Miracle-dz/UniFAR-FTUs huggingface dataset:
The Cleavage of the Urokinase Receptor Regulates Its Multiple Functions*

The urokinase-type plasminogen activator (uPA) is able to cleave its cell surface receptor (uPAR) anchored to the cell membrane through a glycophosphatidylinositol tail. The cleavage leads to the formation of cell surface truncated forms, devoid of the N-terminal domain 1 (D1) and unmasks or disrupts, depending on the cleavage site, a sequence in the D1-D2 linker region (residues 88–92), which in the soluble form is a potent chemoattractant for monocyte-like cells. To investigate the possible role(s) of the cleaved forms of cell surface glycophosphatidylinositol-anchored uPAR, uPAR-negative human embrional kidney 293 cells were transfected with the cDNA of intact uPAR (uPAR-293) or with cDNAs corresponding to the truncated forms of uPAR exposing (D2D3-293) or lacking (D2D3wc-293) the peptide 88–92 (P88–92). Cell adhesion assays and co-immunoprecipitation experiments indicated that the removal of D1, independently of the presence of P88–92, abolished the lateral interaction of uPAR with integrins and its capability to regulate integrin adhesive functions. The expression of intact uPAR induced also a moderate increase in 293 cell proliferation, which was accompanied by the activation of ERK. Also this effect was abolished by D1 removal, independently of the presence of P88–92. The expression of intact and truncated uPARs regulated cell directional migration toward uPA, the specific uPAR ligand, and toward fMLP, a bacterial chemotactic peptide. In fact, the uPA-dependent cell migration required the expression of intact uPAR, including D1, whereas the fMLP-dependent cell migration required the expression of a P88–92 containing uPAR and was independent of the presence of D1. Together these observations indicate that uPA-mediated uPAR cleavage and D1 removal, occurring on the cell surface of several cell types, can play a fundamental role in the regulation of multiple uPAR functions.
Improving comparability between microarray probe signals by thermodynamic intensity correction

Signals from different oligonucleotide probes against the same target show great variation in intensities. However, detection of differences along a sequence e.g. to reveal intron/exon architecture, transcription boundary as well as simple absent/present calls depends on comparisons between different probes. It is therefore of great interest to correct for the variation between probes. Much of this variation is sequence dependent. We demonstrate that a thermodynamic model for hybridization of either DNA or RNA to a DNA microarray, which takes the sequence-dependent probe affinities into account significantly reduces the signal fluctuation between probes targeting the same gene transcript. For a test set of tightly tiled yeast genes, the model reduces the variance by up to a factor ∼1/3. As a consequence of this reduction, the model is shown to yield a more accurate determination of transcription start sites for a subset of yeast genes. In another application, we identify present/absent calls for probes hybridized to the sequenced Escherichia coli strain O157:H7 EDL933. The model improves the correct calls from 85 to 95% relative to raw intensity measures. The model thus makes applications which depend on comparisons between probes aimed at different sections of the same target more reliable.
How landscape organization and scale shape catchment hydrology and biogeochemistry: insights from a long‐term catchment study

Catchment science plays a critical role in the protection of water resources in the face of ongoing changes in climate, long‐range transport of air pollutants, and land use. Addressing these challenges, however, requires improved understanding of how, when, and where changes in water quantity and quality occur within river networks. To reach these goals, we must recognize how different catchment features are organized to regulate surface chemistry at multiple scales, from processes controlling headwaters, to the downstream mixing of water from multiple landscape sources and deep aquifers. Here we synthesize 30‐years of hydrological and biogeochemical research from the Krycklan catchment study (KCS) in northern Sweden to demonstrate the benefits of coupling long‐term monitoring with multi‐scale research to advance our understanding of catchment functioning across space and time. We show that the regulation of hydrological and biogeochemical patterns in the KCS can be decomposed into four, hierarchically structured landscape features that include: (1) transmissivity and reactivity of dominant source layers within riparian soils, (2) spatial arrangement of groundwater input zones that govern water and solute fluxes at reach‐ to segment‐scales, (3) landscape scale heterogeneity (forests, mires, and lakes) that generates unique biogeochemical signals downstream, and (4) broad‐scale mixing of surface streams with deep groundwater contributions. While this set of features are perhaps specific to the study region, analogous hierarchical controls are likely to be widespread. Resolving these scale dependent processes is important for predicting how, when, and where different environmental changes may influence patterns of surface water chemistry within river networks. WIREs Water 2018, 5:e1265. doi: 10.1002/wat2.1265
THE DISTRIBUTION OF LATTICE POINTS IN ELLIPTIC ANNULI

