Miracle-dz/UniFAR-FTUs huggingface dataset:
Algorithms for Characterization and Trend Detection in Spatial Databases

The number and the size of spatial databases, e.g. for geo-marketing, traffic control or environmental studies, are rapidly growing which results in an increasing need for spatial data mining. In this paper, we present new algorithms for spatial characterization and spatial trend analysis. For spatial characterization it is important that class membership of a database object is not only determined by its non-spatial attributes but also by the attributes of objects in its neighborhood. In spatial trend analysis, patterns of change of some non-spatial attributes in the neighborhood of a database object are determined. We present several algorithms for these tasks. These algorithms were implemented within a general framework for spatial data mining providing a small set of database primitives on top of a commercial spatial database management system. A performance evaluation using a real geographic database demonstrates the effectiveness of the proposed algorithms. Furthermore, we show how the algorithms can be combined to discover even more interesting spatial knowledge.
Angiopoietin‐1 but not angiopoietin‐2 induces IL‐8 synthesis and release by human neutrophils

We previously reported Tie2 receptor expression on human neutrophils, which promote chemotactic activities upon activation by both angiopoietins (Ang1 and Ang2). Moreover, we observed that neutrophil pretreatment with Ang1 or Ang2 enhances interleukin‐8 (IL‐8) chemotactic effect. Therefore, we assessed the capacity of Ang1 and/or Ang2 to modulate neutrophil IL‐8 synthesis and release. Neutrophils isolated from healthy donors were stimulated in a time‐ (1–6 h) and concentration‐(10−10–10−8 M) dependent manner with both angiopoietins. IL‐8 mRNA production was measured by RT‐qPCR, whereas its protein synthesis and release from neutrophils was assessed by ELISA. Ang1 (10−8 M) induced a significant and maximal increase of IL‐8 mRNA (4.7‐fold) within 1 h, and promoted maximal IL‐8 protein synthesis (3.6‐fold) and release (5.5‐fold) within 2 h as compared to control PBS‐treated neutrophils. Treatment with Ang2 alone did not modulate IL‐8 synthesis or release, and its combination to Ang1 did not affect Ang1 activity. Neutrophil pretreatment with a protein synthesis inhibitor (CHX) increased IL‐8 mRNA synthesis by 18‐fold, and reduced Ang1‐mediated IL‐8 protein synthesis and release by 96% and 92%, respectively. Pretreatment with a transcription inhibitor (ActD) reduced IL‐8 mRNA synthesis by 54% and IL‐8 protein synthesis and release by 52% and 79%, respectively. Using specific kinase inhibitors, we observed that Ang1‐driven IL‐8 mRNA and protein synthesis is p42/44 MAPK‐dependent and ‐independent from p38 MAPK and PI3K activity. Our study is the first to report the capacity of Ang1 (as opposed to Ang2) to promote neutrophil IL‐8 synthesis and release through the activation of p42/44 MAPK pathway. J. Cell. Physiol. 227: 3099–3110, 2012. © 2011 Wiley Periodicals, Inc.
Intra-Genomic Internal Transcribed Spacer Region Sequence Heterogeneity and Molecular Diagnosis in Clinical Microbiology

Internal transcribed spacer region (ITS) sequencing is the most extensively used technology for accurate molecular identification of fungal pathogens in clinical microbiology laboratories. Intra-genomic ITS sequence heterogeneity, which makes fungal identification based on direct sequencing of PCR products difficult, has rarely been reported in pathogenic fungi. During the process of performing ITS sequencing on 71 yeast strains isolated from various clinical specimens, direct sequencing of the PCR products showed ambiguous sequences in six of them. After cloning the PCR products into plasmids for sequencing, interpretable sequencing electropherograms could be obtained. For each of the six isolates, 10–49 clones were selected for sequencing and two to seven intra-genomic ITS copies were detected. The identities of these six isolates were confirmed to be Candida glabrata (n = 2), Pichia (Candida) norvegensis (n = 2), Candida tropicalis (n = 1) and Saccharomyces cerevisiae (n = 1). Multiple sequence alignment revealed that one to four intra-genomic ITS polymorphic sites were present in the six isolates, and all these polymorphic sites were located in the ITS1 and/or ITS2 regions. We report and describe the first evidence of intra-genomic ITS sequence heterogeneity in four different pathogenic yeasts, which occurred exclusively in the ITS1 and ITS2 spacer regions for the six isolates in this study.
SMOG 2: A Versatile Software Package for Generating Structure-Based Models

