bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure and evolution of Alanine/Serine Decarboxylases and the engineering of theanine production
Authors: Wang Hao , Zhu Biying , Qiao Siming , Dong Chunxia , Wan Xiaochun , Gong Weimin , Zhang Zhaoliang 
Published: September 2023

AbstractEthylamine (EA), the precursor of theanine biosynthesis, is synthesized from alanine decarboxylation by alanine decarboxylase (AlaDC) in tea plants. AlaDC evolves from serine decarboxylase (SerDC) through neofunctionalization and has lower catalytic activity. However, lacking structure information hinders the understanding of the evolution of substrate specificity and catalytic activity. In this study, we solved the X-ray crystal structures of AlaDC fromCamellia sinensis(CsAlaDC) and SerDC fromArabidopsis thaliana(AtSerDC). Tyr341of AtSerDC or the corresponding Tyr336of CsAlaDC is essential for their enzymatic activity. Tyr111of AtSerDC and the corresponding Phe106of CsAlaDC determine their substrate specificity. Both CsAlaDC and AtSerDC have a distinctive zinc finger and have not been identified in any other Group II PLP-dependent amino acid decarboxylases. Based on the structural comparisons, we conducted mutation screen of CsAlaDC. The results indicated that the mutation of L110F or P114A in the CsAlaDC dimerization interface significantly improved the catalytic activity by 110% and 59%, respectively. Combining a double mutant of CsAlaDCL110F/P114Awith theanine synthetase increased theanine production 672% in anin vitrosystem. This study provides the structural basis for the substrate selectivity and catalytic activity of CsAlaDC and AtSerDC and provides a route to more efficient biosynthesis of theanine.
“CandidatusSiderophilus nitratireducens”: a psychrophilic,nap-dependent nitrate-reducing iron oxidizer within the new order Siderophiliales
Authors: Corbera-Rubio Francesc , Stouten Gerben R. , Bruins Jantinus , Dost Simon F. , Merkel Alexander Y. , Müller Simon , van Loosdrecht Mark C. M. , van Halem Doris , Laureni Michele 
Published: September 2023

AbstractNitrate leaching from agricultural soils is increasingly found in groundwater, a primary source of drinking water worldwide. This nitrate influx can potentially stimulate the biological oxidation of iron in anoxic groundwater reservoirs. Nitrate-reducing iron-oxidizing (NRFO) bacteria have been extensively studied in laboratory settings, yet their ecophysiology in natural environments remains largely unknown. To this end, we established a pilot-scale filter on nitrate-rich groundwater to elucidate the structure and metabolism of nitrate-reducing iron-oxidizing microbiomes under oligotrophic conditions mimicking natural groundwaters. The enriched community stoichiometrically removed iron and nitrate consistently with NRFO metabolism. Genome-resolved metagenomics revealed the underlying metabolic network between the dominant iron-dependent denitrifying autotrophs and the less abundant organoheterotrophs. The most abundant genome belonged to a newCandidateorder, named Siderophiliales. This new species, “CandidatusSiderophilus nitratireducens”, carries central genes to iron oxidation (cytochromec cyc2), carbon fixation (rbc), and for the sole periplasmic nitrate reductase (nap). To our knowledge, this is the first report ofnap-based lithoautotrophic growth, and we demonstrate that iron oxidation coupled to dissimilatory reduction of nitrate to nitrite is thermodynamically favourable under realistic Fe3+/Fe2+andconcentration ratios. Ultimately, by bridging the gap between laboratory investigations and real-world conditions, this study provides insights into the intricate interplay between nitrate and iron in groundwater ecosystems, and expands our understanding of NRFOs taxonomic diversity and ecological role.
Comparative Analysis of Multiple Consensus Genomes of the Same Strain of Marek’s Disease Virus Reveals Intrastrain Variation
Authors: Ortigas-Vasquez Alejandro , Pandey Utsav , Renner Daniel , Bowen Chris , Baigent Susan J. , Dunn John , Cheng Hans , Yao Yongxiu , Read Andrew F. , Nair Venugopal , Kennedy Dave A. , Szpara Moriah L. 
Published: September 2023

