Miracle-dz/UniFAR-FTUs huggingface dataset:
A Microfluidics and Agent-Based Modeling Framework for Investigating Spatial Organization in Bacterial Colonies: The Case of Pseudomonas Aeruginosa and H1-Type VI Secretion Interactions

The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models.
Assays to Assess Freeze Injury of Satsuma Mandarin

Containerized 'Owari' satsuma mandarin (Citrus unshiu Marc.) on Poncirus trifoliata 'Flying Dragon' rootstock were exposed to one of two acclimation regimes (cold acclimated and unacclimated) and frozen in a computer-controlled freezer to five different low temperatures. Whole plant survival was measured and compared to the results of four leaf and stem injury assays. Acclimating plants in growth chambers at 20 °C day and 10 °C night for 14 days, followed by 15 °C day and 4 °C night for 14 to 21 days resulted in an 81% and 80% increase in leaf and stem survival, respectively, when frozen to a low of-8 °C. Electrolyte leakage and phenolic leakage assays effectively detected changes in percent leaf survival, but the TTC stain assay, using leaf disks, did not. Stem survival was best predicted by the TTC assay, using the phloem as the indicator tissue for survival. Electrolyte leakage and phenolic leakage were also reliable assays for predicting stem survival, although survival percentages were different at the same electrolyte leakage values reported in other studies. The callus growth assay accurately predicted survival for cold acclimated satsuma mandarin stems only. Chemical name used: triphenyl tetrazolium chloride (TTC).
Physical Disruption and Antibiotic Treatment of Pseudomonas aeruginosa with Gentamicin and Ciprofloxacin Biofilms has No

Pseudomonas aeruginosa is an opportunistic pathogen, armed with multiple resistance mechanisms that render it resistant to many antibiotics. One such mechanism is the ability to form biofilms. A previous study assessed the viability of P. aeruginosa cells within biofilms after physical disruption and antibiotic treatment, and found that there was no difference in cell viability despite physical disruption. However, an increase in green color, thought to be pyocyanin, was observed at higher amounts in the biofilms that had been exposed to both stresses. The purpose of this study was to determine if the lack of change in cell viability during antibiotic treatment and physical disruption was due to an increase in rough small colony variants of P. aeruginosa. The relative proportions of these variants within biofilms were assessed by quantitatively measuring changes in pyocyanin and qualitatively measuring pilin production over a 4-hour antibiotic treatment period following disruption compared to undisrupted biofilms. Antibiotic treatment caused an equal decrease in cell viability, regardless of biofilm disruption, indicating that physical disruption of biofilms was not sufficient to increase susceptibility to antibiotic treatment. Additionally, the results of the pyocyanin and pilin assays showed no relative change between the antibiotic treatment and/ or biofilm disruption conditions over the course of treatment. Therefore, no supporting evidence was generated for the hypothesis that P. aeruginosa within biofilms respond to physical disruption and antibiotic stress by increasing the proportion of rough small colony variants.
Retina Quantification of Macular Microvascular Changes in Patients With Retinitis Pigmentosa Using Optical Coherence Tomography Angiography

Citation: Inooka D, Ueno S, Kominami T, et al. Quantification of macular microvascular changes in patients with retinitis pigmentosa using optical coherence tomography angiography. Invest Ophthalmol Vis Sci. 2018;59:433–438. https://doi.org/ 10.1167/iovs.17-23202 PURPOSE. To evaluate the microvascular changes in eyes with RP quantitatively using optical coherence tomography angiography (OCTA) and to determine whether the correlations between these indices and the severity of RP are significant.
Tumor BRCA1 Reversion Mutation Arising during Neoadjuvant Platinum-Based Chemotherapy in Triple-Negative Breast Cancer Is Associated with Therapy Resistance

Purpose: In germline BRCA1 or BRCA2 (BRCA1/2) mutation carriers, restoration of tumor BRCA1/2 function by a secondary mutation is recognized as a mechanism of resistance to platinum and PARP inhibitors, primarily in ovarian cancer. We evaluated this mechanism of resistance in newly diagnosed patients with BRCA1/2-mutant breast cancer with poor response to neoadjuvant platinum-based therapy. Experimental Design: PrECOG 0105 was a phase II neoadjuvant study of gemcitabine, carboplatin, and iniparib in patients with stage I–IIIA triple-negative or BRCA1/2 mutation–associated breast cancer (n = 80). All patients underwent comprehensive BRCA1/2 genotyping. For mutation carriers with moderate or extensive residual disease after neoadjuvant therapy, BRCA1/2 status was resequenced in the residual surgical breast tumor tissue. Results: Nineteen patients had a deleterious germline BRCA1/2 mutation, and four had moderate residual disease at surgery. BRCA1/2 sequencing of residual tissue was performed on three patients. These patients had BRCA1 1479delAG, 3374insGA, and W1712X mutations, respectively, with LOH at these loci in the pretreatment tumors. In the first case, a new BRCA1 mutation was detected in the residual disease. This resulted in a 14–amino acid deletion and restoration of the BRCA1 reading frame. A local relapse biopsy 4 months later revealed the identical reversion mutation, and the patient subsequently died from metastatic breast cancer. Conclusions: We report a BRCA1 reversion mutation in a patient newly diagnosed with triple-negative breast cancer that developed over 18 weeks of platinum-based neoadjuvant therapy. This was associated with poor therapy response, early relapse, and death. Clin Cancer Res; 23(13); 3365–70. ©2017 AACR.
Effects of exercise training on pulmonary hemodynamics, functional capacity and inflammation in pulmonary hypertension

