Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Throughput Assay Development for Cystine-Glutamate Antiporter (xc -) Highlights Faster Cystine Uptake than Glutamate Release in Glioma Cells

The cystine-glutamate antiporter (system xc -) is a Na+-independent amino acid transporter that exchanges extracellular cystine for intracellular glutamate. It is thought to play a critical role in cellular redox processes through regulation of intracellular glutathione synthesis via cystine uptake. In gliomas, system xc - expression is universally up-regulated while that of glutamate transporters down-regulated, leading to a progressive accumulation of extracellular glutamate and excitotoxic cell death of the surrounding non-tumorous tissue. Additionally, up-regulation of system xc - in activated microglia has been implicated in the pathogenesis of several neurodegenerative disorders mediated by excess glutamate. Consequently, system xc - is a new drug target for brain cancer and neuroinflammatory diseases associated with excess extracellular glutamate. Unfortunately no potent and selective small molecule system xc - inhibitors exist and to our knowledge, no high throughput screening (HTS) assay has been developed to identify new scaffolds for inhibitor design. To develop such an assay, various neuronal and non-neuronal human cells were evaluated as sources of system xc -. Human glioma cells were chosen based on their high system xc - activity. Using these cells, [14C]-cystine uptake and cystine-induced glutamate release assays were characterized and optimized with respect to cystine and protein concentrations and time of incubation. A pilot screen of the LOPAC/NINDS libraries using glutamate release demonstrated that the logistics of the assay were in place but unfortunately, did not yield meaningful pharmacophores. A larger, HTS campaign using the 384-well cystine-induced glutamate release as primary assay and the 96-well 14C-cystine uptake as confirmatory assay is currently underway. Unexpectedly, we observed that the rate of cystine uptake was significantly faster than the rate of glutamate release in human glioma cells. This was in contrast to the same rates of cystine uptake and glutamate release previously reported in normal human fibroblast cells.
Kleene Algebras, Regular Languages and Substructural Logics

We introduce the two substructural propositional logics KL, KL+, which use disjunction, fusion and a unary, (quasi-)exponential connective. For both we prove strong completeness with respect to the interpretation in Kleene algebras and a variant thereof. We also prove strong completeness for language models, where each logic comes with a different interpretation. We show that for both logics the cut rule is admissible and both have a decidable consequence relation.
Access to versus Use of Loans: What are the True Determinants of Access? *

Access to finance is a prerequisite for economic development. Existing studies measure access by the use of finance. We develop a direct measurement for access to finance from the Business Environment and Enterprise Performance Survey 2005 data. We determine whether a firm without a loan does not need one or is indeed credit-constrained. The determinants of access estimated in a Heckman selection model are compared with those of use. Our results show that firm age and sector effects do not influence access although they are significant in the use regression. The reasons are differences in demand.
Emplacement of giant radial dikes in the northern Tharsis region of Mars

[1] Three distinct sets of graben are associated with the volcano Alba Patera on Mars. One set, approximately circumferential to the edifice, has long been accepted to have formed as a tectonic response to an extensional stress regime associated with the evolution of the Alba Patera edifice. A second set includes mainly linear structures interpreted by many workers to have formed in response to very large-scale regional stresses. We infer that the third set of graben, all of which are relatively linear, none of which are strictly parallel to members of the second set, and many of which contain numerous pit craters, formed above long (∼1000 km), laterally propagating regional dikes emanating from a volcanic center located to the south within the Tharsis region. The expected geometries of such dikes (several hundred meters depth to dike top, ∼20 km depth to dike base, mean dike width ∼30–90 m) are modeled on the assumption that they were fed from a shallow magma reservoir centered on a neutral buoyancy horizon, expected to be present at a depth of ∼10 km on Mars. The volumes of magma in the dikes are consistent with a reservoir similar in size to those inferred to be present under the Tharsis shield volcanoes provided that the dikes were emplaced during caldera collapse episodes. The sizes of the graben associated with these dikes are consistent with the relaxation, during or immediately after dike emplacement, of preexisting regional extensional stresses of a few tens of MPa.
Chemical PARP Inhibition Enhances Growth of Arabidopsis and Reduces Anthocyanin Accumulation and the Activation of Stress Protective Mechanisms

