Grouping annotating and filtering history information in VKB

History mechanisms available in hypertext systems allow users access to past interactions with the system and help users incorporate those interactions into the current context. The history information can be useful to both the system and the user. The Visual Knowledge Builder (VKB) creates spatial hypertexts - visual workspaces for collecting, organizing, and sharing. It is based on prior work on VIKI. VKB records all edit events and presents them in the form of a "navigable history" as end-users work within an information workspace. My thesis explores attaching user interpretations of history via the grouping and annotation of edit events. Annotations can take the form of a plain text statement or one or more attribute/value pairs attached to individual events or group of events in the list. Moreover, I explore the value of history event filtering, limiting the edits and groups presented to those that match user descriptions. My contribution in this thesis is the addition of mechanisms whereby users can cope with larger history records in VKB via the process of grouping, annotating and filtering history information

IL-7R-mediated signaling in T-cell acute lymphoblastic leukemia: an update

© 2018 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/BY-NC-ND/4.0/)Interleukin 7 (IL-7) and its receptor (IL-7R, a heterodimer of IL-7Rα and γc) are essential for normal lymphoid development. In their absence, severe combined immunodeficiency occurs. By contrast, excessive IL-7/IL-7R-mediated signaling can drive lymphoid leukemia development, disease acceleration and resistance to chemotherapy. IL-7 and IL-7R activate three main pathways: STAT5, PI3K/Akt/mTOR and MEK/Erk, ultimately leading to the promotion of leukemia cell viability, cell cycle progression and growth. However, the contribution of each of these pathways towards particular functional outcomes is still not completely known and appears to differ between normal and malignant states. For example, IL-7 upregulates Bcl-2 in a PI3K/Akt/mTOR-dependent and STAT5-independent manner in T-ALL cells. This is a 'symmetric image' of what apparently happens in normal lymphoid cells, where PI3K/Akt/mTOR does not impact on Bcl-2 and regulates proliferation rather than survival. In this review, we provide an updated summary of the knowledge on IL-7/IL-7R-mediated signaling in the context of cancer, focusing mainly on T-cell acute lymphoblastic leukemia, where this axis has been more extensively studied.Publication costs were supported by LISBOA-01-0145-FEDER-007391, project cofunded by FEDER, through POR Lisboa2020 Programa Operacional Regional de Lisboa, PORTUGAL 2020, and Fundação para a Ciência e a Tecnologia (FCT, Portugal). The research work in JTB's lab related to the present review was supported by the grants FAPESP/20015/2014 and PTDC/MEC-HEM/31588/2017, from FCT; and by the consolidator grant ERC CoG-648455 from the European Research Council, under the European Union's Horizon 2020 research and innovation programme. JTB is an FCT investigator (consolidator). MLO is a LisbonBioMed PhD student and received a fellowship from FCT. PA received a PhD fellowship from the EU Marie Sklodowska-Curie ITN Protein Conjugates.info:eu-repo/semantics/publishedVersio

Machine intelligence decrypts β-lapachone as an allosteric 5-lipoxygenase inhibitor.

Using machine learning, targets were identified for β-lapachone. Resorting to biochemical assays, β-lapachone was validated as a potent, ligand efficient, allosteric and reversible modulator of 5-lipoxygenase (5-LO). Moreover, we provide a rationale for 5-LO modulation and show that inhibition of 5-LO is relevant for the anticancer activity of β-lapachone. This work demonstrates the power of machine intelligence to deconvolute complex phenotypes, as an alternative and/or complement to chemoproteomics and as a viable general approach for systems pharmacology studies

A fully human anti-IL-7Rα antibody promotes antitumor activity against T-cell acute lymphoblastic leukemia.

T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological cancer for which treatment options often result in incomplete therapeutic efficacy and long-term side-effects. Interleukin 7 (IL-7) and its receptor IL-7Rα promote T-ALL development and mutational activation of IL-7Rα associates with very high risk in relapsed disease. Using combinatorial phage-display libraries and antibody reformatting, we generated a fully human IgG1 monoclonal antibody (named B12) against both wild-type and mutant human IL-7Rα, predicted to form a stable complex with IL-7Rα at a different site from IL-7. B12 impairs IL-7/IL-7R-mediated signaling, sensitizes T-ALL cells to treatment with dexamethasone and can induce cell death per se. The antibody also promotes antibody-dependent natural killer-mediated leukemia cytotoxicity in vitro and delays T-cell leukemia development in vivo, reducing tumor burden and promoting mouse survival. B12 is rapidly internalized and traffics to the lysosome, rendering it an attractive vehicle for targeted intracellular delivery of cytotoxic cargo. Consequently, we engineered a B12-MMAE antibody-drug conjugate and provide proof-of-concept evidence that it has increased leukemia cell killing abilities as compared with the naked antibody. Our studies serve as a stepping stone for the development of novel targeted therapies in T-ALL and other diseases where IL-7Rα has a pathological role

Chemoselective Installation of Amine Bonds on Proteins through Aza-Michael Ligation.

