Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo.

Enhancers control gene expression and have crucial roles in development and homeostasis1-3. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here we combine deep learning and transfer learning to design tissue-specific enhancers for five tissues in the Drosophila melanogaster embryo: the central nervous system, epidermis, gut, muscle and brain. We first train convolutional neural networks using genome-wide single-cell assay for transposase-accessible chromatin with sequencing (ATAC-seq) datasets and then fine-tune the convolutional neural networks with smaller-scale data from in vivo enhancer activity assays, yielding models with 13% to 76% positive predictive value according to cross-validation. We designed and experimentally assessed 40 synthetic enhancers (8 per tissue) in vivo, of which 31 (78%) were active and 27 (68%) functioned in the target tissue (100% for central nervous system and muscle). The strategy of combining genome-wide and small-scale functional datasets by transfer learning is generally applicable and should enable the design of tissue-, cell type- and cell state-specific enhancers in any system.

Systematic identification and characterization of repressive domains in Drosophila transcription factors.

All multicellular life relies on differential gene expression, determined by regulatory DNA elements and DNA-binding transcription factors that mediate activation and repression via cofactor recruitment. While activators have been extensively characterized, repressors are less well studied: the identities and properties of their repressive domains (RDs) are typically unknown and the specific co-repressors (CoRs) they recruit have not been determined. Here, we develop a high-throughput, next-generation sequencing-based screening method, repressive-domain (RD)-seq, to systematically identify RDs in complex DNA-fragment libraries. Screening more than 200,000 fragments covering the coding sequences of all transcription-related proteins in Drosophila melanogaster, we identify 195 RDs in known repressors and in proteins not previously associated with repression. Many RDs contain recurrent short peptide motifs, which are conserved between fly and human and are required for RD function, as demonstrated by motif mutagenesis. Moreover, we show that RDs that contain one of five distinct repressive motifs interact with and depend on different CoRs, such as Groucho, CtBP, Sin3A, or Smrter. These findings advance our understanding of repressors, their sequences, and the functional impact of sequence-altering mutations and should provide a valuable resource for further studies.

Enhancers display constrained sequence flexibility and context-specific modulation of motif function.

The information about when and where each gene is to be expressed is mainly encoded in the DNA sequence of enhancers, sequence elements that comprise binding sites (motifs) for different transcription factors (TFs). Most of the research on enhancer sequences has been focused on TF motif presence, whereas the enhancer syntax, that is, the flexibility of important motif positions and how the sequence context modulates the activity of TF motifs, remains poorly understood. Here, we explore the rules of enhancer syntax by a two-pronged approach in Drosophila melanogaster S2 cells: we (1) replace important TF motifs by all possible 65,536 eight-nucleotide-long sequences and (2) paste eight important TF motif types into 763 positions within 496 enhancers. These complementary strategies reveal that enhancers display constrained sequence flexibility and the context-specific modulation of motif function. Important motifs can be functionally replaced by hundreds of sequences constituting several distinct motif types, but these are only a fraction of all possible sequences and motif types. Moreover, TF motifs contribute with different intrinsic strengths that are strongly modulated by the enhancer sequence context (the flanking sequence, the presence and diversity of other motif types, and the distance between motifs), such that not all motif types can work in all positions. The context-specific modulation of motif function is also a hallmark of human enhancers, as we demonstrate experimentally. Overall, these two general principles of enhancer sequences are important to understand and predict enhancer function during development, evolution, and in disease.

Utilizing COVID-19 as a Model for Diagnostics Using an Electrochemical Sensor.

This paper reports a rapid and sensitive sensor for the detection and quantification of the COVID-19 N-protein (N-PROT) via an electrochemical mechanism. Single-frequency electrochemical impedance spectroscopy was used as a transduction method for real-time measurement of the N-PROT in an immunosensor system based on gold-conjugate-modified carbon screen-printed electrodes (Cov-Ag-SPE). The system presents high selectivity attained through an optimal stimulation signal composed of a 0.0 V DC potential and 10 mV RMS-1 AC signal at 100 Hz over 300 s. The Cov-Ag-SPE showed a log response toward N-PROT detection at concentrations from 1.0 ng mL-1 to 10.0 µg mL-1, with a 0.977 correlation coefficient for the phase (θ) variation. An ML-based approach could be created using some aspects observed from the positive and negative samples; hence, it was possible to classify 252 samples, reaching 83.0, 96.2 and 91.3% sensitivity, specificity, and accuracy, respectively, with confidence intervals (CI) ranging from 73.0 to 100.0%. Because impedance spectroscopy measurements can be performed with low-cost portable instruments, the immunosensor proposed here can be applied in point-of-care diagnostics for mass testing, even in places with limited resources, as an alternative to the common diagnostics methods.

