Miracle-dz/UniFAR-FTUs huggingface dataset:
The Basis and Promise of Programmable RNA Editing and Modification

One key advantage of RNA over genomic editing is its temporary effects. Aside from current use of DNA-targeting CRISPR-Cas9, the more recently discovered CRISPR-Cas13 has been explored as a means of editing due to its RNA-targeting capabilities. Specifically, there has been a recent interest in identifying and functionally characterizing biochemical RNA modifications, which has spurred a new field of research known as “epitranscriptomics”. As one of the most frequently occurring transcriptome modifications, N6-methyladenosine (m6A) has generated much interest. The presence of m6A modifications is under the tight control of a series of regulators, and the ability of fusing these proteins or demethylases to catalytically inactive CRISPR proteins have resulted in a new wave of programmable RNA methylation tools. In addition, studies have been conducted to develop different CRISPR/Cas and base editor systems capable of more efficient editing, and some have explored the effects of in vivo editing for certain diseases. As well, the application of CRISPR and base editors for screening shows promise in revealing the phenotypic outcomes from m6A modification, many of which are linked to physiological, and pathological effects. Thus, the therapeutic potential of CRISPR/Cas and base editors for not only m6A related, but other RNA and DNA related disease has also garnered insight. In this review, we summarize/discuss the recent findings on RNA editing with CRISPR, base editors and non-CRISPR related tools and offer a perspective regarding future applications for basic and clinical research.
Editorial: Ecology, Evolution, and Behavior of Viviparous Fishes

Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico, Mexico, 2 Population and Conservation Biology Group, Department of Biology, Texas State University, San Marcos, TX, United States, 3 Evolutionary Ecology Laboratories, Department of Biology, Brigham Young University, Provo, UT, United States, 4 Experimental Zoology Group, Department of Animal Sciences, Wageningen University,
Measuring and Modeling the Effect of Audio on Human Focus in Everyday Environments Using Brain-Computer Interface Technology

The goal of this study was to investigate the effect of audio listened to through headphones on subjectively reported human focus levels, and to identify through objective measures the properties that contribute most to increasing and decreasing focus in people within their regular, everyday environment. Participants (N = 62, 18–65 years) performed various tasks on a tablet computer while listening to either no audio (silence), popular audio playlists designed to increase focus (pre-recorded music arranged in a particular sequence of songs), or engineered soundscapes that were personalized to individual listeners (digital audio composed in real-time based on input parameters such as heart rate, time of day, location, etc.). Audio stimuli were delivered to participants through headphones while their brain signals were simultaneously recorded by a portable electroencephalography headband. Participants completed four 1-h long sessions at home during which different audio played continuously in the background. Using brain-computer interface technology for brain decoding and based on an individual’s self-report of their focus, we obtained individual focus levels over time and used this data to analyze the effects of various properties of the sounds contained in the audio content. We found that while participants were working, personalized soundscapes increased their focus significantly above silence (p = 0.008), while music playlists did not have a significant effect. For the young adult demographic (18–36 years), all audio tested was significantly better than silence at producing focus (p = 0.001–0.009). Personalized soundscapes increased focus the most relative to silence, but playlists of pre-recorded songs also increased focus significantly during specific time intervals. Ultimately we found it is possible to accurately predict human focus levels a priori based on physical properties of audio content. We then applied this finding to compare between music genres and revealed that classical music, engineered soundscapes, and natural sounds were the best genres for increasing focus, while pop and hip-hop were the worst. These insights can enable human and artificial intelligence composers to produce increases or decreases in listener focus with high temporal (millisecond) precision. Future research will include real-time adaptation of audio for other functional objectives beyond affecting focus, such as affecting listener enjoyment, drowsiness, stress and memory.
PyNeval: A Python Toolbox for Evaluating Neuron Reconstruction Performance

