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Abstract Introduction Acute myeloid leukemia (AML) remains one of the deadliest hematopoietic malignancies. A better understanding of the molecular biology governing AML may lead to improved risk stratification and facilitate the development of novel therapies. Proteins are responsible for much of the biology of cells. Several studies have examined the global proteome in bulk mononuclear cells (MNCs) from AML specimens, which are comprised a heterogenous population of cells at various stages of differentiation. Methods Given the potential impact of the nonleukemic cells on protein expression profiles, we applied an integrative proteogenomic approach utilizing next‐generation sequencing and mass spectrometry‐based proteomics to identify novel protein biomarkers in unsorted MNCs and viable leukemic blasts (VLBs) isolated from blood and bone marrow specimens obtained at the time of AML diagnosis. Results We identified significant differences in protein expression between VLBs and MNCs. Subsequent studies (N = 27) focused on proteomic profiling of VLBs that identified novel candidate biomarkers associated with mutational genotypes and clinical outcome, some of which were recapitulated in an independent cohort of patients. Using mass spectrometry, we also detected mutated protein products, some of which were predicted via in silico analyses to be potential neoantigens amenable to adoptive immunotherapy. As previously described, analyses comparing transcript and protein expression showed an overall modest correlation between mRNA and protein dataset, but enriching for genes associated with mutations significantly improved the protein–RNA correlation. Conclusion Together, the results provide insight into the biology of VLBs and demonstrate the gains derived from examining the proteome in addition to genome and transcriptome.

Abstract Immunotherapies are revolutionizing cancer care, but many patients do not achieve durable responses and immune-related adverse events are difficult to predict. Quantifying the hundreds of proteins involved in cancer immunity has the potential to provide biomarkers to monitor and predict tumor response. We previously developed robust, multiplexed quantitative assays for immunomodulatory proteins using targeted mass spectrometry, providing measurements that can be performed reproducibly and harmonized across laboratories. Here, we expand upon those efforts in presenting data from a multiplexed immuno-oncology (IO)-3 assay panel targeting 43 peptides representing 39 immune- and inflammation-related proteins. A suite of novel monoclonal antibodies was generated as assay reagents, and the fully characterized antibodies are made available as a resource to the community. The publicly available dataset contains complete characterization of the assay performance, as well as the mass spectrometer parameters and reagent information necessary for implementation of the assay. Quantification of the proteins will provide benefit to correlative studies in clinical trials, identification of new biomarkers, and improve understanding of the immune response in cancer.

Abstract Having a direct or indirect band gap can influence the potential applications of a semiconductor, for indirect band gap materials are usually not suitable for optoelectronic devices. Even though this is a fundamental property of semiconducting materials, discussed in textbooks, no unified theory exists to explain why a material has a direct or indirect band gap. Here we used an interpretable machine learning model, the multiVariate dAta eXplanation (VAX) method, to gather information from a dataset of materials extracted from the Materials Project. The dataset contains more than 10000 entries, and atomic properties such as the number of electrons, electronic affinity and orbital energies were used as features to build random forest models that successfully explain the directness of the band gaps. Our results indicate that symmetry is an important feature that dictates the target property, which is the reason why our analysis is made based on sub-groups with similar structures. These sub-groups include materials with zincblende, rocksalt, wurtzite, and perovskite structures. Besides the symmetry of the materials, the existence or not of d bands and the relative energy of atomic orbitals were found to be important in defining whether a material’s band gap is direct or indirect. In conclusion, interpretable machine learning methods such as VAX can be useful in obtaining physical interpretation from materials databases.

Abstract A wealth of proteogenomic data has been generated using cancer samples to deepen our understanding of the mechanisms of cancer and how biological networks are altered in association with somatic mutation of tumor suppressor genes, such as TP53 and PTEN. To generate functional signatures of TP53 or PTEN loss, we profiled the RNA and phosphoproteomes of the MCF10A epithelial cell line, along with its congenic TP53- or PTEN-knockout derivatives, upon perturbation with the monofunctional DNA alkylating agent methyl methanesulfonate (MMS) vs. mock treatment. To enable quantitative and reproducible mass spectrometry data generation, the cell lines were SILAC-labeled (stable isotope labeling with amino acids in cell culture), and the experimental design included label swapping and biological replicates. All data are publicly available and may be used to advance our understanding of the TP53 and PTEN tumor suppressor genes and to provide functional signatures for bioinformatic analyses of proteogenomic datasets.

