Miracle-dz/UniFAR-FTUs huggingface dataset:
Wake effects on drift in two-dimensional inviscid incompressible flows

This investigation analyzes the effect of vortex wakes on the Lagrangian displacement of particles induced by the passage of an obstacle in a two-dimensional incompressible and inviscid fluid. In addition to the trajectories of individual particles, we also study their drift and the corresponding total drift areas in the Foppl and Kirchhoff potential flow models. Our findings, which are obtained numerically and in some regimes are also supported by asymptotic analysis, are compared to the wakeless potential flow which serves as a reference. We show that in the presence of the Foppl vortex wake, some of the particles follow more complicated trajectories featuring a second loop. The appearance of an additional stagnation point in the Foppl flow is identified as a source of this effect. It is also demonstrated that, while the total drift area increases with the size of the wake for large vortex strengths, it is actually decreased for small circulation values. On the other hand, the Kirchhoff flow model is sh.
Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation

We have solved at 1.07 Å resolution the X-ray crystal structure of a polyriboadenylic acid (poly(rA)) parallel and continuous double helix. Fifty-nine years ago, double helices of poly(rA) were first proposed to form at acidic pH. Here, we show that 7-mer oligo(rA), i.e. rA7, hybridizes and overlaps in all registers at pH 3.5 to form stacked double helices that span the crystal. Under these conditions, rA7 forms well-ordered crystals, whereas rA6 forms fragile crystalline-like structures, and rA5, rA8 and rA11 fail to crystallize. Our findings support studies from ∼50 years ago: one showed using spectroscopic methods that duplex formation at pH 4.5 largely starts with rA7 and begins to plateau with rA8; another proposed a so-called ‘staggered zipper’ model in which oligo(rA) strands overlap in multiple registers to extend the helical duplex. While never shown, protonation of adenines at position N1 has been hypothesized to be critical for helix formation. Bond angles in our structure suggest that N1 is protonated on the adenines of every other rAMP−rAMP helix base pair. Our data offer new insights into poly(rA) duplex formation that may be useful in developing a pH sensor.
A Cut‐and‐Paste Approach to 3D Graphene‐Oxide‐Based Architectures

Properly cut sheets can be converted into complex 3D structures by three basic operations including folding, bending, and pasting to render new functions. Folding and bending are extensively employed in crumpling, origami, and pop‐up fabrications for 3D structures. Pasting joins different parts of a material together, and can create new geometries that are fundamentally unattainable by folding and bending. However, it has been much less explored, likely due to limited choice of weldable thin film materials and residue‐free glues. Here it is shown that graphene oxide (GO) paper is one such suitable material. Stacked GO sheets can be readily loosened up and even redispersed in water, which upon drying, restack to form solid structures. Therefore, water can be utilized to heal local damage, glue separated pieces, and release internal stress in bent GO papers to fix their shapes. Complex and dynamic 3D GO architectures can thus be fabricated by a cut‐and‐paste approach, which is also applicable to GO‐based hybrid with carbon nanotubes or clay sheets.
Thin graphite membranes for laser photoacoustic spectroscopy

The mechanical behavior of thin suspended graphite membranes (thickness of about 100 nm) has been investigated by a method utilizing Laser Photoacoustic Absorption Spectroscopy (PAS). Membranes prepared by multiple mechanical cleavage of highly ordered pyrolytic graphite (HOPG) were attached to a glass window with circular opening (diameter 4 mm). The movement of the membranes was induced by pressure changes inside a photoacoustic cell and detected via a laser beam reflected from the membranes onto a position sensitive detector. The movement of graphite membranes has been compared to the movement of a membrane of a condenser microphone. Several membranes have been tested, differing in method of preparation and/or in design. The pressure induced movement of the membranes is influenced by mechanical properties of the membranes itself, as well as by the acoustic properties of the photoacoustic cell. The free volume on the sides of the membranes had the most significant influence on its movement. On the other hand, metallization by thin layer of gold (70 nm) had negligible effect. The sensitivity of membranes utilized as an optical microphone employed in PAS method has been tested. Using methanol vapor as testing gas, we have found that the sensitivity of the membranes is comparable with the sensitivity of a top class microphone and is expected to be further enhanced by reducing the thickness of the membrane, by increasing its diameter or different (e.g. cantilever like) geometry.
Challenges in Enabling Quality of Analytics in the Cloud

Currently, domain scientists (DSs) face challenges in managing quality across multiple data analytics contexts (DACs). We identify and define quality of analytics (QoA) in dynamic and diverse environments, e.g., based on cloud computing resources for big data sources, as a composition of quality of data (data quality), performance, and cost, to name just the main factors. QoA is a complex matter and not just about quality of data or performance, which are typically considered separately when evaluating existing data analytics frameworks/algorithms. Frequently, the DS needs to utilize multiple frameworks to run different (sub)analytics, and, at the same time, the sub-analytics executed in these frameworks exchange inputs and outputs each other. In these cases, we observe different DACs, where a DAC refers to a particular situation in which the DS works with a specific framework to run a sub-analytics carried out by pipeline(s) or tasks in a pipeline. Each DAC has a set of interactions in the following categories:
Improvement of Chemical Properties of Jameed by Fortification with Whey Protein

