Miracle-dz/UniFAR-FTUs huggingface dataset:
Invertibility of graph translation and support of Laplacian Fiedler vectors

The graph Laplacian operator is widely studied in spectral graph theory largely due to its importance in modern data analysis. Recently, the Fourier transform and other time-frequency operators have been defined on graphs using Laplacian eigenvalues and eigenvectors. We extend these results and prove that the translation operator to the $i$'th node is invertible if and only if all eigenvectors are nonzero on the $i$'th node. Because of this dependency on the support of eigenvectors we study the characteristic set of Laplacian eigenvectors. We prove that the Fiedler vector of a planar graph cannot vanish on large neighborhoods and then explicitly construct a family of non-planar graphs that do exhibit this property.
Improving finger force control with vibrational haptic feedback for Multiple Sclerosis

Pathologies including stroke and multiple sclerosis can leave patients with impaired tactile and proprioceptive sensation, which contributes to their difficulty in performing everyday tasks. We present the results that indicate that a combination of fingertip force sensing and vibrational feedback can help patients with multiple sclerosis improve their performance in manipulation tasks. The feedback can take the form of an "event cue" in which patients are alerted when forces at the fingertips stray outside of a recommended range, or proportional feedback, in which trains of vibration pulses are correlated directly with the fingertip forces. While both types of feedback allow the patients to handle objects with more accurate force control, the former approach is more successful and preferred by subjects with mild impairment while the latter approach appears to be most effective for patients with severe impairment.
Another look at “Stem cell fate dictated solely by altered nanotube dimension”

In their article, Oh et al. (1) reported that stem cell behavior on TiO2 nanotubes can be controlled solely by altering nanotube diameter. Culturing human mesenchymal stem cells (MSCs) on a range of nanotubes with diameters between 30 and 100 nm, cell stretching and expression of osteogenic differentiation markers was highest on 100-nm nanotubes, whereas cell-adhesion rates increased with decreasing tube diameter, with a maximum at 30 nm. This finding is particularly striking in light of previous contrary reports showing that nanoscale-dependent differentiation of MSCs to osteoblasts followed in the opposite direction (2, 3). In these studies, data were presented showing that not only adhesion, proliferation, and migration, but also osteogenic differentiation of rat bone marrow MSCs were highest on 15-nm nanotubes and decreased dramatically on 70- and 100-nm nanotubes. A nanospacing of 15 nm is consistent with an optimal support of clustering of integrins, which are ≈10 nm in diameter, on the nanotube grid (2, 4, 5). Also, Arnold et al. (6) have shown that nanospacing >73 nm dramatically reduced cell spreading and the formation of focal adhesions. This discrepancy is disturbing and may have escaped the attention of Oh et al. In contrast, they presented the hypothesis that cell stretching and formation of stress fibers in MSCs observed on 70-nm but not on 30-nm TiO2 nanotubes promoted differentiation into osteogenic cells, not taking into account the critical role of integrin clustering and focal-contact formation for cell differentiation. Further discussion and experimentation will be necessary to resolve this apparent conflict.
Population Dynamics of Phage and Bacteria in Spatially Structured Habitats Using Phage λ and Escherichia coli

