The American College of Obstetrics and Gynecology (ACOG) has emphasized that curriculum-based simulation should be utilized in resident education. These simulations give learners a realistic hands-on learning approach. Currently, sacrospinous ligament fixation (SSLF) models are not readily available and are unrealistic. The purpose of the study was to implement a SSLF simulation for Obstetric and Gynecology (OBGYN) residents and create an low fidelity SSLF model that was more realistic in replicating the narrow surgical space and required proper dissection(IRB exempt). The model was created using a bony pelvis, a vagina made from silicone and cornstarch, ligaments made from silk tape, and fibrous tissue and membranes using plastic wrap and polyfil (Figure 1). Before instruction, residents completed a pre-test knowledge assessment and SSLF. Residents then received curriculum teaching and SSLF simulation demonstration. Following instruction, residents then performed the post SSLF simulation and the post-knowledge assessment. Simulation skills were assessed using the modified Objective Structures Assessment of Technical Skills (mOSATS). The primary outcome was to compare changes in the mOSATS. The secondary outcome was to compare changes in the pre and post knowledge assessment scores. Thirty residents participated in two simulation sessions over two academic years. The majority had neither seen nor performed a SSLF. For the primary outcome, there was a significant difference in all mOSATS components: instrument handling and movement, suturing time, and proper location and placement on the ligament (Table 1). In addition, it was observed that the model provided challenging surgical simulation due to the narrow surgical space and if the required dissection was not completed properly, sutures were placed incorrectly (Figure 2). For the knowledge assessment, there was a significant improvement in the majority of questions testing anatomy and suture placement, but not for success or complication questions. Our SSLF model can be easily created for SSLF simulation, can be used multiple times, and only costs $82.58 per model. In addition, our study demonstrated an improvement in both mOSATS as well as SSLF knowledge. Given ACOG recommendations for simulation training, OBGYN residency programs should consider creating similar SSLF simulation labs to provide learners better understanding of SSLF surgery as well as proper dissection and suture placement.

In this chapter, formation, environmental concerns, and remediation of air pollutions, including particulate matter (PM) and gaseous pollutants, are introduced. Owing to the characteristic differences between PM and gaseous pollutants, the capture mechanisms may differ. Capture of PM is well described by conventional capture mechanism, while gaseous pollutants are captured mainly by physical adsorption and chemical adsorption. The characterization for both filters is also addressed. Metal oxide nanofibers (NFs) have already been proved to be one the most effective and promising solution for air remediation. Fibrous metal oxide has several advantages, such as high surface area, stronger mechanic strength, chemical stability, thermal stability, and photocatalytic ability. The examples of metal oxide NFs for air remediation in form of filter, catalyst, catalyst support, and photocatalyst are discussed.

The work described below was carried out to understand how to control the morphology of nanostructured titania calcined from electrospun nanofibers. This is the first report of hollow rutile nanofibers synthesized from electrospun nanofibers with short calcination time. Titanium isopropoxide was incorporated into the nanofibers as the titania precursor. The electrospinning technique was used to fabricate ceramic/polymer hybrid nanofibers. The electrospun nanofibers were then calcined to produce rutile titania nanofibers with different morphologies (hollow or solid nanofibers), which were characterized by SEM and TEM. The initial concentration of ceramic precursor and the calcination time were shown to control the morphology of the nanofiber. The hollow morphology was only obtained with a concentration of the precursor within a certain level and with short calcination times. The heat treatment profile contributed to particle growth. At longer times, the particle growth led to the closure of the hollow core and all the nanofibers resembled strings of solid particles. A formation mechanism for the hollow nanofibers is also proposed.

