Miracle-dz/UniFAR-FTUs huggingface dataset:
Reynolds and froude number effect on the flow past an interface-piercing circular cylinder

Abstract The two-phase turbulent flow past an interface-piercing circular cylinder is studied using a high-fidelity orthogonal curvilinear grid solver with a Lagrangian dynamic subgrid-scale model for large-eddy simulation and a coupled level set and volume of fluid method for air-water interface tracking. The simulations cover the sub-critical and critical and post critical regimes of the Reynolds and sub and super-critical Froude numbers in order to investigate the effect of both dimensionless parameters on the flow. Significant changes in flow features near the air-water interface were observed as the Reynolds number was increased from the sub-critical to the critical regime. The interface makes the separation point near the interface much delayed for all Reynolds numbers. The separation region at intermediate depths is remarkably reduced for the critical Reynolds number regime. The deep flow resembles the single-phase turbulent flow past a circular cylinder, but includes the effect of the free-surface and the limited span length for sub-critical Reynolds numbers. At different Froude numbers, the air-water interface exhibits significantly changed structures, including breaking bow waves with splashes and bubbles at high Froude numbers. Instantaneous and mean flow features such as interface structures, vortex shedding, Reynolds stresses, and vorticity transport are also analyzed. The results are compared with reference experimental data available in the literature. The deep flow is also compared with the single-phase turbulent flow past a circular cylinder in the similar ranges of Reynolds numbers. Discussion is provided concerning the limitations of the current simulations and available experimental data along with future research
Population Pharmacokinetics of Oral Topotecan in Infants and Very Young Children with Brain Tumors Demonstrates a Role of ABCG2 rs4148157 on the Absorption Rate Constant

For infants and very young children with brain tumors, chemotherapy after surgical resection is the main treatment due to neurologic and neuroendocrine adverse effects from whole brain irradiation. Topotecan, an anticancer drug with antitumor activity against pediatric brain tumors, can be given intravenous or orally. However, high interpatient variability in oral drug bioavailability is common in children less than 3 years old. Therefore, this study aimed to determine the population pharmacokinetics of oral topotecan in infants and very young children, specifically evaluating the effects of age and ABCG2 and ABCB1 on the absorption rate constant (Ka), as well as other covariate effects on all pharmacokinetic parameters. A nonlinear mixed effects model was implemented in Monolix 4.3. 2 (Lixoft, Orsay, France). A one-compartment model with first-order input and first-order elimination was found to adequately characterize topotecan lactone concentrations with population estimates as [mean (S.E.)]; Ka = 0.61 (0.11) h−1, apparent volume of distribution (V/F) = 40.2 (7.0) l, and apparent clearance (CL/F) = 40.0 (2.9) l/h. After including the body surface area in the V/F and CL/F as a power model centered on the population median, the ABCG2 rs4148157 allele was found to play a significant role in the value of Ka. Patients homozygous or heterozygous for G>A demonstrated a Ka value 2-fold higher than their GG counterparts, complemented with a 2-fold higher maximal concentration as well. These results demonstrate a possible role for the ABCG2 rs4148157 allele in the pharmacokinetics of oral topotecan in infants and very young children, and warrants further investigation.
Quantifying Regional Vegetation Cover Variability in North China during the Holocene: Implications for Climate Feedback

Validating model simulations of vegetation-climate feedback needs information not only on changes in past vegetation types as reconstructed by palynologists, but also on other proxies such as vegetation cover. We present here a quantitative regional vegetation cover reconstruction for North China during the Holocene. The reconstruction was based on 15 high-quality lake sediment profiles selected from 55 published sites in North China, along with their modern remote sensing vegetation index. We used the surface soil pollen percentage to build three pollen-vegetation cover transfer models, and used lake surface sediment pollen data to validate their accuracy. Our results showed that vegetation cover in North China increased slightly before its maximum at 6.5 cal ka BP and has since declined significantly. The vegetation decline since 6.5 cal ka BP has likely induced a regional albedo change and aerosol increase. Further comparison with paleoclimate and paleovegetation dynamics in South China reproduced the regional cooling effect of vegetation cover decline in North China modelled in previous work. Our discussion demonstrates that, instead of reconstructing vegetation type from a single site, reconstructing quantitative regional vegetation cover could offer a broader understanding of regional vegetation-climate feedback.
Large‐Scale Synthesis and Medical Applications of Uniform‐Sized Metal Oxide Nanoparticles

