Miracle-dz/UniFAR-FTUs huggingface dataset:
A new frequency domain waveform relaxation algorithm for PEEC models

Waveform relaxation (WR) is conventionally a time domain algorithm for the solution of linear and nonlinear partial and ordinary differential equation problems. It is especially suited for large systems and parallel processing due to the large compute-to-communication ratio and its ability to break up large problems into smaller ones. In this paper, we investigate the new application of WR to linear frequency domain problems. We show that we can use the insights gained from the extensive time domain WR research results to come up with a new frequency domain approach. For this purpose, we compute frequency response waveforms rather than time domain waveforms. Fortunately, some techniques such as partitioning are similar for both approaches. In this paper, we test some of the new algorithms for the frequency domain analysis. The new approach is aimed at the solution of large problems using single and parallel processor solutions.
Structure and agency: reflections from an exploratory study of Vancouver indoor sex workers

Sex work research continues to be characterised by debates around decriminalization. Central to these debates are claims about the agency of those involved in the sex trade. Some researchers argue that individuals involved in the sex trade are victims of structural and interpersonal constraint, whilst others depict them as workers exercising choice. Drawing on structure-agency theory, a review of legal and media accounts of the sex trade and qualitative interviews with 21 indoor sex workers in Vancouver, Canada, we argue that both of these perspectives are insufficient. Rather than reducing the sex trade to part of a binary, we suggest that it is necessary to analyse sex work through the complex interplay of both structure and agency. Specifically, structural analyses undercover the numerous ways that sex workers are controlled, observed and influenced whilst agency perspectives elicit the means that sex workers continue to exercise control in spite of disadvantage. While we do not finalise decriminalisation debates, we do critique current Canadian laws for the lack of responsiveness to the lives of sex workers and their exploitative and contradictory stance on sex work.
The effects of dietary protein intake on appendicular lean mass and muscle function in elderly men: a 10-wk randomized controlled trial.

Background: The Recommended Daily Allowance (RDA) for protein intake in the adult population is widely promoted as 0.8 g · kg-1 · d-1 Aging may increase protein requirements, particularly to maintain muscle mass.Objective: We investigated whether controlled protein consumption at the current RDA or twice the RDA (2RDA) affects skeletal muscle mass and physical function in elderly men.Design: In this parallel-group randomized trial, 29 men aged >70 y [mean ± SD body mass index (in kg/m2): 28.3 ± 4.2] were provided with a complete diet containing either 0.8 (RDA) or 1.6 (2RDA) g protein · kg-1 · d-1, aimed to balance energy needs. Before treatment and after 10 wk of intervention, whole-body and appendicular lean mass were measured by using dual-energy X-ray absorptiometry. Knee-extension peak power was measured with dynamometry.Results: Both groups were found to have been in a moderate negative energy balance (mean ± SD RDA: 209 ± 213 kcal/d; 2RDA 145 ± 214 kcal/d; P= 0.427 for difference between the groups). In comparison with RDA, whole-body lean mass increased in 2RDA (P = 0.001; 1.49 ± 1.30 kg, P < 0.001 compared with -0.55 ± 1.49 kg, P = 0.149). This difference was mostly accounted for by an increase in trunk lean mass found in 2RDA (+1.39 ± 1.09 kg, P < 0.001). Appendicular lean mass also decreased in RDA compared with 2RDA (P = 0.022), driven by a reduction in RDA (-0.64 ± 0.91 kg, P = 0.005 compared with 0.11 ± 0.57 kg, P = 0.592). Adjusting for energy imbalances did not alter these findings. Knee-extension peak power was also differently affected (P = 0.012; 26.6 ± 47.7 W, P = 0.015 in 2RDA compared with -11.7 ± 31.0 W, P = 0.180 in RDA). Conclusions: Consumption of a diet providing 2RDA for protein compared with the current guidelines was found to have beneficial effects on lean body mass and leg power in elderly men. These effects were not explained by differences in energy balance. This trial was registered at the Australia New Zealand Clinical Trial Registry (www.anzctr.org.au) as ACTRN12616000310460.
Ability of Black Soldier Fly (Diptera: Stratiomyidae) Larvae to Recycle Food Waste

