Miracle-dz/UniFAR-FTUs huggingface dataset:
A dimension-independent extrusion algorithm using generalised maps

One solution to the integration of additional characteristics, for example, time and scale, into GIS data sets is to model them as extra geometric dimensions perpendicular to the spatial ones, creating a higher-dimensional model. While this approach has been previously described and advocated, it is scarcely used in practice because of a lack of high-level construction algorithms and accompanying implementations. We present in this paper a dimension-independent extrusion algorithm permitting us to construct from any (n–1)-dimensional linear cell complex represented as a generalised map, an n-dimensional one by assigning to each (n–1)-cell one or more intervals where it exists along the nth dimension. We have implemented the algorithm in C++11 using CGAL, made the source code publicly available and tested it in experiments using real-world 2D GIS data sets which were extruded to construct up to 5D models.
Back to the future: Brake reaction times for manual and automated vehicles

Rear-end collisions are often quoted as being a major cause of road traffic accidents. In response to this, a great deal of ergonomics research effort has been directed towards the analysis of brake reaction times. However, the engineering solution has been to develop advanced systems for longitudinal control, which, it is argued, will mitigate the problem of rear-end collisions. So far, though, there have been few empirical studies to determine how brake reaction times will be affected by such vehicle automation. This paper presents a literature review summarizing the current state of knowledge about driver responses in non-automated vehicles. The review covers driver factors, vehicle factors and situational factors. Following the review, some empirical data are presented from a driving simulator experiment assessing brake reaction times of skilled and unskilled drivers under two different levels of automation. When compared to previous data gathered during manual driving, there seems to be a striking increase in reaction times for these automated conditions. Implications for the design and safety of automated vehicle systems are discussed.
A compact highly-selective filter inspired by Negative-Refractive-Index Transmission Lines

A Negative-Refractive-Index Transmission-Line (NRI-TL) inspired filter is realized by replacing the traditional shunt inductive loading with a series LC resonator to ground. Design equations for the filter are compared with full-wave simulations and experimental results are presented for a highly-selective folded implementation exhibiting 5% bandwidth at 2.03 GHz , 1 dB insertion-loss and a maximum band-edge slope of 2.15 dB/MHz.
Plastic Fibre Reinforced Soil Blocks as a Sustainable Building Material

Solid waste management, especially the huge quantity of waste plastics, is one of the major environmental concerns nowadays. Their employability in block making in the form of fibres, as one of the methods of waste management, can be investigated through a fundamental research. This paper highlights the salient observations from a systematic investigation on the effect of embedded fibre from plastic waste on the performance of stabilised mud blocks. Stabilisation of the soil was done by adding cement, lime and their combination. Plastic fibre in chopped form from carry bags and mineral water bottles were added (0.1% & 0.2% by weight of soil) as reinforcement. The blocks were tested for density, and compressive strength, and observed failure patterns were analysed. Blocks with 0.1% of plastic fibres showed an increase in strength of about 3 to 10%. From the observations of failure pattern it can be concluded that benefits of fibre reinforcement includes both improved ductility in comparison with raw blocks and inhibition of crack propogation after its initial formation.
Volumetric imaging of erythrocytes using label‐free multiphoton photoacoustic microscopy

Photoacoustic microscopy (PAM) is an imaging modality well suited to mapping vasculature and other strong absorbers in tissue. However, one of the primary drawbacks to PAM when used for high‐resolution imaging is the relatively poor axial resolution due to the inverse dependence on the transducer bandwidth. While submicron lateral resolution PAM can be achieved by tightly focusing the excitation light, the axial resolution is fundamentally limited to 10s of microns for typical transducer frequencies. Here we present a multiphoton PAM technique called transient absorption ultrasonic microscopy (TAUM), which results in a completely optically resolved voxel with an experimentally measured axial resolution of 1.5 microns. This technique is demonstrated by imaging individual red blood cells in three dimensions in blood smear and ex vivo tissues. To the best of our knowledge, this is the first demonstration of fully resolved, volumetric photoacoustic imaging of erythrocytes. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Using structured analysis and design technique (SADT) for simulation conceptual modelling

ed diagram of the conceptual model As per table 6.7, participant A produced the abstracted diagram of figure 6.3. Figure 6.3: Abstracted diagram of conceptual model (participant A) A1 Load TV to Pallet (OP10) R1 A2 LCD assembly (OP20) R1+R2 A3 Circuit board assembly R1+R3 A4 Electrical assembly
[Suicide and suicidal behavior among asylum seekers in Denmark during the period 2001-2003. A retrospective study].

