New York State's WAVE Method - Evaluation of a Method for Water Quality Monitoring by Citizen Scientists using Benthic Macroinvertebrates.

New York State Department of Environmental Conservation (NYSDEC) has developed a robust citizen science macroinvertebrate sampling method. The metric relies on the presence and not the absence of key macroinvertebrates and therefore is resistant to collection and sorting errors. It identifies unimpaired streams with high confidence (0.1% type 1 errors) and at a reasonable efficiency compared to NYSDEC's multimetric index of biological integrity (54%). We rank remaining stream samples for further investigation using a calculated probability of impairment. This method is valuable as a tool for large monitoring programs with limited resources for quality assurance checks. The value of this method goes beyond data collection, however, as data of known quality is an effective communication tool between citizen scientists and state regulatory agencies and/or local decision makers.

Synthetic studies on the indane SHIP1 agonist AQX-1125.

AQX-1125 is an indane based SHIP1 agonist that has been evaluated in the clinic for the treatment of bladder pain syndrome/interstitial cystitis. To support our own studies on SHIP1 agonists as potential treatments for IBD and Crohn's disease, a new synthetic route to the SHIP1 agonist AQX-1125 has been developed. This sequence utilizes a hydroxy-acid intermediate which allows for ready differentiation of the C6 and C7 positions. The role of the C17 alkene in the biological activity of the system is also investigated, and this functional group is not required for SHIP1 agonist activity. While AQX-1125 shows SHIP1 agonist activity in enzyme assays, it does not show activity in cell based assays similar to other SHIP1 agonists, which limits the utility of this molecule.

Perineal Injury via Personal Watercraft Hydrostatic Jet: A Case Report.

BACKGROUND: Traumatic injuries resulting from personal watercraft hydrostatic jets are expected to increase as personal watercrafts are affordable, portable, and used in an increasingly wide range of locales. CASE PRESENTATION: This case study presents an unusual severe perineal injury in a 17-year-old adolescent girl resulting from a fall from a personal watercraft and contact with the vehicle's hydrostatic jet. This case report provides an overview of the mechanism, treatment, and prevention of personal watercraft injuries. CONCLUSION: Knowledge of this mechanism's potential for serious morbidity and mortality, patient assessment and management principles, and injury prevention strategies are essential to providing effective trauma center care.

MyPOD: an EMR-Based Tool that Facilitates Quality Improvement and Maintenance of Certification.

Maintenance of Certification (MOC) was designed to assess physician competencies including operative case volume and outcomes. This information, if collected consistently and systematically, can be used to facilitate quality improvement. Information automatically extracted from the electronic medical record (EMR) can be used as a prompt to compile these data. We developed an EMR-based program called MyPOD (My Personal Outcomes Data) to track surgical outcomes at our institution. We compared occurrences reported in the first 18 months to those captured in the American College of Surgeons National Surgical Quality Improvement Program-Pediatric (ACS NSQIP-P) over the same time period. During the first 18 months of using MyPOD, 691 cases were captured in both MyPOD and NSQIP-P. There were 48 cases with occurrences in NSQIP-P (6.9% occurrence rate). MyPOD captured 33% of the occurrences and 83% of the deaths reported in NSQIP-P. Use of the MyPOD program helped to identify series of complications and facilitated systematic change to improve outcomes. MyPOD provides comparative data that is essential in performance evaluation and facilitates quality improvement in surgery. This program and similar EMR-driven tools are becoming essential components of the MOC process. Our initial review has revealed opportunities for improvement in self-reporting which we can continue to measure by comparison to NSQIP-P. In addition, it has identified systems issues that have led to hospital-wide improvements.

Formation of DPM ethers using O-diphenylmethyl trichloroacetimidate under thermal conditions.

Alcohols are effectively converted to their corresponding diphenylmethyl (DPM) ethers by reaction with O-diphenylmethyl trichloroacetimidate in refluxing toluene without the requirement of a catalyst or other additives. A number of acid and base sensitive substrates were protected in excellent yield using this new method without disturbing the pre-existing functionality present in these molecules. This reaction is the first example of the formation of an ether from stoichiometric amounts of a trichloroacetimidate and an alcohol without the addition of a Brønsted or Lewis acid catalyst.

Evaporation of droplets on strongly hydrophobic substrates.

The manner in which the extreme modes of droplet evaporation (namely, the constant contact radius and the constant contact angle modes) become indistinguishable on strongly hydrophobic substrates is described. Simple asymptotic expressions are obtained which provide good approximations to the evolutions of the contact radius, the contact angle, and the volume of droplets evaporating in the extreme modes for a wide range of hydrophobic substrates. As a consequence, on strongly hydrophobic substrates it is appropriate to use the so-called "2/3 power law" to extrapolate the lifetimes of droplets evaporating in the constant contact radius mode as well as in the constant contact angle mode.

