Miracle-dz/UniFAR-FTUs huggingface dataset:
Leukocyte recruitment during onset of experimental allergic encephalomyelitis is CCR1 dependent

We have shown that macrophages and microglia present within demyelinating plaques of patients with multiple sclerosis (MS) are immunoreactive for the chemokine receptor CCR1 and its ligand, macrophage inflammatory protein‐1α. To test the importance of CCR1 to the pathogenesis of MS, we studied the progression of experimental allergic encephalomyelitis (EAE) in CCR1+/+ vs. CCR1–/– mice. After immunization with myelin oligodendrocyte glycoprotein (MOG) 35–55 peptide, nearly all CCR1+/+ mice developed EAE (95% incidence, severity 2.5±0.1), whereas CCR1–/– mice had less severe disease (55% incidence, p<0.001; severity 1.2±0.2, p<0.001). CCR1+/+ mice showed elevated brain mRNA for the chemokines immune protein (IP)‐10, RANTES and monocyte chemoattractant protein‐1 prior to disease onset, whereas only IP‐10 mRNA was elevated in CCR1–/– mice. Both groups of mice had comparable in vitro lymphocyte proliferation and cytokine production upon stimulation with MOG peptide, and similar cutaneous hypersensitivity responses to 2,4‐dinitrofluorobenzene, suggesting that CCR1–/– mice were not systemically immunosuppressed. These data demonstrate that deletion of a chemokine receptor is at least partially protective in EAE, and suggest that targeting of CCR1 may be of therapeutic significance clinically.
The association of dermatologist‐diagnosed and self‐reported skin diseases with skin‐related quality of life in Latino migrant farmworkers

Background Skin diseases are known to affect the quality of life (QoL), but data to support this are based on clinical samples. Few data document the skin‐related QoL in the general population, and whether its association differs with self‐reported or dermatologist‐diagnosed skin ailments. Farmworkers are at high risk for skin diseases, and are an appropriate population in which to explore these associations.
Joint Gaussian processes for inverse modeling

Solving inverse problems is central in geosciences and remote sensing. Very often a mechanistic physical model of the system exists that solves the forward problem. Inverting the implied radiative transfer model (RTM) equations numerically implies, however, challenging and computationally demanding problems. Statistical models tackle the inverse problem and predict the biophysical parameter of interest from radiance data, exploiting either in situ data or simulated data from an RTM. We introduce a novel nonlinear and nonparametric statistical inversion model which incorporates both real observations and RTM-simulated data. The proposed Joint Gaussian Process (JGP) provides a solid framework for exploiting the regularities between the two types of data, in order to perform inverse modeling. Advantages of the JGP method over competing strategies are shown on both a simple toy example and in leaf area index (LAI) retrieval from Landsat data combined with simulated data generated by the PROSAIL model.
Relationship between Cognitive Impairment and Retinal Morphological and Visual Functional Abnormalities in Alzheimer Disease

Background:There is conflicting evidence as to whether Alzheimer disease (AD) is accompanied by loss of retinal ganglion cells. To evaluate this issue, we have used optical coherence tomography (OCT) to assess the thickness and volume of the retina. We have also sought to correlate our findings with visual function and cognitive impairment. Methods:We evaluated 28 eyes of 14 patients with AD and 30 eyes of 15 age-matched control subjects. In these two groups, we measured retinal nerve fiber layer (RNFL) thickness, macular thickness, and macular volume with OCT, visual function through latency of the pattern visual evoked potential (VEP) signal, and cognitive impairment through the Mini-Mental State Examination (MMSE). Results:The parapapillary and macular RNFL thickness in all quadrants and positions of AD patients were thinner than in control subjects. The mean total macular volume of AD patients was significantly reduced as compared with control subjects (P < 0.05). Total macular volume and MMSE scores were significantly correlated. No significant difference was found in the latency of the VEP P100 of AD patients and control subjects. Conclusions:Our study confirms some other studies in showing that in AD patients there is a reduction of parapapillary and macular RNFL thickness and macular volume as measured by OCT. The reduction in macular volume was related to the severity of cognitive impairment.
Retromer function in endosome-to-Golgi retrograde transport is regulated by the yeast Vps34 PtdIns 3-kinase

