Miracle-dz/UniFAR-FTUs huggingface dataset:
A Coevolution Approach for Database Schemas and Related Ontologies

Ontologies are one of the key technologies for data integration and meta-databases, by connecting databases on a semantical level. Still, everything fails when one of the database schemas changes: specific parts of the ontology have to be reconstructed by hand. We propose an approach that allows the database schema and the ontology to change and evolve, without ever losing their connection to each other. We call that "coevolution". Coevolution cannot be completely automated, as data definition languages do not define the change of semantical concepts, but only technical schema changes. In this paper we present our mapping of database schemas to ontologies, describe how these ontologies can be enriched by semantical information and show our approach to transfer schema changes to the ontology
Network traffic shaping based on prediction of polynomial trend self-similar time series

In the present paper shaping algorithms development is considered. Most attention is paid to shaping algorithms based on network traffic prediction. Estimates of prediction-based shapers efficiency for different forecasting techniques are obtained. It is shown that a shaping algorithm should take into account both the prehistory and future values of the traffic in order to achieve the maximum of its operation efficiency. The paper presents an adaptive linear predictor of the fractal network traffic and compares it to the simple autoregressive predictor. According to our simulation results, the autoregressive shaper grants significantly smoother output while the adaptive predictor grants significantly lower packet loss ratio.
Identification of a Repressor of a Truncated Denitrification Pathway in Moraxella catarrhalis

ABSTRACT Growth of Moraxella catarrhalis in a biofilm resulted in marked upregulation of two open reading frames (ORFs), aniA and norB, predicted to encode a nitrite reductase and a nitric oxide reductase, respectively (W. Wang, L. Reitzer, D. A. Rasko, M. M. Pearson, R. J. Blick, C. Laurence, and E. J. Hansen, Infect. Immun. 75:4959-4971, 2007). An ORF designated nsrR, which was located between aniA and norB, was shown to encode a predicted transcriptional regulator. Inactivation of nsrR resulted in increased expression of aniA and norB in three different M. catarrhalis strains, as measured by both DNA microarray analysis and quantitative reverse transcriptase PCR. Provision of a wild-type nsrR gene in trans in an nsrR mutant resulted in decreased expression of the AniA protein. DNA microarray analysis revealed that two other ORFs (MC ORF 683 and MC ORF 1550) were also consistently upregulated in an nsrR mutant. Consumption of both nitrite and nitric oxide occurred more rapidly with cells of an nsrR mutant than with wild-type cells. However, growth of nsrR mutants was completely inhibited by a low level of sodium nitrite. This inhibition of growth by nitrite was significantly reversed by introduction of an aniA mutation into the nsrR mutant and was completely reversed by the presence of a wild-type nsrR gene in trans. NsrR regulation of the expression of aniA was sensitive to nitrite, whereas NsrR regulation of norB was sensitive to nitric oxide.
Dynamic security credentials PANA-based provisioning for IoT smart objects

The integration of physical devices into the Internet infrastructure raises significant security concerns, since many of the assumptions of the current Internet cannot be maintained in the so-called IoT. Due to the scale and requirements of these devices, the IoT should provide automated and self-managing mechanisms coping with security requirements during the life-cycle of smart objects, in order to foster the deployment of IoT scenarios. In this direction, this work addresses the bootstrapping of a smart object as a crucial stage in its lifecycle, through the use and extension of PANA as an IoT bootstrapping protocol, to enable a security credentials provisioning phase for secure M2M communications. Additionally, a set of initial evaluation results is also provided as part of our ongoing work in this area.
Characteristics of the sequence effect in Parkinson's disease

