Miracle-dz/UniFAR-FTUs huggingface dataset:
Receptor tyrosine kinase signaling required for integrin alpha v beta 5- directed cell motility but not adhesion on vitronectin

FG human pancreatic carcinoma cells adhere to vitronectin using integrin alpha v beta 5 yet are unable to migrate on this ligand whereas they readily migrate on collagen in an alpha 2 beta 1-dependent manner. We report here that epidermal growth factor receptor (EGFR) activation leads to de novo alpha v beta 5-dependent FG cell migration on vitronectin. The EGFR specific tyrosine kinase inhibitor tyrphostin 25 selectively prevents EGFR autophosphorylation thereby preventing the EGF-induced FG cell migration response on vitronectin without affecting constitutive migration on collagen. Protein kinase C (PKC) activation also leads to alpha v beta 5-directed motility on vitronectin; however, this is not blocked by tyrosine kinase inhibitors. In this case, PKC activation appears to be associated with and downstream of EGFR signaling since calphostin C, an inhibitor of PKC, blocks FG cell migration on vitronectin induced by either PKC or EGF. These findings represent the first report implicating a receptor tyrosine kinase in a specific integrin mediated cell motility event independent of adhesion.
Use of a multi-thermal washer for DNA microarrays simplifies probe design and gives robust genotyping assays

DNA microarrays are generally operated at a single condition, which severely limits the freedom of designing probes for allele-specific hybridization assays. Here, we demonstrate a fluidic device for multi-stringency posthybridization washing of microarrays on microscope slides. This device is called a multi-thermal array washer (MTAW), and it has eight individually controlled heating zones, each of which corresponds to the location of a subarray on a slide. Allele-specific oligonucleotide probes for nine mutations in the beta-globin gene were spotted in eight identical subarrays at positions corresponding to the temperature zones of the MTAW. After hybridization with amplified patient material, the slides were mounted in the MTAW, and each subarray was exposed to different temperatures ranging from 22 to 40°C. When processed in the MTAW, probes selected without considering melting temperature resulted in improved genotyping compared with probes selected according to theoretical melting temperature and run under one condition. In conclusion, the MTAW is a versatile tool that can facilitate screening of a large number of probes for genotyping assays and can also enhance the performance of diagnostic arrays.
118GHz fundamental VCO with 7.8% tuning range in 65nm CMOS

This paper presents a 118GHz fundamental voltage controlled oscillator in a 65nm low power CMOS technology. Using accumulation mode varactors, the oscillator covers a frequency range from 113.4GHz to 122.6GHz, which corresponds to a 7.8% tuning range. This is the widest tuning range in a D-band VCO reported to date. Combined with a variable supply voltage, the tuning range is extended to 11GHz (9.3%). The VCO draws 5.6mA from a 1V supply and the output is higher than −28.5 dBm. The measured phase noise at 118.3GHz is −83.9dBc/Hz at 1MHz offset. The FOMT is −175.7dB, which is the highest reported for a D-band VCO.
Abstract Argumentation and Answer-Set Programming ?

Argumentation and Answer-Set Programming Sarah Alice Gaggl, Stefan Woltran Vienna University of Technology, Austria Abstract. In this article, we overview encodings for problems associated to abstract argumentation frameworks (AFs) in the language of Answer-Set Programming (ASP). Our encodings are formulated as fixed queries, such that the input is the only part depending on the actual AF to process. We illustrate the functioning of this approach, which is underlying the argumentation system ASPARTIX, briefly report on our experimental experiences, and give links to the relevant articles in the literature. In this article, we overview encodings for problems associated to abstract argumentation frameworks (AFs) in the language of Answer-Set Programming (ASP). Our encodings are formulated as fixed queries, such that the input is the only part depending on the actual AF to process. We illustrate the functioning of this approach, which is underlying the argumentation system ASPARTIX, briefly report on our experimental experiences, and give links to the relevant articles in the literature.
Forecasting Out-of-the-Ordinary Financial Events