Quality assessment of tree-like structures obtained from a neuron reconstruction algorithm is necessary for evaluating the performance of the algorithm. The lack of user-friendly software for calculating common metrics motivated us to develop a Python toolbox called PyNeval, which is the first open-source toolbox designed to evaluate reconstruction results conveniently as far as we know. The toolbox supports popular metrics in two major categories, geometrical metrics and topological metrics, with an easy way to configure custom parameters for each metric. We tested the toolbox on both synthetic data and real data to show its reliability and robustness. As a demonstration of the toolbox in real applications, we used the toolbox to improve the performance of a tracing algorithm successfully by integrating it into an optimization procedure.
Evaluation of Disk Halo Size and Identification of Correlated Factors in Myopic Adults

This study aimed to evaluate glare source-induced disk halo size and assess its correlation with higher-order aberrations (HOAs), pupillometry findings, and contrast sensitivity in myopic adults (aged 23.8 ± 4.4 years). In this cross-sectional study, 150 eyes of 150 patients were assessed. All patients underwent routine ophthalmic examinations, wavefront aberrometry, halo size measurement, dynamic pupillometry, and contrast sensitivity tests. Spearman's correlation analysis and independent sample t-tests were performed for data analysis. The mean halo radius was 82.5 ± 21.8 and 236.7 ± 52.2 arc min at 5 and 1 cd/m2 luminance levels, respectively. The values were inversely correlated with internal spherical aberration (SA) (r = −0.175, p = 0.032 and r = −0.241, p = 0.003, respectively), but not correlated with spherical equivalent (SE, both p > 0.05). Positive correlations were observed between halo radius and pupil size, contraction amplitude, and dilation speed during pupillary light reflex. Halo radii at 5 and 1 cd/m2 luminance levels were not significantly correlated with the area under the log contrast sensitivity function (r = −0.093, p = 0.258 and r = −0.149, p = 0.069, respectively). The mean halo radius was not clinically different between myopic and healthy eyes at 5 cd/m2 luminance level and did not differ significantly between the high and low-to-moderate myopia at 5 and 1 cd/m2 luminance levels (all p > 0.05). According to a stepwise linear regression model, the internal SA had a negative effect on the halo radius under low photpic condition; the average pupil diameter, internal SA and corneal HOAs played a large role in determining the halo radius under mesopic condition.
P. granatum Peel Polysaccharides Ameliorate Imiquimod-Induced Psoriasis-Like Dermatitis in Mice via Suppression of NF-κB and STAT3 Pathways

Psoriasis is a chronic and refractory inflammatory and autoimmune-mediated cutaneous disease affecting approximately 2%–3% of the global population. Most of the current therapies could relieve symptoms rapidly, while the side effects cannot be negligible. Hence, it is urgent to explore much safer and more effective treatments. In the current work, we evaluated the potential beneficial effect of Punica granatum peel polysaccharides (PPPs) in an imiquimod-elicited psoriasis-like mouse model and unraveled their mechanism of action. Firstly, PPPs were isolated from P. granatum peels, and then the molecular weight was determined and monosaccharide analysis was performed. The results revealed that PPPs significantly ameliorated psoriasis-like skin lesions and reduced the Psoriasis Area and Severity Index (PASI) scores and transepidermal water loss (TEWL). PPPs also attenuated the expressions of CD3 and Ki67 in psoriasis-like mouse skin and suppressed the serum or skin levels of pro-inflammatory cytokines, such as tumor necrosis factor alpha (TNF-α), interleukin 6 (IL-6), IL-1β, IL-8, IL-17, and IL-23. Moreover, PPPs were able to upregulate the mRNA and protein expressions of aquaporin-3 (AQP3) and filaggrin (FLG) in the skin of mice. In addition, PPPs inhibited the NF-κB and STAT3 signaling pathways. Overall, these results indicated that PPPs ameliorated the symptoms of psoriasis through inhibition of the inflammatory cytokines by suppressing the NF-κB and STAT3 signaling pathways and improved skin barrier protection via enhancing AQP3 and FLG. These observations potentially contribute to providing theoretical and experimental evidence for the clinical application of PPPs for psoriasis.
Comparison of the Agronomic, Cytological, Grain Protein Characteristics, as Well as Transcriptomic Profile of Two Wheat Lines Derived From Wild Emmer