The sequence effect (SE) in Parkinson's disease (PD) is progressive slowing of sequential movements. It is a feature of bradykinesia, but is separate from a general slowness without deterioration over time. It is commonly seen in PD, but its physiology is unclear. We measured general slowness and the SE separately with a computer‐based, modified Purdue pegboard in 11 patients with advanced PD. We conducted a placebo‐controlled, four‐way crossover study to learn whether levodopa and repetitive transcranial magnetic stimulation (rTMS) could improve general slowness or the SE. We also examined the correlation between the SE and clinical fatigue. Levodopa alone and rTMS alone improved general slowness, but rTMS showed no additive effect on levodopa. Levodopa alone, rTMS alone, and their combination did not alleviate the SE. There was no correlation between the SE and fatigue. This study suggests that dopaminergic dysfunction and abnormal motor cortex excitability are not the relevant mechanisms for the SE. Additionally, the SE is not a component of clinical fatigue. Further work is needed to establish the physiology and clinical relevance of the SE. © 2010 Movement Disorder Society.
Estimation of Inertial Sensor to Camera Rotation from Single Axis Motion

The aim of the present work is to define a calibration framework to estimate the relative orientation between a camera and an inertial orientation sensor AHRS (Attitude Heading Reference System). Many applications in computer vision and in mixed reality frequently work in cooperation with such class of inertial sensors, in order to increase the accuracy and the reliability of their results. In this context the heterogeneous measurements must be represented in a unique common reference frame (rf.) in order to carry out a joint processing. The basic framework is given by the estimation of the vertical direction, defined by a 3D vector expressed in the camera rf. as well as in the AHRS rf. In this paper a new approach has been adopted to retrieve such direction by using different geometrical entities which may be inferred from the analysis of single axis motion projective geometry. Their performances have been evaluated on simulated data as well as on real data.
Family Functioning in Families with Alcohol and Other Drug Addiction

Alcohol and other drug addiction, a societal problem that is steadily growing, contributes to the destruction of families and communities. Research has identified a strong connection between disrupted family relationships and alcohol and other drug addiction. Individual in-depth interviews were undertaken with 12 participants who were residents and ex-residents in the Higher Ground Alcohol and Drug Rehabilitation Trust, Auckland, New Zealand. These interviews were analysed using a qualitative framework. The findings are discussed in the context of a broad range of academic research on addiction and its effects on families. The results show that the majority of participants had experienced painful and traumatic childhoods in their families of origin, which contributed to their subsequent addictive behaviour and which they felt had affected their current familial relationships. All participants and their families had suffered from various forms of family disruption, such as loss of custody of their children, loss of employment, marital breakdown, physical and psychological abuse, depression and ill health. Some participants had also committed drug-related crimes and experienced accidents as a result of their addictions, which also affected their relationships with their families.
Wavelength demultiplexing by chirped waveguide gratings

The spectral response of a chirped sinusoidal surface relief grating in an optical waveguide has been studied by means of Local Normal Mode Expansion theory. A matrix technique has been applied to account for the varying grating period. The grating is divided into segments with constant periods and coupling coefficients. Nonslanted grating is considered in a first-order diffraction. Also, contradirectional coupling between guided modes in phase synchronism at an arbitrary angle of incidence is considered. Performance considerations include TE-TE, TE- TM, and TM-TM mode coupling for different grating geometry and waveguide parameters. We show the effect of geometry and waveguide parameters on the performance of the chirped grating as a wavelength demultiplexer. Also, we demonstrate how the filtering and demultiplexing characteristics and the spectral shift between different polarization modes can be controlled.
Inter-rater reliability of modified modified Ashworth scale in the assessment of plantar flexor muscle spasticity in patients with spinal cord injury.