Molecular dynamics simulations with coarse-grained or simplified Hamiltonians have proven to be an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Originally developed in the context of protein folding, structure-based models (SBMs) have since been extended to probe a diverse range of biomolecular processes, spanning from protein and RNA folding to functional transitions in molecular machines. The hallmark feature of a structure-based model is that part, or all, of the potential energy function is defined by a known structure. Within this general class of models, there exist many possible variations in resolution and energetic composition. SMOG 2 is a downloadable software package that reads user-designated structural information and user-defined energy definitions, in order to produce the files necessary to use SBMs with high performance molecular dynamics packages: GROMACS and NAMD. SMOG 2 is bundled with XML-formatted template files that define commonly used SBMs, and it can process template files that are altered according to the needs of each user. This computational infrastructure also allows for experimental or bioinformatics-derived restraints or novel structural features to be included, e.g. novel ligands, prosthetic groups and post-translational/transcriptional modifications. The code and user guide can be downloaded at http://smog-server.org/smog2.
T-Cell Responses to Treponema pallidumsubsp. pallidum Antigens during the Course of Experimental Syphilis Infection

ABSTRACT In this study we describe the development of the T-cell response to a panel of Treponema pallidum antigens over the course of syphilis infection in the rabbit and determine whether these antigens induce the expression of Th1 cytokines. It was determined that the membrane proteins TpN17 and TpN47, as well as the endoflagellar sheath protein TpN37, induce strong proliferation responses through most of syphilis infection; Tromp1 induced only weak proliferative responses. An unexpected drop in proliferative response to these antigens at day 90 of infection, followed by a dramatic increase in response at day 180, suggests that there may be a secondary dissemination of T. pallidum which induces a recall response. Crude epitope mapping of TpN17 and TpN37 showed that multiple epitopes may be present on both antigens, which is likely a contributing factor in the immunodominance of these antigens. The T-cell response to the TpN37 molecule shows acquisition of newly recognized epitopes during the course of infection. Sonicated T. pallidum was found to induce the expression of interleukin-2 (IL-2) and gamma interferon and not IL-10 mRNA, showing that the general T-cell response to T. pallidum antigens in syphilis infection is biased towards the Th1 phenotype. Of the antigens tested, TpN37 appears to contribute the most to the Th1 cytokine response and therefore may play a key role in the clearance of T. pallidum from lesions.
Gene Expression of the Tumour Suppressor LKB1 Is Mediated by Sp1, NF-Y and FOXO Transcription Factors

The serine/threonine kinase LKB1 is a tumour suppressor that regulates multiple biological pathways, including cell cycle control, cell polarity and energy metabolism by direct phosphorylation of 14 different AMP-activated protein kinase (AMPK) family members. Although many downstream targets have been described, the regulation of LKB1 gene expression is still poorly understood. In this study, we performed a functional analysis of the human LKB1 upstream regulatory region. We used 200 base pair deletion constructs of the 5′-flanking region fused to a luciferase reporter to identify the core promoter. It encompasses nucleotides −345 to +52 relative to the transcription start site and coincides with a DNase I hypersensitive site. Based on extensive deletion and substitution mutant analysis of the LKB1 promoter, we identified four cis-acting elements which are critical for transcriptional activation. Using electrophoretic mobility shift assays as well as chromatin immunoprecipitations, we demonstrate that the transcription factors Sp1, NF-Y and two forkhead box O (FOXO) family members FOXO3 and FOXO4 bind to these elements. Overexpression of these factors significantly increased the LKB1 promoter activity. Conversely, small interfering RNAs directed against NF-Y alpha and the two FOXO proteins greatly reduced endogenous LKB1 expression and phosphorylation of LKB1's main substrate AMPK in three different cell lines. Taken together, these results demonstrate that Sp1, NF-Y and FOXO transcription factors are involved in the regulation of LKB1 transcription.
Improved detection of allergen‐specific T‐cell responses in allergic contact dermatitis through the addition of ‘cytokine cocktails’

