Miracle-dz/UniFAR-FTUs huggingface dataset:
The Influence of Mucus Microstructure and Rheology in Helicobacter pylori Infection

The bacterium Helicobacter pylori (H. pylori), has evolved to survive in the highly acidic environment of the stomach and colonize on the epithelial surface of the gastric mucosa. Its pathogenic effects are well known to cause gastritis, peptic ulcers, and gastric cancer. In order to infect the stomach and establish colonies on the mucus epithelial surface, the bacterium has to move across the gel-like gastric mucus lining of the stomach under acidic conditions. In this review we address the question of how the bacterium gets past the protective mucus barrier from a biophysical perspective. We begin by reviewing the molecular structure of gastric mucin and discuss the current state of understanding concerning mucin polymerization and low pH induced gelation. We then focus on the viscoelasticity of mucin in view of its relevance to the transport of particles and bacteria across mucus, the key first step in H. pylori infection. The second part of the review focuses on the motility of H. pylori in mucin solutions and gels, and how infection with H. pylori in turn impacts the viscoelastic properties of mucin. We present recent microscopic results tracking the motion of H. pylori in mucin solutions and gels. We then discuss how the biochemical strategy of urea hydrolysis required for survival in the acid is also relevant to the mechanism that enables flagella-driven swimming across the mucus gel layer. Other aspects of the influence of H. pylori infection such as, altering gastric mucin expression, its rate of production and its composition, and the influence of mucin on factors controlling H. pylori virulence and proliferation are briefly discussed with references to relevant literature.
Caenorhabditis briggsae methods.

Copyright: © 2006 Scott E. Baird and Helen M. Chamberlin. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. To whom correspondence should be addressed. E-mail: scott.baird@wright.edu or chamberlin.27@osu.edu Caenorhabditis briggsae methods* Scott E. Baird, Department of Biological Sciences, Wright State University, Dayton, OH 45435-0001 USA Helen M. Chamberlin, Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210-1292 USA
SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation

Significance RNA-directed DNA methylation (RdDM) has traditionally been associated with transposable elements, but more recent studies have shown that RdDM also targets regulatory regions of protein-coding genes. Moreover, DNA methylation in Arabidopsis appears to be more dynamic than previously believed and may correlate with transcriptional responses to environmental stresses, such as pathogens. Therefore, the identification and characterization of RdDM mechanisms is fundamental to our understanding of how biological traits are controlled at an epigenetic level. We have performed a screen based on available coexpression data and identified two previously uncharacterized genes, FRG1 and -2, involved in RdDM. This work also shows the validity of coexpression data as an approach to assign new gene functions for RdDM. DNA methylation in Arabidopsis thaliana is maintained by at least four different enzymes: DNA METHYLTRANSFERASE1 (MET1), CHROMOMETHYLASE3 (CMT3), DOMAINS REARRANGED METHYLTRANSFERASE2 (DRM2), and CHROMOMETHYLASE2 (CMT2). However, DNA methylation is established exclusively by the enzyme DRM2, which acts in the RNA-directed DNA methylation (RdDM) pathway. Some RdDM components belong to gene families and have partially redundant functions, such as the endoribonucleases DICER-LIKE 2, 3, and 4, and INVOLVED IN DE NOVO2 (IDN2) interactors IDN2-LIKE 1 and 2. Traditional mutagenesis screens usually fail to detect genes if they are redundant, as the loss of one gene can be compensated by a related gene. In an effort to circumvent this issue, we used coexpression data to identify closely related genes that are coregulated with genes in the RdDM pathway. Here we report the discovery of two redundant proteins, SNF2-RING-HELICASE–LIKE1 and -2 (FRG1 and -2) that are putative chromatin modifiers belonging to the SNF2 family of helicase-like proteins. Analysis of genome-wide bisulfite sequencing shows that simultaneous mutations of FRG1 and -2 cause defects in methylation at specific RdDM targeted loci. We also show that FRG1 physically associates with Su(var)3-9–related SUVR2, a known RdDM component, in vivo. Combined, our results identify FRG1 and FRG2 as previously unidentified components of the RdDM machinery.
A CORPORATE GOVERNANCE STUDY ON ITALIAN FAMILY FIRMS