INTRODUCTION Our aim was to examine suicidal behaviours among asylum seekers in Denmark. MATERIALS AND METHODS A retrospective quantitative analysis of data from reports to the Danish Red Cross Asylum Department on suicidal behaviours among persons over 15 years of age in the period 2001-2003 and from 54 medical records of suicidal asylum seekers in Denmark in 2001 was carried out. RESULTS The number of suicide attempts by asylum seekers in 2001 was 3.4 times higher than by Danish residents. Furthermore, the rate of suicide attempts by asylum seekers grew in the following two years. Suicidal behaviours are most frequent among asylum seekers between 30 and 39 years of age. There are national differences. The preferred method of suicide attempt is intake of medicine. Stress-related diagnoses constitute three fourths of all diagnoses. One analysis suggests that the long waiting time (average 20.8 months) faced by asylum seekers combined with rejection of asylum cases may trigger a rapid suicidal reaction. Other factors may also be active, as 44% of suicide attempts occur within six months after arrival in the country. DISCUSSION The results are discussed in relation to other research on the vulnerability of refugees, immigrants and asylum seekers and also in relation to length of waiting time, growing mental morbidity and the increasing number of rejections of asylum applications during recent years, a period characterized by a reduction of staff at the asylum centers. It is recommended that prevention of suicidal behaviour shall be given higher legal and administrative priority.
Investigations with phage-host system [ H 3 : H 3 / 1 ]

When host bacterium H3 is cultivated in artificial seawater a t a concentration of 0.6 mg organic nutrients ml-l, its reaction to infection by phage H3/1 changes dramatically with the duration of incubation before phage attack. Cells infected when stlll In their logar~thmic growth phase rapidly produce progeny phage until breakdown of the phage-sensitive population. For cells infected after entering the stationary phase, rate and extent of phage propagation by resting cells decreases for some time, but both parameters rather suddenly increase again for cells infected after prolonged ~ncubation. Phage production may then reach the same level attained by cells infected during logarithmic growth phase; although, with increasing phage concentration, resting cells very effectively become protected from phage attack by pseudolysogeny. This course of events is mainly influenced by the method of incubation of the host (shaken vs still), by the age of the cells before ~nfection, and presumedly by changes in physiological traits of the bacteria when serially subcultured for extended periods of time. The reduct~on in volume of bacterial culture by repeated w~thdrawal of aliquots was found to be of minor importance; however, phaga production was measurably affected by the transfer of cells to fresh receptacles. With cells which entered thcir stationary phase up to 36 h before infection, a n initial phage concentration of between 10 and 10" PFIJ (plaque forming units) ml-' was found to determine the extent, but not the rate, of phage production. The aforementioned observations were also made with cells stal-ved for 3, 8, and 22 additional days before inoculation, except with ~nitial PFU concentrations of 10 and 10' PFU ml-l, when an appreciable increase in phage production was found. In cell suspensions seeded with phage 48 d after set up of the experiment, the highest phage production was found with the lowest initial phage concentration and vice versa. This finding, i.e. the inverse relationship between production and initial concentrat~on, is not in agreement with any of the current hypotheses concerning bacteriophage ecology. K E Y WORDS: Virus. Phage Bacteria. Reproduction
THE VERTICAL TRANSMISSION OF HUMAN IMMUNODEFICIENCY VIRUS TYPE 1: Molecular and Biological Properties of the Virus

