Step Of Project Research Articles

Methodology for Good Machine Learning with Multi-Omics Data.

In 2020, Novartis Pharmaceuticals Corporation and the U.S. Food and Drug Administration (FDA) started a 4-year scientific collaboration to approach complex new data modalities and advanced analytics. The scientific question was to find novel radio-genomics-based prognostic and predictive factors for HR+/HER- metastatic breast cancer under a Research Collaboration Agreement. This collaboration has been providing valuable insights to help successfully implement future scientific projects, particularly using artificial intelligence and machine learning. This tutorial aims to provide tangible guidelines for a multi-omics project that includes multidisciplinary expert teams, spanning across different institutions. We cover key ideas, such as "maintaining effective communication" and "following good data science practices," followed by the four steps of exploratory projects, namely (1) plan, (2) design, (3) develop, and (4) disseminate. We break each step into smaller concepts with strategies for implementation and provide illustrations from our collaboration to further give the readers actionable guidance.

“This Land of Thorns Is Not Habitable”: Diagnosing the Despair of Racialized Meta-oppression

ABSTRACT This article addresses the growing literature in critical race studies, which holds that racism is permanent or incurable, and that by adopting this pessimistic view of racism, we can enact improved and healthier racialized lives. I argue that the focus on curing anti-Black racism, and the failure to do so in the civil rights era and its aftermath has left people of all races, to varying degrees, stuck in pessimistic states of racialized anger, resentment, guilt, and shame. These pessimistic states have brought about an additional level of oppression for targets of racialized oppression. I call it “meta-oppression,” and it is the oppression of being oppressed. I argue that this oppression has exacerbated the effects of the social disease of racism, and it has literally affected the physiologies of many African Americans. This article provides a diagnosis of these existential and physiological states of meta-oppression and a clarification of its characteristics. This diagnosis is an initial step in a larger project of formulating and enacting effective treatments for it. I then argue that meta-oppression is a helpful diagnostic tool for clarifying the characteristics and ramifications on Blacks of US systemic racism during the post–civil rights movement period. I aim to establish meta-oppression as an existential and physiological condition that requires attention so as to expand the social imaginations of people of color and to allow us to engage in more systemic joyful affirmations of our racialized lives while still living within racist conditions.

Kuura-An automated workflow for analyzing WES and WGS data.

The advent of high-throughput sequencing technologies has revolutionized the field of genomic sciences by cutting down the cost and time associated with standard sequencing methods. This advancement has not only provided the research community with an abundance of data but has also presented the challenge of analyzing it. The paramount challenge in analyzing the copious amount of data is in using the optimal resources in terms of available tools. To address this research gap, we propose "Kuura-An automated workflow for analyzing WES and WGS data", which is optimized for both whole exome and whole genome sequencing data. This workflow is based on the nextflow pipeline scripting language and uses docker to manage and deploy the workflow. The workflow consists of four analysis stages-quality control, mapping to reference genome & quality score recalibration, variant calling & variant recalibration and variant consensus & annotation. An important feature of the DNA-seq workflow is that it uses the combination of multiple variant callers (GATK Haplotypecaller, DeepVariant, VarScan2, Freebayes and Strelka2), generating a list of high-confidence variants in a consensus call file. The workflow is flexible as it integrates the fragmented tools and can be easily extended by adding or updating tools or amending the parameters list. The use of a single parameters file enhances reproducibility of the results. The ease of deployment and usage of the workflow further increases computational reproducibility providing researchers with a standardized tool for the variant calling step in different projects. The source code, instructions for installation and use of the tool are publicly available at our github repository https://github.com/dhanaprakashj/kuura_pipeline.

