bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ancient Sheep Genomes reveal four Millennia of North European Short-Tailed Sheep in the Baltic Sea region
Authors: Larsson Martin NA , Miranda Pedro Morell , Pan Li , Başak Vural Kıvılcım , Kaptan Damla , Rodrigues Soares André Elias , Kivikero Hanna , Kantanen Juha , Somel Mehmet , Özer Füsun , Johansson Anna M , Storå Jan , Günther Torsten 
Published: June 2023

AbstractSheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this breed diversity goes, with formal documentation only dating back a few centuries. North European short-tailed breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia less than 6000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from Late Neolithic (∼4100 calBP) to historical times (∼1600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern North European short-tailed breeds, suggesting a substantial degree of long-term continuity of this breed type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit higher genetic diversity when compared to modern breeds, implying a loss of diversity in recent centuries associated with breed formation. Finally, we see a potential signature of an even earlier, genetically different form of sheep in Scandinavia as these samples do not represent the first sheep in Northern Europe. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.
Alternative reproductive tactics and evolutionary rescue
Authors: Knell Robert J , Parrett Jonathan M. 
Published: June 2023

AbstractAlternative reproductive tactics (ARTs), whereby males within a species exhibit qualitatively different behaviours in their pursuit of matings, are common throughout the animal kingdom. Here, using an individual-based modelling approach, we consider the possible impacts on adaptation and evolutionary rescue arising from one class of ARTs, those expressed through condition-dependent polyphenism such that high-quality, well-adapted males compete aggressively for mates and low-quality, poorly adapted males attempt to acquire matings via other, non-aggressive behaviours. When the ART is simultaneous, meaning that low-quality males do engage in contests but also pursue other tactics, adaptive capacity is reduced and evolutionary rescue, where a population is able to adapt to a changing environment, becomes less likely. This is because the use of the ART allows low-quality males to contribute more maladaptive genes to the population than would happen otherwise. When the ART is fixed, however, such that low-quality males will only use the alternative tactic and do not engage in contests, we find the opposite: adaptation happens more quickly and evolutionary rescue when the environment changes is more likely. This surprising effect results from an increase in the mating success of the highest quality males who face many fewer competitors in this scenario—counterintuitively, the presence of males pursuing the ART increases reproductive skew towards those males in the best condition.
Aneuploidies are an ancestral feature of trypanosomatids, and an ancient chromosome duplication is maintained in extant species
Authors: Reis-Cunha João Luís , Carvalho Samuel Alexandre Pimenta , Almeida Laila Viana , Anderson Coqueiro-dos-Santos A , Marques Catarina De Almeida , Black Jennifer , Damasceno Jeziel , McCulloch Richard , Bartholomeu Daniella Castanheira , Jeffares Daniel Charlton 
Published: June 2023

AbstractBackgroundAneuploidy is widely observed in both unicellular and multicellular eukaryotes, usually associated with adaptation to stress conditions. Chromosomal duplication stability is a tradeoff between the fitness cost of having unbalanced gene copies and the potential fitness gained from increased dosage of specific advantageous genes. Trypanosomatids, a family of protozoans which include species that cause neglected tropical diseases, are a relevant group to study aneuploidies, as their life cycle has several stressors that would benefit from the rapid adaptation provided by aneuploidies.ResultsBy evaluating the data from 866 isolates covering 7 Trypanosomatids genera, we have observed that aneuploidies are present in the majority of clades, and have a reduced occurrence in a specific monophyletic clade that has undergone large genomic reorganisation and chromosomal fusions. We have also identified an ancient chromosomal duplication that was maintained across these parasite’s speciations, which has increased sequence diversity, unusual gene structure and expression regulation.ConclusionAneuploidies are an important and ancestral feature in Trypanosomatids. Chromosomal duplication/loss is a constant event in these protozoans, common inLeishmaniaandLeptomonasand repressed inT. bruceiand closely related protozoans. The number of chromosomes with extra copies in a given isolate is usually low, and only one chromosomal duplication was kept for long enough to greatly impact its nucleotide diversity. The thigh control of gene expression in this chromosome suggests that these parasites have adapted to mitigate the fitness cost of having this ancient chromosomal duplication.
SAP domain facilitates efficient loading of Ku onto DNA ends
Authors: Fulneček Jaroslav , Klimentová Eva , Cairo Albert , Bukovcakova Sona Valuchova , Alexiou Panagiotis , Prokop Zbynek , Riha Karel 
Published: June 2023