AbstractCurrent strategies to understand the molecular basis of Marek’s disease virus (MDV) virulence primarily consist of cataloguing divergent nucleotides between strains with different phenotypes. However, each MDV strain is typically represented by a single consensus genome despite the confirmed existence of mixed viral populations. To assess the reliability of single-consensus interstrain genomic comparisons, we obtained two additional consensus genomes of vaccine strain CVI988 (Rispens) and two additional consensus genomes of the very virulent strain Md5 by sequencing viral stocks and cultured field isolates. In conjunction with the published genomes of CVI988 and Md5, this allowed us to perform 3-way comparisons between consensus genomes of the same strain. We found that consensus genomes of CVI988 can vary in as many as 236 positions involving 13 open reading frames (ORFs). In contrast, we found that Md5 genomes varied only in 11 positions involving a single ORF. Phylogenomic analyses showed all three Md5 consensus genomes clustered closely together, while also showing that CVI988GenBank.BACdiverged from CVI988Pirbright.laband CVI988USDA.PA.field. Comparison of CVI988 consensus genomes revealed 19 SNPs in the unique regions of CVI988GenBank.BACthat were not present in either CVI988Pirbright.labor CVI988USDA.PA.field. Finally, we evaluated the genomic heterogeneity of CVI988 and Md5 populations by identifying positions with >2% read support for alternative alleles in two ultra-deeply sequenced samples. We were able to confirm that both populations of CVI988 and Md5 were mixed, exhibiting a total of 29 and 27 high-confidence minor variant positions, respectively. We did not find any evidence of minor variants in the positions corresponding to the 19 SNPs in the unique regions of CVI988GenBank.BAC. Taken together, our findings confirm that consensus genomes of the same strain of MDV can vary and suggest that multiple consensus genomes per strain are needed in order to maximize the accuracy of interstrain genomic comparisons.
Algorithms for the identification of prevalent diabetes in the All of Us Research Program validated using polygenic scores – a new resource for diabetes precision medicine
Authors: Szczerbinski Lukasz , Mandla Ravi , Schroeder Philip , Porneala Bianca C. , Li Josephine H. , Florez Jose C. , Mercader Josep M. , Manning Alisa K. , Udler Miriam S. 
Published: September 2023

ABSTRACTOBJECTIVEThe study aimed to develop and validate algorithms for identifying people with type 1 and type 2 diabetes in the All of Us Research Program (AoU) cohort, using electronic health record (EHR) and survey data.RESEARCH DESIGN AND METHODSTwo sets of algorithms were developed, one using only EHR data (EHR), and the other using a combination of EHR and survey data (EHR+). Their performance was evaluated by testing their association with polygenic scores for both type 1 and type 2 diabetes.RESULTSFor type 1 diabetes, the EHR-only algorithm showed a stronger association with T1D polygenic score (p=3×10−5) than the EHR+. For type 2 diabetes, the EHR+ algorithm outperformed both the EHR-only and the existing AoU definition, identifying additional cases (25.79% and 22.57% more, respectively) and showing stronger association with T2D polygenic score (DeLongp=0.03 and 1×10−4, respectively).CONCLUSIONSWe provide new validated definitions of type 1 and type 2 diabetes in AoU, and make them available for researchers. These algorithms, by ensuring consistent diabetes definitions, pave the way for high-quality diabetes research and future clinical discoveries.GRAPHICAL ABSTRACTArticle Highlightsa.Why did we undertake this study?This study was conducted to develop and validate algorithms for identifying type 1 and type 2 diabetes cases in the All of Us Research Program (AoU).b.What is the specific question(s) we wanted to answer?Can accurate algorithms for type 1 and type 2 diabetes identification be developed and validated using AoU cohort Electronic Health Record (EHR) and survey data? Do the identified diabetes cases show association with polygenic scores in diverse populations?c.What did we find?We developed a new validated type 1 diabetes definition and expanded upon the existing type 2 diabetes definition.d.What are the implications of our findings?The developed algorithms can be universally implemented in AoU for identifying study participants for well-defined case-control diabetes studies.
A fuzzy logic evolution of the functional resonance analysis method (FRAM) to assess risk in ground operation
Authors: Tengiz Ertan , Unal Gulay 
Published: September 2023

Purpose
The basis of safe flight is the management of risks. This paper aims to present a new process-based risk assessment model, with an approach to calculate the risk score.

