Miracle-dz/UniFAR-FTUs huggingface dataset:
New Approaches Indicate Constant Viral Diversity despite Shifts in Assemblage Structure in an Australian Hypersaline Lake

ABSTRACT It is widely stated that viruses represent the most significant source of biodiversity on Earth, yet characterizing the diversity of viral assemblages in natural systems remains difficult. Viral diversity studies are challenging because viruses lack universally present, phylogenetically informative genes. Here, we developed an approach to estimate viral diversity using a series of functional and novel conserved genes. This approach provides direct estimates of viral assemblage diversity while retaining resolution at the level of individual viral populations in a natural system. We characterized viral assemblages in eight samples from hypersaline Lake Tyrrell (LT), Victoria, Australia, using 39,636 viral contigs. We defined viral operational taxonomic units (OTUs) in two ways. First, we used genes with three different functional predictions that were abundantly represented in the data set. Second, we clustered proteins of unknown function based on sequence similarity, and we chose genes represented by three clusters with numerous members to define OTUs. In combination, diversity metrics indicated between 412 and 735 sampled populations, and the number of populations remained relatively constant across samples. We determined the relative representation of each viral OTU in each sample and found that viral assemblage structures correlate with salinity and solution chemistry. LT viral assemblages were near-replicates from the same site sampled a few days apart but differed significantly on other spatial and temporal scales. The OTU definition approach proposed here paves the way for metagenomics-based analyses of viral assemblages using ecological models previously applied to bacteria and archaea.
How to Combine Parameter and Compositional Adaptation in the Modeling of Self-Adaptive Applications

ABSTRACT Computing technology quickly pervades our living environment. We are getting used to carrying with us powerful devices with computing and communication capabilities. The execution context of applications on these devices changes continuously and applications need to adapt in a self-organizing manner, to retain their usefulness. Parameter and compositional adaptation are two frequently used mechanisms for self-adaptive applications in pervasive computing environments. Both of them have advantages as well as disadvantages. Our aim is to provide a comprehensive model-driven application development approach that combines the two concepts, in order to benefit from the advantages of both mechanisms and to reduce development effort. In this paper, we present a modeling approach for self-adaptive applications that combines parameter and compositional adaptation in an integrated, homogeneous fashion. The resulting adaptation model is automatically transformed to source code which is used by the middleware to manage the adaptation at application run-time. The approach was successfully tested in the development of two comprehensive pilot applications.
VERY FAST REAL-TIME OCEAN WAVE FOAM RENDERING USING HALFTONING

We introduce an efficient method for emulating sea foam dissipation suitable for use in real-time interactive environments such as video games. By using a precomputed dither array with controlled spectral characteristics adopted from halftone research as a control mechanism in the pixel shader, we can animate the appearance of foam bubbles popping in a random manner while allowing them to clump naturally.
Antimicrobial photodynamic therapy: An overview

Inflammatory periodontal disease caused by dental plaque is characterized by the clinical signs of inflammation and loss of periodontal tissue support. The mechanical removal of this biofilm and adjunctive use of antibacterial disinfectants and antibiotics have been the conventional methods of periodontal therapy. But the removal of plaque and the reduction in the number of infectious organisms can be impaired in sites with difficult access. The possibility of development of resistance to antibiotics by the target organism has led to the development of a new antimicrobial concept with fewer complications. Photodynamic therapy (PDT) involves the use of low power lasers with appropriate wavelength to kill micro organisms treated with a photosensitizer drug. PDT could be a useful adjunct to mechanical as well as antibiotics in eliminating periopathogenic bacteria.
Combined Intravitreal Bevacizumab and Trabeculectomy With Mitomycin C Versus Trabeculectomy With Mitomycin C Alone for Neovascular Glaucoma