Thanks to recent advances in the synthesis of high‐quality inorganic nanoparticles, more and more types of nanoparticles are becoming available for medical applications. Especially, metal oxide nanoparticles have drawn much attention due to their unique physicochemical properties and relatively inexpensive production costs. To further promote the development and clinical translation of these nanoparticle‐based agents, however, it is highly desirable to reduce unwanted interbatch variations of the nanoparticles because characterizing and refining each batch are costly, take a lot of effort, and, thus, are not productive. Large‐scale synthesis is a straightforward and economic pathway to minimize this issue. Here, the recent achievements in the large‐scale synthesis of uniform‐sized metal oxide nanoparticles and their biomedical applications are summarized, with a focus on nanoparticles of transition metal oxides and lanthanide oxides, and clarifying the underlying mechanism for the synthesis of uniform‐sized nanoparticles. Surface modification steps to endow hydrophobic nanoparticles with water dispersibility and biocompatibility are also briefly described. Finally, various medical applications of metal oxide nanoparticles, such as bioimaging, drug delivery, and therapy, are presented.
Source Localization in Cross Modality Matching of Brightness and Loudness of Young Adults

Source Localization in Cross Modality Matching of Brightness and Loudness in Young Adults Tawnya Nadine Coates Department of Communication Disorders, BYU Master of Science Cross modality matching is a magnitude matching procedure, developed to study the relationships between sensory modalities. Auditory and visual sensory integration can be examined through cross modality matching of brightness and loudness. Brightness and loudness are natural correlates of one another as they both represent the parameter of intensity for their respective sensory modalities. Past studies have demonstrated that typical individuals tend to match brighter lights with louder sounds and dimmer lights with softer sounds. The current study utilized a modified cross modality matching procedure, combined with electroencephalography (EEG) data, to examine the cortical response to sensory integration. It was hypothesized that the response latency and cortical distribution of the EEG data would show differences between matched and unmatched conditions of light and sound stimuli. Light and sound stimuli were presented to 10 participants (five males and five females between the ages of 18 and 28 years) in a forced choice paradigm. The behavioral responses, reaction times, and EEG data were recorded for each patient. Results demonstrated that there were significant differences in behavioral reaction time among the stimulus conditions. However, reaction times were only significantly faster for the loudest sound paired with the brightest light. No other pairs of matched stimuli resulted in faster reaction times. Event related potentials (ERPs) were identified for matched and unmatched stimulus conditions. No differences were identified in latency of the ERPs among conditions. Additionally, source localization revealed that dipole locations for each stimulus condition remained relatively constant in the prefrontal cortex. As the prefrontal cortex has been found to be associated with decision-making and sensory integration, it can be concluded that sensory integration did occur. However, the processing of sensory information did not change for matched or unmatched conditions of light and sound.
PrEP on Twitter: Information, Barriers, and Stigma

Abstract On May 14, 2014 the Centers for Disease Control and Prevention (CDC) endorsed the drug Truvada as an HIV preventative, called pre-exposure prophylaxis (PrEP). PrEP has been shown to dramatically reduce the risk of HIV infection, but its rate of adoption has been slow, and discourse surrounding it has been marked by stigma and uncertainty. The purpose of this study was to investigate how PrEP was discussed on Twitter. Our analysis focused on barriers to PrEP adoption and stigmatization of PrEP users. We analyzed a random sample of 1,093 top tweets about PrEP posted to Twitter a year before and a year after the CDC’s endorsement. Our results showed that tweets likely reinforced uncertainty about barriers to PrEP adoption and that users employed Twitter’s functionality to counter stigmatizing narratives about PrEP. We suggest that our findings illuminate both the limitations and strengths of Twitter as a mechanism for health promotion.
Transient external force induces phenotypic reversion of malignant epithelial structures via nitric oxide signaling

