Introduction The demand for data science skills across disciplines has led to massive growth of data-related programs in universities, standalone courses, and other learning materials 1. The Open ...Educational Resources (OER) movement has propelled data science forward by improving the quality, depth, and availability of free materials 4. ...our course “Introduction to R for Public Health Researchers” (Fig 1) 12 takes place during the Johns Hopkins University Summer and Winter Institutes, over 9 days of 3 hour sessions each. A teaching team provides a broader range of skills, knowledge, and personalities when going over materials. In the age of code-ready large language models like ChatGPT, it is more essential to teach how to interpret, test, and debug, rather than recall specific functions.
Primary angle‐closure glaucoma: an update Wright, Carrie; Tawfik, Mohammed A.; Waisbourd, Michael ...
Acta ophthalmologica (Oxford, England),
20/May , Letnik:
94, Številka:
3
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Primary angle‐closure glaucoma is potentially a devastating disease, responsible for half of glaucoma‐related blindness worldwide. Angle closure is characterized by appositional approximation or ...contact between the iris and trabecular meshwork. It tends to develop in eyes with shallow anterior chambers, anteriorly positioned or pushed lenses, and angle crowding. Risk of primary angle‐closure glaucoma is high among women, the elderly and the hyperopic, and it is most prevalent in Asia. Investigation into genetic mechanisms of glaucoma inheritance is underway. Diagnosis relies on gonioscopy and may be aided by anterior segment optical coherence tomography and ultrasound biomicroscopy. Treatment is designed to control intraocular pressure while monitoring changes to the angle and optic nerve head. Treatment typically begins with medical management through pressure‐reducing topical medications. Peripheral iridotomy is often performed to alleviate pupillary block, while laser iridoplasty has been found effective for mechanisms of closure other than pupillary block, such as plateau iris syndrome. Phacoemulsification, with or without goniosynechialysis, both in eyes with existing cataracts and in those with clear lenses, is thus far a viable treatment alternative. Long‐term research currently underway will examine its efficacy in cases of angle closure in early stages of the disease. Endoscopic cyclophotocoagulation is another treatment option, which can be combined with cataract surgery. Trabeculectomy remains effective therapy for more advanced cases.
This paper explores the suitability of lip-based authentication as a behavioural biometric for mobile devices. Lip-based biometric authentication is the process of verifying an individual based on ...visual information taken from the lips while speaking. It is particularly suited to mobile devices because it contains unique information; its potential for liveness over existing popular biometrics such as face and fingerprint and lip movements can be captured using a device’s front-facing camera, requiring no dedicated hardware. Despite its potential, research and progress into lip-based biometric authentication has been significantly slower than other biometrics such as face, fingerprints, or iris.This paper investigates a state-of-the-art approach using a deep Siamese network, trained with the triplet loss for one-shot lip-based biometric authentication with real-world challenges. The proposed system, LipAuth, is rigourously examined with real-world data and challenges that could be expected on lip-based solution deployed on a mobile device. The work in this paper shows for the first time how a lip-based authentication system performs beyond a closed-set protocol, benchmarking a new open-set protocol with an equal error rates of 1.65% on the XM2VTS dataset.New datasets, qFace and FAVLIPS, were collected for the work in this paper, which push the field forward by enabling systematic testing of the content and quantities of data needed for lip-based biometric authentication and highlight problematic areas for future work. The FAVLIPS dataset was designed to mimic some of the hardest challenges that could be expected in a deployment scenario and include varied spoken content, miming and a wide range of challenging lighting conditions. The datasets captured for this work are available to other university research groups on request.
RNA sequencing offers advantages over other quantification methods for microRNA (miRNA), yet numerous biases make reliable quantification challenging. Previous evaluations of these biases have ...focused on adapter ligation bias with limited evaluation of reverse transcription bias or amplification bias. Furthermore, evaluations of the quantification of isomiRs (miRNA isoforms) or the influence of starting amount on performance have been very limited. No study had yet evaluated the quantification of isomiRs of altered length or compared the consistency of results derived from multiple moderate starting inputs. We therefore evaluated quantifications of miRNA and isomiRs using four library preparation kits, with various starting amounts, as well as quantifications following removal of duplicate reads using unique molecular identifiers (UMIs) to mitigate reverse transcription and amplification biases.
