Miracle-dz/UniFAR-FTUs huggingface dataset:
Multi-scale Mining of fMRI Data with Hierarchical Structured Sparsity

Inverse inference, or "brain reading", is a recent paradigm for analyzing functional magnetic resonance imaging (fMRI) data, based on pattern recognition tools. By predicting some cognitive variables related to brain activation maps, this approach aims at decoding brain activity. Inverse inference takes into account the multivariate information between voxels and is currently the only way to assess how precisely some cognitive information is encoded by the activity of neural populations within the whole brain. However, it relies on a prediction function that is plagued by the curse of dimensionality, as we have far more features than samples, i.e., more voxels than fMRI volumes. To address this problem, different methods have been proposed. Among them are univariate feature selection, feature agglomeration and regularization techniques. In this paper, we consider a hierarchical structured regularization. Specifically, the penalization we use is constructed from a tree that is obtained by spatially constrained agglomerative clustering. This approach encodes the spatial prior information in the regularization process, which makes the overall prediction procedure more robust to inter-subject variability. We test our algorithm on a real data acquired for studying the mental representation of objects, and we show that the proposed algorithm yields better prediction accuracy than reference methods.
Evaluation of the Gamma-H2AX Assay for Radiation Biodosimetry in a Swine Model

There is a paucity of large animal models to study both the extent and the health risk of ionizing radiation exposure in humans. One promising candidate for such a model is the minipig. Here, we evaluate the minipig for its potential in γ-H2AX-based biodosimetry after exposure to ionizing radiation using both Cs137 and Co60 sources. γ-H2AX foci were enumerated in blood lymphocytes and normal fibroblasts of human and porcine origin after ex vivo γ-ray irradiation. DNA double-strand break repair kinetics in minipig blood lymphocytes and fibroblasts, based on the γ-H2AX assay, were similar to those observed in their human counterparts. To substantiate the similarity observed between the human and minipig we show that minipig fibroblast radiosensitivity was similar to that observed with human fibroblasts. Finally, a strong γ-H2AX induction was observed in blood lymphocytes following minipig total body irradiation. Significant responses were detected 3 days after 1.8 Gy and 1 week after 3.8 and 5 Gy with residual γ-H2AX foci proportional to the initial radiation doses. These findings show that the Gottingen minipig provides a useful in vivo model for validation of γ-H2AX biodosimetry for dose assessment in humans.
Insulin-like growth factor-1 stimulates regulatory T cells and suppresses autoimmune disease

The recent precipitous rise in autoimmune diseases is placing an increasing clinical and economic burden on health systems worldwide. Current therapies are only moderately efficacious, often coupled with adverse side effects. Here, we show that recombinant human insulin‐like growth factor‐1 (rhIGF‐1) stimulates proliferation of both human and mouse regulatory T (Treg) cells in vitro and when delivered systemically via continuous minipump, it halts autoimmune disease progression in mouse models of type 1 diabetes (STZ and NOD) and multiple sclerosis (EAE) in vivo. rhIGF‐1 administration increased Treg cells in affected tissues, maintaining their suppressive properties. Genetically, ablation of the IGF‐1 receptor specifically on Treg cell populations abrogated the beneficial effects of rhIGF‐1 administration on the progression of multiple sclerotic symptoms in the EAE model, establishing a direct effect of IGF‐1 on Treg cell proliferation. These results establish systemically delivered rhIGF‐1 as a specific, effective stimulator of Treg cell action, underscoring the clinical feasibility of manipulating natural tolerance mechanisms to suppress autoimmune disease.
A stable clustering algorithm for efficiency applications in VANETs

Efficiency applications in VANETs are focused on increasing the productivity of the road resources by managing the traffic flow and monitoring the road conditions. The performance of most such applications is dependent on an effective density estimation of the vehicles in the surroundings. Of the various methods, clustering demonstrates to be an effective concept to implement this. However due to high mobility a stable cluster, within a vehicular framework, is difficult to implement. In this work, we propose a direction based clustering algorithm with a clusterhead switching mechanism. This mechanism is aimed to overcome the influence of overtaking within the clusters. The proposed algorithm facilitates to attain better stability and thus accurate density estimation within the clusters. Simulation results show that the proposed clustering algorithm is rendered stability through switching mechanism and hence provides a better accuracy in density estimation.
Analytical solution for a class of network dynamics with mechanical and financial applications