Abstract In this paper we investigate three corporate governance issues in 30 Italian family firms: (i) the RULHQWDWLRQHLWKHUWRWKH$JHQF\7KHRU\RUWRWKH6WHZDUGVKLS7KHRU\  LL WKHERDUGRIGLUHFWRUV¶comSRVLWLRQ  LLL WKHDELOLW\WRLQYROYHQRQIDPLO\LQGLYLGXDOVLQWKHFRPSDQ\¶VPDQDJHPHQWDQGgovernance (Openness Index) and the decision-making quality (Extension Index) and we analyze empirical results through a cluster analysis by following the Gubitta DQG *LDQHFFKLQL¶V DSSURDFK(2002). Our conclusion suggests that (i) VPDOO,WDOLDQIDPLO\ILUPV¶FRUSRUDWHJRYHUQDQFHV\VWHPVVHHPto be consistent with the guidelines suggested by the Stewardship Theory and LL ,WDOLDQIDPLO\ILUPV¶boards are characterized by a relevant presence of family members. Keywords: family business, corporate governance, small firms *Department of Management, Economics, and Industrial Engineering, Politecnico di Milano ** Department of Management, Economics, and Industrial Engineering, Politecnico di Milano ***Department of Management, Economics, and Industrial Engineering, Politecnico di Milano ****Corresponding Author, Department of Industrial and Management Engineering
Alternative Splicing of the Pituitary Adenylate Cyclase-Activating Polypeptide Receptor PAC1: Mechanisms of Fine Tuning of Brain Activity

Alternative splicing of the precursor mRNA encoding for the neuropeptide receptor PAC1/ADCYAP1R1 generates multiple protein products that exhibit pleiotropic activities. Recent studies in mammals and zebrafish have implicated some of these splice isoforms in control of both cellular and body homeostasis. Here, we review the regulation of PAC1 splice variants and their underlying signal transduction and physiological processes in the nervous system.
A GPU-Accelerated Finite-Difference Time-Domain Scheme for Electromagnetic Wave Interaction With Plasma

A graphical processing unit (GPU)-accelerated finite-difference time-domain (FDTD) scheme for the simulation of radio-frequency (RF) wave propagation in a dynamic, magnetized plasma is presented. This work builds on well-established FDTD techniques with the inclusion of new time advancement equations for the plasma fluid density and temperature. The resulting FDTD formulation is suitable for the simulation of the time-dependent behavior of an ionospheric plasma due to interaction with an RF wave and the excitation of plasma waves and instabilities. The stability criteria and the dependence of accuracy on the choice of simulation parameters are analyzed and found to depend on the choice of simulation grid parameters. It is demonstrated that accelerating the FDTD code using GPU technology yields significantly higher performance, with a dual-GPU implementation achieving a rate of node update almost two orders of magnitude faster than a serial implementation. Optimization techniques such as memory coalescence are demonstrated to have a significant effect on code performance. The results of numerical tests performed to validate the FDTD scheme are presented, with a good agreement achieved when the simulation results are compared to both the predictions of plasma theory and to the results of the Tech-X VORPAL 4.2. 2 software that was used as a benchmark.
Exogenous Glucose Administration Impairs Glucose Tolerance and Pancreatic Insulin Secretion during Acute Sepsis in Non-Diabetic Mice