Two advanced wheat lines BAd7-209 and BAd23-1 without the functional gene GPC-B1 were obtained from a cross between common wheat cultivar Chuannong 16 (CN16) and wild emmer wheat accession D97 (D97). BAd7-209 showed superior quality parameters than those of BAd23-1 and CN16. We found that the components of glutenins and gliadins in BAd7-209 and BAd23-1 were similar, whereas BAd7-209 had higher amount of glutenins and gliadins than those of BAd23-1. RNA sequencing analysis on developing grains of BAd7-209 and BAd23-1 as well as their parents revealed 382 differentially expressed genes (DEGs) between the high–grain protein content (GPC) (D97 + BAd7-209) and the low-GPC (CN16 + BAd23-1) groups. DEGs were mainly associated with transcriptional regulation of the storage protein genes, protein processing in endoplasmic reticulum, and protein export pathways. The upregulated gluten genes and transcription factors (e.g., NAC, MYB, and bZIP) may contribute to the high GPC in BAd7-209. Our results provide insights into the potential regulation pathways underlying wheat grain protein accumulation and contribute to make use of wild emmer for wheat quality improvement.
PSMA PET in Imaging Prostate Cancer

After prostate malignancy diagnosis, precise determination of disease extent are fundamental steps for tailored made therapy. The earlier the diagnosis of the burden of the disease, the longer the survival in many cases. National and international guidelines are based on “classic” imaging technics combining radiological and nuclear medicine scans like CT, MRI and bone scintigraphy (BS). The most recent nuclear medicine development is the prostate specific membrane antigen (PSMA) PET and is emerging as the most promising tool of medical imaging, gaining ground every day. Nevertheless, the different onset among multiple studies fails to establish a worldwide admission and incorporation of this technique in guidelines and its position in workaday medical algorithms. It seems that the medical community agrees not to utilize PSMA PET for low-risk patients; intense debate and research is ongoing for its utility in intermediate risk patients. Contrariwise, in high-risk patients PSMA PET is confirmed outperforming CT and BS combined. Additionally, irrespectively to their castration status, patients with biochemical failure should be referred for PSMA PET. Even though PSMA PET reveals more extended disease than expected or exonerates equivalent lesions, thus impacting treatment optimization. Studies being in progress and future trials with clarify whether PSMA PET will be the new gold standard technic for specific groups of patients.
Mast Cell Chymase/Mcpt4 Suppresses the Host Immune Response to Plasmodium yoelii, Limits Malaria-Associated Disruption of Intestinal Barrier Integrity and Reduces Parasite Transmission to Anopheles stephensi

An increase in mast cells (MCs) and MCs mediators has been observed in malaria-associated bacteremia, however, the role of these granulocytes in malarial immunity is poorly understood. Herein, we studied the role of mouse MC protease (Mcpt) 4, an ortholog of human MC chymase, in malaria-induced bacteremia using Mcpt4 knockout (Mcpt4 -/-) mice and Mcpt4 +/+ C57BL/6J controls, and the non-lethal mouse parasite Plasmodium yoelii yoelii 17XNL. Significantly lower parasitemia was observed in Mcpt4 -/- mice compared with Mcpt4 +/+ controls by day 10 post infection (PI). Although bacterial 16S DNA levels in blood were not different between groups, increased intestinal permeability to FITC-dextran and altered ileal adherens junction E-cadherin were observed in Mcpt4 -/- mice. Relative to infected Mcpt4 +/+ mice, ileal MC accumulation in Mcpt4 -/- mice occurred two days earlier and IgE levels were higher by days 8-10 PI. Increased levels of circulating myeloperoxidase were observed at 6 and 10 days PI in Mcpt4 +/+ but not Mcpt4 -/- mice, affirming a role for neutrophil activation that was not predictive of parasitemia or bacterial 16S copies in blood. In contrast, early increased plasma levels of TNF-α, IL-12p40 and IL-3 were observed in Mcpt4 -/- mice, while levels of IL-2, IL-10 and MIP1β (CCL4) were increased over the same period in Mcpt4 +/+ mice, suggesting that the host response to infection was skewed toward a type-1 immune response in Mcpt4 -/- mice and type-2 response in Mcpt4 +/+ mice. Spearman analysis revealed an early (day 4 PI) correlation of Mcpt4 -/- parasitemia with TNF-α and IFN-γ, inflammatory cytokines known for their roles in pathogen clearance, a pattern that was observed in Mcpt4 +/+ mice much later (day 10 PI). Transmission success of P. y. yoelii 17XNL to Anopheles stephensi was significantly higher from infected Mcpt4 -/- mice compared with infected Mcpt4 +/+ mice, suggesting that Mcpt4 also impacts transmissibility of sexual stage parasites. Together, these results suggest that early MCs activation and release of Mcpt4 suppresses the host immune response to P. y. yoelii 17XNL, perhaps via degradation of TNF-α and promotion of a type-2 immune response that concordantly protects epithelial barrier integrity, while limiting the systemic response to bacteremia and parasite transmissibility.
The Value of Nasal and Oral Clinical Examination in Febrile Neutropenic Patients for Initiating Antifungal Therapy as a Preemptive Method

