bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population genomics of adaptive radiations: Exceptionally high levels of genetic diversity and recombination in an endemic spider from the Canary Islands
Authors: Escuer Paula , Guirao-Rico Sara , Arnedo Miquel A. , Sánchez-Gracia Alejandro , Rozas Julio 
Published: May 2024

AbstractThe spider genusDysderahas undergone a remarkable diversification in the oceanic archipelago of the Canary Islands, ∼60 endemic species originated during the 20 million years since the origin of the archipelago. This evolutionary radiation has been accompanied by substantial dietary shifts, often characterized by phenotypic modifications encompassing morphological, metabolic and behavioral changes. Hence, these endemic spiders represent an excellent model for understanding the evolutionary drivers and to pinpoint the genomic determinants underlying adaptive radiations. Recently, we achieved the first chromosome-level genome assembly of one of the endemic species,D. silvatica,providing a high-quality reference sequence for evolutionary genomics studies. Here, we conducted a low-coverage based resequencing study of a natural population ofD. silvaticafrom La Gomera island. Taking advantage of the new high-quality genome, we characterized genome-wide levels of nucleotide polymorphism, divergence, and linkage disequilibrium, and inferred the demographic history of this population. We also performed comprehensive genome-wide scans for recent positive selection. Our findings uncovered exceptionally high levels of nucleotide diversity and recombination in this geographically restricted endemic species, indicative of large historical effective population sizes. Furthermore, we identified genomic regions potentially under positive selection, shedding light on relevant biological processes, such as vision and nitrogen extraction as possible targets of adaptation and eventually, as drivers of the species diversification. This pioneering study in spiders endemic of an oceanic archipelago lays the groundwork for broader population genomics investigations aimed at understanding the genetic mechanisms driven adaptive radiations in island ecosystems.
Reconstitution of Arp2/3-Nucleated Actin Assembly with CP, V-1 and CARMIL
Authors: Mooren Olivia L. , McConnell Patrick , DeBrecht James D. , Jaysingh Anshuman , Cooper John A. 
Published: May 2024

SummaryActin polymerization is often associated with membrane proteins containing capping-protein-interacting (CPI) motifs, such as CARMIL, CD2AP, and WASHCAP/Fam21. CPI motifs bind directly to actin capping protein (CP), and this interaction weakens the binding of CP to barbed ends of actin filaments, lessening the ability of CP to functionally cap those ends. The protein V-1 / myotrophin binds to the F-actin binding site on CP and sterically blocks CP from binding barbed ends. CPI-motif proteins also weaken the binding between V-1 and CP, which decreases the inhibitory effects of V-1, thereby freeing CP to cap barbed ends. Here, we address the question of whether CPI-motif proteins on a surface analogous to a membrane lead to net activation or inhibition of actin assembly nucleated by Arp2/3 complex. Using reconstitution with purified components, we discovered that CARMIL at the surface promotes and enhances actin assembly, countering the inhibitory effects of V-1 and thus activating CP. The reconstitution involves the presence of an Arp2/3 activator on the surface, along with Arp2/3 complex, V-1, CP, profilin and actin monomers in solution, recreating key features of cell physiology.
Commensal or pathogen: computationally vectorizing microbial genomes forde novorisk assessment and virulence feature discovery inKlebsiella pneumoniae
Authors: Beck Kristen L. , Agarwal Akshay , Halpin Alison Laufer , McDonald L. Clifford , McKay Susannah L. , Kent Alyssa G. , Kaufman James H. , Mukherjee Vandana , Elkins Christopher A. , Seabolt Edward 
Published: May 2024

AbstractBacterial pathogenicity has traditionally focused on gene-level content with experimentally-confirmed functional properties. Hence, significant inferences are made based on similarity to known pathotypes and DNA-based genomic subtyping for risk. Herein, we achievedde novoprediction of human virulence inKlebsiella pneumoniaeby expanding known virulence genes with spatially proximal gene discoveries linked by functional domain architectures across all prokaryotes. This approach identified gene ontology functions not typically associated with virulencesensu stricto. By leveraging machine learning models with these expanded discoveries, public genomes were assessed for virulence prediction using categorizations derived from isolation sources captured in available metadata. Performance forde novostrain-level virulence prediction achieved 0.81 F1-Score. Virulence predictions using expanded “discovered” functional genetic content were superior to that restricted to extant virulence database content. Additionally, this approach highlighted the incongruence in relying on traditional phylogenetic subtyping for categorical inferences. Our approach represents an improved deconstruction of genome-scale datasets for functional predictions and risk assessment intended to advance public health surveillance of emerging pathogens.
Unconstrained Precision Mitochondrial Genome Editing with αDdCBEs
Authors: Castillo Santiago R. , Simone Brandon W. , Clark Karl J. , Devaux Patricia , Ekker Stephen C. 
Published: May 2024