Summary This curriculum development project on multiphase transport phenomena draws on the research experiences from nine research laboratories at The University of Akron, Michigan State University, and the University of Tulsa. The objective of the project is to develop a new curriculum for teaching undergraduate and graduate students multiphase computational fluid dynamics for advanced design. The impact of multiphase flow research on solving practical engineering problems is an integral part of the learning experience. Industrial participants in the project provide specific design problems related to emerging technologies. Students are taught the fundamentals of computational fluid dynamics (CFD) during a one-week workshop. This is followed by an Internet course on multiphase transport phenomena. The students work in teams on CFD design problems with a faculty and industrial mentor. The salient results of this NSF/CRCD project are presented in this paper. I. Introduction Courses on transport phenomena associated with multicomponent, single-phase fluids play a major role in training undergraduate and graduate students in chemical, mechanical, and petroleum engineering. However, like thermodynamics and other multidisciplinary courses, these academic offerings have been developed separately within each engineering discipline in order to emphasize applied problems encountered in each field. So far, student training in the area of transport phenomena for multiphase fluids has been limited to specialized courses and workshops. Consequently, important advances in multiphase flow research and analysis tend to remain isolated within a discipline. Moreover, access to post graduate courses on multiphase transport phenomena and particulate processing remains a difficult challenge for most graduates. Therefore, the objective of this NSF- Combined Research and Curriculum Development (CRCD) initiative is to bridge the gap between traditional training in fluid mechanics, heat transfer, and mass transfer received by most

Polycaprolactone (PCL) nanofiber scaffolds with attached cadaveric human periosteum or its cells were investigated in this study as a tissue-engineering approach to repair nonunion injuries of bone. Addition of silica nanoparticles (silica or nSiO2 ) to PCL scaffolds was examined for effects on the growth of human periosteal cells in vitro and in vivo. Electrospun PCL nanofiber (nanoPCL) scaffolds were fabricated with different silica contents (0, 0.5, and 1.0 wt %) and utilized as substrates on which periosteal cells were seeded. Human periosteal cell growth analyzed in vitro over 21 days with a PrestoBlue viability assay increased as a function of culture time on each of the three different silica/nanoPCL scaffolds. Cadaveric periosteum attached to nanoPCL scaffolds with or without silica was wrapped around allograft bone and implanted for 10 or 20 weeks in athymic (nude) mice. Histological and immunohistochemical analyses of these experiments in vivo confirmed the presence of viable cells populating the constructs after their retrieval from host mice. Osterix, a marker for osteoblasts, increased in retrieved constructs over time and indicated remodeling of the underlying allograft bone. Summary results suggest that silica/nanoPCL scaffolds may be utilized as substrates for periosteal cell and tissue expansion to augment and support clinical applications for treatment and healing of bone defects, including segmental bone injuries and nonunions. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 791-801, 2019.

Fetal fraction (FF) is one of the many factors that influence the performance of non-invasive prenatal screening (NIPS). Low FF is associated with early gestational age, a compromised placenta (eg. from triploidy and certain aneuploidies), and high body mass index (BMI). By far, the most common of these is high BMI: patients with high BMI (>29.9) constitute ∼25% of US pregnancies and ∼20% of UK pregnancies. The most recent American College of Genetics and Genomics statement recommends “offering aneuploidy screening other than NIPS in cases of significant obesity.” We sought to examine whether high-BMI patients benefit from NIPS versus standard maternal serum screening for the purpose of common aneuploidy screening. 51,737 patients who received NIPS were stratified into standard BMI classes. For each BMI group, the aggregate analytical sensitivity was calculated by summing, over the range of FF values, the product of (1) the sensitivity for a given FF and depth based on a model of whole-genome sequencing (WGS) NIPS and (2) the BMI-specific probability of observing a patient at that FF. Scaled sensitivities were incorporated into residual-risk calculations to assess impact on patient results reporting. Due to downward shifts in the FF distribution, NIPS sensitivity drops as BMI increases: non-obese analytical sensitivity for Trisomy 21 (T21) is 99.8%, whereas for class III obesity (BMI >40) it is 95.4%. Nevertheless, even those patients with class III BMI have expected T21 sensitivity in excess of that obtainable via standard maternal serum screening (92.9%). NIPS is a reasonable option for high-BMI patients when using methods that improve the performance at low FF (eg. high-depth WGS), allowing providers to offer the same high level of care to all of their patients, regardless of body habitus. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Expanded carrier screening (ECS) identifies couples whose future children are at increased risk of Mendelian conditions. Historically, ECS has been performed with limited or no copy number variant (CNV) calling, often restricted to a handful of founder deletions. The lack of broad CNV calling may reduce the detection rate of ECS. We performed panel-wide copy number deletion calling on a large ECS patient cohort to determine its impact on detecting at-risk couples. For >10,000 anonymized patient samples tested on a validated 176-disease ECS panel, we performed CNV deletion calling on 161 autosomal-recessive disease genes and 10 genes associated with X-linked conditions (calls for several conditions such as SMN1, are treated as special cases and excluded from this analysis). Copy number calling was performed using a Hidden Markov Model on next generation sequencing depth data, and CNVs were identified down to single-exon resolution. Positive and low-confidence CNV calls emitted by the bioinformatics pipeline were reviewed manually by certified experts prior to being curated and reported to patients if found to be deleterious. Approximately 2% of patients have at least one pathogenic deletion CNV. Importantly, the collective frequency of novel pathogenic CNVs exceeds the rate with which founder CNVs (in CLN3, CTNS, GALC, HEXA, MCOLN1, and NEB) were identified in our previous 112-gene panel. Most of the observed deletions are not the six founder deletions we called in previous work, indicating that broader use of CNV calling will improve detection rates in ECS. The presented findings support inclusion of CNV deletion calling in clinical ECS panels such that at-risk couples can be identified with maximal sensitivity. Our large and growing CNV dataset will enable statistically powered studies of CNV frequencies by size, gene, and ethnicity.

