Miracle-dz/UniFAR-FTUs huggingface dataset:
Simultaneous Multicolor Detection System of the Single‐Molecular Microbial Antigen with Total Internal Reflection Fluorescence Microscopy

Immunological diagnostic methods have been widely performed and showed high performance in molecular and cellular biology, molecular imaging, and medical diagnostics. We have developed novel methods for the fluorescent labeling of several antibodies coupled with fluorescent nanocrystal QDs. In this study we demonstrated that two bacterial toxins, diphtheria toxin and tetanus toxin, were detected simultaneously in the same view field of a cover slip by using directly QD‐conjugated antibodies. We have succeeded in detecting bacterial toxins by counting luminescent spots on the evanescent field with using primary antibody conjugated to QDs. In addition, each bacterial toxin in the mixture can be separately detected by single excitation laser with emission band pass filters, and simultaneously in situ pathogen quantification was performed by calculating the luminescent density on the surface of the cover slip. Our results demonstrate that total internal reflection fluorescence microscopy (TIRFM) enables us to distinguish each antigen from mixed samples and can simultaneously quantitate multiple antigens by QD‐conjugated antibodies. Bioconjugated QDs could have great potentialities for in practical biomedical applications to develop various high‐sensitivity detection systems.
Longitudinal evaluation of fluoride levels in nails of 18-30-month-old children that were using toothpastes with 500 and 1100 μg F/g.

OBJECTIVES This study aimed to evaluate the fluoride concentration in the fingernails and toenails of children aged 18-30 months during use of fluoride-containing toothpastes supplemented with calcium glycerophosphate (CaGP) or sodium trimetaphosphate (TMP). METHODS According to the toothpaste used, children (n = 56) were randomly assigned into three groups: 500 μg F/g with 1% TMP, 500 μg F/g with 0.25% CaGP, and 1100 μg F/g. Fingernails and toenails were collected monthly over a period of 330 days, from the beginning of toothpaste use. Fluoride concentration in the water consumed by the volunteers and fluoride intake from diet and toothpaste were also determined. Fluoride analyses were performed with the electrode after hexamethyldisiloxane-facilitated diffusion or by the direct method, according to the samples. Data passed normality and homoscedasticity tests and were analyzed by 2-way analysis of variance (anova) and 1-way anova followed by Student-Newman-Keuls test (P < 0.05). RESULTS Fluoride levels in the fingernails and toenails as well as fluoride intake from toothpaste were similar for the groups treated with 500 μg F/g with 1% TMP and 500 μg F/g with 0.25% CaGP toothpastes, but significantly lower than the 1100 μg F/g group (P < 0.05). No significant differences were noted among the groups regarding fluoride intake from diet and that by water consumed by the volunteers (P > 0.05). CONCLUSION The results of the longitudinal study suggest that the level of fluoride present in nails was lower with the use of toothpastes with a low fluoride concentration.
A probabilistic approach to building defect prediction model for platform-based product lines

: Determining when software testing should be begun and the resources that may be required to find and fix defects is complicated. Being able to predict the number of defects for an upcoming software product given the current development team enables the project managers to make better decisions. A majority of reported defects are managed and tracked using a repository system, which tracks a defect throughout its lifetime. The Defect Life Cycle (DLC) begins when a defect is found and ends when the resolution is verified and the defect is closed. Defects transition through different states according to the evolution of the project, which involves testing, debugging, and verification. All of these defect transitions should be logged using the Defect Tracking Systems (DTS). We construct a Markov chain theory-based defect prediction model for consecutive software products using defect transition history. During model construction, the state of each defect is modelled using the defect life cycle states. The proposed model can predict the defect trends such as total number of defects and defect distribution states in the consecutive products. The model is evaluated using an actual industrial mobile product software project and found to be well suited for the selected domain.
Are We Overdiagnosing Acute Kidney Injury in Pediatric Patients Following Cardiac Surgery?

