Miracle-dz/UniFAR-FTUs huggingface dataset:
Standardization of clinical protocols in oral malodor research

The objective of this study is to standardize protocols for clinical research into oral malodor caused by volatile sulfur compounds (VSCs). To detect VSCs, a gas chromatograph (GC) using a flame photometric detector equipped with a bandpass filter (at 393 nm) is the gold standard (sensitivity: 5 × 10−11 gS s−1). The baselines of VSC concentrations in mouth air varied considerably over a week. When the subjects refrained from eating, drinking and oral hygiene including mouth rinsing, the VSC concentrations remained constant until eating. Over a 6 h period after a meal, VSC concentrations decreased dramatically (p < 0.01). These results point to optimal times and conditions for sampling subjects. Several portable devices were compared with the measurements by the GCs. Portable GCs demonstrated capabilities similar to those of the GCs. We also applied the recommended protocols described below to clinical research testing the efficacy of ZnCl2 products, and confirmed that using the recommended protocols in a randomized crossover design would provide very clear results. Proposed protocols include: (a) a short-term study rather than a long-term study is strongly recommended, since the VSC concentrations are constant in the short term; (b) a crossover study would be the best design to avoid the effects of individual specificities on each clinical intervention; (c) measurements of VSCs should preferably be carried out using either a GC or portable GCs.
Evaluating the Construct Validity of Ryff’s Scales of Psychological Well-Being Using Exploratory Structural Equation Modeling

The purpose of this study was to evaluate the construct validity of Ryff’s Scales of Psychological Well-Being (SPWB) using exploratory structural equation modeling (ESEM). The data were drawn from the national survey of Midlife in the United States conducted during 1994 and 1995. Measurement models assuming different number of factors (1-6 factors) and considering the effect of negatively wording items were specified and compared to determine optimal number of underlying factors. The discriminant validity was assessed following Farrell’s suggestions. The results showed the discriminant validity was questionable due to five indicators with considerable cross-loadings.
Evaluation of a hybrid anaerobic biofilm reactor treating winery effluents and using grape stalks as biofilm carrier

ABSTRACT Wine production processes generate large amount of both winery wastewater and solid wastes. Furthermore, working periods, volumes and pollution loads greatly vary over the year. Therefore, it is recommended to develop a low-cost treatment technology for the treatment of winery effluents taking into account the variation of the organic loading rate (OLR). Accordingly, we have investigated the sequential operation of an anaerobic biofilm reactor treating winery effluents and using grape stalks (GSs) as biofilm carrier with an OLR ranging from 0.65 to 27 gCOD/L/d. The result showed that, during the start-up with wastewater influent, the chemical oxygen demand (COD) removal rate ranged from 83% to 93% and was about 91% at the end of the start-up period that lasted for 40 days. After 3 months of inactivity period of the reactor (no influent feeding), we have succeeded in restarting-up the reactor in only 15 days with a COD removal of 82% and a low concentration of volatile fatty acids (1 g/L), which confirms the robustness of the reactor. As a consequence, GSs can be used as an efficient carrier support, allowing a fast reactor start-up, while the biofilm conserves its activity during a non-feeding period. The proposed hybrid reactor thus permits to treat both winery effluents and GSs.
Detection of influenza A virus nucleoprotein antibodies in oral fluid specimens from pigs infected under experimental conditions using a blocking ELISA.