Design/methodology/approach
Since thousands of minor changes occur within ground operations, it is difficult to calculate how much risk these variations will pose. This paper proposes a risk assessment model fed from analysis of ground operation processes using functional resonance analysis method (FRAM) and fuzzy logic.

Findings
FRAM is used to detect variations in ground operation. Using the FRAM analysis, it has been revealed how much risk the process steps described in the procedures involve. The risk score was calculated by combining the probability value obtained from the airline’s database and the severity assessment of the expert group in fuzzy logic. The risk level can be monitored dynamically with the transfer of events in the airline’s database to the process-based risk assessment model.

Originality/value
FRAM analysis, which is used to detect function variations before undesirable risk occurs, has brought a proactive approach to risk assessment. The process-based risk assessment model allows the creation of new safety parameter indicators to be followed to reduce the risk level of the function with a high-risk level. The proposed approach can be used for other operational areas in aviation as well.
Does the analytical hierarchy process help appraisers make better decisions? A quasi-experimental approach for property investment comparables
Authors: Aihie Vincent Uwaifiokun , Oyetunji Abiodun Kolawole , Omotayo Temitope , Ekundayo Damilola 
Published: September 2023

PurposeIncome from investment properties can fluctuate depending on the state of the economy. The idea that there is always a potential exit (sale) value whenever the property stops performing at its optimum or deflation in the economy will always appeal to investors. To determine housing prices, investors would rely on a direct comparison approach (DCA) of recent substitute sales in the open market. Appraisers use this approach to develop an opinion of value when there is a plethora of recent sales to analyse.Design/methodology/approachThe study was designed to establish the use of the analytical hierarchy process (AHP) approach as a support tool for deciding property appraisals. A case study of an industrial single-storey stand-alone building with grade-level parking in the south-east of Calgary, Canada, was investigated with the AHP approach. The result was cross-referenced with the DCA.FindingsUsing a consistency index of 0.077321 and a consistency ratio of 0.085912, the matrix multiplication was determined to be 0.456706. The average valuations derived from the adjusted price per square foot using the direct comparison method and the unadjusted price per square foot using the AHP were deemed the best value estimate in the light of available comparables. The implications of the findings suggest that AHP, as a quantitative technique, can support and validate the use of similar non-recent sale comparables when appraising investment properties with the DCA.Originality/valueAHP is an alternative aid in quantitatively deciding the most significant value attribute for comparison before subjective adjustments. When intuitively applied in the DCA, these subjective adjustments almost always lead to an overvaluation of properties.
Characterizing digital service innovation: phases, actors, functions and interactions in the context of a digital service platform
Authors: Narvaiza Lorea , Campos José Antonio , Martín-Peña María Luz , Díaz-Garrido Eloísa 
Published: September 2023

PurposeDigital service innovation (DSI) is a type of technological innovation that is recognized in practice in the innovation structure of companies. Given the breadth of digital technologies that enable digital services and the variety of these services, analysis is needed to discern the nature of these services, as well as the process that culminates in co-innovation. The literature on DSI is fragmented and spread across multiple research areas. This fragmentation impedes conceptualization of the elements that constitute DSI. This paper describes the nature of DSI through the process and elements of initiation, adoption and routinization of DSI in the context of digital service platforms (DSPs).Design/methodology/approachThis paper presents a single exploratory case study of a provider of a leading digital solution in customer relations. The data analysis is based on abductive reasoning.FindingsThe paper conceptualizes the nature of DSI and describes the process and elements of DSI (phases, actors, functions and interactions). It contributes to building a common language for DSI research in service management. The analysis shows that DSI in DSPs is synonymous with co-innovation. This paper offers insight into how co-innovation occurs, using hybrid agile methodologies with the coordination of multiple actors and multilateral interactions.Originality/valueThe originality and value of the study reside in its conceptualization and analysis of what is meant by DSI. The components of the service and the technological requirements for not only provision but also ideation and development appear to be inseparable. The study unveils the mechanisms that turn a digital service solution into a co-innovative proposal. This knowledge can facilitate scalability in digital services.
Getting along and getting ahead: voice trails of status pursuit
Authors: Khan Nabila , Dyaram Lata , Dayaram Kantha , Burgess John 
Published: September 2023

