Average Reading Research Articles

RANCANG BANGUN SISTEM PRESENSI KULIAH MENGGUNAKAN QRCODE BERBASIS ESP32CAM

Rapid Response Codes are a kind of digital bar code that are becoming more and more popular since they can store a lot of data fast and in big quantities. This research aims to design a device for collecting attendance data using QR codes. This QR code contains information about the user's identity and location when used. We may determine the user's distance from the designated area using this location data. This location information is used to find out how far the user is from the area we have set.The presence method used the ESP Cam device to scan a QR code from the user which contains information on student identification number, date and location (latitude and longitude).Before scanning the QR code, users must confirm via the Telegram application which has been prepared in advance to carry out the attendance process at each class session.Ifthe information matches that is stored in the database and the user's location is still within the radius of the reader device, the user's identity data is then uploaded to the online presence system.After the hardware and software have been prepared, it continues with testing on Electrical Engineering students at Muhammadiyah University of Surakarta as attendance at the Electrical Engineering Laboratory.Scanning this QR code takes an average reading time of 3.5 seconds with the fastest estimated time being 3 seconds and the longest 5 seconds.

Readability of Spanish-Language Online Patient Educational Materials for Peripheral Artery Disease Do Not Meet Recommended Standards and Represent a Literacy Barrier to Care

Online resources are a valuable source of information for patients and have been reported to improve engagement and adherence to medical care. However, readability of online patient educational materials (OPEMs) is crucial for them to serve their intended purpose. The American Medical Association (AMA) recommends that OPEM be written at or below the sixth grade reading level. To avoid disparities in access to comprehensible health information on peripheral artery disease (PAD), it is imperative that the readability of PAD OPEM is appropriate for both English-speaking and Spanish-speaking patients. The aim of this study is to evaluate the readability of PAD OPEM in Spanish and compare to English-language OPEM. We conducted a Google search in English and Spanish using "peripheral arterial disease" and "enfermedad arterial periferica", respectively, and the top 25 patient-accessible articles were collected for each. Articles were categorized by source type: hospital, professional society, or other. Readability of English-language OPEM was measured using the Flesch Reading Ease Readability Formula, Automated Readability Index, Coleman-Liau Index, Flesch-Kincaid Grade Level, Gunning Fog, Linsear Write Formula, and the Simple Measure of Gobbledygook Index. Readability of Spanish OPEM was measured using the Fernández-Huerta Index and Índice Flesch-Szigriszt Scale. Readability of the articles was compared to the AMA recommendation, between English- and Spanish-language, and across sources using statistical tests appropriate to the data. OPEM from professional societies represented the fewest number of English- (n=7, 28%) and Spanish-language (n=6, 24%) articles. Most English-speaking (n=18, 72%) and Spanish-language (n=20, 80%) OPEM were considered difficult as measured by the Flesch Reading Ease Readability Formula and Fernández-Huerta Index, respectively, but did not significantly differ between languages (P=0.59). There were no significant differences in the average readability of all readability measurements across sources (hospital, professional society, or other). All the average readability grade levels for English-speaking and Spanish-language OPEM was significantly higher than the sixth grade reading level (P<0.01). Only 3 (6%) OPEM met the AMA recommended reading level and there was no significant difference between English-language and Spanish-language OPEM (P=1.0). Nearly all Spanish-language and English-language PAD OPEM assessed were written at a reading grade level higher than recommended by the AMA. There was no significant difference in the readability of materials from hospitals or professional societies. To prevent further widening of health disparities related to literacy, health content creators, particularly hospitals and professional societies, should prioritize, develop, and ensure that English-language and Spanish-language patient education materials are written at a level appropriate for the public.

