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565 results for “immunodeficiency”
Characterization of the anti-spike IgG immune response to COVID-19 vaccines in people with a wide variety of immunodeficiencies
<p>Participants submitted saliva using the OME-505 collection device (OMNIgene Oral, Ottawa, Canada) every two weeks from vaccination through six months post-dose 3 to detect breakthrough SARS-CoV-2 infections. Viral RNA was extracted using the NucliSENS easyMag automated extraction system from 200ul of saliva in stabilizing solution and eluted in a total volume of 50ul. First strand cDNA synthesis was performed from 5ul of eluted RNA using SuperScript IV VILO Master Mix (Thermo Fisher). Positive specimens were then sequenced. Multiplex tiled amplicon libraries were prepared using the Midnight panel and Rapid barcoding kit RBK-004 (Oxford Nanopore technologies) using previously published protocol. Twelve sample pooled libraries were sequenced on a GridION X5 nanopore sequencer using Flongle adapters. After sequencing, raw data were processed using interARTIC to generate consensus sequences and variant calls. SARS-CoV-2<strong> </strong>lineages were determined using these consensus sequences and the NextClade and Pangolin platforms.</p>
Evaluation of two 4th generation point-of-care assays for the detection of Human Immunodeficiency Virus infection.
<p>Background. Fourth generation assays detect simultaneously antibodies for HIV and the p24 antigen, identifying HIV infection earlier than previous generation tests. Previous studies have shown that the Alere Determine HIV-1/2 Combo has lower than anticipated performance in detecting antibodies for HIV and the p24 antigen. Furthermore, there are currently very few studies evaluating the performance of Standard Diagnostics BIOLINE HIV Ag/Ab Combo.</p> <p>Objective: To evaluate the performance of the Alere Determine HIV-1/2 Combo and the Standard Diagnostics BIOLINE HIV Ag/Ab Combo in a panel of frozen serum samples.</p> <p>Study Design: The testing panel included 133 previously frozen serum specimens from the UCLA Clinical Microbiology & Immunoserology laboratory. Reference testing included testing for HIV antibodies by a 3<sup>rd</sup> generation enzyme immunoassay followed by HIV RNA detection. Antibody negative and RNA positive sera were also tested by a laboratory 4<sup>th</sup> generation HIV Ab/Ag enzyme immunoassay.</p> <p>Results: Reference testing yielded 97 positives for HIV infection and 36 negative samples. Sensitivity of the Alere test was 95% (88-98%), while the SD Bioline sensitivity was 91% (83-96%). Both assays showed 100% (90-100%) specificity. No indeterminate or invalid results were recorded. Among 13 samples with acute infection (HIV RNA positive, HIV antibody negative), 12 were found positive by the first assay and 8 by the second. The antigen component of the Alere assay detected 10 acute samples, while the SD Bioline assay detected only one.</p> <p>Conclusions: Both rapid assays showed very good overall performance in detecting HIV infection in frozen serum samples, but further improvements are required to improve the performance in acute infection.</p>
Data from: A host-adapted auxotrophic gut symbiont induces mucosal immunodeficiency
<p>The microbiome holds great promise as a source of novel therapeutic targets for many diseases. Mining for causative microorganisms that impact processes underlying disease states should utilize Koch's postulates. Here we show a functional screen for the bacterial microbiota of intestinal immunoglobulin A (IgA)-deficient mice; we identified a novel Gram-negative bacterium, proposed to be named as <em>Tomasiella immunophila</em> that induces and degrades IgA in mouse intestine. <em>T. immunophila</em> is auxotrophic for the bacterial cell wall amino sugar N-acetylmuramic acid (MurNAc). <em>T. immunophila</em> secretes IgA-degrading enzymes into outer membrane vesicles that preferentially degrade rodent antibodies with kappa but not lambda light chains. We propose this study uncovers a new paradigm for the role of symbionts in immunodeficiency that can ultimately be applied to human disease.</p>
Fig. 1 in Equal contributions of feline immunodeficiency virus and coinfections to morbidity in African lions
Fig. 1. FIV infection is common in lions of Kruger National Park. Within the sample population, 72.8% (142/195) of lions were infected with FIV. Prevalence of FIV infection was similar between males and females (75.6% versus 70.2%; n = 74 and 121, respectively), but increased with host age (a). For ease of visualization, age has been broken up by life stage into cubs (0–2yrs), subadults (2.1–4yrs), young adults (4.1–6yrs), prime adults (6.1–8yrs), and seniors (>8yrs) based on previous age classifications (Schaller, 1976). Regional prevalence of FIV was highest in the central region and lowest in the north (b). The map to the right shows locations where lion prides were sampled.