In commercial swine populations, influenza is an important component of the porcine respiratory disease complex (PRDC) and a pathogen with major economic impact. Previously, a commercial blocking ELISA (FlockChek(™) Avian Influenza Virus MultiS-Screen(®) Antibody Test Kit, IDEXX Laboratories, Inc., Westbrook, ME, USA) designed to detect influenza A nucleoprotein (NP) antibodies in avian serum was shown to accurately detect NP antibodies in swine serum. The purpose of this study was to determine whether this assay could detect NP antibodies in swine oral fluid samples. Initially, the procedure for performing the NP-blocking ELISA on oral fluid was modified from the serum testing protocol by changing sample dilution, sample volume, incubation time and incubation temperature. The detection of NP antibody was then evaluated using pen-based oral fluid samples (n = 182) from pigs inoculated with either influenza A virus subtype H1N1 or H3N2 under experimental conditions and followed for 42 days post inoculation (DPI). NP antibodies in oral fluid were detected from DPI 7 to 42 in all inoculated groups, that is, the mean sample-to-negative (S/N) ratio of influenza-inoculated pigs was significantly different (P < 0.0001) from uninoculated controls (unvaccinated or vaccinated-uninoculated groups) through this period. Oral fluid versus serum S/N ratios from the same pen showed a correlation of 0.796 (Pearson's correlation coefficient, P < 0.0001). The results showed that oral fluid samples from influenza virus-infected pigs contained detectable levels of NP antibodies for ≥42 DPI. Future research will be required to determine whether this approach could be used to monitor the circulation of influenza virus in commercial pig populations.
Strict Hierarchy of Bell Theorems

As proved by John Bell, quantum mechanics exhibits correlations in spacelike separated bipartite systems that are impossible to reproduce by classical means. There are three levels of "Bell theorems", depending on which aspects of the quantum correlations can or cannot be reproduced classically. The original "Bell inequalities" (Bl) require a perfect classical simulation of all quantum probabilities. With "Bell theorems without inequalities" (BTWI), we ask the classical simulation to be able to produce precisely the outputs that could occur according to quantum mechanics, but we do not worry about their exact probabilities. With "pseudo-telepathy" (PT), we are satisfied if the classical simulation produces only outputs allowed by quantum mechanics, but not necessarily all of them. Bell's original proof of Bl involved a maximally entangled 2times2 bipartite state such as the singlet state. Hardy proved that BTWI are possible in dimension 2times2, but his construction used a non-maximally entangled state. Here, we prove that no 2times2 maximally entangled state can serve to produce BTWI. Combining this with the fact that 2times2 entangled states cannot be used at all for the purpose of PT, it follows a strict hierarchy on the quantum resources that are required to exhibit the various levels of Bell theorems.
Adaptive coping strategies among adults with dental fear. Further development of a new version of the Dental Coping Strategy Questionnaire

Abstract Objective. The aim of this study was to further develop and investigate a newly constructed 15-item questionnaire on strategies for coping with dental treatment, used by fearful adult patients undergoing regular dental care and those with phobic avoidance. Materials and Methods. The dental coping strategy questionnaire (DCSQ-15) was distributed to 77 individuals with dental phobic avoidance and 94 fearful patients undergoing regular dental care. Previous analyses of a 20-item coping questionnaire (DCSQ-20) revealed that 2 of 4 identified factors predicted regularity or phobic avoidance of dental care. However, one of these factors was considered related to catastrophizing thoughts and not to coping strategies and it was therefore removed in the present study. Results. The reduced 15-item questionnaire was analyzed to identify its factor structure and a 5-factor solution was found. The five factors were labeled (i) ‘self-efficacy’, (ii) ‘self-distraction’, (iii) ‘distancing’, (iv) ‘praying’ and (v) ‘optimism’. The factors of ‘praying’ and ‘optimism’ correlated significantly with dental anxiety and were assessed significantly higher and lower respectively, among individuals with phobic avoidance. A logistic regression analysis revealed that ‘optimism’, together with gender and dental anxiety, was predictive of the regularity or phobic avoidance of dental care.
Compact bandpass filter with reconfigurable X-band using stepped impedance resonator and folded structure

A reconfigurable X-band microstrip bandpass filter based on the stepped impedance resonator topology with two folded stubs is proposed. Reconfiguration is enabled in the microstrip filter using positive–intrinsic–negative (PIN) diode and the proposed filter performs frequency switching between uplink and downlink X-band services. The prototype filter is realised ideally using open-circuit and shortcircuit conditions that are designed in a way similar to the design using PIN diodes that provide the same results. From the simulation and measured results, it is inferred that by altering the ON/OFF states, the filter can work from downlink frequency range of 7.25–7.9 GHz to the uplink frequency range of 8.00–8.4 GHz. Comprehensive studies are conducted on a fabricated prototype to assess its performance from which encouraging results are obtained.
Optimization of De Novo Short Read Assembly of Seabuckthorn (Hippophae rhamnoides L.) Transcriptome