Chemical modification of proteins is essential for a variety of important diagnostic and therapeutic applications. Many strategies developed to date lack chemo- and regioselectivity as well as result in non-native linkages that may suffer from instability in vivo and adversely affect the protein's structure and function. We describe here the reaction of N-nucleophiles with the amino acid dehydroalanine (Dha) in a protein context. When Dha is chemically installed in proteins, the addition of a wide-range N-nucleophiles enables the rapid formation of amine linkages (secondary and tertiary) in a chemoselective manner under mild, biocompatible conditions. These new linkages are stable at a wide range of pH values (pH 2.8 to 12.8), under reducing conditions (biological thiols such as glutathione) and in human plasma. This method is demonstrated for three proteins and is shown to be fully compatible with disulfide bridges, as evidenced by the selective modification of recombinant albumin that displays 17 structurally relevant disulfides. The practicability and utility of our approach is further demonstrated by the construction of a chemically modified C2A domain of Synaptotagmin-I protein that retains its ability to preferentially bind to apoptotic cells at a level comparable to the native protein. Importantly, the method was useful for building a homogeneous antibody-drug conjugate with a precise drug-to-antibody ratio of 2. The kinase inhibitor crizotinib was directly conjugated to Dha through its piperidine motif, and its antibody-mediated intracellular delivery results in 10-fold improvement of its cancer cell-killing efficacy. The simplicity and exquisite site-selectivity of the aza-Michael ligation described herein allows the construction of stable secondary and tertiary amine-linked protein conjugates without affecting the structure and function of biologically relevant proteins

Antibody based therapy for T-cell acute lymphoblastic leukemia : targeting IL-7 receptor