AbstractRecognition and processing of DNA ends play a central role in maintaining genome integrity. The evolutionarily conserved DNA repair complex Ku serves as the primary sensor of free DNA ends in eukaryotic cells. Its rapid association with DNA ends is crucial for several cellular processes, including non-homologous end joining (NHEJ) DNA repair and telomere protection. In this study, we conducted a transient kinetic analysis to investigate the impact of the SAP domain on individual phases of the Ku-DNA interaction. Specifically, we examined the initial binding, the subsequent docking of Ku onto DNA, and the sliding of Ku along DNA. Our findings revealed that the C-terminal domain of Ku70, known as SAP ((SAF-A/B, Acinus and PIAS), facilitates the initial phases of Ku-DNA interaction, but does not affect the sliding process. This suggests that SAP may either establish the first interactions with DNA, or stabilize these initial interactions during loading. To assess the biological role of SAP, we generated Arabidopsis plants expressing Ku lacking the SAP domain (ΔSAP). Intriguingly, despite the decreased efficiency of the ΔSAP Ku complex in loading onto DNA, the mutant plants exhibited full proficiency in classical NHEJ and telomere maintenance. This indicates that the speed of Ku loading onto telomeres or DNA double-strand breaks (DSBs) is not the decisive factor in stabilizing these DNA structures.
Genetic atlas of hygro- and thermosensory cells in the vinegar flyDrosophilamelanogaster
Authors: Corthals Kristina , Andersson Vilma , Churcher Allison , Reimegård Johan , Enjin Anders 
Published: June 2023

AbstractThe ability of animals to perceive and respond to sensory information is essential for their survival in diverse environments. While much progress has been made in understanding various sensory modalities, the sense of hygrosensation, which involves the detection and response to humidity, remains poorly understood. In this study, we focused on the hygrosensory, and closely related thermosensory, systems in the vinegar flyDrosophila melanogasterto unravel the molecular profile of the cells of these senses. Using a transcriptomic analysis of over 37,000 nuclei, we identified twelve distinct clusters of cells corresponding to temperature-sensing arista neurons, humidity-sensing sacculus neurons, and support cells relating to these neurons. By examining the expression of known and novel marker genes, we validated the identity of these clusters and characterized their gene expression profiles. We found that each cell type could be characterized by a unique expression profile of ion channels, GPCR signaling molecules, synaptic vesicle cycle proteins, and cell adhesion molecules. Our findings provide valuable insights into the molecular basis of hygro- and thermosensation. Understanding the mechanisms underlying hygro- and thermosensation may shed light on the broader understanding of sensory systems and their adaptation to different environmental conditions in animals.
C2CAplus: a one-pot isothermal circle-to-circle DNA amplification system
Authors: Grasemann Laura , Pizarro Paula Thiel , Maerkl Sebastian J. 
Published: June 2023

AbstractRolling circle amplification (RCA) is a widely used DNA amplification method that uses circular template DNA as input and produces multimeric, linear single or double stranded DNA. Circle-to-circle amplification (C2CA) has further expanded this method by implementing product re-circularization using restriction and ligation, leading to a higher amplification yield, and enabling the generation of circular products. However, C2CA is a multistep, non-isothermal method, requiring multiple fluid manipulations and thereby compromises several advantages of RCA. Here, we improved C2CA to implement a one-pot, single step, isothermal reaction at temperatures ranging from 25 to 37°C. Our C2CAplus method is simple, robust, and produces large quantities of product DNA that can be seen with the naked eye.
Deep speech-to-text models capture the neural basis of spontaneous speech in everyday conversations
Authors: Goldstein Ariel , Wang Haocheng , Niekerken Leonard , Zada Zaid , Aubrey Bobbi , Sheffer Tom , Nastase Samuel A. , Gazula Harshvardhan , Schain Mariano , Singh Aditi , Rao Aditi , Choe Gina , Kim Catherine , Doyle Werner , Friedman Daniel , Devore Sasha , Dugan Patricia , Hassidim Avinatan , Brenner Michael , Matias Yossi , Devinsky Orrin , Flinker Adeen , Hasson Uri 
Published: June 2023

AbstractHumans effortlessly use the continuous acoustics of speech to communicate rich linguistic meaning during everyday conversations. In this study, we leverage 100 hours (half a million words) of spontaneous open-ended conversations and concurrent high-quality neural activity recorded using electrocorticography (ECoG) to decipher the neural basis of real-world speech production and comprehension. Employing a deep multimodal speech-to-text model named Whisper, we develop encoding models capable of accurately predicting neural responses to both acoustic and semantic aspects of speech. Our encoding models achieved high accuracy in predicting neural responses in hundreds of thousands of words across many hours of left-out recordings. We uncover a distributed cortical hierarchy for speech and language processing, with sensory and motor regions encoding acoustic features of speech and higher-level language areas encoding syntactic and semantic information. Many electrodes—including those in both perceptual and motor areas—display mixed selectivity for both speech and linguistic features. Notably, our encoding model reveals a temporal progression from language-to-speech encoding before word onset during speech production and from speech-to-language encoding following word articulation during speech comprehension. This study offers a comprehensive account of the unfolding neural responses during fully natural, unbounded daily conversations. By leveraging a multimodal deep speech recognition model, we highlight the power of deep learning for unraveling the neural mechanisms of language processing in real-world contexts.
Protein engineering, production, reconstitution in lipid nanoparticles, and initial characterization of theMycobacterium tuberculosisEfpA drug exporter
Authors: Ishola Olamide , Ogunbowale Adeyemi , Islam Md Majharul , Hadadianpour Elaheh , Majeed Saman , Adetuyi Oluwatosin , Georgieva Elka R. 
Published: June 2023