Being able to understand the financial market is very important for investors and, given the width and complexity of the topic, tools to support investor decisions are badly needed. In this paper we present Mercurio, a system that supports the decision-making process of financial investors through the automatic extraction and analysis of financial data coming from the Web. Mercurio formalizes the knowledge and reasoning of an expert in financial journalism and uses it to identify relevant events within financial newspapers. Moreover, it performs automatic analysis of financial indexes to identify relevant events related to the stock market. Then, sequential pattern mining is used to predict exceptional events on the basis of the knowledge of their past occurrences and relationships with other events, in order to to warn investors about them.
Structural Brain Alterations in Community Dwelling Individuals with Chronic Joint Pain

BACKGROUND AND PURPOSE: Central sensitization in chronic pain involves structural brain changes that influence vulnerability to pain. Identifying brain regions involved in pain processing and sensitization can provide more insight into chronic pain. This study examines structural brain changes in chronic pain and experimental pain in a large population-based study. MATERIALS AND METHODS: For 3892 participants in the Rotterdam study, global and regional MR imaging brain volumes were automatically segmented and quantified. Chronic joint pain was defined as pain for more than half of all days during the past 6 weeks. Heat pain thresholds were measured in a subset of 1538 individuals. The association between the presence of chronic joint pain and global and lobar brain volumes was studied. Subsequently, literature was reviewed and the association of chronic pain and heat pain thresholds with 11 brain regions associated with musculoskeletal pain in previous publications was studied. RESULTS: Total gray matter volume was smaller in women with chronic pain (β = −0.066, P = .016). This effect was primarily driven by lower gray matter volume in the temporal lobe (β = 0.086, P = .005), the frontal lobe (β = −0.060, P = .039), and the hippocampus (β = −0.099, P = .002). In addition, we observed that a lower heat pain threshold was associated with smaller volumes of the hippocampus (β = 0.017, P = .048), the thalamus (β = 0.018, P = .009), and the anterior cingulate cortex (β = −0.016, P = .037). In men, no significant associations were observed. CONCLUSIONS: The primary identified brain areas, the temporal and frontal lobes and the hippocampus, indicated involvement of emotional processing. The volumetric differences found indicated a sex-specific neuroplasticity in chronic pain. These results emphasized sex-specific and multidisciplinary pain treatment.
The Landscape of Clinical Trials Evaluating the Theranostic Role of PET Imaging in Oncology: Insights from an Analysis of ClinicalTrials.gov Database

In the war on cancer marked by personalized medicine, positron emission tomography (PET)-based theranostic strategy is playing an increasingly important role. Well-designed clinical trials are of great significance for validating the PET applications and ensuring evidence-based cancer care. This study aimed to provide a comprehensive landscape of the characteristics of PET clinical trials using the substantial resource of ClinicalTrials.gov database. We identified 25,599 oncology trials registered with ClinicalTrials.gov in the last ten-year period (October 2005-September 2015). They were systematically reviewed to validate classification into 519 PET trials and 25,080 other oncology trials used for comparison. We found that PET trials were predominantly phase 1-2 studies (86.2%) and were more likely to be single-arm (78.9% vs. 57.9%, P <0.001) using non-randomized assignment (90.1% vs. 66.7%, P <0.001) than other oncology trials. Furthermore, PET trials were small in scale, generally enrolling fewer than 100 participants (20.3% vs. 25.7% for other oncology trials, P = 0.014), which might be too small to detect a significant theranostic effect. The funding support from industry or National Institutes of Health shrunk over time (both decreased by about 5%), and PET trials were more likely to be conducted in only one region lacking international collaboration (97.0% vs. 89.3% for other oncology trials, P <0.001). These findings raise concerns that clinical trials evaluating PET imaging in oncology are not receiving the attention or efforts necessary to generate high-quality evidence. Advancing the clinical application of PET imaging will require a concerted effort to improve the quality of trials.
PERCEPTUAL ORGANIZATION OF 3D SURFACE POINTS