Background Invasive fungal infections (IFIs) are complications that lead to mortality and morbidity in hematologic malignancies. The time of starting antifungal therapy is vital. Preemptive antifungal therapy has appeared recently as a new policy for the management of IFIs based on noninvasive ways in neutropenic patients. Methods We enrolled leukemia patients with neutropenia after chemotherapy in Imam Khomeini Hospital Complex, Tehran, Iran. Patients who entered the neutropenic phase were divided into two categories (empirical and preemptive) for receiving antifungal agents. The patients were clinically examined in the preemptive group every day to find IFIs. As soon as clinical evidence of IFIs was observed, antifungal was prescribed. The empirical group patients received antifungals based on the ward protocol. Based on the data in each group, the diagnostic and therapeutic results of cases are followed-up to 3 months. To compare percentages between the two groups, the chi-squared test was used. And to compare two means between the two groups, the independent t-test was used. All the statistical analyses were done in the Statistical Package for the Social Sciences (SPSS) version 24 software (IBM Corporation, Armonk, New York, USA). Results We assessed 132 leukemic patients with inclusion and exclusion criteria. Eventually, 80 patients were enrolled. The mean age was 35.52 years. Demographics data and distribution of leukemia type show no significant differences between the two groups. Despite a higher percentage of IFIs discovered in the preemptive group than the empirical group (25 vs. 18.75%, respectively), but data show no significant differences. The average days of IFIs diagnosis since the beginning of neutropenia in the empirical group were 9.5 days while in the preemptive group, the average days were 5.4 days (p < 0.05). Totally, there were 15 patients with a proven IFI in each group (40% in the empirical group and 60% in the preemptive group). Results significantly show an increase in surgical sinus debridement in the empirical groups (83.3%) vs. the preemptive groups (55.5%), (p < 0.05). The mortality rate differed significantly among the two groups; it was 7.5% in the preemptive group and 25% in the empirical group (p < 0.05). Conclusion Daily oral and nasal cavities examination to find the symptoms of IFIs and then start preemptive antifungal agents may be able to lead to accurate diagnosis, earlier treatment, and decreasing sinus surgery debridement in leukemia patients with neutropenia.
Leptin: A Potential Link Between Obstructive Sleep Apnea and Obesity