Abstract Background Applying directed acyclic graph (DAG) models to proteogenomic data has been shown effective for detecting causal biomarkers of complex diseases. However, there remain unsolved challenges in DAG learning to jointly model binary clinical outcome variables and continuous biomarker measurements. Results In this paper, we propose a new tool, DAGBagM, to learn DAGs with both continuous and binary nodes. By using appropriate models, DAGBagM allows for either continuous or binary nodes to be parent or child nodes. It employs a bootstrap aggregating strategy to reduce false positives in edge inference. At the same time, the aggregation procedure provides a flexible framework to robustly incorporate prior information on edges. Conclusions Through extensive simulation experiments, we demonstrate that DAGBagM has superior performance compared to alternative strategies for modeling mixed types of nodes. In addition, DAGBagM is computationally more efficient than two competing methods. When applying DAGBagM to proteogenomic datasets from ovarian cancer studies, we identify potential protein biomarkers for platinum refractory/resistant response in ovarian cancer. DAGBagM is made available as a github repository at https://github.com/jie108/dagbagM .

Background: Patients with relapsed/refractory (R/R) chronic lymphocytic leukemia (CLL) have limited treatment options. Ceralasertib, a selective ataxia telangiectasia and Rad-3-related protein (ATR) inhibitor, demonstrated synergistic preclinical activity with a Bruton tyrosine kinase (BTK) inhibitor in TP53 - and ATM -defective CLL cells. Acalabrutinib is a selective BTK inhibitor approved for treatment of CLL. Objectives: To evaluate ceralasertib ± acalabrutinib in R/R CLL. Design: Nonrandomized, open-label phase I/II study. Methods: In arm A, patients received ceralasertib monotherapy 160 mg twice daily (BID) continuously (cohort 1) or 2 weeks on/2 weeks off (cohort 2). In arm B, patients received acalabrutinib 100 mg BID continuously (cycle 1), followed by combination treatment with ceralasertib 160 mg BID 1 week on/3 weeks off from cycle 2. Co-primary objectives were safety and pharmacokinetics. Efficacy was a secondary objective. Results: Eleven patients were treated [arm A, n = 8 (cohort 1, n = 5; cohort 2, n = 3); arm B, n = 3 (acalabrutinib plus ceralasertib, n = 2; acalabrutinib only, n = 1)]. Median duration of exposure was 3.5 and 7.2 months for ceralasertib in arms A and B, respectively, and 15.9 months for acalabrutinib in arm B. Most common grade ⩾3 treatment-emergent adverse events (TEAEs) in arm A were anemia (75%) and thrombocytopenia (63%), with four dose-limiting toxicities (DLTs) of grade 4 thrombocytopenia. No grade ⩾3 TEAEs or DLTs occurred in arm B. Ceralasertib plasma concentrations were similar when administered as monotherapy or in combination. At median follow-up of 15.1 months in arm A, no responses were observed, median progression-free survival (PFS) was 3.8 months, and median overall survival (OS) was 16.9 months. At median follow-up of 17.2 months in arm B, overall response rate was 100%, and median PFS and OS were not reached. Conclusion: Ceralasertib alone showed limited clinical benefit. Acalabrutinib plus ceralasertib was tolerable with preliminary activity in patients with R/R CLL, though findings are inconclusive due to small sample size. Registration: NCT03328273

O aumento na expectativa de vida dos cães em resposta à evolução da medicina veterinária com relação à prevenção e tratamento de doenças é notável. Assim também, é evidente a ascensão de patologias que acometem animais com idade avançada, como o caso das neoplasias mamárias, que abala principalmente fêmeas, idosas, não castradas ou castradas após diversos ciclos estrais, sem predisposição racial. Esta pesquisa tem como objetivo levantar dados a partir da análise de dados clínicos e laudos histopatológicos de cadelas atendidas em Dourados, Mato Grosso com tumor mamário. Neste levantamento, observou-se que de 15 cadelas com neoplasia mamária, 87% apresentaram neoplasia maligna enquanto 13% apresentaram neoplasia benigna. As mamas abdominais caudais (M4) foram as mais acometidas. Os tamanhos tumorais variaram entre um e cinco centímetro de diâmetro, sendo que os tumores com tamanho de até três centímetros foram os mais recorrentes. Os dois únicos tumores benignos mediram 1,5 cm. Contudo, conclui-se que as mamas abdominais caudais (M4) foram as mais acometidas com neoplasias mamárias. Neoformações malignas são as mais comuns e neoplasias com conformações benignas possuem tamanhos menores.

