Miracle-dz/UniFAR-FTUs huggingface dataset:
Human color constancy based on the geometry of color distributions

The physical inputs to our visual system are dictated by the interplay between lights and surfaces; thus, for surface color to be stably perceived, the influence of the illuminant must be discounted. To reveal our strategy to infer the illuminant color, we conducted three psychophysical experiments designed to test our optimal color hypothesis that we internalize the physical color gamut under various illuminants and apply the prior to estimate the illuminant color. In each experiment, we presented 61 hexagons arranged without spatial gaps, where the surrounding 60 hexagons were set to have a specific shape in their color distribution. We asked participants to adjust the color of a center test field so that it appeared to be a full-white surface placed under a test illuminant. Results and computational modeling suggested that, although our proposed model is limited in accounting for estimation of illuminant intensity by human observers, it agrees fairly well with the estimates of illuminant chromaticity in most tested conditions. The accuracy of estimation generally outperformed other tested conventional color constancy models. These results support the hypothesis that our visual system can utilize the geometry of scene color distribution to achieve color constancy.
Emission characteristic of hydrogen and gasoline blend in spark-ignited engine

Hydrogen is an energy carrier that can transform our fossil fuel-dependent economy into a hydrogen economy, which can provide an emission-free transportation fuel. Hydrogen-fuelled engines are known for several advantages, among which is the very low concentration of pollutants in the exhaust gases compared with internal combustion engines using traditional or other alternative fuels. Hydrogen-driven vehicles thus reduce both local and global emissions. It is an energy carrier that can be used in internal combustion engines or fuel cells producing virtually no greenhouse gas emissions when combusted with oxygen. The only significant emission is water vapour. The effect of blending of hydrogen with gasoline is analysed in this current paper. Both HC and NOx concentration decrease with the increase in hydrogen fractions. The results were analysed by collecting data on different crank angles and at 5%, 10%, 15% and 20% of hydrogen introduction into combustion chamber along with gasoline as base fuel.
Using molecular transmission networks to understand the epidemic characteristics of HIV-1 CRF08_BC across China

ABSTRACT HIV-1 CRF08_BC has become a major epidemic in heterosexuals and intravenous drug users (IDUs) in southern China. In order to evaluate the trends of its epidemic and facilitate targeted HIV prevention, we constructed the genetic transmission networks based on its pol sequences, derived from the National HIV Molecular Epidemiology Survey. Through retrospective network analysis, to study the epidemiological and demographic correlations with the transmission network. Of the 1,829 study subjects, 639 (34.9%) were clustered in 151 transmission networks. Factors associated with increased clustering include IDUs, heterosexual men, young adults and people with lower education (P < 0.05 for all). The IDUs, MSM, young adult and person with low education had more potential transmission links as well (P < 0.05 for all). The most crossover links were found between heterosexual women and IDUs, with 30.9% heterosexual women linked to IDUs. The crossover links heterosexual women were mainly those with middle age and single (P < 0.001). This study indicated that the HIV-1 CRF08_BC epidemic was still on going in China with more than one third of the infected people clustered in the transmission networks. Meanwhile, the study could help identify the active CRF08_BC spreader in the local community and greatly facilitate précising AIDS prevention with targeted intervention.
Inverse probability weighted estimation for recurrent events data with missing category

Modeling recurrent event data with multiple event types has drawn interest in recent biomedical studies due to its flexibility for understanding different risk factors for multiple recurrent event processes. However, in such data type, missing event type appears frequently because of various reasons such as recording ignorance or resource limitation. In this study, we aim to propose an inverse probability weighted estimation that is commonly used in the missing data literature to correct possibly biased estimation by a complete‐case analysis. This approach is not limited to a specific form of the recurrent event model. We derive the large sample theory in a general form. We demonstrate that our approach can be applied to either multiplicative or additive rates model with practical sample size via comprehensive simulations. Nonmucoid and mucoid Pseudomonas aeruginosa infections of 14 888 patients in 2016 Cystic Fibrosis Foundation Patient Registry data are analyzed to show that, without including 12% events with missing event type in the analysis, several factors may be misidentified as risk factors for the nonmucoid type of infections.
Modulation of intercolumnar synchronization by endogenous electric fields in cerebral cortex