Role of professional expertise in the decision-making process for periodontally compromised teeth.

The objective of this study was to evaluate factors that may influence decision-making with regard to extraction or maintenance of periodontally compromised teeth. A questionnaire with 2 distinct clinical scenarios, each including a radiographic image, was provided to students in their final year of dental school and practicing dentists. The participants were asked to record the action that they would take in each case (tooth maintenance vs extraction) and provide a justification for their decision. The questionnaires were answered by 158 dental students and 57 dentists (N = 215). Among the sample as a whole, 31.16% of participants recommended extraction in scenario 1, while only 5.58% recommended that action in scenario 2. In scenario 1, there was a statistically significant difference in the recommendations of the dental students and the dentists, with the former group significantly more disposed to conservative action, that is, maintenance of the tooth (P < 0.001; chi-square test). When the actions recommended by participants specializing in implants or periodontics (or both) were compared with those recommended by other specialists, there was a statistically significant difference between the groups regarding maintenance and extraction (P = 0.012; Fisher exact test), with the former group recommending fewer extractions. When the responses were evaluated in terms of the participants' years of specialty practice, it was observed that professionals with fewer than 20 years of practice were more conservative in their decisions, choosing tooth maintenance significantly more often than specialists with longer experience (P = 0.031; Fisher exact test). Among the majority of both dental students and practicing dentists, the decision in both scenarios was to maintain the compromised teeth; however, the results suggested that that both the years of experience of the individual and the specialty of the practitioner can influence decision-making.

Interplay of Magnetic Properties and Doping in Epitaxial Films of h-REFeO3 Multiferroic Oxides.

Multiferroic materials demonstrating coexistence of magnetic and ferroelectric orders are promising candidates for magnetoelectric devices. While understanding the underlying mechanism of interplaying of ferroic properties is important, tailoring their properties to make them potential candidates for magnetoelectric devices is challenging. Here, the antiferromagnetic Neel ordering temperature above 200 K is realized in successfully stabilized epitaxial films of (Lu,Sc)FeO3 multiferroic oxide. The first-principles calculations show the shrinkage of in-plane lattice constants of the unit cells of the films on different substrates which corroborates well the enhancement of the Neel ordering temperature (TN ). The profound effect of lattice strain/stress at the interface due to differences of in-plane lattice constants on out of plane magnetic properties and on spin reorientation temperature in the antiferromagnetic region is further elucidated in the epitaxial films with and without buffer layer of Mn-doped LuFeO3 . Writing and reading ferroelectric domains reveal the ferroelectric response of the films at room temperature. Detailed electron microscopy shows the presence of lattice defects in atomic scale. First-principles calculations show that orbital rehybridization of rare-earth ions and oxygen is one of the main driving force of ferroelectricity along c-axis in thin films of hexagonal ferrites.

Functionalized magnetic composite nano/microfibres with highly oriented van der Waals CrI3 inclusions by electrospinning.

This study reports on the synthesis of highly oriented chromium triiodide (CrI3) magnetic inclusions inside nano/microfibres with a polyethylene oxide matrix, prepared by the electrospinning technique. The structural, microstructural and spectroscopic analysis shows uniformly dispersed CrI3 nanosized inclusions inside the fibres, presenting a C2/m monoclinic structure at room temperature, where their c-axis is perpendicular to the fibre mat plane and the ab layers are in-plane. Analysis of the magnetic properties show that the samples have a ferromagnetic-paramagnetic phase transition at ∼55-56 K, lower than that of bulk CrI3. Noticeably, a field-driven metamagnetic transition is observed below ∼45 K, from M versus H curves, when the applied magnetic field is perpendicular to the fibre mat plane, while it is strongly reduced when the field is in-plane. This anisotropic behaviour is attributed to the field-induced changes from antiferromagnetic to ferromagnetic interlayer magnetic moment alignment along the CrI3 c-axis stacked layers. These CrI3 electrospun fibres then show an efficient cost-effective route to synthesize magnetic composite fibres with highly oriented van der Walls inclusions, for spintronic applications, taking advantage of their anisotropic 2D layered materials properties.

Rapid Serological Tests for SARS-CoV-2: Diagnostic Performance of 4 Commercial Assays.

