Electronic Clinical Decision Support Tools to Manage Patients with Lower Respiratory Tract Infection: Clinicians' Perspectives in Sri Lanka.

In low-resource settings, providers often manage lower respiratory tract infections (LRTIs) without diagnostic tests, which may cause antibacterial overuse. Electronic clinical decision support tools (eCDSTs) can support evidence-based decision-making and judicious use of antibacterials. This study aimed to explore the potential of an eCDST to help providers in Sri Lanka effectively manage LRTI.

Clinical performance of Abbott ID NOW™ COVID-19 2.0 rapid molecular point-of-care test compared to three real-time RT-PCR assays.

Unlabelled: Timely diagnosis of SARS-CoV-2 is important for infection control and treatment. Real-time reverse transcriptase PCR (rRT-PCR) tests are the reference standard for diagnosis but often require a centralized laboratory, making them time-intensive and unsuitable for resource-limited settings. The Abbott ID NOW™ COVID-19 2.

A Rapid Host Response Blood Test for Bacterial/Viral Infection Discrimination Using a Portable Molecular Diagnostic Platform.

Background: Difficulty discriminating bacterial versus viral etiologies of infection drives unwarranted antibacterial prescriptions and, therefore, antibacterial resistance.

Methods: Utilizing a rapid portable test that measures peripheral blood host gene expression to discriminate bacterial and viral etiologies of infection (the HR-B/V assay on Biomeme's polymerase chain reaction-based Franklin platform), we tested 3 cohorts of subjects with suspected infection: the HR-B/V training cohort, the HR-B/V technical correlation cohort, and a coronavirus disease 2019 cohort.

Results: The Biomeme HR-B/V test showed very good performance at discriminating bacterial and viral infections, with a bacterial model accuracy of 84.

Electronic Clinical Decision Support Tools: Strategies to Improve the Management of Lower Respiratory Tract Infections in Low-Resource Settings.

Lower respiratory tract infection (LRTI) is a common reason for hospitalization and antibacterial use globally. There is considerable overlap in the clinical presentation of bacterial and viral LRTIs. Low- or middle-income countries (LMICs) face the dual challenge of appropriately targeting antibacterials for bacterial LRTI while reducing inappropriate antibacterials for viral LRTI.

The Human Immunodeficiency Virus 1 ASP RNA promotes viral latency by recruiting the Polycomb Repressor Complex 2 and promoting nucleosome assembly.

Various epigenetic marks at the HIV-1 5'LTR suppress proviral expression and promote latency. Cellular antisense transcripts known as long noncoding RNAs (lncRNAs) recruit the polycomb repressor complex 2 (PRC2) to gene promoters, which catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3), thus promoting nucleosome assembly and suppressing gene expression. We found that an HIV-1 antisense transcript expressed from the 3'LTR and encoding the antisense protein ASP promotes proviral latency.

A Randomized Study Evaluating Oral Fusidic Acid (CEM-102) in Combination With Oral Rifampin Compared With Standard-of-Care Antibiotics for Treatment of Prosthetic Joint Infections: A Newly Identified Drug-Drug Interaction.

Background:  Fusidic acid (FA) has been used for decades for bone infection, including prosthetic joint infection (PJI), often in combination with rifampin (RIF). An FA/RIF pharmacokinetic interaction has not previously been described.

Methods:  In a phase 2 open-label randomized study, we evaluated oral FA/RIF vs standard-of-care (SOC) intravenous antibiotics for treatment of hip or knee PJI.

HIV reservoirs: the new frontier.

Current antiretroviral therapies suppress viremia to very low levels, but are ineffective in eliminating reservoirs of persistent HIV infection. Efforts toward the development of therapies aimed at HIV reservoirs are complicated by the evidence that HIV establishes persistent productive and nonproductive infection in a number of cell types and through a variety of mechanisms. Moreover, immunologically privileged sites such as the brain also act as HIV sanctuaries.

Msh6 protects mature B cells from lymphoma by preserving genomic stability.

Most human B-cell non-Hodgkin's lymphomas arise from germinal centers. Within these sites, the mismatch repair factor MSH6 participates in antibody diversification. Reminiscent of the neoplasms arising in patients with Lynch syndrome III, mice deficient in MSH6 die prematurely of lymphoma.