A direct role for phosphoinositides in vesicular trafficking has been demonstrated by the identification of the yeast VPS34 gene encoding the phosphatidylinositol 3-kinase responsible for the synthesis of phosphatidylinositol 3-phosphate (PtdIns3P). Vps34p binds the protein kinase Vps15p, and it has recently been shown that Vps15p and Vps34p associate with Vps30p and Vps38p to form a multimeric complex, termed complex II. We observed that mutations in the VPS30 and VPS38 genes led to a selective sorting and maturation phenotype of the soluble vacuolar protease CPY. Localization studies revealed that the CPY receptor Vps10p and the Golgi-endoprotease Kex2p were mislocalized to vacuolar membranes in strains deficient for either Vps30p or Vps38p, respectively. Interestingly, we measured decreased PtdIns3P levels in Δvps30 andΔ vps38 cells and observed redistribution of Vps5p and Vps17p to the cytoplasm in these mutants. Vps5p and Vps17p are subunits of the retromer complex that is required for endosome-to-Golgi retrograde transport. Both proteins contain the Phox homology (PX) domain, a recently identified phosphoinositide-binding motif. We demonstrate that the PX domains of Vps5p and Vps17p specifically bind to PtdIns3P in vitro and in vivo. On the basis of these and other observations, we propose that the PtdIns 3-kinase complex II directs the synthesis of a specific endosomal pool of PtdIns3P, which is required for recruitment/activation of the retromer complex, thereby ensuring efficient endosome-to-Golgi retrograde transport.
Improving Germination Rate of Medicago Scutellata and Medicago Rigidula as Affected by Seed-Coat Dormancy Breaking Techniques

Medicago scutellata and Medicago rigidula are two species of lucerne. As other legumes these exhibit dormancy, which delays and reduces germination. The germination response of these species to mechanical, physical and chemical scarification, applied for overcoming dormancy, has been studied. The almost full and rapid germination achieved by hand scarification with sandpaper, demonstrated that dormancy was exclusively imposed by seed coat (hardseededness). Soaking in hot water partially removed coat-imposed dormancy in these species, but in M. scutellata even after 2 min at 100 °C, 97.9% of seeds still remained hard. Low temperature by keeping in refrigerator was also effective in final germination and germination rate in seeds of M. scutellata. After 10 days of freezing the germination rate increased by 90%. Keeping seeds on surface run off also had a great result. After 7 days germination rate in seed of M. scutellata became 90%. Chemical scarification with sodium hypochlorite was also effective in reducing hardseededness at the lowest concentration (2%) for the shortest time (2 min) in seeds of M. rigidula.
A ~100 mHz QPO in the X-ray emission from IGR J17361-4441

IGR J17361-4441 was discovered by INTEGRAL undergoing its first detectable X-ray outburst in 2011 and was initially classified as an accreting X-ray binary in the globular cluster NGC 6388. A reanalysis of the outburst data collected with INTEGRAL and Swift suggested that the enhanced X-ray emission from IGR J17361-4441 could have been caused by a rare tidal disruption event of a terrestrial-icy planet by a white dwarf. In this letter we report on the analysis of XMM-Newton data collected in 2011 during the outburst from IGR J17361-4441. Our analysis revealed the presence of a 100 mHz quasi-periodic oscillation in the X-ray emission from the source and confirmed the presence of a soft thermal component (kT∼0.08 keV) in its spectrum. We discuss these findings in the context of the different possibilities proposed to explain the nature of IGR J17361-4441.
Discretize and Conquer: Scalable Agglomerative Clustering in Hamming Space