Scientific Literacy Ability Through Speed Reading Methods in Class V Elementary School Students

The teacher has not provided a special method to improve reading skills, the teacher has not measured the students' reading speed and the percentage of understanding of the reading content that the students have achieved, apart from that, the students also think that reading is a very boring lesson Reading is an important skill that can have implications for other literacy skills. However, the average reading ability of SDN 1 Nameng students is still not optimal. The aim of this research is to improve students' reading literacy skills by using the speed reading method on students' science lesson material. The method used in this research is action research which refers to the Kemmis and Mc Taggart model using a spiral system cycle consisting of planning, implementing actions, observation and reflection. The results of class actions in cycle I averaged 72.34% and increased in cycle II with an average of 80.46%. The conclusion of the class action carried out shows that the speed reading method is able to improve students' reading literacy skills in science subject matter

Design and Build a Control and Monitoring System in a Cat Cage Based on the Internet of Things (IoT) (Case Study in Violet Pet Shop &amp; Clinic)

Violet Pet Clinic &amp; Shop is a place to day care and care for pets such as cats which is located at Jalan Borobudur No.11, Mojolangu, Kec. Lowokwaru, Malang City, East Java Province. At Violet Pet Clinic &amp; Shop, it provides various facilities including grooming, day care, doctor consultation, and ultrasound. The type of research carried out includes the type of development research, which functions to produce certain products and test product effectiveness. Equipment testing results show good performance. The tools developed can be a solution to problems at Violet Pet Shop &amp; Clinic. The temperature sensor has an average reading error of 0.88 percent with an accuracy percentage of 99.12 percent, the ESP32 camera can capture images properly. In one of the control systems, feeding in large quantities with a feed dose weighing 150g can only provide 4 times of feed with a delay of 10 seconds.

Düşük Kapsamlı WGS Verileri Kullanılarak Hızlı ve Yüksek Doğruluklu Guppy Baz Çağırma Modellerinin Varyant Çağırma Üzerine Etkisinin İncelenmesi

Long-read sequencing technologies such as Oxford Nanopore Technologies (ONT) enabled researchers to sequence long reads fast and cost-effectively. ONT sequencing uses nanopores integrated into semiconductor surfaces and sequences the genomic materials using changes in current across the surface as each nucleotide passes through the nanopore. The default output of ONT sequencers is in FAST5 format. The first and one of the most important steps of ONT data analysis is the conversion of FAST5 files to FASTQ files using “base caller” tools. Generally, base caller tools pre-trained deep learning models to transform electrical signals into reads. Guppy, the most commonly used base caller, uses 2 main model types, fast and high accuracy. Since the computation duration is significantly different between these two models, the effect of models on the variant calling process has not been fully understood. This study aims to evaluate the effect of different models on performance on variant calling.&#x0D; In this study, 15 low-coverage long-read sequencing results coming from different flow cells of NA12878 (gold standard data) were used to compare the variant calling results of Guppy. &#x0D; Obtained results indicated that the number of output FASTQ files, read counts and average read lengths between fast and high accuracy models are not statistically significant while pass/fail ratios of the base called datasets are significantly higher in high accuracy models. Results also indicated that the difference in pass/fail ratios arises in a significant difference in the number of called Single Nucleotide Polymorphisms (SNPs), insertions and deletions (InDels). Interestingly the true positive rates of SNPs are not significantly different. These results show that using fast models for SNP calling does not affect the true positive rates statistically. The primary observation in this study, using fast models does not decrease the true positive rate but decreases the called variants that arise due to altered pass/fail ratios. Also, it is not advised to use fast models for InDel calling while both the number of InDels and true positive rates are significantly lower in fast models.&#x0D; This study, to the best of our knowledge, is the first study that evaluates the effect of different base calling models of Guppy, one of the most common and ONT-supported base callers, on variant calling.

A Review on Measurement of Radon Gas Concentration in Drinking Water

Radon is a noble gas that has a high risk to the human body, and existence at various rates in soil, air and different source of water. Moreover, radon has a short lifetime but it can produce more risk to public health. Humans are good users of water by food, drinking water, vegetable, shower and dishwashing, however, we do have not good knowledge about the risk of radon, and we need to do more research because it’s one of the main factors to various types of cancer such as lung and stomach cancer. This review used different data in some research in different countries (Romania, Chania, Brazil, Sudan, India, Syria, Iraq, and Yemen) in (2012-2020) with the help of the RAD7 detector because it has higher resolution and is faster in measurement. In current review, higher average reading of radon was found in Nigeria, its reading was (36.1 Bq/L) which was more than the standard value in the world for drinking water (11.1 Bq/L). In any country there are so many factors to high and low concentration of radon in drinking water which are discussed and explained in this review.