Pulmonary hypertension (PH) is characterized by severe exercise limitation mainly attributed to the impairment of right ventricular function resulting from a concomitant elevation of pulmonary vascular resistance and pressure. The unquestioned cornerstone in the management of patients with pulmonary arterial hypertension (PAH) is specific vasoactive medical therapy to improve pulmonary hemodynamics and strengthen right ventricular function. Nevertheless, evidence for a beneficial effect of exercise training (ET) on pulmonary hemodynamics and functional capacity in patients with PH has been growing during the past decade. Beneficial effects of ET on regulating factors, inflammation, and metabolism have also been described. Small case-control studies and randomized clinical trials in larger populations of patients with PH demonstrated substantial improvements in functional capacity after ET. These findings were accompanied by several studies that suggested an effect of ET on inflammation, although a direct link between this effect and the therapeutic benefit of ET in PH has not yet been demonstrated. On this background, the aim of the present review is to describe current concepts regarding the effects of exercise on the pulmonary circulation and pathophysiological limitations, as well as the clinical and mechanistic effects of exercise in patients with PH.
Pocket milling of carbon fiber-reinforced plastics using 532-nm nanosecond pulsed laser: An experimental investigation

Non-traditional machining of carbon fiber-reinforced plastics, such as laser machining, has great advantages over mechanical machining in the aspect of machinability and flexibility. In this article, a laser milling method using diode pumped and frequency doubled Nd:YVO4 nanosecond pulsed laser system is presented. The effects of processing parameters including laser power, scanning speed, and hatch distance were analyzed. It was found that machining quality and efficiency are seriously influenced by laser power and pulses overlapping rate. The features of micro-pit and chopped fibers on the machined surface were observed with metallographic microscope, and ablation mechanism involved was studied to explain the phenomenon. Depth-controlled milling strategy was realized in the laser focusing environment. Finally, challenges and suggestions are presented for wide application of the method.
Particle Swarm Optimization for Object-Based Feature Selection of VHSR Satellite Images

With the advent of very high spatial resolution (VHSR) satellite imagery, object-based classification (OBC) has attracted a great deal of attention in the remote sensing community. However, due to the numerous spectral, textural, and structural features which can be extracted for each object, feature selection is needed to address the curse-of-dimensionality issue. In this letter, a new wrapper object-based feature (OBF) selection method was applied in order to select the best combination of spectral, textural, and structural OBFs. In the first step, the image is segmented into objects using the multiresolution segmentation method. Subsequently, OBFs are extracted for each object. Last, optimal OBFs are selected using the proposed method based on particle swarm optimization (PSO) combined with the minimum distance classifier. Two VHSR remotely sensed images, acquired by a WorldView-2 sensor, were used to test the proposed method. The results of the experiment indicated that OBC using optimal OBFs led to significant improvement over the case where all extracted features were used. Furthermore, PSO has a better performance than do the three metaheuristic optimization algorithms: genetic algorithm, artificial bee colony, and honey-bee mating, according to the technique of order of preference by similarity to ideal solution analysis.
Late-Onset Puberty Induction by Transdermal Estrogen in Turner Syndrome Girls—A Longitudinal Study