Abstract: The gold standard for the diagnosis of allergic hypersensitivity is skin patch testing with the suspected allergens. This diagnostic tool, however, has distinct disadvantages, and therefore the development of alternative or complementary in vitro tests is of great importance. In this study, we evaluate the applicability of an in vitro test method, as developed earlier for nickel allergy, to detect allergen‐specific T cells in the blood of patients allergic to frequent sensitizers (chromate, cobalt, paraphenylenediamine, fragrances and chloromethyl‐isothiazolinone). Peripheral blood mononuclear cells (PBMCs) of allergic patients and healthy controls were cultured in the absence or presence of allergen. Additionally, type 1 (IL‐7 and IL‐12) or type 2 (IL‐7 and IL‐4) stimulating cytokines were added; after 6‐day proliferation, IFN‐γ and IL‐5 secretions were determined. Without the addition of cytokines, consistent allergen‐induced proliferation was observed in PBMCs of nickel‐allergic patients only. By contrast, the addition of type 1 or type 2 stimulating cytokines resulted in a significantly enhanced allergen‐specific proliferation for all allergens tested (sensitivity increased from 26 to 43% or 38%, respectively, P < 0.05). In these cultures, allergen‐induced IFN‐γ and IL‐5 secretion was also significantly increased, compared to healthy controls (P < 0.05, for IFN‐γ sensitivity 79%, specificity 93%; for IL‐5 sensitivity 74%, specificity 81%). In conclusion, these results demonstrate an increased proliferative capacity and cytokine production by allergen‐specific T cells from allergic patients, but not of healthy individuals upon stimulation with allergens in combination with type 1 or 2 skewing cytokines. The present data warrant further exploration of the application of this test to a broader set of allergens.
Seismic Power Generator Using High-Performance Polymer Electret

Development of a micro electret generator prototype for energy harvesting applications is presented. MEMS-friendly perfluoropolymer, CYTOP is adopted as high-performance electret material. When corona charging is employed, charge density as large as 1.37 mC/m2is obtained for a 15 mm-thick CYTOP film, which is much larger than that of Teflon AF. In power generation experiments using a prototype seismic generator, maximum output power of 38 mW is obtained with 2 mmp-poscillation at 20 Hz.
Self-assembled InAs quantum dots within a vertical cavity structure for all-optical switching devices

An all-optical switching device has been proposed by using self-assembled InAs/GaAs quantum dots (QDs) within a vertical cavity structure for ultrafast optical communications. This device has several desirable properties, such as the ultra-low power consumption, the micrometre size, and the polarization insensitive operation. Due to the threedimensional confined carrier state and the broad size distribution of self-assembled InAs/GaAs QDs, it is crucial to enhance the interaction between QDs and the cavity with appropriately designed 1D periodic structure. Significant QD/cavity nonlinearity is theoretically observed by increasing the GaAs/AlAs pair number of the bottom mirror. By this consideration, we have fabricated vertical-reflection type QD switches with 12 periods of GaAs/Al0.8Ga0. 2As for the top mirror and 25 periods for the bottom mirror to give an asymmetric vertical cavity. Optical switching via the QD excited state exhibits a fast switching process with a time constant down to 23 ps, confirming that the fast intersubband relaxation of carriers inside QDs is an effective means to speed up the switching process. A technique by changing the light incident angle realizes wavelength tunability over 30 nm for the QD/cavity switch.
Rostafuroxin Protects from Podocyte Injury and Proteinuria Induced by Adducin Genetic Variants and Ouabain

