Bottom-up Identification Research Articles

Capturing the situated, dynamic nature of EMI-lecture listening comprehension in real time

Abstract English-medium instruction (EMI) potentially offers pedagogical efficiency by simultaneously providing access to academic content and English affordances. EMI’s efficacy and effectiveness, however, remain unproven with questions concerning students’ language proficiency unresolved. As listening to lectures holds a central role in tertiary education and the development of language skills is founded on second-language listening ability, key concerns for stakeholders are knowing how much of an EMI lecture students can understand and what factors impact their lecture listening comprehension. Current methodologies used to capture listening comprehension data, such as tests, surveys, summaries, and transcript markings do not capture the idiosyncratic, volatile, and multifaceted reactions to aural text phenomena that learners encounter during a lecture. This study, therefore, uses an innovative foot switch mechanism to capture comprehension data in real time as students participated in an EMI lecture. These data were then used to guide a stimulated recall. The data showed learners failing to comprehend extensive sections of the lecture while deeper analysis identified sections of the lecture where issues concerning prior taught knowledge, top-down schema building, lexical, and bottom-up identification of sounds coincided for multiple learners. Extrapolating from these points of convergence, pedagogical recommendations are provided.

A cascading model of stakeholder engagement for large-scale regional development using structured dialogical design

We present a large-scale systemic intervention conducted in the wine village communities of Cyprus. The scientific aim of this paper is to contribute to expanding community operational research's purpose, scope, and tools by reflecting on a cascading engagement model of stakeholders toward regional development in Cyprus. An ad-hoc committee comprising three representatives of the Department of Town Planning and Housing, three members of the Cyprus Academy of Public Administration, and a few external consultants came up initially with about a dozen stakeholders’ categories they considered “relevant.” Using a stepwise (cascading) expansion, they eventually engaged over 200 actors representing 26 stakeholder categories. The first 29 stakeholders identified 71 obstacles to developing the wine villages using Structured Democratic Dialogue (SDD). They clustered the obstacles into themes and formed working groups to address them. Each group identified and invited experts and additional stakeholders they considered relevant to form extended theme-specific groups. Each group conducted a SWOT analysis to deepen understanding and produced a thematic vision map using SDD. A holistic vision map was constructed through a final SDD process in which participants were the authors of the most influential factors from each thematic vision map. The approach adheres to the bottom-up, community-led method and falls within community operational research and citizen science. The cascading model offers a formula for multi-methodological intervention. The stepwise bottom-up identification and engagement of stakeholders empowers and engages authentically, especially those marginalised. The expansion in numbers and the effective engagement of stakeholders creates the required momentum for societal change. We discuss the model's broader applicability, frame it within third-phase science, and suggest future directions.

Deliberate simple rule creation and use: Activities and challenges

Using ‘simple rules’ may enable managers to take organizational decisions more rapidly. While prior research presents advantages of simple rule use during strategy formation, we lack insights into how firms can deliberately create simple rules and mitigate the challenges during strategy implementation. This is particularly interesting for established firms struggling to leverage their wealth of experience. We explore how managers of a multinational corporation deliberately create and use simple rules to implement the firm's growth strategy. Drawing on interviews and secondary data, we reveal the activities through which managers ensure the relevance and legitimacy of codified simple rules, yet also establish causality between simple rules and outcomes. Simple rule creation is accomplished via bottom-up identification and lateral validation, its use via consistent top-down guiding and timely adaptation. Our findings contribute to the growing body of research on the evolution of simple rules and aspects of strategy implementation more generally.