ABSTRACT Accumulation of organic wastes, especially in livestock facilities, can be a potential pollution issue. The black soldier fly, Hermetia illucens L. (Diptera: Stratiomyidae), can consume a wide range of organic material and has the potential to be used in waste management. In addition, the prepupae stage of this insect can be harvested and used as a valuable nutritious feed for animal livestock. Five waste types with a wide range of organic source matter were specifically chosen to evaluate the consumption and reduction ability of black soldier fly larvae. H. illucens was able to reduce all waste types examined: 1) control poultry feed, 2) pig liver, 3) pig manure, 4) kitchen waste, 5) fruits and vegetables, and 6) rendered fish. Kitchen waste had the greatest mean rate of reduction (consumption by black soldier fly) per day and produced the longest and heaviest black soldier flies. Larvae reared on liver, manure, fruits and vegetables, and fish were approximately the same length and weight as larvae fed the control feed, although some diets produced larvae with a higher nutritional content. The black soldier fly has the ability to consume and reduce organic waste and be utilized as valuable animal feed. Exploration of the potential use of black soldier flies as an agent for waste management on a large-scale system should continue.
Analysis of Arf GTP‐Binding Protein Function in Cells

This unit describes techniques and approaches that can be used to study the functions of the ADP‐ribosylation factor (Arf) GTP‐binding proteins in cells. There are six mammalian Arfs and many more Arf‐like proteins (Arls), and these proteins are conserved in eukaryotes from yeast to humans. Like all GTPases, Arfs cycle between GDP‐bound, inactive and GTP‐bound active conformations, facilitated by guanine nucleotide exchange factors (GEFs) and GTPase‐activating proteins (GAPs) that catalyze GTP binding and hydrolysis, respectively. This unit describes approaches that can be taken to examine the localization and function of Arf and Arl proteins in cells. A simple protocol for measuring activation (GTP‐binding) of specific Arf proteins in cells using a pull‐down assay is also described. Approaches that can be taken to assess function of GEFs and GAPs in cells is described. Curr. Protoc. Cell Biol. 48:14.12. 1‐14.12. 17. © 2010 by John Wiley & Sons, Inc.
Concomitant Analysis of Salivary Tumor Markers—A New Diagnostic Tool for Oral Cancer

Purpose: Oral squamous cell carcinoma (OSCC) is a common human malignancy. Circulatory epithelial tumor markers were previously investigated in the serum of OSCC patients but almost never in their saliva, in spite of the fact that there is a direct contact between the saliva and the oral cancer lesion. The purpose of the current study was to examine tumor markers in the saliva of OSCC patients. Experimental Design: We measured the concentrations of the six most studied epithelial serum circulatory tumor markers in the saliva of OSCC (tongue) patients. Results: Significant increases (of 400%) in salivary concentrations of Cyfra 21-1, tissue polypeptide antigen, and CA125 were shown. Salivary concentrations of CA19-9, SCC, and carcinoembryonic antigen were increased without statistical significance. A concurrent analysis of the three significantly increased markers revealed sensitivity, specificity, and negative and positive predictive values of 71%, 75%, 71%, and 75%, respectively. Conclusions: The increase reported in salivary tumor markers may be used as a diagnostic tool, especially when a concurrent analysis for significantly increased markers is done. Salivary testing is noninvasive, making it an attractive, effective alternative to serum testing, and the possibility of developing home testing kits would further facilitate it as a diagnostic aid, enabling patients to monitor their own health at home and is important for those who live far from their treatment centers and especially for those at risk of developing OSCC.
Cytosine Arabinoside Induces Apoptosis in Cerebellar Neurons in Culture