Abstract The vertical (mother-to-infant) transmission of human immunodeficiency virus type 1 (HIV-1) occurs at an estimated rate of more than 30% and is the major cause of AIDS in children. Numerous maternal parameters, including advanced clinical stages, low CD4+ lymphocyte counts, high viral load, immune response, and disease progression have been implicated in an increased risk of vertical transmission. While the use of antiretroviral therapy (ART) during pregnancy has been shown to reduce the risk of vertical transmission, selective transmission of ART-resistant mutants has also been documented. Elucidation of the molecular mechanisms of vertical transmission might provide relevant information for the development of effective strategies for prevention and treatment. By using HIV-1 infected mother-infant pairs as a transmitter-recipient model, the minor genotypes of HIV-1 with macrophage-tropic and non-syncytium-inducing phenotypes (R5 viruses) in infected mothers were found to be transmitted to their infants and were initially maintained in the infants with the same properties. In addition, the transmission of major and multiple genotypes has been suggested. Furthermore, HIV-1 sequences found in non-transmitting mothers (mothers who failed to transmit HIV-1 to their infants in the absence of ART) were less heterogeneous than those from transmitting mothers, suggesting that viral heterogeneity may play an important role in vertical transmission. In the analysis of other regions of the HIV-1 genome, we have shown a high conservation of intact and functional gag p17, vif, vpr, vpu, tat, and nef open reading frames following mother-to-infant transmission. Moreover, the accessory genes, vif and vpr, were less functionally conserved in the isolates of non-transmitting mothers than transmitting mothers and their infants. We, therefore, should target the properties of transmitted viruses to develop new and more effective strategies for the prevention and treatment of HIV-1 infection.
Targeting nitric oxide in the subacute restorative treatment of ischemic stroke

Introduction: Stroke remains the leading cause of adult disability. Thus, it is imperative to develop restorative therapies for ischemic stroke designed specifically to treat the intact brain tissue to stimulate functional benefit. Therapies targeting amplification of brain repair processes with nitric oxide (NO) donors and phosphodiesterase type 5 (PDE5) inhibitors in preclinical studies are emerging and showing improvement of functional recovery after stroke. Areas covered: This review will mainly cover the effect of NO donors, which produce NO, and PDE5 inhibitors, which elevate cyclic guanosine 3′,5′-monophosphate (cGMP), on neural restorative events in ischemic brain and highlight mechanisms underlying their restorative therapeutic activity. Expert opinion: During stroke recovery, interwoven restorative events occur in ischemic brain, which include angiogenesis, neurogenesis, oligodendrogenesis, astrogliosis and neurite outgrowth. Emerging preclinical data indicate that restorative therapies targeting multiple parenchymal cells including neural stem cells, cerebral endothelial cells, astrocytes, oligodendrocytes, neurons would be more effective than agents with a single cell target. Preclinical data suggest that elevated cGMP levels induced by NO donors and PDE5 inhibitors act on cerebral endothelial cells, neural stem cells and oligodendrocyte progenitor cells to enhance stroke-induced angiogenesis, neurogenesis and oligodendrogenesis, respectively. These interacting remodeling events collectively improve neurological function after stroke.
Current methods of testing for human papillomavirus.

Human papillomavirus DNA testing is gaining wider acceptance, yet the majority of testing is still undertaken in the research setting using protocols that are unsuitable for clinical diagnostic laboratories. Large-scale clinical human papillomavirus DNA testing is likely to be introduced as an adjunct to cervical cytology, so the cytology laboratory is an appropriate place for it to be undertaken. This poses a challenge for any human papillomavirus DNA test since it will be performed by technicians not specifically trained in virology or molecular biology, and will need to produce consistently reliable results in this setting. This is only realistically possible with a standardized and quality-controlled, commercially produced human papillomavirus DNA test. There is currently only one such commercially available assay, although there are a number of research-based tests that could logically lead to additional commercial products. The technological basis of these assays, together with available performance data, is reviewed in this chapter and the clinical utility of the tests is evaluated.
Automatic Annotation of Bacterial Community Sequences and Application to Infections Diagnostic

