Biology subjects

Stanley, D. A.

Publications and source records attributed to Stanley, D. A..

7 recordsLinked to original sources

bioRxiv2025

MetaBeeAI: an AI pipeline for full-text systematic reviews in biology

The volume and complexity of scientific literature are expanding rapidly, making it increasingly difficult to extract and synthesise information across studies. This challenge is particularly acute in the biological sciences, where evidence spans multiple levels of organisation and heterogeneous experimental designs. Large Language Model (LLM) pipelines offer a scalable route to evidence synthesis, but many existing approaches lack transparency, modularity, and effective mechanisms for human oversight. We present MetaBeeAI, an open-source, modular pipeline that integrates established LLM techniques into a coherent, auditable workflow for structured data extraction in biology. MetaBeeAI combines modular prompting, multi-pass extraction, and expert-in-the-loop validation within an interface that presents model outputs alongside source text, enabling inspection, correction, and iterative refinement. The pipeline produces machine-readable records of prompts, configurations, and expert annotations, supporting reproducibility and continuous improvement. We apply MetaBeeAI to 924 research papers on bees and pesticides, extracting structured information on species, compounds, exposure designs, and experimental context. Evaluation demonstrates improved consistency, convergence with expert judgement, and robustness across heterogeneous biological studies, highlighting the value of expert-guided refinement. MetaBeeAI provides a transparent and extensible framework for scalable evidence synthesis, supporting reliable integration of LLMs into biological research workflows.

ecology↗

bioRxiv2024

A Single-shot ChAd3 Vaccine Provides Protection from Intramuscular and Aerosol Sudan Virus Exposure

Infection with Sudan virus (SUDV) is characterized by an aggressive disease course with case fatality rates between 40-100% and no approved vaccines or therapeutics. SUDV causes sporadic outbreaks in sub-Saharan Africa, including a recent outbreak in Uganda which has resulted in over 100 confirmed cases in one month. Prior vaccine and therapeutic efforts have historically prioritized Ebola virus (EBOV), leading to a significant gap in available treatments. Two vaccines, Erbevo(R) and Zabdeno(R)/Mvabea(R), are licensed for use against EBOV but are ineffective against SUDV. Recombinant adenovirus vector vaccines have been shown to be safe and effective against filoviruses, but efficacy depends on having low seroprevalence to the vector in the target human population. For this reason, and because of an excellent safety and immunogenicity profile, ChAd3 was selected as a superior vaccine vector. Here, a ChAd3 vaccine expressing the SUDV glycoprotein (GP) was evaluated for immunogenicity and efficacy in nonhuman primates. We demonstrate that a single dose of ChAd3-SUDV confers acute and durable protection against lethal SUDV challenge with a strong correlation between the SUDV GP-specific antibody titers and survival outcome. Additionally, we show that a bivalent ChAd3 vaccine encoding the GP from both EBOV and SUDV protects against both parenteral and aerosol lethal SUDV challenge. Our data indicate that the ChAd3-SUDV vaccine is a suitable candidate for a prophylactic vaccination strategy in regions at high risk of filovirus outbreaks. One Sentence Summary: A single-dose of ChAd3 vaccine protected macaques from lethal challenge with Sudan virus (SUDV) by parenteral and aerosol routes of exposure.

immunology↗

bioRxiv2023

Moving Past Neonicotinoids and Honeybees: A Systematic Review of Existing Research on Other Insecticides and Bees

Synthetic pesticides are used widely in agriculture to protect crops from pests, weeds and disease. However, their use also comes with a range of environmental concerns. One of which is effects of insecticides on non-target organisms such as bees, who provide pollination services for crops and wild plants. This systematic literature review quantifies the existing research on bees and insecticides broadly, and then focuses more specifically on non-neonicotinoid insecticides and non-honeybees. We find that articles on honeybees (Apis sp.) and insecticides account for 80% of all research, with all other bees combined making up 20%. Neonicotinoids were studied in 34% of articles across all bees and were the most widely studied insecticide class for non-honeybees overall, with almost three times as many studies than the second most studied class. Of non-neonicotinoid insecticide classes and non-honeybees; the most studied were pyrethroids and organophosphates followed by carbamates, and the most widely represented bee taxa were bumblebees (Bombus), followed by leaf-cutter bees (Megachile) and mason bees (Osmia). Research has taken place across several countries, with the highest numbers of articles from Brazil and the US, and with notable gaps from countries in Asia, Africa and Oceania. Mortality was the most studied effect type, while sub-lethal effects such as on behaviour were less studied. Few studies tested how insecticides were influenced by other multiple pressures, such as climate change and co-occurring pesticides (cocktail effects). As anthropogenic pressures do not occur in isolation, we suggest that future research also addresses these knowledge gaps. Given the changing global patterns in insecticide use, and the increasing inclusion of both non-honeybees and sub-lethal effects in pesticide risk assessment, there is a need for expanding research beyond current state to ensure a strong scientific evidence base for the development of risk assessment and associated policy.

