Studying social network sites with the combination of traditional social science and computational approaches

Social Network Sites (SNSs) are fundamentally changing the way humans connect, communicate and relate to one another and have attracted a considerable amount of research attention. In general, two distinct research approaches have been followed in the pursuit of results in this research area. First, established traditional social science methods, such as surveys and interviews, have been extensively used for inquiry-based research on SNSs. More recently, however, the advent of Application Programming Interfaces (APIs) has enabled data-centric approaches that have culminated in theory-free “big data” studies. Both of these approaches have advantages, disadvantages and limitations that need to be considered in SNS studies. The objective of this dissertation is to demonstrate how a suitable combination of these two approaches can lead to a better understanding of user behavior on SNSs and can enhance the design of such systems. To this end, I present two two-part studies that act as four pieces of evidence in support of this objective. In particular, these studies investigate whether a combination of survey and API-collected data can provide additional value and insights when a) predicting Facebook motivations, b) understanding social media selection, c) understanding patterns of communication on Facebook, and d) predicting and modeling tie strength, compared to what can be gained by following a traditional social science or a computational approach in isolation. I then discuss how the findings from these studies contribute to our understanding of online behavior both at the individual user level, e.g. how people navigate the SNS ecosystem, and at the level of dyadic relationships, e.g. how tie strength and interpersonal trust affect patterns of dyadic communication. Furthermore, I describe specific implications for SNS designers and researchers that arise from this work. For example, the work presented has theoretical implications for the Uses and Gratifications (U&G) framework and for the application of Rational Choice Theory (RCT) in the context of SNS interactions, and design implications such as enhancing SNS users’ privacy and convenience by supporting reciprocity of interactions. I also explain how the results of the conducted studies demonstrate the added value of combining traditional social science and computational methods for the study of SNSs, and, finally, I provide reflections on the strengths and limitations of the overall research approach that can be of use to similar research efforts.As Redes Sociais (SNSs - Social Network Sites) estão a mudar de form fundamental a maneira como os seres humanos estabelecem ligações entre si, como comunicam e como relacionam-se uns com os outros, tendo atraído uma considerável quantidade de atenção investigativa. Em geral, duas abordagens de investigação distintas foram seguidas na procura de resultados nesta área de investigação. Em primeiro lugar, os já estabelecidos métodos tradicionais das ciências sociais, tais como inquéritos e entrevistas foram amplamente utilizados na investigação baseada em SNSs. Contudo, o surgimento mais recente das Interfaces de Programação de Aplicações (APIs - Application Programming Interfaces) tem permitido abordagens centradas em dados que têm culminado em estudos de "dados extensos", livres de teoria. Ambas estas abordagens têm vantagens, desvantagens e limitações que precisam de ser consideradas nos estudos de SNS. O objectivo desta dissertação é demonstrar como uma combinação adequada destas duas abordagens pode levar a uma melhor compreensão do comportamento do utilizador em SNSs e pode melhorar a concepção de tais sistemas. Para esse efeito, apresento dois estudos, em duas partes, que funcionam como quatro peças de prova em apoio a este objectivo. Estes estudos investigam, em particular, se uma combinação de dados recolhidos através de inquéritos e API pode fornecer valor adicional e conhecimentos ao a) prever as motivações do Facebook, b) compreender a selecção dos meios de comunicação social, c) compreender os padrões de comunicação no Facebook, e d) prever e modelar a força dos laços, em comparação com o que pode ser ganho seguindo uma ciência social tradicional ou uma abordagem computacional isolada. Abordo em seguida como os resultados destes estudos contribuem para uma compreensão do comportamento online tanto a nível do utilizador individual, por exemplo, como as pessoas percorrem o ecossistema SNS, e ao nível das relações diádicas, por exemplo, como a força dos laços e a confiança interpessoal afectam os padrões de comunicação diádica. Além disso, descrevo as implicações específicas para os designers e investigadores do SNS que decorrem deste trabalho. Por exemplo, o trabalho apresentado tem implicações teóricas para o quadro de Usos e Gratificações (U&G - Uses and Gratifications framework) e para a aplicação da Teoria da Escolha Racional (RCT - Rational Choice Theory) no contexto das interacções SNS, e implicações de design, como o reforço da privacidade e conveniência dos utilizadores de SNS, com o apoio à reciprocidade das interacções. Explico também como os resultados dos estudos realizados demonstram o valor acrescentado de combinar as ciências sociais tradicionais e os métodos computacionais para o estudo de SNS, e, por fim, apresento reflexões sobre os pontos fortes e limitações da abordagem global de investigação que podem ser úteis a esforços de investigação semelhantes

