Personal transcriptome variation is poorly explained by current genomic deep learning models.

Genomic deep learning models can predict genome-wide epigenetic features and gene expression levels directly from DNA sequence. While current models perform well at predicting gene expression levels across genes in different cell types from the reference genome, their ability to explain expression variation between individuals due to cis-regulatory genetic variants remains largely unexplored. Here, we evaluate four state-of-the-art models on paired personal genome and transcriptome data and find limited performance when explaining variation in expression across individuals. In addition, models often fail to predict the correct direction of effect of cis-regulatory genetic variation on expression.

Fabrication of Multifunctional Electronic Textiles Using Oxidative Restructuring of Copper into a Cu-Based Metal-Organic Framework.

This paper describes a novel synthetic approach for the conversion of zero-valent copper metal into a conductive two-dimensional layered metal-organic framework (MOF) based on 2,3,6,7,10,11-hexahydroxytriphenylene (HHTP) to form Cu3(HHTP)2. This process enables patterning of Cu3(HHTP)2 onto a variety of flexible and porous woven (cotton, silk, nylon, nylon/cotton blend, and polyester) and non-woven (weighing paper and filter paper) substrates with microscale spatial resolution. The method produces conductive textiles with sheet resistances of 0.1-10.1 MΩ/cm2, depending on the substrate, and uniform conformal coatings of MOFs on textile swatches with strong interfacial contact capable of withstanding chemical and physical stresses, such as detergent washes and abrasion. These conductive textiles enable simultaneous detection and detoxification of nitric oxide and hydrogen sulfide, achieving part per million limits of detection in dry and humid conditions. The Cu3(HHTP)2 MOF also demonstrated filtration capabilities of H2S, with uptake capacity up to 4.6 mol/kgMOF. X-ray photoelectron spectroscopy and diffuse reflectance infrared spectroscopy show that the detection of NO and H2S with Cu3(HHTP)2 is accompanied by the transformation of these species to less toxic forms, such as nitrite and/or nitrate and copper sulfide and Sx species, respectively. These results pave the way for using conductive MOFs to construct extremely robust electronic textiles with multifunctional performance characteristics.

Internuclear Ophthalmoplegia Characterizes Multiple Sclerosis Rather Than Neuromyelitis Optica Spectrum Disease.

BACKGROUND: Neuromyelitis optica spectrum disease (NMOSD) and multiple sclerosis (MS) share clinical presentations including optic neuritis and brainstem syndromes. Internuclear ophthalmoplegia (INO) is characterized by slowed ipsilateral adduction saccades and results from a lesion in the medial longitudinal fasciculus (MLF). Although INO is a common clinical finding in MS, its prevalence in NMOSD is unknown. The objective of this work is to determine the comparative frequencies of INO in patients with NMOSD and MS and compare clinical features of both disease processes. METHODS: This is a retrospective study of patients 18 years and older who have an established diagnosis of NMOSD or MS and were evaluated by both neuro-ophthalmology and neuro-immunology specialists between 2014 and 2020. Electronic medical records were screened for documentation of an acute INO at any time during follow-up. Incidence rates were calculated from number of cases of new-onset INO and patient years observed. Logistic regression was used to evaluate the likelihood of developing an INO at any time point for NMOSD vs MS patients. Multivariable analysis was performed by adjusting for age, race, gender, and length of follow-up. RESULTS: Two hundred eighty patients (80 NMOSD, 200 MS) were included. Age range was 18-79 years with a mean age of 35.14 (SD ± 12.41 years). Average length of follow-up in MS and NMOSD patients was 4.18 years vs 3.79 years, respectively (P > 0.05), and disease duration before the start of the study in MS and NMOSD was 8.76 years vs 4.65 years, respectively (P < 0.01). Mean disease duration and follow-up time of both groups was 7.58 years and 4.07 ± 2.51 years, respectively. NMOSD patients were predominantly seropositive for AQP4 antibody (61.25%, n = 49). Individuals who had MOG antibody but also met NMOSD criteria were also included (18.75%, n = 15). The frequency of INO at any time point was 1.25% (n = 1) in NMOSD compared with 16% (n = 32) in MS. The incidence rate of new-onset INO in NMOSD (excluding MOGAD) was 3.8/1,000 person years and 23.9/1,000 person years in MS. Adjusted analysis showed that NMOSD patients were 13.89 times (odds ratio [OR] 0.07, 95% confidence interval [CI] 0.01-0.598, P = 0.015) less likely to develop an INO compared with those with MS when including MOGAD patients, 12.5 times less likely (OR 0.08, 95% CI: 0.10-0.67, P = 0.02) when excluding MOGAD patients and 9.62 times less likely (OR 0.10, 95% CI: 0.01-0.87, P = 0.036) for AQP4+ patients. CONCLUSIONS: Our study shows that the incidence of new INO (3.8 vs 23.9 per 1,000 person years), and the odds of having INO at any time point are significantly lower in NMOSD than MS. This suggests that INO and consequently MLF lesions are less common in NMOSD. The presence of an INO may help in the differentiation of NMOSD from MS and may aid in earlier implementation of disease appropriate therapy.

