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The development of complete mitochondrial genome (mitogenome) reference data for inclusion in publicly available population databases is currently underway, and the generation of more high-quality mitogenomes will only enhance the statistical power of this forensically useful locus. To characterize mitogenome variation in Sweden, the mitochondrial DNA (mtDNA) reads from the SweGen whole genome sequencing (WGS) dataset were analyzed. To overcome the interference from low-frequency nuclear mtDNA segments (NUMTs), a 10% variant frequency threshold was applied for the analysis. In total, 934 forensic-quality mitogenome haplotypes were characterized. Almost 45% of the SweGen haplotypes belonged to haplogroup H. Nearly all mitogenome haplotypes (99.1%) were assigned to European haplogroups, which was expected based on previous mtDNA studies of the Swedish population. There were signature northern Swedish and Finnish haplogroups observed in the dataset (e.g., U5b1, W1a), consistent with the nuclear DNA analyses of the SweGen data. The complete mitogenome analysis resulted in high haplotype diversity (0.9996) with a random match probability of 0.15%. Overall, the SweGen mitogenomes provide a large mtDNA reference dataset for the Swedish population and also contribute to the effort to estimate global mitogenome haplotype frequencies.

Whole-genome sequencing (WGS) data present a readily available resource for mitochondrial genome (mitogenome) haplotypes that can be utilized for genetics research including population studies. However, the reconstruction of the mitogenome is complicated by nuclear mitochondrial DNA (mtDNA) segments (NUMTs) that co-align with the mtDNA sequences and mimic authentic heteroplasmy. Two minimum variant detection thresholds, 5% and 10%, were assessed for the ability to produce authentic mitogenome haplotypes from a previously generated WGS dataset. Variants associated with NUMTs were detected in the mtDNA alignments for 91 of 917 (~8%) Swedish samples when the 5% frequency threshold was applied. The 413 observed NUMT variants were predominantly detected in two regions (nps 12,612-13,105 and 16,390-16,527), which were consistent with previously documented NUMTs. The number of NUMT variants was reduced by ~97% (400) using a 10% frequency threshold. Furthermore, the 5% frequency data were inconsistent with a platinum-quality mitogenome dataset with respect to observed heteroplasmy. These analyses illustrate that a 10% variant detection threshold may be necessary to ensure the generation of reliable mitogenome haplotypes from WGS data resources.

A total of 1327 platinum-quality mitochondrial DNA haplotypes from United States (U.S.) populations were generated using a robust, semi-automated next-generation sequencing (NGS) workflow with rigorous quality control (QC). The laboratory workflow involved long-range PCR to minimize the co-amplification of nuclear mitochondrial DNA segments (NUMTs), PCR-free library preparation to reduce amplification bias, and high-coverage Illumina MiSeq sequencing to produce an average per-sample read depth of 1000 × for low-frequency (5%) variant detection. Point heteroplasmies below 10% frequency were confirmed through replicate amplification, and length heteroplasmy was quantitatively assessed using a custom read count analysis tool. Data analysis involved a redundant, dual-analyst review to minimize errors in haplotype reporting with additional QC checks performed by EMPOP. Applying these methods, eight sample sets were processed from five U.S. metapopulations (African American, Caucasian, Hispanic, Asian American, and Native American) corresponding to self-reported identity at the time of sample collection. Population analyses (e.g., haplotype frequencies, random match probabilities, and genetic distance estimates) were performed to evaluate the eight datasets, with over 95% of haplotypes unique per dataset. The platinum-quality mitogenome haplotypes presented in this study will enable forensic statistical calculations and thereby support the usage of mitogenome sequencing in forensic laboratories.

Given the enhanced discriminatory power of the mitochondrial DNA (mtDNA) genome (mitogenome) over the commonly sequenced control region (CR) portion, the scientific merit of mitogenome sequencing is generally accepted. However, many laboratories remain beholden to CR sequencing due to privacy policies and legal requirements restricting the use of disease information or coding region (codR) information. In this report, we present an approach to obviate the reporting of sensitive codR data in forensic haplotypes. We consulted the MitoMap database to identify 92 mtDNA codR variants with confirmed pathogenicity. We determined the frequencies of these pathogenic variants in literature-quality and forensic-quality databases to be very low, at 1.2% and 0.36%, respectively. The observed effect of pathogenic variant filtering on random match statistics in 2488 forensic-quality mitogenome haplotypes from four populations was nil. We propose that pathogenic variant filtering should be incorporated into variant calling algorithms for mitogenome haplotype reporting to maximize the discriminatory power of the locus while minimizing the reveal of sensitive genetic information.