Sensitive recovery of recombinant antibody clones after their in silico identification within NGS datasets

Recently the analytical power of the latest high throughput next generation DNA sequencing platforms has been used to analyse phage that have been selected from the panning of large combinatorial libraries displaying either peptide or antibody ligands. This process, commonly referred to as next generation phage display (NGPD), allows the researcher to determine the identity of specific phage that are being enriched against an antigen target by analysis of the DNA sequence encoding the displayed ligand. This method bypasses several steps in conventional phage panning that include laborious colony picking and functional ligand screening. A downside of this approach is that the only output from such experiments is the DNA sequence information of such enriched phage particles. In the case of peptides, the peptide sequence can be synthesised directly and used for further screening; however this is more difficult with larger antibody fragments such as ScFvs. In the case of ScFvs, their coding sequence would have to be fully elucidated, synthesised and re-cloned before expression. We describe here the application of an inverse PCR-ligation methodology that enables the specific recovery of ScFvs of interest from enriched sub-libraries of phage clones. Phagemid particles are recovered using sequence information derived from their unique heavy chain CDR3/FR4 domains and specific clones can be recovered irrespective of CDR3 size and at levels of abundance that would be refractory to their discovery during conventional phage panning and screening

A Simple Whole-Plasmid PCR Method to Construct High-Diversity Synthetic Phage Display Libraries

Phage display technology utilises peptide and antibody libraries with very high diversities to select ligands with specific binding properties. The production of such libraries can be labour intensive and technically challenging and whilst there are commercial sources of libraries, the exploitation of the resulting binders is constrained by ownership of the libraries. Here, a peptide library of ~ 1 × 109 variants for display on gene VIII was produced alongside three VHH antibody libraries with similar diversity, where 12mer, 16mer or 21mer CDR3s were introduced into the highly stable cAbBCII10 scaffold displayed on gene III. The cloning strategy used a simple whole-plasmid PCR method and type IIS restriction enzyme assembly that facilitate the seamless insertion of diversity into any suitable phage coat protein or antibody scaffold. This method reproducibly produced 1 × 109 variants from just 10 transformations and the four libraries had relatively low bias with 82 to 86% of all sequences present as single copies. The functionality of both peptide and antibody libraries were demonstrated by selection of ligands with specific binding properties by biopanning. The peptide library was used to epitope map a monoclonal antibody. The VHH libraries were pooled and used to select an antibody to recombinant human collagen type 1

Mapping B-cell responses to Salmonella enterica serovars Typhimurium and Enteritidis in chickens for the discrimination of infected from vaccinated animals

Serological surveillance and vaccination are important strategies for controlling infectious diseases of food production animals. However, the compatibility of these strategies is limited by a lack of assays capable of di erentiating infected from vaccinated animals (DIVA tests) for established killed or attenuated vaccines. Here, we used next generation phage-display (NGPD) and a 2-proportion Z score analysis to identify peptides that were preferentially bound by IgY from chickens infected with Salmonella Typhimurium or S. Enteritidis compared to IgY from vaccinates, for both an attenuated and an inactivated commercial vaccine. Peptides that were highly enriched against IgY from at least 4 out of 10 infected chickens were selected: 18 and 12 peptides for the killed and attenuated vaccines, respectively. The ten most discriminatory peptides for each vaccine were identi ed in an ELISA using a training set of IgY samples. These peptides were then used in multi-peptide assays that, when analysing a wider set of samples from infected and vaccinated animals, diagnosed infection with 100% sensitivity and speci city. The data describes a method for the development of DIVA assays for conventional attenuated and killed vaccines