Clustering is one of the most fundamental tasks in many machine learning and information retrieval applications. Roughly speaking, the goal is to partition data instances such that similar instances end up in the same group while dissimilar instances lie in different groups. Quite surprisingly though, the formal and rigorous definition of clustering is not at all clear mainly because there is no consensus about what constitutes a cluster. That said, across all disciplines, from mathematics and statistics to genetics, people frequently try to get a first intuition about the data through identifying meaningful groups. Finding similar instances and grouping them are two main steps in clustering, and not surprisingly, both have been the subject of extensive study over recent decades. It has been shown that using large datasets is the key to achieving acceptable levels of performance in data-driven applications. Today, the Internet is a vast resource for such datasets, each of which contains millions and billions of high-dimensional items such as images and text documents. However, for such large-scale datasets, the performance of the employed machine-learning algorithm quickly becomes the main bottleneck. Conventional clustering algorithms are no exception, and a great deal of effort has been devoted to developing scalable clustering algorithms. Clustering tasks can vary both in terms of the input they have and the output that they are expected to generate. For instance, the input of a clustering algorithm can hold various types of data such as continuous numerical, and categorical types. This thesis on a particular setting; in it, the input instances are represented with binary strings. Binary representation has several advantages such as storage efficiency, simplicity, lack of a numerical-data-like concept of noise, and being naturally normalized. The literature abounds with applications of clustering binary data, such as in marketing, document clustering, and image clustering. As a more-concrete example, in marketing for an online store, each customer’s basket is a binary representation of items. By clustering customers, the store can recommend items to customers with the same interests. In document clustering, documents can be represented as binary codes in which each element indicates whether a word exists in the document or not. Another notable application of binary codes is in binary hashing, which has been the topic of significant research in the last decade. The goal of binary hashing is to encode high-dimensional items, such as images, with compact binary strings so as to preserve a given notion of similarity. Such codes enable extremely fast nearest neighbour searches, as the distance between two codes (often the Hamming distance) can be computed quickly using bit-wise operations implemented at the hardware level.
Realized laplace transforms for pure-jump semimartingales

We consider specification and inference for the stochastic scale of discretely-observed pure-jump semimartingales with locally stable Levy densities in the setting where both the time span of the data set increases, and the mesh of the observation grid decreases. The estimation is based on constructing a nonparametric estimate for the empirical Laplace transform of the stochastic scale over a given interval of time by aggregating high-frequency increments of the observed process on that time interval into a statistic we call realized Laplace transform. The realized Laplace transform depends on the activity of the driving pure-jump martingale, and we consider both cases when the latter is known or has to be inferred from the data.
Prostate cancer bone metastases promote both osteolytic and osteoblastic activity

Advanced prostate cancer is frequently accompanied by the development of metastasis to bone. In the past, prostate cancer bone metastases were characterized as being osteoblastic (i.e., increasing bone density) based on radiographs. However, emerging evidence suggests that development of prostate cancer bone metastases requires osteoclastic activity in addition to osteoblastic activity. The complexities of how prostate tumor cells influence bone remodeling are just beginning to be elucidated. Prostate cancer cells produce a variety of pro‐osteoblastic factors that promote bone mineralization. For example, both bone morphogenetic proteins and endothelin‐1 have well recognized pro‐osteoblastic activities and are produced by prostate cancer cells. In addition to factors that enhance bone mineralization prostate cancer cells produced factors that promote osteoclast activity. Perhaps the most critical pro‐osteoclastogenic factor produced by prostate cancer cells is receptor activator of NFκB ligand (RANKL), which has been shown to be required for the development of osteoclasts. Blocking RANKL results in inhibiting prostate cancer‐induced osteoclastogenesis and inhibits development and progression of prostate tumor growth in bone. These findings suggest that targeting osteoclast activity may be of therapeutic benefit. However, it remains to be defined how prostate cancer cells synchronize the combination of osteoclastic and osteoblastic activity. We propose that as the bone microenvironment is changed by the developing cancer, this in turn influences the prostate cancer cells' balance between pro‐osteoclastic and pro‐osteoblastic activity. Accordingly, the determination of how the prostate cancer cells and bone microenvironment crosstalk are important to elucidate how prostate cancer cells modulate bone remodeling. © 2003 Wiley‐Liss, Inc.
The suitability of different cellular in vitro immunotoxicity and genotoxicity methods for the analysis of nanoparticle-induced events