Background: Adjuvant maneuvers are often necessary to correct residual curvature during inflatable penile prosthesis (IPP) placement in patients with Peyronie's disease (PD)., Aim: We present our multicenter experience using collagen fleece as graft material for plaque incision and grafting (PIG) during IPP placement in patients with moderate to severe PD., Methods: We retrospectively reviewed 51 patients with IPP from 3 sites who underwent PIG with Tachosil (Baxter, IL) collagen fleece. Coloplast (Minneapolis, MN) IPP devices were used. Factors associated with residual curvature, revision, and patient satisfaction were performed using chi-squared analysis., Outcomes: We evaluated postoperative outcomes including factors associated with residual curvature, revision, and patient satisfaction., Results: The mean compound curvature was 69.6°. The mean follow-up was 10.6 (range 1-38) months. All patients reported erections sufficient for penetrative intercourse at the last follow-up. Residual curvature <15° was noted in 6 of 51 (12%) patients. 3 patients required device revision. 2 patients experienced temporary glanular paresthesia, and no patients experienced device infection., Clinical Implications: In our multicenter study, patients experienced substantial curve correction with minimal complications, and in the few patients who had persistent mild curvature, severe preoperative curvature (>60°) was found to be the only risk factor., Strengths & Limitations: Our study represents the largest series of patients coming from multiple centers undergoing surgical correction of PD with IPP and collagen fleece grafting. Limitations of this study include the retrospective study design, lack of a comparison group, and modest follow-up., Conclusion: PIG using collagen fleece is a safe and effective means of correcting residual curvature after IPP placement in patients with moderate to severe PD. Hatzichristodoulou G, Yang DY, Ring JD, et al. Multicenter Experience Using Collagen Fleece for Plaque Incision With Grafting to Correct Residual Curvature at the Time of Inflatable Penile Prosthesis Placement in Patients With Peyronie's Disease. J Sex Med 2020;17:1168-1174., (Copyright © 2020 International Society for Sexual Medicine. Published by Elsevier Inc. All rights reserved.)

Objectives: Complete primary repair of exstrophy (CPRE) was established as a method to reduce numbers of procedures for the reconstruction of bladder exstrophy (BE). Performed since 1989, some suggest it as a replacement for the staged reconstructive procedure, the gold standard. Does CPRE reduce the numbers of procedures for reconstruction of BE?, Methods: Literature was reviewed from 1989 to 2016, and articles evaluating outcomes of patients undergoing CPRE, extracted. Effort was made to obtain final data from each reporting institution/group. Eleven articles meeting criteria were evaluated for qualitative systematic review. Age at initial closure, complications, additional procedures, and outcomes were evaluated to provide an overview of CPRE., Results: Ten groups reported BE management using the CPRE technique. 236 patients (153 boys; 72 girls; 11 unknown sex) had primary closure ranging from birth to 5.6 years. Osteotomy was favored by most in infants closed beyond the first 72 h of life along with spica cast immobilization. Three groups recommended concomitant augmentation for infants with small bladder capacities. Ureteral reimplantation was required in 58 patients with recurrent urinary tract infections resistant to prophylaxis. Hypospadias repair was required for most boys having complete penile disassembly, and most children eventually required bladder neck reconstruction (BNR) for continence. Overall, voiding without BNR was noted in 16-37% of children in the reported series., Conclusions: Complete primary repair of exstrophy has been suggested as a single procedure for the management of BE. Literature review suggests most patients require multiple procedures to complete reconstruction and attain continence., (Copyright © 2020 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.)

