bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenges and best practices for digital unstructured data enrichment in health research: a systematic narrative review
Authors: Sedlakova Jana , Daniore Paola , Wintsch Andrea Horn , Wolf Markus , Stanikic Mina , Haag Christina , Sieber Chloé , Schneider Gerold , Staub Kaspar , Ettlin Dominik Alois , Grübner Oliver , Rinaldi Fabio , von Wyl Viktor ,   University of Zurich Digital Society Initiative (UZH-DSI) Health Community
Published: July 2022

AbstractDigital data play an increasingly important role in advancing medical research and care. However, most digital data in healthcare are in an unstructured and often not readily accessible format for research. Specifically, unstructured data are available in a non-standardized format and require substantial preprocessing and feature extraction to translate them to meaningful insights. This might hinder their potential to advance health research, prevention, and patient care delivery, as these processes are resource intensive and connected with unresolved challenges. These challenges might prevent enrichment of structured evidence bases with relevant unstructured data, which we refer to as digital unstructured data enrichment. While prevalent challenges associated with unstructured data in health research are widely reported across literature, a comprehensive interdisciplinary summary of such challenges and possible solutions to facilitate their use in combination with existing data sources is missing.In this study, we report findings from a systematic narrative review on the seven most prevalent challenge areas connected with the digital unstructured data enrichment in the fields of cardiology, neurology and mental health along with possible solutions to address these challenges. Building on these findings, we compiled a checklist following the standard data flow in a research study to contribute to the limited available systematic guidance on digital unstructured data enrichment. This proposed checklist offers support in early planning and feasibility assessments for health research combining unstructured data with existing data sources. Finally, the sparsity and heterogeneity of unstructured data enrichment methods in our review call for a more systematic reporting of such methods to achieve greater reproducibility.
Mutational analysis of a conserved positive charge in the c-ring of E. coli ATP synthase
Authors: Shrestha Rashmi K. , Founds Michael W. , Shepard Sam J. , Rothrock Mallory M. , Defnet Amy E. , Steed P. Ryan 
Published: July 2022

ABSTRACTF1Fo ATP synthase is a ubiquitous molecular motor that utilizes a rotary mechanism to synthesize adenosine triphosphate (ATP), the fundamental energy currency of life. The membrane-embedded Fo motor converts the electrochemical gradient of protons into rotation, which is then used to drive the conformational changes in the soluble F1 motor that catalyze ATP synthesis. In E. coli, the Fo motor is composed of a c10 ring (rotor) alongside subunit a (stator), which together provide two aqueous half channels that facilitate proton translocation. Previous work has suggested that Arg50 and Thr51 on the cytoplasmic side of each subunit c are involved in the proton translocation process, and positive charge is conserved in this region of subunit c. To investigate the role of these residues and the chemical requirements for activity at these positions, we generated eleven substitution mutants and assayed their in vitro ATP synthesis, H+ pumping, and passive H+ permeability activities, as well as the ability of mutants to carry out oxidative phosphorylation in vivo. While polar and hydrophobic mutations were generally tolerated in either position, introduction of negative charge caused a substantial defect. We discuss the possible effects of altered electrostatics on the interaction between the rotor and stator, water structure in the aqueous channel, and interaction of the rotor with phospholipids.
Characterization of heterogeneity in nanodisc samples using Feret signatures
Authors: Vilela Fernando , Bezault Armel , de Francisco Borja Rodriguez , Sauvanet Cécile , Xu Xiao-Ping , Swift Mark F. , Yao Yong , Marrasi Francesca M. , Hanein Dorit , Volkmann Niels 
Published: July 2022

ABSTRACTNanodiscs have become a popular tool in structure determination of membrane proteins using cryogenic electron microscopy and single particle analysis. However, the structure determination of small membrane proteins remains challenging. When the embedded protein is in the same size range as the nanodisc, the nanodisc can significantly contribute to the alignment and classification during the structure determination process. In those cases, it is crucial to minimize the heterogeneity in the nanodisc preparations to assure maximum accuracy in the classification and alignment steps of single particle analysis. Here, we introduce a new in-silico method for the characterization of nanodisc samples that is based on analyzing the Feret diameter distribution of their particle projection as imaged in the electron microscope. We validated the method with comprehensive simulation studies and show that Feret signatures can detect subtle differences in nanodisc morphologies and composition that might otherwise go unnoticed. We used the method to identify a specific biochemical nanodisc preparation with low size variations, allowing us to obtain a structure of the 23-kDa single-span membrane protein Bcl-xL while embedded in a nanodisc. Feret signature analysis can steer experimental data collection strategies, allowing more efficient use of high-end data collection hardware, as well as image analysis investments in studies where nanodiscs significantly contribute to the total volume of the full molecular species.GRAPHICAL ABSTRACTHIGHLIGHTSNew methodology to characterize nanodiscs based on Feret signaturesFeret signatures distinguish nanodisc morphologies and compositionsAnalysis is highly sensitive to sample qualityMethod selected condition to solve structure of small membrane protein Bcl-xL
Spatiotemporal Distribution of Vector Mosquito Species and Areas at Risk for Arbovirus Transmission in Maricopa County, Arizona
Authors: Wilke André B. B. , Damian Dan , Litvinova Maria , Byrne Thomas , Zardini Agnese , Poletti Piero , Merler Stefano , Mutebi John-Paul , Townsend John , Ajelli Marco 
Published: July 2022

