Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosphatidylserine Targets Single-Walled Carbon Nanotubes to Professional Phagocytes In Vitro and In Vivo

Broad applications of single-walled carbon nanotubes (SWCNT) dictate the necessity to better understand their health effects. Poor recognition of non-functionalized SWCNT by phagocytes is prohibitive towards controlling their biological action. We report that SWCNT coating with a phospholipid “eat-me” signal, phosphatidylserine (PS), makes them recognizable in vitro by different phagocytic cells - murine RAW264.7 macrophages, primary monocyte-derived human macrophages, dendritic cells, and rat brain microglia. Macrophage uptake of PS-coated nanotubes was suppressed by the PS-binding protein, Annexin V, and endocytosis inhibitors, and changed the pattern of pro- and anti-inflammatory cytokine secretion. Loading of PS-coated SWCNT with pro-apoptotic cargo (cytochrome c) allowed for the targeted killing of RAW264.7 macrophages. In vivo aspiration of PS-coated SWCNT stimulated their uptake by lung alveolar macrophages in mice. Thus, PS-coating can be utilized for targeted delivery of SWCNT with specified cargoes into professional phagocytes, hence for therapeutic regulation of specific populations of immune-competent cells.
Power Allocation and Achievable Secrecy Rates in MISOME Wiretap Channels

We consider transmission of confidential data over multiple-input single-output multiple-eavesdropper (MISOME) Rayleigh-fading wiretap channels. The transmitter has access to full channel state information (CSI) of a legitimate link but only partial CSI of an eavesdropper link in forms of the average received signal-to-noise power ratio (SNR). In this location-aware scenario, we develop the optimal power allocation strategy that maximizes the secrecy rate achievable by beamforming. The optimal power control is regulated in an on-off fashion with the threshold depending only on the numbers of antennas and the average SNRs. By rescuing the vanishing high-SNR degree of freedom for secure communication from this optimal on-off beamforming with the artificial noise scheme, we further derive the achievable ergodic secrecy rate of MISOME wiretap channels in closed form.
Memory for the Random: A Simulation of Computer Program Recall

Contrary to a widely held belief, experts recall random material better than non-experts. This phenomenon, predicted by the CHREST computational model, was first established with chess players. Recently, it has been shown through a meta-analysis that it generalises to nearly all domains where the effect has been tested. In this paper, we carry out computer simulations to test whether the mechanism postulated with chess experts – the acquisition and use of a large number of chunks – also applies to computer programming experts. The results show that a simplified version of CHREST (without the learning and use of highlevel schemata known as templates) broadly captures the skill effect with scrambled programs. However, it fails to account for the differences found in humans between different types of randomisation. To account for these differences, additional mechanisms are necessary that use semantic processing.
Electron tomographic analysis of synaptic ultrastructure

Synaptic function depends on interactions among sets of proteins that assemble into complex supramolecular machines. Molecular biology, electrophysiology, and live‐cell imaging studies have provided tantalizing glimpses into the inner workings of the synapse, but fundamental questions remain regarding the functional organization of these “nano‐machines. ” Electron tomography reveals the internal structure of synapses in three dimensions with exceptional spatial resolution. Here we report results from an electron tomographic study of axospinous synapses in neocortex and hippocampus of the adult rat, based on aldehyde‐fixed material stabilized with tannic acid in lieu of postfixation with osmium tetroxide. Our results provide a new window into the structural basis of excitatory synaptic processing in the mammalian brain. J. Comp. Neurol. 520:2697–2711, 2012. © 2012 Wiley Periodicals, Inc.
Adaptive Algorithms for Deterministic and Stochastic Differential Equations