Seabuckthorn ( Hippophae rhamnoides L.) is known for its medicinal, nutritional and environmental importance since ancient times. However, very limited efforts have been made to characterize the genome and transcriptome of this wonder plant. Here, we report the use of next generation massive parallel sequencing technology (Illumina platform) and de novo assembly to gain a comprehensive view of the seabuckthorn transcriptome. We assembled 86,253,874 high quality short reads using six assembly tools. At our hand, assembly of non-redundant short reads following a two-step procedure was found to be the best considering various assembly quality parameters. Initially, ABySS tool was used following an additive k-mer approach. The assembled transcripts were subsequently subjected to TGICL suite. Finally, de novo short read assembly yielded 88,297 transcripts (> 100 bp), representing about 53 Mb of seabuckthorn transcriptome. The average length of transcripts was 610 bp, N50 length 1198 BP and 91% of the short reads uniquely mapped back to seabuckthorn transcriptome. A total of 41,340 (46.8%) transcripts showed significant similarity with sequences present in nr protein databases of NCBI (E-value < 1E-06). We also screened the assembled transcripts for the presence of transcription factors and simple sequence repeats. Our strategy involving the use of short read assembler (ABySS) followed by TGICL will be useful for the researchers working with a non-model organism’s transcriptome in terms of saving time and reducing complexity in data management. The seabuckthorn transcriptome data generated here provide a valuable resource for gene discovery and development of functional molecular markers.
Cytochrome P450 structure–function: insights from molecular dynamics simulations

Abstract Cytochrome P450 (CYP) family 1, 2, and 3 enzymes play an essential role in the metabolic clearance and detoxification of a myriad of structurally and chemically diverse drugs and non-drug xenobiotics. The individual CYP enzymes exhibit distinct substrate and inhibitor selectivities, and hence differing patterns of inhibitory drug–drug interactions. In addition, CYP enzymes differ in terms of regulation of expression, genetic polymorphism, and environmental factors that alter activity. The availability of three-dimensional structures from X-ray crystallography have been invaluable for understanding the structural basis of the ligand selectivity of CYP enzymes. Moreover, the X-ray crystal structures demonstrate that CYP proteins exhibit marked flexibility, particularly around the active site, and the principle of ligand-induced conformational changes is now well accepted. Recent studies have demonstrated that molecular dynamics simulations (MDS) provide an additional approach for modeling the structural flexibility of CYP enzymes, both in the presence and absence of bound ligand, and understanding the functional consequences of plasticity. However, most of the MDS studies reported to date have utilized short simulation time scales, and few have validated the computationally-generated data experimentally (e.g. by site-directed mutagenesis and enzyme kinetic approaches). Although modeling approaches require further development and validation, MDS has the potential to provide a deeper understanding of CYP structure–function than is available from experimental techniques such as X-ray crystallography alone.
NATURAL RADIOACTIVITY AND ASSOCIATED RADIATION HAZARDS IN LOCAL PORTLAND AND POZZOLANIC CEMENTS USED IN JORDAN

: Activity concentration of the natural gamma-emitting radionuclides ( 40 K, 226 Ra and 232 Th) in at least forty samples of local Portland and Pozzolanic cement types is measured. The measurements were performed using gamma spectrometric techniques. The range of the mean specific activity (minimum and maximum values) due to all the three radionuclides is found. Radiological hazards of the different samples are estimated using five approaches; the representative level index, the external hazard index, the internal hazard index, the radium equivalent index and the absorbed dose rate. Some of the measured radiological hazard parameters are compared to similar parameters in different countries. The activity concentration of 226 Ra for all types of cements varies from 29.1±2.01 to 79.2±3.90 Bq.kg −1 . The activity concentration of 232 Th for all types of cements varies from 5.8±1.1 to 26.4±1.9 Bq.kg −1 . The activity concentration of 40 K for all types of cements varies from 231.9±9.8 to 298.0±10.7 Bq.kg −1 . The radium equivalent activity concentration, Ra eq , of the total activity of each cement type is obtained. The highest value of Ra eq was seen in white cement (125.49 Bq.kg −1 ) and the lowest in Portland Pozzolanic cement (5%) with an average value of (78.08 Bq.kg −1 ). Based on the assessment of potential radiological hazards as inferred from the calculations of Ra eq , representative level index and the dose rate, the investigated cement samples fall within the category of accepted building materials and are safe to use for the construction of inhabited
Functional characterization of core genes from patients with acute hepatitis C virus infection.