ABSTRACTDddA-derived cytosine base editors (DdCBEs) enable the targeted introduction of C•G-to-T•A conversions in mitochondrial DNA (mtDNA). DdCBEs are often deployed as pairs, with each arm comprised of a transcription activator-like effector (TALE), a split double-stranded DNA deaminase half, and a uracil glycosylase inhibitor. This pioneering technology has helped improve our understanding of cellular processes involving mtDNA and has paved the way for the development of models and therapies for genetic disorders caused by pathogenic mtDNA variants. Nonetheless, given the intrinsic properties of TALE proteins, several target sites in human mtDNA remain out of reach to DdCBEs and other TALE-based technologies. Specifically, due to the conventional requirement for a thymine immediately upstream of the TALE target sequences (i.e., the 5’-T constraint), over 150 loci in the human mitochondrial genome are presumed to be inaccessible to DdCBEs. Previous attempts at circumventing this constraint, either by developing monomeric DdCBEs or utilizing DNA-binding domains alternative to TALEs, have resulted in suboptimal specificity profiles with reduced therapeutic potential. Here, aiming to challenge and elucidate the relevance of the 5’-T constraint in the context of DdCBE-mediated mtDNA editing, and to expand the range of motifs that are editable by this technology, we generated αDdCBEs that contain modified TALE proteins engineered to recognize all 5’ bases. Notably, 5’-T-noncompliant, canonical DdCBEs efficiently edited mtDNA at diverse loci. However, DdCBEs were frequently outperformed by αDdCBEs, which consistently displayed significant improvements in activity and specificity, regardless of the 5’-most bases of their TALE binding sites. Furthermore, we showed that αDdCBEs are compatible with DddAtoxand its derivatives DddA6, and DddA11, and we validated TALE shifting with αDdCBEs as an effective approach to optimize base editing outcomes at a single target site. Overall, αDdCBEs enable efficient, specific, and unconstrained mitochondrial base editing.
Flavin-containing siderophore-interacting protein ofShewanella putrefaciensDSM 9451 reveals substrate specificity in ferric-siderophore reduction
Authors: Trindade Inês B. , Fonseca Bruno M. , Catarino Teresa , Matias Pedro M. , Moe Elin , Louro Ricardo O. 
Published: May 2024

AbstractShewanellaare bacteria widespread in marine and brackish water environments and emergent opportunistic pathogens. Their environmental versatility is highly dependent on the ability to produce an abundance of iron-rich proteins, mainly multihemec-type cytochromes. Although iron plays a vital role in the ability ofShewanellaspecies to survive in various environments, very few studies exist regarding the strategies by which these bacteria scavenge iron from the environment. Small molecule siderophore-mediated iron transport is a strategy commonly employed for iron acquisition, and it was identified amongstShewanellaspp. over two decades ago.Shewanellaspecies produce hydroxamate-type siderophores and iron removal from these compounds can occur in the cytoplasm via Fe(III)-siderophore reduction mediated by siderophore-interacting proteins (SIPs). The genome ofShewanella putrefaciensDSM 9451 isolated from an infected child contains representatives of the two different cytosolic families of SIPs: the flavin-containing siderophore interacting protein family (SIP) and the iron−sulfur cluster-containing ferric siderophore reductase family (FSR).Here, we report the expression and purification of the flavin-containing (SbSIP) and iron-sulfur cluster-containing (SbFSR) Fe(III)-siderophore reductases ofShewanella putrefaciensDSM 9451. The structural and functional characterization ofSbSIP shows distinct features from the highly homologous SIP fromShewanella frigidimarina(SfSIP). These include significant structural differences, different binding affinities for NADH and NADPH, and lower rates of Fe(III)-siderophore reduction, results which consolidate in the putative identification of the binding pocket for these proteins.Overall our work highlights NADH and NADPH specificity and the different Fe(III)- siderophore reduction abilities of the SIP family suggesting a tailoring of these enzymes towards meeting different microbial iron requirements.
Structure of the lens MP20 mediated adhesive junction
Authors: Nicolas William J. , Shiriaeva Anna , Martynowycz Michael W. , Grey Angus C , Ruma Yasmeen , Donaldson Paul J , Gonen Tamir 
Published: May 2024