Mitochondrial haplogroup information can be useful in forensic contexts that rely primarily on mitochondrial DNA (mtDNA) testing, which often involve limited or degraded DNA. Due to the phylogeographic patterning of mtDNA in human populations, mitochondrial haplogroups are indicative of maternal ancestry (as mtDNA is a maternally inherited marker). In certain circumstances, maternal ancestry inferred from mitochondrial haplogrouping could be beneficial to forensic investigations. For example, ancestry information could assist in the identification of unknown service members from past conflicts, such as the World War II Battle of Tarawa involving American and Japanese forces. In this context, it could be useful to distinguish Native American mtDNA from Asian mtDNA to bolster the anthropological and circumstantial evidence leading to an identification or foreign national determination. Although most of the founding Native American haplogroups contain diagnostic variants in the mitochondrial control region (CR), haplogroup B2 does not, and this makes it more difficult to distinguish B2 from the parental B4 and closely related B4b haplogroups found in Asia. In this paper, the amount of mtDNA information required to distinguish Native American haplotypes from Asian haplotypes within haplogroup B was examined. Fifty-six samples belonging to subtypes of B2 and B4 were sequenced for the entire mitogenome. Haplogroups were estimated from three ranges of mitochondrial DNA (HV1 and 2, CR, and full mitogenome). Half of the samples could not be precisely haplogrouped without full mitogenome data, although enough variants were often provided to make an accurate B2 versus B4 distinction. Native American B2 haplotypes were distinguishable using CR data alone in 82% of samples, though the remaining samples required full mitogenome data for haplogroup B2 designation. The use of full mitogenome data consistently enables accurate haplogroup determination, and opens the possibility for gaining information on maternal ancestry., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Nuclear mitochondrial DNA segments (NUMTs) have arisen because of the transposition of segments of the mitochondrial DNA genome (mitogenome) into the nuclear genome. When using a "mitotiling" strategy, NUMTs may be more readily amplified when targeting the entire mitogenome compared to the control region, as hundreds of primers are required for complete sequencing coverage. In samples with a high percentage of nuclear DNA copies per cell, such as whole blood, NUMT coenrichment may be exacerbated. The present study examined bioinformatic approaches for removing NUMTs and NUMT-associated variants (NAVs) from next-generation sequence data generated using two mitotiling kits (Precision ID and QIAseq). Across 16 samples with low mtDNA copy number, NUMT coenrichment produced 890 NAVs with >5% variant frequency. The use of the consensus sequence to eliminate NUMT reads proved to be effective for QIAseq data, and resulted in >85% NAV removal in Precision ID data. This method was bolstered by NAV filtering in Precision ID analysis. Alternative high stringency mapping to the revised Cambridge Reference Sequence (rCRS) and the human genome reference GRCh38 for the QIAseq data caused a reduction in mitogenome coverage without complete NUMT removal. These bioinformatic solutions facilitate mitotiling sequence data analysis for low-level variant detection., (Published 2018. This article is a U.S. Government work and is in the public domain in the USA.)

Next-generation sequencing (NGS) facilitates the rapid and high-throughput generation of human mitochondrial genome (mitogenome) data to build population and reference databases for forensic comparisons. To this end, long-range amplification provides an effective method of target enrichment that is amenable to library preparation assays employing DNA fragmentation. This study compared the Nextera XT DNA Library Preparation Kit (Illumina, San Diego, CA) and the KAPA HyperPlus Library Preparation Kit (Kapa Biosystems, Wilmington, MA) for enzymatic fragmentation and indexing of ∼8500bp mitogenome amplicons for Illumina sequencing. The Nextera XT libraries produced low-coverage regions that were consistent across all samples, while the HyperPlus libraries resulted in uniformly high coverage across the mitogenome, even with reduced-volume reaction conditions. The balanced coverage observed from KAPA HyperPlus libraries enables not only low-level variant calling across the mitogenome but also increased sample multiplexing for greater processing efficiency., (Copyright © 2017 Elsevier B.V. All rights reserved.)

