and cognitive performance, mood and human error at work. Cannabis users and controls completed a battery of laboratory based computer tasks measuring mood and cognitive function pre- and post-work at the start and end of a working week. They also completed daily diaries reporting their work performance. Cannabis use was associated with impairment in both cognitive function and mood, though cannabis users reported no more workplace errors than controls. Cannabis use was associated with lower alertness and slower response organization. In addition, users experienced working memory problems at the start, and psychomotor slowing and poorer episodic recall at the end of the working week. This pattern of results suggests two possible effects. First a ‘hangover’-type effect which may increase with frequency of use. Second a subtle effect on cognitive function, perhaps more apparent under cognitive load and/or fatigue, which may increase with more prolonged use. The results also highlight the importance of the timing of testing within the context and routine of everyday life.
Xeroderma pigmentosum genes and melanoma risk

Xeroderma pigmentosum is a rare autosomal recessive disease that is associated with a severe deficiency in nucleotide excision repair. The presence of a distinct the nucleotide excision repair (NER) mutation signature in melanoma suggests that perturbations in this critical repair process are likely to be involved with disease risk. We hypothesized that persons with polymorphic NER gene(s) are likely to have reduced NER activity and are consequently at an increased risk of melanoma development. We assessed the association between 94 SNPs within seven XP genes (XPA–XPG) and the melanoma risk in the Polish population. We genotyped 714 unselected melanoma patients and 1,841 healthy adults to determine if there were any polymorphisms differentially represented in the disease group. We found that a significantly decreased risk of melanoma was associated with the Xeroderma pigmentosum complementation (XPC) rs2228000_CT genotype (odds ratio [OR] = 0.15; p < 0.001) and the rs2228000_TT genotype (OR = 0.11; p < 0.001) compared to the reference genotype. Haplotype analysis within XPC revealed the rs2228001_A + G1475A_G + G2061A_A + rs2228000_T + rs3731062_C haplotype (OR = 0.26; p < 0.05) was associated with a significantly decreased disease risk. The haplotype analysis within the Xeroderma pigmentosum group D (XPD) showed a modest association between two haplotypes and a decrease in melanoma risk. There were no major differences between the prevalence of the XP polymorphisms among young or older patients with melanoma. Linkage disequilibrium of XPC: rs2228001, G1475A, G2061A, rs2228000 and rs3731062 was found. The data from our study support the notion that only XPC and XPD genes are associated with melanoma susceptibility.
New trends in computational modeling: A Neuroid-based retina model

It is thought that using detailed neuron-models could lead to a better understanding of how the nervous system works. However, neural networks preserve their collective computational properties, regardless of the level of description used for modeling the main building block. In this paper, we built a Neuroid-based retina model. As a result of the implementation, the Neuroid was able to reproduce the essential features of the photoreceptor response to light. Likewise, the retina model responded to specific visual effects such as simultaneous contrast, Mach bands and Hermann grid. All of these suggest that the Neuroid comprises enough functional characteristics, such that we could focus not only on the most relevant computational aspects of nerve cells, but also in the collective capabilities of large-scale neural networks.
A probabilistic model for message propagation in two-dimensional vehicular ad-hoc networks

Vehicular ad-hoc networks (VANET) promise to enhance the road safety and travel comfort significantly in both highway and city scenarios. Message propagation, either for emergency or pleasure purposes, constitutes a major category of VANET applications, and is particularly challenging in infrastructure-less vehicle-to-vehicle communication scenarios. In this paper, we study the connectivity property of message propagation in two-dimensional VANET. We first derive the exact expression for the average size of the connected components in the one-dimensional case, i.e., messages propagating along a main street, and give a close approximation to the size distribution. We further derive the connectivity of message propagation in the two-dimensional ladder case, i.e., covering the main and two side streets, and formulate the problem for the two-dimensional lattice case to cover all the blocks in a district. Extensive simulation has been conducted to verify the analytical model and provide further insights in message propagation with and without geographic constraints, respectively. The simulation results show the efficacy of the model and the tradeoff between these two message forwarding strategies, and provide guidelines for future network planning and protocol development.
Microvasculature of the mouse epididymis, with special reference to fenestrated capillaries localized in the initial segment

The blood supply, microvasculature, and ultrastructure of the capillaries in the epididymis in adult mice were regionally examined. The epididymal duct of the initial segment is surrounded with a dense network of fenestrated capillaries running just under the epithelium. The other segments have loose networks of nonfenestrated capillaries running in the interductal connective tissue. The fenestration of capillaries in the initial segment was markedly reduced in frequency immediately after cutting the efferent duct. In adult mice which were subjected to cutting of the efferent duct neonatally, the dense capillary network did not develop, and fenestrated capillaries were absent in the initial segment. We interpret our results to indicate that the fenestrated capillaries in the initial segment provide for absorption of the testicular fluid and that their development is dependent upon the testicular fluid entering the epididymal duct.