OBJECTIVE: To assess the diagnostic performance of lateral flow immunochromatographic assays (LFAs) of 4 different manufacturers to identify SARS-CoV-2 antibodies (IgM, IgG, or total), comparing them with the nucleic acid amplification test (NAAT) or the clinical defined test (definite or probable SARS-CoV-2 infection, respectively). METHODS: One hundred nineteen serum samples were randomly selected by convenience and distributed in the following groups: (1) group with SARS-CoV-2 infection (n = 82; RT-qPCR positive [definite, n = 70] and probable [n = 12]); (2) other diseases (n = 27; other viruses identified [n = 8] and SARS of other etiologies [n = 19]); and (3) healthy control group (n = 10). LFAs of 4 manufacturers were compared: MedTest Coronavirus (COVID-19) IgG/IgM (MedLevensohn, Brazil); COVID-19 IgG/IgM ECO Test (Ecodiagnóstica, Brazil); Camtech COVID-19 IgM/IgG Rapid Test Kit (Camtech Diagnostics Pte Ltd, Singapore); and 1-Step COVID-19 Test for total antibodies (Guangzhou Wondfo Biotech Co., China). RESULTS: The 4 tests studied showed high diagnostic performance characteristics for the diagnoses of definite or probable SARS-CoV-2 infection. The best measures were for the Wondfo test: sensitivity (86.59%; 95% CI: 77.26-93.11%), specificity (100%; 90.51-100%), DOR (257; 60-1,008), LR+ (33.43; 4.82-231.85), LR- (0.13; 0.08-0.23), accuracy (90.76%; 84.06-95.29%), and Matthews correlation coefficient (MCC) 0.82. Although considering only the probable SARS-CoV-2 infection (PCR-) cases, all the kits studied showed limited values. CONCLUSION: Our data demonstrate the excellent performance of LFA for the diagnoses of definite or probable SARS-CoV-2 infection. There was substantial heterogeneity in sensitivities of IgM and IgG antibodies among the different kits. LFA tests cannot replace molecular diagnostics but should be used as an additional screening tool.

Pan-cancer association of a centrosome amplification gene expression signature with genomic alterations and clinical outcome.

Centrosome amplification (CA) is a common feature of human tumours and a promising target for cancer therapy. However, CA's pan-cancer prevalence, molecular role in tumourigenesis and therapeutic value in the clinical setting are still largely unexplored. Here, we used a transcriptomic signature (CA20) to characterise the landscape of CA-associated gene expression in 9,721 tumours from The Cancer Genome Atlas (TCGA). CA20 is upregulated in cancer and associated with distinct clinical and molecular features of breast cancer, consistently with our experimental CA quantification in patient samples. Moreover, we show that CA20 upregulation is positively associated with genomic instability, alteration of specific chromosomal arms and C>T mutations, and we propose novel molecular players associated with CA in cancer. Finally, high CA20 is associated with poor prognosis and, by integrating drug sensitivity with drug perturbation profiles in cell lines, we identify candidate compounds for selectively targeting cancer cells exhibiting transcriptomic evidence for CA.

Charlson comorbidity index scores and in-hospital prognosis of patients with severe acute respiratory infections.

BACKGROUND: Respiratory infections are one of the leading causes of mortality, and comorbid conditions play a significant role in the severity and fatality of these infections. AIMS: We evaluated the Charlson Comorbidity Index (CCI) score and possible predictors of mortality in hospitalised patients with severe acute respiratory infection (SARI), aiming to test if the CCI is a valid in-hospital prognostic indicator. METHODS: Patients older than 14 years, hospitalised from 2010 to 2016 due to SARI by viral infection and who were submitted to respiratory virus testing were included. We assessed comorbidity retrospectively through chart review and calculated four variants of the CCI. RESULTS: Of the 291 patients assessed, 72.8% (n = 212) presented comorbidities, and 24% died (n = 70). The most recurrent comorbidities were chronic pulmonary disease (n = 76/212, 36%) and HIV (n = 50/212, 23.6%). The 1994 age-adjusted CCI predicted in-hospital mortality in SARI patients (P = 0.04), and HIV was associated with in-hospital mortality (P = 0.032). CONCLUSIONS: The comorbidity scores used to assess mortality risk in hospitalised patients with SARI displayed poor results, but HIV infection was considered a marker of severity. However, other factors should be considered in order to compose a score system that allows us to specifically assess the risk of mortality in patients with SARI.