Abstract: Cytosine arabinoside (AraC) is a pyrimidine antimetabolite that prevents cell proliferation by inhibiting DNA synthesis. We report that AraC kills cultured cerebellar neurons in a concentration‐dependent fashion with an EC50 of ∼60 µM when added shortly after seeding. This cell death has apoptotic features because we observed (1) morphology of apoptotic nuclei as judged by DNA staining with Hoechst 33258, (2) DNA fragmentation with typical ladder pattern on agarose gel, (3) positive nuclear labeling with a specific in situ DNA fragmentation staining, (4) prevention by deoxycytidine (IC50 = 1 µM), protein, and RNA synthesis inhibitors, and (5) release of DNA fragments in the incubating medium. We have also observed that several proteins were overexpressed in AraC‐treated neurons by two‐dimensional polyacrylamide gel electrophoresis. We conclude that AraC induces a signal that triggers a cascade of new mRNA and protein synthesis, leading to apoptotic cell death in cultured cerebellar granule cells.
Effect of intramammary infection by Staphylococcus caprae on somatic cell counts and milk composition in goats

Since its identification by Devirese et al. (1983), Staphylococcus caprae has been frequently isolated from udder halves of goats with subclinical intramammary infection (IMI) (Contreras et al. 1995; Poutrel et al. 1996). Several different studies have demonstrated the capacity of Staph. caprae to persist throughout lactation (Poutrel et al. 1996; Contreras et al. 1997; Bedidi-Madani et al. 1998a) and during the dry period (Poutrel, 1984). Bedidi-Madani et al. (1998a) found that isolates of Staph. caprae from udders of uninfected goats express potential virulence factors (different exoproteins and slime); other researchers have occasionally isolated it from clinical cases of goat mastitis (Deinhofer & Pernthaner, 1995), or from human clinical specimens associated with bone and joint infection (Vandenesh et al. 1995; Shuttleworth et al. 1997). In spite of these forms of pathogenicity, some studies have not shown significant increases in somatic cell count (SCC) of milk from goat udder halves infected by Staph. caprae (Deinhofer & Pernthaner, 1995; Poutrel et al. 1996). Moreover, there is a lack of information on the effect of infection by this mammary pathogen on milk yield and composition. Knowledge of repercussions for hygiene and production would be useful in mastitis control programmes in view of the high frequency of isolation (higher than 22% of the staphylococci isolated) of Staph. caprae in dairy goat herds (Contreras et al. 1995; Poutrel et al. 1996). The aim of the present investigation was to ascertain the significance of persistent subclinical IMI by Staph. caprae on SCC, milk yield and physical-chemical parameters of Murciano-Granadina goat milk at mid-lactation.
Genotypic Diversity among Bacillus cereus and Bacillus thuringiensis Strains

Twenty-four strains of Bacillus cereus were analyzed by pulsed-field gel electrophoresis (PFGE) and compared with 12 Bacillus thuringiensis strains. In addition, the 36 strains were examined for variation in 15 chromosomal genes encoding enzymes (by multilocus enzyme electrophoresis [MEE]). The genome of each strain had a distinct NotI restriction enzyme digestion profile by PFGE, and the 36 strains could be assigned to 27 multilocus genotypes by MEE. However, neither PFGE nor MEE analysis could distinguish between the two species. Two of the B. cereus strains contained extrachromosomal DNA that hybridized to a cryIA insecticidal toxin probe, and seven strains contained DNA with homology to a Tn4430 transposon probe derived from B. thuringiensis. The results strongly indicate that B. cereus and B. thuringiensis should be regarded as one species.
Enzymes of the SUMO Modification Pathway Localize to Filaments of the Nuclear Pore Complex

ABSTRACT SUMOs are small ubiquitin-related polypeptides that are reversibly conjugated to many nuclear proteins. Although the number of identified substrates has grown rapidly, relatively little is still understood about when, where, and why most proteins are modified by SUMO. Here, we demonstrate that enzymes involved in the SUMO modification and demodification of proteins are components of the nuclear pore complex (NPC). We show that SENP2, a SUMO protease that is able to demodify both SUMO-1 and SUMO-2 or SUMO-3 protein conjugates, localizes to the nucleoplasmic face of the NPC. The unique amino-terminal domain of SENP2 interacts with the FG repeat domain of Nup153, indicating that SENP2 associates with the nucleoplasmic basket of the NPC. We also investigated the localization of the SUMO conjugating enzyme, Ubc9. Using immunogold labeling of isolated nuclear envelopes, we found that Ubc9 localizes to both the cytoplasmic and the nucleoplasmic filaments of the NPC. In vitro binding studies revealed that Ubc9 and SUMO-1-modified RanGAP1 bind synergistically to form a trimeric complex with a component of the cytoplasmic filaments of the NPC, Nup358. Our results indicate that both SUMO modification and demodification of proteins may occur at the NPC and suggest a connection between the SUMO modification pathway and nucleocytoplasmic transport.
A Fuzzy Logic Approach in Emotion Detection and Recognition and Formulation of an Odor-Based Emotional Fitness Assistive System