Objectives The development of hyperglycemia and the use of early parenteral feeding are associated with poor outcomes in critically ill patients. We therefore examined the impact of exogenous glucose administration on the integrated metabolic function of endotoxemic mice using our recently developed frequently sampled intravenous glucose tolerance test (FSIVGTT). We next extended our findings using a cecal ligation and puncture (CLP) sepsis model administered early parenteral glucose support. Methods Male C57BL/6J mice, 8-12 weeks, were instrumented with chronic indwelling arterial and venous catheters. Endotoxemia was initiated with intra-arterial lipopolysaccharide (LPS; 1 mg/kg) in the presence of saline or glucose infusion (100 µL/hr), and an FSIVGTT was performed after five hours. In a second experiment, catheterized mice underwent CLP and the impact of early parenteral glucose administration on glucose homeostasis and mortality was assessed over 24 hrs. Measurements And MAIN RESULTS: Administration of LPS alone did not impair metabolic function, whereas glucose administration alone induced an insulin sensitive state. In contrast, LPS and glucose combined caused marked glucose intolerance and insulin resistance and significantly impaired pancreatic insulin secretion. Similarly, CLP mice receiving parenteral glucose developed fulminant hyperglycemia within 18 hrs (all > 600 mg/dl) associated with increased systemic cytokine release and 40% mortality, whereas CLP alone (85 ± 2 mg/dL) or sham mice receiving parenteral glucose (113 ± 3 mg/dL) all survived and were not hyperglycemic. Despite profound hyperglycemia, plasma insulin in the CLP glucose-infused mice (3.7 ± 1.2 ng/ml) was not higher than sham glucose infused mice (2.1 ± 0.3 ng/ml). Conclusions The combination of parenteral glucose support and the systemic inflammatory response in the acute phase of sepsis induces profound insulin resistance and impairs compensatory pancreatic insulin secretion, leading to the development of fulminant hyperglycemia.
Effect of the food traceability system for building trust: Price premium and buying behavior

Facing a series of food-related accidents, consumers worldwide have become more concerned with the safety of the food they consume. The Food Traceability System has been introduced in many countries to reduce the uncertainties originating in the food purchasing process by providing information about the entire food process, from farm to table, in terms of quality and safety. However, this relatively new information system has not yet been explored with an academic approach. The main goal of this study was to determine whether reduced uncertainty provides benefits for producers and consumers, thereby warranting the adoption of the food traceability system. We also analyzed the factors and mechanisms that explain consumer behavior within the system. We have modified and applied the uncertainty model of Pavlou et al. (MIS Quarterly 31(1):105–136, 2007) derived from the principal–agent perspective in order to fulfill our research objectives. Through a survey conducted in Korea, we found that Korean consumers were not only willing to purchase greater quantities of food, but also willing to pay more for food managed with the traceability system. The results of this study indicate that the mitigated uncertainty given by the traceability system plays a key role in price premium and purchase intention. In addition, mitigated uncertainty has a larger impact on purchase intention than on price premium, implying that consumers are inclined to buy more rather than pay more. These results provide valuable suggestions for producers for how to deal with increased costs resulting from adoption of the system. We also found that in the context of the Food Traceability System, perceived uncertainty was mitigated as a result of a reduced fear of seller opportunism originating from increased trust and reduced information asymmetry originating from increased product diagnosticity, informativeness, and trust. Reduced fear of seller opportunism had a stronger impact than reduced information asymmetry on perceived mitigated uncertainty.
Measurable and Immeasurable in Relativistic Quantum Information MSc Dissertation

The field of relativistic quantum information (RQI) has emerged from studying quantum information (QI) in a relativistic context. Since its inception it has become useful as a means of tackling problems ranging from QI processing techniques to black hole physics. The increased use of quantum fields in RQI research has necessitated a better understanding of measurement in QFT. An analysis of possible operators in QFT demonstrates that causality limits the number of possible quantum operations, arriving at definitions of operations which are causal, acausal or semicausal, and localisable, semilocalisable and nonlocal. Then an example is given where an idealised measurement, generalised from nonrelativistic quantum mechanics to QFT, produces superluminal signalling. Furthermore this problem persists even with arbitrarily long measurement times on spatially localised Gaussian-like wavepackets. Finally arguments are presented for strategies to avoid such unphysical behaviour before concluding that the path integral formulation of quantum mechanics is the most suitable for working with relativistic quantum field theory.
Artificial Intelligence in the NASA Volcano Sensorweb: Over a Decade in Operations