Objective Estrogen replacement therapy (ERT) for Turner syndrome (TS) is a widely discussed topic; however, the optimal model of ERT for patients with delayed diagnosis and/or initiation of therapy is still unclear, mainly due to insufficient data. We present the results of a prospective observational single-center study in which the efficacy of late-onset puberty induction by one-regimen transdermal ERT in TS girls was evaluated. Methods The analysis encompassed 49 TS girls (63.3% with 45,X) with hypergonadotropic hypogonadism in whom unified transdermal ERT protocol was used for puberty induction (first two months 12.5 μg/24 h, thereafter 25.0 μg/24 h until breakthrough bleeding). Clinical visits for examination and therapy modification took place every 3–6 months. Transabdominal pelvic ultrasound examinations were performed at least twice: at the beginning and at the end of follow-up. Results The mean (SD) age at ERT induction was 15.1 (1.3) years. The duration of follow-up was 2.4 (1.1) years. Half of all the patients had at least B2 after 0.57 years, B3 after 1.1 years, B4 after 1.97 years, and menarche after 1.82 years from ERT initiation. With earlier initiation of ERT (≤14 years), B2 (p = 0.059) was achieved faster and B4 (p = 0.018) significantly slower than with the later start of ERT. Thirty-four (94.4%) patients had at least stage B3 at menarche. The karyotype, initial weight, and body mass index had no impact on puberty tempo during ERT. The uterine volume increased significantly during ERT in all the study group (p < 0.0001), and in half of the patients, the increase was at least 12.4-fold. It did not correlate with the duration of treatment (p = 0.84) or the dose of estradiol per kilogram (p = 0.78), nor did it depend on karyotype (p = 0.71) or age at ERT initiation (p = 0.28). There were no differences in ΔhSDS during ERT (p = 0.63) between the two age groups (ERT ≤14 and >14 years). Conclusion The presented easy-to-use fixed-dose regimen for late-onset puberty induction allowed for a satisfactory rate of achieving subsequent puberty stages and did not influence the growth potential.
HIF-1α promotes ZEB1 expression and EMT in a human bladder cancer lung metastasis animal model

Lung is one of the most common sites for bladder cancer to metastasize. Although the involvement of the epithelial-to-mesenchymal transition (EMT) in bladder cancer progression has been established, the mechanism of EMT induction remains unclear. In order to investigate this, T24-parental (P) and T24-lung (L) bladder cancer cells were obtained from primary tumors and lung metastatic sites of an animal model with orthotopic spontaneous metastatic bladder cancer, according to a protocol previously described. Compared with T24-P cells, mesenchymal-like T24-L cells exhibited an increased ability in tumor invasion and metastasis, as well as an increased expression of hypoxia-inducible factor (HIF)-1α, zinc finger E-box-binding homeobox 1 (ZEB1), vimentin and N-cadherin and lower level of cytokeratin 18 were observed. Mechanistically, it was identified that HIF-1α increases ZEB1 expression and subsequently regulates the expression of EMT-related genes in both HIF-1α knocking down by siRNA and gain-in HIF-1α by hypoxia culture cell models. In addition, the expression of HIF-1α and ZEB1 in bladder cancer tissues were increased compared with normal bladder epithelial tissues, as well as significantly increased in the high-grade, invasive and metastatic bladder cancer tissues compared with low-grade, superficial and non-metastatic bladder cancer tissues by using immune-histochemical staining assay. Notably, the protein level of HIF-1α was positively associated with that of ZEB1 in bladder cancer tissues. Results from the present study indicate that HIF-1α promotes ZEB1 expression and EMT in the T24-L human bladder cancer lung metastasis animal model, suggesting that HIF-1α serves an important function in the metastasis of bladder cancer, and HIF-1α and ZEB1 may be potential targets for inhibiting bladder metastasis in the future.
Phanerozoic survivors: Actinopterygian evolution through the Permo‐Triassic and Triassic‐Jurassic mass extinction events

Actinopterygians (ray‐finned fishes) successfully passed through four of the big five mass extinction events of the Phanerozoic, but the effects of these crises on the group are poorly understood. Many researchers have assumed that the Permo‐Triassic mass extinction (PTME) and end‐Triassic extinction (ETE) had little impact on actinopterygians, despite devastating many other groups. Here, two morphometric techniques, geometric (body shape) and functional (jaw morphology), are used to assess the effects of these two extinction events on the group. The PTME elicits no significant shifts in functional disparity while body shape disparity increases. An expansion of body shape and functional disparity coincides with the neopterygian radiation and evolution of novel feeding adaptations in the Middle‐Late Triassic. Through the ETE, small decreases are seen in shape and functional disparity, but are unlikely to represent major changes brought about by the extinction event. In the Early Jurassic, further expansions into novel areas of ecospace indicative of durophagy occur, potentially linked to losses in the ETE. As no evidence is found for major perturbations in actinopterygian evolution through either extinction event, the group appears to have been immune to two major environmental crises that were disastrous to most other organisms.
Clinical features, course, and outcomes of a UK cohort of pediatric moyamoya