Dealing with the Very Small: First Steps of a Picohydro Demonstration Project in an University Campus

This paper presents the implementation, project and design of a small run-of-river hydropower plant, designed for demonstration purposes, under a Project aimed to be a framework of wide spread dissemination of renewable energies and energy efficiency in an University Campus. The details of the hydroelectric power plant, from the project design until the final use of the produced electric energy, are described. The main requirements of the implementation are presented, with regards to the environmental footprint and topography of the site and the adopted solutions are also described. Considering the demonstration purposes, two different electrical systems were installed in the power house: stand-alone and grid-connected. The latter establishes a case study in the development and application of picohydro power plants as microgeneration units in the context of distributed generation systems. The evaluation of both systems is also presented, based on the experimental results obtained from tests experiments and from monitoring the first months of operation at the site.

Empirical Analysis of Drug Targets for Nervous System Disorders.

The discovery and development of drugs to treat diseases of the nervous system remains challenging. There is a higher attrition rate in the clinical stage for nervous system experimental drugs compared to other disease areas. In the preclinical stage, additional challenges arise from the considerable effort required to find molecules that penetrate the blood-brain barrier (BBB) coupled with the poor predictive value of many preclinical models of nervous system diseases. In the era of target-based drug discovery, the critical first step of drug discovery projects is the selection of a therapeutic target which is largely driven by its presumed pathogenic involvement. For nervous system diseases, however, the feasibility of identifying potent molecules within the stringent range of molecular properties necessary for BBB penetration should represent another important factor in target selection. To address the latter, the present review analyzes the distribution of human protein targets of FDA-approved drugs for nervous system disorders and compares it with drugs for other disease areas. We observed a substantial difference in the distribution of therapeutic targets across the two clusters. We expanded on this finding by analyzing the physicochemical properties of nervous and non-nervous system drugs in each target class by using the central nervous system multiparameter optimization (CNS MPO) algorithm. These data may serve as useful guidance in making more informed decisions when selecting therapeutic targets for nervous system disorders.

The ethical assessment of Assisted Reproductive Technologies (ART) in wildlife conservation

The application of Assisted Reproductive Technologies (ART) in breeding programs to save wild animal species is a relatively new approach to conservation and their ethical implications seem still to be underestimated. However, the ethical evaluation is a decisive step for conservation projects employing ART to address crucial questions like the welfare and life of the animals involved, the survival of the targeted species, the quality and safety of the procedures and the very idea of biodiversity conservation we want to pursue. Balancing the potential benefits of ART with the risks involved requires careful ethical analysis. This paper highlights the increasing role of ART in species conservation and emphasizes the need to address their ethical implications. After discussing the lack of ethical discussion in ART application to wildlife, the contribution outlines an ethical frame to address this gap and introduces an ETHical ASsessment tool (ETHAS) for the ethical self-assessment of ART procedures in vertebrate conservation. The tool allows respondents to highlight ethical aspects to be improved and risks related to the procedure, from its design to each application. The ethical approach to the ART application, relatively novel to wildlife conservation, can contribute to assure the ethical acceptability of conservation programs while favoring discussion and communication among project partners and the integration of ethical aspects in conservation programs.

Arguing and bargaining in international forums: The need for a novel approach

Most of the literature examining forum-based social interactions considers arguing and bargaining as the main modes of communication used by negotiating parties, and authors have often claimed that arguing interactions can be distinguished from bargaining ones on the basis of the presence/absence of some validation mechanisms. Starting from this assumption, authors have tried to study real-world international negotiations and to distinguish arguing from bargaining empirically. These attempts, however, have encountered several paralyzing methodological hindrances. This paper claims that the current differentiation between arguing and bargaining is built on erroneous assumptions and on a certain degree of undertheorization of bargaining types of forum interaction. The position advanced in this paper is that both arguing and bargaining types of interaction rely on similar validation mechanisms. Furthermore, the study shows that this erroneous distinction is the reason why authors have hitherto been unable to isolate and distinguish arguing from bargaining while looking at real-world international negotiations. The final goal of this paper is to challenge the current definitions of arguing and bargaining, and to provide the first step of a long-term research project aiming at the reconceptualization of these two types of interaction.