Associations between students’ reading performance and literacy instruction in first grade: a cross-lagged study

This cross-lagged study examined the classroom-level associations between the reading performance of first-grade students (N = 537) and observed literacy instruction activities in classrooms (N = 30) in the autumn and spring terms. The multilevel analyses indicated that lower average word reading skills in the classrooms (i.e., there were more students who were learning to read) in the autumn were associated with higher amount of activities supporting consolidation of reading and spelling skills in the spring. In contrast, higher average word reading skills in the classrooms in the autumn were associated with higher amount of independent meaning-focused activities in the spring. Higher extent of whole-group meaning-focused activities in the autumn was positively associated with reading comprehension at classroom level in the spring, whereas independent phonological recoding practice in the autumn was negatively associated with reading comprehension in the spring. The study provides novel understanding of the associations between students’ reading performance and literacy instruction especially showing how students’ reading skills at classroom level may inform instruction in the classroom. This information may guide teachers to adapt their instruction at classroom level but also to identify the students needing differentiation. The results also acknowledge the affordances and limitations students’ skills may set for the instruction.

Improving traumatic fracture detection on radiographs with artificial intelligence support: a multi-reader study.

The aim of this study was to evaluate the diagnostic performance of nonspecialist readers with and without the use of an artificial intelligence (AI) support tool to detect traumatic fractures on radiographs of the appendicular skeleton. The design was a retrospective, fully crossed multi-reader, multi-case study on a balanced dataset of patients (≥2 years of age) with an AI tool as a diagnostic intervention. Fifteen readers assessed 340 radiographic exams, with and without the AI tool in 2 different sessions and the time spent was automatically recorded. Reference standard was established by 3 consultant radiologists. Sensitivity, specificity, and false positives per patient were calculated. Patient-wise sensitivity increased from 72% to 80% (P < .05) and patient-wise specificity increased from 81% to 85% (P < .05) in exams aided by the AI tool compared to the unaided exams. The increase in sensitivity resulted in a relative reduction of missed fractures of 29%. The average rate of false positives per patient decreased from 0.16 to 0.14, corresponding to a relative reduction of 21%. There was no significant difference in average reading time spent per exam. The largest gain in fracture detection performance, with AI support, across all readers, was on nonobvious fractures with a significant increase in sensitivity of 11 percentage points (pp) (60%-71%). The diagnostic performance for detection of traumatic fractures on radiographs of the appendicular skeleton improved among nonspecialist readers tested AI fracture detection support tool showed an overall reader improvement in sensitivity and specificity when supported by an AI tool. Improvement was seen in both sensitivity and specificity without negatively affecting the interpretation time. The division and analysis of obvious and nonobvious fractures are novel in AI reader comparison studies like this.

Can Large Language Models Generate Outpatient Clinic Letters at First Consultation That Incorporate Complication Profiles From UK and USA Aesthetic Plastic Surgery Associations?