ATHLATES: accurate typing of human leukocyte antigen through exome sequencing.

Human leukocyte antigen (HLA) typing at the allelic level can in theory be achieved using whole exome sequencing (exome-seq) data with no added cost but has been hindered by its computational challenge. We developed ATHLATES, a program that applies assembly, allele identification and allelic pair inference to short read sequences, and applied it to data from Illumina platforms. In 15 data sets with adequate coverage for HLA-A, -B, -C, -DRB1 and -DQB1 genes, ATHLATES correctly reported 74 out of 75 allelic pairs with an overall concordance rate of 99% compared with conventional typing. This novel approach should be broadly applicable to research and clinical laboratories.

Three-dimensional fiber segment orientation distribution using X-ray microtomography.

The orientation of fibers in assemblies such as nonwovens has a major influence on the anisotropy of properties of the bulk structure and is strongly influenced by the processes used to manufacture the fabric. To build a detailed understanding of a fabric's geometry and architecture it is important that fiber orientation in three dimensions is evaluated since out-of-plane orientations may also contribute to the physical properties of the fabric. In this study, a technique for measuring fiber segment orientation as proposed by Eberhardt and Clarke is implemented and experimentally studied based on analysis of X-ray computed microtomographic data. Fiber segment orientation distributions were extracted from volumetric X-ray microtomography data sets of hydroentangled nonwoven fabrics manufactured from parallel-laid, cross-laid, and air-laid webs. Spherical coordinates represented the orientation of individual fibers. Physical testing of the samples by means of zero-span tensile testing and z-directional tensile testing was employed to compare with the computed results.

A Comparison of Two Macroinvertebrate Multi-Plate Sampling Methods to Inform Great Lakes Monitoring and Remediation Efforts.

Hester-Dendy (HD) multi-plate samplers have been widely used by state and federal government agencies for bioassessment of water quality through use of macroinvertebrate community data. To help guide remediation and restoration efforts at the Niagara River Great Lakes Area of Concern site, a multi-agency study was conducted in 2014 to assess the contribution of seven major urban tributaries on the US side of the river toward the impairment of the Niagara River. As part of this study, macroinvertebrate communities were sampled using two co-located versions of HD samplers: one version used by the New York State Department of Environmental Conservation (NYSDEC) and another by the US Environmental Protection Agency Office of Research and Development. Samplers were deployed in tributaries in highly developed watersheds with high percent impervious surface. The two sampling methods varied in terms of number and size of plates, between-plate spacing, and deployment method. Comparison of the similarity/grouping of communities with multivariate ordination techniques, Nonmetric Multidimensional Scaling and Multi-Response Permutation Procedure, showed that both methods were able to detect differences in communities at stations, despite some grouping by month and method. The indices and metrics derived from the two HD methods were found to give comparable but not identical assessments of water quality. Despite their differences, the methods were robust with respect to water quality categories derived from indices used nationally (HBI) and by NY state (BAP). For the common richness metrics, total taxa and EPT richness, there was no statistical difference between means from 3 samplings. Some metrics, especially percent tolerant collector-gatherer individuals, did show significant differences at certain stations. Indicator Species Analysis showed some taxa associated with each method. The observed community differences were thought mostly due to the difference in sampler deployment position.

Weak-anchoring effects in a thin pinned ridge of nematic liquid crystal.

A theoretical investigation of weak-anchoring effects in a thin two-dimensional pinned static ridge of nematic liquid crystal resting on a flat solid substrate in an atmosphere of passive gas is performed. Specifically, we solve a reduced version of the general system of governing equations recently derived by Cousins et al. [Proc. R. Soc. A 478, 20210849 (2022)10.1098/rspa.2021.0849] valid for a symmetric thin ridge under the one-constant approximation of the Frank-Oseen bulk elastic energy with pinned contact lines to determine the shape of the ridge and the behavior of the director within it. Numerical investigations covering a wide range of parameter values indicate that the energetically preferred solutions can be classified in terms of the Jenkins-Barratt-Barbero-Barberi critical thickness into five qualitatively different types of solution. In particular, the theoretical results suggest that anchoring breaking occurs close to the contact lines. The theoretical predictions are supported by the results of physical experiments for a ridge of the nematic 4^{'}-pentyl-4-biphenylcarbonitrile (5CB). In particular, these experiments show that the homeotropic anchoring at the gas-nematic interface is broken close to the contact lines by the stronger rubbed planar anchoring at the nematic-substrate interface. A comparison between the experimental values of and the theoretical predictions for the effective refractive index of the ridge gives a first estimate of the anchoring strength of an interface between air and 5CB to be (9.80±1.12)×10^{-6}Nm^{-1} at a temperature of (22±1.5)^{∘}C.