ABSTRACT Bacteria living in physically structured habitats are exposed heterogeneously to both resources and different types of phages. While there have been numerous experimental approaches to examine spatially distributed bacteria exposed to phages, there is little theory to guide the design of these experiments, interpret their results, or expand the inferences drawn to a broader ecological and evolutionary context. Plaque formation provides a window into understanding phage-bacterium interactions in physically structured populations, including surfaces, semisolids, and biofilms. We develop models to address the plaque dynamics for a temperate phage and its virulent mutants. The models are compared with phage λ-Escherichia coli system to quantify their applicability. We found that temperate phages gave an increasing number of gradually smaller colonies as the distance increased from the plaque center. For low-lysogen frequency this resulted in plaques with most of the visible colonies at an intermediate distance between the center and periphery. Using spot inoculation, where phages in excess of bacteria were inoculated in a circular area, we measured the frequency and spatial distribution of lysogens. The spot morphology of cII-negative (cII−) and cIII− mutants of phage λ displays concentric rings of high-density lysogenic colonies. The simplest of these ring morphologies was reproduced by including multiplicity of infection (MOI) sensitivity in lysis-lysogeny decisions, but its failure to explain the occasional observation of multiple rings in cIII− mutant phages highlights unknown features of this phage. Our findings demonstrated advantages of temperate phages over virulent phages in exploiting limited resources in spatially distributed microbial populations. IMPORTANCE Phages are the most abundant organisms on earth, and yet little is known about how phages and bacterial hosts are influencing each other in density and evolution. Phages can be either virulent or temperate, a difference that is highlighted when a spatially structured bacterial population is infected. Phage λ is a temperate phage, with a capacity for dormancy that can be modified by single gene knockouts. The stochastic bias in the lysis-lysogeny decision's probability is reflected in plaque morphologies on bacterial lawns. We present a model for plaque morphology of both virulent and temperate phages, taking into account the underlying survival of bacterial microcolonies. It reproduces known plaque morphologies and speaks to advantages of temperate phages in a spatially structured environment.
Using pluggable procedures and ontology to realize semantic virtual environments 2.0

Allowing users to design animation procedures and share their designs with other users is a crucial function for creating personalized 3D avatar behaviors on multi-user virtual environments (MUVE's). By describing the ontology of the virtual objects in the environment to animation procedures, we allow these procedures to create customized animations for an avatar to interact with the environment or other avatars. In this paper, we attempt to realize a semantic virtual environment (SVE) in our MUVE system (called IMNET) with the concept of web 2.0 through three mechanisms: dynamical installation of animation procedures, ontology design of semantic description for virtual objects and avatars, and interaction-oriented message delivery. Based on our demonstrative applications, we have designed example semantics for the objects in the virtual world by the use of ontology. We have used two application scenarios about automatic generation of navigation path and casual interactions between users to illustrate the potential of creating sharable rich contents in a semantic virtual environment.
Branched polyethylene glycol for protein precipitation

The use of linear PEGs for protein precipitation raises the issues of high viscosity and limited selectivity. This paper explores PEG branching as a way to alleviate the first problem, by using 3‐arm star as the model branched structure. 3‐arm star PEGs of 4,000 to 9,000 Da were synthesized and characterized. The effects of PEG branching were then elucidated by comparing the branched PEG precipitants to linear versions of equivalent molecular weights, in terms of IgG recovery from CHO cell culture supernatant, precipitation selectivity, solubility of different purified proteins, and precipitation kinetics. Two distinct effects were observed: PEG branching reduced dynamic viscosity; secondly, the branched PEGs precipitated less proteins and did so more slowly. Precipitation selectivity was largely unaffected. When the branched PEGs were used at concentrations higher than their linear counterparts to give similar precipitation yields, the dynamic viscosity of the branched PEGs were noticeably lower. Interestingly, the precipitation outcome was found to be a strong function of PEG hydrodynamic radius, regardless of PEG shape and molecular weight. These observations are consistent with steric mechanisms such as volume exclusion and attractive depletion. Biotechnol. Bioeng. 2012; 109:736–746. © 2011 Wiley Periodicals, Inc.
Evolution and change in data management — issues and directions

One of the fundamental aspects of information and database systems is that they change. Moreover, in so doing they evolve, although the manner and quality of this evolution is highly dependent on the mechanisms in place to handle it. While changes in data are handled well, changes in other aspects, such as structure, rules, constraints, the model, etc., are handled to varying levels of sophistication and completeness. In order to study this in more detail a workshop on Evolution and Change in Data Management was held in Paris in November 1999. It brought together researchers from a wide range of disciplines with a common interest in handling the fundamental characteristics and the conceptual modelling of change in information and database systems. This short report of the workshop concentrates on some of the general lessons that emerged during the four days.
A nanobody inhibitor of Fascin-1 actin-bundling activity and filopodia formation

