Miracle-dz/UniFAR-FTUs huggingface dataset:
Priming Endothelial Cells With a Melanoma‐Derived Extracellular Matrix Triggers the Activation of αvβ3/VEGFR2 Axis

The unique composition of tumor‐produced extracellular matrix (ECM) can be a determining factor in changing the profile of endothelial cells in the tumor microenvironment. As the main receptor for ECM proteins, integrins can activate a series of signaling pathways related to cell adhesion, migration, and differentiation of endothelial cells that interact with ECM proteins. We studied the direct impact of the decellularized ECM produced by a highly metastatic human melanoma cell line (MV3) on the activation of endothelial cells and identified the intracellular signaling pathways associated with cell differentiation. Our data show that compared to the ECM derived from a human melanocyte cell line (NGM‐ECM), ECM produced by a melanoma cell line (MV3‐ECM) is considerably different in ultrastructural organization and composition and possesses a higher content of tenascin‐C and laminin and a lower expression of fibronectin. When cultured directly on MV3‐ECM, endothelial cells change morphology and show increased adhesion, migration, proliferation, and tubulogenesis. Interaction of endothelial cells with MV3‐ECM induces the activation of integrin signaling, increasing FAK phosphorylation and its association with Src, which activates VEGFR2, potentiating the receptor response to VEGF. The blockage of αvβ3 integrin inhibited the FAK‐Src association and VEGFR activation, thus reducing tubulogenesis. Together, our data suggest that the interaction of endothelial cells with the melanoma‐ECM triggers integrin‐dependent signaling, leading to Src pathway activation that may potentiate VEGFR2 activation and up‐regulate angiogenesis. J. Cell. Physiol. 231: 2464–2473, 2016. © 2016 Wiley Periodicals, Inc.
Prenatal betaine exposure modulates hypothalamic expression of cholesterol metabolic genes in cockerels through modifications of DNA methylation

&NA; Cholesterol is essential for neuronal development and brain function. Previously we reported that in ovo administration of betaine modulates hepatic cholesterol metabolism in the chicken, yet it remains unknown whether maternal betaine affects the cholesterol content and the expression of cholesterol metabolic genes in chicken hypothalamus. In this study, eggs were injected with saline or betaine at 2.5 mg/egg, and the hatchlings were raised under the same condition until 64 d of age. Maternal betaine significantly (P = 0.05) increased the body weight and suppressed aggressive behavior of 64‐day‐old cockerels, in association with significantly (P < 0.05) up‐regulated expression of 5‐HTR1A receptor in the hypothalamus. Concurrently, betaine in ovo significantly increased (P < 0.05) the hypothalamic content of total cholesterol and cholesterol ester, which coincided with significantly up‐regulated (P < 0.05) hypothalamic expression of cholesterol biosynthetic genes, such as sterol‐regulatory element binding protein 2 and 3‐hydroxy‐3‐methyl‐glutaryl‐CoA reductase as well as acetyl‐CoA cholesterol acyltransferase 1, which converts free cholesterol to cholesterol ester for storage. In contrast, low density lipoprotein receptor, which mediates the cholesterol uptake, was significantly down‐regulated (P < 0.05). In ovo betaine administration significantly enhanced the expression of betaine‐homocysteine methyltransferase and DNA methyltransferase 1 (P < 0.05), which was associated with alterations of CpG methylation on the promoter of modified cholesterol metabolic genes. These results indicate that maternal betaine modulates hypothalamic cholesterol metabolism in cockerels through modifying DNA methylation on the promoter of cholesterol metabolic genes.
Sensitive Quantification of Clostridium difficile Cells by Reverse Transcription-Quantitative PCR Targeting rRNA Molecules