: Perceptual organization is proposed as a promising intermediate process toward object recognition and reconstruction from 3D surface points, which can be derived from aerial stereo-images, LIDAR data or InSAR data. Here, perceptual organization is to group sensory primitives originating from the same object and has been emphasized as a robust intermediate-level grouping process toward object recognition in human and computer vision. Despite intensive research on 2D data, perceptual organization of 3D entities is still in its infancy, however. Therefore, the purpose of this research is to develop a robust approach for constructing perceptual organization particularly with irregularly distributed 3D surface points. The scope of perceptual organization presented in this paper is limited to signal, primitive and structural levels. At the signal level, we organize raw 3D points into spatially coherent patches. Then, at the primitive level, we merge the patches into co-parametric surfaces. Finally, at the structural level, we group the surfaces into perceptually meaningful surface clusters. We establish a novel approach and implement the approach as an autonomous system. The system is evaluated with real LIDAR data by inspecting the quality of organized output. The evaluation substantiates a promising performance of the system. The organized output serves as a valuable input to higher order perceptual processes, including the generation and validation of hypotheses in object recognition tasks.
Heterochromatic Threads Connect Oscillating Chromosomes during Prometaphase I in Drosophila Oocytes

In Drosophila oocytes achiasmate homologs are faithfully segregated to opposite poles at meiosis I via a process referred to as achiasmate homologous segregation. We observed that achiasmate homologs display dynamic movements on the meiotic spindle during mid-prometaphase. An analysis of living prometaphase oocytes revealed both the rejoining of achiasmate X chromosomes initially located on opposite half-spindles and the separation toward opposite poles of two X chromosomes that were initially located on the same half spindle. When the two achiasmate X chromosomes were positioned on opposite halves of the spindle their kinetochores appeared to display proper co-orientation. However, when both Xs were located on the same half spindle their kinetochores appeared to be oriented in the same direction. Thus, the prometaphase movement of achiasmate chromosomes is a congression-like process in which the two homologs undergo both separation and rejoining events that result in the either loss or establishment of proper kinetochore co-orientation. During this period of dynamic chromosome movement, the achiasmate homologs were connected by heterochromatic threads that can span large distances relative to the length of the developing spindle. Additionally, the passenger complex proteins Incenp and Aurora B appeared to localize to these heterochromatic threads. We propose that these threads assist in the rejoining of homologs and the congression of the migrating achiasmate homologs back to the main chromosomal mass prior to metaphase arrest.
DipM, a new factor required for peptidoglycan remodelling during cell division in Caulobacter crescentus

In bacteria, cytokinesis is dependent on lytic enzymes that facilitate remodelling of the cell wall during constriction. In this work, we identify a thus far uncharacterized periplasmic protein, DipM, that is required for cell division and polarity in Caulobacter crescentus. DipM is composed of four peptidoglycan binding (LysM) domains and a C‐terminal lysostaphin‐like (LytM) peptidase domain. It binds to isolated murein sacculi in vitro, and is recruited to the site of constriction through interaction with the cell division protein FtsN. Mutational analyses showed that the LysM domains are necessary and sufficient for localization of DipM, while its peptidase domain is essential for function. Consistent with a role in cell wall hydrolysis, DipM was found to interact with purified murein sacculi in vitro and to induce cell lysis upon overproduction. Its inactivation causes severe defects in outer membrane invagination, resulting in a significant delay between cytoplasmic compartmentalization and final separation of the daughter cells. Overall, these findings indicate that DipM is a periplasmic component of the C. crescentus divisome that facilitates remodelling of the peptidoglycan layer and, thus, coordinated constriction of the cell envelope during the division process.
Wild Edible Fruit of Prunus nepalensis Ser. (Steud), a Potential Source of Antioxidants, Ameliorates Iron Overload-Induced Hepatotoxicity and Liver Fibrosis in Mice