Fascin-1-mediated actin-bundling activity is central to the generation of plasma membrane protrusions required for cell migration. Dysregulated formation of cellular protrusions is observed in metastatic cancers, where they are required for increased invasiveness, and is often correlated with increased Fascin-1 abundance. Therefore, there is interest in generating therapeutic Fascin-1 inhibitors. We present the identification of Nb 3E11, a nanobody inhibitor of Fascin-1 actin-bundling activity and filopodia formation. The crystal structure of the Fascin-1/Nb 3E11 complex reveals the structural mechanism of inhibition. Nb 3E11 occludes an actin-binding site on the third β-trefoil domain of Fascin-1 that is currently not targeted by chemical inhibitors. Binding of Nb 3E11 to Fascin-1 induces a conformational change in the adjacent domains to stabilize Fascin-1 in an inhibitory state similar to that adopted in the presence of small-molecule inhibitors. Nb 3E11 could be used as a tool inhibitor molecule to aid in the development of Fascin-1 targeted therapeutics.
Measuring phase synchrony in brain signals

This article presents, for the first time, a practical method for the direct quantification of frequency‐specific synchronization (i.e., transient phase‐locking) between two neuroelectric signals. The motivation for its development is to be able to examine the role of neural synchronies as a putative mechanism for long‐range neural integration during cognitive tasks. The method, called phase‐locking statistics (PLS), measures the significance of the phase covariance between two signals with a reasonable time‐resolution (<100 ms). Unlike the more traditional method of spectral coherence, PLS separates the phase and amplitude components and can be directly interpreted in the framework of neural integration. To validate synchrony values against background fluctuations, PLS uses surrogate data and thus makes no a priori assumptions on the nature of the experimental data. We also apply PLS to investigate intracortical recordings from an epileptic patient performing a visual discrimination task. We find large‐scale synchronies in the gamma band (45 Hz), e.g., between hippocampus and frontal gyrus, and local synchronies, within a limbic region, a few cm apart. We argue that whereas long‐scale effects do reflect cognitive processing, short‐scale synchronies are likely to be due to volume conduction. We discuss ways to separate such conduction effects from true signal synchrony. Hum Brain Mapping 8:194–208, 1999. © 1999 Wiley‐Liss, Inc.
Regenerative Therapeutic Potential of Adipose Stromal Cells in Early Stage Diabetic Retinopathy

Diabetic retinopathy (DR) is the leading cause of blindness in working-age adults. Early stage DR involves inflammation, vascular leakage, apoptosis of vascular cells and neurodegeneration. In this study, we hypothesized that cells derived from the stromal fraction of adipose tissue (ASC) could therapeutically rescue early stage DR features. Streptozotocin (STZ) induced diabetic athymic nude rats received single intravitreal injection of human ASC into one eye and saline into the other eye. Two months post onset of diabetes, administration of ASC significantly improved “b” wave amplitude (as measured by electroretinogram) within 1–3 weeks of injection compared to saline treated diabetic eyes. Subsequently, retinal histopathological evaluation revealed a significant decrease in vascular leakage and apoptotic cells around the retinal vessels in the diabetic eyes that received ASC compared to the eyes that received saline injection. In addition, molecular analyses have shown down-regulation in inflammatory gene expression in diabetic retina that received ASC compared to eyes that received saline. Interestingly, ASC were found to be localized near retinal vessels at higher densities than seen in age matched non-diabetic retina that received ASC. In vitro, ASC displayed sustained proliferation and decreased apoptosis under hyperglycemic stress. In addition, ASC in co-culture with retinal endothelial cells enhance endothelial survival and collaborate to form vascular networks. Taken together, our findings suggest that ASC are able to rescue the neural retina from hyperglycemia-induced degeneration, resulting in importantly improved visual function. Our pre-clinical studies support the translational development of adipose stem cell-based therapy for DR to address both retinal capillary and neurodegeneration.
Online and Stochastic Gradient Methods for Non-decomposable Loss Functions