Stealth Magnetoliposomes Based on Calcium-Substituted Magnesium Ferrite Nanoparticles for Curcumin Transport and Release.

Despite the promising pharmacological properties of curcumin, the transport and effective release of curcumin is still a challenge. The advances in functionalized nanocarriers for curcumin have also been motivated by the anticancer activity of this natural compound, aiming at targeted therapies. Here, stealth (aqueous and solid) magnetoliposomes containing calcium-substituted magnesium ferrite nanoparticles, CaxMg1-xFe2O4 (with x = 0.25, 0.50, 0.75) were developed as nanocarriers for curcumin. The magnetic nanoparticles exhibit superparamagnetic properties and crystalline structure, with sizes below 10 nm. The magnetoliposomes based on these nanoparticles have hydrodynamic diameters around or below 150 nm and a low polydispersity. The influence of an alternating magnetic field (AMF) on drug release over time was evaluated and compared with curcumin release by diffusion. The results suggest the potential of drug-loaded magnetoliposomes as nanocarriers that can be magnetically guided to the tumor sites and act as agents for a synergistic effect combining magnetic hyperthermia and controlled drug release.

Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers.

BACKGROUND: Breast cancer is a highly heterogeneous disease resulting in diverse clinical behaviours and therapeutic responses. DNA methylation is a major epigenetic alteration that is commonly perturbed in cancers. The aim of this study is to characterize the relationship between DNA methylation and aberrant gene expression in breast cancer. METHODS: We analysed DNA methylation and gene expression profiles from breast cancer tissue and matched normal tissue in The Cancer Genome Atlas (TCGA). Genome-wide differential methylation analysis and methylation-gene expression correlation was performed. Gene expression changes were subsequently validated in the METABRIC dataset. The Oncoscore tool was used to identify genes that had previously been associated with cancer in the literature. A subset of genes that had not previously been studied in cancer was chosen for further analysis. RESULTS: We identified 368 CpGs that were differentially methylated between tumor and normal breast tissue (Ƨ > 0.4). Hypermethylated CpGs were overrepresented in tumor tissue and were found predominantly (56%) in upstream promoter regions. Conversely, hypomethylated CpG sites were found primarily in the gene body (66%). Expression analysis revealed that 209 of the differentially-methylated CpGs were located in 169 genes that were differently expressed between normal and breast tumor tissue. Methylation-expression correlations were predominantly negative (70%) for promoter CpG sites and positive (74%) for gene body CpG sites. Among these differentially-methylated and differentially-expressed genes, we identified 7 that had not previously been studied in any form of cancer. Three of these, TDRD10, PRAC2 and TMEM132C, contained CpG sites that showed diagnostic and prognostic value in breast cancer, particularly in estrogen-receptor (ER)-positive samples. A pan-cancer analysis confirmed differential expression of these genes together with diagnostic and prognostic value of their respective CpG sites in multiple cancer types. CONCLUSION: We have identified 368 DNA methylation changes that characterize breast cancer tumor tissue, of which 209 are associated with genes that are differentially-expressed in the same samples. Novel DNA methylation markers were identified, of which cg12374721 (PRAC2), cg18081940 (TDRD10) and cg04475027 (TMEM132C) show promise as diagnostic and prognostic markers in breast cancer as well as other cancer types.

Natural product-drug conjugates for modulation of TRPV1-expressing tumors.

We report the design, synthesis and biological evaluation of natural product-drug conjugates for treatment of prostate cancers over-expressing the transient receptor potential vanilloid 1 (TRPV1) channel. We validate the relevance of TRPV1 as a target in prostate cancer patients by using a bioinformatics approach and provide proof-of-concept for the drug delivery strategy through bioorthogonal chemistry and stability assays under simulated physiological conditions. In cell-based assays, the constructs displayed modest activity. Moreover, we serendipitously discover that a stoichiometric combination of a TRPV1 agonist with a small, positively charged cytotoxic may provide new research avenues in personalized medicines for prostate cancer.

Flavivirus cross-reactivity in serological tests and Guillain-Barré syndrome in a hematopoietic stem cell transplant patient: A case report.