Abstract The importance of written communication between clinicians and patients, especially in the wake of the Supreme Court case of Montgomery vs Lanarkshire, has led to a shift toward patient-centric care in the United Kingdom. This study investigates the use of large language models (LLMs) like ChatGPT and Google Bard in enhancing clinic letters with gold-standard complication profiles, aiming to improve patients’ understanding and save clinicians’ time in aesthetic plastic surgery. The aim of this study is to assess the effectiveness of LLMs in integrating complication profiles from authoritative sources into clinic letters, thus enhancing patient comprehension and clinician efficiency in aesthetic plastic surgery. Seven widely performed aesthetic procedures were chosen, and complication profiles were sourced from the British Association of Aesthetic Plastic Surgeons (BAAPS) and the American Society of Plastic Surgeons (ASPS). We evaluated the proficiency of the ChatGPT4, ChatGPT3.5, and Google Bard in generating clinic letters which incorporated complication profiles from online resources. These letters were assessed for readability using an online tool, targeting a recommended sixth-grade reading level. ChatGPT4 achieved the highest compliance in integrating complication profiles from BAAPS and ASPS websites, with average readability grades between eighth and ninth. ChatGPT3.5 and Google Bard showed lower compliance, particularly when accessing paywalled content like the ASPS Informed Consent Bundle. In conclusion, LLMs, particularly ChatGPT4, show promise in enhancing patient communications in aesthetic plastic surgery by effectively incorporating standard complication profiles into clinic letters. This aids in informed decision making and time saving for clinicians. However, the study underscores the need for improvements in data accessibility, search capabilities, and ethical considerations for optimal LLM integration into healthcare communications. Future enhancements should focus on better interpretation of inaccessible formats and a Human in the Loop approach to combine Artifical Intelligence capabilities with clinician expertise. Level of Evidence: 3

Exploration of Cultural Teaching Mechanisms of Ideology and Politics Courses under the Background of “Internet Plus”

Abstract As the cradle of cultivating and conveying talents, colleges and universities should innovate the education of ideological and political courses under the background of “Internet+”, focusing on cultivating students’ cultural self-confidence. This paper first explains blockchain-related technology in Internet technology, including the basic principle and structure of blockchain, the consistency Hash algorithm, the consensus mechanism and the credit mechanism of blockchain. Secondly, it discusses the fit between the blockchain and the cultural teaching mechanism of the Civics course, through which blockchain technology can effectively realize the interactive sharing of the cultural teaching resources of the Civics course. Based on the blockchain technology and MVC network structure, an interactive model of cultural teaching resources for Civic and Political Science courses is constructed, which further improves the way students access cultural teaching resources. Finally, a simulation test is conducted to evaluate the interactivity of the cultural teaching resources in the Civics and Political Science course and the effectiveness of the model. The results show that the average write bandwidth of the consistent Hash algorithm is 756.68MBps, and the average read bandwidth is 215.42MBps, and when the total amount of data exceeds 64GB, the relative standard deviation of the Hash algorithm decreases to about 0.15% and remains stable. The cultural teaching mechanism of the Civics course with the introduction of blockchain technology is based on a digital platform, and when the number of network nodes is 150, the delay of the consensus mechanism is 236.73ms, and the throughput reaches about 98 data interactions per second. The cultural teaching mechanism of the Civics and Politics course in the background of the Internet needs to be based on digitization, fully combining with information technology to realize the common construction and sharing of cultural teaching resources and cultivate new-age talents with higher cultural self-confidence for the development of society.

Quality and Readability Analysis of Online Information on First Metatarsophalangeal Joint Fusion

Patients frequently turn to the internet to learn about their orthopedic procedures. This study evaluates the readability and quality of first metatarsophalangeal (MTP) joint fusion information found online. We evaluated websites based on classification, search term, readability, HON code, DISCERN score, Journal of the American Medical Association benchmark criteria, and an author-created MTP fusion index (MFI). The average readability of websites was 8.48 ± 1.99, above the recommended sixth- or eighth-grade reading level. Almost half of all websites (48.98%) provided “poor” information. Keywords had no significant impact on the readability or quality of information. Academic/governmental websites had the highest quality of information, with the highest DISCERN and second highest MFI. Most websites (52.04%) were commercial and were the easiest to read, but had the second lowest DISCERN and MFI scores. Our results suggest that inappropriate information on the MTP joint fusion procedure is abundant online. Academic/governmental websites have the highest quality of information, but may be difficult for patients to comprehend. Many websites do have readable and relevant information. We recommend that physicians create a list of websites with accurate, relevant information for patients to circumvent the misinformation they may find while navigating and reading online.

