Deconstruction of rheumatoid arthritis synovium defines inflammatory subtypes.

Rheumatoid arthritis is a prototypical autoimmune disease that causes joint inflammation and destruction1. There is currently no cure for rheumatoid arthritis, and the effectiveness of treatments varies across patients, suggesting an undefined pathogenic diversity1,2. Here, to deconstruct the cell states and pathways that characterize this pathogenic heterogeneity, we profiled the full spectrum of cells in inflamed synovium from patients with rheumatoid arthritis. We used multi-modal single-cell RNA-sequencing and surface protein data coupled with histology of synovial tissue from 79 donors to build single-cell atlas of rheumatoid arthritis synovial tissue that includes more than 314,000 cells. We stratified tissues into six groups, referred to as cell-type abundance phenotypes (CTAPs), each characterized by selectively enriched cell states. These CTAPs demonstrate the diversity of synovial inflammation in rheumatoid arthritis, ranging from samples enriched for T and B cells to those largely lacking lymphocytes. Disease-relevant cell states, cytokines, risk genes, histology and serology metrics are associated with particular CTAPs. CTAPs are dynamic and can predict treatment response, highlighting the clinical utility of classifying rheumatoid arthritis synovial phenotypes. This comprehensive atlas and molecular, tissue-based stratification of rheumatoid arthritis synovial tissue reveal new insights into rheumatoid arthritis pathology and heterogeneity that could inform novel targeted treatments.

Sperm cryopreservation in the Burmese python Python bivittatus as a model for endangered snakes.

Burmese pythons Python bivittatus captured in the Florida Everglades as part of an invasive species monitoring program served as a model for the development of sperm cryopreservation protocols for endangered snakes. Spermatozoa were collected from the vas deferens and initial motility, plasma membrane integrity and acrosome integrity were recorded before cryopreservation. Spermatozoa were extended in TES and Tris (TEST) yolk buffer with glycerol (GLY) or dimethyl sulfoxide (DMSO) concentrations of 8%, 12% or 16%, or combinations of GLY and DMSO with final concentrations of 4%:4%, 6%:6% or 8%:8%, and frozen at a rate of 0.3°C min-1 . Sperm frozen in combinations of GLY and DMSO exhibited greater post-thaw motility and plasma membrane integrity than those frozen in GLY or DMSO alone. All DMSO and GLY:DMSO treatments preserved a greater proportion of intact acrosomes than GLY alone. To determine the best overall cryopreservation protocol for this species, a sperm quality index was calculated, giving equal weight to each of the three measured indicators of cryosurvival. This analysis revealed that Burmese python spermatozoa frozen in 6% GLY:6% DMSO or 4% GLY:4% DMSO exhibited the highest post-thaw viability. This study represents the first comparative, comprehensive attempt to develop a sperm cryopreservation protocol for any snake species.

Identification of protein interactions of grapevine fanleaf virus RNA-dependent RNA polymerase during infection of Nicotiana benthamiana by affinity purification and tandem mass spectrometry.

The RNA-dependent RNA polymerase (1EPol) is involved in replication of grapevine fanleaf virus (GFLV, Nepovirus, Secoviridae) and causes vein clearing symptoms in Nicotiana benthamiana. Information on protein 1EPol interaction with other viral and host proteins is scarce. To study protein 1EPol biology, three GFLV infectious clones, i.e. GHu (a symptomatic wild-type strain), GHu-1EK802G (an asymptomatic GHu mutant) and F13 (an asymptomatic wild-type strain), were engineered with protein 1EPol fused to a V5 epitope tag at the C-terminus. Following Agrobacterium tumefaciens-mediated delivery of GFLV clones in N. benthamiana and protein extraction at seven dpi, when optimal 1EPol:V5 accumulation was detected, two viral and six plant putative interaction partners of V5-tagged protein 1EPol were identified for the three GFLV clones by affinity purification and tandem mass spectrometry. This study provides insights into the protein interactome of 1EPol during GFLV systemic infection in N. benthamiana and lays the foundation for validation work.

Using reproductive technologies to assess the development of secondary sexual characteristics, ovarian senescence and hermaphroditism in the endangered mountain yellow-legged frog Rana muscosa.