Poly-ADP-ribose polymerase (PARP) post-translationally modifies proteins through the addition of ADP-ribose polymers, yet its role in modulating plant development and stress responses is only poorly understood. The experiments presented here address some of the gaps in our understanding of its role in stress tolerance and thereby provide new insights into tolerance mechanisms and growth. Using a combination of chemical and genetic approaches, this study characterized phenotypes associated with PARP inhibition at the physiological level. Molecular analyses including gene expression analysis, measurement of primary metabolites and redox metabolites were used to understand the underlying processes. The analysis revealed that PARP inhibition represses anthocyanin and ascorbate accumulation under stress conditions. The reduction in defense is correlated with enhanced biomass production. Even in unstressed conditions protective genes and molecules are repressed by PARP inhibition. The reduced anthocyanin production was shown to be based on the repression of transcription of key regulatory and biosynthesis genes. PARP is a key factor for understanding growth and stress responses of plants. PARP inhibition allows plants to reduce protection such as anthocyanin, ascorbate or Non-Photochemical-Quenching whilst maintaining high energy levels likely enabling the observed enhancement of biomass production under stress, opening interesting perspectives for increasing crop productivity.
poLCA : Polytomous Variable Latent Class Analysis Version

poLCA is a software package for the estimation of latent class and latent class regression models for polytomous outcome variables, implemented in the R statistical computing environment. Both models can be called using a single simple command line. The basic latent class model is a ﬁnite mixture model in which the component distributions are assumed to be multi-way cross-classiﬁcation tables with all variables mutually independent. The latent class regression model further enables the researcher to estimate the eﬀects of covariates on predicting latent class membership. poLCA uses expectation-maximization and Newton-Raphson algorithms to ﬁnd maximum likelihood estimates of the model parameters. This user’s guide to the poLCA software package draws extensively from Linzer and Lewis (Forthcoming).
Enhancing partner matching with recommendation systems

Collaboration is vital for the survival of companies in today’s fast moving economy and, therefore, finding and matching partners is an important task. This is true for many different scenarios ranging from companies building consortiums over organizations frequently staffing project teams to the recruitment of new employees. An empirical survey among the Top 1000 companies in Germany on state-of-the-art recruitment practices shows that the Internet is already heavily used to attract and identify large sets of potential partners or applicants. However, the selection of the most suitable candidates from this pool by predicting the quality of the resulting partnership is only merely supported by information technology. Building on existing research in the fields of team building and information systems, we first outline the enhanced information requirements for online partner matching compared to partner information currently available on the Internet. Based on this, we then delineate how recommendation systems can assist in improving matching quality by incorporating relational information when bringing partners together online.
Inattentional Deafness in Simulated Air Traffic Control Tasks:A Behavioral and P300 Analysis

The acoustic environment is critical in Air Traffic Control (ATC), as operators exchange information with planes and must also be aware of the occurrence of auditory alarms. In such situations, observing inattentional deafness is likely. In this study, we aimed to identify the physiological indicators of inattentional deafness through the analysis of the P300 evoked potential, known to be an indicator of attention allocation, an important step to a stimulus reaching consciousness. Based on the assumption that the high mental load generated by an ATC task may reduce the alarm detection rate, we wished to test whether this effect would be reflected in the alarm-evoked P300 amplitude. Participants had to perform simulated ATC tasks within the LABY microworld while electroencephalographic (EEG) activity was recorded. Simultaneously to the LABY tasks, participants were asked to respond to target tones (the “alarm”) and to ignore standard tones. Behavioral results showed that 4.6% of alarms were not reported. For these alarm detection failures, the EEG analysis showed a diminution of the P300 amplitude in comparison to a control condition in which participants only focused on the tones. These results suggest that the P300 amplitude seems to be a valid physiological indicator of vulnerability to inattentional deafness in complex environments. Relevant applications include the prevention of alarm omission and the assessment of warning designs.
Short-Range Wireless Communications for Next-Generation Networks: UWB, 60 GHz Millimeter-Wave WPAN, And ZigBee

This article presents standardization, regulation, and development issues associated with short-range wireless technologies for next-generation personal area networks (PAN). Ultra-wideband (UWB) and 60 GHz millimeter-wave communication technologies promise unprecedented short-range broadband wireless communication and are the harbingers of multigigabit wireless networks. Despite the huge potential for PAN, standardization and global spectrum regulations challenge the success of UWB. On the other hand, ZigBeetrade is expected to be a crucial short-range technology for low throughput and ultra low-power consumption networks. The current status and direction of future development of UWB, emerging 60 GHz millimeter-wave PAN, and low data rate ZigBee are described. This article also addresses wireless MAC protocol issues of 60 GHz multigigabit PAN.
Measuring Stress in Money Markets : The CDSS Index ∗ November 2012

We develop an index that allows us to assess, in real time, the level of stress in money markets, the functioning of which is crucial for banks to fulfill their marginal funding needs and for other financial institutions to meet their liquidity needs. We estimate a dynamic factor model to synthesize information from various money market segments into a single measure—the CDSS index. Using nonlinear versions of the dynamic factor model, we identify phases of money market stress cycles during and after the recent financial crisis. We show that the crisis period has been characterized by three distinct phases—states of low, high, and extreme stress. The switches from high to low stress states generally coincide with various actions by the Federal Reserve that are intended to alleviate funding stress. In the aftermath of the crisis, using a two state model, we find that the level of stress in money markets is generally low with the exception of a brief period in mid-2010 and late-2011.
A weighted voting scheme for recognition of faces with illumination variation