Readability of information on stem cell therapies: a comparison between commercial websites and scientific articles

The aim of this paper is to evaluate and compare the readability level of the stem cell companies’ websites content and scientific articles devoted to this topic. Eight readability formulas were utilised to assess the readability of the information available on the 2020 top ten stem cell companies’ websites and of 24 scientific articles (12 research articles and 12 reviews) published in npj Regenerative Medicine between 2018 and 2020, selected on the basis of the search term “stem cell therapy human”. The average Flesch Reading Ease Score was 32.6 (difficult) for website pages, 35.8 (difficult) for original articles, and 22.4 (very difficult) for reviews. Based on the other seven readability algorithms applied here, none of the examined texts was written beyond the sixth-grade level of readability, indicating that neither scientific articles nor commercial materials from the companies’ websites delivered information on stem cell-based therapies that would be easily readable for an average adult.

Design And Development Of A Portable Alcohol Testing Device For Motorists

This research aims to design and develop a portable alcohol testing device that can be used to check whether prospective drivers have consumed alcohol before driving. The device is designed with the goal of improving road safety by reducing the risk of accidents caused by intoxicated drivers.In this study, we used the Figaro TGS 2620 alcohol sensor. The device is also equipped with a 16x2 LCD that displays test results directly and accurately. Additionally, we added indicators in the form of LEDs and a buzzer for signaling. The device we designed utilizes an Arduino UNO microcontroller.The test results and evaluations indicate that the portable alcohol testing device can respond to changes in alcohol levels around the sensor. When subjected to a non-alcohol condition, the device shows an average voltage reading of 0.69 V, whereas when subjected to the presence of alcohol, the device exhibits an average voltage reading of 3.97 V.

Eye radiation dose from breast cancer screening using full field digital mammography and digital breast tomosynthesis: A phantom study

IntroductionThe eye lens is recently classified as one of the most radiosensitive tissues by the International Commission on Radiological Protection (ICRP), and it has been suggested that the eye lens receives radiation dose during mammography due to scatter radiation. The aim of this study was to investigate the radiation dose received by the lens of the clients’ eye from Full Field Digital Mammography (FFDM) and Digital Breast Tomosynthesis (DBT) screening. MethodsThe eye radiation dose received by ATOM dosimetry phantom was estimated with thermo-luminescent dosemeters (TLDs). One TLD was utilised for each eye. A breast phantom was exposed for four-view screening mammography using 16 FFDM machines and one DBT machine. The breast phantom was exposed three times for each mammographic position and an average TLD dose reading was considered to minimise random error. ResultsFor four-view FFDM screening, the phantom eye radiation dose ranges from 0.013 mGy to 0.029 mGy with a mean±sd of 0.019 ± 0.005 mGy. A higher eye radiation dose of 0.041 mGy was recorded from four-view DBT screening. The statistical analysis demonstrated that the eye lens radiation dose is strongly and significantly correlated to breast organ dose and X-ray tube voltage. ConclusionThe phantom eye lens was exposed to scatter radiation from FFDM and DBT screening. The measured dose via the four-view DBT screening was higher than the four-view FFDM screening, but sits below the internationally acceptable ranges. If the findings of our paper hold true in practice, then the risk to the lens of the eyes for women attending breast screening is acceptable. Implications for practiceThe new lens radiation dose levels recommended by the ICRP necessitate the reevaluation of eye radiation dose from different radiographic examinations, especially those used for screening purpose where healthy individuals involved.

Presence of Recurrent Somatic Mutations in Mesenchymal Stromal Cell Fractions Isolated from Acute Myeloid Leukemia As an Evidence of Clonality