Serological diagnosis of flavivirus infection is a challenge, particularly in the context of a disease associated with immune response enhancement in a transplant patient, where aspects such as previous flavivirus infections may be involved with the outcome. We report a case of a pediatric patient who developed Guillain-Barré syndrome (GBS) after matched-unrelated hematopoietic stem cell transplantation (HSCT). The patient lives in a Brazilian region that is experiencing an epidemic of Zika virus (ZIKV) and dengue virus (DENV). Because an increasing number of cases of GBS, likely triggered by ZIKV infection, are being reported in Brazil, samples from the patient were tested for both ZIKV and DENV infection. Serological assays strongly suggested a recent ZIKV infection, although infection by DENV or co-infection with both viruses cannot be ruled out. The presence of anti-DENV immunoglobulin-G in donor serum led to the hypothesis that antibodies from the donor could have enhanced the severity of the ZIKV infection. This hypothesis is in agreement with the recent findings that DENV sero-cross-reactivity drives antibody-dependent enhancement of ZIKV infection. These findings highlight the need for discussion of the indication to perform previous flavivirus tests in HSCT donors, especially in areas where ZIKV and other flaviviruses co-circulate.

Magnetic liposomes based on nickel ferrite nanoparticles for biomedical applications.

Nickel ferrite nanoparticles with superparamagnetic behavior at room temperature were synthesized using a coprecipitation method. These magnetic nanoparticles were either covered with a lipid bilayer, forming dry magnetic liposomes (DMLs), or entrapped in liposomes, originating aqueous magnetoliposomes (AMLs). A new and promising method for the synthesis of DMLs is described. The presence of the lipid bilayer in DMLs was confirmed by FRET (Förster Resonance Energy Transfer) measurements between the fluorescent-labeled lipids NBD-C12-HPC (NBD acting as a donor) included in the second lipid layer and rhodamine B-DOPE (acceptor) in the first lipid layer. An average donor-acceptor distance of 3 nm was estimated. Assays of the non-specific interactions of magnetoliposomes with biological membranes (modeled using giant unilamellar vesicles, GUVs) were performed. Membrane fusion between both aqueous and dry magnetoliposomes and GUVs was confirmed by FRET, which is an important result regarding applications of these systems both as hyperthermia agents and antitumor drug nanocarriers.

Positive tip culture with Candida and negative blood culture: to treat or not to treat? A systematic review with meta-analysis.

BACKGROUND: Invasive candidiasis is a major invasive fungal infection. It has high lethality, and even higher if not treated early. There is no consensus on antifungal treatment in patients with positive catheter tip culture for Candida spp. The objective of this study was to evaluate the impact of antifungal therapy and mortality of patients with positive culture for Candida spp. in catheter tip that have negative blood culture. METHODS: The PubMed database was searched to identify articles related to Candida and catheter. Articles with adequate data were included. RESULTS: Of 1208 studies initially screened, 5 met the selection criteria. All were retrospective studies. In all, 265 patients were evaluated for outcomes 'candidemia' and 'invasive candidiasis' and 158 for the outcome 'mortality.' Antifungal therapy had no impact on the development of invasive fungal disease (Odds ratio (OR) = 1.41; 95% confidence interval (CI) = 0.56-3.52). Also there was no benefit of therapy on mortality (OR = 1.02; 95% CI = 0.54-1.95). CONCLUSION: Due to the poor quality of the studies no conclusion can be made. Randomized prospective studies are needed to better evaluate this therapeutic strategy.

Flexible Magnetocaloric Fiber Mats for Room-Temperature Energy Applications.

Currently, magnetocaloric refrigeration technologies are emerging as ecofriendly and more energy-efficient alternatives to conventional expansion-compression systems. However, major challenges remain. A particular concern is the mechanical properties of magnetocaloric materials, namely, their fatigue under cycling and difficulty in processing and shaping. Nevertheless, in the past few years, using multistimuli thermodynamic cycles with multicaloric refrigerants has led to higher heat-pumping efficiencies. To address simultaneously the challenges and develop a multicaloric material, in this work, we have prepared magnetocaloric-based flexible composite mats composed of micrometric electroactive (EA) polyvinylidene fluoride (PVDF) fibers with embedded magnetocaloric/strictive La(Fe,Si)13 particles by the simple and cost-effective electrospinning technique. The composite's structural characterization, using X-ray diffraction (XRD) analysis, Fourier transform infrared (FTIR) spectroscopy, and measurements of the local-scale piezoresponse, revealed a cubic NaZn13-type structure of the La(Fe,Si)13 phase and the formation of the dominant polar ß-phase of the PVDF polymer. The PVDF-La(Fe,Si)13 composite showed an enhancement of the longitudinal piezoelectric coefficient (effective d33) (-11.01 pm/V) compared with the single PVDF fiber matrix (-9.36 pm/V). The main magnetic properties of La(Fe,Si)13 powder were retained in the PVDF-La(Fe,Si)13 composite, including its giant magnetocaloric effect. By retaining the unique magnetic properties of La(Fe,Si)13 embedded in the electroactive piezoelectric polymer fiber mats, we have designed a flexible, easily shapeable, and multifunctional composite enabling its potential application in multicaloric heat-pumping devices and other sensing and actuating devices.

