The current landscape of software tools for the climate-sensitive infectious disease modelling community.

Climate-sensitive infectious disease modelling is crucial for public health planning and is underpinned by a complex network of software tools. We identified only 37 tools that incorporated both climate inputs and epidemiological information to produce an output of disease risk in one package, were transparently described and validated, were named (for future searching and versioning), and were accessible (ie, the code was published during the past 10 years or was available on a repository, web platform, or other user interface). We noted disproportionate representation of developers based at North American and European institutions.

Discriminating protein tags on a dsDNA construct using a Dual Nanopore Device.

We report Brownian dynamics simulation results with the specific goal to identify key parameters controlling the experimentally measurable characteristics of protein tags on a dsDNA construct translocating through a double nanopore setup. First, we validate the simulation scheme in silico by reproducing and explaining the physical origin of the asymmetric experimental dwell time distributions of the oligonucleotide flap markers on a 48 kbp long dsDNA at the left and the right pore. We study the effect of the electric field inside and beyond the pores, critical to discriminate the protein tags based on their effective charges and masses revealed through a generic power-law dependence of the average dwell time at each pore.

Patterns of sexual and HIV-related stigma among men who have sex with men and women living with HIV in Haiti.

Vulnerability to contracting HIV among Men who have Sex with Men and Women (MSMW) was recognized early in the epidemic. However, while global HIV efforts have made tremendous progress for the heterosexually-identified population, the specific needs of MSMW were not directly addressed with tailored and context-adapted interventions. The purpose of this study was to inform this area of research by exploring patterns of stigma through sexual identity developmental history as well as coping mechanisms among MSMW living with HIV in Haiti.

Electronic Mapping of a Bacterial Genome with Dual Solid-State Nanopores and Active Single-Molecule Control.

We present an electronic mapping of a bacterial genome using solid-state nanopore technology. A dual-nanopore architecture and active control logic are used to produce single-molecule data that enables estimation of distances between physical tags installed at sequence motifs within double-stranded DNA. Previously developed "DNA flossing" control logic generates multiple scans of each captured DNA.

Co-learning during the co-creation of a dengue early warning system for the health sector in Barbados.

Over the past decade, the Caribbean region has been challenged by compound climate and health hazards, including tropical storms, extreme heat and droughts and overlapping epidemics of mosquito-borne diseases, including dengue, chikungunya and Zika. Early warning systems (EWS) are a key climate change adaptation strategy for the health sector. An EWS can integrate climate information in forecasting models to predict the risk of disease outbreaks several weeks or months in advance.

A realist evaluation of the continuum of HIV services for men who have sex with men.

Background: Men who have Sex with Men (MSM) represent the risk group that are disproportionately most affected by the human immunodeficiency virus (HIV) and continue to drop-off from the steps of the continuum of HIV services that have been adopted to overcome poor engagement and retention in care. This realist evaluation aimed at: (1) describing the evaluation carried out in Haiti aiming to ascertain why, how and under which circumstances MSM are linked and retained along the continuum, (2) assessing the outcomes of this approach and (3) exploring the motivators and facilitators for the HIV continuum of services through mechanisms and pathways.

Methods: Guided by a realist approach, first, an initial program theory (IPT) was developed based on literature and frameworks review, participant observations and discussions with stakeholders.

HIV among men who have sex with men in the Caribbean: reaching the left behind.

Objectives: To present the epidemiology, social and cultural factors driving the HIV epidemic among men who have sex with men (MSM) in the Caribbean region and to highlight the regional and national responses, and what remains to be addressed to close the gaps in order to ending AIDS by 2030.

Methods: A literature review was performed in the following databases: PubMed and Scopus. Articles published in the past 10 years were selected.

Attitudes of medical students towards men who have sex with men living with HIV: implications for social accountability.

Objectives: To explore the attitudes that medical students in Haiti harbour toward Men who have Sex with Men living with HIV in order to better understand how stigma and other factors may impair healthcare, and to explore suggestions of opportunities in line with the values of social accountability.

Methods: This study employed a qualitative design by using a grounded theory approach regarding the context of Haiti. We used purposive sampling to select the 22 research participants.

A realist systematic review of stigma reduction interventions for HIV prevention and care continuum outcomes among men who have sex with men.

While stigma associated with human immunodeficiency virus (HIV) infection among men who have sex with men (MSM) is well recognized, there remains relatively limited intervention data on effective stigma reduction strategies. This systematic review was conducted to highlight the mechanisms through which sexual and HIV stigma is reduced in relation to HIV prevention and care engagement. Search of PubMed and Scopus resulted in 11 tested interventions to include in our preliminary model constructed from programme frameworks and recommendations.

Fast and accurate quantification of insertion-site specific transgene levels from raw seed samples using solid-state nanopore technology.

Many modern crop varieties contain patented biotechnology traits, and an increasing number of these crops have multiple (stacked) traits. Fast and accurate determination of transgene levels is advantageous for a variety of use cases across the food, feed and fuel value chain. With the growing number of new transgenic crops, any technology used to quantify them should have robust assays that are simple to design and optimize, thereby facilitating the addition of new traits to an assay.

Flossing DNA in a Dual Nanopore Device.

Solid-state nanopores are a single-molecule technique that can provide access to biomolecular information that is otherwise masked by ensemble averaging. A promising application uses pores and barcoding chemistries to map molecular motifs along single DNA molecules. Despite recent research breakthroughs, however, it remains challenging to overcome molecular noise to fully exploit single-molecule data.