Adaptive methods for numerical solutions of differential equations are useful to combine the two goals of good accuracy and efficiency. This thesis contributes to the theoretical understanding of optimal convergence rates of adaptive algorithms. In particular, this work studies stopping, accuracy and efficiency behavior of adaptive algorithms for solving ordinary differential equations (ODEs), partial differential equations (PDEs) and Itô stochastic differential equations (SDEs). The main ingredient of the adaptive algorithms is an error expansion of the form “Global error = ∑ local error ·weight+higher order error”, with computable leading order terms. The algorithm uses additional computational work to obtain the error estimate because of the weights. However, the approximation of the weights is required to inform where to refine the mesh to achieve optimal efficiency. Based on the a posteriori error expansions with “error indicator := |local error · weight|”, the adaptive algorithm subdivides the time steps or elements if the error indicators are greater than TOL/N , and stops if all N time steps or elements have sufficiently small error indicators. Similar algorithms are derived with either stochastic or deterministic time steps for weak approximations of SDEs including stopped diffusions using Monte Carlo Euler method. There are two main results on efficiency and accuracy of the adaptive algorithms. For accuracy, the approximation errors are asymptotically bounded by the specified error tolerance times a problem independent factor as the tolerance parameter tends to zero. For efficiency, the algorithms decrease the maximal error indicator with a factor, less than 1, or stop with asymptotically optimal number of final time steps or elements. Note that the optimal here refers to error densities of one sign, i.e. possible cancellation of the errors is not taken into account. For a p-th order accurate method, the L 1 p+1 quasi-norm of the error density is a good measure of the convergence rate for the adaptive approximation, while the number of uniform steps is measured by the larger L-norm of the error density. This analysis of convergence rates of the adaptive algorithms is based on the convergence of an error density, which measures the approximation error for each time step or element. In particular, the error density is proven to converge pointwise on structured adaptive meshes allowing hanging nodes for tensor finite elements and to converge almost surely for SDEs as the error tolerance tends to zero. Finally, numerical experiments illustrate the behavior of the adaptive methods and show that adaptive methods can be more efficient than methods with uniform step sizes. 2000 Mathematics Subject Classification. Primary 65L50, 65C30, 65N50
WIP Regulates Signaling via the High Affinity Receptor for Immunoglobulin E in Mast Cells

Wiskott-Aldrich syndrome protein–interacting protein (WIP) stabilizes actin filaments and is important for immunoreceptor-mediated signal transduction leading to actin cytoskeleton rearrangement in T and B cells. Here we report a role for WIP in signaling pathways downstream of the high affinity receptor for immunoglobulin (Ig)E (FcεRI) in mast cells. WIP-deficient bone marrow–derived mast cells (BMMCs) were impaired in their capacity to degranulate and secrete interleukin 6 after FcεRI ligation. Calcium mobilization, phosphorylation of Syk, phospholipase C-g2, and c-Jun NH2-terminal kinase were markedly decreased in WIP-deficient BMMCs. WIP was found to associate with Syk after FcεRI ligation and to inhibit Syk degradation as evidenced by markedly diminished Syk levels in WIP-deficient BMMCs. WIP-deficient BMMCs exhibited no apparent defect in their subcortical actin network and were normal in their ability to form protrusions when exposed to an IgE-coated surface. However, the kinetics of actin changes and the cell shape changes that follow FcεRI signaling were altered in WIP-deficient BMMCs. These results suggest that WIP regulates FcεRI-mediated mast cell activation by regulating Syk levels and actin cytoskeleton rearrangement.
Wisdom of crowds versus wisdom of linguists – measuring the semantic relatedness of words