INTRODUCTION Spasticity occurs in disorders of the central nervous system such as stroke, spinal cord injury (SCI), multiple sclerosis and traumatic brain injury. The recently developed clinical measurement for the measurement of spasticity is the Modified Modified Ashworth Scale (MMAS) PURPOSE OF STUDY: The purpose of this study is to determine the inter-rater reliability of the MMAS in the assessment of plantar flexor spasticity in patients with SCI. METHODOLOGY Thirty-eight subjects (32 males and six females, mean age 31.9 ± 12.6 years) were recruited for the study. Excluded from the study were patients with contracture in the lower limb and where passive movements were contraindicated. PROCEDURE Each patient was assessed by two raters in a single session. After the performance of the procedure by the first assessor and rating of the patient's muscle tone with the MMAS, the same procedure was repeated by the second assessor after 1 hour. The evaluation was carried out in side-lying position. The extent of agreement was analysed by non-weighted Cohen kappa. RESULTS The agreement between the raters was good (soleus - ĸ: 0.75, SE = 0 .084, p < 0.0001, gastrocnemius - ĸ:0.70, SE = 0.105, p < 0.0001). CONCLUSION The MMAS has good inter-rater reliability in the assessment of plantar flexor muscle spasticity in patients with SCI.
Allele polymorphisms of tumor integrins correlate with peritoneal carcinosis capability of gastric cancer cells in radically resected patients.

BACKGROUND Preclinical studies suggested that integrins are relevant for gastric cancer diffusion. We investigated integrins polymorphisms role in determining peritoneal carcinosis or hematogenous metastases in radically resected gastric cancer. PATIENTS AND METHODS Integrins genotyping was carried out on pT3 radically resected gastric tumors recurring with either peritoneal-only carcinosis or hematogenous metastases. RESULTS The following factors resulted independently associated with peritoneal carcinosis or hematogenous metastases: the A genotype of rs2269772 (ITGA3) [odds ratio (OR) for peritoneal carcinosis: 22.2, 95% confidence interval 1.2-40, P=0.03], the G genotype of rs2269772 (ITGA3) (OR for hematogenous metastases: 5.5, 95% confidence interval 2.2-14.15, P=0.0003), the C genotype of rs11902171 (ITGV) (OR for peritoneal carcinosis: 6.8, 95% confidence interval 1.3-33.4, P=0.01), the G genotype of rs11902171 (ITGV) (OR for hematogenous metastases: 2.5, 95% confidence interval 1.1-5.7, P = 0.02), diffuse histology (OR for peritoneal carcinosis: 4.7, 95% confidence interval 1.9-11.3, P=0.0005) and intestinal histology (OR for hematogenous metastases: 4.2, 95% confidence interval 1.9-9.9, P=0.0008). CONCLUSIONS Tumor histology represents a crucial issue conditioning tumoral behavior; genotyping of rs2269772 (ITGA3) and rs11902171 (ITGV) may be a further asset in the definition of high-risk patients for peritoneal carcinosis among those relapsing after curative resection. The selection tool deriving from this analysis may allow an optimal use of innovative treatment strategies.
Neofunction of ACVR1 in fibrodysplasia ossificans progressiva

Significance By utilizing patient-specific induced pluripotent stem cells (iPSCs) of fibrodysplasia ossificans progressiva (FOP) and gene-corrected (rescued) FOP-iPSCs, we discovered a novel mechanism in ectopic bone formation: The disease-causing mutation endows ACVR1 with the ability to transmit the signal of an unexpected ligand, Activin-A. We believe this is a milestone study for FOP research and provides a novel platform for searching therapeutic targets of this intractable disease. Fibrodysplasia ossificans progressiva (FOP) is a rare genetic disease characterized by extraskeletal bone formation through endochondral ossification. FOP patients harbor point mutations in ACVR1 (also known as ALK2), a type I receptor for bone morphogenetic protein (BMP). Two mechanisms of mutated ACVR1 (FOP-ACVR1) have been proposed: ligand-independent constitutive activity and ligand-dependent hyperactivity in BMP signaling. Here, by using FOP patient-derived induced pluripotent stem cells (FOP-iPSCs), we report a third mechanism, where FOP-ACVR1 abnormally transduces BMP signaling in response to Activin-A, a molecule that normally transduces TGF-β signaling but not BMP signaling. Activin-A enhanced the chondrogenesis of induced mesenchymal stromal cells derived from FOP-iPSCs (FOP-iMSCs) via aberrant activation of BMP signaling in addition to the normal activation of TGF-β signaling in vitro, and induced endochondral ossification of FOP-iMSCs in vivo. These results uncover a novel mechanism of extraskeletal bone formation in FOP and provide a potential new therapeutic strategy for FOP.
Improving packet transport network efficiency using capacity aware routing