We study the distribution of the number of lattice points lying in thin elliptical annuli. It has been conjectured by Bleher and Lebowitz that if the width of the annuli tends to zero and their area tends to infinity, then the distribution of this number, normalized to have zero mean and unit variance, is Gaussian. This has been proved by Hughes and Rudnick for circular annuli whose width shrinks to zero sufficiently slowly. We prove this conjecture for ellipses whose aspect ratio is transcendental and strongly Diophantine, also assuming the width shrinks slowly to zero.
High frequency of GJA12/GJC2 mutations in Turkish patients with Pelizaeus–Merzbacher disease

Bilir B, Yapici Z, Yalcinkaya C, Baris I, Carvalho CMB, Bartnik M, Ozes B, Eraksoy M, Lupski JR, Battaloglu E. High frequency of GJA12/GJC2 mutations in Turkish patients with Pelizaeus–Merzbacher disease.
Visual servoing based on intersample disturbance rejection by multirate sampling control-time delay compensation and experimental verification

Multirate sampling controllers are proposed for digital control systems, where the speed of the A/D converters is restricted to be slower than that of the D/A converters. The proposed feedback controller assures perfect disturbance rejection at M intersample points in the steady state. The proposed method is extended to systems with time delay, and the compensation method is proposed based on the observer including time delay model. Next, the scheme of repetitive control is proposed based on the open-loop estimation and switching function, which enables the rejection of periodical disturbance without any sacrifice of the closed-loop characteristics. Finally, the proposed controllers are applied to a visual servo system by introducing the workspace controller and nonlinear perspective transformation. The advantages of these approaches are demonstrated by simulations and experiments using a robot manipulator.
A discriminative approach to polyphonic piano note transcription using supervised non-negative matrix factorization

We introduce a novel method for the transcription of polyphonic piano music by discriminative training of support vector machines (SVMs). As features, we use pitch activations computed by supervised non-negative matrix factorization from low-level spectral features. Different approaches to low-level feature extraction, NMF dictionary learning and activation feature extraction are analyzed in a large-scale evaluation on eight hours of piano music including synthesized and real recordings. We conclude that the proposed method delivers state-of-the-art results and clearly outperforms SVMs using simple spectral features.
The knowledge in multiple human relevance judgments

We show first that the pooling of multiple human judgments of relevance provides predictor of relevance that is superior to that obtained from a single human's relevance judgemts. A learning algorithm applied to a set of relevance judgments obtained from a single human would be expected to perform on new material at a level somewhat below that human. However, we examine two learning methods which when trained on the superior source of pooled human relevance judgments are able to perform at the level of a single human on new material. All performance comparisons are based on an independent human judge. Both algorithms function by producing term weights—one by a log odds calculation and the other by producing a least-squares fit to human relevance ratings. Some characteristics of the algorithms are examined.
Coordinating Resistance Through Communication and Repeated Interaction

Successful deterrence of leader expropriation is important for economic development. This article studies experimentally how repeated interactions and communication can help deter leaders from extracting surplus from their subordinates. We show that repetition alone is far from sufficient in deterring leader expropriation. Communication between subordinates is critical for increasing coordinated resistance even when the information communicated is highly restrictive. Adding communication reduces expropriation significantly even in the presence of repetition.
rBCG Induces Strong Antigen-Specific T Cell Responses in Rhesus Macaques in a Prime-Boost Setting with an Adenovirus 35 Tuberculosis Vaccine Vector