Endogenous electric fields modulate synchronization across cerebral cortex columns compatible with electric-dipole interactions. Neurons synaptically interacting in a conductive medium generate extracellular endogenous electric fields (EFs) that reciprocally affect membrane potential. Exogenous EFs modulate neuronal activity, and their clinical applications are being profusely explored. However, whether endogenous EFs contribute to network synchronization remains unclear. We analyzed spontaneously generated slow-wave activity in the cerebral cortex network in vitro, which allowed us to distinguish synaptic from nonsynaptic mechanisms of activity propagation and synchronization. Slow oscillations generated EFs that propagated independently of synaptic transmission. We demonstrate that cortical oscillations modulate spontaneous rhythmic activity of neighboring synaptically disconnected cortical columns if layers are aligned. We provide experimental evidence that these EF-mediated effects are compatible with electric dipoles. With a model of interacting dipoles, we reproduce the experimental measurements and predict that endogenous EF–mediated synchronizing effects should be relevant in the brain. Thus, experiments and models suggest that electric-dipole interactions contribute to synchronization of neighboring cortical columns.
Cas9-expressing chickens and pigs as resources for genome editing in livestock

Significance Genetically modified animals are crucial for functional studies and translational biomedical research. However, the generation of genome-edited large animals is time consuming and inefficient. Here, we report the generation of transgenic pigs and chickens that ubiquitously express Cas9 nuclease. The functionality of Cas9 was demonstrated for different target genes, a variety of cell types, and in vivo for the heart and the developing brain. Genome editing can now easily be carried out in vivo in specific organs or tissues without the need to generate germline-modified animals. These Cas9 transgenic animals provide an innovative and efficient resource for in vivo genome editing in biomedical and agricultural sciences. Genetically modified animals continue to provide important insights into the molecular basis of health and disease. Research has focused mostly on genetically modified mice, although other species like pigs resemble the human physiology more closely. In addition, cross-species comparisons with phylogenetically distant species such as chickens provide powerful insights into fundamental biological and biomedical processes. One of the most versatile genetic methods applicable across species is CRISPR-Cas9. Here, we report the generation of transgenic chickens and pigs that constitutively express Cas9 in all organs. These animals are healthy and fertile. Functionality of Cas9 was confirmed in both species for a number of different target genes, for a variety of cell types and in vivo by targeted gene disruption in lymphocytes and the developing brain, and by precise excision of a 12.7-kb DNA fragment in the heart. The Cas9 transgenic animals will provide a powerful resource for in vivo genome editing for both agricultural and translational biomedical research, and will facilitate reverse genetics as well as cross-species comparisons.
Urinary cytokines in women with refractory detrusor overactivity: A longitudinal study of rotating antibiotic versus placebo treatment

Over 50% of women with detrusor overactivity (DO), who do not respond to therapy have been shown to have bacteriuria, which may stimulate the release of inflammatory cytokines than can enhance nerve signalling, leading to symptoms of urgency. This study made use of a consecutive series of urine samples collected from women with refractory DO, who participated in a clinical trial of rotating antibiotic therapy. The aim was to determine the effect of bacteriuria and antibiotic treatment on the levels of urinary cytokines, and to correlate the cytokine concentration with patient outcome measures relating to urgency or urge incontinence. The urinary cytokines chosen were IL-1α, IL-1 receptor antagonist, IL-4, IL-6, IL-8, IL-10, CXCL10 (IP-10), MCP-1 and TNF-α. The presence of bacteriuria stimulated a significant increase in the concentrations of IL-1α (P 0.0216), IL-1 receptor antagonist (P 0.0264), IL-6 (P 0.0003), IL-8 (P 0.0043) and CXCL-10 (P 0.009). Antibiotic treatment significantly attenuated the release of IL-1α (P 0.005), IL-6 (P 0.0027), IL-8 (P 0.0001), IL-10 (P 0.049), and CXCL-10 (P 0.042), i.e. the response to the presence of bacteria was less in the antibiotic treated patients. Across the 26 weeks of the trial, antibiotic treatment reduced the concentration of five of the nine cytokines measured (IL-1α, IL-6, IL-8, IL-10 and CXCL-10); this did not reach significance at every time point. In antibiotic treated patients, the urinary concentration of CXCL-10 correlated positively with four of the six measures of urgency. This study has shown that cytokines associated with activation of the innate immune system (e.g. cytokines chemotactic for or activators of macrophages and neutrophils) are reduced by antibiotic therapy in women with refractory DO. Antibiotic therapy is also associated with symptom improvement in these women, therefore the inflammatory response may have a role in the aetiology of refractory DO.
The Quality of Dying and Death of Advanced Cancer Patients in Palliative Care and Its Association With Place of Death and Quality of Care