Fig. 4 in Equal contributions of feline immunodeficiency virus and coinfections to morbidity in African lions
Fig. 4. FIV has strong direct and indirect effects on overall health. The final path model (a) shows only statistically significant relationships between manifest variables (rectangles) and latent variables (circles) for FIV infection, immune response (IMM), coinfections with hemoparasites (Hemoparasites), co-infections with gastrointestinal parasites (Helminths), and morbidity (Morbidity). Note that the parameter βx,z between each variable of interest represents the path coefficient obtained from least squares regression examining the relationship between one latent variable and the next (for example, FIV to IMM). Blue arrows represent positive relationships, whereas red arrows denote negative relationships. Final sample size was 106 lions.
Fig. 3 in Equal contributions of feline immunodeficiency virus and coinfections to morbidity in African lions
Fig. 3. FIV significantly increases the prevalence of select gastrointestinal and hemoparasitic coinfections, as well as overall parasite richness for both groups. Graph (a) shows the prevalence of coinfecting parasites isolated in lions from this study. Sample size for the parasite groups included is as follows: n = 114 for gastrointestinal parasites; n = 190 for hemoparasites; and n = 195 for viral parasites. Coinfections are broken down by FIV status (positive versus negative). The two additional graphs illustrate the relationship between FIV status and gastrointestinal parasite richness (b) and hemoparasite richness (c).
Fig. 2 in Equal contributions of feline immunodeficiency virus and coinfections to morbidity in African lions
Fig. 2. FIV has broad effects on lion health and is associated with progressive immune impairment. Box (2a) above provides a complete list of the health metrics measured for the purposes of this study. Arrows to the right of each variable summarize the directionality of statistically significant changes with FIV infection. Descriptive statistics and reference values can be found in Table 2. Complete model output can be found in supplementary tables S1–S4. For ease of visualization, each parameter has been broken into categories of clinical relevance. To the right, age-related changes in lymphocyte profiles are shown for total lymphocyte counts in FIV-positive versus FIV-negative lions (b); as well as specific lymphocyte subsets in FIV-positive lions (c). Due to small sample size for lymphocyte subsets, subadults, and cubs have been included together under the 'juvenile' category.