Molecular characterization of hybridoma subclones spontaneously switching at high frequencies in vitro.

The hybridoma technology allows the production of large quantities of specific antibodies of a single isotype. Since different isotypes have special effector functions and are distributed distinctively throughout the body, it is often useful to have a library of switch variants from the original monoclonal antibody. We have shown previously that forced expression of activation induced cytidine deaminase (AID) in hybridomas increased their very low frequency of class switch recombination (CSR) in vitro only approximately 7-13 fold.

The biochemistry of somatic hypermutation.

Affinity maturation of the humoral response is mediated by somatic hypermutation of the immunoglobulin (Ig) genes and selection of higher-affinity B cell clones. Activation-induced cytidine deaminase (AID) is the first of a complex series of proteins that introduce these point mutations into variable regions of the Ig genes. AID deaminates deoxycytidine residues in single-stranded DNA to deoxyuridines, which are then processed by DNA replication, base excision repair (BER), or mismatch repair (MMR).

Detection of chromatin-associated single-stranded DNA in regions targeted for somatic hypermutation.

After encounter with antigen, the antibody repertoire is shaped by somatic hypermutation (SHM), which leads to an increase in the affinity of antibodies for the antigen, and class-switch recombination (CSR), which results in a change in the effector function of antibodies. Both SHM and CSR are initiated by activation-induced cytidine deaminase (AID), which deaminates deoxycytidine to deoxyuridine in single-stranded DNA (ssDNA). The precise mechanism responsible for the formation of ssDNA in V regions undergoing SHM has yet to be experimentally established.

Forced expression of AID facilitates the isolation of class switch variants from hybridoma cells.

Monoclonal antibodies are used in the treatment and diagnosis of diseases and to study the protective and adverse functions of antibodies in vitro and in vivo. Since the isotype determines the effector function, half-life in the serum and distribution throughout the body, it would be useful to have a battery of antibodies with the same binding site associated with different isotypes. However, since hybridomas switch isotypes at very low frequencies in tissue culture, it has been difficult and very labor intensive to isolate panels of class switch variants.

The mismatch repair protein Msh6 influences the in vivo AID targeting to the Ig locus.

Somatic hypermutation (SHM) and class switch recombination (CSR) are initiated by activation-induced cytidine deaminase (AID), which preferentially deaminates deoxycytidines at WRC (W = A/T, R = A/G) motifs in vitro. The mechanisms responsible for targeting AID and for organizing the queue of enzymes involved in vivo have been elusive. Here, we examined point mutant knockin Msh6 mice (Msh6(TD/TD)), which lack the second phase of SHM but retain all the proteins involved, and found that AID was frequently targeted to non-WRC motifs.

Complex regulation of somatic hypermutation by cis-acting sequences in the endogenous IgH gene in hybridoma cells.

To create high-affinity antibodies, B cells target a high rate of somatic hypermutation (SHM) to the Ig variable-region genes that encode the antigen-binding site. This mutational process requires transcription and is triggered by activation-induced cytidine deaminase (AID), which converts deoxycytidine to deoxyuridine. Mistargeting of AID to non-Ig genes is thought to result in the malignant transformation of B cells, but the mechanism responsible for targeting SHM to certain DNA regions and not to others is largely unknown.

Msh2 ATPase activity is essential for somatic hypermutation at a-T basepairs and for efficient class switch recombination.

Somatic hypermutation (SHM) and class switch recombination (CSR) are initiated by activation-induced cytidine deaminase-mediated cytidine deamination of immunoglobulin genes. MutS homologue (Msh) 2-/- mice have reduced A-T mutations and CSR. This suggests that Msh2 may play a role in repairing activation-induced cytidine deaminase-generated G-U mismatches.

In vitro analysis of human immunodeficiency virus type 1 resistance to nevirapine and fitness determination of resistant variants.

Nevirapine-resistant variants were generated by serial passages in MT-2 cells in the presence of increasing drug concentrations. In passage 5, mutations V106A, Y181C and G190A were detected in the global population, associated with a 100-fold susceptibility decrease. Sequence analysis of biological clones obtained from passage 5 and subsequent passages showed that single mutants, detected in first passages, were progressively replaced in passage 15 by double mutants, correlating with a 500-fold increase in phenotypic resistance.