Background: Jameed is a dried fermented milk food commonly used as a traditional dairy product in several Mediterranean countries including Jordan, Syria, Saudi Arabia, Iraq and Egypt.The aim of this work was to study the effect of blending whey protein paste (a byproduct in Ras cheese production) with jameed curd on the chemical composition and microbial properties of the produced jameed. Materials and Methods: Nine treatments of jameed were made from sheep buttermilk, goat and cow skim milk with adding 10, 15 and 20% whey protein paste to jameed curd. Jameed samples were stored at room temperature for 180 days and chemically and microbiologically analysed every month.The obtained results were statistically analyzed using a software package based on analysis of variance (One-factor analysis of variance, ANOVA, with SPSS software). Results: The obtained results showed that acidity, total solids, ash, total protein and non-protein-nitrogen values of jameed made from sheep buttermilk were higher than that of jameed prepared from goat or cow skim milk. Mixing whey protein paste with jameed curd increased acidity, total solids, total protein, ash, non-proteinnitrogen, total free amino acids and lactic acid bacteria count. Economic study for utilization of whey protein in jameed production showed that incorporation of 10 and 15% whey protein paste with goat or cow skim milk jameed curd increased the net profit. Conclusion: To improve the chemical characteristics, to enhance the nutritional values and to increase the profit of jameed manufacture, it is recommended to add 10 or 15% whey protein paste to jameed curd.
Cognitive Associates of Current and More Intensive Control of Hypertension: Findings From the Hispanic Community Health Study/Study of Latinos

BACKGROUND Hypertension control in Hispanics/Latinos lag behind general US trends by 10-15%. Intensive systolic blood pressure (SBP) management <120 mm Hg may significantly reduce morbidity/mortality risk in adults with hypertension; less is known about cognition. We investigated cross-sectional associations of cognition with observed hypertension control at currently recommended (SBP < 140 mm Hg) and more intensive (SBP < 120 mm Hg) levels using baseline data from the Hispanic Community Health Study/Study of Latinos. METHODS From this multicenter cohort study, we focused on 1,735 Hispanic/Latino men and women ages 45-74 years with hypertension and verified antihypertensive use. Verbal fluency, information processing speed, learning, and memory were tested in Spanish or English. RESULTS Separate linear regressions revealed that being on 1 vs. >1 antihypertensive medication was not associated with cognition; however, individuals with SBP controlled to currently recommended levels outperformed individuals with uncontrolled SBP on verbal fluency [Beta = 1.44 (0.52), P < 0.01] and information processing speed [Beta = 3.01 (0.89), P < 0.001] in age-adjusted regression analyses; only information processing speed remained significant (P < 0.05) after additional adjustments including acculturation, health insurance, and other cardiovascular disease risk factors. When regrouping individuals based on more intensive SBP control, individuals with levels <120 mm Hg outperformed individuals with higher SBP on verbal fluency regardless of adjustments (P < 0.01). More intensive rather than currently recommended levels of control associated with higher verbal fluency performance regardless of adjustments (P < 0.05). CONCLUSIONS Individual cognitive test scores related to distinct SBP management with more intensive management appearing more robust against confounders. While cognitive associations with hypertension in Hispanics/Latinos may be multifactorial, different levels of SBP control should be considered in future prospective intervention studies.
Transcriptomic reprogramming in soybean seedlings under salt stress.

To obtain a comprehensive understanding of transcriptomic reprogramming under salt stress, we performed whole-transcriptome sequencing on the leaf and root of soybean seedlings subjected to salt treatment in a time-course experiment (0, 1, 2, 4, 24, and 48 hr). This time series dataset enabled us to identify important hubs and connections of gene expressions. We highlighted the analysis on phytohormone signaling pathways and their possible crosstalks. Differential expressions were also found among those genes involved in carbon and nitrogen metabolism. In general, the salt-treated seedlings slowed down their photosynthetic functions and ramped up sugar catabolism to provide extra energy for survival. Primary nitrogen assimilation was shut down whereas nitrogen resources were redistributed. Overall, the results from the transcriptomic analyses indicate that the plant uses a multipronged approach to overcome salt stress, with both fast-acting, immediate physiological responses, and longer term reactions that may involve metabolic adjustment.
Accumulated promoter methylation as a potential biomarker for esophageal cancer