A new method for face recognition based on weighted votes on different sub-images of a picture is proposed. The proposed method is robust under illumination variations and achieves the illumination invariants based on the reflectance-illumination model. The proposed method does not require any prior information about the face shape or illumination and can be applied on each image separately. It does not need multiple images in training stage to get the illumination invariants and is computationally efficient. Support vector machines are used as classifier. Several experiments are performed on Yale B and CMU-PIE databases. The system achieved 99.82% recognition rate in the Yale B and 99.74% for the CMU-PIE database.
Functional Metagenomics of the Bronchial Microbiome in COPD

The course of chronic obstructive pulmonary disease (COPD) is frequently aggravated by exacerbations, and changes in the composition and activity of the microbiome may be implicated in their appearance. The aim of this study was to analyse the composition and the gene content of the microbial community in bronchial secretions of COPD patients in both stability and exacerbation. Taxonomic data were obtained by 16S rRNA gene amplification and pyrosequencing, and metabolic information through shotgun metagenomics, using the Metagenomics RAST server (MG-RAST), and the PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) programme, which predict metagenomes from 16S data. Eight severe COPD patients provided good quality sputum samples, and no significant differences in the relative abundance of any phyla and genera were found between stability and exacerbation. Bacterial biodiversity (Chao1 and Shannon indexes) did not show statistical differences and beta-diversity analysis (Bray-Curtis dissimilarity index) showed a similar microbial composition in the two clinical situations. Four functional categories showed statistically significant differences with MG-RAST at KEGG level 2: in exacerbation, Cell growth and Death and Transport and Catabolism decreased in abundance [1.6 (0.2–2.3) vs 3.6 (3.3–6.9), p = 0.012; and 1.8 (0–3.3) vs 3.6 (1.8–5.1), p = 0.025 respectively], while Cancer and Carbohydrate Metabolism increased [0.8 (0–1.5) vs 0 (0–0.5), p = 0.043; and 7 (6.4–9) vs 5.9 (6.3–6.1), p = 0.012 respectively]. In conclusion, the bronchial microbiome as a whole is not significantly modified when exacerbation symptoms appear in severe COPD patients, but its functional metabolic capabilities show significant changes in several pathways.
Pieri-type formulas for maximal isotropic Grassmannains via triple intersections

We give an elementary proof of the Pieri-type formula in the cohomology of a Grassmannian of maximal isotropic subspaces of an odd orthogonal or symplectic vector space. This proof proceeds by explicitly computing a triple intersection of Schubert varieties. The decisive step is an exact description of the intersection of two Schubert varieties, from which the multiplicities (which are powers of 2) in the Pieri-type formula are immediately obvious.
Algebraic approach for R-peak detection in the ElectroCardioGram (ECG) signal

In this paper, we present a novel method for R-peak detection in the ElectroCardioGram (ECG) signal in a noisy environment. We interpret the R-peak occurrence as an irregularity in the signal. Thereby, we transform the problem of R-peaks detection into irregularity instants estimation. To point out these irregularities, we use an algebraic approach based on differential algebra and operational calculus. To make the R-peak detection more accuracy, we propose a new decision rule permitting a reliable distinction between R-peaks and false alarms. To assess the validity of theoretical analysis, numerical simulations, according to signals from the MIT-BIH arrhythmias database, are performed. To carry out the performance of the proposed method, a comparison with the most used technique in literature is achieved. The obtained results show the robustness of the algebraic method in the context of complicated pathologies as well as to various types of noises.
Variational theory of elastic manifolds with correlated disorder and localization of interacting quantum particles.

We apply the gaussian variational method (GVM) to study the equilibrium statistical mechanics of the two related systems: (i) classical elastic manifolds, such as flux lattices, in presence of columnar disorder correlated along the $\tau$ direction (ii) interacting quantum particles in a static random potential. We find localization by disorder, the localized phase being described by a replica symmetry broken solution confined to the mode $\omega=0$. For classical systems we compute the correlation function of relative displacements. In $d=2+1$, in the absence of dislocations, the GVM allows to describes the Bose glass phase. Along the columns the displacements saturate at a length $l_{\perp}$ indicating flux-line localization. Perpendicularly to the columns long range order is destroyed. We find divergent tilt modulus $c_{44}=\infty$ and a $x \sim \tau^{1/2}$ scaling. Quantum systems are studied using the analytic continuation from imaginary to real time $\tau \to i t$. We compute the conductivity and find that it behaves at small frequency as $\sigma(\omega) \approx \omega^2$ in all dimensions ($d < 4$) for which disorder is relevant. We compute the quantum localization length $\xi$. In $d=1$, where the model also describes interacting fermions in a static random potential, we find a delocalization transition and obtain analytically both the low and high frequency behavior of the conductivity for any value of the interaction. We show that the marginality condition appears as the condition to obtain the correct physical behavior. Agreement with renormalization group results is found whenever it can be compared.
Potent Immunity to Low Doses of Influenza Vaccine by Probabilistic Guided Micro-Targeted Skin Delivery in a Mouse Model