Chronic intermittent hypoxia (CIH), a pathophysiological manifestation of obstructive sleep apnea (OSA), is strongly correlated with obesity, as patients with the disease experience weight gain while exhibiting elevated plasma levels of leptin. This study was done to determine whether a relationship may exist between CIH and obesity, and body energy balance and leptin signaling during CIH. Sprague-Dawley rats were exposed to 96 days of CIH or normoxic control conditions, and were assessed for measures of body weight, food and water intake, and food conversion efficiency. At the completion of the study leptin sensitivity, locomotor activity, fat pad mass and plasma leptin levels were determined within each group. Additionally, the hypothalamic arcuate nucleus (ARC) was isolated and assessed for changes in the expression of proteins associated with leptin receptor signaling. CIH animals were found to have reduced locomotor activity and food conversion efficiency. Additionally, the CIH group had increased food and water intake over the study period and had a higher body weight compared to normoxic controls at the end of the study. Basal plasma concentrations of leptin were significantly elevated in CIH exposed animals. To test whether a resistance to leptin may have occurred in the CIH animals due to the elevated plasma levels of leptin, an acute exogenous (ip) leptin (0.04 mg/kg carrier-free recombinant rat leptin) injection was administered to the normoxic and CIH exposed animals. Leptin injections into the normoxic controls reduced their food intake, whereas CIH animals did not alter their food intake compared to vehicle injected CIH animals. Within ARC, CIH animals had reduced protein expression of the short form of the obese (leptin) receptor (isoform OBR100) and showed a trend toward an elevated protein expression of the long form of obese (leptin) receptor (OBRb). In addition, pro-opiomelanocortin (POMC) protein expression was reduced, but increased expression of the phosphorylated extracellular-signal-regulated kinase 1/2 (pERK1/2) and of the suppressor of cytokine signaling 3 (SOCS3) proteins was observed in the CIH group, with little change in phosphorylated signal transducer and activator of transcription 3 (pSTAT3). Taken together, these data suggest that long-term exposure to CIH, as seen in obstructive sleep apnea, may contribute to a state of leptin resistance promoting an increase in body weight.
Improving Work-Life Fit in Hourly Jobs: An Underutilized Cost-Cutting Strategy in a Globalized World

This report provides employers with the tools they need to gain a competitive edge by improving what workforce experts call schedule effectiveness. One key to schedule effectiveness is to gain an understanding of the constraints that need to be programmed in to develop an effective schedule — including the constraints employees face as they fulfill their family responsibilities. This report offers a better understanding of those constraints by providing vivid, capsule descriptions of how work and family fit together for low-wage and higher-wage hourly workers. Knowing your workforce is a vital first step. The report also provides concrete tools to allow employers to improve schedule effectiveness in hourly jobs.
A Method to Evaluate Vehicle Impact Speeds in Passenger Car-Pedestrian Accidents

This paper aimed to research the relationship between the wrap around distance (WAD) to head contact and vehicle impact speed based on real pedestrian traffic accidents with video. A team was established to collect passenger car-pedestrian accident cases occurring between July 2011 and July 2015 in Chongqing, China. A total of 15 pedestrian crashes were selected into the sample. Impact speeds were calculated by a video analysis technology, and the WAD was revised according to the average height of pedestrians involved in the sample. The relationship between the WAD and impact speed was analyzed using linear regression analysis. We propose a method to evaluate the impact speed in passenger car-pedestrian. These results will contribute to the development of judicial identification and research of pedestrian injury.
Noise analysis and modeling of low-voltage power line

After the lowvoltage power line's channel properties are analyzed, noises in the frequency range between 1～30 MHz are sorted and their properties are given in detail. Based on experimentation, the three main noises including background (colored) noise,narrowband interference and impulse noise are presented in the approximate function models. 
Theoretic Analysis of Optical Fiber Ring Resonators Based on A Collinear 3×3 Fiber Coupler

We present a systemic theoretical analysis of three different types of optical fiber ring resonator using a collinear 3×3 fiber coupler. It is the first time that the theoretical analysis of dual ring resonator based on a collinear 3×3 fiber coupler is presented. Expressions for the output fields and output intensities of the fiber ring resonator are obtained. By using computer system software one can obtain these output intensities easily. The three types of resonators all use a collinear 3×3 fiber coupler as key device in which the three fibers are in the same plane. It is found that these fiber ring resonators have their own special characteristics. They can be used as fiber filter, a sensor with high_phase sensitivity and densely spaced two_channel wavelength division multi/demultiplexer(WDM/WDDM).