Volcanic activity can occur with little or no warning. Increasing numbers of space borne assets can enable coordinated measurements of volcanic events to enhance both scientific study and hazard response. We describe the use of space and ground measurements to target further measurements as part of a worldwide volcano monitoring system. We utilize a number of alert systems including the MODVOLC, GOESVOLC, US Air Force Weather Advisory, and Volcanic Ash Advisory Center (VAAC) alert systems. Additionally we use in-situ data from ground instrumentation at a number of volcanic sites, including Iceland. Artificial Intelligence Software plays a key role in the Volcano Sensorweb. First, several in-situ volcano monitoring networks use “intelligent” data interpretation software to trigger alerts that can then be used to allocate network resources, notify human agents, and even task space observations. Second, the Earth Observing One (EO-1) spacecraft uses Artificial Intelligence Software to automatically task the spacecraft to execute observations. Third, EO-1 also interprets thermal data onboard to allow for faster notifications of volcanic activity. Finally some data interpretation steps use intelligent software such as Random Decision Forest Methods used to automatically estimate volcanic plume heights in Worldview-2 Imagery.
Class-Discriminative Kernel Sparse Representation-Based Classification Using Multi-Objective Optimization

In this paper, we propose class-discriminative kernel sparse representation-based classification (KSRC) using multi-objective optimization (MOO) called KSRC 2.0. In sparse representation-based classification (SRC), both dictionary and residuals (reconstruction errors) play an important role in classifying a sample. Thus, discriminative dictionary and residuals are required to achieve high classification performance. To generate discriminative dictionary and residuals from training data sets, we formulate multi-objective functions via the Fisher discrimination criterion that minimizes distances within and maximizes distances between classes. Then, we solve them by using MOO, which can optimize conflicting objectives at the same time, and obtain component importance factors to make dictionary and residuals class-discriminative. Extensive experiments on publicly available databases demonstrate that the proposed KSRC 2.0 enhances the class separability of KSRC and achieves high classification performance.
On the Use of Voice Signals for Studying Sclerosis Disease

Multiple sclerosis (MS) is a chronic demyelinating autoimmune disease affecting the central nervous system. One of its manifestations concerns impaired speech, also known as dysarthria. In many cases, a proper speech evaluation can play an important role in the diagnosis of MS. The identification of abnormal voice patterns can provide valid support for a physician in the diagnosing and monitoring of this neurological disease. In this paper, we present a method for vocal signal analysis in patients affected by MS. The goal is to identify the dysarthria in MS patients to perform an early diagnosis of the disease and to monitor its progress. The proposed method provides the acquisition and analysis of vocal signals, aiming to perform feature extraction and to identify relevant patterns useful to impaired speech associated with MS. This method integrates two well-known methodologies, acoustic analysis and vowel metric methodology, to better define pathological compared to healthy voices. As a result, this method provides patterns that could be useful indicators for physicians in identifying patients affected by MS. Moreover, the proposed procedure could be a valid support in early diagnosis as well as in monitoring treatment success, thus improving a patient’s life quality.
Tracking transport-layer evolution with PATHspider

The ossification of the Internet protocol stack, due in large part to mangling of packets by middleboxes, has led to a relatively slow rate of change in today's Internet. We have developed the PATHspider active Internet measurement tool which performs onesided measurements of a variety of transport-layer features and extensions, to investigate these impairments to protocol evolution along an Internet path. Data collected with PATHspider can be used both to determine the degree of support for these features, as well as to detect connectivity issues caused by attempting to use them. The wider aim of this effort is to provide quantifiable input to protocol design and deployment choices that can be based on the level of impairment present in the Internet. This paper details PATHspider's design, and applies it to trace the evolution of deployment of two extensions to TCP, Explicit Congestion Notification (ECN) and the newer TCP Fast Open (TFO); as well as the degree of interference with the Differentiated Services Code Point (DSCP) carried in the IP header. Our ECN results, in particular, expand on a long-term study beginning in 2012, and show continued linear adoption of ECN. Automating PATHspider measurements has allowed us to collect far more data than in previous campaigns, allowing us to better distinguish ECN-linked connectivity failures from transient effects. Interestingly, we observe a correlation between ECN-linked connectivity failure in the core of the network with the presence of large-scale, heterogeneous Internet censorship infrastructure.
SELF-ASSEMBLY OF MICRO PUMPS WITH HIGH UNIFORMITY IN PERFORMANCE