We show that for a certain class of dynamics at the nodes the response of a network of any topology to arbitrary inputs is defined in a simple way by its response to a monotone input. The nodes may have either a discrete or continuous set of states and there is no limit on the complexity of the network. The results provide both an efficient numerical method and the potential for accurate analytic approximation of the dynamics on such networks. As illustrative applications, we introduce a quasistatic mechanical model with objects interacting via frictional forces and a financial market model with avalanches and critical behavior that are generated by momentum trading strategies.
Antigen recognition by H-2-restricted T cells. I. Cell-free antigen processing

We examined the ability of a set of cloned chicken ovalbumin (cOVA)- specific, Id-restricted, T cell hybridomas to produce interleukin-2 in response to cOVA presented by the Ia+ B cell lymphoma line, A20-2J. Although viable A20-2J cells presented native, denatured, and fragmented cOVA more or less equally well, A20-2J cells that were glutaraldehyde-fixed could present only enzymatically or chemically fragmented cOVA. These results suggest that antigen fragmentation may be both necessary and sufficient to define accessory cell processing of soluble antigens so that they may be recognized in association with I- region molecules by T cells.
Altered State and Trait Disgust in Borderline Personality Disorder

Abstract Clinical experience suggests that the emotion disgust plays an important role in borderline personality disorder (BPD). We investigated 30 female patients with BPD and 30 healthy women who answered different measures of trait disgust, specifically disgust proneness, disgust sensitivity, and self-disgust. Moreover, all participants rated affective facial expressions as well as affective scenes according to perceived or elicited basic emotions. The patients with BPD reported elevated trait disgust, especially for the area of self-disgust. They also rated facial expressions of disgust as more intense than did the healthy women but only when the person who displayed this emotion was male. This sex-specific disgust bias was independent of depression and experienced sexual/physical abuse in the clinical group. Altogether, the patients with BPD showed a broad spectrum of altered disgust processes, which was positively correlated with disorder severity. Consequently, the assessment of disgust reactivity should be introduced as a diagnostic tool for this disorder.
Generating Valid 4 ◊ 4 Correlation Matrices

In this article, we provide an algorithm for generating valid 4 ◊ 4 correlation matrices by creating bounds for the remaining three correlations that insure positive semidefiniteness once correlations between one variable and the other three are supplied. This is achieved by attending to the constraints placed on the leading principal minor determinants. Prior work in this area is restricted to 3 ◊ 3 matrices or provides a means to investigate whether a 4 ◊ 4 matrix is valid but does not oer a method of construction. We do oer such a method and supply a computer program to deliver a 4 ◊ 4 positive semidefinite correlation matrix.
An enhanced multilevel algorithm for circuit placement

This paper presents several important enhancements to the recently published multilevel placement package mPL. The improvements include (i) unconstrained quadratic relaxation on small, noncontiguous subproblems at every level of the hierarchy; (ii) improved interpolation (declustering) based on techniques from algebraic multigrid (AMG), and (iii) iterated V-cycles with additional geometric information for aggregation in subsequent V-cycles. The enhanced version of mPL, named mPL2, improves the total wirelength result by about 12% compared to the original version. The attractive scalability properties of the mPL run time have been largely retained, and the overall run time remains very competitive. Compared to GORDIAN-L-DOMINO on uniform-cell-size IBM/ISPD98 benchmarks, a speed-up of well over 8/spl times/ on large circuits (/spl ges/100,000 cells or nets) is obtained along with an average improvement in total wirelength of about 2%. Compared to Dragon on the same benchmarks, a speed-up of about 5/spl times/ is obtained at the cost of about 4% increased wirelength. On the recently published PEKO synthetic benchmarks, mPL2 generates surprisingly high-quality placements-roughly 60% closer to the optimal than those produced by Capo 8.5 and Dragon-in run time about twice as long as Capo's and about 1/10th of Dragon's.
What's on Users' Minds? Toward a Usable Smart Phone Security Model