Inferring human immunodeficiency virus 1 proviral integration dates with Bayesian Inference
<p>Human immunodeficiency virus 1 (HIV) proviruses archived in the persistent reservoir currently pose the greatest obstacle to HIV cure due to their evasion of combined antiretroviral therapy and ability to reseed HIV infection. Understanding the dynamics of the HIV persistent reservoir is imperative for discovering a durable HIV cure. Here, we explore Bayesian methods using the software BEAST2 to estimate HIV proviral integration dates. We started with within-host longitudinal HIV sequences collected prior to therapy, along with sequences collected from the persistent reservoir during suppressive therapy. We built a BEAST2 model to estimate integration dates of proviral sequences collected during suppressive therapy, implementing a tip date random walker to adjust the sequence tip dates and a latency-specific prior to inform the dates. To validate our method, we implemented it on both simulated and empirical data sets. Consistent with previous studies, we found that proviral integration dates were spread throughout active infection. Path sampling to select an alternative prior for date estimation in place of the latency-specific prior produced unrealistic results in one empirical data set, while on another data set the latency-specific prior was selected as best-fitting. Our Bayesian method outperforms current date estimation techniques with a root mean squared error of 0.89 years on simulated data relative to 1.23–1.89 years with previously developed methods. Bayesian methods offer an adaptable framework for inferring proviral integration dates.</p>
Characterization of the anti-spike IgG immune response to COVID-19 vaccines in people with a wide variety of immunodeficiencies
<p>Research on COVID-19 vaccination in immune-deficient/disordered people (IDP) has primarily focused on cancer and organ transplantation populations. In a prospective cohort of 195 IDP and 35 healthy volunteers, anti-spike IgG was detected in 88% of IDP post-dose 2, increasing to 93% by six months post-dose 3. Despite high seroconversion, median IgG levels for IDP never surpassed 1/3 that of healthy volunteers. IgG binding to Omicron BA.1 was lower than all other variants. Angiotensin-converting enzyme 2 pseudo-neutralization (% inhibition) was only modestly correlated with anti-spike IgG concentration. IgG levels were not significantly altered by participants' use of different mRNA-based vaccines, immunomodulating treatments, and prior SARS-CoV-2 infections. While our data show that three doses of COVID-19 vaccinations induce anti-spike IgG in most IDP, additional doses are needed to achieve the levels of protection in healthy volunteers. Due to the strikingly reduced IgG response to Omicron BA.1, the efficacy of additional vaccinations, including bivalent vaccines, should be studied in this population.</p>
Characterization of the anti-spike IgG immune response to COVID-19 vaccines in people with a wide variety of immunodeficiencies
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Data from: A host-adapted auxotrophic gut symbiont induces mucosal immunodeficiency (Part I)
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A host-adapted auxotrophic gut symbiont induces mucosal immunodeficiency (Part II)
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Inferring human immunodeficiency virus 1 proviral integration dates with Bayesian Inference
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Outgrowth of transferred tumors expressing libraries of PresentER minigenes in immunocompetent and immunodeficient mice
<p>Minigene sequencing of RMA/S tumors grown in RAG deficient mice, harvested and then transferred and grown in WT or RAG mice. "Pool 13" are wild type peptide minigenes. "Pool 18" are mutant peptide minigenes.</p>
GRACE: A Study to Compare the Effectiveness, Safety and Tolerability of PREZISTA (Darunavir)/Ritonavir by Gender and Race When Administered With Other Antiretroviral Medications in Human Immunodeficie
ClinicalTrials.gov study NCT00381303. IPD Sharing: Not stated. Countries: 3. Publications: 3.
Safety and Immunogenicity Study of a Candidate Tuberculosis Vaccine in Human Immunodeficiency Virus (HIV)-Positive Adults
ClinicalTrials.gov study NCT01262976. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Safety, Tolerability and Immunogenicity Study of 3 Prime-boost Regimens for Ebola Vaccines Ad26.ZEBOV/MVA-BN-Filo in Healthy Adults, Children and Human Immunodeficiency Virus Positive (HIV+) Adults
ClinicalTrials.gov study NCT02564523. IPD Sharing: Not stated. Countries: 4. Publications: 3.
A Study of Heterologous Vaccine Regimen of Adenovirus Serotype 26 Mosaic4 Human Immunodeficiency Virus(Ad26.Mos4.HIV), Adjuvanted Clade C gp140 and Mosaic gp140 to Prevent HIV-1 Infection Among Cis-ge
ClinicalTrials.gov study NCT03964415. IPD Sharing: YES. Countries: 9. Publications: 1.
Study of Immune Globulin Intravenous (Human) GC5107 in Subjects With Primary Humoral Immunodeficiency
ClinicalTrials.gov study NCT02783482. IPD Sharing: NO. Countries: 2. Publications: 1.
Extension Study of Subcutaneous Immunoglobulin Human in Patients With Primary Immunodeficiency (PID)
ClinicalTrials.gov study NCT00719680. IPD Sharing: Not stated. Countries: 1. Publications: 1.
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Allen Brain Atlas
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.