IntroductionImmunotherapy is an effective treatment for a subset of cancer patients, and expanding the benefits of immunotherapy to all cancer patients will require predictive biomarkers of response and immune-related adverse events (irAEs). To support correlative studies in immunotherapy clinical trials, we are developing highly validated assays for quantifying immunomodulatory proteins in human biospecimens.MethodsHere, we developed a panel of novel monoclonal antibodies and incorporated them into a novel, multiplexed, immuno-multiple reaction monitoring mass spectrometry (MRM-MS)-based proteomic assay targeting 49 proteotypic peptides representing 43 immunomodulatory proteins.Results and discussionThe multiplex assay was validated in human tissue and plasma matrices, where the linearity of quantification was >3 orders of magnitude with median interday CVs of 8.7% (tissue) and 10.1% (plasma). Proof-of-principle demonstration of the assay was conducted in plasma samples collected in clinical trials from lymphoma patients receiving an immune checkpoint inhibitor. We provide the assays and novel monoclonal antibodies as a publicly available resource for the biomedical community.

Early diagnosis of cattle diseases such as mastitis caused by Staphylococcus aureus (S. aureus) can be made effective if on-site detection methods with portable instruments are available. In this work, we fabricated immunosensors based on a layer-by-layer (LbL) film of chitosan and carbon nanotubes coated with a layer of antibodies to detect S. aureus. Using electrical and electrochemical impedance spectroscopies, detection was possible in buffer solutions and in milk with limits of detection which could be as low as 2.6 CFU/mL for milk, sufficient to detect mastitis at early stages. This high sensitivity is ascribed to the specific interactions involving the antibodies, as demonstrated with polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). The selectivity of the immunosensor was verified by distinguishing S. aureus-containing samples from possible interferents found in milk, for which the interactive document mapping (IDMAP) was employed. Because the interferents affected the spectra, in spite of this distinguishability, we treated the data with a machine learning technique with decision tree models. A multidimensional calibration space was then obtained with rules that permit interpretability and predictability in detecting S. aureus in matrices with high variability as in milk.

As governments take measures against COVID-19, the epidemic situation is expected to improve, but public sentiment is likely to fluctuate during this process, potentially influencing the best course of action. Social media has become a prevalent way for the public to express emotions and opinions in recent times. So that, the sentiment analysis on top of it may detect and provide valuable evidence of public attitude and help governments subsequent formulation of measures and policies. We present Senti-COVID19, an interactive visual analytic system for reflecting and analyzing public sentiment and detecting sentiment fluctuation triggers on social media. Senti-COVID19 adopts lexicon-based sentiment analysis to divulge the public opinion to COVID-19 events, employing libraries to extract keywords and statistics for providing detailed information. In addition, it offers visualizations for presenting the analysis, allowing users to quickly discover relevant information. Our results show that Senti-COVID19 can be used effectively to analyze sentiment from social media text, allowing users to explore derived data and identify insights from the collected tweets.

Immunotherapies are revolutionizing cancer care, producing durable responses and potentially cures in a subset of patients. However, response rates are low for most tumors, grade 3/4 toxicities are not uncommon, and our current understanding of tumor immunobiology is incomplete. While hundreds of immunomodulatory proteins in the tumor microenvironment shape the anti-tumor response, few of them can be reliably quantified. To address this need, we developed a multiplex panel of targeted proteomic assays targeting 52 peptides representing 46 proteins using peptide immunoaffinity enrichment coupled to multiple reaction monitoring-mass spectrometry. We validated the assays in tissue and plasma matrices, where performance figures of merit showed over 3 orders of dynamic range and median inter-day CVs of 5.2% (tissue) and 21% (plasma). A feasibility study in clinical biospecimens showed detection of 48/52 peptides in frozen tissue and 38/52 peptides in plasma. The assays are publicly available as a resource for the research community.

Knowing how to construct text-based Search Queries (SQs) for use in Search Engines (SEs) such as Google or Wikipedia has become a fundamental skill. Though much data are available through such SEs, most structured datasets live outside their scope. Visualization tools aid in this limitation, but no such tools come close to the sheer amount of information available through general-purpose SEs. To fill this gap, this paper presents Q4EDA, a novel framework that converts users’ visual selection queries executed on top of time series visual representations, providing valid and stable SQs to be used in general-purpose SEs and suggestions of related information. The usefulness of Q4EDA is presented and validated by users through an application linking a Gapminder’s line-chart replica with a SE populated with Wikipedia documents, showing how Q4EDA supports and enhances exploratory analysis of United Nations world indicators. Despite some limitations, Q4EDA is unique in its proposal and represents a real advance towards providing solutions for querying textual information based on user interactions with visual representations.

