Biology subjects

Martins, A. L.

Publications and source records attributed to Martins, A. L..

7 recordsLinked to original sources

bioRxiv2025

Sardine: a modular framework for developing data acquisition and near real-time analysis applications

We present Sardine, a software framework built with.NET to control experimental setups through the reliable execution of dynamic networks of independent modules, where each module can interface with a hardware device (e.g., camera, motor) or represent an operation over data (e.g., image filter, data stream). The Sardine framework delivers robust fault-tolerant hardware control and eliminates downstream delays by implementing dedicated data processing queues for each module. Any.NET class can be seamlessly adapted into a Sardine module, enabling effortless integration with existing codebases. Sardines modular architecture ensures flexibility to accommodate changes in experimental paradigms, simplifying the adaptation of essential features, such as swapping hardware components or redefining the logic of their interactions. The core of Sardine is a novel aggregation system that connects modules in two layers, designed to streamline complex workflows such as those in microscopy applications. The first layer (link layer) enables concurrent operations between modules, such as synchronizing a camera module with a stage controller or a laser module, while maintaining a dependency tree to ensure devices operate as intended. For example, in an imaging experiment, Sardine oversees individual module malfunctions, such as a camera failure or stage misalignment, gracefully handling errors and dynamically restoring functionality to impacted network segments to minimize disruption. The second layer (data layer) facilitates the transmission of information across modules by associating them with operations that produce, consume, or transform data. In an imaging context, this could involve processing raw image data from a camera module, passing it through a real-time analysis module for feature detection, and forwarding the results to a visualization module for immediate feedback. This two-layer architecture ensures seamless data flow and robust error handling, making Sardine ideal for dynamic and complex experimental setups. Sardine also integrates logging, a metadata collection system, and tools to create graphical applications.

neuroscience↗

bioRxiv2022

Processing and evaluating the quality of genome-wide nascent transcription profiling libraries

Precision genomic run-on assays (PRO-seq) quantify nascent RNA at single nucleotide resolution with strand specificity. Here we deconstruct a recently published genomic nascent RNA processing pipeline (PEPPRO) into its components and link the analyses to the underlying molecular biology. PRO-seq experiments are evolving and variations can be found throughout the literature. The analyses are presented as individual code chunks with comprehensive details so that users can modify the framework to accommodate different protocols. We present the framework to quantify the following quality control metrics: library complexity, nascent RNA purity, nuclear run-on efficiency, alignment rate, sequencing depth, and RNA degradation.

bioinformatics↗

bioRxiv2022

Correction of transposase sequence bias in ATAC-seq data with rule ensemble modeling

Chromatin accessibility assays have revolutionized the field of transcription regulation by providing single-nucleotide resolution measurements of regulatory features such as promoters and transcription factor binding sites. ATAC-seq directly measures how well the Tn5 transpose accesses chromatinized DNA. Tn5 has a complex sequence bias that is not effectively scaled with traditional bias-correction methods. We model this complex bias using a rule ensemble machine learning approach that integrates information from many input k-mers proximal to the ATAC sequence reads. We effectively characterize and correct single-nucleotide sequence biases and regional sequence biases of the Tn5 enzyme. Correction of enzymatic sequence bias is an important step in interpreting chromatin accessibility assays that aim to infer transcription factor binding and regulatory activity of elements in the genome.

bioinformatics↗

bioRxiv2021

Instruments to assess Evidence-Based Practice among healthcare professionals: a systematic review