The quality of dying and death is currently considered an objective to achieve at the end of life. The aim of this study is to analyze the quality of dying and death of advanced cancer patients in palliative care and its association with place of death and quality of care from the perspective of family caregivers. This is a cross-sectional study. The study sample included 72 family caregivers of advanced cancer patients in palliative care. For the evaluation of the quality of dying and death, the Spanish version of the Quality of Dying and Death Questionnaire was used. Quality of care was evaluated with the Palliative Care Outcome Scale. The mean (SD) total score on the Spanish version of the Quality of Dying and Death Questionnaire was 64.56 (20.97). The quality of dying and death was higher when the patients died at home, 70.45 (19.70), and it was positively correlated with quality of care (r = 0.61). Palliative care contributes to achieving a satisfactory quality of dying and death in Spanish advanced cancer patients. Further studies that evaluate interventions for improving the quality of dying and death in the advanced cancer population are needed.
Patient Characteristics Independently Associated With Knee Osteoarthritis Symptom Severity at Initial Orthopedic Consultation

Background/Objective The objective of this study was to identify patient and disease characteristics associated with the symptomatic severity of knee osteoarthritis (OA) at the time of initial knee OA diagnosis by an orthopedist. Methods This medical records review included patients initially diagnosed with knee OA during 2016 to 2017 by a single orthopedic surgeon in a university-based tertiary care setting. All variables were assessed at first OA diagnosis. Main outcomes were subscales of the Knee Injury and Osteoarthritis Outcome Score–Pain, other Symptoms, knee-related quality of life, and function in daily living. Multivariable regression analyses examined the following predictors of main outcomes: sex, race, age, insurance type, body mass index, Charlson comorbidity index, and radiographic OA severity (Kellgren-Lawrence grade). Results Of the 559 patients included in the study, most were African American (52.1%), female (71.7%), and had severe radiographic OA (Kellgren-Lawrence grade, 4; 68.7%). Female sex, African American racial/ethnic group, Medicaid insurance, younger age, and severe radiographic OA were independently statistically significantly associated with worse symptoms, pain, and function (p < 0.05 for all). Body mass index and Charlson comorbidity index were not statistically significant predictors of any outcome. Conclusions This study identified disparities in the perception of knee OA problems at initial orthopedist diagnosis based on sex, age, race, insurance, and radiographic OA severity. Because most of these variables are also associated with more rapid progression of OA, identifying their biopsychosocial underpinnings may help determine which interventions are most likely to redress these disparities and delay progression to end-stage knee OA.
Characteristics and nature of the halogen-bonding interactions between CCl3F and ozone: a supermolecular and SAPT study

The strength and nature of the halogen-bond interactions in CCl3F···O3 complexes were examined by means of ab initio quantum-chemical calculations and symmetry-adapted perturbation theory (SAPT). Our calculations predict a trifurcated C–Cl···O interaction for the global minimum of CCl3F···O3 complex and several local minima, differing slightly in energy, separated by very low barriers. The calculations, which include a rigorous decomposition of the interaction energies, also indicate that the interaction of CCl3F molecule with O3 is characterised by contributions from both electrostatic and dispersion energies, with the contribution of the latter being dominant. The evaluated SAPT interaction energies for the CCl3F···O3 complexes are generally in good agreement with those obtained using the supermolecule CCSD(T) method, suggesting that SAPT is a proper method to study the intermolecular interactions in these complexes.
Diffuse Large B-Cell Lymphoma.