K-means quantization for a web-based open-source flow cytometry analysis platform.

Flow cytometry (FCM) is an analytic technique that is capable of detecting and recording the emission of fluorescence and light scattering of cells or particles (that are collectively called "events") in a population1. A typical FCM experiment can produce a large array of data making the analysis computationally intensive2. Current FCM data analysis platforms (FlowJo3, etc.), while very useful, do not allow interactive data processing online due to the data size limitations. Here we report a more effective way to analyze FCM data on the web. Freecyto is a free and intuitive Python-flask-based web application that uses a weighted k-means clustering algorithm to facilitate the interactive analysis of flow cytometry data. A key limitation of web browsers is their inability to interactively display large amounts of data. Freecyto addresses this bottleneck through the use of the k-means algorithm to quantize the data, allowing the user to access a representative set of data points for interactive visualization of complex datasets. Moreover, Freecyto enables the interactive analyses of large complex datasets while preserving the standard FCM visualization features, such as the generation of scatterplots (dotplots), histograms, heatmaps, boxplots, as well as a SQL-based sub-population gating feature2. We also show that Freecyto can be applied to the analysis of various experimental setups that frequently require the use of FCM. Finally, we demonstrate that the data accuracy is preserved when Freecyto is compared to conventional FCM software.

Rapture facilitates inexpensive and high-throughput parent-based tagging in salmonids.

Accurate methods for tracking individuals are crucial to the success of fisheries and aquaculture management. Management of migratory salmonid populations, which are important for the health of many economies, ecosystems, and indigenous cultures, is particularly dependent on data gathered from tagged fish. However, the physical tagging methods currently used have many challenges including cost, variable marker retention, and information limited to tagged individuals. Genetic tracking methods combat many of the problems associated with physical tags, but have their own challenges including high cost, potentially difficult marker design, and incompatibility of markers across species. Here we show the feasibility of a new genotyping method for parent-based tagging (PBT), where individuals are tracked through the inherent genetic relationships with their parents. We found that Rapture sequencing, a combination of restriction-site associated DNA and capture sequencing, provides sufficient data for parentage assignment. Additionally, the same capture bait set, which targets specific restriction-site associated DNA loci, can be used for both Rainbow Trout Oncorhynchus mykiss and Chinook Salmon Oncorhynchus tshawytscha. We input 248 single nucleotide polymorphisms from 1,121 samples to parentage assignment software and compared parent-offspring relationships of the spawning pairs recorded in a hatchery. Interestingly, our results suggest sperm contamination during hatchery spawning occurred in the production of 14% of offspring, further confirming the need for genetic tagging in accurately tracking individuals. PBT with Rapture successfully assigned progeny to parents with a 98.86% accuracy with sufficient genetic data. Cost for this pilot study was approximately $3 USD per sample. As costs vary based on the number of markers used and individuals sequenced, we expect that when implemented at a large-scale, per sample costs could be further decreased. We conclude that Rapture PBT provides a cost-effective and accurate alternative to the physical coded wire tags, and other genetic-based methods.

Refractive Errors and Amblyopia Among Children Screened by the UCLA Preschool Vision Program in Los Angeles County.