Abstract Suitable assays and test strategies are needed to analyze potential genotoxic and immunotoxic health effects caused by nanoparticle exposure. The development and validation of such methods is challenging because nanoparticles may show unexpected behavior, like aggregation or interference with optical measurements, when routine in vitro assays are performed. In our interdisciplinary study, the effects of inorganic gold (4.5 nm) and iron oxide (7.3 nm) nanoparticles with a narrow size distribution were tested on human cells using different assay systems. The results show that cytotoxicity as well as immunotoxicity and genotoxicity induced by these two inorganic nanoparticles was low or absent when using a panel of cell-based tests in different laboratories. However, several technical issues had to be tackled that were specific for working with nanoparticles. The methods used, their suitability for nanotoxicity testing, and the technical problems encountered are carefully described and discussed in this paper.
Resolution of proteinuria in a patient with X-linked Alport syndrome treated with cyclosporine

We report a 9-year-old Icelandic male with Alport syndrome and nephrotic-range proteinuria who responded well to cyclosporine therapy. He presented at the age of 2 years with gross hematuria and proteinuria during an episode of upper respiratory tract infection. Three years later he had developed persistent proteinuria; kidney function was normal. A renal biopsy revealed marked irregularities in the glomerular basement membrane consistent with Alport syndrome. Mutation analysis revealed a single base insertion in COL4A5 which was predicted to cause a major structural defect in the collagen IV α5 chain. Despite angiotensin-converting enzyme inhibitor therapy his proteinuria progressed to the nephrotic range associated with edema. At the age of 7 years, cyclosporine therapy was instituted, which promptly resulted in almost complete resolution of proteinuria. Three years later his urinary protein excretion was close to the normal range and serum creatinine remained within normal limits. We conclude that closely monitored cyclosporine therapy may be a safe and effective treatment in patients with severe proteinuria and Alport syndrome.
High Prevalence of blaNDM-1 Carbapenemase-Encoding Gene and 16S rRNA armA Methyltransferase Gene among Acinetobacter baumannii Clinical Isolates in Egypt

ABSTRACT The main objective of this study was to decipher the molecular mechanism of resistance to carbapenems and aminoglycosides in a large series of 150 Acinetobacter baumannii clinical isolates collected from July 2012 to September 2013 in Egypt. We report for the first time the emergence of blaNDM-1 and the cooccurrence of 16S rRNA methylase armA with blaNDM-1 and blaOXA-23 in Egyptian hospitals. Multilocus sequence typing identified 27 distinct sequence types, 11 of which were novel.
Analysis of an inductive charging system for a commercial electric vehicle

The growing awareness that the use of fossil fuels is limited in time and that the growing awareness of the world population about environmental issues have been accelerating the search for environmentally friendly solutions that can contribute to decrease the oil dependency. Considering the world panorama of the transportation sector, mainly their pollutant emissions and oil consumption, different technological challenges must be overcome in the coming years. Under the nowadays context, electric vehicles constitute a promising solution merging several subsystems that do not have standard solutions. One challenge related with electric vehicles is the technical solution of the charging system. This paper addresses this subject by studying the adoption of a less conventional charging system (wireless electrical charging) in a commercial electric vehicle (“Fiat Seicento Elettra”) [1]-[5]. In a first approach, a “Matlab/Simulink” computational model about this system was developed. The studied model allows computing and analyzing the main impairments of the inductive charging theory, by determining the current and/or voltages, in several points of the circuit. With this method, it is also possible to study the power transfer capabilities of this type of system and its influence on low voltage power grids. The obtained values were evaluated and compared with the requirements of the charging system of the commercial car.
Privacy landscape in online social networks

These days a large number of people are actively using online social networks (OSNs). OSN users can freely interact with their digital friends and build and maintain their online as well as their offline relationships. Intentionally or unintentionally users share a lot of their personal information on these networks which results in privacy threats and unwanted privacy breaches. One of the major reasons for this is the lack of privacy awareness among users and their inability to effectively make correct use of privacy settings. Privacy in an OSN can be viewed from different perspectives but we mainly focus on user privacy. We present an elaborative privacy landscape where we compare and contrast previous literature, review existing definitions covering taxonomy and privacy concerns in OSNs, discuss different perceptions of privacy amongst users and some privacy preserving approaches to guarantee maximum privacy.
The impact of church contextual factors on church-going youth's HIV prevention behaviour in Nairobi, Kenya: A cross-denominational study