Abstract In this article, we present a comprehensive study aimed at computing semantic relatedness of word pairs. We analyze the performance of a large number of semantic relatedness measures proposed in the literature with respect to different experimental conditions, such as (i) the datasets employed, (ii) the language (English or German), (iii) the underlying knowledge source, and (iv) the evaluation task (computing scores of semantic relatedness, ranking word pairs, solving word choice problems). To our knowledge, this study is the first to systematically analyze semantic relatedness on a large number of datasets with different properties, while emphasizing the role of the knowledge source compiled either by the ‘wisdom of linguists’ (i.e., classical wordnets) or by the ‘wisdom of crowds’ (i.e., collaboratively constructed knowledge sources like Wikipedia). The article discusses benefits and drawbacks of different approaches to evaluating semantic relatedness. We show that results should be interpreted carefully to evaluate particular aspects of semantic relatedness. For the first time, we employ a vector based measure of semantic relatedness, relying on a concept space built from documents, to the first paragraph of Wikipedia articles, to English WordNet glosses, and to GermaNet based pseudo glosses. Contrary to previous research (Strube and Ponzetto 2006; Gabrilovich and Markovitch 2007; Zesch et al. 2007), we find that ‘wisdom of crowds’ based resources are not superior to ‘wisdom of linguists’ based resources. We also find that using the first paragraph of a Wikipedia article as opposed to the whole article leads to better precision, but decreases recall. Finally, we present two systems that were developed to aid the experiments presented herein and are freely available1 for research purposes: (i) DEXTRACT, a software to semi-automatically construct corpus-driven semantic relatedness datasets, and (ii) JWPL, a Java-based high-performance Wikipedia Application Programming Interface (API) for building natural language processing (NLP) applications.
Scalable Uplink Signal Detection in C-RANs via Randomized Gaussian Message Passing

Cloud radio access network (C-RAN) is a promising architecture for unprecedented capacity enhancement in next-generation wireless networks thanks to the centralization and virtualization of base station processing. However, centralized signal processing in C-RANs involves high computational complexity that quickly becomes unaffordable when the network grows to a huge size. First, this paper endeavors to design a scalable uplink signal detection algorithm, in the sense that both the complexity per unit network area and the total computation time remain constant when the network size grows. To this end, we formulate the signal detection in C-RAN as an inference problem over a bipartite random geometric graph. By passing messages among neighboring nodes, message passing (a.k.a. belief propagation) provides an efficient way to solve the inference problem over a sparse graph. However, the traditional message-passing algorithm is not guaranteed to converge, because the corresponding bipartite random geometric graph is locally dense and contains many short loops. As a major contribution of this paper, we propose a randomized Gaussian message passing (RGMP) algorithm to improve the convergence. Instead of exchanging messages simultaneously or in a fixed order, we propose to exchange messages asynchronously in a random order. The proposed RGMP algorithm demonstrates significantly better convergence performance than conventional message passing. The randomness of the message updating schedule also simplifies the analysis, and allows the derivation of the convergence conditions for the RGMP algorithm. In addition, we generalize the RGMP algorithm to a blockwise RGMP (B-RGMP) algorithm, which allows parallel implementation. The average computation time of B-RGMP remains constant when the network size increases.
Investigating the Flow Dynamics in the Obstructed and Stented Ureter by Means of a Biomimetic Artificial Model

Double-J stenting is the most common clinical method employed to restore the upper urinary tract drainage, in the presence of a ureteric obstruction. After implant, stents provide an immediate pain relief by decreasing the pressure in the renal pelvis (P). However, their long-term usage can cause infections and encrustations, due to bacterial colonization and crystal deposition on the stent surface, respectively. The performance of double-J stents - and in general of all ureteric stents - is thought to depend significantly on urine flow field within the stented ureter. However very little fundamental research about the role played by fluid dynamic parameters on stent functionality has been conducted so far. These parameters are often difficult to assess in-vivo, requiring the implementation of laborious and expensive experimental protocols. The aim of the present work was therefore to develop an artificial model of the ureter (i.e. ureter model, UM) to mimic the fluid dynamic environment in a stented ureter. The UM was designed to reflect the geometry of pig ureters, and to investigate the values of fluid dynamic viscosity (μ), volumetric flow rate (Q) and severity of ureteric obstruction (OB%) which may cause critical pressures in the renal pelvis. The distributed obstruction derived by the sole stent insertion was also quantified. In addition, flow visualisation experiments and computational simulations were performed in order to further characterise the flow field in the UM. Unique characteristics of the flow dynamics in the obstructed and stented ureter have been revealed with using the developed UM.
The Prefrontal Cortex and Oculomotor Delayed Response: A Reconsideration of the “Mnemonic Scotoma”