Summary: A primary goal of the US National Cancer Institute's Ras initiative at the Frederick National Laboratory for Cancer Research is to develop methods to quantify RAS signaling to facilitate development of novel cancer therapeutics. We use targeted proteomics technologies to develop a community resource consisting of 256 validated multiple reaction monitoring (MRM)-based, multiplexed assays for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. As proof of concept, we quantify the response of melanoma (A375 and SK-MEL-2) and colorectal cancer (HCT-116 and HT-29) cell lines to BRAF inhibition by PLX4720. These assays replace over 60 western blots with quantitative mass-spectrometry-based assays of high molecular specificity and quantitative precision, showing the value of these methods for pharmacodynamic measurements and mechanism-of-action studies. Methods, fit-for-purpose validation, and results are publicly available as a resource for the community at assays.cancer.gov. Motivation: A lack of quantitative, multiplexable assays for phosphosignaling limits comprehensive investigation of aberrant signaling in cancer and evaluation of novel treatments. To alleviate this limitation, we sought to develop assays by using targeted mass spectrometry for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. The resulting assays provide a resource for replacing over 60 western blots in examining cancer signaling and tumor biology with high molecular specificity and quantitative rigor.

Summary: Many gene products exhibit great structural heterogeneity because of an array of modifications. These modifications are not directly encoded in the genomic template but often affect the functionality of proteins. Protein glycosylation plays a vital role in proper protein functions. However, the analysis of glycoproteins has been challenging compared with other protein modifications, such as phosphorylation. Here, we perform an integrated proteomic and glycoproteomic analysis of 83 prospectively collected high-grade serous ovarian carcinoma (HGSC) and 23 non-tumor tissues. Integration of the expression data from global proteomics and glycoproteomics reveals tumor-specific glycosylation, uncovers different glycosylation associated with three tumor clusters, and identifies glycosylation enzymes that were correlated with the altered glycosylation. In addition to providing a valuable resource, these results provide insights into the potential roles of glycosylation in the pathogenesis of HGSC, with the possibility of distinguishing pathological outcomes of ovarian tumors from non-tumors, as well as classifying tumor clusters.

Early detection of Primary Immunodeficiencies Disorders (PIDDs) is of paramount importance for effective treatment and disease management. Many PIDDs would be strong candidates for newborn screening (NBS) if robust screening methods could identify patients from dried blood spots (DBS) during the neonatal period. As majority of congenital PIDDs result in the reduction or absence of specific proteins, direct quantification of these target proteins represents an attractive potential screening tool. Unfortunately, detection is often limited by the extremely low protein concentrations in blood cells and limited blood volume present in DBS. We have recently developed a robust novel method for quantification of low abundance proteins in DBS for PIDDs using peptide immunoaffinity enrichment coupled to selected reaction monitoring (immuno-SRM). Here, we further generated a multiplexed Immuno-SRM panel for simultaneous screening of eight signature peptides representing five PIDD-specific and two cell-type specific proteins from DBS. In samples from 28 PIDD patients including two carriers, representing X-Linked Agammaglobulinemia (XLA), Wiskott-Aldrich Syndrome (WAS), X-Linked Chronic Granulomatous Disease (XL-CGD), DOCK8 Deficiency and ADA deficiency, peptides representing each disease are significantly reduced relative to normal controls and patient identification had excellent agreement with clinical and molecular diagnosis. Also included in the multiplex panel are cell specific markers for platelets (CD42) and Natural Killer Cells (CD56). In patients with WAS, CD42 levels were found to be significantly reduced consistent with characteristic thrombocytopenia. A patient with WAS analyzed before and after bone marrow transplant showed normalized WAS protein and platelet CD42 after treatment highlighting the ability of immuno-SRM to monitor the effects of PIDD treatment. The assay was readily reproduced in two separate laboratories with similar analytical performance and complete agreement in patient diagnosis demonstrating the effective standardized methods. A high-throughput Immuno-SRM method screens PIDD-specific peptides in a 2.5-min runtime meeting high volume NBS workflow requirements was also demonstrated in this report. This high-throughput method returned identical results to the standard Immuno-SRM PIDD panel. Immuno-SRM peptide analysis represents a robust potential clinical diagnostic for identifying and studying PIDD patients from easily collected and shipped DBS and supports a significant potential for early PIDD diagnosis through newborn screening.

