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.

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.

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.

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.

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 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.

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.

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 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.

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.

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.

Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing.

Oxford Nanopore Technologies' MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-of-care human leukocyte antigen (HLA) typing, an assay routinely used to assess the immunologic compatibility between organ donors and recipients, but the platform's high error rate makes it challenging to type alleles with accuracy. We developed and validated accurate typing of HLA by Oxford nanopore (Athlon), a bioinformatic pipeline that i) maps nanopore reads to a database of known HLA alleles, ii) identifies candidate alleles with the highest read coverage at different resolution levels that are represented as branching nodes and leaves of a tree structure, iii) generates consensus sequences by remapping the reads to the candidate alleles, and iv) calls the final diploid genotype by blasting consensus sequences against the reference database. Using two independent data sets generated on the R9.4 flow cell chemistry, Athlon achieved a 100% accuracy in class I HLA typing at the two-field resolution.

Accelerated humoral renal allograft rejection due to HLA-C14 mediated allosensitization to HLA-Bw6.

OBJECTIVES: To investigate immunological mechanisms underlying accelerated antibody-mediated rejection (AMR) of a living-related renal allograft in a patient with no detectable antibodies to donor human leukocyte antigens (HLA) in pre-transplant sera. METHODS: Pre- and post-transplant HLA antibody specificities were determined by single-antigen bead assay, and crossmatching was performed by flow cytometry- and complement-dependent cytotoxicity-based methods. Intermediate- and high-resolution HLA typing were performed by molecular methods. RESULTS: Pre-transplant patient serum reacted weakly against Bw6-positive beads; cytotoxicity and flow crossmatches were negative. The patient was mismatched for the donor antigens B62 and C10 (Bw6-positive). Following transplantation, strong antibody responses against B62, C10, and all Bw6-positive beads were detected. This reactivity was initially masked by complement interference, but became apparent at 1:20 dilution. High-resolution typing suggested that the anti-C16 antibody reactivity detected was an allele-specific response to donor C∗16:01 (Bw6-positive) but not recipient C∗16:02 (Bw6-negative). Alloimmunization likely occurred during pregnancy, during which HLA-C14 (Bw6-positive) was the only mismatched paternal HLA Class I allele. CONCLUSIONS: Sensitization to HLA-Bw6 via exposure to paternal HLA-C14 during pregnancy likely predisposed this patient to AMR. The case demonstrates the immunogenicity of HLA-C14-associated Bw6 epitopes in vivo and the clinical significance of low-level antibodies to HLA-Bw6.

Rapid detection of donor cell free DNA in lung transplant recipients with rejections using donor-recipient HLA mismatch.

Fiberoptic bronchoscopy and transbronchial lung biopsy are currently the gold standard for detection of acute rejection following human lung transplantation (LTx). However, these surveillance procedures are expensive and invasive. Up to now, there are few new methods that have demonstrated clinical utility for detecting early stages of rejection following human lung transplantation. We optimized and technically validated a novel method to quantify donor-derived circulating cell free DNA (DcfDNA) that can be used as an early biomarker for lung allograft rejection. The method involves the initial development of a panel of probes in which each probe will specifically target a unique sequence of a human leukocyte antigen (HLA) allele. After transplantation, donor/recipient specific probes are chosen based on the mismatched HLA loci, followed by droplet digital PCR (ddPCR) used as a quantitative assay to accurately track the trace amount of DcfDNA in an ample excess of recipient DNA background. The average false positive rate noted was about 1 per 800,000 molecules. Serially 2-fold diluted cfDNA, representing donor fractions of cfDNA, were spiked into a constant level of cfDNA representing the recipient cfDNA. The fraction of spiked cfDNA was measured and quantitative linearity was observed across seven serially diluted cfDNA samples. We were able to measure the minor portion of cfDNA as low as 0.2% of total cfDNA. We subsequently applied the method to a pilot set of 18 LTx recipients grouped into biopsy-proven acute rejection, bronchiolitis obliterans syndrome (BOS) or stable groups. Serial plasma samples were used to identify the percentage of DcfDNA over total cfDNA. The level of DcfDNA was significantly elevated in patients diagnosed with acute rejection (10.30±2.80, n=18), compared to that from stable (1.71±0.50, n=24) or from BOS patients (2.52±0.62, n=20). In conclusion, we present results validating the application of digital PCR to quantify DcfDNA assay in primary clinical specimens, which demonstrate that DcfDNA can be used as an early non-invasive biomarker for acute lung allograft rejection.

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.

Laparoscopic Excision of Congenital Hepatic Cysts in the Pediatric Population: A Case Series and Literature Review.

PURPOSE: Congenital hepatic cysts are rare. Surgical excision is indicated for symptoms, complications, and to rule out malignancy. Laparoscopic management in the pediatric population has not been extensively documented. We present a series involving laparoscopic excision of pediatric congenital hepatic cysts and review the literature. METHODS: Data were collected over 15 years from two pediatric surgeons at three medical centers. Presence of a hepatic cyst excised laparoscopically was the only inclusion criterion. Data were collected on the cyst size, type, pathology, and location, as well as on length of hospital stay, complications, and 1 year recurrence rate. RESULTS: Four patients were identified: a 7-week-old male presenting with feeding intolerance due to a hepatic cyst; a 6-year-old male presenting with a hepatic cyst identified by ultrasound during evaluation for appendicitis; a male neonate diagnosed at birth with a left thoracic cyst that communicated through the diaphragm with a hepatic cystic lesion; and a 14-year-old male presenting with a 25 cm × 11 cm hepatic cyst. All lesions were excised laparoscopically. CONCLUSION: Our series is the largest documenting complete laparoscopic excision of congenital solitary hepatic cysts in the pediatric population. Laparoscopic excision is a safe and effective approach for the pediatric population.

Fluid-dynamical model for antisurfactants.

We construct a fluid-dynamical model for the flow of a solution with a free surface at which surface tension acts. This model can describe both classical surfactants, which decrease the surface tension of the solution relative to that of the pure solvent, and antisurfactants (such as many salts when added to water, and small amounts of water when added to alcohol) which increase it. We demonstrate the utility of the model by considering the linear stability of an infinitely deep layer of initially quiescent fluid. In particular, we predict the occurrence of an instability driven by surface-tension gradients, which occurs for antisurfactant, but not for surfactant, solutions.

Parental Perspectives of Communication at the End of Life at a Pediatric Oncology Institution.

BACKGROUND: The interaction of health care providers and hospital staff with patients and families at the end of life affects the parental grief experience. Both verbal and nonverbal communication are key components of this interaction. OBJECTIVE: The study objective was to explore the communication between hospital staff members and patients and families at the time of patients' health decline near the end of life. METHODS: Twelve bereaved parents participated in a focus group. Semantic content analysis was used to analyze the transcript. RESULTS: Parents' responses to the prompt about typical ways the medical team communicated yielded 109 codes, which were grouped into 12 themes. The most common themes were "patient inclusion" and "explanation of medical plan," both used in 17% of responses. Responses to the prompt about positive and negative aspects of communication generated 208 codes, yielding 15 different themes. The most common theme about positive communication was the "strong relationship between family and staff." The theme "variations in care with a negative impact" was used most frequently in describing negative communication. CONCLUSION: This study helps to identify techniques that should be used by clinicians as they work with children with cancer and their families, particularly including patients in treatment decisions, ongoing relationship building, communicating with caring and empathy, using an interdisciplinary team for additional support, and pairing bad news with a plan of action.