Empirical-Likelihood-Based Inference for Partially Linear Models

Partially linear models find extensive application in biometrics, econometrics, social sciences, and various other fields due to their versatility in accommodating both parametric and nonparametric elements. This study aims to establish statistical inference for the parametric component effects within these models, employing a nonparametric empirical likelihood approach. The proposed method involves a projection step to eliminate the nuisance nonparametric component and utilizes an empirical-likelihood-based technique, along with the Bartlett correction, to enhance the coverage probability of the confidence interval for the parameter of interest. This method demonstrates robustness in handling normally and non-normally distributed errors. The proposed empirical likelihood ratio statistic converges to a limiting chi-square distribution under certain regulations. Simulation studies demonstrate that this method provides better inference in terms of coverage probabilities compared to the conventional normal-approximation-based method. The proposed method is illustrated by analyzing the Boston housing data from a real study.

Implementasi Profil Pelajar Pancasila Dalam Menghadapi Perundungan Di Sekolah Dasar: Perspektif Glokalisasi

Profil Pelajar Pancasila is a Standar Kompetensi Lulusan (SKL) it is mean a Graduate Competency Standard which refers to the character and competencies that Indonesian students are expected to have. This profile consists of six dimensions: faith, devotion to God Almighty, noble character; global diversity; collaboration; creativity; critical thinking; and independence. This profile reflects the quality of the generation by the National Education Goals and acts as the main reference that directs education policies. Character is the main part that must be built to realize student welfare. However, on the other hand, the results of the National Assessment through the 2022 Character Survey show that the rate of bullying is still quite high, namely 36.31% of students have the potential to experience bullying, which means 1 in 3 children experience bullying at school. This research method is a position paper with a literary study approach, aimed at conveying the author's view or position on a particular topic or issue. In this research, starting with identifying issues or problems related to the Pancasila student profile and its application to overcome bullying in educational units is the first step in this research project. In addition, this research aims to investigate the glocalization process in the profile of Pancasila students by collecting evidence using literary studies.

Ab. No. 78 Validation of a Retrospective Injury Questionnaire for Competitive Indian Athletes

Introduction: The purpose of the current study is to develop and validate a new questionnaire for measuring Injuries (Present acute, Present overuse, Past acute, and Past overuse) among Competitive Indian Athletes. Measuring injuries is a preliminary step of any epidemiological project. Though vast scientific literature on injury measurements and questionnaire development is available, work done among Indian athletes is negligible. Recording injury-related data in forms or questionnaires is a common data collection practice. Developing a new questionnaire becomes necessary when existing ones cannot cover the research area of interest. Methods: 10 experts were recruited for the validation study and 50 subjects were recruited for questionnaire administration. A Delphi panel consensus study was conducted to validate an initial 126-item questionnaire by recruiting 10 experts. After two rounds, a 125-item questionnaire was obtained that was administered to 50 track and road runners (ages 15-35 years) practicing at Dharamshala. Athletes preparing for army or forest services, para-athletes, and those who did not have working smartphones were excluded. The data obtained was cleaned and coded for further analysis. The content validity ratio (CVR) score for each item was calculated to finalize the final items. To test the internal consistency, Cronbach’s alpha was calculated. Results: The final questionnaire had an overall alpha value of 0.812 indicating an adequate internal consistency. Conclusion: The newly generated retrospective injury questionnaire for Indian athletes is valid and reliable. Implications: The application of the questionnaire on a wider population can give an estimated injury incidence and prevalence data in the country.

End-of-life management of consumer products and industrial assets: a state of the art analysis of decision-making approaches and methodologies

This paper presents a state-of-the-art review of decision-making methodologies for the end-of-life management in consumer products and industrial assets domains, traditionally studied separately. The findings anticipate substantial benefits in uniting these domains, identifying best practices, and learning opportunities. This is the first step of a wider research project whose overall aim is to identify synergies, opportunities, and cross-domain learning to enhance sustainable and efficient end-of-life practices. Future steps will deepen the comparison of end-of-life decision-making methodologies and empirically investigate industry needs and challenges in end-of-life management practices or absence thereof.