Background BCG vaccination, combined with adenoviral-delivered boosts, represents a reasonable strategy to augment, broaden and prolong immune protection against tuberculosis (TB). We tested BCG (SSI1331) (in 6 animals, delivered intradermally) and a recombinant (rBCG) AFRO-1 expressing perfringolysin (in 6 animals) followed by two boosts (delivered intramuscullary) with non-replicating adenovirus 35 (rAd35) expressing a fusion protein composed of Ag85A, Ag85B and TB10.4, for the capacity to induce antigen-specific cellular immune responses in rhesus macaques (Macaca mulatta). Control animals received diluent (3 animals). Methods and Findings Cellular immune responses were analyzed longitudinally (12 blood draws for each animal) using intracellular cytokine staining (TNF-alpha, IL-2 and IFN-gamma), T cell proliferation was measured in CD4+, CD8alpha/beta+, and CD8alpha/alpha+ T cell subsets and IFN-gamma production was tested in 7 day PBMC cultures (whole blood cell assay, WBA) using Ag85A, Ag85B, TB10.4 recombinant proteins, PPD or BCG as stimuli. Animals primed with AFRO-1 showed i) increased Ag85B-specific IFN-gamma production in the WBA assay (median >400 pg/ml for 6 animals) one week after the first boost with adenoviral-delivered TB-antigens as compared to animals primed with BCG (<200 pg/ml), ii) stronger T cell proliferation in the CD8alpha/alpha+ T cell subset (proliferative index 17%) as compared to BCG-primed animals (proliferative index 5% in CD8alpha/alpha+ T cells). Polyfunctional T cells, defined by IFN-gamma, TNF-alpha and IL-2 production were detected in 2/6 animals primed with AFRO-1 directed against Ag85A/b and TB10.4; 4/6 animals primed with BCG showed a Ag85A/b responses, yet only a single animal exhibited Ag85A/b and TB10.4 reactivity. Conclusion AFRO-1 induces qualitatively and quantitatively different cellular immune responses as compared with BCG in rhesus macaques. Increased IFN-gamma-responses and antigen-specific T cell proliferation in the CD8alpha/alpha+ T cell subset represents a valuable marker for vaccine-take in BCG-based TB vaccine trials
Pelvic Organ Distribution of Mesenchymal Stem Cells Injected Intravenously after Simulated Childbirth Injury in Female Rats

The local route of stem cell administration utilized presently in clinical trials for stress incontinence may not take full advantage of the capabilities of these cells. The goal of this study was to evaluate if intravenously injected mesenchymal stem cells (MSCs) home to pelvic organs after simulated childbirth injury in a rat model. Female rats underwent either vaginal distension (VD) or sham VD. All rats received 2 million GFP-labeled MSCs intravenously 1 hour after injury. Four or 10 days later pelvic organs and muscles were imaged for visualization of GFP-positive cells. Significantly more MSCs home to the urethra, vagina, rectum, and levator ani muscle 4 days after VD than after sham VD. MSCs were present 10 days after injection but GFP intensity had decreased. This study provides basic science evidence that intravenous administration of MSCs could provide an effective route for cell-based therapy to facilitate repair after injury and treat stress incontinence.
Extracciones selectivas y secuenciales de Al, Fe y Si en un Andisol del Oriente antioqueño, Colombia

The selective and sequential extraction of the fractions of Al, Fe and Si (potassium chloride, sodium pyrophosphate, ammonium acid oxalate, dithionite-citrate-bicarbonate and sodium hydroxide) was studied in an Andisol of the East of Antioquia to separate allophane and non-allophane horizons. In the A and 2B/A horizons, the colloidal fraction was dominated by organometallic complexes, whereas in the 3C/A and 4Bs horizons the aluminosilicates and the non-crystalline oxides and hydroxides predominated. This method also managed to differentiate within the horizon A, at least, two sub-horizons not visualized in the field. The low Ald, Fed and Sid and Aln and Fen contents reported be due to the previous extractions made in the soil with sodium pyrophosphate and ammonium acid oxalate, in which the highest proportion of Al, Fe and Si was released, and to the low amounts of crystalline inorganic colloids as hematite, goethite and gibbsite present in the Andisols.
Optimal Exercise Policies and Simulation-Based Valuation for American-Asian Options