Good practices in Italian therapeutic communities. Outcomes 2020 of quality accreditation program “Visiting DTC Project”

PurposeThis paper aims to present results achieved by the first, and to date only, Democratic Therapeutic Communities (DTC) quality improvement program developed in Italy, in the past 10 years, named “Visiting DTC Project.” Process of bottom-up identification, definition and evaluation of good practices of TCs for adult users with long term severe mental disorders will be described. In addition, a five-phase clinical care pathway will be presented for the same user category, developed by the “Visiting DTC Project” to comply with Italian National Health Service accreditation standards for TCs.Design/methodology/approach“Visiting DTC Project” involved 40 Italian TCs, since 2012 until 2020, in an action research on good practices developed throw a democratic and bottom-up methodology. Project’s methodology is the “Democratic Peer-to-peer Accreditation,” a kind of professional scientific quality accreditation and continuous improvement process for community mental health services. Scientific model for the definition of service standards and principles of treatment is the British “Democratic Therapeutic Community,” which the “Visiting DTC Project” is organizationally inspired by.FindingsIn the eighth annual cycle of the program for TC with adult users of mental health services a significantly effective good practice procedure (GPP), with good practical efficacy, was finally identified (for the first time after eight years), but still no best practice. GPP with the title “Multi-family Community Meeting” is the Good Practice of the year 2020. No Best Practice has yet been identified. An integrated clinical care pathway for Adult DTCs Users in five phases is also presented. This care pathway organizes advanced standards of Community Group Quality in a map, to support the description and planning of the five phases of the user’s clinical work in DTC treatment.Originality/valueCooperation with local community services, organizations and networks, as well as a therapeutic environment based on informal coexistence and cooperation between TC members, are thus, together with care of family relationships, the main characteristics of the Italian experience of implementing and developing the Italian DTC treatment model. These characteristics make it clear how fragile Italian DTCs are at this moment. They are still in an early stage of development. All the most applied and effective best practice procedures are dependent on a wide and dense network of relationships, formal and informal, which cross the therapeutic environment and interconnect TC members with all other stakeholders.

Perceived characteristics of hazard-managing organizations for institutional stereotypes and their effects on trust

Institutional stereotypes’ contents and effects on trust of hazard managers can be determined by directly eliciting ratings of government, business, and nonprofit institutions (‘top-down’ approach), or by a bottom-up approach used here. U.S. residents were recruited in 2015 through an opportunity sample from Amazon Mechanical Turk (n = 752). Americans’ views of positive and negative attributes of 11 organizations each within the institutions of government agencies, corporations, and nonprofit advocacy groups (which try to influence policy) were elicited to test four hypotheses. First, relative positions of organizations within these three institutions on positive and negative attributes converged with these institutions’ relative top-down positions. Second, given great variation in reported familiarity across institutions, organizations, and individuals, familiarity increased distinctions among organizations within an institution while attenuating both positive and negative attributions. Inter-individual differences in demographics, political views, and worldviews produced small variations in positive and negative attributes, supporting their culturally shared (stereotypical) nature. Familiarity did not greatly distinguish ratings per organization of its typicality for its institution, a critical variable for bottom-up identification of stereotypical attributes, but top ‘typical’ organizations for familiar and unfamiliar respondents rarely overlapped. Third, explained variance in trust in ‘typical’ organizations was greatly affected by perceived positive and negative organizational attributes. Fourth, familiarity increased attributes’ effects on trust, probably reflecting influence of both institutional stereotypes and organization-specific beliefs. Low organizational familiarity limited this bottom-up study’s ability to confirm that high-familiarity ‘typical’ organizations and the top-down approach converged on the same stereotypical attributes, but results were not inconsistent with such convergence. Replication with more representative samples, and extending stereotypes research to other cultures, is warranted.