Large B-cell lymphomas, with an estimated 150,000 new cases annually worldwide, represent almost 30% of all cases of non-Hodgkin’s lymphoma. Patients typically present with progressive lymphadenopathy, extranodal disease, or both and require therapy. Despite the advanced stage at presentation in the majority of patients, more than 60% can be cured with R-CHOP (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) immunochemotherapy (Fig. 1A). Patients with treatment failure after R-CHOP often have a poor outcome — in particular, those with disease that is refractory to frontline or subsequent therapies — although some patients can have a durable remission and be cured after secondary therapies. Over the past two decades, improved insights into large B-cell lymphomas, in terms of epidemiology, prognostic factors, and biologic heterogeneity, have led to a refinement of disease classification and the development of new therapeutic approaches.
Frequency response characteristics of IPMC sensors with current/voltage measurements

This paper discusses a model of IPMC sensors and the characteristics of the frequency responses. There are two different methods of measurements, the current sensing and the voltage sensing, which exhibit completely different frequency responses each other. A simple model based on Onsager's equation is shown in order to explain the experimental results of the current sensing. The voltage sensing model is derived by the equivalent transform of the voltage and the current sources. In contrast to the constant gain of the charge response, the characteristics of the voltage response are directly related to the impedance dynamics. In the experiments, the frequency responses of the charge/current sensing and the voltage sensing for two species of counter ion are measured. The ratio of the obtained frequency responses and the measured impedance are also compared to validate the voltage sensing model. Though the theoretical prediction of the sensor coefficient does not match the experimental one, the structure of the model agrees with the experimental data.
A Rare Case of Congenitally Acquired Ocular Toxocariasis in A Five-Week-Old Infant

ABSTRACT Purpose To report a case of strabismus in a five-week-old infant, likely secondary to a rare occurrence of congenitally acquired ocular toxocariasis. Methods Retrospective case report. Results A five-week-old male infant with left exotropia was referred to pediatric ophthalmology and to a vitreoretinal specialist. Fundoscopic examination revealed a granuloma with associated retinal folds and tractional retinal detachment typical for ocular toxocariasis. Serology revealed positivity for Toxocara antibodies, consistent with the clinical diagnosis of ocular toxocariasis. Conclusion Ocular toxocariasis is typically thought to be secondary to acquired Toxocara infection secondary to fecal-oral transmission. In this case of early-onset strabismus secondary to ocular toxocariasis, it is hypothesized that this is a presentation of congenitally acquired toxocariasis.
Investigation into surface composition of nitrogen-doped niobium for superconducting RF cavities

Systematic analysis of the surface morphology, crystalline phase, chemical composition and elemental distribution along depth for nitrogen-doped niobium was carried out using different methods of characterization, including Scanning Electron Microscopy (SEM), Atomic-Force Microscopy (AFM), Grazing Incidence X-ray Diffraction (GIXRD), Rutherford Backscattering Spectrometry (RBS) and layer-by-layer X-ray Photoelectron Spectroscopy (XPS) analysis. The results showed that, after nitrogen doping, the surface was covered by densely distributed trigonal precipitates with an average crystallite size of 32 ± 8 nm, in line with the calculation result (29.9 nm) of nitrogen-enriched β-Nb2N from GIXRD, demonstrating the phase composition of trigonal precipitates. The depth analysis through RBS and XPS indicated that β-Nb2N was dominant in the topmost 9.7 nm and extended to a depth of 575 nm, with gradually decreased content. In addition, the successive change along depth in the naturally oxidized states of niobium after nitrogen doping, was revealed. It was interesting to find that the oxygen diffusion depth could be moderately enhanced by the nitridation process. These results established the near-surface phase composition of nitrided niobium, which is of great significance in evaluating the effect of nitrogen doping and further understanding the Q improvement of the superconducting radio frequency cavities.
Complete revascularization in stable multivessel coronary artery disease: A real world analysis from the British Columbia Cardiac Registry