AbstractHuman lens fiber membrane intrinsic protein MP20 is the second most abundant membrane protein of the human eye lens. Despite decades of effort its structure and function remained elusive. Here, we determined the MicroED structure of full-length human MP20 in lipidic-cubic phase to a resolution of 3.5 Å. MP20 forms tetramers each of which contain 4 transmembrane α-helices that are packed against one another forming a helical bundle. Both the N- and C-termini of MP20 are cytoplasmic. We found that each MP20 tetramer formed adhesive interactions with an opposing tetramer in a head-to-head fashion. These interactions were mediated by the extracellular loops of the protein. The dimensions of the MP20 adhesive junctions are consistent with the 11 nm thin lens junctions. Investigation of MP20 localization in human lenses indicated that in young fiber cells MP20 was stored intracellularly in vesicles and upon fiber cell maturation MP20 inserted into the plasma membrane and restricted the extracellular space. Together these results suggest that MP20 forms lens thin junctions in vivo confirming its role as a structural protein in the human eye lens, essential for its optical transparency.
Prospective neuroimaging and neuropsychological evaluation in adults with newly diagnosed focal epilepsy
Authors: de Bezenac Christophe , Leek Nicola , Adan Guleed , Ali Ahmad , Mohanraj Rajiv , Biswas Shubhabrata , Mcginty Ronan , Murphy Kieran , Malone Helen , Baker Gus , Moore Perry , Marson Anthony G , Keller Simon S. 
Published: May 2024

AbstractObjectiveThere are few prospective longitudinal studies in patients with newly diagnosed epilepsy (NDE) despite that this is a key time point to understand the underlying biology of epilepsy and to identify potential interventions and biomarkers for seizure and cognitive outcomes. Here we have performed a prospective combined neuroimaging and neuropsychological study in a cohort of patients with focal NDE and healthy controls.MethodsWe recruited 104 patients with NDE and 45 healthy controls for research-grade 3 Tesla MRI (diagnostic and structural imaging, diffusional kurtosis imaging, resting-state functional MRI, task-based functional MRI), EEG, comprehensive neuropsychological, and blood biomarker investigations. We report here on the baseline clinical, neuroradiological, MRI morphometric, and neuropsychological findings in this cohort.Results38% of patients had unremarkable MRI features, 12% had lesions of known significance in epilepsy, 49% with abnormalities of unknown significance in epilepsy, and 23% with incidental findings. In comparison, 56% of controls had unremarkable MRI features, 7% had lesions of known significance in epilepsy, 33% with abnormalities of unknown significance in epilepsy, and 16% had incidental findings. Patients had a higher incidence of white matter hyperintensities compared to controls. Reduced bihemispheric frontal lobe cortical thickness and thalamic volumes were observed in patients with moderate effect sizes. Patients scored significantly lower on tasks of executive function, processing speed, and visual, delayed, and immediate memory, and significantly higher on depression and anxiety assessments compared to controls. Patient neuropsychological performance was related to various brain morphometric features.SignificancePeople with adult focal NDE have a greater proportion of MRI-positive findings than previously reported. Subtle white matter lesions may represent an important diagnostic criterion and have a pathophysiological basis in focal epilepsy. Morphometric and neuropsychological alterations are present at the point of diagnosis of epilepsy, which suggests that brain and cognitive changes are not exclusively due to the deleterious impact of chronic epilepsy.
Farmer sentiment and farm service agency direct loan applications
Authors: Fiechter Chad M. , Hughes Megan N. , Atkinson Sarah A. , Mintert James , Langemeier Michael R. 
Published: May 2024

PurposeFarmer sentiment may be an important indicator for the agricultural sector, similar to the way that consumer sentiment is linked to the general economy. This study uses the Purdue University–CME Group Ag Economy Barometer to test the degree to which farmer sentiment is correlated with demand for United States Department of Agriculture Farm Service Agency (FSA) direct loan applications.Design/methodology/approachWe estimate the dynamics between farmer sentiment and applications to FSA direct operating or farm ownership loans using monthly measures of farmer sentiment and loan applications from October 2015 to April 2023 and pairwise vector autoregression.FindingsA negative relationship exists between farmer sentiment and FSA direct operating loan applications. In contrast, a positive relationship exists between farmer sentiment and FSA direct farm ownership loan applications. Together, the estimated nonzero relationships suggests that the Ag Economy Barometer may be a leading indicator for the Agricultural Economy and that FSA loan programs play a nuanced role in the agricultural credit market.Originality/valueThis study uses unique data sources to further the discussion on the link between farmer sentiment and real economic outcomes and the role of an important US Federal Government farmer lending program: FSA direct loans.
Digital twin publications in construction (2017–2023): a bibliometrics-based visualization analysis
Authors: Foudah Alshaymaa , Tarek May , Essam Sarah , El Hawary Mostafa , Adel Kareem , Marzouk Mohamed 
Published: May 2024

Purpose
This study aims to thoroughly explore and visualize the trends and developments of digital twin (DT) literature in the construction field while revealing future research directions for further exploration and exploitation.

Design/methodology/approach
The research follows a three-stage methodology. First, the bibliographic data is acquired using the Web of Science database. Second, the bibliometric methods are defined to include co-authorship analysis, citation analysis, keywords co-occurrence, thematic mapping while the software tools include MS Excel, VOSviewer and Biblioshiny. Third, analysis and findings include yearly DT publication output, influential DT publications, leading DT contributors, top DT sources and science mapping of DT literature.