A novel HLA-DQA1*01 allele, HLA-DQA1*01:99, identified by next-generation sequencing.

DQA1*01:99 differs from DQA1*01:01 by a missense nucleotide substitution in exon 4.

Young and Young-Laplace equations for a static ridge of nematic liquid crystal, and transitions between equilibrium states.

Motivated by the need for greater understanding of systems that involve interfaces between a nematic liquid crystal, a solid substrate and a passive gas that include nematic-substrate-gas three-phase contact lines, we analyse a two-dimensional static ridge of nematic resting on a solid substrate in an atmosphere of passive gas. Specifically, we obtain the first complete theoretical description for this system, including nematic Young and Young-Laplace equations, and then, making the assumption that anchoring breaking occurs in regions adjacent to the contact lines, we use the nematic Young equations to determine the continuous and discontinuous transitions that occur between the equilibrium states of complete wetting, partial wetting and complete dewetting. In particular, in addition to continuous transitions analogous to those that occur in the classical case of an isotropic liquid, we find a variety of discontinuous transitions, as well as contact-angle hysteresis, and regions of parameter space in which there exist multiple partial wetting states that do not occur in the classical case.

HLA-B evolutionary divergence is associated with outcomes after SARS-CoV-2 infection.

We examined the correlation between class I HLA evolutionary divergence (HED), a surrogate for the capacity to present different peptides, and the outcomes of 234 adult inpatients with confirmed SARS-CoV-2 infection. Genomic DNA was extracted from peripheral blood and genotyped by next-generation sequencing (NGS). HED scores for HLA class I (HLA-A, -B, and -C) genotypes were calculated using Grantham's distance. Higher HED scores for HLA-B, but not HLA-A or -C, are significantly associated with a decreased probability of poor outcomes including ICU admission, mechanical ventilation, and death (OR = 0.93; P = 0.04) in the univariate analysis. In the multivariate analysis, increased HLA-B HED score, younger age, and no comorbidity were independently associated with favorable outcomes (P = 0.02, P = 0.01, and P = 0.05, respectively). This finding is consistent with the notion that broader peptide repertoires presented by class I HLA may be beneficial in infection control.

A novel B*07 variant allele, B*07:416, identified by next-generation sequencing.

HLA-B*07:416 differs from HLA-B*07:02 by a missense mutation at codon 92 of the cDNA sequence.

HLA genetic polymorphism in patients with Coronavirus Disease 2019 in Midwestern United States.

The experience of individuals with Coronavirus Disease 2019 (COVID-19) ranges from asymptomatic to life threatening multi-organ dysfunction. Specific HLA alleles may affect the predisposition to severe COVID-19 because of their role in presenting viral peptides to launch the adaptive immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this population-based case-control study in the midwestern United States, we performed high-resolution HLA typing of 234 cases hospitalized for COVID-19 in the St. Louis metropolitan area and compared their HLA allele frequencies with those of 22,000 matched controls from the National Marrow Donor Program (NMDP). We identified two predisposing alleles, HLA-DRB1*08:02 in the Hispanic group (OR = 9.0, 95% confidence interval: 2.2-37.9; adjusted p = 0.03) and HLA-A*30:02 in younger African Americans with ages below the median (OR = 2.2, 1.4-3.6; adjusted p = 0.01), and several candidate alleles with potential associations with COVID-19 in African American, White, and Hispanic groups. We also detected risk-associated amino acid residues in the peptide binding grooves of some of these alleles, suggesting the presence of functional associations. These findings support the notion that specific HLA alleles may be protective or predisposing factors to COVID-19. Future consortium analysis of pooled cases and controls is warranted to validate and extend these findings, and correlation with viral peptide binding studies will provide additional evidence for the functional association between HLA alleles and COVID-19.

High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells.

Nanopore sequencing has been investigated as a rapid and cost-efficient option for HLA typing in recent years. Despite the lower raw read accuracy, encouraging typing accuracy has been reported, and long reads from the platform offer additional benefits of the improved phasing of distant variants. The newly released R10.3 flow cells are expected to provide higher read-level accuracy than previous chemistries. We examined the performance of R10.3 flow cells on the MinION device in HLA typing after enrichment of target genes by multiplexed PCR. We also aimed to mimic a 1-day workflow with 8-24 samples per sequencing run. A diverse collection of 102 unique samples were typed for HLA-A, -B, -C, -DPA1, -DPB1, -DQA1, -DQB1, -DRB1, -DRB3/4/5 loci. The concordance rates at 2-field and 3-field resolutions were 99.5% (1836 alleles) and 99.3% (1710 alleles). We also report important quality metrics from these sequencing runs. Continued research and independent validations are warranted to increase the robustness of nanopore-based HLA typing for broad clinical application.