AbstractMosquito-borne diseases are a major global public health concern and mosquito surveillance systems are essential for the implementation of effective mosquito control strategies. The objective of our study is to determine the spatiotemporal distribution of vector mosquito species in Maricopa County, AZ from 2011 to 2021, and to identify the hotspot areas for West Nile virus (WNV) and St. Louis Encephalitis virus (SLEV) transmission in 2021. The Maricopa County Mosquito Control surveillance system utilizes BG-Sentinel and EVS-CDC traps throughout the entire urban and suburban areas of the county. We estimated specific mosquito species relative abundance per unit area using the Kernel density estimator in ArcGIS 10.2. We calculated the distance between all traps in the surveillance system and created a 4 km buffer radius around each trap to calculate the extent to which each trap deviated from the mean number ofCx. quinquefasciatusandCx. tarsaliscollected in 2021. Our results show that vector mosquito species are widely distributed and abundant in the urban areas of Maricopa County. A total of 691,170Culex quinquefasciatus, 542,733Culex tarsalis, and 292,305Aedes aegyptiwere collected from 2011 to 2022. The relative abundance ofAe. aegyptiwas highly seasonal peaking in the third and fourth quarters of the year.Culex quinquefasciatus, on the other hand, was abundant throughout the year with several regions consistently yielding high numbers of mosquitoes.Culex tarsaliswas abundant but it only reached high numbers in well-defined areas bordering natural and rural areas. We also detected high levels of heterogeneity in the risk of WNV and SLEV transmission to humans disregarding traps geographical proximity. The well-defined species-specific spatiotemporal and geographical patterns found in this study can be used to inform vector control operations.
Structure of a LRRC8 chimera with physiologically relevant properties reveals heptameric assembly and pore-blocking lipids
Authors: Takahashi Hirohide , Yamada Toshiki , Denton Jerod S. , Strange Kevin , Karakas Erkan 
Published: July 2022

ABSTRACTVolume-regulated anion channels (VRACs) mediate Cl- and organic solute efflux from vertebrate cells and are essential for cell volume homeostasis. VRACs are heteromeric assemblies of LRRC8A-E proteins with unknown stoichiometries. Homomeric LRRC8A and LRRC8D channels have a hexameric structure. However, these channels are either non-functional or exhibit abnormal functional properties limiting their utility for structure-function analyses. We circumvented these limitations by developing novel homomeric LRRC8 chimeric channels with physiologically relevant functional properties. We demonstrate here that the LRRC8C-LRRC8A(IL125) chimera comprising LRRC8C and 25 amino acids unique to the first intracellular loop (IL1) of LRRC8A has a heptameric structure like that of homologous pannexin channels. Membrane lipids are a key structural element of the channel and are located between subunits and occluding the channel pore. Our results suggest that native VRAC/LRRC8 channels are heptamers and that associated lipids are likely essential for normal channel gating and regulation.
Structural conservation of MALAT1 long non-coding RNA in cells and in evolution
Authors: Monroy-Eklund Anais , Taylor Colin , Weidmann Chase , Burch Christina , Laederach Alain 
Published: July 2022

AbstractAlthough not canonically polyadenylated, the long non-coding RNA MALAT1 (Metastasis Associated Lung Adenocarcinoma Transcript 1) is stabilized by a highly conserved 159 nucleotide triple helix structure on its 3’ end. The entire MALAT1 transcript is over 8,000 nucleotides long in humans and is considered one of the most conserved lncRNAs, at both the sequence and structure levels. The strongest structural conservation signal (as measured by co-variation of base-pairs) is in the triple helix structure. Primary sequence analysis of co-variation alone cannot confirm the degree of structural conservation of the entire full-length transcript. Furthermore, RNA structure is often context dependent; RNA binding proteins that are differentially expressed in different cell types may alter structure. We investigate here the in cell and cell free structures of the full-length human and green monkey (Chlorocebus sabaeus) MALAT1 transcripts in multiple tissue-derived cell lines using SHAPE chemical probing. Our data reveals surprising levels of uniform structural conservation in different cell lines, in cells and cell free, and even between species, despite significant differences in primary sequence. The uniformity of the structural conservation across the entire transcript suggests that, despite seeing co-variation signals only in the three-helix junction of the lncRNA, the rest of the transcript’s structure is remarkably conserved at least in primates and across multiple cell types and conditions.
Student use of digital libraries during COVID-19: structural equation modelling in Indonesian and Malaysian contexts
Authors: Habibi Akhmad , Yaakob Mohd Faiz Mohd , Sofwan Muhammad 
Published: July 2022

Purpose
This paper aims to examine the determinants that drive digital library use by university students in Indonesia and Malaysia during COVID-19. A proposed model based on the unified theory of acceptance and use of technology model-2 was implemented.