In this paper we report a novel capillary-force-driven selfassembly technique which proceeds in an air environment. We demonstrate this technique for the self-assembly of piezoelectric driving elements (PZT) for diffuser valve micropumps: with the agitation of an orbital shaker, square PZT actuators self-align and mount to the hydrophilic trench binding sites with electric connections by heat curable lubricant oil and conductive physical contact between the PZT actuators and the substrate. 28 pumps are fabricated on a 4-inch bonded pyrex/silicon substrate. The resonance frequencies of all the pumps show high performance uniformity: the average is 80.1 kHz and standard deviation is 2.0 kHz. This technique provides fast, parallel and well-controlled bonding of bulk PZTs for micro pumps with yield ratio up to 100%.
Defining a Link between Gap Junction Communication, Proteolysis, and Cataract Formation*

Disruption of the connexin α3 (Cx46) gene (α3 (−/−)) in mice results in severe cataracts within the nuclear portion of the lens. These cataracts are associated with proteolytic processing of the abundant lens protein γ-crystallin, leading to its aggregation and subsequent opacification of the lens. The general cysteine protease inhibitor, E-64, blocked cataract formation and γ-crystallin cleavage in α3 (−/−) lenses. Using a new class of activity-based cysteine protease affinity probes, we identified the calcium-dependent proteases, m-calpain and Lp82, as the primary targets of E-64 in the lens. Profiling changes in protease activities throughout cataractogenesis indicated that Lp82 activity was dramatically increased in α3 (−/−) lenses and correlated both spatially and temporally with cataract formation. Increased Lp82 activity was due to calcium accumulation as a result of increased influx and decreased outflux of calcium ions in α3 (−/−) lenses. These data establish a role for α3 gap junctions in maintaining calcium homeostasis that in turn is required to control activity of the calcium-dependent cysteine protease Lp82, shown here to be a key initiator of the process of cataractogenesis.
Gender differences in the association between metabolic syndrome and periodontal disease: the Hisayama Study

Aims: Periodontal disease and metabolic syndrome (MS) are more prevalent in males than in females. However, whether there is a gender difference in the association between these health conditions has not yet been investigated. This study examined the gender difference in this association, considering the definition of periodontal disease. Materials and Methods: We recruited 1040 males and 1330 females, aged ≥40 years, with at least ten teeth from subjects of the 2007 Hisayama health examination. We performed a logistic regression analysis with various definitions of periodontal disease the dependent variable and MS as the independent variable. Following the analysis, the data were reanalysed with the structural equations model. Results: The logistic regression analysis suggested a stronger association between periodontal disease and MS in females than that in males when periodontal disease was more severely defined. When we constructed the structural equations model in each gender, the model showed a good fit to the data of females, suggesting the association between periodontal disease and MS in females, but not in males. Conclusions: Gender differences seem to exist in the association between periodontal disease and MS; MS might show a stronger association with periodontal disease in females than in males. Furuta M, Shimazaki Y, Takeshita T, Shibata Y, Akifusa S, Eshima N, Kiyohara Y, Ninomiya T, Hirakawa Y, Mukai N, Nagata M, Yamashita Y. Gender differences in the association between metabolic syndrome and periodontal disease: the Hisayama Study. J Clin Periodontol 2013; 40: 743–752. doi: 10.1111/jcpe.12119.
Changing legal systems: legal abrogations and annulments in Defeasible Logic

In this paper we investigate how to represent and reason about legal abrogations and annulments in Defeasible Logic. We examine some options that embed in this setting, and in similar rule-based systems, ideas from belief and base revision. In both cases, our conclusion is negative, which suggests to adopt a different logical model. This model expresses temporal aspects of legal rules, and distinguishes between two main timelines, one internal to a given temporal version of the legal system, and another relative to how the legal system evolves over time. Accordingly, we propose a temporal extension of Defeasible Logic suitable to express this model and to capture abrogation and annulment. We show that the proposed framework overcomes the difficulties discussed in regard to belief and base revision, and is sufficiently flexible to represent many of the subtleties characterizing legal abrogations and annulments.