To annotate bacterial sequences from an environmental sample, we have developed an automatic annotation pipeline Fgenesb_annotator that includes self-training of gene-finding parameters, prediction of CDS, RNA genes, operons, promoters and terminators. New version of pipeline includes frame shift corrections and special module with improved prediction accuracy of ribosomal proteins. To analyze next-generation sequencing data we have developed OligiZip assembler and Transomics pipeline that provide solutions to the following tasks: 1) de novo reconstruction of genomic sequence; 2) reconstruction of sequence with a reference genome; 3) SNP discovery; 4) mapping RNA-Seq data to a reference genome, assemble them into alternative transcripts and quantify the abundance of these transcripts. Using the OligoZip assembler and gene Fgenesb pipeline we have developed a novel computational approach of identification toxic and nontoxic bacterial serotypes using next-generation sequencing data. It can be used for detection of bacterial infections in wounds, water or food contamination.
Isolation and Characterization of Agar-degrading Paenibacillus spp. Associated with the Rhizosphere of Spinach

Agar-degrading bacteria in spinach plant roots cultivated in five soils were screened, and four strains of Paenibacillus sp. were isolated from roots cultivated in three soils. The agar-degrading bacteria accounted for 1.3% to 2.5% of the total bacteria on the roots. In contrast, no agar-degrading colony was detected in any soil (non-rhizosphere soil samples) by the plate dilution method, and thus these agar-degrading bacteria may specifically inhabit plant roots. All isolates produced extracellular agarase, and could grow using agar in the culture medium as the sole carbon source. Zymogram analyses of agarase showed that all four isolates extracellularly secreted multiple agarases (75-160 kDa). In addition, the isolates degraded not only agar but also various plant polysaccharides, i.e., cellulose, pectin, starch, and xylan.
Modelling and analysing the TLS protocol using Casper and FDR

This paper analyses the TLS Handshake protocol in a progressive manner, by gradually building the protocol's messages and message fields. Messages constituting the TLS protocol are described by Casper, a compiler for the analysis of security protocols. FDR, a model checking tool is then used to test whether the protocol achieves its goals. It has been shown that TLS achieves its security goals for the systems tested. By using this progressive approach of the TLS Handshake analysis, this paper identifies the importance of each message and message field to the overall achievement of the security goal of the TLS protocol. The study also shows that the TLS protocol contains much redundancy. A few important points that show how TLS has been carefully designed to thwart some attacks that have appeared in many of the previous security protocols are also emphasized.
Clustering of Metagenomic Data by Combining Different Distance Functions

Metagenomics allows researchers to sequence genomes of many microorganisms directly from a natural environment, without the need to isolate them. The results of this type of sequencing are a huge set of DNA fragments of different organisms. These results pose a new computational challenge to identify the groups of DNA sequences that belong to the same organism. Even when there are big databases of known species genomes and some similarity-based supervised algorithms, they only have a very small representation of existing microorganisms and the process to identify a set of short fragments is very time consuming. For all those reasons, the reconstruction and identification process in a set of metagenomics fragments has a binning process, as a preprocess step, in order to join fragments into groups of the same taxonomic levels. In this paper, we propose a clustering algorithm based on k-means iterative and a consensus of clusters using different distance functions. The results achieved by the proposed method are divided using different lengths of sequences and different combinations of distances. The proposed method outperforms the simple and iterative k-means.
Enhancement of phosphorylation and transcriptional activity of the glucocorticoid receptor in human synovial fibroblasts by nimesulide, a preferential cyclooxygenase 2 inhibitor.