Smart phones pose new challenges to usable security. Current means of specifying security policies or preferences for resource sharing are either woefully inadequate or too hard to use. This article presents a policy model approach toward usable security for smart phones. In particular, the approach adopts a semantic-based policy representation to help users' understanding of security policies and to better reflect what users really want. Furthermore, given the special nature of smart phones' usage, social awareness plays an important role. In this regard, the authors present propose a socially-aware policy reasoning model based on the results of a user study.
miR‐221 redirects precursor B cells to the BM and regulates their residence

Pluripotent hematopoietic stem cells and multipotent myeloid/lymphoid progenitors express miR‐221 and miR‐222. When Pax5 expression commits these progenitors to monopotent pre‐B lymphocytes the two microRNAs (miRNAs) are downregulated. Upon transplantation, stem cells and progenitors can reside in the BM, while pre‐B cells, after their commitment, no longer do so. Retrovirally transduced, doxycycline‐induced overexpression of either miR‐221 or miR‐222 in pre‐B‐I cells does not revert their monopotency to multipotency. However, upon transplantation miR‐221, but not miR‐222, transduced pre‐B‐I cells regain the capacity to reside in the BM. Upon subsequent termination of miR‐221‐expression by removal of doxycycline, the transplanted cells leave the BM again. Microarray analyses identified 25 downregulated miR‐221‐target genes, which could function to localize phases of B‐lymphocyte development in BM before and after commitment.
Evolution of Resistance and Progression to Disease during Clonal Expansion of Cancer

Inspired by previous work of Iwasa, Nowak, and Michor (2006), and Haeno, Iwasa, and Michor (2007), we consider an exponentially growing population of cancerous cells that will evolve resistance to treatment after one mutation or display a disease phenotype after two or more mutations. We prove results about the distribution of the first time when k mutations have accumulated in some cell, and about the growth of the number of type k cells. We show that our results can be used to derive the previous results about the tumor grown to a fixed size.
The Impact of Interpixel Capacitance in CMOS Detectors on PSF Shapes and Implications for WFIRST

Unlike optical CCDs, near-infrared detectors, which are based on CMOS hybrid readout technology, typically suffer from electrical crosstalk between the pixels. The interpixel capacitance (IPC) responsible for the crosstalk affects the point-spread function (PSF) of the telescope, increasing the size and modifying the shape of all objects in the images while correlating the Poisson noise. Upcoming weak lensing surveys that use these detectors, such as WFIRST, place stringent requirements on the PSF size and shape (and the level at which these are known), which in turn must be translated into requirements on IPC. To facilitate this process, we present a first study of the effect of IPC on WFIRST PSF sizes and shapes. Realistic PSFs are forward-simulated from physical principles for each WFIRST bandpass. We explore how the PSF size and shape depends on the range of IPC coupling with pixels that are connected along an edge or corner; for the expected level of IPC in WFIRST, IPC increases the PSF sizes by ∼5%. We present a linear fitting formula that describes the uncertainty in the PSF size or shape due to uncertainty in the IPC, which could arise for example due to unknown time evolution of IPC as the detectors age or due to spatial variation of IPC across the detector. We also study of the effect of a small anisotropy in the IPC, which further modifies the PSF shapes. Our results are a first, critical step in determining the hardware and characterization requirements for the detectors used in the WFIRST survey.
Effects of biomass burning on climate, accounting for heat and moisture fluxes, black and brown carbon, and cloud absorption effects