Anurans can display a host of intriguing sexual syndromes, including hermaphroditism and sex reversal. Using a multifaceted approach for diagnosing and characterising hermaphroditism in the endangered anuran species Rana mucosa, we tracked changes in female reproductive status using hormone monitoring, ultrasound examinations, individual life history, fertilisation records and post-mortem findings. Seven individuals originally sexed as females developed secondary male sexual characteristics, behaviour and hormone profiles and, in some cases, had testicular tissue despite having previously laid eggs. Our results suggest that reproductive technologies can shed light on life history patterns and reproductive anomalies that may affect endangered anuran survival.

Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions.

T-cells recognize antigens and induce specialized gene expression programs (GEPs) enabling functions including proliferation, cytotoxicity, and cytokine production. Traditionally, different classes of helper T-cells express mutually exclusive responses - for example, Th1, Th2, and Th17 programs. However, new single-cell RNA sequencing (scRNA-Seq) experiments have revealed a continuum of T-cell states without discrete clusters corresponding to these subsets, implying the need for new analytical frameworks. Here, we advance the characterization of T-cells with T-CellAnnoTator (TCAT), a pipeline that simultaneously quantifies pre-defined GEPs capturing activation states and cellular subsets. From 1,700,000 T-cells from 700 individuals across 38 tissues and five diverse disease contexts, we discover 46 reproducible GEPs reflecting the known core functions of T-cells including proliferation, cytotoxicity, exhaustion, and T helper effector states. We experimentally characterize several novel activation programs and apply TCAT to describe T-cell activation and exhaustion in Covid-19 and cancer, providing insight into T-cell function in these diseases.

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease.

The human leukocyte antigen (HLA) locus is associated with more complex diseases than any other locus in the human genome. In many diseases, HLA explains more heritability than all other known loci combined. In silico HLA imputation methods enable rapid and accurate estimation of HLA alleles in the millions of individuals that are already genotyped on microarrays. HLA imputation has been used to define causal variation in autoimmune diseases, such as type I diabetes, and in human immunodeficiency virus infection control. However, there are few guidelines on performing HLA imputation, association testing, and fine mapping. Here, we present a comprehensive tutorial to impute HLA alleles from genotype data. We provide detailed guidance on performing standard quality control measures for input genotyping data and describe options to impute HLA alleles and amino acids either locally or using the web-based Michigan Imputation Server, which hosts a multi-ancestry HLA imputation reference panel. We also offer best practice recommendations to conduct association tests to define the alleles, amino acids, and haplotypes that affect human traits. Along with the pipeline, we provide a step-by-step online guide with scripts and available software ( https://github.com/immunogenomics/HLA_analyses_tutorial ). This tutorial will be broadly applicable to large-scale genotyping data and will contribute to defining the role of HLA in human diseases across global populations.

Cardiovascular effects of dexmedetomidine sedation in children.

BACKGROUND: Dexmedetomidine (DEX) affects heart rate (HR), mean arterial blood pressure, cardiac index (CI), stroke index (SI), and systemic vascular resistance index (SVRI) in adults. In this study we sought to determine whether similar effects occur in children undergoing DEX sedation. METHODS: Hemodynamic changes in children were followed during IV DEX sedation for radiological procedures. One group of 8 patients (DEX-brief) received a bolus (2 mcg/kg bolus over 10 minutes) and completed the procedure within 10 minutes. The second group of 9 patients (DEX-prolong) received the bolus plus additional DEX as needed to maintain sedation for procedures lasting longer than 10 minutes (additional 1 mcg/kg/hr infusion with second bolus if needed). CI, SI, and SVRI were measured using a continuous noninvasive cardiac output monitor. Changes in hemodynamic variables at minutes 10, 20, and discharge (time at which patient achieved Aldrete Score ≥9) were compared to baseline by repeated measures ANOVA with effect sizes reported as mean [95% confidence interval]. RESULTS: Data were obtained during 8 DEX-brief and 9 DEX-prolong procedures. In DEX-brief, HR and CI decreased (18.9 [2.3 to 35.5] bpm and 0.74 [0.15 to 1.33] L/min/m(2); respectively) at T1. There was no change in any other hemodynamic variables and all hemodynamic variables returned to baseline at recovery. In DEX-prolong, both HR and CI remained decreased (24.0 [8.3 to 39.6] bpm, 1.51 [0.95 to 2.06] L/min/m(2); respectively) at recovery. In addition, SI was decreased (8.01 [1.71 to 14.31] mL/m(2)) and SVRI was increased (776.0 [271.9 to 1280.4] dynes-sec/cm(5)/m(2)) at recovery in the DEX-prolong group. There were no significant changes in mean arterial blood pressure in either group. CONCLUSION: DEX decreases CI in children and has a cumulative effect. For patients undergoing prolonged procedures HR and CI remained decreased at the time of discharge together with a decrease in SI and an increase in SVRI.