This paper aims at a Fuzzy relational approach for similar emotions expressed by different subjects by facial expressions and predefined parameters. Different Facial attributes contribute to a wide variety of emotions under varied circumstances. These same features also vary widely from person to person, introducing uncertainty to the process. Facial features like eye-opening, mouth-opening and length of eye-brow constriction from localized areas from a face are Fuzzified and converted into emotion space by employing relational models. This is dealt with Fuzzy Type-2 logic, which reigns supreme in reducing uncertainty.
Contrast independence of cardinal preference: stable oblique effect in orientation maps of ferret visual cortex

The oblique effect was first described as enhanced detection and discrimination of cardinal orientations compared with oblique orientations. Such biases in visual processing are believed to originate from a functional adaptation to environmental statistics dominated by cardinal contours. At the neuronal level, the oblique orientation effect corresponds to the numerical overrepresentation and narrower tuning bandwidths of cortical neurons representing the cardinal axes. The anisotropic distribution of orientation preferences over large cortical regions was revealed with optical imaging, providing further evidence for the cortical oblique effect in several mammalian species. Our present study explores whether the dominant representation of cardinal contours persists at different stimulus contrasts. Performing intrinsic optical imaging in the ferret visual cortex and presenting drifting gratings at various orientations and contrasts (100%, 30% and 10%), we found that the overrepresentation of vertical and horizontal contours was invariant across stimulus contrasts. In addition, the responses to cardinal orientations were also more robust and evoked larger modulation depths than responses to oblique orientations. We conclude that orientation maps remain constant across the full range of contrast levels down to detection thresholds. Thus, a stable layout of the functional architecture dedicated to processing oriented edges seems to reflect a fundamental coding strategy of the early visual cortex.
Statistical inference from power law distributed web-based social interactions

Purpose – to propose a method for statistical inference on data from power law distributions in order to explain behavior and social phenomena associated with web-based social spaces such as discussion forums, question-and-answer sites, web 2.0 applications and the like. Design/methodology/approach – The paper starts by highlighting the importance of explaining behavior in social networks. Next, the power law nature of social interactions is described and a hypothetical example is used to explain why analyzing sub-sets of data might misrepresent the relationship between variables having power law distributions. Analysis requires the use of the complete distribution. We propose logarithmic transformation prior to correlation and regression analysis and show why it works using the hypothetical example and field data retrieved from Microsoft's Netscan project. Findings – The hypothetical example emphasizes the importance of analyzing complete datasets harvested from social spaces. The Netscan example shows the importance of the logarithmic transformation for enabling the development of a predictive regression model based on the power law distributed data. Specifically, we show that the number of new and returning participants are the main predictors of discussion forum activity. Originality/value – This paper offers a useful analysis tool for anyone interested in social aspects of the Internet as well as corporate intra-net systems, knowledge management systems or other systems which support social interaction such as cellular phones and mobile devices. It also explains how to avoid errors by paying attention to assumptions and range restriction issues.
Nasoduodenal Feeding Tubes: Prevention of Occlusion

&NA; Blockage of nasoduodenal feeding tubes is costly in terms of materials and nursing time, and traumatic to the neuroscience patient. A laboratory experimental study explored ways to decrease obstruction of small bore nasoduodenal feeding tubes when medications are given concurrently with continuous tube feeding. The first part of the study examined type and form of 4 medications in relation to frequency and timing of tube blockage. Trimethoprim sulfamethoxazole (Septra) in dissolved pill form blocked tubes most frequently (F10,77 =10.333, p<.001) and in the shortest time (F10,77=10.534, p<.001). The second part of the study examined different irrigation methods. Irrigation before and after administration of medication and irrigation after medication administration only were significantly better than no irrigation in preventing blockage, both in terms of number of occlusions (F2,87=5.486, p<.01) and time to occlusion (F2,87=4.556, p<.02). The fact the study was performed in vitro rather than in vivo was a limiting factor. However, results of the study suggest trimethoprim sulfamethoxazole forms occlusions, especially in dissolved form. Elixir of this medication should probably be used whenever available. This study also found that irrigating the tube before and after administration of medications was the most effective of the 3 options examined.
Influence of Apical Clearance on Mini-Scleral Lens Settling, Clinical Performance, and Corneal Thickness Changes