This paper examines the effects on climate and air pollution of open biomass burning (BB) when heat and moisture fluxes, gases and aerosols (including black and brown carbon, tar balls, and reflective particles), cloud absorption effects (CAEs) I and II, and aerosol semidirect and indirect effects on clouds are treated. It also examines the climate impacts of most anthropogenic heat and moisture fluxes (AHFs and AMFs). Transient 20 year simulations indicate BB may cause a net global warming of ~0.4 K because CAE I (~32% of BB warming), CAE II, semidirect effects, AHFs (~7%), AMFs, and aerosol absorption outweigh direct aerosol cooling and indirect effects, contrary to previous BB studies that did not treat CAEs, AHFs, AMFs, or brown carbon. Some BB warming can be understood in terms of the anticorrelation between instantaneous direct radiative forcing (DRF) changes and surface temperature changes in clouds containing absorbing aerosols. BB may cause ~250,000 (73,000–435,000) premature mortalities/yr, with >90% from particles. AHFs from all sources and AMFs + AHFs from power plants and electricity use each may cause a statistically significant +0.03 K global warming. Solar plus thermal‐IR DRFs were +0.033 (+0.027) W/m2 for all AHFs globally without (with) evaporating cooling water, +0.009 W/m2 for AMFs globally, +0.52 W/m2 (94.3% solar) for all‐source BC outside of clouds plus interstitially between cloud drops at the cloud relative humidity, and +0.06 W/m2 (99.7% solar) for BC inclusions in cloud hydrometeor particles. Modeled post‐1850 biomass, biofuel, and fossil fuel burning, AHFs, AMFs, and urban surfaces accounted for most observed global warming.
Mapping of the Plasmodium falciparum multidrug resistance gene 5′‐upstream region, and evidence of induction of transcript levels by antimalarial drugs in chloroquine sensitive parasites

The Plasmodium falciparum multidrug resistance gene, pfmdr1, has been shown to be involved in the mediation of the parasite's response to various antimalarial drugs. Previous studies of pfmdr1 expression have shown that transcript levels are increased in drug‐resistant isolates. However, a detailed examination of the transcriptional regulation of this gene has not been completed. The aim of this study was to map the 5′ UTR of pfmdr1, and to examine the transcriptional profile of the gene in sensitive parasites treated with four different antimalarial drugs. RT‐PCR and 5′‐RACE mapping showed that the 5′ UTR has a length of 1.94 kb. A putative promoter has been identified via transient transfection. Northern analysis revealed a 2.1‐ to 2.7‐fold increase in pfmdr1 expression in 3D7 parasites treated with 50 nM chloroquine for 6 h, confirming results from Serial Analysis of Gene Expression. 3D7 parasites were subsequently treated with experimentally derived IC50 concentrations of mefloquine, quinine and pyrimethamine. pfmdr1 transcript levels specifically increased 2.5‐fold at 6 h in mefloquine‐treated parasites and threefold in parasites treated with quinine for 30 min. There was no evidence of transcript induction in pyrimethamine‐treated parasites. This is the first evidence of induction of pfmdr1 expression in sensitive cells; and suggests a novel method of transcriptional control for this gene.
Genetic Ablation of CaV3.2 Channels Enhances the Arterial Myogenic Response by Modulating the RyR-BKCa Axis

Objective—In resistance arteries, there is an emerging view that smooth muscle CaV3.2 channels restrain arterial constriction through a feedback response involving the large-conductance Ca2+-activated K+ channel (BKCa). Here, we used wild-type and CaV3.2 knockout (CaV3.2−/−) mice to definitively test whether CaV3.2 moderates myogenic tone in mesenteric arteries via the CaV3.2-ryanodine receptor-BKCa axis and whether this regulatory mechanism influences blood pressure regulation. Approach and Results—Using pressurized vessel myography, CaV3.2−/− mesenteric arteries displayed enhanced myogenic constriction to pressure but similar K+-induced vasoconstriction compared with wild-type C57BL/6 arteries. Electrophysiological and myography experiments subsequently confirmed the inability of micromolar Ni2+, a CaV3.2 blocker, to either constrict arteries or suppress T-type currents in CaV3.2−/− smooth muscle cells. The frequency of BKCa-induced spontaneous transient outward K+ currents dropped in wild-type but not in knockout arterial smooth muscle cells upon the pharmacological suppression of CaV3.2 channel. Line scan analysis performed on en face arteries loaded with Fluo-4 revealed the presence of Ca2+ sparks in all arteries, with the subsequent application of Ni2+ only affecting wild-type arteries. Although CaV3.2 channel moderated myogenic constriction of resistance arteries, the blood pressure measurements of CaV3.2−/− and wild-type animals were similar. Conclusions—Overall, our findings establish a negative feedback mechanism of the myogenic response in which CaV3.2 channel modulates downstream ryanodine receptor-BKCa to hyperpolarize and relax arteries.
Semi-Supervised Learning Using Sparse Eigenfunction Bases