Creating value with eHealth: identification of the value proposition with key stakeholders for the resilience navigator app

BackgroundFor a stress-management app to be persuasive and impactful, designers and developers should obtain a clear perspective of the value proposition according to key stakeholders before development. However, this is often not the case. In order to increase the chance of creating an impact by means of the Resilience Navigator app, this study aims to identify key stakeholders and work with them to gain an in-depth understanding of the value proposition of this stress-management app.MethodsThe approach used in this study builds on the approaches taken by Van Limburg et al. and Van Woezik et al. An initial list of stakeholders was identified by means of a literature scan. Stakeholders on this initial list took an online survey to identify key stakeholders with a ranking system. Semi-structured interviews were conducted with a subset of key stakeholders to identify the value proposition using the value proposition canvas as a framework for data collection. Finally, the value proposition was validated by key stakeholders during focus groups.ResultsThe key stakeholders identified included employees, employers, participation councils within organisations, HR advisors, product owners, company doctors, and business analysts. The interviews produced a list of approximately one hundred values from which fifteen core values were distilled. One example is to take into account time constraints experienced by users during stress periods. In general, the Resilience Navigator app’s main goal is to increase awareness of personal stress levels and causes of stress. In addition, the sub-goal is to increase skills for effective stress management. The focus groups validated the idea that the most important values were reflected in the value proposition and had been appropriately translated into design elements, according to key stakeholders.ConclusionsA thorough, bottom-up identification and validation of the value proposition for the Resilience Navigator app was obtained, reflecting key stakeholders’ varying ideas on this piece of eHealth technology. The results will facilitate the continued development of the Resilience Navigator app from the value specification phase to the design phase. In the design phase, the remaining assumptions regarding the app’s value proposition should be tested using rapid prototyping.

Glocal Tourism and Resilient Cities: The Case of Matera “European Capital of Culture 2019”

This research paper presents the key elements of the strategic project “European Capital of Culture 2019” initiated by the city of Matera in 2014. Through the “big event”, defined by the combination “diluted time/diffuse space”, the “Città dei Sassi”, UNESCO World Heritage since 1993, is innovating the symbolic, material, and organizational levels of all the Basilicata municipalities whose tourist resources were almost unknown both at national and international levels, thus showing high resiliency, i.e., flexibility, inclusiveness, integration, and initiative. Through a self-centered and sustainable model of tourist accommodation that minimizes the infrastructure fixed capital investment aiming, at the same time, to increase collective empowerment processes, it is planned to accommodate about 700,000 “temporary citizens” who, by adopting an active and participative approach, wish to live a unique and unrepeatable identity experience in the Lucanian community instead of being mere spectators. Special attention is paid to “virtual” communication by using the world wide web not only as a showcase to promote the bottom-up identification and enhancement process of the heritage, but also as a tool to manage contacts with potential visitors in order to avoid any adverse impact of the event on the environmental and cultural components of the city and of the regional planning.

Acetonitrile-assisted enzymatic digestion can facilitate the bottom-up identification of proteins of cancer origin

The main objective of this study was to develop an effective in-gel trypsin digestion protocol using aqueous-acetonitrile solvent system to facilitate MS analysis and maximize the number of identified proteins from biological samples. The procedure, where 80% acetonitrile was present in the trypsin reaction mixture, increased the number of matched peptides, and allowed the identification of more proteins with higher coverage than the common digestion protocol. Vimentin, annexins, tubulin, actin, peptidyl-prolyl cis-trans isomerase or alpha-enolase are examples of important proteins that change during the progress cancer. These were isolated from human breast cancer cells and were used for this study.

The Evolution of the Systems of Cities Literature Since 1995: Schools of Thought and their Interaction

The study of relations between cities has long been a major focus in urban research. For decades, this field has grown integrating contributions from many disciplines. But today, the field appears rather fragmented. This study analyses the body of literature that has developed over the last 23 years to identify schools of thought on interurban relationships and to see to what extent these interact with each other. It does so by innovatively employing bibliometric analysis to the study of systems of cities, which allows a bottom-up identification of five schools of thought: one predominantly focusing on the regional or intra-metropolitan scale and centred on concepts of polycentricity; one addressing the global scale with a focus on world city networks; one employing simulation and complexity theories to understand behaviour of agents building the urban system bottom-up; one rooted in (new) economic geography and focusing on growth and decline in the urban system; and, one seeking regularities with respect to city size distributions. The conceptual, methodological and empirical aspects of these different schools are discussed by means of a ‘semantic map’ derived from the vocabulary of titles and abstracts of papers. The coupling of the semantic map with the citation networks of these schools of thought confirms the increasing fragmentation of the field over the last decades. However, in the most recent years, the different schools of thought start to interact slightly more. The desirability and feasibility of a move from multidisciplinarity to interdisciplinarity in urban systems research needs further exploration.