The antioxidant and restoration potentials of hepatic injury by Prunus nepalensis Ser. (Steud), a wild fruit plant from the Northeastern region of India, were investigated. The fruit extract (PNME) exhibited excellent antioxidant and reducing properties and also scavenged the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical (IC50 = 30.92 ± 0.40 μg/ml). PNME demonstrated promising scavenging potency, as assessed by the scavenging of different reactive oxygen and nitrogen species. Moreover, the extract revealed an exceptional iron chelation capacity with an IC50 of 25.64 ± 0.60 μg/ml. The extract induced significant improvement of hepatic injury and liver fibrosis against iron overload induced hepatotoxicity in mice in a dose-dependent manner, and this effect was supported by different histopathological studies. The phytochemical constitutions and their identification by HPLC confirmed the presence of purpurin, tannic acid, methyl gallate, reserpine, gallic acid, ascorbic acid, catechin and rutin. The identified compounds were investigated for their individual radical scavenging and iron chelation activity; some compounds exhibited excellent radical scavenging and iron chelation properties, but most were toxic towards normal cells (WI-38). On the other hand, crude PNME was found to be completely nontoxic to normal cells, suggesting its feasibility as a safe oral drug. The above study suggests that different phytochemicals in PNME contributed to its free radical scavenging and iron chelation activity; however, further studies are required to determine the pathway in which PNME acts to treat iron-overload diseases.
Income and Nutritional Effects of the Commercialization of Agriculture in Southwestern Kenya

This 1984-85 study evaluated the effects of cash crop production on agricultural production income and food consumption. It assessed the impact of cash cropping on the health and nutritional status of women and preschoolers in Kenya. This study was unique in its focus on the process through which commercial agriculture may affect household behavior. Data were obtained from a sample of 504 farmers who lived in Nyanza province South Nyanza District southwest Kenya. 139 were sugar farmers. Illness among children and women ranged from 50-70% at any one time. Analysis pertained to a comparison of maize and sugar cropping distribution of income and expenditure energy consumption among subpopulations and the determinants of household food consumption nutritional status and morbidity. The health and sanitation environments were deficient. Sugar cane farmers had 25% higher income than non-sugar farmers but had less area under cultivation as food crops. Returns to land were greater for sugar cane compared to maize due to a lower need for labor and the governments pricing policy. Household calorie consumption but not preschool nutritional status was significantly indirectly affected by the sugarcane outgrowers program. Child health was mostly affected by sanitation and morbidity patterns. Child health status was better in female headed households. Gender determined type of household expenditure. Agricultural contracts should include wives in order to establish the concept of household income. Income payments should be periodic. The outgrowers scheme should be integrated into primary health care delivery.
Specific sequence determinants of miR-15/107 microRNA gene group targets

MicroRNAs (miRNAs) target mRNAs in human cells via complex mechanisms that are still incompletely understood. Using anti-Argonaute (anti-AGO) antibody co-immunoprecipitation, followed by microarray analyses and downstream bioinformatics, ‘RIP-Chip’ experiments enable direct analyses of miRNA targets. RIP-Chip studies (and parallel assessments of total input mRNA) were performed in cultured H4 cells after transfection with miRNAs corresponding to the miR-15/107 gene group (miR-103, miR-107, miR-16 and miR-195), and five control miRNAs. Three biological replicates were run for each condition with a total of 54 separate human Affymetrix Human Gene 1.0 ST array replicates. Computational analyses queried for determinants of miRNA:mRNA binding. The analyses support four major findings: (i) RIP-Chip studies correlated with total input mRNA profiling provides more comprehensive information than using either RIP-Chip or total mRNA profiling alone after miRNA transfections; (ii) new data confirm that miR-107 paralogs target coding sequence (CDS) of mRNA; (iii) biochemical and computational studies indicate that the 3′ portion of miRNAs plays a role in guiding miR-103/7 to the CDS of targets; and (iv) there are major sequence-specific targeting differences between miRNAs in terms of CDS versus 3′-untranslated region targeting, and stable AGO association versus mRNA knockdown. Future studies should take this important miRNA-to-miRNA variability into account.
Reproducibility of oxidative stress biomarkers in breath condensate: are they reliable?