High-molecular-weight DNA extraction for broadleaved and conifer tree species

Abstract Plant genome sequencing based on long reads has increasingly been applied also to tree species in recent years. A crucial step in these genome projects is the successful extraction of high-molecular-weight DNA in high quality and sufficient quantity, which is imperative for long-read sequencing. The extraction of high-molecular-weight DNA in trees has been limited and difficult to conduct. To achieve successful extraction, modification of the protocol for tree species is necessary. Here, we present a protocol for high-molecular-weight DNA extraction from the broadleaved tree species Fraxinus excelsior and from the conifer species Taxus baccata. The protocol is based on nuclei isolation and is divided into two main steps, i.e. nuclei separation based on the nuclei isolation buffer and DNA extraction using the Nanobind® plant nuclei kit by Pacific Biosciences (PacBio). The protocol can be applied to different tree species to obtain high-molecular-weight DNA in high quality, which can be used for Oxford Nanopore Technologies (ONT) and PacBio sequencing. ONT sequencing using four high-molecular-weight DNA preparations from Fraxinus excel-sior resulted in different read length N50 values (12.91-38.19 kb) and total base output (5.81-23.17 Gb), emphasizing the complex nature of the sequencing pipeline of high-molecular-weight DNA. PacBio HiFi sequencing of Taxus baccata produced circular consensus sequencing reads with an average length of 12.9 kb and an N50 of 13.59 kb. Altogether, this study presents a protocol to obtain high-molecular-weight DNA from different challenging tree species and discusses several important points that can be considered when adapting the protocol to additional species.

Using Ubuntu as a Research Paradigm to Unpack How Ghanaian Novice Teachers and Their Collaborators Engaged Virtually in Collaborative International Qualitative Research

The article details how Ubuntu was incorporated into each step of the research project, shares the authors’ experiences and key learnings, and provides recommendations for researchers utilizing Ubuntu as a research paradigm. Ubuntu is an ancient African philosophy emphasizing a way of life grounded in interdependence, collaboration, harmony, and community. In recent years, researchers have incorporated Ubuntu as a research paradigm to decolonize research in a sub-Saharan African context. The present article used international collaborative qualitative research conducted virtually during the COVID-19 pandemic to demonstrate the application of Ubuntu as a research paradigm for conducting research in the African context. Some of the key takeaways include technological factors to consider, establishing connections during the planning stage, and ultimately nurturing productive collaboration within virtual groups.

Data-Driven Hypothesis Generation in Clinical Research: What We Learned from a Human Subject Study?

Hypothesis generation is an early and critical step in any hypothesis-driven clinical research project. Because it is not yet a well-understood cognitive process, the need to improve the process goes unrecognized. Without an impactful hypothesis, the significance of any research project can be questionable, regardless of the rigor or diligence applied in other steps of the study, e.g., study design, data collection, and result analysis. In this perspective article, the authors provide a literature review on the following topics first: scientific thinking, reasoning, medical reasoning, literature-based discovery, and a field study to explore scientific thinking and discovery. Over the years, scientific thinking has shown excellent progress in cognitive science and its applied areas: education, medicine, and biomedical research. However, a review of the literature reveals the lack of original studies on hypothesis generation in clinical research. The authors then summarize their first human participant study exploring data-driven hypothesis generation by clinical researchers in a simulated setting. The results indicate that a secondary data analytical tool, VIADS-a visual interactive analytic tool for filtering, summarizing, and visualizing large health data sets coded with hierarchical terminologies, can shorten the time participants need, on average, to generate a hypothesis and also requires fewer cognitive events to generate each hypothesis. As a counterpoint, this exploration also indicates that the quality ratings of the hypotheses thus generated carry significantly lower ratings for feasibility when applying VIADS. Despite its small scale, the study confirmed the feasibility of conducting a human participant study directly to explore the hypothesis generation process in clinical research. This study provides supporting evidence to conduct a larger-scale study with a specifically designed tool to facilitate the hypothesis-generation process among inexperienced clinical researchers. A larger study could provide generalizable evidence, which in turn can potentially improve clinical research productivity and overall clinical research enterprise.