All methods resulted in false isomiR detection; however, the adapter-free method tested was especially prone to false isomiR detection. We demonstrate that using UMIs improves accuracy and we provide a guide for input amounts to improve consistency.
Our data show differences and limitations of current methods, thus raising concerns about the validity of quantification of miRNA and isomiRs across studies. We advocate for the use of UMIs to improve accuracy and reliability of miRNA quantifications.
The role of boron in terrestrial plant physiology is diverse and increasingly well understood, but its role in marine aquatic eukaryotes is less clear. Our research reveals a distinctive and large ...offset in boron isotopes from seawater, irrespective of seaweed type or season. We show that the offset is consistent with the incorporation of borate from seawater. Boron is a known micronutrient in plants but very few studies have used boron isotopes to investigate boron’s role in plant physiology. Seaweed, as the most primitive multicellular plant, has an important role in investigating wider plant adaptations that use boron to meet functional needs. Furthermore, seaweed and other plants are a key base nutrient provider in food webs, supplying boron to consumers and playing a critical role in boron environmental cycling.
Data science education provides tremendous opportunities but remains inaccessible to many communities. Increasing the accessibility of data science to these communities not only benefits the ...individuals entering data science, but also increases the field's innovation and potential impact as a whole. Education is the most scalable solution to meet these needs, but many data science educators lack formal training in education. Our group has led education efforts for a variety of audiences: from professional scientists to high school students to lay audiences. These experiences have helped form our teaching philosophy which we have summarized into three main ideals: 1) motivation, 2) inclusivity, and 3) realism. To put these ideals better into practice, we also aim to iteratively update our teaching approaches and curriculum as we find ways to better reach these ideals. In this manuscript we discuss these ideals as well practical ideas for how to implement these philosophies in the classroom.
The results from a four-year study of a freshwater pond on Long Island, NY, USA, do not point to a single source of boron (and by proxy other elements including nutrients) in this system. However, ...boron data from samples associated with this pond can be explained by mixing between average precipitation (weighted average δ11B = 22.7) in the area and the local sources of boron, both natural and anthropogenic. This multiyear study provided the opportunity to see both yearly and seasonal differences. One algae sample from the pond showed significant fractionation and enrichment in light boron relative to the water and suggests algae may act as a boron sink. This type of biological fractionation could explain an observed down-gradient trend to heavier boron isotope values in pond water, which corresponds to the slight reduction in boron concentration seen in 2021. However, the trend was subdued in the following year, likely due to differences in the water flow rates and/or rate of algal growth. An opposite trend was seen with depth in the water, where δ11B showed a positive correlation to boron concentration, which increased with depth from the surface of the pond. This gradient may be explained by the stratification of the pond with a heavy source concentrating in the bottom waters. The bottom water composition was consistent with goose feces (δ11B = 25.8) or the addition of chemicals from the application of rock salt to local roads in winter. Surprisingly, boron from seawater (average δ11B = 39.8) did not appear to have a direct impact on Setauket Pond, other than its influence on precipitation, providing heavy δ11B and very low boron concentrations.
Background: Drinking during pregnancy has been associated with learning disabilities in affected offspring. At present, there are no clinically effective pharmacotherapeutic interventions for these ...learning deficits. Here, we examined the effects of ABT‐239, a histamine H3 receptor antagonist, on fetal ethanol‐induced fear conditioning and spatial memory deficits.