We present a new framework for semi-supervised learning with sparse eigenfunction bases of kernel matrices. It turns out that when the cluster assumption holds, that is, when the high density regions are sufﬁciently separated by low density valleys, each high density area corresponds to a unique representative eigenvector. Linear combination of such eigenvectors (or, more precisely, of their Nystrom extensions) provide good candidates for good classiﬁcation functions. By ﬁrst choosing an appropriate basis of these eigenvectors from unlabeled data and then using labeled data with Lasso to select a classiﬁer in the span of these eigenvectors, we obtain a classiﬁer, which has a very sparse representation in this basis. Importantly, the sparsity appears naturally from the cluster assumption. Experimental results on a number of real-world datasets show that our method is competitive with the state of the art semi-supervised learning algorithms and out-performs the natural base-line algorithm (Lasso in the Kernel PCA basis).
The Multicopper Ferroxidase Hephaestin Enhances Intestinal Iron Absorption in Mice

Hephaestin is a vertebrate multicopper ferroxidase important for the transfer of dietary iron from intestinal cells to the blood. Hephaestin is mutated in the sex-linked anemia mouse, resulting in iron deficiency. However, sex-linked anemia mice still retain some hephaestin ferroxidase activity. They survive, breed, and their anemia improves with age. To gain a better understanding of the role of hephaestin in iron homeostasis, we used the Cre-lox system to generate knockout mouse models with whole body or intestine-specific (Villin promoter) ablation of hephaestin. Both types of mice were viable, indicating that hephaestin is not essential and that other mechanisms, multicopper ferroxidase-dependent or not, must compensate for hephaestin deficiency. The knockout strains, however, both developed a microcytic, hypochromic anemia, suggesting severe iron deficiency and confirming that hephaestin plays an important role in body iron acquisition. Consistent with this, the knockout mice accumulated iron in duodenal enterocytes and had reduced intestinal iron absorption. In addition, the similarities of the phenotypes of the whole body and intestine-specific hephaestin knockout mice clarify the important role of hephaestin specifically in intestinal enterocytes in maintaining whole body iron homeostasis. These mouse models will serve as valuable tools to study the role of hephaestin and associated proteins in iron transport in the small intestine and other tissues.
Class and Status: The Conceptual Distinction and its Empirical Relevance

In this article, we return to Max Weber's distinction between class and status as related but different forms of social stratification. We argue that this distinction is not only conceptually cogent, but empirically important as well. Indeed, class and status do have distinct explanatory power when it comes to studying varying areas of social life. Consistent with Weber's assertions, we show that economic security and prospects are stratified more by class than by status, while the opposite is true for outcomes in the domain of cultural consumption. Within politics, class rather than status predicts Conservative versus Labour Party voting in British general elections and also Left-Right political attitudes. But it is status rather than class that predicts Libertarian-Authoritarian attitudes.
Methods of detection of Chlamydia psittaci in domesticated and wild birds.

OBJECTIVE To study the occurrence of Chlamydia psittaci in domesticated and wild birds and compare the sensitivity of molecular detection with cell culture isolation. DESIGN Study of cell culture isolation and PCR detection of C psittaci in avian samples. PROCEDURE Samples were obtained from 485 birds. Domesticated birds were selected at random from pet shops, private aviaries and zoos, while wild birds were captured locally, sampled, and immediately released. Swabs were collected from choanal slit, conjunctiva and cloaca of each bird and pooled. Samples were divided into equal portions for use in PCR dot-blot and cell culture detection. PCR and dot-blot detection was based on the ompB gene. RESULTS Prevalence of infection varied markedly between flocks of captive birds. It was highest where there were frequent changes in the flock members or where there were many birds confined in small areas. C psittaci was not detected in wild birds or water birds. The sensitivity of cell culture compared to PCR dot-blot detection was 68%. All samples positive by cell culture were also positive by PCR. CONCLUSIONS PCR-dot blot detection of C psittaci in birds appears to be more sensitive than cell culture isolation in this study. C psittaci infection of birds may occur in clinically normal captive birds.