Objective To describe characteristics and course of a large UK cohort of children with moyamoya from multiple centers and examine prognostic predictors. Methods Retrospective review of case notes/radiology, with use of logistic regression to explore predictors of outcome. Results Eighty-eight children (median presentation age 5.1 years) were included. Thirty-six presented with arterial ischemic stroke (AIS) and 29 with TIA. Eighty had bilateral and 8 unilateral carotid circulation disease; 29 patients had posterior circulation involvement. Acute infarction was present in 36/176 hemispheres and chronic infarction in 86/176 hemispheres at the index presentation. Sixty-two of 82 with symptomatic presentation had at least one clinical recurrence. Fifty-five patients were treated surgically, with 37 experiencing fewer recurrences after surgery. Outcome was categorized as good using the Recovery and Recurrence Questionnaire in 39/85 patients. On multivariable analysis, presentation with TIA (odds ratio [OR] 0.09, 95% confidence interval [CI] 0.02–0.35), headache (OR 0.10, 95% CI 0.02–0.58), or no symptoms (OR 0.08, 95% CI 0.01–0.68) was less likely to predict poor outcome than AIS presentation. Posterior circulation involvement predicted poor outcome (OR 4.22, 95% CI 1.23–15.53). Surgical revascularization was not a significant predictor of outcome. Conclusions Moyamoya is associated with multiple recurrences, progressive arteriopathy, and poor outcome in half of patients, especially with AIS presentation and posterior circulation involvement. Recurrent AIS is rare after surgery. Surgery was not a determinant of overall outcome, likely reflecting surgical case selection and presentation clinical status.
Asymmetry of Preoperative Incision Design Markings for Upper Blepharoplasty

Purpose: To compare preoperative incision design markings between both eyelids in upper blepharoplasty. Methods: This retrospective study examined 22 patients who underwent bilateral upper blepharoplasty surgery resulting from senile dermatochalasis and/or blepharoptosis. The initial preoperative incision design markings were drawn with the patient sitting upright. Then, with the patient in a supine position, preoperative design photographs were taken. The authors measured medial canthal excision angle, maximal lid excision height, maximal lid excision width, peak point angle, and peak point distance and compared measurements between both upper eyelids designs using Image J software. Results: The mean medial canthal excision angle, maximal lid excision height, and maximal lid excision width for the right side (30.68° ± 10.16°, 1.17 ± 0.24 cm, and 0.72 ± 0.19 cm) were significantly different from those for the left side (35.39° ± 13.82°; P < 0.001, 1.24 ± 0.25 cm; P = 0.002, and 0.77 ± 0.21 cm; P = 0.011). The mean peak point angle and peak point distance for the right side (15.67° ± 5.09°, 2.41° ± 0.31°) were significantly different from those for the left side (18.11° ± 5.49°; P = 0.001, 2.22 ± 0.28 cm; P = 0.001). Conclusions: In upper blepharoplasty, the preoperative incision marking design measurements of the left side were significantly greater than those of the right side. The symmetry can therefore be maximized by including the asymmetries in the preoperative design.
More Similar Than Different: Gender Differences in Children's Basic Numerical Skills Are the Exception Not the Rule.

This study investigates gender differences in basic numerical skills that are predictive of math achievement. Previous research in this area is inconsistent and has relied upon traditional hypothesis testing, which does not allow for assertive conclusions to be made regarding nonsignificant findings. This study is the first to compare male and female performance (N = 1,391; ages 6-13) on many basic numerical tasks using both Bayesian and frequentist analyses. The results provide strong evidence of gender similarities on the majority of basic numerical tasks measured, suggesting that a male advantage in foundational numerical skills is the exception rather than the rule.
Short and long time MR signal behavior of randomly distributed water and fat—numerical simulations

The MR time‐signal behavior of water has been reported to be different on short and long time scales for systems of randomly distributed perturbers in water in the static dephasing regime. Up to now, the signal of the perturbers in such systems has not been taken into consideration. Water–fat emulsions are macroscopically homogeneous systems and can be considered as microscopically randomly distributed perturbing fat spheres embedded in water. In such water–fat systems, the signal of the perturber, fat, cannot be ignored. Since water and fat are within the same system, the fat signal behavior may show similarities with water, with differences in short and long time scales. This could complicate fat‐referenced MR thermometry (MRT) methods such as multi‐gradient echo‐based (MGE) MRT. Simulations were performed using a numerical phantom comprising spherical fat objects embedded in a spherical water medium. To characterize the fat signal, the theoretical signal description of water was fitted to the simulated fat signal. The simulated signals were sampled as an MGE signal and MGE MRT was used to calculate temperatures. The sampling was done with and without delay, to investigate the effect on the temperature error of the time ranges in which the signal was sampled. It was confirmed that the fat signal behavior was similar to that of water and consisted of two regimes. The separation between the short and long time scales was approximately at 55 ms for fat, as compared with 8.9 ms for water. Without delayed signal sampling, the MGE MRT temperature error was about 2.5°C. With delayed sampling such that both the water and the fat signals were either in the short or in the long time scale the error was reduced to 0.2°C.