ecology↗

bioRxiv2022

Honey contamination from plant protection products approved for cocoa cultivation: a systematic review of existing research and methods

Cocoa (Theobroma cocoa), which is the key ingredient of chocolate, is an important economic crop plant which supports the livelihoods of an estimated forty to fifty million people directly involved in its cultivation. Many cocoa producing countries, especially those from the developing world, rely on the income from cocoa export to support their economies. The plant is, however, prone to disease and pest attacks and therefore requires the application of large volumes of pesticides to guarantee satisfactory productions. Even though pesticides help protect the cocoa plant from disease and pest attacks, unintended effects of environmental contamination are also a possibility. Honey, a product of nectar collected by honeybees from flowers during foraging, may be a useful proxy for the extent to which landscapes are exposed to pesticides and the degree of pesticide accumulation in the environment. The overreaching question is: to what extent has the effect of pesticides imputed for cocoa production on honey received attention in research? In this present study, we conducted a systematic approach to quantify existing studies on honey contamination from plant protection products approved for cocoa cultivation. We observed that one hundred and sixty-nine different compounds, comprising some recommended and other unapproved compounds for cocoa cultivation, were detected in 81% of the reviewed 104 publications. Our results further point to the neonicotinoids as the most detected class of pesticides, with imidacloprid particularly being the single most detected compound. However, the most remarkable observation made from this study points to disproportionate studies of honey contamination from pesticides conducted in cocoa and non-cocoa producing countries with only 19% of the publications taking place in the latter. To bridge the gap, we suggest prioritising increased research in cocoa growing countries to ameliorate the significant gaps in knowledge owing to limited studies emanating from these geographic regions.

ecology↗

bioRxiv2021

Rapid and Durable Protection Against Marburg Virus with a Single-Shot ChAd3-MARV GP Vaccine

Marburg virus (MARV) causes a severe hemorrhagic fever disease in primates with mortality rates in humans up to 90%. Since 2018, MARV has been identified as a priority pathogen by the WHO, needing urgent research and development of countermeasures due to the high public health risk it poses. Recently, the first case of MARV in West Africa underscored the significant outbreak potential of this virus. The potential for cross border spread as had occurred during the Ebola 2014-2016 outbreak illustrates the critical need for Marburg vaccines. To support regulatory approval of the ChAd3-Marburg vaccine that has completed Phase I trials, we show that a non-replicating chimpanzee-derived adenovirus vector with a demonstrated safety profile in humans (ChAd3) protected against a uniformly lethal challenge with Marburg-Angola. Protective immunity was achieved within 7 days of vaccination and was maintained through one year post vaccination, antigen-specific antibodies were a significant immune correlate of protection in the acute challenge model (p=0.0003), and predictive for protection with an AUC = 0.88. These results demonstrate that a single-shot ChAd3 MARV vaccine generated a protective immune response that was both rapid and durable with a significant immune correlate of protection that will support advanced clinical development. One Sentence SummaryA single-shot of non-replicating ChAd3-MARV vaccine demonstrated both rapid (within 1 week) and durable (12 months) protection against lethal Marburg virus infection in macaques.

immunology↗

bioRxiv2020

Differential contributions of synaptic and intrinsic inhibitory currents to parsing via flexible phase-locking in neural oscillators