The concept of the “mnemonic scotoma,” a spatially circumscribed region of working memory impairment produced by unilateral lesions of the PFC, is central to the view that PFC is critical for the short-term retention of information. Presented here, however, are previously unpublished data that offer an alternative, nonmnemonic interpretation of this pattern of deficit. In their study, Wajima and Sawaguchi [Wajima, K. , & Sawaguchi, T. The role of GABAergic inhibiton in suppressing perseverative responses in the monkey prefrontal cortex. Neuroscience Research, 50(Suppl. 1), P3–P317, 2004] applied the GABAA antagonist bicuculline methiodide unilaterally to the PFC of two monkeys while they performed an oculomotor delayed-response task. Consistent with previous studies, errors for the initial memory-guided saccade were markedly higher when the cued location fell into the region of the visual field affected by the infusion. These erroneous saccades tended to select an alternative target location (out of a possible 16) that had not been cued on that trial. By extending the analysis window, however, it was observed that the second, “corrective” saccade often acquired the location that had been cued on that trial. Further analysis of the erroneous initial saccades indicated that they tended to be directed to a location that had been relevant on the previous trial. Thus, the deficit was not one of “forgetting” the cued location. Rather, it was one of selecting between currently and previously relevant locations. These findings suggest a need for a reconsideration of the concept of the mnemonic scotoma, which in turn invites a reconsideration of functional interpretations of sustained neuronal activity in PFC.
Confronting the natural variability and modeling uncertainty of nonpoint source pollution in water quality management

ii ACKNOWLEDGMENTS . iv DEDICATION . v LIST OF TABLES . x LIST OF FIGURES . xii Chapter 1: INTRODUCTION . 1 1.1. Overview and research goals . 1 1.2. Background, specific objectives, and propositions . 3 1.2. 1. Objectives: . 5 1.2.2. Propositions . 5 1.3. Significance of the dissertation . 6 1.4. Organization of the dissertation . 7 Bibliography . 8 Chapter 2: THE RELATIONSHIP BETWEEN LAND USE AND VULNERABILITY TO NITROGEN AND PHOSPHOROUS POLLUTION IN AN URBANIZING WATERSHED . 13 2.2. Materials and methods . 16 2.2. 1. Study watershed . 16 2.2.2. Geospatial analysis . 18 2.2.3. Water quality data . 18 2.2. 4. Hydrologic modeling. 19 2.2. 5. Statistical analysis . 20 2.2. 6. Analysis of land use-water quality relationships . 20 2.2. 7. Characterization of the vulnerability to nutrient pollution . 21 2.2. 8. The role of climatic variability on the relationship between land use and nutrient levels . 22 2.3. Results and discussion . 22 2.3. 1. Calibration and testing of the hydrologic model . 22 2.3. 2. The relationship between land use and water quality . 23 2.3. 3. The effects of the inter-annual variability of precipitation on land use-water quality relationships . 27
Reactions to Stigmas

Reactions toward older adults have been widely researched, but the question of whether such reactions are due to age per se or due to the presence of other stigmas (e.g., physical disabilities) has received little attention. This study was designed to investigate emotional reactions and willingness to help older versus younger adults who exhibited a wide range of stigmas, including AIDS, leg amputation, depression, and so on. Guided by attribution theory, the cause of the stigmas was further ascribed to either uncontrollable or controllable factors. Older adults evoked less anger than younger individuals, particularly in the case of blindness, depression, leg amputation, lung cancer, and unemployment. Subjects were also more willing to help an older than a younger amputee. Moreover, stigmas ascribed to uncontrollable factors generally produced less anger, more pity, and greater willingness to help than stigmas described as due to controllable causes. These results provide little support for the notion of ageism, at least within an age range of up to 65 years, but suggest that responses to older adults with stigmas may be subject to positive stereotyping.
Evidence of increased microvessel density and activation of the hypoxia pathway in tumours from the hereditary leiomyomatosis and renal cell cancer syndrome

