Microbial interactions with nanoscale features

Bacteria and other microbes interact with their environment through nanoscale mechanical and chemical processes. Understanding these interactions is critical for controlling bacteria, both in preventing biofilm formation and in using these interactions to control bacterial metabolism and behavior in industrially relevant applications such as fermentation and biomaterial generation. Biofilm formation is a key step in the process of biofouling, a process of great importance in shipping and food processing industries and especially in healthcare where it is of utmost importance to prevent the formation of biofilms on medical equipment which would further prevent infections. In this dissertation, I examine the biological responses of the Gram-negative bacterium, Escherichia coli (E. coli) to alterations in the surface nanostructure, persistent photoconductivity, and the stiffness of the surface material. In my characterization of Bacterial interactions with nanostructured surfaces, I examined the behavior of E. coli bacteria, when exposed to twenty-one different nanostructured polymeric substrates etched from seven common and industrially relevant polymers. I demonstrated that in the bacteria respond to the surfaces by changing their adhesion, morphology and biofilm formation. Interestingly neither surface energy nor structure appeared to control these behaviors. The predominant effect on bacterial behavior appeared to be directed by the composition of the surface. To investigate the mechanisms that control the bacterial response to a surface phenomenon known as persistent photoconductivity (PPC), I used E. coli strains that were mutant for genes that encoded specific components of adhesion and/or biofilm formation. One goal of microbial bioelectronics is to develop hybrid organic/inorganic interfaces between living cells and electronic devices. Type III semiconductors such as GaN are a good candidate for such interfaces; Gallium nitride and Oxide materials are biocompatible, a growing material system for electronics, and have a property known as persistent photoconductivity (PPC), which is the persistence of a charge after excitation energy such as ultraviolet light is removed. Work in the Ivanisevic and LaJeunesse labs have shown that PPC changes the physiology of the bacterial cells and results in both an increase in intracellular Ca2+ and alteration to cell adhesion. To determine which cell surface and adhesive components of E. coli are required for the response to PCC, I used a collection of E. coli deletion mutants and examined the loss of these cell structures on the bacteria’s response to PCC. I found that mutation in the synthetic pathways that generate the LPS, curli, and mutations in flagella significantly alter the response of E. coli to PPC. To determine the bacterial adhesive response to material stiffness, I tested the adhesion of E. coli to Polyacrylamide hydrogels of three different stiffnesses (~17kPa, 29kPa and 1547 kPa). Wild type E. coli demonstrated the highest adhesion to the soft PA hydrogel and the least on the hard gel. I used single-gene deletion mutants of E. coli bacterial surface appendages to determine how the loss of these cellular structures would affect bacterial adhesion to these gels. I compared the adhesion trends of the various knockouts to the WT trend and found that they were vastly different, and with no particular pattern. Adhesion of bacteria to the soft gels was significantly lower than the adhesion of the WT except for the csgD mutant. All the knockout bacteria adhered more to the hard gels in comparison to the WT adhesion. Identifying the most important deletion remains a challenge, even though all the deletions resulted in a change in bacterial adhesion. This analysis has provided a framework for the further elucidation of genetic pathways involved in the bacterial responses. [This abstract has been edited to remove characters that will not display in this system. Please see the PDF for the full abstract.]]]> 2019 Escherichia coli $x Biotechnology Microbial biotechnology Nanostructured materials Photoconductivity English http://libres.uncg.edu/ir/uncg/f/Iyer_uncg_0154D_12923.pdf oai:libres.uncg.edu/29255 2020-01-17T11:22:01Z UNCG Traditional vs. self-compassionate expressive writing: differentiating processes through linguistic analysis Kalianivala, Anahita Z. NC DOCKS at The University of North Carolina at Greensboro <![CDATA[Expressive writing (EW) is an experimental paradigm developed by Pennebaker and colleagues (Pennebaker &amp; Beall, 1986). In traditional EW tasks, participants are asked to disclose their deepest thoughts and emotions concerning the most traumatic or stressful event of their lives. Consistent with the notion that EW may be beneficial for those with psychological diagnoses, research has looked to individual differences that infer risk or are associated with the maintenance of psychological disorders. It has been posited that an underlying mechanism of EW is the implicit message for participants to be accepting and non-judgmental towards their emotions and cognitions through the instruction to delve into one’s deepest thoughts and feelings. Thus, EW may be a particularly useful intervention tool for individuals prone to rumination, a repetitive form of thinking about the self, especially one’s sad or depressed feelings (Nolen-Hoeksema, Wisco, &amp; Lyubomirsky, 2008). In particular, Baum and Rude (2013) proposed self-compassion as a related construct that may further enhance the benefit of EW. The current study sought to align multiple arms of EW research that have typically been separately pursued: comparing traditional EW to an adapted paradigm (e.g., providing instructions that guide participants to engage in principles of self-compassion,); measuring individual differences which may impact EW benefit; and conducting linguistic analysis to further understand psychological processes occurring during writing. Overall, participants reported both EW conditions as beneficial, on average. Negative affect increased across writing sessions for the full sample, consistent with typical immediate effects of EW. However, none of the hypothesized differences in affect or cognitive word use by EW condition were supported, nor were the moderation effects of rumination