Current hypotheses suggest that speech segmentation - the initial division and grouping of the speech stream into candidate phrases, syllables, and phonemes for further linguistic processing - is executed by a hierarchy of oscillators in auditory cortex. Theta (~3-12 Hz) rhythms play a key role by phase-locking to recurring acoustic features marking syllable boundaries. Reliable synchronization to quasi-rhythmic inputs, whose variable frequency can dip below cortical theta frequencies (down to ~1 Hz), requires "flexible" theta oscillators whose underlying neuronal mechanisms remain unknown. Using biophysical computational models, we found that the flexibility of phase-locking in neural oscillators depended on the types of hyperpolarizing currents that paced them. Simulated cortical theta oscillators flexibly phase-locked to slow inputs when these inputs caused both (i) spiking and (ii) the subsequent buildup of outward current sufficient to delay further spiking until the next input. The greatest flexibility in phase-locking arose from a synergistic interaction between intrinsic currents that was not replicated by synaptic currents at similar timescales. Flexibility in phase-locking enabled improved entrainment to speech input, optimal at mid-vocalic channels, which in turn supported syllabic-timescale segmentation through identification of vocalic nuclei. Our results suggest that synaptic and intrinsic inhibition contribute to frequency-restricted and -flexible phase-locking in neural oscillators, respectively. Their differential deployment may enable neural oscillators to play diverse roles, from reliable internal clocking to adaptive segmentation of quasi-regular sensory inputs like speech. Author summaryOscillatory activity in auditory cortex is believed to play an important role in auditory and speech processing. One suggested function of these rhythms is to divide the speech stream into candidate phonemes, syllables, words, and phrases, to be matched with learned linguistic templates. This requires brain rhythms to flexibly synchronize with regular acoustic features of the speech stream. How neuronal circuits implement this task remains unknown. In this study, we explored the contribution of inhibitory currents to flexible phase-locking in neuronal theta oscillators, believed to perform initial syllabic segmentation. We found that a combination of specific intrinsic inhibitory currents at multiple timescales, present in a large class of cortical neurons, enabled exceptionally flexible phase-locking, which could be used to precisely segment speech by identifying vowels at mid-syllable. This suggests that the cells exhibiting these currents are a key component in the brains auditory and speech processing architecture.

neuroscience↗

bioRxiv2019

Flexible reset and entrainment of delta oscillations in primate primary auditory cortex: modeling and experiment

Salient auditory stimuli typically exhibit rhythmic temporal patterns. A growing body of evidence suggests that, in primary auditory cortex (A1), attention is associated with entrainment of delta rhythms (1 - 4 Hz) by these auditory stimuli. It is thought that this entrainment involves phase reset of ongoing spontaneous oscillations in A1 by thalamus matrix afferents, but precise mechanisms are unknown. Furthermore, naturalistic stimuli can vary widely in terms of their rhythmicity: some cycles can be longer than others and frequency can drift over time. It is not clear how the auditory system accommodates this natural variability. We show that in rhesus macaque monkey A1 in vivo, bottom-up gamma (40 Hz) click trains influence ongoing spontaneous delta rhythms by inducing an initial delta-timescale transient response, followed by entrainment to gamma and suppression of delta. We then construct a computational model to reproduce this effect, showing that transient thalamus matrix activation can reset A1 delta oscillations by directly activating deep (layer 5) IB cells, promoting bursting, and beginning a new delta cycle. In contrast, long duration gamma-rhythmic input stimuli induce a steady-state containing entrainment of superficial RS and FS cells at gamma, and suppression of delta oscillations. This suppression is achieved in the model by two complementary pathways. First, long-duration thalamus matrix input causes IB cells to switch from bursting to sparse firing, which disrupts the IB bursts associated with delta. Second, thalamus core input activates deep FS cells (by way of layer 4), which fire at gamma frequency and actively inhibit the delta oscillator. Together, these two fundamental operations of reset and suppression can respectively advance and delay the phase of the delta oscillator, allowing it to follow rhythms exhibiting the type of variability found in the natural environment. We discuss these findings in relation to functional implications for speech processing.\n\nAuthor summaryNeurons organize their firing into synchronous, rhythmic patterns. These neural oscillations have been shown to entrain to rhythmic stimuli in the external world, such as patterns of speech or patterns of movement. By entraining to a particular input stimulus, these oscillations are thought to help us attend to that stimulus and to exclude others. To understand how this synchronization emerges, we constructed a physiologically detailed mathematical model of the primary auditory cortex. By fitting this model to a variety of experimental data, we suggest fundamental mechanisms by which neurons of the auditory cortex can synchronize their activity to rhythmic external stimuli. This result will be useful for understanding the mechanism and limitations of oscillatory entrainment, which are thought to underlie the processing of naturalistic auditory inputs like speech or music. Furthermore, this model, though simplified, was shown to generalize and reproduce a wide range of experimental results, and can thus be used as a starting point for building more complex models of auditory cortex.

neuroscience↗