The role of transport in our society is ever growing with increasing globalisation, and new methods are needed to keep up with demand within the frame of available resources. This means using technological advancements in order to utilise currently available capacity to its fullest. In this thesis we focus on improving efficiency of routed packet transport networks by using routing algorithms that take into account real time network package load data. Given a transport network that moves packets between stations in the network, we aim to decrease packet costs and increase the throughput of the network. We do this by utilising data on the network load in order to find more efficient paths for the packets to travel on. For this we develop methods and software to simulate and measure different routing schemes, enabling us to compare how the usage of the network load data affects the network performance. This work resulted in the capacity reserving router, which keeps track of network resource usage in order to avoid congestions under heavier loads. This method was able to increase the network efficiency in our simulations by up to 100%, compared to similar routing without capacity reserving. Additionally, the cost of individual packets decreased by up to 50% under heavy loads. These results enable more efficient usage of packet routing in transport networks.
Biomolecular Simulation of Base Excision Repair and Protein Signaling

The goal of the Biomolecular Simulation of Base Excision Repair and Protein Signaling project is to enhance our understanding of the mechanism of human polymerase-β, one of the key enzymes in base excision repair (BER) and the cell-signaling enzymes cyclic-AMP-dependent protein kinase. This work used molecular modeling and simulation studies to specifically focus on the • dynamics of DNA and damaged DNA • dynamics and energetics of base flipping in DNA • mechanism and fidelity of nucleotide insertion by BER enzyme human polymerase-β • mechanism and inhibitor design for cyclic-AMP-dependent protein kinase. Molecular dynamics simulations and electronic structure calculations have been performed using the computer resources at the Molecular Science Computing Facility at the Environmental Molecular Sciences Laboratory.
A unified approach to approximating resource allocation and scheduling

We present a general framework for solving resource allocation and scheduling problems. Given a resource of fixed size, we present algorithms that approximate the maximum throughput or the minimum loss by a constant factor. Our approximation factors apply to many problems, among which are: (i) real-time scheduling of jobs on parallel machines, (ii) bandwidth allocation for sessions between two endpoints, (iii) general caching, (iv) dynamic storage allocation, and (v) bandwidth allocation on optical line and ring topologies. For some of these problems we provide the first constant factor approximation algorithm. Our algorithms are simple and efficient and are based on the local-ratio technique. We note that they can equivalently be interpreted within the primal-dual schema.
sxtA-Based Quantitative Molecular Assay To Identify Saxitoxin-Producing Harmful Algal Blooms in Marine Waters

ABSTRACT The recent identification of genes involved in the production of the potent neurotoxin and keystone metabolite saxitoxin (STX) in marine eukaryotic phytoplankton has allowed us for the first time to develop molecular genetic methods to investigate the chemical ecology of harmful algal blooms in situ. We present a novel method for detecting and quantifying the potential for STX production in marine environmental samples. Our assay detects a domain of the gene sxtA that encodes a unique enzyme putatively involved in the sxt pathway in marine dinoflagellates, sxtA4. A product of the correct size was recovered from nine strains of four species of STX-producing Alexandrium and Gymnodinium catenatum and was not detected in the non-STX-producing Alexandrium species, other dinoflagellate cultures, or an environmental sample that did not contain known STX-producing species. However, sxtA4 was also detected in the non-STX-producing strain of Alexandrium tamarense, Tasmanian ribotype. We investigated the copy number of sxtA4 in three strains of Alexandrium catenella and found it to be relatively constant among strains. Using our novel method, we detected and quantified sxtA4 in three environmental blooms of Alexandrium catenella that led to STX uptake in oysters. We conclude that this method shows promise as an accurate, fast, and cost-effective means of quantifying the potential for STX production in marine samples and will be useful for biological oceanographic research and harmful algal bloom monitoring.
A 10-bit Low-Power Small-Area High-Swing CMOS DAC