With the recent increase in the use of sea transportation, the importance of maritime surveillance for detecting unusual vessel behavior related to several illegal activities has also risen. Unfortunately, the data collected by surveillance systems are often incomplete, creating a need for the data gaps to be filled using techniques such as interpolation methods. However, such approaches do not decrease the uncertainty of ship activities. Depending on the frequency of the data generated, they may even confuse operators, inducing errors when evaluating ship activities and tagging them as unusual. Using domain knowledge to classify activities as anomalous is essential in the maritime navigation environment since there is a well-known lack of labeled data in this domain. In an area where identifying anomalous trips is a challenging task using solely automatic approaches, we use visual analytics to bridge this gap by utilizing users’ reasoning and perception abilities. In this work, we propose a visual analytics tool that uses spatial segmentation to divide trips into subtrajectories and score them. These scores are displayed in a tabular visualization where users can rank trips by segment to find local anomalies. The amount of interpolation in subtrajectories is displayed together with scores so that users can use both their insight and the trip displayed on the map to determine if the score is reliable.

Graph visualization has been successfully applied in a wide range of problems and applications. Although different approaches are available to create visual representations, most of them suffer from clutter when faced with many nodes and/or edges. Among the techniques that address this problem, edge bundling has attained relative success in improving node-link layouts by bending and aggregating edges. Despite their success, most approaches perform the bundling based only on visual space information. There is no explicit connection between the produced bundled visual representation and the underlying data (edges or vertices attributes). In this paper, we present a novel edge bundling technique, called Similarity-Driven Edge Bundling (SDEB), to address this issue. Our method creates a similarity hierarchy based on a multilevel partition of the data, grouping edges considering the similarity between nodes to guide the bundling. The novel features introduced by SDEB are explored in different application scenarios, from dynamic graph visualization to multilevel exploration. Our results attest that SDEB produces layouts that consistently follow the similarity relationships found in the graph data, resulting in semantically richer presentations that are less cluttered than the state-of-the-art.

Deep Neural Networks are known for impressive results in a wide range of applications, being responsible for many advances in technology over the past few years. However, debugging and understanding neural networks models’ inner workings is a complex task, as there are several parameters and variables involved in every decision. Multidimensional projection techniques have been successfully adopted to display neural network hidden layer outputs in an explainable manner, but comparing different outputs often means overlapping projections or observing them side-by-side, presenting hurdles for users in properly conveying data flow. In this paper, we introduce a novel approach for comparing projections obtained from multiple stages in a neural network model and visualizing differences in data perception. Changes among projections are transformed into trajectories that, in turn, generate vector fields used to represent the general flow of information. This representation can then be used to create layouts that highlight new information about abstract structures identified by neural networks.

Background: Primary immunodeficiency disorders (PIDD) comprise a group of life-threatening congenital diseases characterized by absent or impaired immune responses. Despite the fact that effective, curative treatments are available with optimal clinical outcomes when diagnosed early, newborn screening does not exist for the majority of these diseases due to the lack of detectable, specific biomarkers or validated methods for population-based screening. Peptide immunoaffinity enrichment coupled with selected reaction monitoring mass spectrometry (immuno-SRM) is a sensitive proteomic assay, involving antibody-mediated peptide capture, that allows for concurrent quantification of multiple analytes. This assay has promise for use in potential newborn screening of PIDDs that lead to diminished or absent target proteins in the majority of cases.Objective: To determine and evaluate if a multiplex assay based on immuno-SRM is able to reliably and precisely distinguish affected patients with X-linked agammaglobulinemia (XLA), Wiskott-Aldrich Syndrome (WAS), and CD3ϵ-associated severe combined immunodeficiency (SCID) from one another and from unaffected normal control dried blood spot (DBS) samples.Methods: We performed a blinded, multiplexed analysis of proteolytically-generated peptides from WASp, BTK, and CD3ϵ (for WAS, XLA, and SCID, respectively) in DBS samples from 42 PIDD patients, 40 normal adult controls, and 62 normal newborns. The peptide ATPase copper transporting protein (ATP7B) 1056 was simultaneously monitored for quality assurance purposes.Results: The immuno-SRM assays reliably quantified the target peptides in DBS and accurately distinguished affected patients from normal controls. Analysis of signature peptides found statistically significant reduction or absence of peptide levels in affected patients compared to control groups in each case (WASp and BTK: p = 0.0001, SCID: p = 0.05). Intra and inter-assay precision ranged from 11 to 22% and 11 to 43% respectively; linearity (1.39–2000 fmol peptide), and stability (≤ 0.09% difference in 72 h) showed high precision for the multiplexed assay. Inter-laboratory assay comparison showed high concordance for measured peptide concentrations, with R2 linearity ≥ 0.97 for the WASp 274, CD3ϵ 197, BTK 407, and ATP7B 1056 peptides.Conclusion: Immuno-SRM-based quantification of proteotypic peptides from WASp, BTK, and CD3ϵ in DBS distinguishes relevant PIDD cases from one another and from controls, raising the possibility of employing this approach for large-scale multiplexed newborn screening of selective PIDDs.

