CAMDA 2023: Finding patterns in urban microbiomes.

The Critical Assessment of Massive Data Analysis (CAMDA) addresses the complexities of harnessing Big Data in life sciences by hosting annual competitions that inspire research groups to develop innovative solutions. In 2023, the Forensic Challenge focused on identifying the city of origin for 365 metagenomic samples collected from public transportation systems and identifying associations between bacterial distribution and other covariates. For microbiome classification, we incorporated both taxonomic and functional annotations as features.

Prevalence and spectrum of germline pathogenic variants in cancer susceptibility genes among mexican patients with exocrine pancreatic cancer.

Background: Although universal germline genetic testing is recommended for patients with exocrine pancreatic cancer (PC), access to genetic testing remains limited in low- and middle-income countries. This study aims to narrow the gap in our understanding of the spectrum of germline pathogenic and likely pathogenic variants (PVs) in cancer susceptibility genes in the Mexican population.

Methods: The landscape of PVs in cancer susceptibility genes was identified by next-generation sequencing multigene panel assays among patients with PC who were enrolled in the Clinical Cancer Genomics Community Research Network prospective registry in Mexico City.

Comparative Effectiveness of Switching to Bictegravir From Dolutegravir-, Efavirenz-, or Raltegravir-Based Antiretroviral Therapy Among Individuals With HIV Who are Virologically Suppressed.

Background: We aimed to determine the effectiveness of switching to bictegravir in maintaining an undetectable viral load (<50 copies/mL) among people with HIV (PWH) as compared with continuing dolutegravir-, efavirenz-, or raltegravir-based antiretroviral therapy using nationwide observational data from Mexico.

Methods: We emulated 3 target trials comparing switching to bictegravir vs continuing with dolutegravir, efavirenz, or raltegravir. Eligibility criteria were PWH aged ≥16 years with a viral load <50 copies/mL and at least 3 months of current antiretroviral therapy (dolutegravir, efavirenz, or raltegravir) between July 2019 and September 2021.

Caveats Regarding the Test-Negative Design to Study Mpox (monkeypox) Risk Factors and Vaccine Effectiveness.

The test-negative design (TND) has been commonly used to study vaccine effectiveness (notably regarding COVID-19 and influenza vaccines) and has been recently proposed as a valid design to study causal risk factors of diseases during an outbreak. In April 2022, mpox (previously monkeypox) led to a worldwide outbreak that resulted in an international public health emergency. The TND could be used to study vaccine effectiveness and risk factors of mpox using epidemiologic databases, and a few studies have already done so.

Preventable sources of bias in subgroup analyses and secondary outcomes of randomized trials.

Background: Randomized controlled trials are the gold standard for determining treatment efficacy in medicine. To deter harmful practices such as p-hacking and hypothesizing after the results are known, any analysis of subgroups and secondary outcomes must be documented and pre-specified. However, they can still introduce bias (and routinely do) if they are not treated with the same consideration as the primary analysis.

The Anthropussy: an ecolesbian manifesto.

The Anthropocene is old news. As young queer zine-makers in Singapore, we heard the term on repeat and dared to ask: What about the Anthro? From this queer environmentalist pun we birthed a new take on our relationship to the Earth amidst climate crises - and in doing so, we came out as ecolesbians. Ecolesbianism is a concept we co-created, bringing together queer ecologies, political lesbianism, ecofeminism, transecology, ecosexuality, and our own experiences.

Isolation of human antibodies against influenza B neuraminidase and mechanisms of protection at the airway interface.

Influenza B viruses (IBVs) comprise a substantial portion of the circulating seasonal human influenza viruses. Here, we describe the isolation of human monoclonal antibodies (mAbs) that recognized the IBV neuraminidase (NA) glycoprotein from an individual following seasonal vaccination. Competition-binding experiments suggested the antibodies recognized two major antigenic sites.

Treatment of highly virulent mammarenavirus infections-status quo and future directions.

Introduction: Mammarenaviruses are negative-sense bisegmented enveloped RNA viruses that are endemic in Africa, the Americas, and Europe. Several are highly virulent, causing acute human diseases associated with high case fatality rates, and are considered to be significant with respect to public health impact or bioterrorism threat.

Areas Covered: This review summarizes the status quo of treatment development, starting with drugs that are in advanced stages of evaluation in early clinical trials, followed by promising candidate medical countermeasures emerging from bench analyses and investigational animal research.