Systematic Review of Methods in Low-Consensus Fields: Supporting Commensuration through `Construct-Centered Methods Aggregation’ in the Case of Climate Change Vulnerability Research

There is increasing interest in using systematic review to synthesize evidence on the social and environmental effects of and adaptations to climate change. Use of systematic review for evidence in this field is complicated by the heterogeneity of methods used and by uneven reporting. In order to facilitate synthesis of results and design of subsequent research a method, construct-centered methods aggregation, was designed to 1) provide a transparent, valid and reliable description of research methods, 2) support comparability of primary studies and 3) contribute to a shared empirical basis for improving research practice. Rather than taking research reports at face value, research designs are reviewed through inductive analysis. This involves bottom-up identification of constructs, definitions and operationalizations; assessment of concepts’ commensurability through comparison of definitions; identification of theoretical frameworks through patterns of construct use; and integration of transparently reported and valid operationalizations into ideal-type research frameworks. Through the integration of reliable bottom-up inductive coding from operationalizations and top-down coding driven from stated theory with expert interpretation, construct-centered methods aggregation enabled both resolution of heterogeneity within identically named constructs and merging of differently labeled but identical constructs. These two processes allowed transparent, rigorous and contextually sensitive synthesis of the research presented in an uneven set of reports undertaken in a heterogenous field. If adopted more broadly, construct-centered methods aggregation may contribute to the emergence of a valid, empirically-grounded description of methods used in primary research. These descriptions may function as a set of expectations that improves the transparency of reporting and as an evolving comprehensive framework that supports both interpretation of existing and design of future research.

Top-down and bottom-up identification of proteins by liquid extraction surface analysis mass spectrometry of healthy and diseased human liver tissue.

Liquid extraction surface analysis mass spectrometry (LESA MS) has the potential to become a useful tool in the spatially-resolved profiling of proteins in substrates. Here, the approach has been applied to the analysis of thin tissue sections from human liver. The aim was to determine whether LESA MS was a suitable approach for the detection of protein biomarkers of nonalcoholic liver disease (nonalcoholic steatohepatitis, NASH), with a view to the eventual development of LESA MS for imaging NASH pathology. Two approaches were considered. In the first, endogenous proteins were extracted from liver tissue sections by LESA, subjected to automated trypsin digestion, and the resulting peptide mixture was analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) (bottom-up approach). In the second (top-down approach), endogenous proteins were extracted by LESA, and analyzed intact. Selected protein ions were subjected to collision-induced dissociation (CID) and/or electron transfer dissociation (ETD) mass spectrometry. The bottom-up approach resulted in the identification of over 500 proteins; however identification of key protein biomarkers, liver fatty acid binding protein (FABP1), and its variant (Thr→Ala, position 94), was unreliable and irreproducible. Top-down LESA MS analysis of healthy and diseased liver tissue revealed peaks corresponding to multiple (~15–25) proteins. MS/MS of four of these proteins identified them as FABP1, its variant, α-hemoglobin, and 10 kDa heat shock protein. The reliable identification of FABP1 and its variant by top-down LESA MS suggests that the approach may be suitable for imaging NASH pathology in sections from liver biopsies. Graphical ᅟ Electronic supplementary materialThe online version of this article (doi:10.1007/s13361-014-0967-z) contains supplementary material, which is available to authorized users.

Identification of black market products and potential doping agents in Germany 2010-2013.