BACKGROUND The hepatitis C virus (HCV) core protein is implicated in diverse aspects of HCV-induced pathogenesis. There is a paucity of information on core in acute hepatitis C infection. METHODS We analyzed core gene sequences and protein functions from 13 patients acutely infected with HCV genotype 1. RESULTS Although core isolates differed slightly between patients, core quasispecies were relatively homogeneous within each patient. In 2 of 4 patients studied temporally, core quasispecies did not change over time. Comparison with more than 2700 published core isolates indicated that amino acid changes from a prototype reference strain found in acute core isolates were present in chronically infected persons at low frequency (6.4%; range, 0%-32%). Core isolates associated with lipid droplets to similar degrees in Huh7 cells. Core diffusion in cells was not affected by nonconservative changes F130L and G161S in the lipid targeting domain of core. Core isolates inhibited interferon-stimulated response element- and nuclear factor kappaB-dependent transcription and tumor necrosis factor alpha-induced nuclear translocation of nuclear factor kappaB and were also secreted from Huh7 cells. CONCLUSIONS The data suggest that upon transmission, core quasispecies undergo genetic homogenization associated with amino acid changes that are rarely found in chronic infection and that, despite genetic variation, acute core isolates retain similar functions in vitro.
An exact, high-efficiency PFM DC-DC boost converter with dynamic stored energy

This paper presents an exact and high-efficiency PFM dc-dc boost converter designed with a standard TSMC 3.3/5 V 0.35-mum CMOS technology. The proposed boost converter utilizes a dynamic stored energy technique to reduce output voltage variation and raise power conversion efficiency. This result is realized using a dynamic stored energy controller and a load current detector that accurately generates different energy according to various load conditions. The output up-ripple voltage variation and steady-state accuracy was 2.6 mV (5.7 mV-8.3 mV) and 0.15% whereas its fixed energy counterpart was 11.1 mV (8.1 mV-19.2 mV) and 0.35%, respectively. The proposed circuit has 6.91% higher power-conversion efficiency than conventional fixed energy technique at a 1 mA current. The maximum power-conversion efficiency is 91.75% for 50 mA output current with a 1.5 V supply.
Classification of blood cells and tumor cells using label‐free ultrasound and photoacoustics

A label‐free method that can identify cells in a blood sample using high frequency photoacoustic and ultrasound signals is demonstrated. When the wavelength of the ultrasound or photoacoustic wave is similar to the size of a single cell (frequencies of 100–500 MHz), unique periodic features occur within the ultrasound and photoacoustic power spectrum that depend on the cell size, structure, and morphology. These spectral features can be used to identify different cell types present in blood, such as red blood cells (RBCs), white blood cells (WBCs), and circulating tumor cells. Circulating melanoma cells are ideal for photoacoustic detection due to their endogenous optical absorption properties. Using a 532 nm pulsed laser and a 375 MHz transducer, the ultrasound and photoacoustic signals from RBCs, WBCs, and melanoma cells were individually measured in an acoustic microscope to examine how the signals change between cell types. A photoacoustic and ultrasound signal was detected from RBCs and melanoma cells; only an ultrasound signal was detected from WBCs. The different cell types were distinctly separated using the ultrasound and photoacoustic signal amplitude and power spectral periodicity. The size of each cell was also estimated from the spectral periodicity. For the first time, sound waves generated using pulse‐echo ultrasound and photoacoustics have been used to identify and size single cells, with applications toward counting and identifying cells, including circulating melanoma cells. © 2015 International Society for Advancement of Cytometry
Harmonic Functions and Collision Probabilities

There is a close relationship between harmonic functions— which have recently been proposed for path planning—and hitting probabilities for random processes. The hitting proba bilities for random walks can be cast as a Dirichlet problem for harmonic functions, in much the same way as in path plan ning. This equivalence has implications both for uncertainty in motion planning and in the application of machine-learning techniques to some robot problems. In particular, Erdmann's method can directly incorporate such hitting probabilities. In addition, the value functions obtained by reinforcement learn ing algorithms can be rapidly reconstructed by relaxation or resistive networks, once the extrema for such functions are known.
Development and characterization of a three-dimensional radiochromic film stack dosimeter for megavoltage photon beam dosimetry.