Church doctrine about sexual behaviour has long been assumed to have an impact on aspects of the sub-Saharan AIDS epidemic, and evidence suggests that Pentecostal churches have a stronger influence THAN? on the sexual behaviour of their adherents. However, few studies have investigated the denominational differences in sexual attitudes and behaviour of youths, and virtually no empirical evidence is available regarding what specific aspects of the church environment are associated with differences in the response of youths to church messaging about sexual behaviour. This study examined those factors among church-going youth in Nairobi, Kenya. Separate focus groups with male and female youths were conducted in four mainline and three Pentecostal/evangelical (P/E) churches, and in-depth interviews were conducted with youth pastors or pastors of five of those churches. Content of church teaching as reported by youths and pastors did not differ between denominations. However, amount and context of teaching did vary, with P/E churches reportedly offering more teaching about sex to their youth. In addition, P/E churches appeared to provide a more intense experience of community than mainline churches, a situation that may create a context within which abstinence appears to be a reasonable life choice.
Graph Isomorphism, Sherali-Adams Relaxations and Expressibility in Counting Logics

Two graphs with adjacency matrices A and B are isomorphic if there exists a permutation matrix P for which the identity PAP = B holds. Multiplying through by P and relaxing the permutation matrix to a doubly stochastic matrix leads to the notion of fractional isomorphism. We show that the levels of the Sherali-Adams hierarchy of linear programming relaxations applied to fractional isomorphism interleave in power with the levels of a well-known colorrefinement heuristic for graph isomorphism called the Weisfeiler-Lehman algorithm. This tight connection has quite striking consequences. For example, it follows immediately from a deep result of Grohe in the context of logics with counting quantifiers, that a fixed number of levels of SA suffice to determine isomorphism of planar graphs. We also offer applications both in finite model theory and polyhedral combinatorics. First, we show that certain properties of graphs such as that of having a flow-circulation of a prescribed value, are definable in the infinitary logic with counting with a bounded number of variables. Second, we exploit a lower bound construction due to Cai, Furer and Immerman in the context of counting logics to give simple explicit instances that show that the SA relaxations of the vertex-cover and cut polytopes do not reach their integer hulls for up to Ω(n) levels, where n is the number of vertices in the graph.
ANTIBACTERIAL EFFICACY OF 6% GREEN TEA EXTRACT AND 2% CHLORHEXIDINE AGAINST ENTEROCOCCUS FAECALIS BIOFILM IN VITRO

Objective: This study aimed to compare the antibacterial efficacy of green tea extract to chlorhexidine 2% against Enterococcus faecalis biofilm usingreal-time polymerase chain reaction (RT-PCR). Methods: E. faecalis strain ATCC 29212 colonies were collected from overnight cultures grown on brain–heart infusion agar (BHIA) and resuspendedat 108 CFU/ml according to a 0.5 McFarland standard. Aliquots of bacterial suspension (50 μl) were then inoculated onto sterile nitrocellulose filterdiscs place on BHIA and incubated aerobically at 37°C for 72 h. After incubation, the discs were removed, transferred into 10-ml phosphate-bufferedsaline (PBS) to loosen planktonic bacteria, and then incubated for 10 min at 37°C in 10 ml of 6% green tea extract, 2% chlorhexidine, or sterile PBS(control). Surviving E. faecalis cells were then quantified by RT-PCR.Results: Green tea extract reduced bacterial survival compared to control but was not as effective as chlorhexidine 2%. Conclusion: Green tea extract may help reduce oral E. faecalis biofilm. Moreover, specific antimicrobial compounds in green tea extract such asepigallocatechin-3-gallate should be tested as non-toxic alternatives to chlorhexidine.