PurposeTo evaluate the effects of intravitreal bevacizumab (IVB) before mitomycin C trabeculectomy (MMCT) for neovascular glaucoma (NVG). MethodsThe study is a retrospective, comparative, consecutive case series. The study group consisted of 57 eyes from 50 patients with NVG who underwent a first MMCT: 33 eyes were treated with MMCT alone between June 1, 2005 and May 17, 2007 (Control Group); and, 24 eyes were treated with a combination of IVB and MMCT after May 18, 2007 (IVB Group). Surgical complications, intraocular pressure (IOP), and the probability of success were compared between the 2 groups. Surgical failure was defined as IOP ≥22 mm Hg for 2 consecutive follow-up visits, a deterioration of visual acuity to no light perception, or additional glaucoma surgeries. ResultsThere were no significant differences in preoperative data between the groups. Hyphema associated with MMCT occurred significantly less often in the IVB Group (P=0.006). IOPs at 7 and 10 days after MMCT were significantly lower in the IVB Group (P=0.01 and 0.02, respectively). However, Kaplan-Meier survival-curve analysis showed the probability of success 120, 240, and 360 days after MMCT of 87.5%, 79.2%, and 65.2% in the IVB Group, and 75.0%, 71.9%, and 65.3% in the Control Group. No significant difference in survival times was found between the groups (P=0.76). ConclusionsIVB before MMCT reduced hyphema associated with MMCT for NVG. IVB provided further IOP reduction immediately after MMCT, but did not significantly improve surgical outcomes over longer periods.
Inhibition of protein kinase C promotes differentiation of neuroblastoma × glioma NG108‐15 hybrid cells

Differentiation of neuroblastoma × glioma NG108‐15 hybrid cells can be induced by different means, but the mechanisms involved are unclear. Our aim was to characterize the role of protein kinase C (PKC) in this process. The PKCs present in NG108‐15 cells, i.e. PKCα, PKCδ, PKCε and PKCζ, were inhibited using a cocktail of Go6983 and Ro318220 or were downregulated by treatment with phorbol 12‐myristate 13‐acetate (PMA). In high‐glucose Dulbecco’s modified Eagle medium, neuritogenesis was induced by 24 h treatment with a cocktail of Go6983 and Ro318220 or by 48 h treatment with PMA, the latter process thus requiring a longer treatment. However, when cells treated with PMA for only 24 h were placed in extracellular standard salts solution, e.g. Locke’s buffer, for 3 h, morphological and functional differentiation occurred, with rounding of the cell body, actin polymerization subjacent to the plasma membrane and an increase in voltage‐sensitive Ca2+ channel activity in the absence of cell death. This rapid differentiation was not due to autophagy, growth arrest or increased cyclic AMP response element binding protein phosphorylation, but coincided with combined activation of p38 mitogen‐activated protein kinase (MAPK) and inhibition of extracellular signal‐regulated kinase (ERK) and Akt, as confirmed by the effects of selective inhibitors. Furthermore, PKC activation blocked thapsigargin‐induced neuritogenesis, whereas PKC downregulation did not. These results show that PKC downregulation promotes differentiation and this effect is accelerated by exposure to Locke’s buffer. Although this experimental paradigm cannot be related to the in vivo situation and disease, it implies that combined inhibition of Akt and p44/p42 ERK and activation of p38 MAPK promotes differentiation.
EFFICIENT DESCRIPTION AND RENDERING OF COMPLEX INTERACTIVE ACOUSTIC SCENES

Interactive environmental audio spatialization technology has become commonplace in personal computers and is migrating into portable entertainment platforms (including cell phones) and multiplayer game servers (virtual online worlds). While the primary current application of this technology is 3D game sound track rendering, it is ultimately necessary in the implementation of any personal or shared immersive virtual world (“virtual reality”). The successful development and deployment of such applications in new mobile or online platforms involves maximizing the plausibility of the synthetic 3D audio scene while minimizing the computational and memory footprint of the audio rendering engine. It also requires a flexible, standardized scene description model to facilate the development of applications targeting multiple platforms. This paper reviews a computationally efficient 3-D positional audio and spatial reverberation processing architecture for real-time virtual acoustics over headphones or loudspeakers, compatible with current interactive audio standards (including MPEG-4, OpenAL, JSR 234 and OpenSL ES).
Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard

ABSTRACT Heterotrophic microbial communities in seawater and sediments metabolize much of the organic carbon produced in the ocean. Although carbon cycling and preservation depend critically on the capabilities of these microbial communities, their compositions and capabilities have seldom been examined simultaneously at the same site. To compare the abilities of seawater and sedimentary microbial communities to initiate organic matter degradation, we measured the extracellular enzymatic hydrolysis rates of 10 substrates (polysaccharides and algal extracts) in surface seawater and bottom water as well as in surface and anoxic sediments of an Arctic fjord. Patterns of enzyme activities differed between seawater and sediments, not just quantitatively, in accordance with higher cell numbers in sediments, but also in their more diversified enzyme spectrum. Sedimentary microbial communities hydrolyzed all of the fluorescently labeled polysaccharide and algal extracts, in most cases at higher rates in subsurface than surface sediments. In seawater, in contrast, only 5 of the 7 polysaccharides and 2 of the 3 algal extracts were hydrolyzed, and hydrolysis rates in surface and deepwater were virtually identical. To compare bacterial communities, 16S rRNA gene clone libraries were constructed from the same seawater and sediment samples; they diverged strongly in composition. Thus, the broader enzymatic capabilities of the sedimentary microbial communities may result from the compositional differences between seawater and sedimentary microbial communities, rather than from gene expression differences among compositionally similar communities. The greater number of phylum- and subphylum-level lineages and operational taxonomic units in sediments than in seawater samples may reflect the necessity of a wider range of enzymatic capabilities and strategies to access organic matter that has already been degraded during passage through the water column. When transformations of marine organic matter are considered, differences in community composition and their different abilities to access organic matter should be taken into account.
Plasmid-Mediated Chloramphenicol Resistance in Haemophilus influenzae

A clinical isolate of Haemophilus influenzae HC234 was found to be resistant to chloramphenicol and tetracycline. It was shown that both resistance markers are tranferable as one unit to other Haemophilus influenzae strains and also to Escherichia coli. Data are presented which indicate that conjugation is the most likely mechanism of resistance transfer. HC234 was shown to carry a single plasmid species with a molecular weight of 38 × 106.
CO2‐dependent growth of Succinatimonas hippei YIT 12066T isolated from human feces

Succinatimonas hippei is a new bacterial species isolated from human feces. Here we report that the growth of S. hippei YIT 12066T depends on CO2 or bicarbonate and the headspace gas produced by microbiota. Genetic defect for carbonic anhydrase in this bacterium suggested a reason for the syntrophic property of CO2 dependency and may suggest an adaptation to its habitat.
Novel Mycobacterium avium Complex Species Isolated From Black Wildebeest (Connochaetes gnou) in South Africa

A study was undertaken to isolate and characterize Mycobacterium species from black wildebeest suspected of being infected with tuberculosis in South Africa. This led to the discovery of a new Mycobacterium avium complex species, provisionally referred to as the Gnou isolate from black wildebeest (Connochaetes gnou). Sixteen samples from nine black wildebeest were processed for Mycobacterium isolation. Following decontamination, samples were incubated in an ordinary incubator at 37°C on Löwenstein-Jensen slants and in liquid medium tubes using the BACTEC™ MGIT™ 960 system, respectively. Identification of the isolate was carried out by standard biochemical tests and using the line probe assay from the GenoType® CM/AS kit (Hain Lifescience GmbH, Nehren, Germany). The DNA extract was also analysed using gene sequencing. Partial gene sequencing and analysis of 16S rRNA gene, and 16S-23S rRNA (ITS), rpoB and hsp65 and phylogenetic analyses by searching GenBank using the BLAST algorithm were conducted. Phylogenetic trees were constructed using four methods, namely Bayesian inference, maximum likelihood, maximum parsimony and neighbour-joining methods. The isolate was identified as Mycobacterium intracellulare using the GenoType® CM/AS kit and as Mycobacterium avium complex (MAC) by gene sequencing. The gene sequence targeting all the genes, ITS, 16S rRNA, rpoB and hsp65 and phylogenetic analyses indicated that this isolate presented a nucleotide sequence different from all currently published sequences, and its position was far enough from other MAC species to suggest that it might be a new species.
Recommendations for recruiting and retaining adolescent girls in chronic exercise (training) research studies