Modern applications in sensitive domains such as biometrics and medicine frequently require the use of non-decomposable loss functions such as [email protected]k, F-measure etc. Compared to point loss functions such as hinge-loss, these offer much more fine grained control over prediction, but at the same time present novel challenges in terms of algorithm design and analysis. In this work we initiate a study of online learning techniques for such non-decomposable loss functions with an aim to enable incremental learning as well as design scalable solvers for batch problems. To this end, we propose an online learning framework for such loss functions. Our model enjoys several nice properties, chief amongst them being the existence of efficient online learning algorithms with sublinear regret and online to batch conversion bounds. Our model is a provable extension of existing online learning models for point loss functions. We instantiate two popular losses, Prec@k and pAUC, in our model and prove sublinear regret bounds for both of them. Our proofs require a novel structural lemma over ranked lists which may be of independent interest. We then develop scalable stochastic gradient descent solvers for non-decomposable loss functions. We show that for a large family of loss functions satisfying a certain uniform convergence property (that includes Prec@k, pAUC, and F-measure), our methods provably converge to the empirical risk minimizer. Such uniform convergence results were not known for these losses and we establish these using novel proof techniques. We then use extensive experimentation on real life and benchmark datasets to establish that our method can be orders of magnitude faster than a recently proposed cutting plane method.
Locally Adaptive Nonparametric Binary Regression

We propose a nonparametric and locally adaptive Bayesian estimator for estimating a binary regression. Flexibility is obtained by modeling the binary regression as a mixture of probit regressions with the argument of each probit regression having a thin plate spline prior with its own smoothing parameter and with the mixture weights depending on the covariates. The estimator is compared to a single spline estimator and to a recently proposed locally adaptive estimator. The methodology is illustrated by applying it to both simulated and real examples.
A Multivariate Analytic Approach to the Differential Diagnosis of Apraxia of Speech.

Purpose Apraxia of speech (AOS) is a consequence of stroke that frequently co-occurs with aphasia. Its study is limited by difficulties with its perceptual evaluation and dissociation from co-occurring impairments. This study examined the classification accuracy of several acoustic measures for the differential diagnosis of AOS in a sample of stroke survivors. Method Fifty-seven individuals were included (mean age = 60.8 ± 10.4 years; 21 women, 36 men; mean months poststroke = 54.7 ± 46). Participants were grouped on the basis of speech/language testing as follows: AOS-Aphasia (n = 20), Aphasia Only (n = 24), and Stroke Control (n = 13). Normalized Pairwise Variability Index, proportion of distortion errors, voice onset time variability, and amplitude envelope modulation spectrum variables were obtained from connected speech samples. Measures were analyzed for group differences and entered into a linear discriminant analysis to predict diagnostic classification. Results Out-of-sample classification accuracy of all measures was over 90%. The envelope modulation spectrum variables had the greatest impact on classification when all measures were analyzed together. Conclusions This study contributes to efforts to identify objective acoustic measures that can facilitate the differential diagnosis of AOS. Results suggest that further study of these measures is warranted to determine the best predictors of AOS diagnosis. Supplemental Materials https://doi.org/10.23641/asha.5611309.
On Capacity of Large-Scale MIMO Multiple Access Channels with Distributed Sets of Correlated Antennas

In this paper, a deterministic equivalent of ergodic sum rate and an algorithm for evaluating the capacity-achieving input covariance matrices for the uplink large-scale multiple-input multiple-output (MIMO) antenna channels are proposed. We consider a large-scale MIMO system consisting of multiple users and one base station with several distributed antenna sets. Each link between a user and an antenna set forms a two-sided spatially correlated MIMO channel with line-of-sight (LOS) components. Our derivations are based on novel techniques from large dimensional random matrix theory (RMT) under the assumption that the numbers of antennas at the terminals approach to infinity with a fixed ratio. The deterministic equivalent results (the deterministic equivalent of ergodic sum rate and the capacity-achieving input covariance matrices) are easy to compute and shown to be accurate for realistic system dimensions. In addition, they are shown to be invariant to several types of fading distribution.
Restriction Fragment Length Polymorphism of hsp 70 Gene , Localized in the RT 1 Complex , Is Associated With Hypertension in Spontaneously Hypertensive Rats