"Not a perfect situation, but..." A single-practice survey of patient experience of phone consultations during COVID-19 Alert Level 4 in New Zealand.

AIM: To explore patients' experiences of virtual consultations during the COVID-19 Alert Level 4 lockdown in New Zealand. METHOD: A single-practice retrospective phone survey exploring patients' satisfaction with the phone consultation process during Alert Level 4 lockdown. RESULTS: Of 259 eligible patients, 108 (42%) participated in the survey. Overall satisfaction with phone consultations was high, with a median score 9 out of 10 (95% CI 9-9). Participants were highly likely to recommend phone consultations to others, with a median score of 9 (95% CI 7-9). This was consistent across age groups, ethnicities and socioeconomic groupings. Men were less satisfied with phone consultations than women, with a 2 point (95% CI -3--1) lower median score than women, but they were not less likely to recommend phone consultations. Most participants found phone consultations to be convenient and time-saving and considered not seeing the doctor to be acceptable in the context of the lockdown. Few participants experienced technical difficulties over the phone. Issues of communication and appropriateness of consultations to the medium of the phone were raised. CONCLUSION: This single-centre study demonstrates the acceptability of phone consults for most patients presenting to general practice during a pandemic. These findings need further exploration in broader general practice settings and non-pandemic contexts.

Improved Ablation Efficiency in PVI Guided by Contact Force and Local Impedance: Chronic Canine Model.

Background: The purpose of this study was to assess the effect local impedance (LI) has on an ablation workflow when combined with a contact force (CF) ablation catheter. Methods: Left pulmonary vein isolation was performed in an in vivo canine model (N = 8) using a nominal (30 W) or an elevated (50 W) power strategy with a CF catheter. The catheter was enabled to measure LI prior to and during ablation. LI was visible for only one of the vein isolations. Results: Chronic block was achieved in all animals when assessed 30 ± 5 days post-ablation procedure with a median LI drop during RF ranging from 23.0 to 34.0 Ω. In both power cohorts, the median radiofrequency (RF) duration decreased if LI was visible to the operator (30 W only CF: 17.0 s; 30 W CF + LI: 14.0 s, p = 0.009; 50 W only CF: 6.0 s; 50 W CF + LI: 4.0 s, p = 0.019). An inverse relationship between the LI prior to RF delivery and the RF duration required to achieve an effective lesion was observed. There was no correlation between the magnitude of the applied force and the drop in LI, once at least 5 g was achieved. Conclusions: An elevated power strategy with the context of CF and LI led to the most efficient titration of successful RF energy delivery. The combination of feedback allows for customization of the ablation strategy based on local tissue variation rather than a uniform approach that could potentially lead to overtreatment. Higher LI drops were more readily achievable when an elevated power strategy was utilized, especially in conditions where the catheter was coupled against tissue with low resistivity. Clinical study is warranted to determine if there is an additive safety benefit to visualizing the dynamics of the tissue response to RF energy with LI when an elevated power strategy is used.

Reproductive Techniques for Ovarian Monitoring and Control in Amphibians.