Background: The use of two diagnostic criteria in the current literature has led to some degree of ambiguity in the precise diagnosis of acute kidney injury in pediatric patients undergoing surgery for congenital heart disease. This study aims to determine which criteria is the most accurate diagnostic indicator of acute kidney injury and determine whether the incidence is being overestimated based on the current criteria. Methods: This retrospective study consisted of 389 patients with congenital heart disease from birth to 18 years, who underwent cardiac surgery. The statistical tests conducted were the student t test and chi-square test. Outcomes measured included hospital length of stay, duration of mechanical ventilation, and mortality. Results: The incidence rate of acute kidney injury diagnosed by the pediatric Risk, Injury, Failure, Loss, and End-Stage Renal Disease (RIFLE) criterion was 56% compared to 24.4% for the Acute Kidney Injury Network criterion. The pediatric RIFLE criterion consists of the following subsets: risk, injury, failure, loss, and end-stage renal disease. Patients classified in the “risk” subset of the pediatric RIFLE criterion who failed to meet Acute Kidney Injury Network criterion were compared to patients without acute kidney injury. Comparison of intensive care unit outcomes between these groups lacked statistical significance for all variables except the duration of mechanical ventilation postoperatively. Conclusion: Although recent research in this field identified the pediatric RIFLE criterion as the most sensitive indicator of acute kidney injury, the results of this study suggest the pediatric RIFLE criterion overestimates acute kidney injury incidence and that the Acute Kidney Injury Network criterion is the more accurate diagnostic indicator.
Rapid alterations in cortical protein profiles underlie spontaneous sleep and wake bouts

Existing data indicate that sleep–wakefulness is an essential behavior. The biological function(s) of sleep, however, remains unknown, due, in part, to the lack of information available at the intracellular level. Preliminary microarray analyses show that changes in behavioral state influence regional mRNA profiles; however, the impact of sleep on protein signatures is virtually unexplored. In these studies, cortical protein profiles were examined after timed bouts of spontaneous sleep–wakefulness. Within minutes of each behavioral state examined, a small number of spots showing unique expression were detected. Mass spectroscopy analyses of sleep‐ and wake‐related spots identified proteins associated with multiple functional categories. Two sleep‐associated proteins were further validated using a sleep deprivation paradigm. We found preliminary evidence for two different post‐transcriptional mechanisms—one (GAPDH) in which the amount of protein was increased in the recovery sleep following prolonged waking, while the other (actin) suggested that post‐translational modifications may underlie sleep. The similarities between the effects of sleep on both protein and mRNA profiles indicate that dynamic intracellular changes underlie sleep–wake states and are consistent with roles for sleep in multiple biological functions. J. Cell. Biochem. 105: 1472–1484, 2008. © 2008 Wiley‐Liss, Inc.
Age Differences in the Experience of Daily Life Events: A Study Based on the Social Goals Perspective

This study examined age differences in daily life events related to different types of social goals based on the socioemotional selectivity theory (SST), and determined whether the positivity effect existed in the context of social goals in older adults’ daily lives. Over a course of 14 days, 49 older adults and 36 younger adults wrote about up to three life events daily and rated the valence of each event. The findings indicated that (1) although both older and younger adults recorded events related to both emotional and knowledge-acquisition goals, the odds ratio for reporting a higher number of events related to emotional goals compared to the number of events related to knowledge-acquisition goals was 2.12 times higher in older adults than that observed in younger adults. (2) Considering the number of events, there was an age-related positivity effect only for knowledge-related goals, and (3) older adults’ ratings for events related to emotional and knowledge-acquisition goals were significantly more positive compared to those observed in younger adults. These findings supported the SST, and to some extent, the positivity effect was demonstrated in the context of social goals.
‘Church hurt can be the worst hurt’: community stakeholder perceptions of the role of Black churches in HIV prevention among young Black gay and bisexual men