We performed a two-stage molecular epidemiological study to explore DNA methylation profiles for potential biomarkers of esophageal squamous cell carcinoma (ESCC) in a Chinese population. Infinium Methylation 450K BeadChip was used to identify genes with differentially methylated CpG sites. Sixteen candidate genes were validated by sequencing 1160 CpG sites in their promoter regions using the Illumina MiSeq platform. When excluding sites with negative changes, 10 genes (BNIP3, BRCA1, CCND1, CDKN2A, HTATIP2, ITGAV, NFKB1, PIK3R1, PRDM16 and PTX3) showed significantly different methylation levels among cancer lesions, remote normal-appearing tissues, and healthy controls. PRDM16 had the highest diagnostic value with the AUC (95% CI) of 0.988 (0.965–1.000), followed by PIK3R1, with the AUC (95% CI) of 0.969 (0.928–1.000). In addition, the methylation status was higher in patients with advanced cancer stages. These results indicate that aberrant DNA methylation may be a potential biomarker for the diagnosis of ESCC.
‘I am not a man’: Trans-specific barriers and facilitators to PrEP acceptability among transgender women

ABSTRACT The frequent conflation of transgender (‘trans’) women with ‘men who have sex with men (MSM)’ in HIV prevention obscures trans women's unique gender identities, social and behavioural vulnerabilities, and their disproportionately high rates of HIV infection. Pre-exposure prophylaxis (PrEP) is an efficacious biomedical HIV prevention approach. However, trans women are underrepresented in PrEP research, and are often aggregated with MSM without consideration for their unique positions within sociocultural contexts. This study examined PrEP acceptability among trans women via three focus groups and nine individual interviews (total N = 30) in San Francisco. While knowledge of PrEP was low, interest was relatively high once participants were informed. Due to past negative healthcare experiences, ability to obtain PrEP from a trans-competent provider was cited as essential to PrEP uptake and adherence. Participants noted that PrEP could address situations in which trans women experience reduced power to negotiate safer sex, including sex work. Trans-specific barriers included lack of trans-inclusive marketing of PrEP, prioritisation of hormone use, and medical mistrust due to transphobia. Findings underscore the importance of disaggregating trans women from MSM in HIV prevention strategies to mitigate disparate risk among this highly vulnerable population.
Effect of a preceptor education workshop: part 1. Quantitative results of a hospital-wide study.

BACKGROUND This study examined the hospital-wide effect of a mandatory 8-hour preceptor workshop on preceptors and orientees. METHODS A mixed-methods approach (QUAN + qual) with a quasi-experimental design was used to test nurse preceptors' self-reported confidence and comfort (pre- to postworkshop) in five specific roles in addition to the frequency of coaching critical thinking and providing formal feedback. Additionally, survey items compared cross-sectional cohorts of preceptors and orientees pre- to postworkshop. Orientee retention rates were compared for 1 year before and 1 year after the workshop. RESULTS Findings from the QUAN portion of the study are presented. Paired t tests showed that preceptors (n = 131) reported significantly improved results for confidence and comfort in all five specific preceptor roles measured 3 to 6 months after workshop attendance; coaching of critical thinking was increased, whereas provision of formal feedback was not. Preceptor-reported comfort and confidence were not significantly greater in the cohort who participated in the workshop compared with the noninterventional cohort (n = 74). Among orientees, satisfaction with preceptors was not significantly improved for the cohort whose preceptors had attended training (n = 53) versus the previous cohort (n = 39). Among orientee cohorts, greater confidence in critical thinking skills on completion of orientation occurred only among experienced transfer nurses. Orientees who had three to four preceptors reported the highest composite satisfaction. One year postintervention, significantly more orientees were retained (125 of 132) than in the previous year (82 of 94) (chi-square, p < .05). CONCLUSION Preceptor workshops are effective in preparing experienced nurses to precept new nurses, as measured by self-reported development of preceptors and retention of orientees.
Physicians' Empathy and Clinical Outcomes for Diabetic Patients

Purpose To test the hypothesis that physicians' empathy is associated with positive clinical outcomes for diabetic patients. Method A correlational study design was used in a university-affiliated outpatient setting. Participants were 891 diabetic patients, treated between July 2006 and June 2009, by 29 family physicians. Results of the most recent hemoglobin A1c and LDL-C tests were extracted from the patients' electronic records. The results of hemoglobin A1c tests were categorized into good control (<7.0%) and poor control (>9.0%). Similarly, the results of the LDL-C tests were grouped into good control (<100) and poor control (>130). The physicians, who completed the Jefferson Scale of Empathy in 2009, were grouped into high, moderate, and low empathy scorers. Associations between physicians' level of empathy scores and patient outcomes were examined. Results Patients of physicians with high empathy scores were significantly more likely to have good control of hemoglobin A1c (56%) than were patients of physicians with low empathy scores (40%, P < .001). Similarly, the proportion of patients with good LDL-C control was significantly higher for physicians with high empathy scores (59%) than physicians with low scores (44%, P < .001). Logistic regression analyses indicated that physicians' empathy had a unique contribution to the prediction of optimal clinical outcomes after controlling for physicians' and patients' gender and age, and patients' health insurance. Conclusions The hypothesis of a positive relationship between physicians' empathy and patients' clinical outcomes was confirmed, suggesting that physicians' empathy is an important factor associated with clinical competence and patient outcomes.
Novel Upper-Limb Rehabilitation System Based on Attention Technology for Post-Stroke Patients: A Preliminary Study