The Mendelian tumour syndromes hereditary leiomyomatosis and renal cell cancer (HLRCC) and hereditary paragangliomatosis with phaeochromocytomas (HPGL) result from mutations in nuclear genes (FH and SDHB/C/D, respectively) that encode Krebs cycle enzymes. HPGL tumours are highly vascular and there is evidence that inactivation of SDH leads to activation of the hypoxia/angiogenesis pathway. In contrast, uterine leiomyomas are not generally regarded as particularly vascular lesions. In order to test the possibility that activation of the hypoxia/angiogenesis pathway contributes to tumourigenesis in HLRCC, increased vascularity and hypoxia pathway activation were searched for in HLRCC tumours. Microvessel density was markedly higher in uterine leiomyomas from HLRCC than in the surrounding myometrium; it was notable that sporadic uterine leiomyomas were actually less vascular than normal myometrium. In HLRCC tumours, there was increased expression of transcripts from the hypoxia‐responsive genes vascular endothelial growth factor (VEGF) and BNIP3; sporadic uterine leiomyomas did not show these changes. All uterine leiomyomas showed decreased expression of thrombospondin 1. Although sporadic and HLRCC uterine leiomyomas appear to have identical morphology, their pathways of tumourigenesis may be fundamentally different. As is the case in HPGL, it is probable that failure of the Krebs cycle in HLRCC tumours causes inappropriate signalling that the cell is in a hypoxic state, leading to angiogenesis and perhaps directly to clonal expansion and tumour growth through some uncharacterized, cell‐autonomous effect. Copyright © 2004 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Farmers’ attitudes and practices towards variety and certified seed use, seed replacement and seed storage in wheat growing areas of Ethiopia

Farmers’ prevailing attitudes and practices towards wheat variety and certified seed use, seed replacement and seed storage were assessed through a field survey following a multistage purposive sampling technique to identify 552 smallholder farmers from 10 districts (wereda) in three regional states (Oromiya, Amhara, and SNNP) in Ethiopia. Data were collected in 2013, using a structured questionnaire and subject to descriptive analysis and cross-tabulations. About 57.6% (n = 514) of respondents preferred wheat varieties with high yield whereas 39.9% of the respondents preferred varieties with disease resistance. Farmers purchased an average amount of 157.2 kg certified seed in one season, and most of them paid for it in cash, regardless of their attitudes to seed prices. Disease susceptibility of the existing variety was a significant reason why most farmers (63.8%, n = 538) purchased certified seed. Farmers in the studied areas have practised storing own saved seed up to one year. In conclusion, farmers have good knowledge of certified wheat seed, but their attitudes that dictated the frequency of purchase of certified seed have to be addressed adequately through backstopping of the certified seed supply chain with disease resistant varieties but that have minimum yield penalty.
Children's Conceptions of Characteristic Features of Category Members

Abstract The authors investigated children's conceptions of the characteristic features of category members and found that their conceptions underwent qualitative developmental changes. They hypothesized that (a) children initially tend to perceive category members in terms of individual characteristics (i.e., internal dispositions and behavioral patterns) and (b) only later do they conceive of category members in terms of their shared beliefs and values. They explored these hypotheses in 2 studies: In Study 1, they investigated how Protestant and Catholic children in Northern Ireland understood the religious intergroup context in their own country; in Study 2, children in Italy were presented with a fictional scenario of intergroup conflict and asked to explain the causes of the conflict. The results of both studies confirmed the 2 hypotheses.