Purpose By identifying pathogenic variants across hundreds of genes, expanded carrier screening (ECS) enables prospective parents to assess risk of transmitting an autosomal recessive or X-linked condition. Detection of at-risk couples depends on the number of conditions tested, the diseases’ respective prevalences, and the screen’s sensitivity for identifying disease-causing variants. Here we present an analytical validation of a 235-gene sequencing-based ECS with full coverage across coding regions, targeted assessment of pathogenic noncoding variants, panel-wide copy-number-variant (CNV) calling, and customized assays for technically challenging genes. Methods Next-generation sequencing, a customized bioinformatics pipeline, and expert manual call review were used to identify single-nucleotide variants, short insertions and deletions, and CNVs for all genes except FMR1 and those whose low disease incidence or high technical complexity precludes novel variant identification or interpretation. Variant calls were compared to reference and orthogonal data. Results Validation of our ECS data demonstrated >99% analytical sensitivity and >99% specificity. A preliminary assessment of 15,177 patient samples reveals the substantial impact on fetal disease-risk detection attributable to novel CNV calling (13.9% of risk) and technically challenging conditions (15.5% of risk), such as congenital adrenal hyperplasia. Conclusion Validated, high-fidelity identification of different variant types—especially in diseases with complicated molecular genetics—maximizes at-risk couple detection.

Expanded carrier screening (ECS) identifies couples whose future children are at increased risk of Mendelian conditions. Historically, ECS has been performed with limited or no copy number variant (CNV) calling, often restricted to a handful of founder deletions. The lack of broad CNV calling may reduce the detection rate of ECS. We performed panel-wide CNV calling on an ECS cohort of 65,732 patients tested between Nov. 2016 and April 2017 to determine its impact on detecting at risk couples. Here we report CNV statistics for a 177-gene ECS panel on a cohort of 65,732 anonymized patient samples. We performed CNV deletion and duplication calling on 161 autosomal genes and 10 genes on chromosome X (calls for six genes, such as SMN1, are treated as special cases and excluded from this analysis). Copy number calling was performed using a Hidden Markov Model on next generation sequencing depth data. Although the genes with the most observed deletions (CLN3, GALC, CTNS) contain known founder mutations, 62% of called CNVs were located outside of the six genes for which we called deletions in our previous 112-gene panel (CLN3, CTNS, GALC, HEXA, MCOLN1, and NEB). Beyond the previously studied six gene subset, we also observe a large number of deletions in HBB (50 observations) and FANCA (58 observations); many of these variants are predicted to be pathogenic and significantly impact the population disease risk burden. Furthermore, HBB deletions are particularly common in Southeast Asians and African Americans. @Using a 65,732 patient cohort, we retrospectively evaluated the impact of CNVs on a 177 gene ECS panel. Most of the observed CNVs were outside the six genes for which we called founder deletions in previous work, indicating that broader use of CNV calling will improve detection rates in ECS. The presented findings have motivated the inclusion of panel-wide deletion calling in our clinical ECS panel, where novel deletions undergo real-time variant interpretation to assess clinical impact.