In this paper, we proposed an upper-limb post-stroke rehabilitation system integrating a motion tracking device (MTD), a portable electroencephalogram (EEG) device for an attentional feedback, and interactive virtual reality (VR) game with the goal to assist patients in upper-limb rehabilitation. Fifteen post-stroke patients were recruited and randomly assigned to a control group (A) or one of two experimental groups (B and C). Group B played the game using a MTD and group C played it using a MTD and brain–computer-interface-based attention-monitoring EEG device. In group C, patients’ attention was measured in real time using the EEG while the patients performed tasks; visual and auditory stimuli were emitted when their attention lowered. The primary outcome was a change in score on the upper extremity section of the Fugl–Meyer assessment, which was used to evaluate the severity of motor impairment and indicate any improvement of motor function. Improvement in motor function, associated with game performance, was found in group C. Based on their performance quality during 12 training sessions, the higher performance of group C patients in the VR game was significantly correlated with attention level and motor performance. Higher attention level is associated with higher game performance after 12 training sessions, and our MTD-EEG-VR training system may facilitate the improvement of motor function and assist patients in upper-limb rehabilitation. Our MTD-EEG-VR game with the attentional EEG-feedback device is a potential intervention for improving motor function in patients with stroke.
Shock-induced star formation in a model of the Mice

Star formation plays an important role in the fate of interacting galaxies. To date, most galactic simulations including star formation have used a density-dependent star formation rule designed to approximate a Schmidt law. Here, I present a new star formation rule which is governed by the local rate of energy dissipation in shocks. The new and old rules are compared using self-consistent simulations of NGC 4676; shock-induced star formation provides a better match to the observations of this system.
Mothers’ experiences of coping with adolescent substance abuse: a phenomenological inquiry

Background and study aim: Adolescent substance abuse significantly impacts on the lives of mothers. This paper explores the coping responses of mothers whose adolescents have been admitted to treatment for substance abuse. Design and method: A multiple case study design was adopted and the data were collected through one-on-one interviews facilitated by the Lifegrid. Interpretative phenomenological analysis was used to interrogate the data. Results: Coping emerged as a complex construct in our analysis. The mothers’ used problem-focused and emotion-focused coping in different combinations of withdrawing, tolerating and engaged coping responses. The mothers’ coping responses were also influenced by individual and relational factors like subjective distress and the mother–adolescent relationship. Conclusions: We argue that research and practice initiatives should consider using a multidimensional perspective of parental coping that recognises the heterogeneity of mothers’ coping responses. Impact statement: The current paper offers new insights into the complexities of mothers’ coping responses to adolescent substance abuse.
Centralized Control for Parallel Operation of Distributed Generation Inverters in Microgrids

This paper presents a centralized control system that coordinates parallel operations of different distributed generation (DG) inverters within a microgrid. The control design for the DG inverters employs a new Model Predictive Control algorithm that allows faster computational time for large power systems by optimizing the steady-state and the transient control problems separately. An overall energy management system is also implemented for the microgrid to coordinate load sharing among different DG units during both grid-connected and islanded operations. The design concept of the proposed control system is evaluated through simulation studies under different test scenarios. The impact of the increased penetration of DG units on the distribution grid is also investigated using the proposed microgrid. The simulation results show that the operations of the DG units within the microgrid can be coordinated effectively under the proposed control system to ensure stable operation of the overall microgrid.
OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations

Summary: OncoSimulR implements forward‐time genetic simulations of biallelic loci in asexual populations with special focus on cancer progression. Fitness can be defined as an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, restrictions in the order of accumulation of mutations, and order effects. Mutation rates can differ among genes, and can be affected by (anti)mutator genes. Also available are sampling from simulations (including single‐cell sampling), plotting the genealogical relationships of clones and generating and plotting fitness landscapes. Availability and Implementation: Implemented in R and C ++, freely available from BioConductor for Linux, Mac and Windows under the GNU GPL license. Version 2.5. 9 or higher available from: http://www.bioconductor. org/packages/devel/bioc/html/OncoSimulR.html. GitHub repository at: https://github.com/rdiaz02/OncoSimul Contact: ramon.diaz@iib.uam. es Supplementary information: Supplementary data are available at Bioinformatics online.