More than half of patients undergoing percutaneous coronary intervention (PCI) have multivessel disease (MVD). The prognostic significance of PCI in stable patients has recently been debated, but little data exists about the potential benefit of complete revascularization (CR) in stable MVD. We investigated the prognostic benefit of CR in patients undergoing PCI for stable disease.
Structural Perturbations of Exon Skipping Edits within the Dystrophin D20:24 Region

Exon skipping is a disease modifying therapy that operates at the RNA level. In this strategy, oligonucleotide analog drugs are used to specifically mask specific exons and prevent them from inclusion in the mature mRNA. Of course, this also results in loss of the corresponding region from the cognate protein, which is one possible therapeutic aim. Exon skipping can also be used to restore protein expression in cases where a genetic frameshift mutation has occurred, and this how it is applied to Duchenne muscular dystrophy, DMD. DMD most commonly arises as a result of large exonic deletions that juxtapose flanking exons of incompatible reading frame in the dystrophin gene, creating a frameshift and abolishing protein expression. Loss of dystrophin protein leads to the pathology of the disease, which is severe, causing death generally in the second or third decade of life. Here, the primary aim of exon skipping is the restoration of the reading frame by skipping an exon adjacent to the patient’s original defect. However, the therapeutically expressed protein is of course edited, and missing both the region of the underlying genetic defect, as well as the therapeutically skipped exon. While restoring some protein expression is good, how removing some region from the middle of a protein effects its structure and function is unclear. Complicating this in the case of DMD is the fact that the dystrophin gene is very large, containing 79 exons. Many different underlying deletions are known, and exon skipping can be applied in many ways. It has previously been shown that many exon-skip edits result in structural perturbations of varying degrees. What has been unclear is whether and how exon editing can be done to minimize these perturbations. In this study we examine a systematic and comprehensive panel of possible exon edits in a region of the dystrophin protein, and identify for the first time, exon edits that appear to maintain structural stability similar to wildtype protein. We also identify factors that appear to be correlated with the degree of structural perturbation, such as the number of cooperative protein domains, as well as how the underlying exon structure interacts with the protein domain structure.
Ca2+ Sensitivity of Anoctamin 6/TMEM16F Is Regulated by the Putative Ca2+-Binding Reservoir at the N-Terminal Domain

Anoctamin 6/TMEM16F (ANO6) is a dual-function protein with Ca2+-activated ion channel and Ca2+-activated phospholipid scramblase activities, requiring a high intracellular Ca2+ concentration (e.g., half-maximal effective Ca2+ concentration [EC50] of [Ca2+]i > 10 μM), and strong and sustained depolarization above 0 mV. Structural comparison with Anoctamin 1/TMEM16A (ANO1), a canonical Ca2+-activated chloride channel exhibiting higher Ca2+ sensitivity (EC50 of 1 μM) than ANO6, suggested that a homologous Ca2+-transferring site in the N-terminal domain (Nt) might be responsible for the differential Ca2+ sensitivity and kinetics of activation between ANO6 and ANO1. To elucidate the role of the putative Ca2+-transferring reservoir in the Nt (Nt-CaRes), we constructed an ANO6-1-6 chimera in which Nt-CaRes was replaced with the corresponding domain of ANO1. ANO6-1-6 showed higher sensitivity to Ca2+ than ANO6. However, neither the speed of activation nor the voltage-dependence differed between ANO6 and ANO6-1-6. Molecular dynamics simulation revealed a reduced Ca2+ interaction with Nt-CaRes in ANO6 than ANO6-1-6. Moreover, mutations on potentially Ca2+-interacting acidic amino acids in ANO6 Nt-CaRes resulted in reduced Ca2+ sensitivity, implying direct interactions of Ca2+ with these residues. Based on these results, we cautiously suggest that the net charge of Nt-CaRes is responsible for the difference in Ca2+ sensitivity between ANO1 and ANO6.