Controlling DNA Tug-of-War in a Dual Nanopore Device.

Methods for reducing and directly controlling the speed of DNA through a nanopore are needed to enhance sensing performance for direct strand sequencing and detection/mapping of sequence-specific features. A method is created for reducing and controlling the speed of DNA that uses two independently controllable nanopores operated with an active control logic. The pores are positioned sufficiently close to permit cocapture of a single DNA by both pores.

Single Molecule DNA Resensing Using a Two-Pore Device.

A nanofluidic device is presented that, enables independent sensing and resensing of a single DNA molecule translocating through two nanopores with sub-micrometer spacing. The device concept is based upon integrating a thin nitride membrane with microchannels etched in borosilicate glass. Pores, coupled to each microchannel, are connected via a fluid-filled half-space on the device backside, enabling translocation of molecules across each pore in sequence.

A handheld platform for target protein detection and quantification using disposable nanopore strips.

Accessible point-of-care technologies that can provide immunoassay and molecular modalities could dramatically enhance diagnostics, particularly for infectious disease control in low-resource settings. Solid-state nanopores are simple and durable sensors with low-energy instrumentation requirements. While nanopore sensors have demonstrated efficacy for nucleic acid targets, selective detection and quantification of target proteins from sample background has not been demonstrated.

Semimembranosus tenosynovitis: Diagnosis and management of a commonly missed cause of posteromedial knee pain.

Background: In orthopedic and sports medicine literature there is minimal information regarding accurate diagnosis and the treatment options for tenosynovitis of the distal semimembranosus tendon. After reviewing the literature, the authors question both the etiology and treatment of this condition. Previous descriptions have associated the condition primarily with the endurance athlete but we have noted multiple cases in which this is a condition common to the 'sprinter' as well.

Identification of lanthanum-specific peptides for future recycling of rare earth elements from compact fluorescent lamps.

As components of electronic scrap, rare earth minerals are an interesting but little used source of raw materials that are highly important for the recycling industry. Currently, there exists no cost-efficient technology to separate rare earth minerals from an electronic scrap mixture. In this study, phage surface display has been used as a key method to develop peptides with high specificity for particular inorganic targets in electronic scrap.

Identification of mineral-binding peptides that discriminate between chalcopyrite and enargite.

Innovative approaches to the separation of minerals and subsequent extraction of metals are imperative owing to the increasing mineralogical complexity of ore deposits that are difficult or even impossible to separate into slurries or solutions containing only the minerals or metals of interest. Low recovery of metal is typical for these complex deposits leading to significant losses to tailings. In addition, the minerals often contain impurities, some toxic, which are difficult and costly to control or manage during the processing of a concentrate or other mineral product.

Biotechnology and the Mine of Tomorrow.

Biotechnology could provide many innovative alternatives for changing the way metals are obtained. Microbes have been used to dissolve metallic minerals and release metal ions into solution, from which pure metal can be obtained by electrolysis. Plants that accumulate metals in their roots and leaves have been used to concentrate metals, and mineral-binding peptides might be used to separate minerals.

Nanopore-Based Target Sequence Detection.

The promise of portable diagnostic devices relies on three basic requirements: comparable sensitivity to established platforms, inexpensive manufacturing and cost of operations, and the ability to survive rugged field conditions. Solid state nanopores can meet all these requirements, but to achieve high manufacturing yields at low costs, assays must be tolerant to fabrication imperfections and to nanopore enlargement during operation. This paper presents a model for molecular engineering techniques that meets these goals with the aim of detecting target sequences within DNA.

Intense cavitation at extreme static pressure.

Cavitation is usually performed at hydrostatic pressures at or near 0.1 MPa. Higher static pressure produces more intense cavitation, but requires an apparatus that can build high amplitude acoustic waves with rarefactions exceeding the cavitation threshold.

Detecting single-abasic residues within a DNA strand immobilized in a biological nanopore using an integrated CMOS sensor.

In this paper, we demonstrate the application of a novel current-measuring sensor (CMS) customized for nanopore applications. The low-noise CMS is fabricated in a 0.35μm CMOS process and is implemented in experiments involving DNA captured in an α-hemolysin (α-HL) nanopore.

A patch-clamp ASIC for nanopore-based DNA analysis.

In this paper, a fully integrated high-sensitivity patch-clamp system is proposed for single-molecule deoxyribonucleic acid (DNA) analysis using a nanopore sensor. This system is composed of two main blocks for amplification and compensation. The amplification block is composed of three stages: 1) a headstage, 2) a voltage-gain difference amplifier, and 3) a track-and-hold circuit, that amplify a minute ionic current variation sensed by the nanopore while the compensation block avoids the headstage saturation caused by the input parasitic capacitances during sensing.

Error analysis of idealized nanopore sequencing.

This numerical study provides an error analysis of an idealized nanopore sequencing method in which ionic current measurements are used to sequence intact single-stranded DNA in the pore, while an enzyme controls DNA motion. Examples of systematic channel errors when more than one nucleotide affects the current amplitude are detailed, which if present will persist regardless of coverage. Absent such errors, random errors associated with tracking through homopolymer regions are shown to necessitate reading known sequences (Escherichia coli K-12) at least 140 times to achieve 99.