Ovarian control and monitoring in amphibians require a multi-faceted approach. There are several applications that can successfully induce reproductive behaviors and the acquisition of gametes and embryos for physiological or molecular research. Amphibians contribute to one-quarter to one-third of vertebrate research, and of interest in this context is their contribution to the scientific community's knowledge of reproductive processes and embryological development. However, most of this knowledge is derived from a small number of species. In recent times, the decimation of amphibians across the globe has required increasing intervention by conservationists. The captive recovery and assurance colonies that continue to emerge in response to the extinction risk make existing research and clinical applications invaluable to the survival and reproduction of amphibians held under human care. The success of any captive population is founded on its health and reproduction and the ability to develop viable offspring that carry forward the most diverse genetic representation of their species. For researchers and veterinarians, the ability to monitor and control ovarian development and health is, therefore, imperative. The focus of this article is to highlight the different assisted reproductive techniques that can be used to monitor and, where appropriate or necessary, control ovarian function in amphibians. Ideally, any reproductive and health issues should be reduced through proper captive husbandry, but, as with any animal, issues of health and reproductive pathologies are inevitable. Non-invasive techniques include behavioral assessments, visual inspection and palpation and morphometric measurements for the calculation of body condition indices and ultrasound. Invasive techniques include hormonal injections, blood sampling, and surgery. Ovarian control can be exercised in a number of ways depending on the application required and species of interest.

Human tissue kallikrein in the treatment of acute ischemic stroke.

Acute ischemic stroke (AIS) remains a major cause of death and disability throughout the world. The most severe form of stroke results from large vessel occlusion of the major branches of the Circle of Willis. The treatment strategies currently available in western countries for large vessel occlusion involve rapid restoration of blood flow through removal of the offending blood clot using mechanical or pharmacological means (e.g. tissue plasma activator; tPA). This review assesses prospects for a novel pharmacological approach to enhance the availability of the natural enzyme tissue kallikrein (KLK1), an important regulator of local blood flow. KLK1 is responsible for the generation of kinins (bradykinin and kallidin), which promote local vasodilation and long-term vascularization. Moreover, KLK1 has been used clinically as a direct treatment for multiple diseases associated with impaired local blood flow including AIS. A form of human KLK1 isolated from human urine is approved in the People's Republic of China for subacute treatment of AIS. Here we review the rationale for using KLK1 as an additional pharmacological treatment for AIS by providing the biochemical mechanism as well as the human clinical data that support this approach.

Transcriptome analyses and biofilm-forming characteristics of a clonal Pseudomonas aeruginosa from the cystic fibrosis lung.

Transmissible Pseudomonas aeruginosa clones potentially pose a serious threat to cystic fibrosis (CF) patients. The AES-1 clone has been found to infect up to 40 % of patients in five CF centres in eastern Australia. Studies were carried out on clonal and non-clonal (NC) isolates from chronically infected CF patients, and the reference strain PAO1, to gain insight into the properties of AES-1. The transcriptomes of AES-1 and NC isolates, and of PAO1, grown planktonically and as a 72 h biofilm were compared using PAO1 microarrays. Microarray data were validated using real-time PCR. Overall, most differentially expressed genes were downregulated. AES-1 differentially expressed bacteriophage genes, novel motility genes, and virulence and quorum-sensing-related genes, compared with both PAO1 and NC. AES-1 but not NC biofilms significantly downregulated aerobic respiration genes compared with planktonic growth, suggesting enhanced anaerobic/microaerophilic growth by AES-1. Biofilm measurement showed that AES-1 formed significantly larger and thicker biofilms than NC or PAO1 isolates. This may be related to expression of the gene PA0729, encoding a biofilm-enhancing bacteriophage, identified by PCR in all AES-1 but few NC isolates (n=42). Links with the Liverpool epidemic strain included the presence of PA0729 and the absence of the bacteriophage gene cluster PA0632-PA0639. No common markers were found with the Manchester strain. No particular differentially expressed gene in AES-1 could definitively be ascribed a role in its infectivity, thus increasing the likelihood that AES-1 infectivity is multi-factorial and possibly involves novel genes. This study extends our understanding of the transcriptomic and genetic differences between clonal and NC strains of P. aeruginosa from CF lung.

Development of a sperm cryopreservation protocol for the Argentine black and white tegu (Tupinambis merianae).