Abstract Black gay and bisexual men aged 15–29 are disproportionately represented among new cases of HIV in the USA. Researchers have argued that community-based prevention cannot succeed without the participation of faith-based organisations, particularly given the salience of religion and spirituality in the lives of young Black gay and bisexual men. Yet some Black churches may be hesitant to engage in HIV prevention efforts given their beliefs about same-sex behaviour. It is less clear, however, whether and how public health practitioners in the field of HIV prevention have approached church inclusion. We therefore explored how community stakeholders describe the involvement of Black churches with the HIV continuum of care. We draw on a qualitative dataset of 50 in-depth semi-structured interviews conducted in Detroit, USA. Participants offered multiple perspectives on the response of Black churches to the HIV epidemic, from overt stigma to gradual acceptance and action. Nevertheless, participants agreed that when stigma was present in the pews and the pulpit, young Black gay and bisexual men were at potential risk of social isolation. Furthermore, tensions may exist between Black churches and secular community-based organisations that are attributable to histories of mistrust. These findings have important implications for future community-based intervention strategies among young Black gay and bisexual men.
Approximation to Default Swaptions in Reduced-Form Framework: Calibration and Comparison of Intensity Dynamics

We develop an approximation to pricing default swaptions in general intensity models which yields a fast and accurate analytic/semi-analytic solution to the valuation problem. We consider several dynamics for intensity and derive 'extended transforms' for inverse Gaussian- and tempered stable Ornstein-Uhlenbeck processes. Having convenient pricing formulae, we are able to provide the first account of calibration of intensity models to credit options. Further, we extend the model by adding a shift, thus resulting in a tractable model that keeps the intensity positive, matches closely implied volatilities of default swaptions, and fits exactly the CDS spreads.
Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2009–2010

This review is the sixth update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2010. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, arrays and fragmentation are covered in the first part of the review and applications to various structural typed constitutes the remainder. The main groups of compound that are discussed in this section are oligo and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Many of these applications are presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis. © 2014 Wiley Periodicals, Inc. Mass Spec Rev 34: 268–422, 2015.
Using Social Media Content in the Visual Analysis of Movement Data

Data about the movement of people and objects is a rich source for visual analysis. However, understanding the data and inferring user behavior from it is often difficult due to missing context information. The goal of our research is to augment movement data by information derived from social media. In this paper, we present a visual concept that extends movement trajectories with terms extracted from geo-coded Twitter posts. The movement data comes from a large sample of e-bikes equipped with GPS devices. The Twitter terms are displayed as word clouds to provide additional context information for visual analysis. They are shown at locations of interests to help understand the movement data and infer possible user behavior. We plan to extend the visual concept in the future by incorporating further social media services. Ultimately, we aim for an integrated view of social media contents that allows for semi-automated reasoning and causality discovery on movement data.
Two-part pricing contracts under competition: the South-to-North Water Transfer Project supply chain system in China

Abstract This study analyzes the water supply chain system of the Eastern Route of the South-to-North Water Transfer Project in China. The article compares the impacts of competition intensity on profits of two water distributors and the water supply chain system under two-part pricing contracts versus wholesale price contracts. When the upstream water supplier offers two-part pricing contracts, the water quantity and expected profits of both distributors decrease as the competition intensity increases. The expected profits of the supply chain system decrease, but are greater than the profits under wholesale price contracts. The government can control fixed costs to balance the profits of suppliers and distributors.
Incidence and clinical manifestations of adenoviral infection among children undergoing allogeneic stem cell transplantation.