Non-malignant breast epithelial cells cultured in three-dimensional laminin-rich extracellular matrix (lrECM) form well organized, growth-arrested acini, whereas malignant cells form continuously growing disorganized structures. While the mechanical properties of the microenvironment have been shown to contribute to formation of tissue-specific architecture, how transient external force influences this behavior remains largely unexplored. Here, we show that brief transient compression applied to single malignant breast cells in lrECM stimulated them to form acinar-like structures, a phenomenon we term ‘mechanical reversion. ’ This is analogous to previously described phenotypic ‘reversion’ using biochemical inhibitors of oncogenic pathways. Compression stimulated nitric oxide production by malignant cells. Inhibition of nitric oxide production blocked mechanical reversion. Compression also restored coherent rotation in malignant cells, a behavior that is essential for acinus formation. We propose that external forces applied to single malignant cells restore cell-lrECM engagement and signaling lost in malignancy, allowing them to reestablish normal-like tissue architecture.
Automatic language identification using deep neural networks

This work studies the use of deep neural networks (DNNs) to address automatic language identification (LID). Motivated by their recent success in acoustic modelling, we adapt DNNs to the problem of identifying the language of a given spoken utterance from short-term acoustic features. The proposed approach is compared to state-of-the-art i-vector based acoustic systems on two different datasets: Google 5M LID corpus and NIST LRE 2009. Results show how LID can largely benefit from using DNNs, especially when a large amount of training data is available. We found relative improvements up to 70%, in Cavg, over the baseline system.
Comic Chat

Comics have a rich visual vocabulary, and people find them appealing. They are also an effective form of communication. We have built a system, called Comic Chat, that represents on-line communications in the form of comics. Comic Chat automates numerous aspects of comics generation, including balloon construction and layout, the placement and orientation of comic characters, the default selection of character gestures and expressions, the incorporation of semantic panel elements, and the choice of zoom factor for the virtual camera. This paper describes the mechanisms that Comic Chat uses to perform this automation, as well as novel aspects of the program’s user interface. Comic Chat is a working program, allowing groups of people to communicate over the Internet. It has several advantages over other graphical chat programs, including the availability of a graphical history, and a dynamic graphical presentation.
Upregulation of distinct collagen transcripts in post-surgery scar tissue: a study of conjunctival fibrosis

ABSTRACT Excessive accumulation of collagen is often used to assess the development of fibrosis. This study aims to identify collagen genes that define fibrosis in the conjunctiva following glaucoma filtration surgery (GFS). Using the mouse model of GFS, we have identified collagen transcripts that were upregulated in the fibrotic phase of wound healing via RNA-seq. The collagen transcripts that were increased the most were encoded by Col8a1, Col11a1 and Col8a2. Further analysis of the Col8a1, Col11a1 and Col8a2 transcripts revealed their increase by 67-, 54- and 18-fold, respectively, in the fibrotic phase, compared with 12-fold for Col1a1, the most commonly evaluated collagen gene for fibrosis. However, only type I collagen was significantly upregulated at the protein level in the fibrotic phase. Type VIII and type I collagens colocalized in fibrous structures and in ACTA2-positive pericytes, and appeared to compensate for each other in expression levels. Type XI collagen showed low colocalization with both type VIII and type I collagens but can be found in association with macrophages. Furthermore, we show that both mouse and human conjunctival fibroblasts expressed elevated levels of the most highly expressed collagen genes in response to TGFβ2 treatment. Importantly, conjunctival tissues from individuals whose GF surgeries have failed due to scarring showed 3.60- and 2.78-fold increases in type VIII and I collagen transcripts, respectively, compared with those from individuals with no prior surgeries. These data demonstrate that distinct collagen transcripts are expressed at high levels in the conjunctiva after surgery and their unique expression profiles may imply differential influences on the fibrotic outcome. Summary: As well as providing an objective quantitative measure, distinct collagen genes may further aid in the characterization and definition of the development of fibrosis.
Immunosuppressive agents in adult kidney transplantation in the National Health Service: a model-based economic evaluation