O presente trabalho avaliou diferenças de patoge-nicidade entre 19 cepas de Brachyspira pilosicoli isoladas de casos de diarréia em suínos no Estado do Rio Grande do Sul, usando um modelo de infecção oral de pintos de um dia. Os animais foram inoculados com uma suspensão de bactérias vivas, 21 dias após foram sacrificados e os cecos examinados por histopatologia através da hematoxilina-eosina, coloração pela prata e a imuno-histoquímica usando um anticorpo policlonal anti-Brachyspira pilosicoli. Com o uso das técnicas da prata e da imuno-histoquímica, respectivamente, 21,59% e 70,96% dos pintos mostraram colonização do epitélio do ceco por B. pilosicoli. Houve diferenças no tipo de colonização, ocorrendo aderência contínua, focal ou presença de bactérias livres na luz intestinal. A imuno-histoquímica foi considerada superior para a avaliação da colonização intestinal, pois foi capaz de detectar 49,37% de animais colonizados a mais do que com o uso da coloração pela prata. Em três cepas foram observadas figuras alongadas dentro do citoplasma das células epiteliais cecais de aves inoculadas.The study assessed differences of pathogenicity among 19 strains of Brachyspira pilosicoli isolated from cases of diarrhea in swine in the State of Rio Grande do Sul, Brazil, using an one-day-old chick model. The chicken inoculated with live bacterial cultures were submitted to euthanasia 21 days later, and the cecum was examined histologically using hematoxylin-eosin, silver staining and immunohistochemistry with a polyclonal antibody anti-Brachyspira pilosicoli. With silver staining and immunohistochemistry, respectively, 21.59% and 70.96% of the chicken showed colonization of the cecal epithelium with B. pilosicoli. Differences in the type of colonization characterized by continuous adhesion, focal adhesion or free bacteria in the intestinal lumen were observed. Immunohistochemistry was more efficient to assess intestinal colonization, because 49.37% more colonized chicken could be detected with silver staining. With three strains, elongated figures inside the cytoplasm of epithelial cecal cells in the inoculated chicken were observed.

Neste artigo relatamos uma investigação sobre a formação dos conceitos algébricos iniciais realizada com estudantes de uma classe de 7ª série de uma escola estadual de ensino fundamental e médio. Como suporte teórico para esta investigação, foi empregada a teoria de formação de conceitos elaborada por Lev Semenovich Vygotsky e descrita no seu livro Pensamento e Linguagem.

Protein folding occurs in a very high dimensional phase space with an exponentially large number of states, and according to the energy landscape theory it exhibits a topology resembling a funnel. In this statistical approach, the folding mechanism is unveiled by describing the local minima in an effective one-dimensional representation. Other approaches based on potential energy landscapes address the hierarchical structure of local energy minima through disconnectivity graphs. In this paper, we introduce a metric to describe the distance between any two conformations, which also allows us to go beyond the one-dimensional representation and visualize the folding funnel in 2D and 3D. In this way it is possible to assess the folding process in detail, e.g., by identifying the connectivity between conformations and establishing the paths to reach the native state, in addition to regions where trapping may occur. Unlike the disconnectivity maps method, which is based on the kinetic connections between states, our methodology is based on structural similarities inferred from the new metric. The method was developed in a 27-mer protein lattice model, folded into a 3×3×3 cube. Five sequences were studied and distinct funnels were generated in an analysis restricted to conformations from the transition-state to the native configuration. Consistent with the expected results from the energy landscape theory, folding routes can be visualized to probe different regions of the phase space, as well as determine the difficulty in folding of the distinct sequences. Changes in the landscape due to mutations were visualized, with the comparison between wild and mutated local minima in a single map, which serves to identify different trapping regions. The extension of this approach to more realistic models and its use in combination with other approaches are discussed.