Purpose: The purpose of this work was to define the timing and magnitude of scleral contact lens settling, the factors influencing settling, and to examine whether the amount of apical clearance has an impact on clinical performance or is associated with hypoxia-induced corneal changes. Methods: Eleven patients (22 eyes) with keratoconus were fitted with a mini-scleral lens (Esclera, Brazil). Three different lenses with successively greater sagittal depths were applied to achieve 3 levels of initial apical clearance: 100 to 200 &mgr;m (low), 200 to 300 &mgr;m (medium), and greater than 300 &mgr;m (high). Corneal apical clearance was measured at 15 min, 1, 2, 4, 6, and 8 hr with optical coherence tomography (OCT). Central corneal thickness was measured with OCT and Pentacam, in the morning and immediately after removal of the contact lens. Results: Mean settling was 26.8±18.8 &mgr;m (42.7%) at 1 hr, 39.5±26.5 &mgr;m (62.9%) at 2 hr, 50.7±31.6 &mgr;m (80.8%) at 4 hr, 57.4±34.6 &mgr;m (91.4%) at 6 hr, and 62.8±38.4 &mgr;m (100%) at 8 hr. Settling rate was significantly lower in low apical clearance group (P=0.01). The smaller diameter lenses settled more (P=0.03). There was a slight statistically significant increase of 1.3% in central corneal thickness measured with OCT (P=0.03). Central corneal thickness measured with Pentacam at three locations increased slightly (P=0.001). Settling showed significant intrasubject and intersubject variations. The amount of corneal swelling and comfort scores did not differ significantly according to apical clearance. Conclusions: The average amount of settling was 62.8 &mgr;m after 8 hr, 80% of which occurred during the first 4 hr. Slight corneal swelling (1.3%) occurred after 8 hr of wear.
High numerical aperture square lattice structure photonic crystal fiber for optical coherence tomography

In optical coherence tomography (OCT) system, high numerical aperture (NA) PCF is required for collecting back scattering light for detailed information from body tissue. In this paper, we propose a new structure of high NA zero dispersion single mode photonic crystal fiber (PCF) for OCT at 0.83 μm, 1.06 μm and 1.31 μm wavelengths which are used for ophthalmology, dermatology and dentistry, respectively. The properties of the proposed PCF are simulated by using finite difference method (FDM) with an anisotropic perfectly matched boundary layer. The PCF offers not only high NA but also both zero dispersion and single mode operation at each center wavelengths. Simulation results show that the designed PCF at target wavelengths improves the transverse resolution of OCT systems.
A comparative study between two different suture materials in oral implantology.

OBJECTIVE The prospective study compares, in split-mouth design, the use of two different suture materials, silk vs. Teflon-coated, multi-filament braided polyester threads suture. MATERIAL AND METHODS Ten edentulous or partially edentulous patients were surgically treated for implant installation. Each side was sutured with either, randomly selected one or the other suture material. Seven days postsurgically, the sutures were removed and three knots per patient and side were collected for microbiological testing. Additionally, a piece of each suture thread was analysed before clinical use to test its susceptibility for bacterial adherence. To evaluate the patient's subjective opinion, a questionnaire based on Visual Analogue Scale had to be filled out by all included patients 1 week after the intervention. RESULTS The results showed a more pronounced plaque accumulation for silk sutures but there was not a statistical difference. The intraoperative handling of the silk sutures was less comfortable and the patient comfort was worse than Teflon-coated polyester suture. CONCLUSION The bacterial adherence on Teflon-coated polyester suture was slightly inferior than silk suture although it did not show the expected differences.