Introduction: Acute myeloid leukemia (AML) involves somatic mutations in hematopoietic stem cells (HSCs). Recent evidence suggests the bone marrow microenvironment, particularly mesenchymal stromal cells (MSCs), also influences AML development. Abnormalities in MSCs from AML patients have been observed (von der Heide et al., 2016), potentially impacting leukemia progression. This study aims to identify MSC somatic mutations and their consequences, further exploring their role in AML. Understanding MSCs' impact on the leukemic microenvironment may shed light on AML pathophysiology and guide targeted therapies, particularly benefiting patients with adverse risk disease. Methods: A total of 28 bone marrow cases were collected from AML patients with adverse risk, including those with complex karyotype, monosomy karyotype, chromosome 5/7/17 abnormalities, TP53 mutation, or relapsed/refractory AML. From these cases, 14 paired MSC and leukemic cell (LC) fractions were analyzed and are presented here. Magnetic bead sorting was used to isolate CD33+ LCs, while the plastic adherence method was employed for MSC culture. Following magnetic isolation, CD33- cells were plated in DMEM-LG with FBS and pen/strep, and MSC colonies formed within 48 hours. Contaminating cells were removed through media changes, and passaging was performed at 70-80% confluency. Flow cytometry at passage 3 characterized MSCs based on cell surface expression of CD105, CD73, and CD90, in accordance with the ISCT guideline. DNA and RNA were extracted from MSCs at passage 3 and subjected to whole exome sequencing (WES) using the Illumina platform, along with the LC fractions. WES aimed for 200X depth for the paired DNA samples. A standard bioinformatics pipeline was used for sequence alignment and variant calling, with variants requiring sufficient read depth (≥30x) and variant allele frequency in the case (&amp;gt;5%) and in the control (&amp;lt;5%). Synonymous variants were filtered out, and gene ontology and pathway enrichment analyses explored the biological significance and potential involvement in leukemogenesis of the identified mutations. Whole transcriptomics for gene expression analyses was also conducted for both MSC and LC fractions. Results: In 14 analyzed cases, a total of 548 somatic variants were identified in the MSC fraction, affecting 480 genes, including 518 nonsynonymous single nucleotide variants (SNVs), 7 stop-gain SNVs, 1 stoploss, 1 non-frameshift insertion, 2 frameshift deletions, 1 frameshift insertion, and 2 non-frameshift deletions, with 16 unknown variants. The average read depth was 75 (range: 15 - 887), and the average variant allele frequency was 50% (range: 11% - 90%). On average, 38 genes were mutated per MSC case, with 8 genes detected in at least 3 cases, 25 in exactly 2 cases, and 447 genes found in only one case. In the leukemic fraction, 686 somatic variants in 595 genes were identified, with an average read depth of approximately 75 (range: 10 - 2596) and an average variant allele frequency of 47% (range: 8% - 85%). On average, 48 mutations were detected per leukemic case, with 12 mutations found in at least 3 cases, 40 in 2 cases, and 543 in only one case. Among the 14 cases, 10 cases (71%) had mutations in known driver genes for AML ( FLT3, NPM1, IDH1, IDH2, DNMT3A, RUNX1, TP53) exclusively in the leukemic fraction. As seen in Figure 1., of the 480 genes mutated in the MSC fraction, 69 overlapped with the 595 genes mutated in the leukemic fraction, while 411 genes were uniquely mutated in the MSC fraction. Further analysis is ongoing, and pathway analysis will be conducted once the remaining 14 cases are processed. Conclusions: This study identifies distinct somatic mutations in AML patients' MSC and leukemic cell fractions, revealing genomic complexity and crosstalk impacting leukemia progression. Understanding the functional implications of these mutations is crucial for unraveling their roles in leukemogenesis and developing personalized therapeutic interventions targeting MSC somatic mutations.

Nanopore Cas9-Targeted Long-Read Sequencing - a Fast and Flexible Diagnostic Tool for the Identification of B-Cell Acute Lymphoblastic Leukemia Associated Gene Rearrangements