Design/methodology/approach
A pilot study was conducted prior to the main data collection to examine the reliability of the instrument. For the structural model assessment, 1,168 responses were analysed through partial least square structural equation modelling (PLS-SEM) and importance and performance analysis (IPMA). A t-test was also conducted to support the main findings.

Findings
Most hypotheses are confirmed by the significant results reported through the PLS-SEM. The strongest determinant of behavioural intention is habits. Digital library use is most significantly predicted by behavioural intention. Through IPMA, habits are reported to be the most important determinant for behavioural intention. Performance expectancy obtains the highest performance in the IPMA procedure. Behavioural intention and digital library use are significantly different based on the respondents’ location.

Originality/value
This study addresses the research gap (comparative studies between two countries) by evaluating digital library use among students in two universities in Indonesia and Malaysia during COVID-19. Findings could facilitate policymakers with insights into digital library use determinants and initiate effective and efficient policies to improve digital library use, especially during school closures due to certain situations or conditions.
A new approach for layout design of an emergency department in hospitals: a case from Jordan
Authors: Khatib Majd , Alshboul Abdulsalam 
Published: July 2022

Purpose
The design of the emergency department (ED) requires high precision in the process of distributing spaces. An increase in population and continuous development during the past years caused the addition of new services, changes in patients’ numbers, movement flow and treatment procedures which makes the existing layout plan of the ED no longer appropriate for its current needs. Therefore, the purpose of this paper is to generate a process of finding better alternatives for ED’s spatial planning.

Design/methodology/approach
The genetic algorithm method as a part of the systematic layout planning strategy was adopted for decision-making in redesigning the ED layout and finding the most appropriate alternative. This methodology was applied to a teaching hospital in Jordan to create layout alternatives with better functional dimensions.

Findings
The design that is based on the study of the movement of users and the relationship of spaces increases the layout performance.

Research limitations/implications
The structural method of this study can be adopted for different hospital designs, but the results are limited only to the study case itself because of the different factors and data for each building.

Originality/value
This study demonstrates the process of making the most appropriate decision to redesign the ED in the hospital; therefore, the method can be adopted in restructuring the scheme of different hospitals and evaluated, especially before implementation.
Severe and multiple disadvantage: development and applications of a concept
Authors: Lemkes Alice 
Published: July 2022

Purpose
This paper aims to remove the self-evidence of the concept of severe and multiple disadvantage (SMD) by drawing upon a historical as well as a critical perspective to show its contingency.

Design/methodology/approach
This paper will introduce the concept of SMD by examining how it has come to be understood in the way that it has. This paper does so by exploring key texts which have informed the development of the concept as well as its conceptual near neighbours such as “multiple needs”. This paper traces some advancements of the concept within practice and further research with a focus on the Fulfilling Lives programme and the Lankelly Chase Foundation. Finally, the author reflects critically upon the concept and the manner in which the concept has become operationalised.

Findings
This analysis demonstrates how a particular definition of SMD has come to dominate over the past few years because of the research and practice of key organisations. On the one hand, this has further marginalised alternative definitions and ways of working, but on the other hand these stakeholders have been able to influence the way in which UK policy has taken up the concept within its governmental priorities.

Originality/value
To date, research has taken the term SMD for granted which limits the ability to critique its definitions and applications. This is an important and timely contribution because concepts are all-too-often taken for granted and at a pivotal moment when SMD has become nationalised through policy, critique is a political, potentially transformative, act.
Urban mix in housing neighbourhoods: challenges, evaluation method and diagnosis of Ayouf in Jijel, Algeria
Authors: Hallal Ibtissem , Sahnoune Tayeb 
Published: July 2022

Purpose
This study aims to identify the challenges of new urban housing zones in Algeria that have permitted the emergence of many habitat neighbourhoods deprived of all services. The objective is to promote social interaction by departing from the zoning and introducing the notion of urban mix.