The desire to increase the athletic performance, to 'optimize' an individual's appearance, and to complement but also to arguably substitute exercise by means of drugs and drug candidates has generated a considerable (illicit) market for compounds such as anabolic-androgenic steroids, stimulants, growth promoting peptide hormones, and so on. Genuinely developed for therapeutic use, their abuse/misuse generates enormous health risks, which has necessitated comprehensive controls of compound trafficking by customs and anti-doping authorities. From 2012 to 2013, the Bureau of Customs Investigation confiscated products containing anabolic-androgenic steroids (AAS; 259 kg), stimulants (13 kg), selective estrogen receptor modulators (SERMs; 24 kg), and human growth hormone (hGH; 3500 ampules). In cooperation with the Bureau and under the umbrella of the European Monitoring Center for Emerging Doping Agents (EuMoCEDA), the Cologne Anti-Doping Laboratory analyzed an additional 337 (black market) products between 2010 and 2013, allowing to monitor developments in drug use and, hence, the anticipation of new challenges in sports drug testing. Main tools utilized in characterizing confiscated materials were liquid chromatography-high resolution mass spectrometry (LC-HRMS), gas chromatography-high resolution mass spectrometry (GC-HRMS), and polyacrylamide gel electrophoresis (PAGE) with subsequent bottom-up identification of peptidic compounds using nano liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS). Among the 337 substances analyzed in the doping control laboratory in Cologne, 67 active ingredients were found, 49 of which being categorized as doping agents by the World Anti-Doping Agency (WADA). A total of 83.7 % accounted for steroidal substances (predominantly testosterone, trenbolone, and nandrolone and corresponding esters), 12.8 % accounted for peptide hormones and growth factors (predominantly hGH and growth hormone releasing peptides (GHRPs)), 3.2 % of the products contained hormones and metabolic modulators, and 0.3 % accounted for diuretic agents. Outstanding findings were the detection of the selective androgen receptor modulator (SARM) LGD-4033, the thymic hormone thymosin β4, and a fusion protein of unknown biological activity. Trafficking of considerable amounts of arguably performance and/or body-enhancing compounds has been observed during the past 4 years, the majority of which is categorized as relevant to sports drug testing. Several substances are of fake/non-approved nature and represent enormous health risks to the 'customer'.

Structural Identification of Nonlinear Dynamic Biomolecular Feedback and Feedforward Loops

Many biomolecular networks are still widely unknown. With high structural uncertainties, bottom-up identification based on model discrimination tends to fail because of combinatorially many possible model structures. Top-down approaches, in contrast, describe general signal processing properties, rather than specific mechanisms. Most of these approaches originated in engineering disciplines where linearity is commonly (approximately) given, but naturally evolved networks exhibit a rather high degree of nonlinearity. Here, we present a top-down structural identification method that is not only applicable to nonlinear biomolecular networks, but indeed requires the network under study to be nonlinear. Similar to traditional frequency domain analysis, we apply an oscillatory input signal to a biomolecular network. However, instead of varying the frequency, we vary the mean value of the oscillatory signal to detect, discriminate, and partly characterize single feedback and feedforward loops in nonlinear networks.

LC–MS/MS identification of doublecortin as abundant beta cell-selective protein discharged by damaged beta cells in vitro

There is a clinical need for plasma tests that can directly detect injury to pancreatic beta cells in type 1 diabetes. Such tests require biomarkers that are abundantly and selectively released into plasma by damaged beta cells. We combined LC-MS/MS proteomics and tissue-comparative transcriptomics of FACS-purified beta cells for bottom-up identification of candidate markers. Less than 10% of 467 proteins detected in beta cells showed endocrine-enriched expression. One surprising candidate was the neuronal migration marker doublecortin: in situ analysis revealed uniform doublecortin expression in the cytoplasm of all beta cells. Western blotting and real-time PCR confirmed its strong beta cell-selectivity outside the brain and its high molar abundance, indicating promising biomarker properties in comparison to GAD65, a more established marker of beta cell injury. DCX potential was validated in vitro: chemically-induced necrosis of rat and human beta cells led to a discharge of intracellular doublecortin into the extracellular space, proportionate to the amount of injured cells, and similar to GAD65. In vivo, recombinant DCX showed favorable pharmacokinetic properties, with a half-life in plasma of around 3h. Combined, our findings provide first proof-of-principle for doublecortin as biomarker for beta cell injury in vitro, advocating its further validation as biomarker in vivo.