Findings
This study identifies top-cited DT publications (35 out of 320) in terms of citations score, local citations score and document average citations per year. Furthermore, the key contributors with respect to authors (58 out of 1147), organizations (55 out of 427) and countries (19 out of 51) are recognized in terms of productivity, influence, activeness and scientific value. Similarly, the major publishing sources (24 out of 58) are identified using the same measures. Regarding science mapping, the DT domain comprises four research frontiers, namely, deep learning and smart city, internet of things and blockchain, DT and building information modeling and machine learning and asset management.

Originality/value
Through a mixed-review strategy, this study introduces a comprehensive analysis of DT literature while avoiding the subjectivity/cognitive bias of traditional review approaches. Moreover, it illuminates the promising and rising DT themes for new/seasoned researchers, institutions, editorial boards and funding agencies.
A framework for aligning training to learner preferences in support of organizational objectives
Authors: Musgrave Jon , Fowler David , Musgrave Jill 
Published: May 2024

Purpose
This paper presents a framework that training professionals may utilize to develop training to align learner preferences with organizational objectives.

Design/methodology/approach
The authors of this paper present a framework they have used throughout the United States to prepare and develop training aligned with organizational objectives and learners' preferences in the workplace.

Findings
This paper highlights the importance of understanding organizational objectives and learner preferences when designing training and provides a framework to assist trainers. Using this framework, the authors have found that they can quickly adjust training sessions to a target audience with a broad range of personalities and preferences with good results.

Originality/value
This framework provides training practitioners with a step-by-step guide for quickly considering the alignment of organizational objectives to learner characteristics to enhance training design.
The middleman dilemma: exploring the relationship between formal ethics and ethics in practice among real estate agents in Sweden
Authors: Engström Rickard , Söderberg Inga-Lill 
Published: May 2024

PurposeThe purpose of this paper is to explore the relationship between formal ethics and ethics in practice in the empirical context of real estate agents (REAs) working in the residential housing market, including owner-occupied houses and owner-occupied apartments, in Sweden. The paper investigates problems with the Swedish middleman model of real estate agency with regard to the acceptance among REAs of borderline professional behavior.Design/methodology/approachWe report on a survey distributed to all Swedish licensed residential REAs to investigate their attitudes towards eight scenarios displaying borderline ethical behavior. Firstly, the means of each scenario were calculated, investigating signs of distance between formal ethics and ethics in practice. Secondly, logistic regressions were run for each scenario separately, thereby investigating factors affecting misconduct among REAs.FindingsThe empirical results show a clear difference between formal ethics and ethics in practice and also illustrate that some scenarios of borderline ethical behavior are creating greater problems for the REAs.Practical implicationsIn Sweden, the seller is the principal, assigning the REA to sell a house or apartment, but the regulation is clear on the role of the licensed REA as responsible for promoting an informed and fair sales process where the buyer is safe to act without their own representative. Our study contributes with information to policymakers on possible areas for the development of the middleman model.Originality/valueThe paper is the first to empirically investigate the middleman model of a Swedish real estate agency in relation to the business ethics of the agents. The use of scenarios in close relation to the everyday working context of REAs as tests of ethics of practice is also of original methodological value to investigate possible diversions of professionals from national regulations.
An investigation of waqf-based Islamic micro financial institution models to identify the most effective model for Indonesia
Authors: Ascarya Ascarya 
Published: May 2024

Purpose
This study aims to determine the best waqf-based Islamic microfinancial institution (IMFI) model by first determining various viable waqf-based IMFI models and then evaluating them based on certain criteria to obtain the best model.

Design/methodology/approach
A combination of Delphi and analytic network process (ANP) methods was used. The Delphi method was used to determine various waqf-based IMFI models and validate them, whereas the ANP method was used to evaluate those models to prioritize and find the best model.

Findings
The Delphi results show nine proposed waqf-based IMFI models that have commercial, social or integrated commercial-social orientation, where each could be in the form of a micro bank, micro venture capital (MV) or micro cooperative (MC). Delphi and ANP then determined the strategic, commercial and social criteria to evaluate the models. Finally, the ANP results show that the best waqf-based IMFI models are the integrated waqf-based micro bank, integrated waqf-based MV and integrated waqf-based MC. Integrated waqf-based IMFI provides Islamic microfinance services as well as Islamic social finance services, including waqf, zakat and infaq.

Research limitations/implications
The adoption of waqf-based IMFI could solve the structural problems of IMFIs, such as funding, low capital, mismatch, liquidity, outreach and sustainability.

Practical implications
The conceptual framework and method used in this study can be applied to determine and evaluate waqf-based IMFI models in other countries.

Originality/value
This study begins by determining various viable waqf-based IMFI models and then evaluating them to determine the priority and best waqf-based IMFI model.