A Leucemia Linfoblástica Aguda de células T (LLA-T) é um cancro hematológico agressivo, para o qual a abordagem terapêutica atual consiste em regimes intensivos de quimioterapia multiagente, frequentemente levando a efeitos secundários a longo prazo que afetam a qualidade de vida dos doentes. Apesar do sucesso terapêutico em casos pediátricos, as recidivas ainda ocorrem em 10-20% dos casos, e o prognóstico é consideravelmente pior em adultos. Assim, existe uma necessidade de encontrar novos tratamentos mais seletivos e como tal, menos tóxicos, bem como de melhorar os resultados associados ao tratamento de LLA-T. A interleucina 7 (IL-7) e seu receptor, IL-7Rα, promovem o desenvolvimento de leucemia na maioria dos pacientes com LLA-T e à ativação mutacional de IL-7Rα, que ocorre em cerca de 10% dos casos, associa-se um elevado risco de recidiva. Utilizando bibliotecas de apresentação de fagos com combinações de scFv e reformatação de anticorpos, conseguimos produzir um anticorpo monoclonal IgG1, totalmente humano contra o IL-7Rα humano (denominado B12). B12 não apresenta reatividade cruzada contra o receptor de murganho e reconhece tanto a forma wild type como as formas mutantes de IL-7Rα, expressas naturalmente em linhas celulares de LLA-T e amostras de pacientes, bem como em células Ba/F3 transduzidas de forma estável com IL-7Rα humano. Simulações de dinâmica molecular sugerem que B12 forma um complexo estável com IL-7Rα num local diferente da IL-7. No entanto, B12 inibe a sinalização mediada por IL-7/IL-7R e induz morte celular per se em algumas linhas celulares de T-ALL, dependentes do eixo de sinalização IL-7/IL-7R (por exemplo, células TAIL7, dependentes de IL-7, e células DND4.1, que possuem IL7R mutante) e amostras de pacientes. Utilizando amostras de xenoenxertos derivados de doentes (PDX), células HPB-ALL e células D1 que sobrexpressam uma forma mutada para ganho de função de IL-7Rα, mostrámos, in vitro, que o anticorpo promove citotoxicidade mediada por células NK dependente deste e, in vivo, atrasos no desenvolvimento de leucemia de células T, reduzindo a carga tumoral e promovendo a sobrevivência do murganho. Além disso, B12 coopera com dexametasona na promoção da morte tanto de células HPB-ALL, resistentes a este fármaco, como de uma amostra de PDX, sensível ao mesmo. De notar, B12 é rapidamente internalizado através de poços revestidos de clatrina para o endossoma inicial, eventualmente traficando para o lisossoma - um efeito que é ligeiramente acelerado na presença de IL-7. Essas características tornam a B12 um veículo atraente para administração intracelular direcionada de uma carga altamente citotóxica. Como tal, desenvolvemos uma molécula de anticorpo conjugada com droga (ADC), B12-mono-metil-auristatina E (MMAE), na qual a conjugação sítio-específica de B12 foi realizada reduzindo-se as ligações dissulfeto inter-cadeias e reagindo o grupo tiol das cisteínas livres com um aceitador de Michael (derivado carbonil acrílico) ligado a um ligante clivável (valina-citrulina) e ao fármaco (MMAE). Testado contra diferentes linhagens celulares, células primárias de pacientes e amostras de PDX, o ADC B12-MMAE demonstra aumento da capacidade matar células leucémicas, in vitro, em comparação com o anticorpo não conjugado. No geral, este trabalho serve como ponto de partida para o desenvolvimento de novas estratégias terapêuticas direcionadas contra LLA-T e outras doenças, nas quais o IL-7Rα desempenha um papel patológico.T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological cancer that is treated with intensive multi-agent chemotherapy, often leading to long-term side-effects impacting the quality of life of survivors. Despite the therapeutic success in children, relapses still occur in 10-20% of the cases, and adults face a considerably poorer prognosis. Novel, more selective treatments that contribute to reducing toxicities and improving outcome are thus in need. Interleukin 7 (IL-7) and its receptor IL-7Rα promote leukemia development in a majority of T-ALL patients and mutational activation of IL-7Rα, which occurs in around 10% of the cases, associates with very high risk in relapsed disease. Using combinatorial scFv phage display libraries and antibody reformatting we have now generated a fully human IgG1 monoclonal antibody (named B12) against human IL-7Rα. B12 does not display cross-reactivity against the mouse receptor and recognizes both wild type and mutant forms of IL-7Rα naturally expressed in T-ALL cell lines and patient samples, as well as in Ba/F3 cells stably transduced with human, but not mouse, IL-7Rα. Interestingly, molecular dynamics simulations suggest that B12 forms a stable complex with IL-7Rα at a different site from IL-7. Nonetheless, B12 inhibits IL-7/IL-7R-mediated signaling and induces cell death per se in at least some IL-7/IL-7Rreliant T-ALL cell lines (e.g. IL-7-dependent TAIL7 cells and mutant IL7R DND4.1 cells) and patient samples. Using patient-derived xenograft (PDX) samples, HPBALL cells and D1 cells overexpressing a mutated gain-of-function form of IL-7Rα, we show that the antibody also promotes antibody-dependent NK-mediated leukemia cytotoxicity in vitro and delays T-cell leukemia development In vivo, reducing tumor burden and promoting mouse survival. Moreover, B12 cooperates with dexamethasone in promoting the death of both dexamethasone-resistant HPBALL cells and a dexamethasone-sensitive PDX sample. Notably, B12 is rapidly internalized via clathrin-coated pits to the early endosome, eventually trafficking to the lysosome - an effect that is slightly accelerated in the presence of IL-7. These characteristics render B12 an attractive vehicle for targeted intracellular delivery of a highly cytotoxic warhead. As such, we engineered a B12- mono-methyl auristatin E (MMAE) antibody-drug conjugate (ADC) in which sitespecific conjugation of B12 was carried out by reducing inter-chain disulfide bonds and reacting the thiol group of the free cysteines with a Michael acceptor (carbonyl acrylic derivate) linked to a cleavable linker (valine-citrulline) and the drug (MMAE). Tested against different cell lines, primary patient cells and PDX samples, B12-MMAE ADC demonstrates increased leukemia cell killing ability in vitro as compared to the naked antibody. Altogether, our studies serve as a stepping stone towards the development of novel targeted therapeutic strategies in T-ALL and other diseases where IL-7Rα was shown to play a pathological role

Fuzzy Programming With Quadratic Membership Functions For Multi-objective Transportation Problem

In the present paper, a fuzzy programming model with quadratic membership functions has been developed for the solution of a Multi-Objective Transportation problem. In literature, several fuzzy programming approaches exist with various types of membership functions such as linear, exponential, hyperbolic etc. These membership functions are defined, by taking the lower and upper values of the objective functions into account.  In some cases, these methods fail to obtain an integer compromise optimal solution. In the present method, two coefficients of the quadratic membership functions are determined by the lower and upper values of the objective functions. The other coefficient is taken as a variable in the fuzzy programming approach. This means that the membership curve is fixed at the two end points and set free in between. Application of the method on numerical examples proved that the approach could generate integer compromise optimal solutions.