Objective Performance of noninvasive prenatal screening (NIPS) methodologies when applied to low fetal fraction samples is not well established. The single-nucleotide polymorphism (SNP) method fails samples below a predetermined fetal fraction threshold, whereas some laboratories employing the whole-genome sequencing (WGS) method report aneuploidy calls for all samples. Here, the performance of the two methods was compared to determine which approach actually detects more fetal aneuploidies. Methods Computational models were parameterized with up-to-date published data and used to compare the performance of the two methods at calling common fetal trisomies (T21, T18, T13) at low fetal fractions. Furthermore, clinical experience data were reviewed to determine aneuploidy detection rates based on compliance with recent invasive screening recommendations. Results The SNP method’s performance is dependent on the origin of the trisomy, and is lowest for the most common trisomies (maternal M1 nondisjunction). Consequently, the SNP method cannot maintain acceptable performance at fetal fractions below ~3%. In contrast, the WGS method maintains high specificity independent of fetal fraction and has >80% sensitivity for trisomies in low fetal fraction samples. Conclusion The WGS method will detect more aneuploidies below the fetal fraction threshold at which many labs issue a no-call result, avoiding unnecessary invasive procedures.

The past two decades have brought many important advances in our understanding of the hereditary susceptibility to cancer. Numerous studies have provided convincing evidence that identification of germline mutations associated with hereditary cancer syndromes can lead to reductions in morbidity and mortality through targeted risk management options. Additionally, advances in gene sequencing technology now permit the development of multigene hereditary cancer testing panels. Here, we describe the 2016 revision of the Counsyl Inherited Cancer Screen for detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy number variants (CNVs) in 36 genes associated with an elevated risk for breast, ovarian, colorectal, gastric, endometrial, pancreatic, thyroid, prostate, melanoma, and neuroendocrine cancers. To determine test accuracy and reproducibility, we performed a rigorous analytical validation across 341 samples, including 118 cell lines and 223 patient samples. The screen achieved 100% test sensitivity across different mutation types, with high specificity and 100% concordance with conventional Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA). We also demonstrated the screen's high intra-run and inter-run reproducibility and robust performance on blood and saliva specimens. Furthermore, we showed that pathogenic Alu element insertions can be accurately detected by our test. Overall, the validation in our clinical laboratory demonstrated the analytical performance required for collecting and reporting genetic information related to risk of developing hereditary cancers.

Purpose The recent growth in pan-ethnic expanded carrier screening (ECS) has raised questions about how such panels might be designed and evaluated systematically. Design principles for ECS panels might improve clinical detection of at-risk couples and facilitate objective discussions of panel choice. Methods Guided by medical-society statements, we propose a method for the design of ECS panels that aims to maximize the aggregate and per-disease sensitivity and specificity across a range of Mendelian disorders considered serious by a systematic classification scheme. We evaluated this method retrospectively using results from 474,644 de-identified carrier screens. We then constructed several idealized panels to highlight strengths and limitations of different ECS methodologies. Results Based on modeled fetal risks for “severe” and “profound” diseases, a commercially available ECS panel (Counsyl) is expected to detect 183 affected conceptuses per 100,000 US births. A screen’s sensitivity is greatly impacted by two factors: (i) the methodology used (e.g., full-exon sequencing finds more affected conceptuses than targeted genotyping) and (ii) the detection rate of the screen for diseases with high prevalence and complex molecular genetics (e.g., fragile X syndrome). Conclusion The described approaches enable principled, quantitative evaluation of which diseases and methodologies are appropriate for pan-ethnic expanded carrier screening.

The past two decades have brought many important advances in our understanding of the hereditary susceptibility to cancer.Numerous studies have provided convincing evidence that identification of germline mutations associated with hereditary cancer syndromes can lead to reductions in morbidity and mortality through targeted risk management options.Additionally, advances in gene sequencing technology now permit the development of multigene hereditary cancer testing panels.Here, we describe the 2016 revision of the Counsyl Inherited Cancer Screen for detecting single-nucleotide variants (SNVs), short insertions and deletions (indels), and copy number variants (CNVs) in 36 genes associated with an elevated risk for breast, ovarian, colorectal, gastric, endometrial, pancreatic, thyroid, prostate, melanoma, and neuroendocrine cancers.To determine test accuracy and reproducibility, we performed a rigorous analytical validation across 341 samples, including 118 cell lines and 223 patient samples.The screen achieved 100% test sensitivity across different mutation types, with high specificity and 100% concordance with conventional Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA).We also demonstrated the screen's high intra-run and inter-run reproducibility and robust performance on blood and saliva specimens.Furthermore, we showed that pathogenic Alu element insertions can be accurately detected by our test.Overall, the validation in our clinical laboratory demonstrated the analytical performance required for collecting and reporting genetic information related to risk of developing hereditary cancers.