The design and measurements of a prototype general purpose digital to analog converter for readout systems in high energy physics experiments are presented. The main goals for the proposed DAC are low power consumption, small die area and high-swing voltage output. The 10-bit DAC design is based on a current steering architecture which includes a high-swing class AB output amplifier. The prototype ASIC is fabricated using 2P-4M 0.35- ¿m technology. Measurements of maximum differential (DNL) and integral (INL) nonlinearity both show 0.42 LSB. The total power consumption is below 0.6 mW while the core area is 0.18 mm2.
Student and supervisor perspectives in a computer-mediated research relationship

A brief narrative description of the journal article, document, or resource. This paper presents the reflective perspectives of the student and supervisor in a successful computer-mediated research relationship at Deakin University (Australia). Key contributing factors are discussed in a dialog format covering the role of computer-mediated communication (CMC), the projection of social presence, student self-efficacy beliefs, the role of information and communication technology (ICT), and interaction in online professional networks. Drawing on relevant theory, inherent challenges are addressed, informing some concluding suggestions as to how supervision might become more responsive to the emergent forms of research learning being experienced by escalating numbers of postgraduate students studying at a distance via ICT.
Monitoring of Human Cytomegalovirus and Virus-Specific T-Cell Response in Young Patients Receiving Allogeneic Hematopoietic Stem Cell Transplantation

In allogeneic hematopoietic stem-cell transplantation (HSCT) recipients, outcome of human cytomegalovirus (HCMV) infection results from balance between viral load/replication and pathogen-specific T-cell response. Using a cut-off of 30,000 HCMV DNA copies/ml blood for pre-emptive therapy and cut-offs of 1 and 3 virus-specific CD4+ and CD8+ T cells/µl blood for T-cell protection, we conducted in 131 young patients a prospective 3-year study aimed at verifying whether achievement of such immunological cut-offs protects from HCMV disease. In the first three months after transplantation, 55/89 (62%) HCMV-seropositive patients had infection and 36/55 (65%) were treated pre-emptively, whereas only 7/42 (17%) HCMV-seronegative patients developed infection and 3/7 (43%) were treated. After 12 months, 76 HCMV-seropositive and 9 HCMV-seronegative patients (cumulative incidence: 90% and 21%, respectively) displayed protective HCMV-specific immunity. Eighty of these 85 (95%) patients showed spontaneous control of HCMV infection without additional treatment. Five patients after reaching protective T-cell levels needed pre-emptive therapy, because they developed graft-versus-host disease (GvHD). HSCT recipients reconstituting protective levels of HCMV-specific T-cells in the absence of GvHD are no longer at risk for HCMV disease, at least within 3 years after transplantation. The decision to treat HCMV infection in young HSCT recipients may be taken by combining virological and immunological findings.
Outer membrane permeation of Bacteroides fragilis by cephalosporins

Outer membrane permeation of Bacteroides fragilis by cephalosporins was examined by a previously described method. The permeation parameters of cephalosporins in B. fragilis were close to 10(-5) cm3/min per microgram of cell dry weight. These values were about an order of magnitude lower than those in Escherichia coli. In B. fragilis, the permeation was not directly proportional to the hydrophilicity of cephalosporins, and the ion selectivity was weak.
A Comparison of Multiple Testing Procedures for the Gold Standard Non-Inferiority Trial

For the three-arm parallel-group design, several procedures have been proposed in the literature to control for the multiple type I error when all groups are to be statistically compared. Mere statements regarding the rejection of the null hypotheses are not satisfactory, but instead confidence intervals are more desirable. For this purpose, the procedure by Koch and Röhmel (2004) is modified and the theoretical reasoning behind it is given. However, one combination of effects occurs where control of the multiple type I error cannot be guaranteed. This pathologic case is discussed theoretically and further investigated in a simulation study.