LasUIE: Unifying Information Extraction with Latent Adaptive Structure-aware Generative Language Model

Universally modeling all typical information extraction tasks (UIE) with one generative language model (GLM) has revealed great potential by the latest study, where various IE predictions are unified into a linearized hierarchical expression under a GLM. Syntactic structure information, a type of effective feature which has been extensively utilized in IE community, should also be beneficial to UIE. In this work, we propose a novel structure-aware GLM, fully unleashing the power of syntactic knowledge for UIE. A heterogeneous structure inductor is explored to unsupervisedly induce rich heterogeneous structural representations by post-training an existing GLM. In particular, a structural broadcaster is devised to compact various latent trees into explicit high-order forests, helping to guide a better generation during decoding. We finally introduce a task-oriented structure fine-tuning mechanism, further adjusting the learned structures to most coincide with the end-task's need. Over 12 IE benchmarks across 7 tasks our system shows significant improvements over the baseline UIE system. Further in-depth analyses show that our GLM learns rich task-adaptive structural bias that greatly resolves the UIE crux, the long-range dependence issue and boundary identifying. Source codes are open at https://github.com/ChocoWu/LasUIE.Comment: NeurIPS2022 conference pape

Facilitating the Expression of Emotions by Alleged Victims of Child Abuse During Investigative Interviews Using the Revised NICHD Protocol.

Children's testimony is often critical to the initiation of legal proceedings in abuse cases. In forensic interviews, the expression of emotions can powerfully enhance both the quality of children's statements and perceptions that their statements are coherent and credible. However, children rarely express their emotions when reporting abusive events. The Revised The National Institute of Child Health and Human Development (NICHD) Protocol (RP) was designed to emphasize socioemotional communication during forensic interviews and thus should be associated with more extensive and diverse expressions of emotions by alleged victims of abuse. The present study focused on forensic interviews (178 using the Revised and 100 using the Standard NICHD Protocol) with victims of physical child abuse whose allegations were corroborated using independent evidence. Detailed content coding showed that the RP was associated with the expression of more different emotions, more expression of abuse-related emotions, and more expression of emotions related to the interview context. Emotional expressiveness was associated with increased informativeness, and the association between the type of protocol and informativeness was fully mediated by emotional expressiveness. These results suggest that the Revised Protocol facilitates the expression of emotions by alleged victims of abuse in a way that enhances the value of children's testimony in multiple ways.Nuffield and Jacobs Foundation

Hacking Smart Machines with Smarter Ones: How to Extract Meaningful Data from Machine Learning Classifiers

Machine Learning (ML) algorithms are used to train computers to perform a variety of complex tasks and improve with experience. Computers learn how to recognize patterns, make unintended decisions, or react to a dynamic environment. Certain trained machines may be more effective than others because they are based on more suitable ML algorithms or because they were trained through superior training sets. Although ML algorithms are known and publicly released, training sets may not be reasonably ascertainable and, indeed, may be guarded as trade secrets. While much research has been performed about the privacy of the elements of training sets, in this paper we focus our attention on ML classifiers and on the statistical information that can be unconsciously or maliciously revealed from them. We show that it is possible to infer unexpected but useful information from ML classifiers. In particular, we build a novel meta-classifier and train it to hack other classifiers, obtaining meaningful information about their training sets. This kind of information leakage can be exploited, for example, by a vendor to build more effective classifiers or to simply acquire trade secrets from a competitor's apparatus, potentially violating its intellectual property rights

The biosemiotic imagination in the Victorian frames of mind : Newman, Eliot and Welby