Previous studies from our laboratory have demonstrated that the intermediate phenotype of thermosensitivity is present in hypertensive mice and rats. Increased expression of hsp70 caused by increased transcription rate was demonstrated in vivo, in organs, and in cultured cells from spontaneously hypertensive rats and hypertensive mice. In this study, a polymorphism of this gene was revealed with BamHl enzyme by using a human hsp70 probe. A 4.4-kb fragment was visualized in normotensive rats (Brown-Norway BN.Ix and Sprague-Dawley), and a 3.0-kb fragment was found in spontaneously hypertensive rats (SHR) of three different origins and in Wistar and Buffalo rats. Both fragments were present in the Wistar-Kyoto rat strain. The present study mapped the polymorphism of hsp70 into the RT1 complex in BN.1K and SHR.1N congenic strains. The hsp70 restriction fragment length polymorphism is associated with a blood pressure difference of IS mm Hg in recombinant inbred strains. These results justify the search for a mechanism by which hsp70 could influence blood pressure. (Hypertension 1992;19:611-614)
Transparency of Environmental Computer Models

Environmental computer models are considered essential tools in supporting environmental decision making, but their main value is that they allow a better understanding of our complex environment. Despite numerous attempts to promote good modelling practice, transparency of current environmental computer models is limited, which hinders progress in both science and policy making. An important cause is that the structure, meaning and context of environmental computer models is often not clear for other people than the model developers. In the proposed research project we would like to find out whether it is possible to increase the transparency of environmental computer models by making their underlying conceptual model explicit. In preliminary research we identi ed the following challenges: 1) many model developers are mainly focused on the computational instead of the descriptive aspects of computer models 2) many environmental modellers may not consider the lack of transparency a big problem nor do they see computer scientists as natural partners in cooperation. However, we think that both environmental and computer science could bene t from an interdisciplinary or even a totally integrated approach. We expect that ex- perimenting with tools and methods from computer science could teach us important lessons on the practice of environmental modelling and hopefully guide us to this novel, integrated way of performing e-science.
Identification of an Export Control Sequence and a Requirement for the KH Domains in ICP27 from Herpes Simplex Virus Type 1

ABSTRACT The herpes simplex virus type 1 (HSV-1) immediate-early protein ICP27 is an RNA-binding protein that performs multiple functions required for the expression of HSV-1 genes during a productive infection. One essential function involves shuttling between the nucleus and the cytoplasm. Some of the domains identified in ICP27 include a leucine-rich nuclear export sequence (NES), a nuclear localization signal, three KH-like RNA-binding domains, and an RGG-box type RNA-binding motif. To study the contribution of two of the essential domains in ICP27 to HSV gene expression, we generated recombinant herpesviruses carrying deleterious mutations in the NES and KH domains of ICP27. To accomplish this, we fused the green fluorescent protein (GFP) to ICP27 and utilized fluorescence as a marker to isolate recombinant herpesviruses. Fusion of GFP to wild-type ICP27 did not disturb its localization or function or significantly reduce virus yield. Analysis of HSV gene expression in cells infected with a recombinant virus carrying a point mutation in the first KH-like RNA-binding domain revealed that nuclear export of ICP27 was not blocked, and the expression of only a subset of ICP27-dependent late genes was affected. These findings suggest that individual KH-like RNA-binding motifs in ICP27 may be involved in binding distinct RNAs. Analysis of recombinant viruses carrying a lethal mutation in the NES of ICP27 was not accomplished because this mutation results in a strong dominant-negative phenotype. Finally, we demonstrate that shuttling by ICP27 is regulated by an export control sequence adjacent to its NES that functions like the inhibitory sequence element found adjacent to the NES of NS1 from influenza virus.