English-Indonesian and Indonesian-English Code Switching Used by the Teachers in Teaching-Learning English at the 11th Grade of SMAN 2 Mataram in the Academic Year of 2022/2023

Language is the most important component of the lives of all individual’s life. People will be able to communicate with one another more conveniently and effectively if they use language. People speak a variety of languages for a variety of reasons. It could be anywhere, including home, work, school, or campus. In a communication process, people may switch language codes, such as the English language, to the Indonesian language or vice versa. This research aimed to identify and describe the types and functions of English-Indonesian and Indonesian-English code switching used by the teachers in teaching-learning English at the 11th Grade of SMAN 2 Mataram. This research concentrates on two English teachers who currently teach students in the 11th grade who are majoring in science during the academic year 2022/2023. This study employed a descriptive qualitative methodology, and observation was the primary data collection method. A pre-observation class will be held as the first step in this research project to choose the topic. From the results, during classrooms, the first English teacher’s utterances caused sixty-seven codes switching and the second English teacher’s utterances caused forty-six codes switching. While for the functions, both English teachers only used five out of six functions of code switching. The research results show that the type of code switching mainly used by the English teachers is inter-sentential code switching and the function used mainly by English teachers is managing class.

CO-PRODUCTION TO TAILOR A DIGITAL TOOL FOR MONITORING SYMPTOMS OF DEMENTIA IN NURSING HOME CARE IN SWEDEN

Abstract Symptoms of dementia change over time, resulting in complex situations that can negatively impact the person with dementia, as well as their relatives, and create challenges for staff members. Behavioral and Psychological Symptoms of Dementia (BPSD), such as delusions, hallucinations, agitation, depression, anxiety, apathy, irritability, aberrant motor behavior, and sleep disturbances, occur in approximately 90% of older people with dementia. The purpose of the study was to identify potential barriers and facilitators prior to introducing a web-based digital tool, the Daily-BPSD. Daily-BPSD is going to be used by staff members for daily registrations of severity levels of BPSD for persons with dementia in nursing home care in Sweden. Qualitative data collection was conducted in co-production with previous users of a similar digital tool in disability care (n = 11) and future users in dementia care (n = 32). The participants were assistant nurses, care managers, nurses, occupational therapists, and relatives. The responses highlight the importance of an accessible and time-effective registration procedure, a manageable number of variables and registrations occasions per day, and ensuring that the same information does not need to be documented in different systems. The findings will be used to tailor Daily-BPSD and adequately prepare staff members for large-scale data collection in the next step of the research project. Daily-BPSD could provide an extended foundation of knowledge of the person with BPSD, which could be used to provide more person-centered and appropriate care.