This thesis traces the development of thought in the philosophical and other writings of three nineteenth-century thinkers, whose work exemplifies that century’s attempts to think beyond the divisions of culture from nature and to reconcile empirical science with metaphysical truth. Drawing on nineteenth-century debates on the origin of language and evolutionary theory, the thesis argues that the ideas of John Henry Newman, George Eliot and Lady Victoria Welby were cultural precursors to the biosemiotic thought of the second half of the twentieth century and beyond, specifically in the way in which these three thinkers sought to find a ‘common grammar’ between natural and human practices. While only Lady Welby communicated with the scientist, logician and father of modern semiotics, Charles S. Peirce (1839-1914), all three contributed to the cultural sensibility that informed subsequent work in biology/ethology (Jakob von Uexküll (1864-1944), zoosemiotics (Thomas A. Sebeok (1920-2001), and the development of biosemiotics (Thomas A. Sebeok and Jesper Hoffmeyer (1943-present), Kalevi Kull (1952-present) among others. Each of these nineteenth-century writer’s intellectual development show strong parallels with the interdisciplinary endeavour of biosemiotics. The latter’s observation that biology is semiotics, its postulation of the continuity between the natural and cultural world through semiosis and evolutionary semiotic scaffolding its emphasis on the coordination of organic life processes on all levels, from simple cells to human beings, via semiotic interactions that depend on interpretation, communication and learning, and its consequent refusal of Cartesian divide, all find distinct resonances with these earlier thinkers. The thesis thus argues that Newman, Eliot and Welby all gave articulation to what the thesis identifies as the growth of a ‘biosemiotic imagination.’ It argues that Newman, Eliot and Lady Welby envisaged a unity, or a holistic understanding, of life based on a European developmental tradition of biology, philosophy and language which was familiar to Charles Darwin himself. This evolutionary ontology called forth a new epistemology grounded in a mode of unconscious creative inference (biosemiotic imagination) akin to Charles S. Peirce’s concept of abduction. Abduction is the logical operation which introduces a new idea and, as such, is the only source of adaptive and creative growth. For Peirce, it is closely tied to the growth of knowledge via the evolutionary action of sign relations. The thesis shows how these thinkers conceptualised their own version of what I suggest can be understood as this biosemiotic imagination and the implications this has for understanding creativity in nature and culture. For John Henry Newman, it was a common source of inspiration in religion and science. For George Eliot, it lay at the basis of any creative process, natural and cultural, between which it forged a link. Similarly to Eliot, Lady Victoria Welby saw abduction as a signifying process that subtends creativity both in nature and culture

Data Minimisation in Communication Protocols: A Formal Analysis Framework and Application to Identity Management

With the growing amount of personal information exchanged over the Internet, privacy is becoming more and more a concern for users. One of the key principles in protecting privacy is data minimisation. This principle requires that only the minimum amount of information necessary to accomplish a certain goal is collected and processed. "Privacy-enhancing" communication protocols have been proposed to guarantee data minimisation in a wide range of applications. However, currently there is no satisfactory way to assess and compare the privacy they offer in a precise way: existing analyses are either too informal and high-level, or specific for one particular system. In this work, we propose a general formal framework to analyse and compare communication protocols with respect to privacy by data minimisation. Privacy requirements are formalised independent of a particular protocol in terms of the knowledge of (coalitions of) actors in a three-layer model of personal information. These requirements are then verified automatically for particular protocols by computing this knowledge from a description of their communication. We validate our framework in an identity management (IdM) case study. As IdM systems are used more and more to satisfy the increasing need for reliable on-line identification and authentication, privacy is becoming an increasingly critical issue. We use our framework to analyse and compare four identity management systems. Finally, we discuss the completeness and (re)usability of the proposed framework

Program evaluation of English language learning for EYL curriculum development in Indonesia: teachers’ perception, challenges, and expectation

Program evaluation (henceforth PE) is a phase of curriculum development in the ELT context and is precious for improving curriculum reform. However, more research needs to be undertaken to investigate PE as a part of the English curriculum development for young learners’ context in Indonesian elementary schools. This case study research aims to scrutinize the teachers’ voices on PE centered on the challenges, perceptions, and expectations of the English to young learners (EYL) curriculum development. A semi-structured interview with three English teachers chosen by purposive sampling in Tasikmalaya, West Java, Indonesia, was employed to gather the data, and the collected data were examined thematically. The results showed that EYL teachers believe PE is vital to conduct since it can encourage curriculum development. They deal with challenges in designing and developing the curriculum related to lesson planning, materials development, instructional methods, and assessment practices. Teachers expected the EYL program to be adjusted with a suitable curriculum, such as contextualized, character-based, and school-based curricula. The study suggests that PE should be performed regularly to gain insightful reforms for the EYL curriculum, so teachers, schools, and stakeholders can advance the quality of the English program at Indonesian elementary schools