Extensive challenges are often encountered when recruiting participants to chronic exercise (training) studies. High participant burden during chronic exercise training programmes can result in low uptake to and/or poor compliance with the study. The aim of this qualitative study was to identify factors affecting adolescent girls’ recruitment and adherence to chronic exercise training research studies. Twenty-six adolescent girls (aged 12 to 15 years) participated in one of five focus groups discussing recruitment and retention to exercise physiology research involving a chronic exercise training programme. A thematic analysis was used to analyse the data and eight final themes were inductively identified. Seven evidence-based practical recommendations are suggested to improve the recruitment and retention of participants for prospective, chronic exercise training studies. Successful recruitment requires: (i) the defining of exercise-related terms; (ii) appropriate choice of recruitment material; and (iii) an understanding of participant motivations. Retention strategies include: (iv) regular monitoring of participant motives; and (v) small groups which foster peer and researcher support. Finally, (vi) friendship and ability groups were favoured in addition to (vii) a variety of activities to promote adherence to an exercise training programme.
Host defenses against metabolic endotoxaemia and their impact on lipopolysaccharide detection

ABSTRACT Bacterial endotoxin (lipopolysaccharide, LPS), is one of the most potent inducers of inflammatory signaling, yet it is abundant in the human gut and the modern diet. Small quantities of LPS routinely translocate from the gut lumen to the circulation (so-called metabolic endotoxaemia), and elevated plasma LPS concentrations are reported in a variety of chronic non-communicable diseases, including obesity, non-alcoholic fatty liver disease, atherosclerosis and type II diabetes. Murine models of experimentally-induced endotoxaemia and Toll-like receptor-4 deficiency suggest that endotoxin may promote the metabolic disturbances that underpin these diseases. However, as bioactive LPS is cleared rapidly from the circulation, and reported levels of endotoxin in human plasma vary widely, the potential relevance of metabolic endotoxaemia to human disease remains unclear. We here review insight into these questions gained from human and murine models of experimental endotoxaemia, focusing on the kinetics of LPS neutralization and its clearance from blood, the limitations of the widely used limulus assay and alternative methods for LPS quantitation. We conclude that although new methods for LPS measurement will be required to definitively quantify the extent of metabolic endotoxaemia in man, evidence from numerous approaches suggests that this molecule may play a key role in the development of diverse metabolic diseases.
Phylogenetic Comparison of the Methanogenic Communities from an Acidic, Oligotrophic Fen and an Anaerobic Digester Treating Municipal Wastewater Sludge

ABSTRACT Methanogens play a critical role in the decomposition of organics under anaerobic conditions. The methanogenic consortia in saturated wetland soils are often subjected to large temperature fluctuations and acidic conditions, imposing a selective pressure for psychro- and acidotolerant community members; however, methanogenic communities in engineered digesters are frequently maintained within a narrow range of mesophilic and circumneutral conditions to retain system stability. To investigate the hypothesis that these two disparate environments have distinct methanogenic communities, the methanogens in an oligotrophic acidic fen and a mesophilic anaerobic digester treating municipal wastewater sludge were characterized by creating clone libraries for the 16S rRNA and methyl coenzyme M reductase alpha subunit (mcrA) genes. A quantitative framework was developed to assess the differences between these two communities by calculating the average sequence similarity for 16S rRNA genes and mcrA within a genus and family using sequences of isolated and characterized methanogens within the approved methanogen taxonomy. The average sequence similarities for 16S rRNA genes within a genus and family were 96.0 and 93.5%, respectively, and the average sequence similarities for mcrA within a genus and family were 88.9 and 79%, respectively. The clone libraries of the bog and digester environments showed no overlap at the species level and almost no overlap at the family level. Both libraries were dominated by clones related to uncultured methanogen groups within the Methanomicrobiales, although members of the Methanosarcinales and Methanobacteriales were also found in both libraries. Diversity indices for the 16S rRNA gene library of the bog and both mcrA libraries were similar, but these indices indicated much lower diversity in the 16S digester library than in the other three libraries.
Experiments on Candidate Data for Collocation Extraction