American-Asian options are average-price options that allow early exercise. In this paper, we derive structural properties for the optimal exercise policy, which are then used to develop an efficient numerical algorithm for pricing such options. In particular, we show that the optimal policy is a threshold policy: The option should be exercised as soon as the average asset price reaches a characterized threshold, which can be written as a function of the asset price at that time. By exploiting this and other structural properties, we are able to parameterize the exercise boundary, and derive gradient estimators for the option payoff with respect to the parameters of the model. These estimators are then incorporated into a simulation-based algorithm to price American-Asian options. Computational experiments carried out indicate that the algorithm is very competitive with other recently proposed numerical algorithms.
Overexpression of 5-Lipoxygenase and Cyclooxygenase 2 in Hamster and Human Oral Cancer and Chemopreventive Effects of Zileuton and Celecoxib

Purpose: Previous studies have suggested an important role of aberrant arachidonic acid metabolism, especially the cyclooxygenase (Cox) pathway, in oral carcinogenesis. However, it is unknown whether the 5-lipoxygenase (5-Lox) pathway contributes to oral carcinogenesis, and whether combination of inhibitors of both pathways may have synergistic or additive effects of chemoprevention. Experimental Design: 5-Lox expression was examined in 7,12-dimethylbenz[a]anthracene (DMBA)–induced hamster and human oral cancer tissues by immunohistochemistry, and Cox2 expression was investigated in hamster oral tissues using in situ hybridization. Zileuton (a specific 5-Lox inhibitor) and celecoxib (a specific Cox2 inhibitor), either alone or in combination, were investigated for their chemopreventive effects on the DMBA-induced hamster model at the post-initiation stage through topical application. Results: 5-Lox was overexpressed during oral carcinogenesis in hamsters and humans, as well as Cox2 in the hamster tissues. In a chemoprevention study using the post-initiation DMBA model, incidence of hamster oral squamous cell carcinoma was reduced from 76.9% (20 of 26) to 45.8% (11 of 24, P < 0.05) and 32.1% (9 of 28, P < 0.01) by 3% and 6% topical zileuton, respectively; and to 57.6% (15 of 26, P > 0.05) and 50% (12 of 24, P < 0.05) by 3% and 6% topical celecoxib, respectively. When used in combination, celecoxib and zileuton (3% of each) had an additive inhibitory effect on the incidence of squamous cell carcinoma (36%, 9 of 25, P < 0.01). Other pathologic variables and the levels of leukotriene B4 and prostaglandin E2 of the hamster tissues were reduced as well. Conclusions: The results clearly showed that both 5-Lox and Cox2 played important roles in oral carcinogenesis. Zileuton and celecoxib prevented oral carcinogenesis at the post-initiation stage through their inhibitory effects on arachidonic acid metabolism.
Biomonitoring of water quality by aquatic bryophytes: Optimization and methodological harmonization

Aquatic bryophytes, native or transplanted, can be used as reliable, simple and economical tools for biomonitoring the aquatic environment but one of the main impediments to the widespread use of these techniques is the lack of standardized protocols. Hence, the first task of this doctoral research was to address this problem in two critical reviews of the methodology used for passive and active biomonitoring (Chapters I and II). Because of the advantages of the use of transplanted mosses over the use of native mosses, the research efforts then focused on optimizing some of the key methodological aspects of applying the moss bag technique. In Chapter III, the optimal devitalizing treatment of moss samples was selected, while in Chapter IV the optimal number and position of moss bags for use in biomonitoring studies were determined
Adrenodoxin Reductase-Adrenodoxin Complex Structure Suggests Electron Transfer Path in Steroid Biosynthesis*

The steroid hydroxylating system of adrenal cortex mitochondria consists of the membrane-attached NADPH-dependent adrenodoxin reductase (AR), the soluble one-electron transport protein adrenodoxin (Adx), and a membrane-integrated cytochrome P450 of the CYP11 family. In the 2.3-Å resolution crystal structure of the Adx·AR complex, 580 Å2 of partly polar surface are buried. Main interaction sites are centered around Asp79, Asp76, Asp72, and Asp39 of Adx and around Arg211, Arg240, Arg244, and Lys27 of AR, respectively. In particular, the region around Asp39 defines a new protein interaction site for Adx, similar to those found in plant and bacterial ferredoxins. Additional contacts involve the electron transfer region between the redox centers of AR and Adx and C-terminal residues of Adx. The Adx residues Asp113 to Arg115 adopt 310-helical conformation and engage in loose intermolecular contacts within a deep cleft of AR. Complex formation is accompanied by a slight domain rearrangement in AR. The [2Fe-2S] cluster of Adx and the isoalloxazine rings of FAD of AR are 10 Å apart suggesting a possible electron transfer route between these redox centers. The AR·Adx complex represents the first structure of a biologically relevant complex between a ferredoxin and its reductase.
Approximation of Uplink Inter-Cell Interference in FDMA Small Cell Networks