PURPOSE Three-dimensional (3D) dosimeters are particularly useful for verifying the commissioning of treatment planning and delivery systems, especially with the ever-increasing implementation of complex and conformal radiotherapy techniques such as volumetric modulated arc therapy. However, currently available 3D dosimeters require extensive experience to prepare and analyze, and are subject to large measurement uncertainties. This work aims to provide a more readily implementable 3D dosimeter with the development and characterization of a radiochromic film stack dosimeter for megavoltage photon beam dosimetry. METHODS A film stack dosimeter was developed using Gafchromic(®) EBT2 films. The dosimeter consists of 22 films separated by 1 mm-thick spacers. A Virtual Water™ phantom was created that maintains the radial film alignment within a maximum uncertainty of 0.3 mm. The film stack dosimeter was characterized using simulations and measurements of 6 MV fields. The absorbed-dose energy dependence and orientation dependence of the film stack dosimeter were investigated using Monte Carlo simulations. The water equivalence of the dosimeter was determined by comparing percentage-depth-dose (PDD) profiles measured with the film stack dosimeter and simulated using Monte Carlo methods. Film stack dosimeter measurements were verified with thermoluminescent dosimeter (TLD) microcube measurements. The film stack dosimeter was also used to verify the delivery of an intensity-modulated radiation therapy (IMRT) procedure. RESULTS The absorbed-dose energy response of EBT2 film differs less than 1.5% between the calibration and film stack dosimeter geometries for a 6 MV spectrum. Over a series of beam angles ranging from normal incidence to parallel incidence, the overall variation in the response of the film stack dosimeter is within a range of 2.5%. Relative to the response to a normally incident beam, the film stack dosimeter exhibits a 1% under-response when the beam axis is parallel to the film planes. Measured and simulated PDD profiles agree within a root-mean-square difference of 1.3%. In-field film stack dosimeter and TLD measurements agree within 5%, and measurements in the field penumbra agree within 0.5 mm. Film stack dosimeter and TLD measurements have expanded (k = 2) overall measurement uncertainties of 6.2% and 5.8%, respectively. Film stack dosimeter measurements of an IMRT dose distribution have 98% agreement with the treatment planning system dose calculation, using gamma criteria of 3% and 2 mm. CONCLUSIONS The film stack dosimeter is capable of high-resolution, low-uncertainty 3D dose measurements, and can be readily incorporated into an existing film dosimetry program.
Diet Quality and Cancer Outcomes in Adults: A Systematic Review of Epidemiological Studies

Dietary patterns influence cancer risk. However, systematic reviews have not evaluated relationships between a priori defined diet quality scores and adult cancer risk and mortality. The aims of this systematic review are to (1) describe diet quality scores used in cohort or cross-sectional research examining cancer outcomes; and (2) describe associations between diet quality scores and cancer risk and mortality. The protocol was registered in Prospero, and a systematic search using six electronic databases was conducted through to December 2014. Records were assessed for inclusion by two independent reviewers, and quality was evaluated using a validated tool. Sixty-four studies met inclusion criteria from which 55 different diet quality scores were identified. Of the 35 studies investigating diet quality and cancer risk, 60% (n = 21) found a positive relationship. Results suggest no relationship between diet quality scores and overall cancer risk. Inverse associations were found for diet quality scores and risk of postmenopausal breast, colorectal, head, and neck cancer. No consistent relationships between diet quality scores and cancer mortality were found. Diet quality appears to be related to site-specific adult cancer risk. The relationship with cancer mortality is less conclusive, suggesting additional factors impact overall cancer survival. Development of a cancer-specific diet quality score for application in prospective epidemiology and in public health is warranted.