Abstract The evaluation of cfDNA allows novel approaches to noninvasive detection of actionable alterations, resistance mechanisms, and tumor monitoring in patients with cancer. Importantly, tumor-specific DNA fragments represent a small minority of the cfDNA and can be obscured by false positive (FP) variants introduced by chemical damage and sequencer error. To address this, we improved key processes in the design of NGS libraries, including a new molecular barcoding approach, that maximize molecular recovery while eliminating spurious variants. We engineered a set of Illumina sequencing chemistry compatible adaptors incorporating unique molecular identifiers (barcodes) enabling reconstruction of the sequence of both strands of the original DNA molecule. These barcodes incorporate a number of key design improvements as compared to published methodologies, which enhance sequencer cluster density, thereby increasing library diversity and molecular recovery. Our new design identified both chemical and sequencer errors, reducing incorrect base calls to rates below 5e-7. We validated our methodology for use in cfDNA using both dilution experiments and patient blood samples with known oncogenic alterations via a custom capture panel targeting actionable genomic alterations in a 55kb region. By identifying the molecular origin of each read, we found that the sensitivity of detection obtained from barcoded libraries followed ideal binomial sampling expectations. We obtained an average molecular depth of 1,000 molecules per site from the plasma extracted from a single blood collection tube, which corresponded to an 80% sensitivity of detection of known oncogenic single-nucleotide and indel mutations at 0.15% mutant allele frequency (MAF) in cfDNA with no FP calls. Furthermore, we successfully detected known gene-fusions at 0.5%, and amplifications (>10 copies) down to 1% MAF. We designed and validated a custom-engineered error-correcting sequencing adapters, ideal for broad range of applications requiring high accuracy detection of ultra-low frequency alterations. Note: This abstract was not presented at the meeting. Citation Format: Carlo G. Artieri, Kyle A. Beauchamp, Valentina S. Vysotskaia, Noah C. Welker, Eric A. Evans, Clement Chu, Haluk Tezcan, Imran S. Haque. Optimized molecular barcoding enables accurate targeted mutation detection in circulating cell-free DNA (cfDNA) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5690. doi:10.1158/1538-7445.AM2017-5690

I Supplementary Materials and Methods 2 1 CNV Deletion Calling 2 2 Census Weighting 2 3 Disease Risk Calculation 2 3.1 Additive Approximation to Disease Risk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 3.2 Example: Autosomal Recessive Disease Risk for one Disease . . . . . . . . . . . . . . . . . . . . . . 3 3.3 Calculating Disease Risk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 3.4 Designing Optimal Targeted Genotyping Panels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 4 References 4

ObjectiveTo tabulate individual allele frequencies and total carrier frequency for Smith-Lemli-Opitz syndrome (SLOS) and compare expected versus observed birth incidences.MethodsA total of 262399 individuals with no known indication or increased probability of SLOS carrier status, primarily US based, were screened for SLOS mutations as part of an expanded carrier screening panel. Results were retrospectively analyzed to estimate carrier frequencies in multiple ethnic groups. SLOS birth incidences obtained from existing literature were then compared with these data to estimate the effect of SLOS on fetal survival.ResultsSmith-Lemli-Opitz syndrome carrier frequency is highest in Ashkenazi Jews (1 in 43) and Northern Europeans (1 in 54). Comparing predicted birth incidence with that observed in published literature suggests that approximately 42% to 88% of affected conceptuses experience prenatal demise.ConclusionSmith-Lemli-Opitz syndrome is relatively frequent in certain populations and, because of its impact on prenatal and postnatal morbidity and mortality, merits consideration for routine screening. (c) 2017 The Authors. Prenatal Diagnosis published by John Wiley & Sons, Ltd.