BACKGROUND Adenoviral infection in children undergoing stem cell transplantation is associated with significant morbidity and mortality. Identification of adenoviral infection by polymerase chain reaction from blood facilitates accurate and rapid diagnosis and surveillance. The incidence of adenoviral infection among children undergoing SCT in Israel is not known. OBJECTIVE To estimate the incidence of adenoviral infection in pediatric SCT patients and to characterize the morbidity associated with proven infection. METHODS Blood samples obtained weekly from children who underwent allogeneic SCT were retrospectively tested for adenovirus using standard PCR. A total of 657 samples collected from 32 patients were examined. Correlation was made between the presence of adenovirus in samples and clinical records. RESULTS Of the 32 patients 4 had adenoviral infection by PCR (12.5%). Clinical disease was present in all four patients concurrent with positive PCR. Gastrointestinal complaints and abnormal hepatocellular enzymes were uniformly present. One patient died due to disseminated disease. T cell depletion was a significant risk factor for adenoviral infection (P = 0.03). CONCLUSIONS In the patient population studied, the incidence of adenoviral infection in children undergoing SCT was 12.5%. The combination of gastrointestinal symptoms and abnormal hepatocellular enzymes should raise the suspicion of adenoviral infection, especially when occurring during the first few months after SCT.
Does Clinical Remission Lead to Normalization of EQ-5D in Patients with Rheumatoid Arthritis and Is Selection of Remission Criteria Important?

Objective. To compare health-related quality of life (HRQOL) of patients with rheumatoid arthritis (RA) to that of the general population and to investigate the association with disease activity, focusing on different clinical remission criteria. Methods. EQ-5D data from 3156 patients with RA from 11 Danish centers were compared with Danish EQ-5D population norms (n = 16,136). The Disease Activity Score (DAS28) and the Clinical Disease Activity Index score (CDAI) were used as definitions of disease activity and clinical remission. The score difference (ΔEQ-5D) was calculated in each patient as the difference from the age and sex-matched general population and adjusted for age, marital status, education, body mass index, smoking, exercise habits, disease duration, IgM-rheumatoid factor status, joint surgery, extraarticular features, treatment, and comorbidity in multiple linear regression models. Results. 37% vs 22% fulfilled the DAS28 and CDAI remission criteria, respectively. The ΔEQ-5D values for women/men in clinical remission were DAS28 0.05/0.06 vs CDAI 0.01/0.02; low disease activity: DAS28 0.12/0.13 vs CDAI 0.11/0.14; moderate disease activity: DAS28 0.18/0.20 vs CDAI 0.20/0.23; and high disease activity: DAS28 0.38/0.28 vs CDAI 0.33/0.26. Adjusting for confounders reduced the ΔEQ-5D values between 0 and 0.04 units. Conclusion. Patients with RA had worse EQ-5D scores than the general population, and the difference was strongly associated with disease activity. The EQ-5D score for patients in clinical remission approached that of the general population, suggesting that strict treatment goals are critical in order to achieve near-normal HRQOL in patients with RA.
The persuasive effects of framing messages on fruit and vegetable consumption according to regulatory focus theory

According to Regulatory Focus theory (RFT), outcomes in persuasive messages can be framed in four different ways, as gains, non-gains, losses or non-losses. In study 1, the persuasiveness of all four frames was compared and the presence/absence effect that was expected on the basis of the feature-positive effect was verified: Statements about present outcomes (gain, loss) were more persuasive than those about absent outcomes (non-gain, non-loss). However, this study failed to support the prediction that a gain-framed message would be more persuasive than a loss-framed message when promoting a prevention behaviour. Study 2 was designed to examine the latter finding. It was hypothesised that the threat posed by the loss-framed message in study 1 was too low to elicit a defensive reaction. Therefore, in study 2, the personal relevance of the gain and the loss framed message was manipulated. Consistent with predictions, the gain-framed message was more persuasive than the loss-framed message, but only when the message was personalised to increase self-relevance. Moreover, the effect was due to a significant drop in persuasion in the loss condition, probably caused by a defensive reaction. These data shed a new light on the findings of past framing studies.
Transfer of the beta-tubulin gene of Botrytis cinerea with resistance to carbendazim into Fusarium graminearum.