PURPOSE: To summarize the results of 5 years of vision screening with the University of California, Los Angeles (UCLA) Preschool Vision Program (UPVP). DESIGN: Retrospective evaluation of a screening program. METHODS: The UPVP performed visual acuity and undilated noncycloplegic refractive screening using an autorefractor on 93,097 children between 2012 and 2017. Of these, 79,451 children, who were between 3 and 5 years old, were screened for the first time, and 14,259 were referred for full cycloplegic examination if they met specific refractive criteria for myopia, hyperopia, astigmatism, or anisometropia. UPVP performed 6779 cycloplegic examinations on this population. Data from the right eye only were included in this analysis. RESULTS: Of the examined population, hyperopia was found in 61% (4018), myopia in 20% (1336), and astigmatism in 93% (6122) of children. Latino children had higher rates of astigmatism and worse visual acuity compared to all other races/ethnicities. An astigmatism cutoff of ≥1.50 diopters (D) in either eye correctly predicted the need for glasses 93% of the time; increasing this cutoff to ≥1.50 D in both eyes increased the positive predictive value to 96%. Refractive amblyopia was found in 780 children (1.0% of the screened population and 11.5% of the examined population), and of these, 211 (27%) were bilaterally amblyopic. CONCLUSIONS: These data represent the largest published sample of vision screening results on preschool-aged children, provide additional insight on the proportion of common refractive errors and their association with race/ethnicity, and can inform screening criteria to more accurately identify children who need intervention to prevent permanent vision loss.

Use of double wire-guided technique and transpancreatic papillary septotomy in difficult ERCP: 4-year experience.

Background and aims: Post-ERCP complications increase with repeated attempts at cannulation. We evaluated several advanced biliary cannulation techniques applied when the standard approach fails. Methods: In total, 1873 consecutive patients underwent ERCP at our institution during the period 2010 - 2014. Guidewire-assisted (GA) cannulation with no contrast injection until deep biliary cannulation was considered the standard technique. Advanced techniques used were double wire-guided (DWG) cannulation, transpancreatic papillary septotomy (TPS), and needle-knife sphincterotomy (NKS). When GA cannulation failed, DWG cannulation was usually attempted first if the pancreatic duct (PD) wire was in place; if that failed, TPS or NKS was performed. Alternatively, TPS or NKS were performed alone. A prophylactic pancreatic stent was placed with repeated PD cannulation or PD contrast injection. During the last 2 years of review, indomethacin suppositories were given post-procedure to all patients who underwent advanced techniques. Results: The overall biliary cannulation success rate was 97 % (1823/1873). Advanced techniques were used in 12 % of ERCPs (230/1873), with 87 % (200/230) success rate. DWG was used alone or in combination with other techniques in 58 % (134/230) of advanced cases, with 68 % (91/134) success rate. Biliary cannulation was achieved in 96 % (91/95) of procedures when DWG was used alone, 76 % (26/34) with TPS alone, 80 % (37/46) for NKS alone, and 84 % (46/55) with multiple techniques. The overall rate of post-ERCP pancreatitis was 0.4 %, with all patients treated conservatively. Conclusion: In our experience at an urban tertiary care center, use of advanced techniques in difficult ERCP improved the overall success rate of biliary cannulation after standard technique failure without a significant increase in complication rate.

Aspect ratio determines the quantity of mesoporous silica nanoparticle uptake by a small GTPase-dependent macropinocytosis mechanism.

Although the aspect ratio (AR) of engineered nanomaterials (ENMs) is one of the key physicochemical parameters that could determine biological outcome, not much is understood about how AR contributes to shaping biological outcome. By using a mesoporous silica nanoparticle (MSNP) library that has been constructed to cover a range of different lengths, we could demonstrate that the AR of rod-shaped particles determines the rate and abundance of MSNP uptake by a macropinocytosis process in HeLa and A549 cancer cell lines. MSNPs with an AR of 2.1-2.5 were taken up in larger quantities compared to shorter or longer length rods by a process that is sensitive to amiloride, cytochalasin D, azide, and 4 °C inhibition. The rods with intermediary AR also induced the maximal number of filopodia, actin polymerization, and activation of small GTP-binding proteins (e.g., Rac1, CDC42) that involve assembly of the actin cytoskeleton and filopodia formation. When assessing the role of AR in the delivery of paclitaxel or camptothecin, the rods with AR 2.1-2.5 were clearly more efficient for drug delivery and generation of cytotoxic killing in HeLa cells. All considered, our data suggest an active sensoring mechanism by which HeLa and A549 cells are capable of detecting AR differences in MSNP to the extent that accelerated macropinocytosis can be used to achieve more efficient drug delivery.