B-cell acute lymphoblastic leukemia (B-ALL) is characterized by a multitude of recurrent genetic alterations, which drive malignant transformation. Besides their essential role in leukemia biology these aberrations also serve as predictors of treatment response and survival, making their reliable detection a prerequisite for risk stratification in state-of-the-art clinical trials. Currently, the genetic characterization of B-ALL in most diagnostic laboratories still relies on an integrative approach combining conventional cytogenetics, reverse transcription polymerase chain reaction (RT-PCR) and fluorescence in situ hybridization (FISH) assays as well as single nucleotide polymorphism (SNP) array analysis. However, these conventional diagnostic tools fail to identify a considerable number of genetic alterations, particularly cryptic rearrangements such as IGH::DUX4, IGH::EPOR or MEF2D involving fusions. Although next generation DNA- and RNA-based sequencing (NGS) assays have significantly improved the reliable detection of fusion genes, the need for large sample numbers to achieve acceptable turnaround times and cost effectiveness impairs their application in small- to medium-sized diagnostic laboratories. To address these issues, we developed a targeted sequencing assay, based on the commercially available combination of Cas9-mediated target enrichment and Nanopore long-read sequencing, which facilitates the identification of B-ALL associated gene rearrangements on the DNA level in a single sample format. The targeted panel design included an initial review of the literature to define the breakpoint-spanning regions involved in fusion gene formation followed by the design of specific guide RNAs (gRNA) to facilitate Cas9-mediated enrichment of these regions of interest (ROIs). We first conducted ROI enrichment and sequencing with a limited number of gRNAs targeting only ETV6, KMT2A and DUX4 fusions. Then we progressively extended the pool of gRNAs with each sequencing run until it comprised 91 gRNAs covering most B-ALL-associated rearrangements. This stepwise approach allowed us to identify negative effects of increasing panel size on overall enrichment efficacy and simplified the identification and replacement of poor performing gRNAs. Our initial cohort consisted of 12 well-characterized samples harboring 13 gene rearrangements, including ETV6::RUNX1, KMT2A::AFF1, MEF2D::BCL9, ZMIZ1::ABL1, SSBP2::CSF1R, PDGFRB::EBF1, IGH::EPOR, IGH::DUX4, IGH::CRLF2, IGH::CEBPE, IGH::MYC, and IGH::BCL2. To ensure easy implementation in diagnostic workflows, we used genomic DNA, isolated according to standard protocols. Cas9-based target enrichment and long-read sequencing on MinION flow cells (v9.4.1) were performed according to protocols provided by Oxford Nanopore and each sample was sequenced for 72 hours. On average, each run yielded 3.72±1.21 Gb, a mean read length of 7.40±1.00 kb with an N50 value of 12.87±1.71 kb and an average read quality (Q) score of 14.72±0.52. For data processing and analysis, we adapted the existing nextflow nf-core bioinformatics pipeline, nanoseq, to include publicly available structural variation callers and quality control tools. Our approach correctly identified 92.3% (12/13) of the rearrangements with a mean of 42 (range 2-97) breakpoint-supporting reads (BSR) per alteration. Only the IGH::MYC translocation was missed as the breakpoint was located outside of our predefined ROIs for MYC. To corroborate these results, we sequenced an additional cohort of 14 B-ALL samples, including ZNF384::DUX4, KMT2A::MLLT10, KMT2A::USP2, PAX5::SOX5, EP300::ZNF384, P2RY8::CRLF2, and IGH::DUX4 positive cases and were able to correctly identify 100% (14/14) of the fusion genes with an average of 83 (range 7-367) BSR. In conclusion, our newly developed targeted sequencing panel correctly identified 96.3% (26/27) analyzed gene rearrangements in B-ALL, including alterations evading standard diagnostic methodologies such as IGH::DUX4 or IGH::EPOR. Importantly, the assay allows individual analysis in a single sample format, thereby representing a valuable tool for B-ALL diagnostics in small to medium-sized laboratories.

Accurate identification of structural variations from cancer samples.

Structural variations (SVs) are commonly found in cancer genomes. They can cause gene amplification, deletion and fusion, among other functional consequences. With an average read length of hundreds of kilobases, nano-channel-based optical DNA mapping is powerful in detecting large SVs. However, existing SV calling methods are not tailored for cancer samples, which have special properties such as mixed cell types and sub-clones. Here we propose the Cancer Optical Mapping for detecting Structural Variations (COMSV) method that is specifically designed for cancer samples. It shows high sensitivity and specificity in benchmark comparisons. Applying to cancer cell lines and patient samples, COMSV identifies hundreds of novel SVs per sample.