ABSTRACT We established a sensitive and accurate quantification system for Clostridium difficile in human intestines, based on rRNA-targeted reverse transcription-quantitative PCR (RT-qPCR). We newly developed a species-specific primer set for C. difficile targeting 23S rRNA gene sequences. Both the vegetative cells and the spores of C. difficile in human feces were quantified by RT-qPCR, with a lower detection limit of 102.4 cells/g of feces. In an analysis of the feces of residents (n = 83; age, 85 ± 8 years) and staff (n = 19; age, 36 ± 10 years) at a care facility for the elderly, C. difficile was detected by RT-qPCR in 43% of the residents (average count, log10 4.0 ± 2.0 cells/g of feces) and 16% of the staff (average count, log10 2.2 ± 0.1 cells/g of feces); these rates were far higher than those detected by qPCR (residents, 19%; staff, 0%) or selective cultivation (residents, 18%; staff, 5%). Another analysis of healthy adults (n = 63; age, 41 ± 11 years) also revealed the significant carriage rate of C. difficile in the intestines (detection rate, 13%; average count, log10 4.9 ± 1.2 cells/g of feces). From these results, it was suggested that rRNA-targeted RT-qPCR should be an effective tool for analyzing population levels of C. difficile in the human intestine.
Increase of Precision on the Top of the List of Retrieved Web Documents Using Global and Local Link Analysis

At present, information derived from the cross-references among pages is used to improve the results of Web-based information retrieval systems, as constantly occur in bibliometric techniques. The references are local when only the links related to the set of documents returned as answers to a user query are treated, as done by the HITS algorithm. If all the links of the documents in the collection are taken into account, we speak of global references. This is the case with the PageRank algorithm, which takes advantage of the whole Web structure. Using the WBR99 reference collection, the article shows the results of the implementation of the HITS and PageRank algorithms and emphasizes the gains in precision on the top of the list compared with the results of the space vector model algorithm (SVM), which is grounded only on the textual analysis of the pages. It was noticed that the use of local links produces higher average precision. However, the use of global links is justified whenever high precision at low recall is important and query processing efficiency is essential, such as in Web search engines.
The type I IFN system in rheumatoid arthritis

Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disorder characterized by joint inflammation, immune cell infiltration of the synovia, and cartilage/bone destruction. Despite noteworthy progress in the treatment of RA in recent years, many patients remain refractory to current therapeutic strategies that target either the adaptive immune system or mediators of the innate system. Type I interferons (IFNs) play a significant role in regulation of the innate immune system, originally being discovered as part of intracellular immune defence against viral infection. IFNs are pleiotropic cytokines, mediating both immunostimulatory and immunosuppressive effects. IFN-alpha and beta have been detected in RA synovial fluid and tissue and subsequent therapeutic approaches using type I IFN in murine models of arthritis and in human RA have produced different and controversial results. Great interest has been directed toward principally plasmacytoid dendritic cells (pDCs), although also toward myeloid dendritic cells, as sources of type I IFN. Furthermore, manipulation of DC populations in murine RA models demonstrated that pDCs could suppress the development of arthritis and autoimmunity and may offer an attractive therapy for T-cell-mediated autoimmune diseases. Finally, dendritic cells (DCs) are vehicles for the delivery of therapeutic vaccines, and clinical trials are ongoing in RA with “tolerogenic” DC populations. Further, studies on animal models of RA will elucidate how IFN and DCs contribute to the establishment of autoimmune arthritis and the potential for manipulation of these cell populations and products to re-establish the immune tolerance.
Tapered Microchannel for Multi-particles Passive Separation Based on Hydrodynamic Resistance

Researches on separation of multi-particles utilizing microfluidic have been flourishing in recent years with the aid from advancements in microfabrication design and technology. Generally, separation is beneficial for biomedical application especially involving heterogeneous samples. Due to inherent problems of samples isolation, a simple and efficient separation device is required. Here, we present a passive tapered microchannel for multi-particles separation using hydrodynamic principle. Our emphasis is on the effect of hydrodynamic resistance coupled with tapered microchannel design. In the experiment, successful multi-particles samples separation was observed. The results were further analyzed and were in agreement with the proposed concept. This method opens the route toward robust, low-cost and high-throughput, thus it may holds potential to be integrated as one functional module in Micro Total Analysis System (µTAS).
STARBENCH: the D-type expansion of an H II region