Introduction: The Kropp and Salle procedures have shown good short-term outcomes for managing neuropathic urinary incontinence. However, few studies have assessed their long-term results., Objective: This study aimed to evaluate the long-term outcomes of Kropp and Salle procedures, including: dryness, secondary interventions for incontinence or complications, upper urinary tract changes, and use of urethral catheterizations., Study Design: Consecutive patients undergoing Kropp and Salle procedures at the present institution (1983-2012) were retrospectively reviewed. Patients with <1-year follow-up or prior bladder neck (BN) continence procedures were excluded. Data were collected on postoperative dryness per urethra at 4-hourly and 3-hourly intervals, secondary interventions, lab tests, and imaging. Non-parametric tests were used for statistical analysis., Results: Thirty-eight patients had Kropp (K: 30 boys) and 12 had Salle procedures (S: 8 boys). Patients underwent surgery at similar median ages (K: 7.4 vs S: 8.7 years old, P = 0.51) and had similar median follow-up (6.9 vs 10.3 years, P = 0.10). Most patients had myelomeningocele, a prior/concomitant bladder augmentation (K: 73.7%, S: 58.3%) and catheterizable channel (K: 81.6%, S: 50.0%). Differences in all outcomes between Kropp and Salle procedures were statistically non-significant. The majority of patients did not have additional BN procedures for dryness (K: 84.2%, S: 66.7%). Of this group, K: 81.3% and S: 75.0% were dry for ≥4 h, K: 93.8% and S: 87.5% were dry for ≥3 h between catheterizations (Table). Of the minority of patients who underwent additional BN procedures for dryness (K: 15.8%, S: 33.3%), most achieved dryness for ≥4 h (K: 66.7%, S: 100%) and ≥3 h (100% for both). Among patients without an initial catheterizable channel, 57.1% had one subsequently created after a Kropp procedure, and 33.3% after a Salle. Among patients without bladder augmentation, approximately half underwent delayed augmentation (K: 50.0%, S: 40.0%). Ultimately, most patients required a secondary intervention under anesthesia for incontinence or complications (K: 79.0%, S: 66.7%). Few patients developed worsening hydronephrosis, vesicoureteral reflux or renal function (K: 2.6%, S: 0.0%). At the end of follow-up, few patients catheterized per urethra (K: 10.5%, S: 33.3%)., Discussion: This was a retrospective study without urodynamic data. Originating from a tertiary center, the results may not apply to other clinical settings., Conclusions: At the present institution the Kropp and Salle procedures attained similar dryness in 75-81% at 4-hourly intervals and 88-94% at 3-hourly intervals without additional BN procedures. Few patients required subsequent BN procedures to achieve dryness. However, the overall need for secondary procedures during long-term follow-up was high for both procedures., (Copyright © 2016. Published by Elsevier Ltd.)

Male factor contributes to 50%-60% of overall infertility but is solely responsible in only 20% of couples. Although most male factor infertility is ascertained from an abnormal semen analysis, other male factors can be contributory especially if the sample returns normal. Male infertility can be due to identifiable hormonal or anatomical etiologies that may be reversible or irreversible. This manuscript will highlight existing guidelines and our recommendations for hormone evaluation for male infertility and empiric therapies including multivitamins, estrogen receptor modulators (clomiphene), estrogen conversion blockers (anastrozole), and hormone replacement.