Methods and Results: Long‐Evans rat dams stably consumed a mean of 2.82 g ethanol/kg during a 4‐hour period each day during pregnancy. This voluntary drinking pattern produced a mean peak serum ethanol level of 84 mg/dl. Maternal weight gain, litter size and birth weights were not different between the ethanol‐consuming and control groups. Female adult offspring from the control and fetal alcohol‐exposed (FAE) groups received saline or 1 mg ABT‐239/kg 30 minutes prior to fear conditioning training. Three days later, freezing time to the context was significantly reduced in saline‐treated FAE rats compared to control. Freezing time in ABT‐239‐treated FAE rats was not different than that in controls. In the spatial navigation study, adult male offspring received a single injection of saline or ABT‐239 30 minutes prior to 12 training trials on a fixed platform version of the Morris Water Task. All rats reached the same performance asymptote on Trials 9 to 12 on Day 1. However, 4 days later, first‐trial retention of platform location was significantly worse in the saline‐treated FAE rats compared control offspring. Retention by ABT‐239‐treated FAE rats was similar to that by controls. ABT‐239’s effect on spatial memory retention in FAE rats was dose dependent.
Conclusions: These results suggest that ABT‐239 administered prior to training can improve retention of acquired information by FAE offspring on more challenging versions of hippocampal‐sensitive learning tasks. Further, the differential effects of ABT‐239 in FAE offspring compared to controls raises questions about the impact of fetal ethanol exposure on histaminergic neurotransmission in affected offspring.
Multiple genetic approaches have identified microRNAs as key effectors in psychiatric disorders as they post-transcriptionally regulate expression of thousands of target genes. However, their role in ...specific psychiatric diseases remains poorly understood. In addition, epigenetic mechanisms such as DNA methylation, which affect the expression of both microRNAs and coding genes, are critical for our understanding of molecular mechanisms in schizophrenia.
Using clinical, imaging, genetic, and epigenetic data of 103 patients with schizophrenia and 111 healthy controls of the Mind Clinical Imaging Consortium (MCIC) study of schizophrenia, we conducted gene set enrichment analysis to identify markers for schizophrenia-associated intermediate phenotypes. Genes were ranked based on the correlation between DNA methylation patterns and each phenotype, and then searched for enrichment in 221 predicted microRNA target gene sets.
We found the predicted hsa-miR-219a-5p target gene set to be significantly enriched for genes (EPHA4, PKNOX1, ESR1, among others) whose methylation status is correlated with hippocampal volume independent of disease status. Our results were strengthened by significant associations between hsa-miR-219a-5p target gene methylation patterns and hippocampus-related neuropsychological variables. IPA pathway analysis of the respective predicted hsa-miR-219a-5p target genes revealed associated network functions in behavior and developmental disorders.
Altered methylation patterns of predicted hsa-miR-219a-5p target genes are associated with a structural aberration of the brain that has been proposed as a possible biomarker for schizophrenia. The (dys)regulation of microRNA target genes by epigenetic mechanisms may confer additional risk for developing psychiatric symptoms. Further study is needed to understand possible interactions between microRNAs and epigenetic changes and their impact on risk for brain-based disorders such as schizophrenia.
•We used gene set enrichment analysis for DNA methylation data in schizophrenia.•Predicted target genes of microRNA miR-219 were associated with hippocampus volume.•This association was independent of disease status.•Epigenetic (dys)regulation of miR targets may confer risk for psychiatric disorders.
Open-source Tools for Training Resources - OTTR Savonen, Candace; Wright, Carrie; Hoffman, Ava M. ...
Journal of Statistics and Data Science Education,
2023, Letnik:
31, Številka:
1
Journal Article
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Data science and informatics tools are developing at a blistering rate, but their users often lack the educational background or resources to efficiently apply the methods to their research. Training ...resources and vignettes that accompany these tools often deprecate because their maintenance is not prioritized by funding, giving teams little time to devote to such endeavors. Our group has developed Open-source Tools for Training Resources (OTTR) to offer greater efficiency and flexibility for creating and maintaining these training resources. OTTR empowers creators to customize their work and allows for a simple workflow to publish using multiple platforms. OTTR allows content creators to publish training material to multiple massive online learner communities using familiar rendering mechanics. OTTR allows the incorporation of pedagogical practices like formative and summative assessments in the form of multiple choice questions and fill in the blank problems that are automatically graded. No local installation of any software is required to begin creating content with OTTR. Thus far, 15 training courses have been created with OTTR repository template. By using the OTTR system, the maintenance workload for updating these courses across platforms has been drastically reduced. For more information about OTTR and how to get started, go to ottrproject.org.
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