In this paper, for the first time, we analytically prove that the uplink (UL) inter-cell interference in frequency division multiple access (FDMA) small cell networks (SCNs) can be well approximated by a lognormal distribution under a certain condition. The lognormal approximation is vital because it allows tractable network performance analysis with closed-form expressions. The derived condition, under which the lognormal approximation applies, does not pose particular requirements on the shapes/sizes of user equipment (UE) distribution areas as in previous works. Instead, our results show that if a path loss related random variable (RV) associated with the UE distribution area, has a low ratio of the 3rd absolute moment to the variance, the lognormal approximation will hold. Analytical and simulation results show that the derived condition can be readily satisfied in future dense/ultra-dense SCNs, indicating that our conclusions are very useful for network performance analysis of the 5th generation (5G) systems with more general cell deployment beyond the widely used Poisson deployment.
Semantically Holistic and Personalized Views Across Heterogeneous Information Sources

A consolidated view of the content within different data repositories would facilitate useful operations such as advanced informational discovery. This paper proposes a methodology and an architecture that uses semantic annotations to enable such holistic views across domain specific information sources. The potential for the personalization of this annotated information is described, and the future work necessary to implement the system is elaborated on.
Effect of High Curvature Point Deletion on the Performance of Two Contour Based Shape Recognition Algorithms

Psychophysical researches on the human visual system have shown that the points of high curvature on the contour of an object play an important role in the recognition process. Inspired by these studies we propose: (i) a novel algorithm to select points of high curvature on the contour of an object which can be used to construct a recognizable polygonal approximation, (ii) a test which evaluates the effect of deletion of contour segments containing such points on the performance of contour based object recognition algorithms. We use complete contour representations of objects as a reference (training) set. Incomplete contour representations of the same objects are used as a test set. The performance of an algorithm is reported using the recognition rate as a function of the percentage of contour retained. We consider two types of contour incompleteness obtained by deletion of contour segments of high or low curvature. We illustrate the test procedure using two shape recognition algorithms that deploy a shape context and a distance multiset as local shape descriptors. Both algorithms qualitatively mimic human visual perception in that the deletion of segments of high curvature has a stronger performance degradation effect than the deletion of other parts of the contour. This effect is more pronounced in the performance of the shape context method.
Testing two screening instruments for autism spectrum disorder in UK community child health services

The aim of this study was to test the accuracy of two screening instruments in UK Community health services: Modified Checklist for Autism in Toddlers (M‐CHAT) and Social Communication Questionnaire (SCQ) for autism spectrum disorder (ASD). A two‐stage screening and in‐depth assessment procedure, combined with sampling stratification and statistical weighting, allowed the accuracy of the screens to be estimated in the entire population of referred children.
Host multicast: a framework for delivering multicast to end users

While the advantages of multicast delivery over multiple unicast deliveries is undeniable, the deployment of the IP multicast protocol has been limited to "islands" of network domains under single administrative control. Deployment of inter-domain multicast delivery has been slow due to both technical and administrative reasons. In this paper we propose a Host Multicast Tree Protocol (HMTP) that (1) automates the interconnection of IP-multicast enabled islands and (2) provides multicast delivery to end hosts where IP multicast is not available. With HMTP, end-hosts and proxy gateways of IP multicast-enabled islands can dynamically create shared multicast trees across different islands. Members of an HMTP multicast group self-organize into an efficient, scalable and robust multicast tree. The tree structure is adjusted periodically to accommodate changes in group membership and network topology. Simulation results show that the multicast tree has low cost, and data delivered over it experiences moderately low latency.