Glomerulopathies are important causes of morbidity and mortality. Selective therapies that address the underlying mechanisms are still lacking. Recently, two mechanisms, mutant β-adducin and ouabain, have been found to be involved in glomerular podocytopathies and proteinuria through nephrin downregulation. The main purpose of the present study was to investigate whether rostafuroxin, a novel antihypertensive agent developed as a selective inhibitor of Src-SH2 interaction with mutant adducin- and ouabain-activated Na,K-ATPase, may protect podocytes from adducin- and ouabain-induced effects, thus representing a novel pharmacologic approach for the therapy of podocytopathies and proteinuria caused by the aforementioned mechanisms. To study the effect of rostafuroxin on podocyte protein changes and proteinuria, mice carrying mutant β-adducin and ouabain hypertensive rats were orally treated with 100 μg/kg per day rostafuroxin. Primary podocytes from congenic rats carrying mutant α-adducin or β-adducin (NB) from Milan hypertensive rats and normal rat podocytes incubated with 10−9 M ouabain were cultured with 10−9 M rostafuroxin. The results indicated that mutant β-adducin and ouabain caused podocyte nephrin loss and proteinuria in animal models. These alterations were reproduced in primary podocytes from NB rats and normal rats incubated with ouabain. Treatment of animals, or incubation of cultured podocytes with rostafuroxin, reverted mutant β-adducin– and ouabain-induced effects on nephrin protein expression and proteinuria. We conclude that rostafuroxin prevented podocyte lesions and proteinuria due to mutant β-adducin and ouabain in animal models. This suggests a potential therapeutic effect of rostafuroxin in patients with glomerular disease progression associated with these two mechanisms.
Solutions to Congruences using Sets with the Property of Baire

Hausdorff's paradoxical decomposition of a sphere with countably many points removed (the main precursor of the Banach–Tarski paradox) actually produced a partition of this set into three pieces A,B,C such that A is congruent to B (i.e. there is an isometry of the set which sends A to B), B is congruent to C, and A is congruent to B ∪ C. While refining the Banach–Tarski paradox, R. Robinson characterized the systems of congruences like this which could be realized by partitions of the sphere with rotations witnessing the congruences: the only nontrivial restriction is that the system should not require any set to be congruent to its complement. Later, J. F. Adams showed that this restriction can be removed if one allows arbitrary isometries of the sphere to witness the congruences. The purpose of this paper is to characterize those systems of congruences which can be satisfied by partitions of the sphere or related spaces into sets with the property of Baire. A paper of Dougherty and Foreman gives a proof that the Banach–Tarski paradox can be achieved using such sets, and gives versions of this result using open sets and related results about partitions of spaces into congruent sets. The same method is used here; it turns out that only one additional restriction on a system of congruences is needed to make it solvable using subsets of the sphere with the property of Baire (or solvable with open sets if one allows meager exceptions to the congruences and the covering of the space) with free rotations witnessing the congruences. Actually, the result applies to any complete metric space acted on in a sufficiently free way by a free group of homeomorphisms. We also characterize the systems solvable on the sphere using sets with the property of Baire but allowing all isometries.
Recycling of the Cell Adhesion Molecule L1 in Axonal Growth Cones

The cell adhesion molecule (CAM) L1 plays crucial roles in axon growth in vitro and in the formation of major axonal tracts in vivo. It is generally thought that CAMs link extracellular immobile ligands with retrogradely moving actin filaments to transmit force that pulls the growth cone forward. However, relatively little is known about the fate of CAMs that have been translocated into the central (C)-domain of the growth cone. We have shown previously that L1 is preferentially endocytosed at the C-domain. In the present study, we further analyze the subcellular distribution of endocytic organelles containing L1 at different time points and demonstrate that internalized L1 is transported into the peripheral (P)-domain of growth cones advancing via an L1-dependent mechanism. Internalized L1 is found in vesicles positioned along microtubules, and the centrifugal transport of these L1-containing vesicles is dependent on dynamic microtubules in the P-domain. Furthermore, we show that endocytosed L1 is reinserted into the plasma membrane at the leading edge of the P-domain. Monitoring recycled L1 reveals that it moves retrogradely on the cell surface into the C-domain. In contrast, the growth cone advancing independently of L1 internalizes and recycles L1 within the C-domain. For the growth cone to advance, the leading edge needs to establish strong adhesive interactions with the substrate while attachments at the rear are released. Recycling L1 from the C-domain to the leading edge provides an effective way to create asymmetric L1-mediated adhesion and therefore would be critical for L1-based growth cone motility.
Interlaboratory Comparison of Epstein‐Barr Virus Viral Load Assays