Performance of a multiplexed amplicon-based next-generation sequencing assay for HLA typing.

BACKGROUND: Next-generation sequencing (NGS) has enabled efficient high-resolution typing of human leukocyte antigen (HLA) genes with minimal ambiguity. Most commercially available assays amplify individual or subgroup of HLA genes by long-range PCR followed by library preparation and sequencing. The AllType assay simplifies the workflow by amplifying 11 transplant-relevant HLA genes in one PCR reaction. Here, we report the performance of this unique workflow evaluated using 218 genetically diverse samples. METHODS: Five whole genes (HLA-A/B/C/DQA1/DPA1) and six near-whole genes (HLA-DRB1/DRB345/DQB1/DPB1; excluding exon 1 and part of intron 1) were amplified in a multiplexed, long-range PCR. Manual library preparation was performed per manufacturer's protocol, followed by template preparation and chip loading on the Ion Chef, and sequencing on the Ion S5 sequencer. Pre-specified rules for quality control and repeat testing were followed; technologists were blinded to the reference results. The concordance between AllType and reference results was determined at 2-field resolution. We also describe the ranges of input DNA and library concentrations, read number per sample and per locus, and key health metrics in relation to typing results. RESULTS: The concordance rates were 98.6%, 99.8% and 99.9% at the sample (n = 218), genotype (n = 1688), and allele (n = 3376) levels, respectively. Three genotypes were discordant, all of which shared the same G group typing results with the reference. Most ambiguous genotypes (116 out of 144, 80.6%) were due to the lack of exon 1 and intron 1 coverage for HLA-DRB1/DRB345/DQB1/DPB1 genes. A broad range of input DNA concentrations and library concentrations were tolerated. Per sample read numbers were adequate for accurate genotyping. Per locus read numbers showed some inter-lot variations, and a trend toward improved inter-locus balance was observed with later lots of reagents. CONCLUSION: The AllType assay on the Ion Chef/Ion S5 platform offers a robust and efficient workflow for clinical HLA typing at the 2-field resolution. The multiplex PCR strategy simplifies the laboratory procedure without compromising the typing accuracy.

Clinical implications of the seat belt sign in blunt trauma.

Patients with the seat belt sign (SBS) from motor vehicle crashes (MVCs) are prone to specific regional injury patterns. Investigators at a Level 1 trauma center analyzed the incidence, clinical implications, and spectrum of regional injuries in patients injured in MVC over 2 years. SBS was seen in 11.3 per cent of patients injured in MVCs and 20.5 per cent of patients with known restraint use. Restrained patients were less severely injured with lower injury severity scores (7.62 vs 11.33) and mortality (1.1 vs 5.7%). Patients with SBS had lower mortality rates than patients without SBS (1.4 vs 3.7%). Thoraco-abdominal injuries were present in 47 per cent (34 of 72) of patients with SBS. Compared with patients without SBS, patients had a higher incidence of hollow viscous injuries (HVI) and solid organ trauma (8 and 17% vs 1 and 3%, P < 0.05); splenic trauma was 24-fold higher (9.7 vs 0.4%), liver injuries 3.1-fold higher (6 vs 3%), and rib fractures 2.4-fold higher (P < 0.05). Children had 2.8-fold higher rates of HVI (18 vs 9%, P < 0.05). SBS is associated with underlying regional injuries in nearly half of patients with a higher prevalence of HVI and solid organ trauma.

Purification of CD45+ hematopoietic cells directly from human bone marrow using a flow-based P-selectin-coated microtube.

Recently, a flow-based selectin-dependent method for capture and enrichment of specific type blood cells (CD34+ hematopoietic stem and progenitor cells) from bone marrow and peripheral blood has been described. Using a similar approach, here we show isolation of CD45+ blood cells directly from human bone marrow to a high purity (90%-97%). The process mimics a ubiquitous mechanism of cell trafficking in the body for the recruitment of neutrophils during inflammation. The method is straightforward, rapid, and may represent a practical alternative to CD45+ cell enrichment procedures required for chimerism analysis following allogenic stem-cell transplantation.

Revisiting histograms and isosurface statistics.

Recent results have shown a link between geometric properties of isosurfaces and statistical properties of the underlying sampled data. However, this has two defects: not all of the properties described converge to the same solution, and the statistics computed are not always invariant under isosurface-preserving transformations. We apply Federer's Coarea Formula from geometric measure theory to explain these discrepancies. We describe an improved substitute for histograms based on weighting with the inverse gradient magnitude, develop a statistical model that is invariant under isosurface-preserving transformations, and argue that this provides a consistent method for algorithm evaluation across multiple datasets based on histogram equalization. We use our corrected formulation to reevaluate recent results on average isosurface complexity, and show evidence that noise is one cause of the discrepancy between the expected figure and the observed one.