Flapjack: Data Management and Analysis for Genetic Circuit Characterization.

Flapjack presents a valuable solution for addressing challenges in the Design, Build, Test, Learn (DBTL) cycle of engineering synthetic genetic circuits. This platform provides a comprehensive suite of features for managing, analyzing, and visualizing kinetic gene expression data and associated metadata. By utilizing the Flapjack platform, researchers can effectively integrate the test phase with the build and learn phases, facilitating the characterization and optimization of genetic circuits.

Genetic Network Design Automation with LOICA.

Genetic design automation (GDA) is the use of computer-aided design (CAD) in designing genetic networks. GDA tools are necessary to create more complex synthetic genetic networks in a high-throughput fashion. At the core of these tools is the abstraction of a hierarchy of standardized components.

Retiring the term AIDS for more descriptive language.

The term acquired immunodeficiency syndrome (AIDS) was coined to describe a condition marked by weakened cell-mediated immunity in the absence of a clear cause. Due to unfortunate messaging during the early days of the HIV epidemic, this term became loaded with stigma. After the discovery of HIV, the term AIDS became redundant, but its use has persisted and has come to embody negative connotations in the current landscape of the HIV epidemic.

Perceptions and experiences of daily and long-acting pre-exposure prophylaxis (PrEP) among MSM in India.

Oral pre-exposure prophylaxis (PrEP) is an effective HIV prevention strategy with high efficacy. An increased willingness to use PrEP among at-risk Indian men who have sex with men (MSM) population has been reported; however, little is known about their real experiences that guide their key motivators, facilitators, and barriers with using oral and Long-Acting (LA) Injectable PrEP. We recruited participants (n = 18) through active MSM social media networks.

Influenza virus immune imprinting dictates the clinical outcomes in ferrets challenged with highly pathogenic avian influenza virus H5N1.

Zoonotic transmission of H5N1 highly pathogenic avian influenza virus (HPAIV) into the human population is an increasing global threat. The recent 2022 HPAIV outbreak significantly highlighted this possibility, increasing concern in the general population. The clinical outcomes of H5N1 influenza virus exposure can be determined by an individual's primary influenza virus infection (imprinting) or vaccination status.

The importance of using disease causal models in studies of preventive interventions: Learning from preeclampsia research.

Objective: Interventions aimed at preventing disease are commonly studied as strategies of primary or secondary prevention. Unfortunately, this dichotomy can be misleading, and studies might unknowingly exclude people at high risk of the disease that could benefit from the intervention. Here I use the example of aspirin for prevention of preeclampsia to illustrate this problem.

Challenges to the HIV Care Continuum During the COVID-19 Pandemic in Mexico: A Mixed Methods Study.

The COVID-19 pandemic has been reported to disrupt the access to care of people who live with HIV (PWH). The impact of the pandemic on the longitudinal HIV care continuum, however, has not been properly evaluated. We performed a mixed-methods study using data from the Mexican System of Distribution, Logistics, and ART Surveillance on PWH that are cared for in the state of Oaxaca.

Longitudinal clinical phenotyping of post COVID condition in Mexican adults recovering from severe COVID-19: a prospective cohort study.

Introduction: Few studies have evaluated the presence of Post COVID-19 conditions (PCC) in people from Latin America, a region that has been heavily afflicted by the COVID-19 pandemic. In this study, we describe the frequency, co-occurrence, predictors, and duration of 23 symptoms in a cohort of Mexican patients with PCC.

Methods: We prospectively enrolled and followed adult patients hospitalized for severe COVID-19 at a tertiary care centre in Mexico City.

Predictors of laboratory-confirmed mpox in people with mpox-like illness.

Objectives: We aimed to identify predictors of confirmed monkeypox (mpox) among people with mpox-like illness and to develop a multivariable model for confirmed mpox.

Methods: We performed an observational study using national epidemiologic surveillance data in Mexico from May to November 2022. People with mpox-like illness were reported to the Mexican Ministry of Health and real-time polymerase chain reaction was performed in clinical samples to confirm mpox.

Home or hospital? An observational study of what affects the place of death of people with COVID-19 in Mexico.

Background: Out-of-hospital deaths increased during peak coronavirus disease 2019 (COVID-19) pandemic periods. However, aside from COVID-19 severity, which variables are related to being hospitalized have not been properly studied. We examine the association of several variables with dying at home from COVID-19 as opposed to in a hospital.