Design/methodology/approach
This study tries to catch different elements that contribute to promote the degree of social interaction. This step ultimately has led to the need to improve the quality conditions of the living environment and focus the analysis on urban mix advantages. The latter aims to organize space by balancing functional, social and spatial magnitudes. Different methods have been adopted to assess each dimension. Starting with the assessment of the functional mix, the functional mix coefficient (C.Mix f) was calculated in a quantitative approach, and attendance rates of various targeted functions were determined in a second qualitative one. However, regarding the social mix, several evaluation criteria were selected. Finally, the spatial mix was evaluated via three modes of occupation; mix on the islet, mix on the parcel and mix on the building.

Findings
The results of this research confirm that urban mix is imperative to counteract problems generated by zoning. It also concludes that urban mix can be assessed through a grid of indicators. The case study of Ayouf-Jijel revealed that it benefits from good coverage of amenities and businesses; the authors also found that most indicators present some qualitative rather than quantitative deficiencies. This concerns the location of businesses in collective and individual housing. This phenomenon is scattered in the neighbourhood’s development.

Originality/value
The objective of this paper is to contribute to the argument on how to develop neighbourhoods in a city in general and particular to the city of Jijel through the urban mix by taking into account several indicators under three measurements: functional, social and spatial. In addition, the paper contributes to discuss new methods for the evaluation and implementation of urban mix. Finally, this paper reveals an opportunity to rethink neighbourhoods regarding new approaches and reflections of cosmopolite development versus zoning.
Exploring the frictional characteristics of kelp liquid as an environmentally friendly lubricant
Authors: Yang Huiyun , Lu Hailin , Wang Changkai , Jia Endong , Xue Bowen , Chai Guiquan 
Published: July 2022

Purpose
Kelp is widely productive and inexpensive. The purpose of this study is to explore kelp liquid (KL) as an environment-friendly water-based lubricant, which is expected to replace some industrial lubricants and protect the environment while satisfying lubricating performance.

Design/methodology/approach
In this experiment, the soaked kelp was broken up by a wall-breaking machine to get the KL by a centrifuge. Elements and crystal structure of KL samples were characterized by X-ray photoelectron spectroscopy, X-ray diffraction and Raman spectra. The friction test is carried out by the relative movement of the polyethylene ball and the aluminum disk on the friction tester.

Findings
Friction experiments showed that 0.1 Wt.% KL has a good lubrication effect, and the average coefficient of friction is 0.063 under the condition of applying a 10 N load and moving at a speed of 2.0 cm/s. KL has good thermal conductivity with excellent cooling effect and high intermolecular force which makes high viscosity for excellent lubricating behavior, at the meantime molecules in solution remain stable which shows an excellent dispersibility.

Originality/value
At present, the research on kelp mainly focuses on its medicinal value and abundant nutritional value, and the research on its lubrication effect is less. Based on this situation, this paper explored the characteristics of KL as an environmentally friendly lubricant, which is expected to be used as a green cutting fluid.
Institutional quality, macroeconomic uncertainty and efficiency of financial institutions in Sub-Saharan Africa
Authors: Abaidoo Rexford , Agyapong Elvis Kwame 
Published: July 2022

PurposeThis paper evaluates how institutions of governance and macroeconomic uncertainty influence efficiency of financial institutions in the subregion of Sub-Saharan Africa (SSA). Data for the empirical inquiry were compiled from relevant sources for 33 countries in the subregion from 2002 to 2019. Empirical estimates verifying hypothesized relationships were carried out using the continuous updating estimator (CUE) by Hansenet al.(1996).Design/methodology/approachThe purpose of this paper is to evaluates how institutions of governance and macroeconomic uncertainty influence efficiency of financial institutions in the subregion of Sub-Saharan Africa (SSA). Data for the empirical inquiry were compiled from relevant sources for 33 countries in the subregion from 2002 to 2019. Empirical estimates verifying hypothesized relationships were carried out using the continuous updating estimator (CUE) by Hansenet al.(1996).FindingsThe results suggest that institutional quality has significant positive effect on financial institution efficiency, supporting the view that improved and supportive structures of governance tend to promote operational efficiency among financial institutions among economies in SSA. In addition, improvement in individual governance indicators such as corruption control, government effectiveness, regulatory quality and rule of law was also found to support or enhance efficiency of financial institutions among economies in the subregion. Macroeconomic uncertainty on the other hand is found to impede efficiency of financial institutions; the same condition (macroeconomic uncertainty) is further found to negate any positive impact corruption control, government effectiveness, regulatory quality and rule of law have on operational efficiency among financial institutions in the subregion.Originality/valueUnlike most of related studies, this study adopts a different approach on the dynamics of financial institutions. Approach pursued in this empirical inquiry examines how the regulatory environment within which financial institutions operate, the form of governance and the quality of government institutions influence efficiency of financial institutions among emerging economies in Sub-Sahara. Empirical analysis conducted examines effects of variables that are unique to this study; these variables are either constructed or econometrically derived specifically for various interactions verified in the study. For instance, institutional quality variable is an index constructed specifically for this study using principal component analysis approach.