STARBENCH is a project focused on benchmarking and validating different star formation and stellar feedback codes. In this first STARBENCH paper we perform a comparison study of the D-type expansion of an H II region. The aim of this work is to understand the differences observed between the 12 participating numerical codes against the various analytical expressions examining the D-type phase of H II region expansion. To do this, we propose two well-defined tests which are tackled by 1D and 3D grid- and smoothed particle hydrodynamics-based codes. The first test examines the ‘early phase’ D-type scenario during which the mechanical pressure driving the expansion is significantly larger than the thermal pressure of the neutral medium. The second test examines the ‘late phase’ D-type scenario during which the system relaxes to pressure equilibrium with the external medium. Although they are mutually in excellent agreement, all 12 participating codes follow a modified expansion law that deviates significantly from the classical Spitzer solution in both scenarios. We present a semi-empirical formula combining the two different solutions appropriate to both early and late phases that agrees with high-resolution simulations to ≲ 2 per cent. This formula provides a much better benchmark solution for code validation than the Spitzer solution. The present comparison has validated the participating codes and through this project we provide a data set for calibrating the treatment of ionizing radiation hydrodynamics codes.
Hypergraph-Based Binary Locally Repairable Codes With Availability

We study a hypergraph-based code construction for binary locally repairable codes (LRCs) with availability. A symbol of a code is said to have <inline-formula> <tex-math notation="LaTeX">$(r, t)$ </tex-math></inline-formula>-availability if it can be recovered from <inline-formula> <tex-math notation="LaTeX">$t$ </tex-math></inline-formula> disjoint repair sets of other symbols, each set of size at most <inline-formula> <tex-math notation="LaTeX">$r$ </tex-math></inline-formula>. We refer a systematic code to an LRC with <inline-formula> <tex-math notation="LaTeX">$(r, t)_{i}$ </tex-math></inline-formula>-availability if its information symbols have <inline-formula> <tex-math notation="LaTeX">$(r, t)$ </tex-math></inline-formula>-availability and a code to an LRC with <inline-formula> <tex-math notation="LaTeX">$(r, t)_{a}$ </tex-math></inline-formula>-availability if its all symbols have <inline-formula> <tex-math notation="LaTeX">$(r, t)$ </tex-math></inline-formula>-availability. We construct binary LRCs with <inline-formula> <tex-math notation="LaTeX">$(r, t)_{i}$ </tex-math></inline-formula>-availability from linear <inline-formula> <tex-math notation="LaTeX">$r$ </tex-math></inline-formula>-uniform <inline-formula> <tex-math notation="LaTeX">$t$ </tex-math></inline-formula>-regular hypergraphs. As a special case, we also construct binary LRCs with <inline-formula> <tex-math notation="LaTeX">$(r, t)_{a}$ </tex-math></inline-formula>-availability from labeled linear <inline-formula> <tex-math notation="LaTeX">$r$ </tex-math></inline-formula>-uniform <inline-formula> <tex-math notation="LaTeX">$t$ </tex-math></inline-formula>-regular hypergraphs. Moreover, we extend the hypergraph-based codes to increase the minimum distance. All the proposed codes achieve a well-known Singleton-like bound with equality.
Formal Verification of Compilers Independent Study Report

This study, completed as part of a Bachelor level independent study course, aims to survey the current landscape of research into the formal verification of compilers. This report includes a technical perspective of several current and past compiler verification projects conducted by researchers at leading universities and a final ending summary giving impressions on the future of formal compiler verification research.
The Effects of Preseason Trunk Muscle Training on Low-Back Pain Occurrence in Women Collegiate Gymnasts