BACKGROUND Resistance to carbendazim and other benzimidazole fungicides in Botrytis cinerea (Pers. ex Fr.) and most other fungi is usually conferred by mutation(s) in a single chromosomal beta-tubulin gene, often with several allelic mutations. In Fusarium graminearum Schwade, however, carbendazim resistance is not associated with a mutation in the corresponding beta-tubulin gene. RESULTS The beta-tubulin gene conferring carbendazim resistance in B. cinerea was cloned and connected with two homologous arms of the beta-tubulin gene of F. graminearum by using a double-joint polymerase chain reaction (PCR). This fragment was transferred into F. graminearum via homologous double crossover at the site where the beta-tubulin gene of F. graminearum is normally located (the beta-tubulin gene of F. graminearum had been deleted). The transformants were confirmed and tested for their sensitivity to carbendazim. CONCLUSION The beta-tubulin gene conferring carbendazim resistance in B. cinerea could not express this resistance in F. graminearum, as transformants were still very sensitive to carbendazim.
Voice conversion with pitch alteration using phase vocoder

A novel approach to pitch transposition is presented, which allows to preserve the spectral envelope or to modify it in a voice conversion task. Pitch-shifted output is synthesized directly from the input signal using the phase vocoder, without explicitly estimating the fundamental frequency, which is often prone to errors. Frequency band extension technique is proposed to address the problem of bandwidth reduction when scaling pitch down. Artificial neural network was applied to transform the signal's spectral envelope in the full voice conversion task. Listening tests showed that 55% of listeners preferred the quality of the pitch modification using the phase vocoder over the one offered by a parametric approach.
Optimizing dual‐energy x‐ray parameters for the ExacTrac clinical stereoscopic imaging system to enhance soft‐tissue imaging

Purpose: Stereoscopic x‐ray image guided radiotherapy for lung tumors is often hindered by bone overlap and limited soft‐tissue contrast. This study aims to evaluate the feasibility of dual‐energy imaging techniques and to optimize parameters of the ExacTrac stereoscopic imaging system to enhance soft‐tissue imaging for application to lung stereotactic body radiation therapy. Methods: Simulated spectra and a physical lung phantom were used to optimize filter material, thickness, tube potentials, and weighting factors to obtain bone subtracted dual‐energy images. Spektr simulations were used to identify material in the atomic number range (3–83) based on a metric defined to separate spectra of high and low‐energies. Both energies used the same filter due to time constraints of imaging in the presence of respiratory motion. The lung phantom contained bone, soft tissue, and tumor mimicking materials, and it was imaged with a filter thickness in the range of (0–0.7) mm and a kVp range of (60–80) for low energy and (120,140) for high energy. Optimal dual‐energy weighting factors were obtained when the bone to soft‐tissue contrast‐to‐noise ratio (CNR) was minimized. Optimal filter thickness and tube potential were achieved by maximizing tumor‐to‐background CNR. Using the optimized parameters, dual‐energy images of an anthropomorphic Rando phantom with a spherical tumor mimicking material inserted in his lung were acquired and evaluated for bone subtraction and tumor contrast. Imaging dose was measured using the dual‐energy technique with and without beam filtration and matched to that of a clinical conventional single energy technique. Results: Tin was the material of choice for beam filtering providing the best energy separation, non‐toxicity, and non‐reactiveness. The best soft‐tissue‐weighted image in the lung phantom was obtained using 0.2 mm tin and (140, 60) kVp pair. Dual‐energy images of the Rando phantom with the tin filter had noticeable improvement in bone elimination, tumor contrast, and noise content when compared to dual‐energy imaging with no filtration. The surface dose was 0.52 mGy per each stereoscopic view for both clinical single energy technique and the dual‐energy technique in both cases of with and without the tin filter. Conclusions: Dual‐energy soft‐tissue imaging is feasible without additional imaging dose using the ExacTrac stereoscopic imaging system with optimized acquisition parameters and no beam filtration. Addition of a single tin filter for both the high and low energies has noticeable improvements on dual‐energy imaging with optimized parameters. Clinical implementation of a dual‐energy technique on ExacTrac stereoscopic imaging could improve lung tumor visibility.