Background Over 14 million people die each year from infectious diseases despite extensive vaccine use [1]. The needle and syringe—first invented in 1853—is still the primary delivery device, injecting liquid vaccine into muscle. Vaccines could be far more effective if they were precisely delivered into the narrow layer just beneath the skin surface that contains a much higher density of potent antigen-presenting cells (APCs) essential to generate a protective immune response. We hypothesized that successful vaccination could be achieved this way with far lower antigen doses than required by the needle and syringe. Methodology/Principal Findings To meet this objective, using a probability-based theoretical analysis for targeting skin APCs, we designed the Nanopatch™, which contains an array of densely packed projections (21025/cm2) invisible to the human eye (110 µm in length, tapering to tips with a sharpness of <1000 nm), that are dry-coated with vaccine and applied to the skin for two minutes. Here we show that the Nanopatches deliver a seasonal influenza vaccine (Fluvax® 2008) to directly contact thousands of APCs, in excellent agreement with theoretical prediction. By physically targeting vaccine directly to these cells we induced protective levels of functional antibody responses in mice and also protection against an influenza virus challenge that are comparable to the vaccine delivered intramuscularly with the needle and syringe—but with less than 1/100th of the delivered antigen. Conclusions/Significance Our results represent a marked improvement—an order of magnitude greater than reported by others—for injected doses administered by other delivery methods, without reliance on an added adjuvant, and with only a single vaccination. This study provides a proven mathematical/engineering delivery device template for extension into human studies—and we speculate that successful translation of these findings into humans could uniquely assist with problems of vaccine shortages and distribution—together with alleviating fear of the needle and the need for trained practitioners to administer vaccine, e.g., during an influenza pandemic.
Bayesian networks

This brief tutorial on Bayesian networks serves to introduce readers to some of the concepts, terminology, and notation employed by articles in this special section. In a Bayesian network, a variable takes on values from a collection of mutually exclusive and collective exhaustive states. A variable may be discrete, having a finite or countable number of states, or it may be continuous. Often the choice of states itself presents an interesting modeling question. For example, in a system for troubleshooting a problem with printing, we may choose to model the variable “print output” with two states—“present” and “absent”—or we may want to model the variable with finer distinctions such as “absent,” “blurred ,” “cut off,” and “ok. ”
DNA Methylation of Imprinted Loci on Autosomal Chromosomes and IGF2 are not Affected in Parkinson's Disease Patients Peripheral Blood Monocytes

Genomic imprinting is an epigenetic phenomenon that results in differential expression of alleles depending on their parental origin. The functional significance of DNA methylation in genomic imprinting has been widely investigated and to date, around 100 imprinted genes have been identified in humans. To investigate, if methylation status of these “known” imprinting genes is associated with Parkinson's disease (PD), we analyzed methylation profile of all these “known” imprinting genes using an epigenome wide approach with Illumina's 450K methylation chip. Strikingly, none of these total autosomal annotated genes show changes of DNA methylation between PD and healthy individuals. We further refined our analysis by evaluating DNA methylation for maternally imprinted human gene encoding insulin-like growth factor 2 (IGF2) by using bisulfite sequencing PCR (BSP) and by considering different dosages of L-dopa. Our results demonstrate that methylation profiles specifically at exon 8-9 genomic region of IGF2 gene in PD are neither influenced by the dosage of L-dopa treatment nor by the disease itself. Thus loss or disruption of imprinting in autosomal chromosomes seems not to apparent in PD and is not relevant for the pathogenesis of the disease.
Does Permafrost Deserve Attention in Comprehensive Climate Models ?

Traditionally, from a climate modeling perspective, permafrost is looked upon as a phenomenon impacted by climate change. However, it is well recognized that thawing permafrost may create climate feedback loops via changes in greenhouse gas emissions and surface hydrology. Only recently, these effects are being introduced in comprehensive climate models. The thermal properties of permanently frozen regions on the other hand have not been much explored in this context, mainly because models rarely resolve soil layers deeper than a few meters. One reason comes from the still rather poor ability of climate models to simulate realistic snowpack behavior, which is vital to allowing for a realistic depiction of below-surface properties. Here, we stress the sensitivities of near-surface atmospheric temperatures to inadequacies in the description of soil processes including retreat of permafrost to deeper layers under warming conditions.