Segmentation of interwoven 3d tubular tree structures utilizing shape priors and graph cuts

The segmentation of tubular tree structures like vessel systems in volumetric datasets is of vital interest for many medical applications. We present a novel approach that allows to simultaneously separate and segment multiple interwoven tubular tree structures. The algorithm consists of two main processing steps. First, the tree structures are identified and corresponding shape priors are generated by using a bottom-up identification of tubular objects combined with a top-down grouping of these objects into complete tree structures. The grouping step allows us to separate interwoven trees and to handle local disturbances. Second, the generated shape priors are utilized for the intrinsic segmentation of the different tubular systems to avoid leakage or undersegmentation in locally disturbed regions. We have evaluated our method on phantom and different clinical CT datasets and demonstrated its ability to correctly obtain/separate different tree structures, accurately determine the surface of tubular tree structures, and robustly handle noise, disturbances (e.g., tumors), and deviations from cylindrical tube shapes like for example aneurysms.

Fragmentation of intra-peptide and inter-peptide disulfide bonds of proteolytic peptides by nanoESI collision-induced dissociation

Characterisation and identification of disulfide bridges is an important aspect of structural elucidation of proteins. Covalent cysteine-cysteine contacts within the protein give rise to stabilisation of the native tertiary structure of the molecules. Bottom-up identification and sequencing of proteins by mass spectrometry most frequently involves reductive cleavage and alkylation of disulfide links followed by enzymatic digestion. However, when using this approach, information on cysteine-cysteine contacts within the protein is lost. Mass spectrometric characterisation of peptides containing intra-chain disulfides is a challenging analytical task, because peptide bonds within the disulfide loop are believed to be resistant to fragmentation. In this contribution we show recent results on the fragmentation of intra and inter-peptide disulfide bonds of proteolytic peptides by nano electrospray ionisation collision-induced dissociation (nanoESI CID). Disulfide bridge-containing peptides obtained from proteolytic digests were submitted to low-energy nanoESI CID using a quadrupole time-of-flight (Q-TOF) instrument as a mass analyser. Fragmentation of the gaseous peptide ions gave rise to a set of b and y-type fragment ions which enabled derivation of the sequence of the amino acids located outside the disulfide loop. Surprisingly, careful examination of the fragment-ion spectra of peptide ions comprising an intramolecular disulfide bridge revealed the presence of low-abundance fragment ions formed by the cleavage of peptide bonds within the disulfide loop. These fragmentations are preceded by proton-induced asymmetric cleavage of the disulfide bridge giving rise to a modified cysteine containing a disulfohydryl substituent and a dehydroalanine residue on the C-S cleavage site.

Recognition of three-dimensional objects from orthographic views

This paper presents a program interpreting orthographic drawings input through a digitizing tablet into three-dimensional (3-D) objects. Ambiguity arises in such a task not only in the case of two views but also with three-view inputs, due to coinciding projections of vertices. The main effort consists in heuristically reducing this ambiguity. The general strategy is a bottom-up identification of the objects starting with the tablet-coordinates and aggregating them into vertices, then faces and finally polyhedra. The program does not contain any high level geometrical concepts or probable properties of 3-D objects but only some basic definitions of polyhedra (as expressed by Euler and Mobius). By applying these definitions to different parts of the scene to recognize, it defines local sets of alternatives and then chooses the right ones by running a mini theorem prover over these sets. A major issue in writing this program has been to limit the drawing constraints imposed on the user. In case that it gets blocked in the recognition process, however, the program can require the user's help.