Background Immunosuppression is required in kidney transplantation to prevent rejection and prolong graft survival. We conducted an economic evaluation to support England's National Institute for Health and Care Excellence in developing updated guidance on the use of immunosuppression, incorporating new immunosuppressive agents, and addressing changes in pricing and the evidence base. Methods A discrete-time state transition model was developed to simulate adult kidney transplant patients over their lifetime. A total of 16 different regimens were modelled to assess the cost-effectiveness of basiliximab and rabbit anti-thymocyte globulin (rabbit ATG) as induction agents (with no antibody induction as a comparator) and immediate-release tacrolimus, prolonged-release tacrolimus, mycophenolate mofetil, mycophenolate sodium, sirolimus, everolimus and belatacept as maintenance agents (with ciclosporin and azathioprine as comparators). Graft survival was extrapolated from acute rejection rates, graft function and post-transplant diabetes rates, all estimated at 12 months post-transplantation. National Health Service (NHS) and personal social services costs were included. Cost-effectiveness thresholds of £20 000 and £30 000 per quality-adjusted life year were used. Results Basiliximab was predicted to be more effective and less costly than rabbit ATG and induction without antibodies. Immediate-release tacrolimus and mycophenolate mofetil were cost-effective as maintenance therapies. Other therapies were either more expensive and less effective or would only be cost-effective if a threshold in excess of £100 000 per quality-adjusted life year were used. Conclusions A regimen comprising induction with basiliximab, followed by maintenance therapy with immediate-release tacrolimus and mycophenolate mofetil, is likely to be effective for uncomplicated adult kidney transplant patients and a cost-effective use of NHS resources.
Polyphenolic content, antiradical activity, stability and microbiological quality of elderberry (Sambucus nigra L.) extracts.

BACKGROUND The pharmaceutical and food industries expect detailed knowledge on the physicochemical properties of elderberry fruit extracts, their stability and microbiological quality, as well as the polyphenol content in elderberry cultivars. The characteristics of the extracts might be additionally modified by citric acid, which improves the stability of anthocyanins and protects processed fruits and syrups from pathogenic microorganisms. The choice of the method with citric acid was a consequence of the physicochemical charac teristics of elderberry pigments, which are not stable under the effect of light in alcoholic solutions. The aim of study was to analyze the properties of elderberry fruit extracts regarding polyphenol content and antiradical activity, as well as their stability and microbiological quality. METHODS The plant material consisted of fruit from four cultivars (Alleso, Korsor, Sampo, Samyl) of black elderberry (Sambucus nigra L.). The following were determined in fruit extracts: polyphe- nolic content (HPLC), antiradical activity (ABTS and DPPH) and stability and microbiological quality. RESULTS The HPLC analysis of polyphenols demonstrated that the extracts from fruits collected from cv. Samyl had the highest 3-sambubioside cyanidin content and those from cv. Korsor contained the highest quantity of 3-glucoside cyanidin. The extracts from cv. Sampo fruit had a dominant 3-sambubioside-5-gluco- side cyanidin and 3,5-diglucoside cyanidin content. The highest quercetin (5.92 mg 100 mg-1 of extract) and caffeic acid (1.21 mg 100 mg-1 of extract) content was found in fruit extracts from cv. Alleso. The cultivars Samyl and Korsor had a higher level of anthocyanins and higher antiradical activity (ABTS) in fruit extracts than cv. Alleso and Sampo. The antiradical activity (DPPH) of fruit extracts from elderberry cultivars as- sessed in this research was similar. The degradation index for all fruit extracts was similar (DI = 1.035). The microbiological species detected in extracts were classified as moulds (Penicillum sp., Aspergillus sp.) and yeasts (Rhodotorula sp., Torulopsis sp., Trichosporon sp., Saccharomyces sp.). CONCLUSIONS The research findings may support the selection of certain cultivars for industrial applications. The high stability of anthocyanins and low level of microbiological impurities in elderberry extracts ensure the high quality of such a raw material in food and pharmaceutical processing.
Host Genetic Variants and Gene Expression Patterns Associated with Epstein-Barr Virus Copy Number in Lymphoblastoid Cell Lines