Of the 934 lizard species evaluated by the International Union for the Conservation of Nature (IUCN), at least one-third is threatened with extinction. However, there are no reports of semen cryopreservation efforts for lizards. Invasive Argentine black and white tegus were captured in the Florida Everglades, and sperm was collected postmortem. Initial motility score (IMS; % motile × speed of progression2 × 100), plasma membrane integrity (IPL), and acrosome integrity (IAC) were recorded. Sperm was diluted in TEST-yolk buffer with a final glycerol or dimethylsulfoxide (DMSO)concentration of 8%, 12%, or 16%, and frozen at 0.3 °C, 1.0 °C, or 6.3 °C/min. At thaw, all variables were expressed as the percentage of initial (%IMS, %IPL, and %IAC). The 0.3 °C freeze rate was more successful than 1.0 °C and 6.3 °C/min in preserving %IMS and %IPL. DMSO preserved %IMS, %IPL, and %IAC better than glycerol. To determine the best overall cryopreservation protocol, a sperm quality index was calculated, giving equal weight to each of the three indicators of cryosurvival. Because there were significant interactions between freeze rate and cryoprotectant concentration, each treatment was compared with all others. The sperm quality index analysis revealed that tegu sperm frozen at 0.3 °C/min with 12% DMSO exhibited the highest postthaw viability compared with all other treatments.

Native low-density lipoprotein induces endothelial nitric oxide synthase dysfunction: role of heat shock protein 90 and caveolin-1.

Although native LDL (n-LDL) is well recognized for inducing endothelial cell (EC) dysfunction, the mechanisms remain unclear. One hypothesis is n-LDL increases caveolin-1 (Cav-1), which decreases nitric oxide (*NO) production by binding endothelial nitric oxide synthase (eNOS) in an inactive state. Another is n-LDL increases superoxide anion (O(2)(*-)), which inactivates *NO. To test these hypotheses, EC were incubated with n-LDL and then analyzed for *NO, O(2)(*-), phospho-eNOS (S1179), eNOS, Cav-1, calmodulin (CaM), and heat shock protein 90 (hsp90). n-LDL increased NOx by more than 4-fold while having little effect on A23187-stimulated nitrite production. In contrast, n-LDL decreased cGMP under basal and A23187-stimulated conditions and increased O(2)(*-) by a mechanism that could be inhibited by L-nitroargininemethylester (L-NAME) and BAPTA/AM. n-LDL increased phospho-eNOS by 149%, eNOS by approximately 34%, and Cav-1 by 28%, and decreased the association of hsp90 with eNOS by 49%. n-LDL did not appear to alter eNOS distribution between membrane fractions (approximately 85%) and cytosol (approximately 15%). Only 3-6% of eNOS in membrane fractions was associated with Cav-1. These data support the hypothesis that n-LDL increases O(2)(*-), which scavenges *NO, and suggest that n-LDL uncouples eNOS activity by decreasing the association of hsp90 as an initial step in signaling eNOS to generate O(2)(*-).

Invader assay for RNA quantitation.

The Invader assay is a homogeneous, isothermal, signal amplification system for the quantitative detection of nucleic acids. The assay can directly detect either DNA or RNA without target amplification or reverse transcription. It is based on the ability of Cleavase enzymes to recognize as a substrate and cleave a specific nucleic acid structure generated through the hybridization of two oligonucleotides to the target sequence. The combination of sequence-specific oligonucleotide hybridization and structure-specific enzymatic cleavage results in a highly specific assay well suited for discriminating closely related gene sequences. This includes detection of single nucleotide polymorphisms directly from genomic DNA as well as highly homologous mRNAs in closely related gene families. Because Cleavase substrate recognition is structure, and not sequence dependent, cleavage and detection can be applied to virtually any DNA or RNA sequence.

Analytical performance of Cervista HPV 16/18 genotyping test for cervical cytology samples.