In this issue of the European Respiratory Journal , Van Hoydonck et al. 1 report a study about the reproducibility of oxidative stress biomarkers, such as hydrogen peroxide (H2O2) and 8‐isoprostane (a member of the F2‐isoprostane class) in nonconcentrated exhaled breath condensate (EBC) obtained from healthy male smokers. The aim of their study was to identify whether these biomarkers could reproducibly be measured on different days of collection to enable identification of a susceptible population to lung diseases and monitoring of disease severity. The authors collected the EBC samples at three time points within 1 week (day 0, day 3 or 4, day 7) from each healthy smoker. Their major findings were: 1) H2O2 and 8‐isoprostane were detected in only 47% and 36% of all EBC samples, respectively; 2) only three of 12 smokers had detectable 8‐isoprostane concentrations on all three occasions (mean 4.6 pg·mL−1; range 3.9–7.7 pg·mL−1), whereas H2O2 was not detected on all three occasions in any of the smokers within 1 week; and 3) 8‐isoprostane and H2O2 concentrations were below the limit of detection in many samples (<3.9 pg·mL−1 for 8‐isoprostane and 0.31 µM forH2O2). They concluded that the levels of H2O2 and 8‐isoprostane could not be reproducibly assessed in the EBCof healthy smokers because of their low concentration and/or the lack of sensitivity/specificity of the available assays. The other major factors that may affect the reproducibility would include intra- and inter-individual variability, sampling time and variability in dilution of respiratory droplets by water vapour 2 …
The spirit of public administration

Introduction: Understanding Public Administration Part One: Governance, Politics, and the Public 1. Finding the Public in Public Administration 2. The Political Context of Public Administration 3. Public Administration as Governance Part Two: Issues of Fairness 4. The Question of Administrative Discretion 5. Fairness and Social Equity in Public Administration 6. Intergenerational Concepts of Public Administration Part Three: Ethics, Citizenship, and Benevolence in Public Administration 7. Ethics and Public Administration 8. The Paradox of Distance and the Problem of Differentiation. (with David G. Frederickson) 9. Patriotism, Benevolence, and Public Administration. (with David Kirkwood Hart) 10. The Public Administrator as a Representative Citizen. (with Ralph Clark Chandler) 11. Pushing Things Up to Their First Principles.
The POLAR gamma-ray burst polarimeter onboard the Chinese Spacelab

POLAR is a joint European-Chinese experiment aimed at a precise measurement of hard X-ray polarization (50-500 keV) of the prompt emission of Gamma-Ray Bursts. The main aim is a better understanding of the geometry of astrophysical sources and of the X-ray emission mechanisms. POLAR is a compact Compton polarimeter characterized by a large modulation factor, effective area, and field of view. It consists of 1600 low-Z plastic scintillator bars read out by 25 at-panel multi-anode photomultipliers. The incoming X-rays undergo Compton scattering in the bars and produce a modulation pattern; experiments with polarized synchrotron radiation and GEANT4 Monte Carlo simulations have shown that the polarization degree and angle can be retrieved from this pattern with the accuracy necessary for identifying the GRB mechanism. The flight model of POLAR is currently under construction in Geneva. The POLAR instrument will be placed onboard the Chinese spacelab TG-2, scheduled for launch in low Earth orbit in 2015. The main milestones of the space qualification campaign will be described in the paper.
Analysis of dynamic morphogen scale invariance

During the development of some tissues, fields of multipotent cells differentiate into distinct cell types in response to the local concentration of a signalling factor called a morphogen. Typically, individual organisms within a population differ in size, but their body plans appear to be scaled versions of a common template. Similarly, closely related species may differ by three or more orders of magnitude in size, yet common structures between species scale to have similar proportions. In standard reaction–diffusion equations, the morphogen range has a length scale that depends on a balance between kinetic and transport processes and not on the length or size of the field of cells being patterned. However, as shown here for a class of morphogen-patterning systems, a number of conditions lead to scale invariance of the morphogen distribution at equilibrium and during the transient approach to equilibrium. Equilibrium scale invariance requires conservation of the total binding site number and total input flux. Dynamic scale invariance additionally requires sufficient binding to slow the diffusion of ligand. The equations derived herein can be extended to the study of other perturbations to gain further insight into the processes regulating the robustness and scaling of morphogen-mediated pattern formation.