OBJECTIVE To examine the effect of 2 nonsteroidal antiinflammatory drugs (NSAIDs), nimesulide (NIM), a preferential cyclooxygenase 2 (COX-2) inhibitor, and naproxen (NAP), on the functional parameters and transcriptional activity of the glucocorticoid receptor (GR) system in cultured human synovial fibroblasts (HSF). METHODS HSF were incubated with NIM (0.3, 3, and 30 microg/ml), NAP (15, 30, and 90 microg/ml), and dexamethasone (DEX; 0.01, 0.1, and 1 microM) on a time- and dose-dependent basis. The numbers of GR binding sites per cell were determined by radioligand receptor assay. Total cellular, cytoplasmic, or nuclear GR protein was measured by Western analysis using a specific anti-human GR antibody. Phosphorylation of GR was determined by specific immunoprecipitation of protein extracts from 32P-orthophosphate-labeled HSF. Mitogen-activated protein kinase p44/42 (MAPK) phosphorylation was followed by Western analysis using a specific anti-phosphoMAPK antibody. Levels of activated nuclear GR capable of binding specifically to a 32P-labeled oligonucleotide harboring the glucocorticoid/hormone response element (GRE) were evaluated by gel electrophoretic mobility shift analysis. The effects of NIM and DEX on transcriptional activation of the mouse mammary tumor virus (MMTV) promoter was determined by transfecting HSF with MMTV-luciferase (reporter gene) constructs. RESULTS NIM had no effect on the number of GR binding sites, in contrast to NAP and DEX. NIM and NAP did not influence cellular GR protein levels or nucleocytoplasmic shuttling, although DEX lowered GR messenger RNA and protein levels after 48 hours. NIM, but not NAP, markedly increased MAPK phosphorylation (suggesting an increase in MAPK cascade activity), GR phosphorylation, GR binding to GRE, and transcriptional activation of MMTV promoter through the GRE site in the promoter. CONCLUSION This study is the first to report that the antiinflammatory effects of NIM, an NSAID, may be partly related to its activation of the GR system.
Application of the skin and bone integrated pylon with titanium oxide nanotubes and seeded with dermal fibroblasts

Background: Direct skeletal attachment of limb prostheses is associated with high rate of transcutaneous infection and loosening of the fixture in the medullary canal prompting for careful assessment of various means for enhancing the skin-device and bone-device interface. The skin and bone integrated pylon system constitutes a technological platform for different modifications being evaluated previously. Objectives: The current study assessed the combination of nano-treatment skin and bone integrated pylon with its pre-seeding with dermal fibroblasts. We hypothesized that this combination will enhance cell interaction with skin and bone integrated pylon compared to nano-treatment and the fibroblast seeding when done separately. Study design: The feasibility and safety of in-bone implantation of the skin and bone integrated pylon with nanotubes was investigated in vitro and in vivo in the animal model. Methods: TiO2 nanotubes were fabricated on the skin and bone integrated pylon, and the fibroblasts taken from rabbit’s skin were cultured on the pylons before implantation. Results: The in vitro experiments demonstrated higher cellular density in the samples with a nanotubular surface than in the non-modified pylons used as control. There were no postoperative complications in any of the animals during the 6-month observation period. Subsequent scanning electron microscopy of the pylon extracted from the rabbit’s femur showed the stable contact between the pylon and soft tissues in comparison to control samples where the patchy fibrovascular ingrowth was detected. Conclusion: The promising results prompt further investigation of the integrative properties of the nanotextured skin and bone integrated pylon system seeded with dermal fibroblasts and its optimization for clinical application. Clinical relevance The study is devoted to the development of more safe and efficient technology of direct skeletal attachment of limb prostheses aimed in improving quality of life of people with amputations.
Experiment on an Onsite Early Warning Method for the Taiwan Early Warning System

As increasing urbanization is taking place worldwide, earthquake hazards pose serious threats to lives and property in urban areas. For seismic hazard mitigation, a practical earthquake forecast method appears to be far from realization, because of the extreme complexity involved in earthquake processes (e.g., Kanamori et al., 1997). Another approach to mitigate seismic hazards is the development of early warning systems (ews) (Nakamura, 1984, 1988; Heaton, 1985; United States National Research Council, 1991; Teng et al., 1997; United States Geological Survey, 1998; Wu et al., 1998; Wu and Teng, 2002; Allen and Kanamori, 2003). An ews provides a few seconds to tens of seconds of warning time for impending ground motions, allowing for mitigation measures in the short term. Early warning systems that estimate the severity of ground shaking and its onset time are in operation in Japan (Nakamura, 1984, 1988, 1989), Mexico (Espinosa-Aranda et al., 1995), and Taiwan (Teng et al., 1997; Wu et al., 1998, 1999; Wu and Teng, 2002). This timely information can be used to minimize property damage and the loss of lives in urban areas. It can also be used for real-time loss estimation to aid emergency response and recovery (Wu et al., 2002).