Bioinspired Cyclic Dipeptide Functionalized Nanofibers for Thermal Sensing and Energy Harvesting.

Nanostructured dipeptide self-assemblies exhibiting quantum confinement are of great interest due to their potential applications in the field of materials science as optoelectronic materials for energy harvesting devices. Cyclic dipeptides are an emerging outstanding group of ring-shaped dipeptides, which, because of multiple interactions, self-assemble in supramolecular structures with different morphologies showing quantum confinement and photoluminescence. Chiral cyclic dipeptides may also display piezoelectricity and pyroelectricity properties with potential applications in new sources of nano energy. Among those, aromatic cyclo-dipeptides containing the amino acid tryptophan are wide-band gap semiconductors displaying the high mechanical rigidity, photoluminescence and piezoelectric properties to be used in power generation. In this work, we report the fabrication of hybrid systems based on chiral cyclo-dipeptide L-Tryptophan-L-Tryptophan incorporated into biopolymer electrospun fibers. The micro/nanofibers contain self-assembled nano-spheres embedded into the polymer matrix, are wide-band gap semiconductors with 4.0 eV band gap energy, and display blue photoluminescence as well as relevant piezoelectric and pyroelectric properties with coefficients as high as 57 CN-1 and 35×10-6 Cm-2K-1, respectively. Therefore, the fabricated hybrid mats are promising systems for future thermal sensing and energy harvesting applications.

Nanostructured Electrospun Fibers with Self-Assembled Cyclo-L-Tryptophan-L-Tyrosine Dipeptide as Piezoelectric Materials and Optical Second Harmonic Generators.

The potential use of nanostructured dipeptide self-assemblies in materials science for energy harvesting devices is a highly sought-after area of research. Specifically, aromatic cyclo-dipeptides containing tryptophan have garnered attention due to their wide-bandgap semiconductor properties, high mechanical rigidity, photoluminescence, and nonlinear optical behavior. In this study, we present the development of a hybrid system comprising biopolymer electrospun fibers incorporated with the chiral cyclo-dipeptide L-Tryptophan-L-Tyrosine. The resulting nanofibers are wide-bandgap semiconductors (bandgap energy 4.0 eV) consisting of self-assembled nanotubes embedded within a polymer matrix, exhibiting intense blue photoluminescence. Moreover, the cyclo-dipeptide L-Tryptophan-L-Tyrosine incorporated into polycaprolactone nanofibers displays a strong effective second harmonic generation signal of 0.36 pm/V and shows notable piezoelectric properties with a high effective coefficient of 22 pCN-1, a piezoelectric voltage coefficient of geff=1.2 VmN-1 and a peak power density delivered by the nanofiber mat of 0.16µWcm-2. These hybrid systems hold great promise for applications in the field of nanoenergy harvesting and nanophotonics.

Data treatment methods for real-time colorimetric loop-mediated isothermal amplification reactions.

With the SARS-CoV-2 pandemic and the need for affordable and rapid mass testing, colorimetric isothermal amplification reactions such as Loop-Mediated Isothermal Amplification (LAMP) are quickly rising in importance. The technique generates data that is similar to quantitative Polymerase Chain Reaction (qPCR), but instead of an endpoint color visualization, it is possible to construct a signal over a time curve. As the number of works using time-course analysis of isothermal reactions increases, there is a need to analyze data and standardize their related treatments quantitatively. Here, we take a step forward toward this goal by evaluating different available data treatments (curve models) for amplification curves, which allows for a cycle threshold-like parameter extraction. In this study, we uncover evidence of a double sigmoid equation as the most adequate model to describe amplification data from our remote diagnostics system and discuss possibilities for similar setups. We also demonstrate the use of multimodal Gompertz regression models. Thus, this work provides advances toward standardized and unbiased data reporting of Reverse Transcription (RT) LAMP reactions, which may facilitate and quicken assay interpretation, potentially enabling the application of machine learning techniques for further optimization and classification.