Discovery of peptide ligands targeting a specific ubiquitin-like domain– binding site in the deubiquitinase USP11

© 2019 Spiliotopoulos et al. Published by The American Society for Biochemistry and Molecular Biology, Inc. Ubiquitin-specific proteases (USPs) reverse ubiquitination and regulate virtually all cellular processes. Defined noncatalytic domains in USP4 and USP15 are known to interact with E3 ligases and substrate recruitment factors. No such interactions have been reported for these domains in the paralog USP11, a key regulator of DNA double-strand break repair by homologous recombination. We hypothesized that USP11 domains adjacent to its protease domain harbor unique peptide-binding sites. Here, using a next-generation phage display (NGPD) strategy, combining phage display library screening with next-generation sequencing, we discovered unique USP11-interacting peptide motifs. Isothermal titration calorimetry disclosed that the highest affinity peptides (K D of 10 M) exhibit exclusive selectivity for USP11 over USP4 and USP15 in vitro. Furthermore, a crystal structure of a USP11–peptide complex revealed a previously unknown binding site in USP11’s noncatalytic ubiquitin-like (UBL) region. This site interacted with a helical motif and is absent in USP4 and USP15. Reporter assays using USP11-WT versus a binding pocket– deficient double mutant disclosed that this binding site modulates USP11’s function in homologous recombination–mediated DNA repair. The highest affinity USP11 peptide binder fused to a cellular delivery sequence induced significant nuclear localization and cell cycle arrest in S phase, affecting the viability of different mammalian cell lines. The USP11 peptide ligands and the paralog-specific functional site in USP11 identified here provide a framework for the development of new biochemical tools and therapeutic agents. We propose that an NGPD-based strategy for identifying interacting peptides may be applied also to other cellular targets

Isolation of antigen-specific, disulphide-rich knob domain peptides from bovine antibodies.

As a novel alternative to established surface display or combinatorial chemistry approaches for the discovery of therapeutic peptides, we present a method for the isolation of small, cysteine-rich domains from bovine antibody ultralong complementarity-determining regions (CDRs). We show for the first time that isolated bovine antibody knob domains can function as autonomous entities by binding antigen outside the confines of the antibody scaffold. This yields antibody fragments so small as to be considered peptides, each stabilised by an intricate, bespoke arrangement of disulphide bonds. For drug discovery, cow immunisations harness the immune system to generate knob domains with affinities in the picomolar to low nanomolar range, orders of magnitude higher than unoptimized peptides from naïve library screening. Using this approach, knob domain peptides that tightly bound Complement component C5 were obtained, at scale, using conventional antibody discovery and peptide purification techniques

Successful treatment of postoperative massive pulmonary embolism with paradoxal arterial embolism through extracorporeal life support and thrombolysis

Pulmonary embolism is a common clinical entity related to high mortality. About 200,000 to 300,000 patients die every year due to pulmonary embolism. The purpose of this article is to describe a case of a patient who on the second postoperative day after undergoing thromboembolectomy of the left femoral artery, manifested a massive pulmonary embolism. Due to cardiorespiratory collapse a combined treatment via extracorporeal life support (ECLS) and parallel catheter thrombolysis was decided and performed. By cardiorespiratory improvement and final stabilization the patient was successfully weaned from ECLS and the system was successfully removed. After a reasonable postoperative time the patient was dismissed in good overall condition. Keywords: Pulmonary embolism, Extracorporeal membrane oxygenation, Thrombolysis, Catheter thrombolysi