IMPLEMENTATION FRAMEWORKS IN ACTION: A QUALITATIVE STUDY OF INTERGENERATIONAL TECHNOLOGY IN HIGHER EDUCATION

Abstract Cyber-Seniors is an intergenerational technology program that bridges the digital divide by training younger people to assist older adults with using technology. While higher education is an ideal setting for utilizing this program for service learning or student internship opportunities, there are often challenges to implementing this program in a higher education setting. In this study, implementation factors must be studied to improve sustainability and increase the potential to scale-up the use of Cyber-Seniors programming within higher education. This study is guided by the dynamic sustainability framework (Chambers et al., 2013) with the goal to investigate prominent contextual factors of implementation that permit and prohibit program sustainability. The study will also identify needed adaptations to Cyber-Seniors’ implementation, which will be documented using Stirman and colleagues’ (2019) Framework for Reporting Adaptations and Modifications-Enhanced (FRAME). In this presentation, we will illustrate the process of infusing implementation science frameworks into a multistage qualitative study designed to allow for in-depth understanding of experiences implementing Cyber-Seniors programming in higher education and designing an adapted checklist for program implementation. We will describe how the implementation science frameworks have been used to design the research instruments, protocols, and the analysis plan. The presentation will conclude with next steps for the research project. A key takeaway from this presentation will be for attendees to gain an understanding of how to infuse implementation science frameworks when designing, implementing, and evaluating research programs and interventions.

EUROPEAN GROUND MOTION SERVICE FOR BRIDGE MONITORING: TEMPORAL AND THERMAL DEFORMATION CROSS-CHECK USING COSMO-SKYMED INSAR

Abstract. This paper elaborates on the potential of the deformation time-series provided by European Ground Motion Service (EGMS) data points for bridge monitoring, in terms of the response of bridge structures to temporal and thermal deformations. For this purpose, high-resolution Cosmo-SkyMed (CSK) Synthetic Aperture Radar (SAR) images have been utilized through Persistent Scatterer SAR Interferometry (PS-InSAR) to derive spatially detailed deformation time-series of two bridges located at the north of Lombardy region, Italy. Then, the Annual Displacement Velocity and Thermal Expansion Coefficient of the data points in both datasets are extracted based on the corresponding deformation time-series. The response parameters are post-processed through projection and compensation steps to become comparable. Cross-checking the results by comparing the response parameters along the bridges showed that the global (for L3 products) and local (for L2b products) differential behaviour and the variation of the values of these parameters from one side to the other side of each bridge are consistent between CSK and EGMS datasets. However, the EGMS L3 information shows a slightly lower magnitude in both displacement velocity and thermal expansion coefficient responses. According to the revealed capability of EGMS information in this work, it can be concluded that the EGMS data points, if spatially cover a bridge, can present a reasonable and sufficient insight into the temporal evolution of displacement and thermal structural response, suitable for structural health monitoring and condition assessment of bridges under operational and environmental loads.

Stable nodal projection method on octree grids

We propose a novel collocated projection method for solving the incompressible Navier-Stokes equations with arbitrary boundaries. Our approach employs non-graded octree grids, where all variables are stored at the nodes. To discretize the viscosity and projection steps, we utilize supra-convergent finite difference approximations with sharp boundary treatments. We demonstrate the stability of our projection on uniform grids, identify a sufficient stability condition on adaptive grids, and validate these findings numerically. We further demonstrate the accuracy and capabilities of our solver with several canonical two- and three-dimensional simulations of incompressible fluid flows. Overall, our method is second-order accurate, allows for dynamic grid adaptivity with arbitrary geometries, and reduces the overhead in code development through data collocation.

A Lunar Perspective (an excerpt)

This is an excerpt from A Lunar Perspective: a piece of writing and performance that travels through irregular orbits around Lunar House, a Home Office Visa and Immigration building, to question our practices of mapping, bordering and othering. Weaving together voices from different writers and thinkers across disciplines and positions, the project steps in to understand the materiality of Lunar House as a site of the enactment of the border and steps out to consider and critique our current politics and practices of othering. A Lunar Perspective reflects on the reality of violence at, of, for and with the border, recognising the continued practice of hostile environment policies within the UK. Understanding a map as a way of situating in relation to others, A Lunar Perspective becomes a map of words, taking language as a practice of cartography. Our languages, our words themselves, are maps of their own journeys, travelling through linguistic roots and resurfacing in partially remembered or imagined times and places. This collection of words, growing from and rooted within my own positionality, becomes a tentative, unfixed map, sloshing like water, in a state of continually shifting relations.