BACKGROUND: Human papillomavirus (HPV) types 16 and 18 are the 2 most frequent types associated with cervical cancer. Identifying their presence or absence in cervical samples may assist in triaging women for subsequent management. The Cervista HPV 16/18 genotyping test specifically detects the presence of HPV 16 and 18 in ThinPrep cervical specimens. OBJECTIVES: The objective was to establish the analytical performance of the CERVISTA HPV 16/18 genotyping test. STUDY DESIGN: These studies were performed in support of a regulatory submission to the US Food and Drug Administration. Here we report the analytical sensitivity (limit of detection), accuracy compared to consensus L1 gene PCR/bi-directional sequencing, precision, reproducibility, and cross-reactivity (specificity) of the genotyping test. RESULTS: Analytical sensitivity for detection of HPV 16 and 18 ranged between 625 and 1250 copies/reaction for both types. When compared to PCR/sequencing for women with atypical squamous cells of undetermined significance cytology, the positive percent agreement was 94.1% (95% confidence interval [CI], 89.8-96.7) and the negative percent agreement was 85.7% (95% CI, 82.4-88.4). The test demonstrated high within-laboratory and inter-operator precision. Reproducibility within sites and between 3 testing sites resulted in 100% agreement with expected results (150 positive, 90 negative results). The genotyping test did not exhibit cross-reactivity to DNA from common low-risk HPV types and other microorganisms found in the human female reproductive tract. CONCLUSIONS: These analytical performance data support the use of CERVISTA HPV 16/18 genotyping test for the detection and differentiation of HPV 16 and 18 in ThinPrep cervical cytology specimens.

Analytical performance of the Investigational Use Only Cervista HPV HR test as determined by a multi-center study.

BACKGROUND: Any HPV test designed to be utilized in cervical cancer screening programs should be highly validated both analytically and clinically. OBJECTIVES: The Investigational Use Only (IUO) Cervista HPV HR test is designed to detect 14 high-risk HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68). The analytical performance of the Cervista HPV HR test was characterized in a multi-center study. RESULTS: Analytical sensitivity for the 14 high-risk HPV types that the test is designed to detect ranged from 1,250 copies to 7,500 copies per reaction depending on HPV type. Accuracy compared to PCR with bi-directional sequencing was 91.4% [95% CI: 86.5 95.0%]. The reproducibility, when tested at three different testing centers, resulted in an overall inter-run reproducibility (between day/within site) agreement of 98.8% [1-sided 95% Confidence Lower Limit = 96.9%] and an overall inter-site reproducibility (between site) agreement of 98.7% [1-sided 95% Confidence Lower Limit = 97.9%]. The Cervista HPV HR test showed no cross-reactivity with DNA from seven non-oncogenic HPV types or 17 different infectious agents at up to 10(7) copies per reaction. CONCLUSIONS: The analytical performance of the Cervista HPV HR test demonstrates sufficient analytical performance for use in cervical cancer screening. As with any clinical laboratory test, analytical characteristics must be evaluated in light of the clinical performance of this assay.

Environmental, policy, and cultural factors related to physical activity in sedentary American Indian women.

Focus group interviews were conducted to explore sociocultural, environmental, and policy-related determinants of physical activity among sedentary American Indian women. Thirty women aged 20 to 50 years (mean = 37.4 +/- 10.6 years) participated. Three sessions were conducted with women aged 20 to 34 years and three with women aged 35 to 50 to evaluate response differences by age. Because no obvious age differences were observed, data were pooled. Barriers to physical activity included inadequate support for household and child care responsibilities and difficulties balancing home-related and societal expectations with physical activity. In addition, women reported little support from their communities and work sites to be physically active. Environmental barriers included lack of safe outdoor areas and accessible walking trails. Weather and stray dogs were also commonly mentioned. Sociocultural barriers included giving family obligations priority above all other things, being expected to eat large portions of high-fat foods, and failing to follow a traditionally active lifestyle. Enablers of physical activity included support from family and coworkers and participation in traditional community events. Suggested intervention approaches included accessible and affordable programs and facilities, community emphasis on physical activity, and programs that incorporated the needs of larger women and of families. Participants emphasized a preference for programs that were compatible with the role expectations of their families and communities, and they expressed the desire for acceptance and encouragement to be physically active from the family, the community, the worksite, and their tribal leaders.