Assessing the Potential of a Deep Learning Tool to Improve Fracture Detection by Radiologists and Emergency Physicians on Extremity Radiographs

To evaluate the standalone performance of a deep learning (DL) based fracture detection tool on extremity radiographs and assess the performance of radiologists and emergency physicians in identifying fractures of the extremities with and without the DL aid. The DL tool was previously developed using 132,000 appendicular skeletal radiographs divided into 87% training, 11% validation, and 2% test sets. Stand-alone performance was evaluated on 2626 de-identified radiographs from a single institution in Ohio, including at least 140 exams per body region. Consensus from three US board-certified musculoskeletal (MSK)radiologists served as ground truth. A multi-reader retrospective study was performed in which 24 readers (eight each of emergency physicians, non-MSK radiologists, and MSK radiologists) identified fractures in 186 cases during two independent sessions with and without DLaid, separated by a one-month washout period. The accuracy (area under the receiver operating curve), sensitivity, specificity, and reading time werecompared withand without model aid. The model achieved a stand-alone accuracy of 0.986, sensitivity of 0.987, and specificity of 0.885, and high accuracy (> 0.95) across stratification for body part, age, gender, radiographic views, and scanner type. With DL aid, reader accuracy increased by 0.047 (95% CI: 0.034, 0.061; p=0.004) and sensitivity significantly improved from 0.865 (95% CI: 0.848, 0.881) to 0.955 (95% CI: 0.944, 0.964). Average reading time was shortened by 7.1s (27%) per exam. When stratified by physician type, this improvement was greater for emergency physicians and non-MSK radiologists. The DL tool demonstrated high stand-alone accuracy, aided physician diagnostic accuracy, and decreased interpretation time.

Association of oral care with periodontitis and glycemic control among US adults with diabetes

BackgroundStudies indicate that treating periodontitis may benefit glycemic control among people with diabetes. It is unclear whether oral self-care such as flossing may reduce risk for periodontitis and improve glycemic control among people with diabetes. The purpose of this study was to examine associations between oral care, specifically, flossing and preventive dental care, with periodontitis and glycemic control, among US dentate adults with diabetes.MethodsWe analyzed data from the National Health and Nutrition Examination Survey 2011–2014 for 892 participants aged 30 years and older with diabetes who completed the periodontal examination and lab test for hemoglobin A1c (HbA1c). Sampling weights were applied. Multivariable logistic regression and multivariable linear modeling were performed to examine the associations of flossing and preventive dental services on periodontal health and HbA1c levels, respectively, controlling for sociodemographic characteristics, health behaviors, and other risk factors.ResultsAmong U.S. dentate adults with diabetes, 52.1% of flossers and 72.1% of non-flossers had periodontitis (p < 0.001). Flossers were 39% less likely to have periodontitis (Adj. OR 0.61, 95% CI 0.43–0.88) compared to non-flossers. Flossers had an average HbA1c reading 0.30% (95% CI 0.02%—0.58%) lower than non-flossers, adjusted for covariates (p = 0.037). Preventive dental visits were associated with reduced risk for periodontitis (Adj. OR 0.54, 95%CI, 0.38–0.75) but not glycemic control.ConclusionFlossing was associated with periodontal health and glycemic control among US adults with diabetes. Although further research is needed, the findings support that oral self-care may be particularly beneficial for adults with diabetes.

Impact evaluation of the turnaround arts pilot program: an interrupted time series analysis

The purpose of this study was to conduct an evaluation of the pilot program of the Turnaround Arts reform using a comparative interrupted time series design. Because the only existing evaluation of the Turnaround Arts pilot program lacks clarity and transparency, reanalyzing this program is important to understand the effects of the initiative. I created a unique dataset with nine variables to specifically evaluate the achievement outcomes of the pilot schools, which I paired with similarly matched control schools. Achievement measures included average math and reading language arts (RLA) percent proficient scores for each of the schools from 2010 to 2014 and were collected from the Stanford Education Data Archive. My results indicated that the original Turnaround Arts reform had no statistically significant impacts on the pilot schools achievement measures, an important link in the initiatives theory of action. These results support previous music education literature that found no positive causal effects between music education and non-music achievement scores. School music and arts programs are important for providing children with a well-rounded education; however, justifying the use of arts education for non-arts gains can undermine high-quality arts program development.