Durall, CJ, Udermann, BE, Johansen, DR, Gibson, B, Reineke, DM, and Reuteman, P. The effects of preseason trunk muscle training on low-back pain occurrence in women collegiate gymnasts. J Strength Cond Res 23(1): 86-92, 2009-Low-back pain (LBP) in women gymnasts is relatively common. This investigation was performed to evaluate the effects of a preseason training program for the trunk extensor, lateral flexor, and flexor muscles on LBP occurrence during the subsequent competitive season. The training group consisted of 15 collegiate women gymnasts. The control group consisted of 15 nonathlete collegiate women. Pre- and posttesting for all participants consisted of static endurance tests for the trunk extensors, lateral flexors, and flexors. After pretesting, the training group completed 10 weeks of biweekly training consisting of non-foot-supported back extensions and side bridges, in addition to their usual trunk flexor exercises. The control group did not perform any specialized trunk muscle training. Mean improvements in trunk endurance, based on multivariate analysis of variance at the 5% level of significance, were significantly greater in the training group than in the control group. Mean improvements in endurance in the training group were 47 seconds for the lateral trunk flexors, 34 seconds for the trunk extensors, and 80 seconds for the trunk flexors. During the subsequent gymnastics season, none of the gymnasts reported new episodes of LBP. One gymnast with chronic LBP reported a recurrence of LBP during the season. None of the gymnasts reported that the training program adversely affected their gymnastic performance. These data suggest that training the trunk musculature twice per week during a 10-week period with a relatively simple floor exercise protocol was an effective stimulus to improve trunk endurance measures. It is encouraging that none of the gymnasts reported new episodes of LBP during the subsequent competitive gymnastics season.
Optimal configuration and weighting of nonuniform arrays according to a maximum ISLR criterion

Proposes of a method for optimizing configuration and weighting of linear or planar arrays. The criterion chosen for the optimization is the maximization of the integrated sidelobe ratio (ISLR), defined as the ratio between the energy of the mainlobe and the energy of the sidelobes of the system impulse response. The choice of the ISLR allows us to take into account, in the optimization procedure, two important quality factors: resolution and contrast. The nonuniform spacing of the resulting optimized array breaks the regularity responsible for the formation of the so called grating lobes. The method can then be used also as a tool for reducing the number of elements in an array strictly necessary for achieving some desired performance. <<ETX>>
Sparrow: An energy harvesting wireless sensor node

Powering a device using solar generated energy can be difficult, especially when that device is meant to function constantly over a long period of time. In this article we present an architecture for energy harvesting wireless sensor networks that can be used to develop solar powered applications. It will cover the hardware as well as the software requirements and specifications for a truly autonomous energy harvesting wireless sensor network. The hardware is composed of a new low power node designed to be a powerful development platform and an efficient energy harvesting module. The software is designed to efficiently use the stored energy by implementing a lightweight but powerful algorithm for scheduling data transmission.
Finger Search Trees

University of Aarhus 11.1 Finger Searching. 11-1 11.2 Dynamic Finger Search Trees . 11-2 11.3 Level Linked (2,4)-Trees . 11-3 11.4 Randomized Finger Search Trees . 11-4 Treaps • Skip Lists 11.5 Applications . 11-6 Optimal Merging and Set Operations • Arbitrary Merging Order • List Splitting • Adaptive Merging and Sorting
A cre/loxP‐deleter transgenic line in mouse strain 129S1/SvImJ

Summary: A Cre recombinase expression cassette was inserted into the X‐linked Hprt locus by gene targeting in a mouse embryonic stem (ES) cell line isogenic to strain 129S1/SvImJ (129S1), then the transgene was introduced into 129S1 mice through ES cell chimeras. When females hemizygous for this transgene were mated to males carrying a neomycin selection cassette flanked by loxP sites, the cassette was always excised regardless of Cre inheritance and without detectable mosaicism. The usefulness of this “Cre‐deleter” transgenic line is in its efficiency and defined genetic status in terms of mouse strain and location of the transgene. genesis 32:199–202, 2002. © 2002 Wiley‐Liss, Inc.
Vehicle-generated data exchange protocol for Remote OBD inspection and maintenance