Introduction: Bladder and renal calculi after bladder augmentation are thought to be primarily infectious, yet few studies have reported stone composition., Objective: The primary aim was to assess bladder stone composition after augmentation, and renal stone composition in those with subsequent nephrolithiasis. The exploratory secondary aim was to screen for possible risk factors for developing infectious stones., Study Design: Patients treated for bladder stones after bladder augmentation at the present institution between 1981 and 2012 were retrospectively reviewed. Data were collected on demographics, surgeries and stone composition. Patients without stone analysis were excluded. Stones containing struvite, carbonate apatite or ammonium acid ureate were classified as infectious. The following variables were analyzed for a possible association with infectious bladder stone composition: gender, history of cloacal exstrophy, ambulatory status, nephrolithiasis, recurrent urea-splitting urinary tract infections, first vs recurrent stones, timing of presentation with a calculus, history of bladder neck procedures, catheterizable channel and vesicoureteral reflux. Fisher's exact test was used for analysis., Results: Of the 107 patients with bladder stones after bladder augmentation, 85 met inclusion criteria. Median age at augmentation was 8.0 years (follow-up 10.8 years). Forty-four patients (51.8%) recurred (14 multiple recurrences, 143 bladder stones). Renal calculi developed in 19 (22.4%) patients with a bladder stone, and 10 (52.6%) recurred (30 renal stones). Overall, 30.8% of bladder stones were non-infectious (Table). Among patients recurring after an infectious bladder stone, 30.4% recurred with a non-infectious one. Among patients recurring after a non-infectious stone, 84.6% recurred with a non-infectious one (P = 0.005). Compared with bladder stones, renal stones were more likely to be non-infectious (60.0%, P = 0.003). Of patients with recurrent renal calculi after an infectious stone, 40.0% recurred with a non-infectious one. No clinical variables were significantly associated with infectious stone composition on univariate (≥0.28) or bivariate analysis (≥0.36)., Discussion: This study had several limitations: it was not possible to accurately assess adherence with bladder irrigations, and routine metabolic evaluations were not performed. The findings may not apply to patients in all clinical settings. While stone analysis was available for 3/4 of the stones, similar rates of incomplete stone analyses have been reported in other series., Conclusions: In patients with bladder augmentation, 1/3 of bladder stones and >1/2 of renal stones were non-infectious. Furthermore, an infectious stone does not imply an infectious recurrent stone and no known clinical variables appear to be associated with stone composition, suggesting that there is a possible metabolic component in stone formation after bladder augmentation., (Copyright © 2015 Journal of Pediatric Urology Company. Published by Elsevier Ltd. All rights reserved.)

Objective: To calibrate a 12-mm high-intensity focused ultrasound (HIFU) probe to produce histologically verifiable complete tissue necrosis through thermal energy delivery while maintaining safety in ablation of porcine renal tissue., Methods: The study was approved by the animal research committee at our institution. A HIFU probe on a fixed arm was introduced, and ablation was subsequently carried out robotically (under computer control) at 2 planned locations within each kidney at varying energy levels. After 4 days of survival, kidneys were retrieved and pathologic analysis of the lesions was carried out for necrotic volume. Planned volume was compared with pathologic necrotic volume., Results: A series of optimizations were carried out as the experiment progressed. Near optimal ablation zone dimensions with complete cell death were achieved when the energy density was between 400 and 460 calories/cm(3). Pathologic analysis demonstrated the average ratio of necrotic zone volume to planned zone volume was 1.0 (standard deviation, 0.18) in the 7 lesions with energy density between 400 and 460 calories/cm(3). All animals survived the surgeries, and no device-related complications were identified during the study. No acute renal failure was identified in analysis of the blood work., Conclusion: A novel 12-mm laparoscopic HIFU probe was successfully calibrated for the ablation of porcine renal tissue. The safety profile of the Sonatherm probe was found to be excellent with no complications identified., (Copyright © 2015 Elsevier Inc. All rights reserved.)

Though investigations into the use of massively parallel sequencing technologies for the generation of complete mitochondrial genome (mtGenome) profiles from difficult forensic specimens are well underway in multiple laboratories, the high quality population reference data necessary to support full mtGenome typing in the forensic context are lacking. To address this deficiency, we have developed 588 complete mtGenome haplotypes, spanning three U.S. population groups (African American, Caucasian and Hispanic) from anonymized, randomly-sampled specimens. Data production utilized an 8-amplicon, 135 sequencing reaction Sanger-based protocol, performed in semi-automated fashion on robotic instrumentation. Data review followed an intensive multi-step strategy that included a minimum of three independent reviews of the raw data at two laboratories; repeat screenings of all insertions, deletions, heteroplasmies, transversions and any additional private mutations; and a check for phylogenetic feasibility. For all three populations, nearly complete resolution of the haplotypes was achieved with full mtGenome sequences: 90.3-98.8% of haplotypes were unique per population, an improvement of 7.7-29.2% over control region sequencing alone, and zero haplotypes overlapped between populations. Inferred maternal biogeographic ancestry frequencies for each population and heteroplasmy rates in the control region were generally consistent with published datasets. In the coding region, nearly 90% of individuals exhibited length heteroplasmy in the 12418-12425 adenine homopolymer; and despite a relatively high rate of point heteroplasmy (23.8% of individuals across the entire molecule), coding region point heteroplasmies shared by more than one individual were notably absent, and transversion-type heteroplasmies were extremely rare. The ratio of nonsynonymous to synonymous changes among point heteroplasmies in the protein-coding genes (1:1.3) and average pathogenicity scores in comparison to data reported for complete substitutions in previous studies seem to provide some additional support for the role of purifying selection in the evolution of the human mtGenome. Overall, these thoroughly vetted full mtGenome population reference data can serve as a standard against which the quality and features of future mtGenome datasets (especially those developed via massively parallel sequencing) may be evaluated, and will provide a solid foundation for the generation of complete mtGenome haplotype frequency estimates for forensic applications., (Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.)