Lymphoblastoid cell lines (LCLs) are commonly used in molecular genetics, supplying DNA for the HapMap and 1000 Genomes Projects, used to test chemotherapeutic agents, and informing the basis of a number of population genetics studies of gene expression. The process of transforming human B cells into LCLs requires the presence of Epstein-Barr virus (EBV), a double-stranded DNA virus which through B-cell immortalisation maintains an episomal virus genome in every cell of an LCL at variable copy numbers. Previous studies have reported that EBV alters host-gene expression and EBV copy number may be under host genetic control. We performed a genome-wide association study of EBV genome copy number in LCLs and found the phenotype to be highly heritable, although no individual SNPs achieved a significant association with EBV copy number. The expression of two host genes (CXCL16 and AGL) was positively correlated and expression of ADARB2 was negatively correlated with EBV copy number in a genotype-independent manner. This study shows an association between EBV copy number and the gene expression profile of LCLs, and suggests that EBV copy number should be considered as a covariate in future studies of host gene expression in LCLs.
Quantitative analysis of image quality for acceptance and commissioning of an MRI simulator with a semiautomatic method

Abstract Magnetic Resonance Imaging (MRI) simulation differs from diagnostic MRI in purpose, technical requirements, and implementation. We propose a semiautomatic method for image acceptance and commissioning for the scanner, the radiofrequency (RF) coils, and pulse sequences for an MRI simulator. The ACR MRI accreditation large phantom was used for image quality analysis with seven parameters. Standard ACR sequences with a split head coil were adopted to examine the scanner's basic performance. The performance of simulation RF coils were measured and compared using the standard sequence with different clinical diagnostic coils. We used simulation sequences with simulation coils to test the quality of image and advanced performance of the scanner. Codes and procedures were developed for semiautomatic image quality analysis. When using standard ACR sequences with a split head coil, image quality passed all ACR recommended criteria. The image intensity uniformity with a simulation RF coil decreased about 34% compared with the eight‐channel diagnostic head coil, while the other six image quality parameters were acceptable. Those two image quality parameters could be improved to more than 85% by built‐in intensity calibration methods. In the simulation sequences test, the contrast resolution was sensitive to the FOV and matrix settings. The geometric distortion of simulation sequences such as T1‐weighted and T2‐weighted images was well‐controlled in the isocenter and 10 cm off‐center within a range of ±1% (2 mm). We developed a semiautomatic image quality analysis method for quantitative evaluation of images and commissioning of an MRI simulator. The baseline performances of simulation RF coils and pulse sequences have been established for routine QA.
Segmenting Proteins into Tripeptides to Enhance Conformational Sampling with Monte Carlo Methods

This paper presents an approach to enhance conformational sampling of proteins employing stochastic algorithms such as Monte Carlo (MC) methods. The approach is based on a mechanistic representation of proteins and on the application of methods originating from robotics. We outline the general ideas of our approach and detail how it can be applied to construct several MC move classes, all operating on a shared representation of the molecule and using a single mathematical solver. We showcase these sampling techniques on several types of proteins. Results show that combining several move classes, which can be easily implemented thanks to the proposed approach, significantly improves sampling efficiency.