The paper describes ongoing work on the evaluation of methods for extracting collocation candidates from large text corpora. Our research is based on a German treebank corpus used as gold standard. Results are available for adjective+noun pairs, which proved to be a comparatively easy extraction task. We plan to extend the evaluation to other types of collocations (e.g., PP+verb pairs).
Implementation of multi-hop time synchronization on miniature test-bed setup of underwater acoustic sensor network

Time synchronization is an important part of any distributed networked embedded system. It is essentially the process of achieving and maintaining common time base among all network nodes of the system. This task is quite challenging for the systems or applications like sensor networks, since these systems are highly resource constrained, yet need to process time-sensitive data in collaborative manner. Though many protocols have been suggested for terrestrial sensor networks (RSB, TPSN, FTSP and LTS) and they perform reasonably well, very few protocols (THSL, Tri-message) have been suggested for the high-latency underwater acoustic networks, since achieving time-synchronization for high-latency networks is even more challenging issue. Here we describe a very simple extension and implementation of Tri-message time synchronization protocol for multi-hop Underwater Acoustic Sensor Network (UASN) on the miniature test-bed setup.
Temperature effects on life-history trade-offs, germline maintenance and mutation rate under simulated climate warming

Mutation has a fundamental influence over evolutionary processes, but how evolutionary processes shape mutation rate remains less clear. In asexual unicellular organism, increased mutation rates have been observed in stressful environments and the reigning paradigm ascribes this increase to selection for evolvability. However, this explanation does not apply in sexually reproducing species, where little is known about how the environment affects mutation rate. Here we challenged experimental lines of seed beetle, evolved at ancestral temperature or under simulated climate warming, to repair induced mutations at ancestral and stressful temperature. Results show that temperature stress causes individuals to pass on a greater mutation load to their grand-offspring. This suggests that stress-induced mutation rates, in unicellular and multicellular organisms alike, can result from compromised germline DNA repair in low condition individuals. Moreover, lines adapted to simulated climate warming had evolved increased longevity at the cost of reproduction, and this allocation decision improved germline repair. These results suggest that mutation rates can be modulated by resource allocation trade-offs encompassing life-history traits and the germline and have important implications for rates of adaptation and extinction as well as our understanding of genetic diversity in multicellular organisms.
Position-based ICI elimination with compressed channel estimation for SIMO-OFDM high speed train systems

In this paper, we consider a typical high speed train (HST) communication system with single-input multiple-output (SIMO) orthogonal frequency-division multiplexing (OFDM). We show that the inter-carrier interference (ICI) caused by large Doppler shifts can be mitigated by exploiting the train position information as well as the sparsity of the basis expansion model (BEM) based channel model. For the complex-exponential BEM (CE-BEM) based channel model, we show that the ICI can be completely eliminated to get the ICI-free pilots at each receive antenna. In addition, we design the pilot pattern to reduce the system coherence so as to improve the compressed sensing (CS) based channel estimation accuracy. In specific, the optimal pilot pattern is independent of the number of receive antennas, the Doppler shifts, the train position, or the train speed. Simulation results confirm the effectiveness of the proposed scheme in high-mobility environments. The results also show that the proposed scheme is robust to the train moving speed.