Forensic mitochondrial DNA (mtDNA) testing requires appropriate, high quality reference population data for estimating the rarity of questioned haplotypes and, in turn, the strength of the mtDNA evidence. Available reference databases (SWGDAM, EMPOP) currently include information from the mtDNA control region; however, novel methods that quickly and easily recover mtDNA coding region data are becoming increasingly available. Though these assays promise to both facilitate the acquisition of mitochondrial genome (mtGenome) data and maximize the general utility of mtDNA testing in forensics, the appropriate reference data and database tools required for their routine application in forensic casework are lacking. To address this deficiency, we have undertaken an effort to: (1) increase the large-scale availability of high-quality entire mtGenome reference population data, and (2) improve the information technology infrastructure required to access/search mtGenome data and employ them in forensic casework. Here, we describe the application of a data generation and analysis workflow to the development of more than 400 complete, forensic-quality mtGenomes from low DNA quantity blood serum specimens as part of a U.S. National Institute of Justice funded reference population databasing initiative. We discuss the minor modifications made to a published mtGenome Sanger sequencing protocol to maintain a high rate of throughput while minimizing manual reprocessing with these low template samples. The successful use of this semi-automated strategy on forensic-like samples provides practical insight into the feasibility of producing complete mtGenome data in a routine casework environment, and demonstrates that large (>2kb) mtDNA fragments can regularly be recovered from high quality but very low DNA quantity specimens. Further, the detailed empirical data we provide on the amplification success rates across a range of DNA input quantities will be useful moving forward as PCR-based strategies for mtDNA enrichment are considered for targeted next-generation sequencing workflows., (Copyright © 2014 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.)

We describe a new class of propagation-invariant light beams with Fourier transform given by an eigenfunction of the quantum mechanical pendulum. These beams, whose spectra (restricted to a circle) are doubly periodic Mathieu functions in azimuth, depend on a field strength parameter. When the parameter is zero, pendulum beams are Bessel beams, and as the parameter approaches infinity, they resemble transversely propagating one-dimensional Gaussian wave packets (Gaussian beam-beams). Pendulum beams are the eigenfunctions of an operator that interpolates between the squared angular momentum operator and the linear momentum operator. The analysis reveals connections with Mathieu beams, and insight into the paraxial approximation.

We present a mathematical analysis of the finite-energy Airy beam with a sharply truncated spectrum, which can be generated by a uniformly illuminated, finite-sized spatial light modulator, or windowed cubic phase mask. The resulting "incomplete Airy beam" is tractable mathematically, and differs from an infinite-energy Airy beam by an additional oscillating modulation and the decay of its fringes. Its propagation can be described explicitly using an incomplete Airy function, from which we derive simple expressions for the beam's total power and mean position. Asymptotic analysis reveals a simple connection between the cutoff and the region of the beam with Airy-like behavior.

We present a new solution of the paraxial equation based on the Pearcey function, which is related to the Airy function and describes diffraction about a cusp caustic. The Pearcey beam displays properties similar not only to Airy beams but also Gaussian and Bessel beams. These properties include an inherent auto-focusing effect, as well as form-invariance on propagation and self-healing. We describe the theory of propagating Pearcey beams and present experimental verification of their auto-focusing and self-healing behaviour.

One of the most serious and prevalent problems associated with the restorative aspect of dental implants is loosening and fracturing of screws. Implant screws should be retightened 10 minutes after the initial torque application as a routine clinical procedure to help compensate for the settling effect. Mechanical torque gauges should be used instead of hand drivers to ensure consistent tightening of implant components to torque values recommended by implant manufacturers.