The study makes it possible to select the most appropriate instruments to evaluate the use of Evidence-Based Practice (EBP) among health professionals. The objective of this study was to assess the measurement properties, summarize and describe the instruments that evaluate the use of EBP in health professionals, currently available through the update of the systematic review. The study was conducted and reported according to recommendations of the PRISMA checklist. A systematic search was conducted in the databases: PubMed, Embase, CINAHL and ERIC. In addition, three groups of search terms: EBP terms; evaluation; cross-cultural adaptation and measurement proprieties. They included studies that showed assessment tools of EBP in healthcare workers in general publication of full-text scientific articles, which tested the measurement properties and publication of an article in English. Searches included published studies from 2006 until July 2020. Evaluation of the methodological quality of the studies was conducted according to the COSMIN initiative. 92 studies were included. Forty new instruments have been identified to assess EBP. From these, most were developed for nursing professionals and physiotherapists. More than 48% of studies have American and Australian English as their native language. Only 28% of the studies included students in the samples. Reliability was considered appropriate (sufficient) in 76% of the instruments. The COSMIN checklist classified 7 (seven) instruments as being suitable for use in the target audience. However, Fresno Test remains the most appropriate instrument for assessing the use of EBP in healthcare professionals. 40 new instruments that assess EBP have been identified. Most are consistent and reliable for measuring the use of EBP in healthcare professionals. The Fresno Test, in a list of seven reliable and valid instruments for analysis, remains the most used and the one that most assesses the domains of EBP.

scientific communication and education↗

bioRxiv2020

Early-life social experience shapes social avoidance reactions in larval zebrafish

Social experiences greatly define successive social behavior. Lack of such experiences, especially during critical phases of development, can severely impede the ability to behave adequately in social contexts. To date it is not well characterized how early-life social isolation leads to social deficits and impacts development. In many model species, it is challenging to fully control social experiences, because they depend on parental care. Moreover, complex social behaviors involve multiple sensory modalities, contexts, and actions. Hence, when studying social isolation effects, it is particularly important to parse apart social deficits from general developmental effects, such as abnormal motor learning. Here, we characterized how social experiences during early development of zebrafish larvae modulate their social behavior, at one week of age, when social avoidance reactions can be measured as discrete swim events. We show that raising larvae in social isolation leads to enhanced social avoidance, in terms of reaction distance and reaction strength. Specifically, larvae raised in isolation use a high-acceleration escape swim bout, the short latency C-start, more frequently during social interactions. These behavioral differences are absent in non-social contexts. By ablating the lateral line and presenting the fish with local water vibrations, we show that lateral line inputs are both necessary and sufficient to drive enhanced social avoidance reactions. Taken together, our results show that social experience during development is a critical factor in shaping mechanosensory avoidance reactions in larval zebrafish. HighlightsO_LILarval zebrafish raised in isolation show enhanced social avoidance reactions C_LIO_LIEnhanced avoidance is composed of increased avoidance distances and usage of high acceleration escape swims C_LIO_LIThe lateral line sensory organ is necessary and sufficient for the increased usage of high acceleration escape swims C_LI

neuroscience↗

bioRxiv2017

Universal correction of enzymatic sequence bias

Coupling molecular biology to high throughput sequencing has revolutionized the study of biology. Molecular genomics techniques are continually refined to provide higher resolution mapping of nucleic acid interactions and structure. Sequence preferences of enzymes can interfere with the accurate interpretation of these data. We developed seqOutBias to characterize enzymatic sequence bias from experimental data and scale individual sequence reads to correct intrinsic enzymatic sequence biases. SeqOutBias efficiently corrects DNase-seq, TACh-seq, ATAC-seq, MNase-seq, and PRO-seq data. We show that seqOutBias correction facilitates identification of true molecular signatures resulting from transcription factors and RNA polymerase interacting with DNA.

genomics↗

bioRxiv2016

Natural Selection has Shaped Coding and Non-coding Transcription in Primate CD4+ T-cells

Transcriptional regulatory changes have been shown to contribute to phenotypic differences between species, but many questions remain about how gene expression evolves. Here we report the first comparative study of nascent transcription in primates. We used PRO-seq to map actively transcribing RNA polymerases in resting and activated CD4+ T-cells in multiple human, chimpanzee, and rhesus macaque individuals, with rodents as outgroups. This approach allowed us to measure transcription separately from post-transcriptional processes. We observed general conservation in coding and non-coding transcription, punctuated by numerous differences between species, particularly at distal enhancers and non-coding RNAs. We found evidence that transcription factor binding sites are a primary determinant of transcriptional differences between species, that stabilizing selection maintains gene expression levels despite frequent changes at distal enhancers, and that adaptive substitutions have driven lineage-specific transcription. Finally, we found strong correlations between evolutionary rates and long-range chromatin interactions. These observations clarify the role of primary transcription in regulatory evolution.

genomics↗