PurposeIntegrating individual and relational centric voice literature, the authors draw on self-presentation theory to analyse the role of status pursuit in employee voice. Status pursuit is believed to be ubiquitous as it is linked to access to scarce resources and social order pecking.Design/methodology/approachThe authors present a cross-level conceptual model outlining relational nuances of employee status pursuit that drive upward voice.FindingsThe model integrates status pursuit with peer- and leader-related facets, focusing on three targets of voice: immediate leader (supervisor), diagonal leader (supervisor of another team/unit) and co-workers. The model highlights how employee voice can be directed to diverse targets, and depending on interpersonal attributes, how it serves as underlying links for upward voice.Originality/valueWhile employee voice can help to address important workplace concerns, it can also be used to advance employees' self-interest. Though there is a wealth of research on the importance of employee voice to organisational performance and individual wellbeing, especially through collective representation such as trade unions, there is a lack of literature on how employees navigate the social-relational work setting to promote their interests and develop status.
Oil spills removal from seawater surface by magnetic biochar composite derived from Heglig tree bark and cobalt ferrite
Authors: Amar Ibrahim A. , Alzarouq Aeshah , Mohammed Wajdan , Zhang Mengfei , Matroed Noarhan 
Published: September 2023

Purpose
This study aims to explore the possibility of using magnetic biochar composite (MBCC) derived from Heglig tree bark (HTB) powder (agricultural solid waste) and cobalt ferrite (CoFe2O4, CFO) for oil spill removal from seawater surface.

Design/methodology/approach
One-pot co-precipitation route was used to synthesize MBCC. The prepared materials were characterized by X-ray diffraction, scanning electron microscopy-energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy. The densities of the prepared materials were also estimated. Crude, diesel engine and gasoline engine oils were used as seawater pollutant models. The gravimetric oil removal (GOR) method was used for removing oil spills from seawater using MBCC as a sorbent material.

Findings
The obtained results revealed that the prepared materials (CFO and MBCC) were able to remove the crude oil and its derivatives from the seawater surface. Besides, when the absorbent amount was 0.01 g, the highest GOR values for crude oil (31.96 ± 1.02 g/g) and diesel engine oil (14.83 ± 0.83 g/g) were obtained using MBCC as an absorbent. For gasoline engine oil, the highest GOR (27.84 ± 0.46 g/g) was attained when CFO was used as an absorbent.

Originality/value
Oil spill removal using MBCC derived from cobalt ferrite and HTB. Using tree bark as biomass (eco-friendly, readily available and low-cost) for magnetic biochar preparation also is a promising method for minimizing agricultural solid wastes (e.g. HTB) and obtaining value-added-products.
The assessment of structural behaviours of steel framing system – affordable house system design
Authors: Hashim Nor Salwani , De’nan Fatimah , Naaim Nurfarhah 
Published: September 2023

Purpose
Nowadays, residential buildings have become increasingly important due to the growing communities. The purpose of this study is to investigate the behavior of a steel structural framing system that incorporates lightweight load-bearing walls and slabs, and to compare the weight of materials used in cold-formed and hot-finished steel structural systems for affordable housing.

Design/methodology/approach
Four types of models consisting of 243 members were simulated. Model 1 is a cold-formed steel structural framing system, while Model 2 is a hot-finished steel structural framing system. Both Models 1 and 2 use lightweight wall panels and lightweight composite slabs. Models 3 and 4 are made with brick walls and precast reinforced concrete systems, respectively. These structures use different wall and slab materials, namely, brick walls and precast reinforced concrete. The analysis includes bending behavior, buckling resistance, shear resistance and torsional rotation analysis.

Findings
This study found that using thinner steel sections can increase the deflection value. Meanwhile, increasing member length and the ratio of slenderness will decrease buckling resistance. As the applied load increases, buckling deformation also increases. Furthermore, decreasing shear area causes a reduction in shear resistance. Thicker sections and the use of lightweight materials can decrease the torsional rotation value.