This paper introduces efficient method for inspection and maintenance of vehicles using existing technology which is aimed primarily at supporting on-board diagnostics (OBD) regulations remotely i.e. Remote OBD. Remote OBD may require remote wireless connectivity with vehicular ECUs and also comply with OBD requirements. Compliance with future remote OBD requirements is achieved through a proposed standard protocol called vehicle-generated data exchange protocol with XML schema for encoding OBD related information. We implemented this protocol on an on-board data acquisition and communications device with simultaneously alternative wireless data links between vehicle and the internet (e.g. mobile devices or data management system).
Virtual flux based direct power control of a three-phase rectifier connected to an LCL filter with sensorless active damping

This paper proposes a simple method for connecting an LCL filter to a three-phase pulse-width modulation (PWM) rectifier with direct power control space vector modulation (DPC-SVM) strategy. The goal is to improve the transient response and reduce the harmonic distortion, as well as size and cost reduction of the input filter. Since the proposed method is sensorless, the AC line voltage sensors are eliminated and the virtual flux block would be used instead. The cost and size of the filter could be reduced since the LCL-filter has lower inductance values and also the harmonic distortions could be reduced as well. The only drawback of the LCL-filter is producing resonance oscillations due to the resonance frequency of its third-order transfer function. In order to eliminate the oscillations, a simple method of active damping is utilized. Finally, simulation results have shown an excellent dynamic response compared with a three-phase converter that uses a conventional L-filter.
Cost Analysis of a Novel Interdisciplinary Model for Advanced Illness Management

Purpose: This research project evaluated cost outcomes for patients in the @HOMe Support program, a novel interdisciplinary home-based program for patients and caregivers facing advanced illness drawing on the Chronic Care Model. Methods: Cost analysis involved paired sample t-tests to examine pre–post differences in health care expenditures obtained from Health Maintenance Organization (HMO) claims data for program participants. Results: Average 6-month costs per month significantly declined for patients older than 65 years of age from 1 HMO (US$9300-US$5900, P = .001). Evaluation of the second HMO showed that patients less than 65 years of age with lower preentry costs (<70 000) had a nonsignificant decline in total costs (US$18 787-US$13 781, P = .08). Conclusions: Study findings suggest @HOMe Support is associated with reductions in the use and cost for most health services over time.
Conserved Residues Ser16 and His20 and Their Relative Positioning Are Essential for TonB Activity, Cross-linking of TonB with ExbB, and the Ability of TonB to Respond to Proton Motive Force*

The cytoplasmic membrane protein TonB couples the proton electrochemical potential of the cytoplasmic membrane to transport events at the outer membrane of Gram-negative bacteria. The amino-terminal signal anchor of TonB and its interaction with the cytoplasmic membrane protein ExbB are essential to this process. The TonB signal anchor is predicted to form an α-helix, with a conserved face comprised of residues Ser16, His20, Leu27, and Ser31. Deletion of either Ser16 or His20 or of individual intervening but not flanking residues rendered TonB inactive and unable to assume a proton motive force-dependent conformation. In vivo formaldehyde cross-linking experiments revealed that the ability of this subset of mutants to form a characteristic heterodimer with ExbB was greatly diminished. Replacement of residues 17–19 by three consecutive alanines produced a wild type TonB allele, indicating that the intervening residues (Val, Cys, and Ile) contributed only to spacing. These data indicated that the spatial relationship of Ser16 to His20 was essential to function and suggested that the motif HXXXS defines the minimal requirement for the coupling of TonB to the cytoplasmic membrane electrochemical gradient. Deletion of Trp11 resulted in a TonB that remained active yet was unable to cross-link with ExbB. Because Trp11 was demonstrably not involved in the actual cross-linking, these results suggest that the TonB/ExbB interaction detected by cross-linking occurred at a step in the energy transduction cycle distinct from the coupling of TonB to the electrochemical gradient.