To assess interlaboratory variability in qualitative and quantitative Epstein‐Barr virus (EBV) viral load (VL) testing, we distributed a panel of samples to 28 laboratories in the USA, Canada and Europe who performed testing using commercially available reagents (n = 12) or laboratory‐developed assays (n = 18). The panel included two negatives, seven constructed samples using Namalwa and Molt‐3 cell lines diluted in plasma (1.30–5.30 log10 copies/mL) and three clinical plasma samples. Significant interlaboratory variation was observed for both actual (range 1.30–4.30 log10 copies/mL) and self‐reported (range, 1.70–3.30 log10 copies/mL) lower limits of detection. The variation observed in reported results on individual samples ranged from 2.28 log10 (minimum) to 4.14 log10 (maximum). Variation was independent of dynamic range and use of commercial versus laboratory‐developed assays. Overall, only 47.0% of all results fell within acceptable standards of variation: defined as the expected result ± 0.50 log10. Interlaboratory variability on replicate samples was significantly greater than intralaboratory variability (p < 0.0001). Kinetics of change in VL appears more relevant than absolute values and clinicians should understand the uncertainty associated with absolute VL values at their institutions. The creation of an international reference standard for EBV VL assay calibration would be an initial important step in quality improvement of this laboratory tool.
Dynamic social networks promote cooperation in experiments with humans

Human populations are both highly cooperative and highly organized. Human interactions are not random but rather are structured in social networks. Importantly, ties in these networks often are dynamic, changing in response to the behavior of one's social partners. This dynamic structure permits an important form of conditional action that has been explored theoretically but has received little empirical attention: People can respond to the cooperation and defection of those around them by making or breaking network links. Here, we present experimental evidence of the power of using strategic link formation and dissolution, and the network modification it entails, to stabilize cooperation in sizable groups. Our experiments explore large-scale cooperation, where subjects’ cooperative actions are equally beneficial to all those with whom they interact. Consistent with previous research, we find that cooperation decays over time when social networks are shuffled randomly every round or are fixed across all rounds. We also find that, when networks are dynamic but are updated only infrequently, cooperation again fails. However, when subjects can update their network connections frequently, we see a qualitatively different outcome: Cooperation is maintained at a high level through network rewiring. Subjects preferentially break links with defectors and form new links with cooperators, creating an incentive to cooperate and leading to substantial changes in network structure. Our experiments confirm the predictions of a set of evolutionary game theoretic models and demonstrate the important role that dynamic social networks can play in supporting large-scale human cooperation.
Assessment of dermal exposure and skin condition of workers exposed to nickel at a South African base metal refinery.

OBJECTIVES The objectives of this study were to assess dermal exposure of cell workers to nickel at a South African base metal refinery and to characterize their skin condition by measuring the skin hydration and trans epidermal water loss (TEWL) indices. METHODS The skin hydration index of the index finger, palm, neck, and forehead was measured before, during and at the end of the shift. The TEWL index was measured before and at the end of the shift. Dermal exposure samples were collected with Ghostwipes from the index finger and palm of the dominant hand, before, during, and at the end of the shift. Neck and forehead samples were collected before and at the end of the shift. Wipe samples of various surfaces in the workplace were also collected. Wipes were analyzed for nickel according to NIOSH method 9102, using inductively coupled plasma-atomic emission spectrometry. RESULTS Hydration indices measured on the hands decreased significantly during the shift, but recovered to normal levels by the end of the shift. TEWL indices for the index finger and palm of the hands are indicative of a low barrier function even before commencement of the shift, which further deteriorated significantly during the shift. During the shift, substantial nickel skin loading occurred on the index finger and palm of the hand. Levels on the neck and forehead were much lower. Various workplace surfaces, which workers come into contact with, were also contaminated with nickel. CONCLUSIONS The skin condition and high levels of nickel on the skin were most probably caused by inadequate chemical protection provided by protective gloves. Although, the permeability of nickel through intact skin is considered to be low, a decreased barrier function of dehydrated or slightly damaged skin will increase its permeability for nickel. The ethnicity of these exposed workers may contribute significantly toward the low incidence of allergic contact dermatitis observed. Several measures to lower dermal exposure to nickel are also recommended.