Originality/value
The weight comparison of the steel structures shows that Model 1, which is a cold-formed steel structure with lightweight wall panels and lightweight composite slabs, is the most suitable model due to its lightweight and affordability for housing. This model can also be used as a reference for the optimal design of modular structural framing using cold-formed steel materials in the field of civil engineering and as a promotional tool.
THE URBAN LEFT IN POWER: Comparing the Profiles of ‘Municipal Socialists’ and the ‘New Urban Left’ in Swiss Cities
Authors: Antoniazza Baptiste , Mach André , Strebel Michael Andrea 
Published: September 2023

AbstractToday, many cities in post‐industrial societies are strongholds of left and progressive political forces. Almost 100 years ago, left parties had instituted municipal socialism in several European cities. In this article, we compare these two periods of left urban rule by focusing on the long‐term changes over the last 120 years in the socio‐demographic profile of urban left elites in four major Swiss cities. Our analysis of left elected representatives at six key dates highlights the main differences between the municipal socialists of the interwar period and the new urban left that rules contemporary cities. The former are members of the working class, blue‐collar workers without university education, while the latter are members of the upper‐middle class, highly educated sociocultural professionals. The results of our analysis contribute to a better understanding of the sociological composition of urban left‐progressive political forces, an aspect that is somewhat neglected in recent research on the urban left. We discuss the potential political implications and further research avenues for contemporary debates in urban studies, in terms of urban policy priorities and political mobilization.
Comparing letrozole and mifepristone pre‐treatment in medical management of first trimester missed miscarriage: a prospective open‐label non‐inferiority randomised controlled trial
Authors: Du Libei , Li Hang Wun Raymond , Gemzell‐Danielsson Kristina , Zhang Zhiqiang , Du Yanhong , Zhang Wenju , Xu Bo , Wang Xiaozhong , Wang Yaokai , Wan Wenjuan , Chang Ying , Diao Weiyu , Wang Yanli , Zhang Li , Ho Pak Chung 
Published: September 2023

AbstractObjectiveTo investigate whether letrozole pre‐treatment is non‐inferior to mifepristone pre‐treatment, followed by misoprostol, for complete evacuation in the medical treatment of first‐trimester missed miscarriage.DesignProspective open‐label non‐inferiority randomised controlled trial.SettingA university‐affiliated hospital.PopulationWe recruited 294 women diagnosed with first‐trimester missed miscarriage who opted for medical treatment.MethodsParticipants were randomly assigned to: (i) the mifepristone group, who received 200 mg mifepristone orally followed 24–48 h later by 800 μg misoprostol vaginally; or (ii) the letrozole group, who received 10 mg letrozole orally once‐a‐day for 3 days, followed by 800 μg misoprostol vaginally on the third (i.e. last) day of letrozole administration.Main outcome measuresThe primary outcome was the rate of complete evacuation without surgical intervention at 42 days post‐treatment. Secondary outcomes included induction‐to‐expulsion interval, adverse effects, women's satisfaction, number of doses of misoprostol required, duration of vaginal bleeding, pain score on the day of misoprostol administration and other adverse events.ResultsThe complete evacuation rates were 97.8% (95% CI 95.1%–100%) and 97.2% (95% CI 94.4%–99.9%) in the letrozole and mifepristone groups, respectively (p ≤ 0.001 for non‐inferiority). The mean induction‐to‐tissue expulsion interval in the letrozole group was longer compared with the mifepristone group (15.4 vs 9.0 h) (p = 0.03). The letrozole group had less heavy post‐treatment bleeding and an earlier return of menses. There were no statistically significant differences in the number of doses of misoprostol required, the duration of vaginal bleeding, the pain score on the day of misoprostol administration and the rate of other adverse events between the two groups. The majority of the women (91.2% and 93.9% in the letrozole and mifepristone groups, respectively) were satisfied with their treatment option.ConclusionsLetrozole is non‐inferior to mifepristone as a pre‐treatment, followed by misoprostol, for the medical treatment of first‐trimester missed miscarriage.