ABSTRACTMycobacterium tuberculosis(Mtb) drug exporters contribute an efficient mechanism for drug resistance. Therefore, understanding the structure–function relationship in these proteins is important. We focused on theMtbEfpA efflux pump, which belongs to the major facilitator superfamily (MSF) and transports anti-tuberculosis drugs outside the bacterial cell. Here, we report on our advancements in producing and characterization of this protein. We engineered a construct of apolipoprotein A-I (apoAI) fused to the N-terminus of EfpA (apoAI-EfpA) and cloned it in anE. coliexpression vector. This fusion construct was found in a membrane-bound form, unlike the deposited in inclusion bodies EfpA without apoAI. We purified the apoAI-EfpA in detergent to a sufficient degree and reconstituted it in DOPC/DOPS lipids. We found that upon reconstitution in lipid, the apoAI-EfpA forms discoidal protein-lipid nanostructures with a diameter of about 20 nm, resembling nanodiscs. We further detected apoAI-EfpA oligomers in β-DDM and lipid. To the best of our knowledge, this is the first complete protocol on the expression, purification, and lipid reconstitution of theMtbEfpA transported. AlphaFold2 also predicted EfpA oligomers and further bioinformatic analysis confirmed the earlier proposed 14-transmembrane helices of theMtbEfpA. We also found very high identity, >80%, among the EfpA-s of diversemycobacterialspecies. Outside ofmycobacteria, EfpA has no close homologues with only low identity with the QacA family of transporters. These findings possibly indicate high specificity of EfpA mechanisms. Our developments provide a foundation for more comprehensive in vitro studies on the EfpA exporter.
Effects of policy and economic uncertainty on investment activities and corporate financial reporting: a study of developing countries in Asia-Pacific
Authors: Kurniawan Firdaus , Amanati Hilma Tsani , Nugroho Albertus Henri Listyanto , Pusparini Nandya Octanti 
Published: June 2023

PurposeThis study investigates the impact of government and economic policy uncertainty (EPU) on companies' business operations, especially risk-taking tendencies and corporate financial reporting quality (FRQ).Design/methodology/approachThe study employs the generalised least squares regression model. The final sample comprised 27,376 company-year observations from eight countries in the Asia-Pacific region.FindingsEPU has a negative and significant effect on investment activity and FRQ. Higher EPU leads to a decline in investment and FRQ.Research limitations/implicationsThere are several limitations in this study. First, the authors used abnormal investments to measure investments, without considering the degree of irreversibility investment objectives. Second, although control variables are included at the company and country levels, they may only partially control for companies' mitigation effects. Third, the sample is limited to developing countries with unique characteristics in Asia-Pacific; therefore, the findings cannot be generalised.Practical implicationsThe findings can help investors, analysts and regulators evaluate EPU's impact on companies' business activities by offering an overview regarding the decline in investment efficiency and FRQ. The results can also be used as input for regulators in formulating policies that encourage companies to regulate investment levels without harming other stakeholders and maintain FRQ during periods of uncertainty.Originality/valueThis research provides intriguing insights into EPU's effects on companies' investment activity and FRQ in developing countries, which are sensitive to changes in macroeconomic conditions.
Exploring innovation deployment of construction contracting firms through the lens of exploratory–exploitative learning: a Hong Kong case study
Authors: Sumanarathna Nipuni , Duodu Bismark , Memon Shoeb Ahmed , Rowlinson Steve 
Published: June 2023

Purpose
This study aims to explore the innovation deployment of construction contracting firms through exploratory–exploitative learning and organisational ambidexterity.

Design/methodology/approach
Firstly, a literature-based conceptual framework was developed to explain innovation implementation through exploratory–exploitative learning and organisational ambidexterity. A prominent Hong Kong construction contracting firm was then selected as the case study to explore its innovation deployment at different organisational levels (i.e. firm and project levels). Qualitative data were attained by conducting 12 semi-structured interviews with industry experts and document analysis. The thematic analysis using NVivo 12 software was adopted to analyse data.

Findings
Findings reveal that the case study firm successfully fosters innovation when ambidexterity is achieved through the balance between exploratory (i.e. radical innovation) and exploitative learnings (i.e. incremental innovation).

Research limitations/implications
Establishing uniform ambidexterity (i.e. 50:50) at the firm or project level is not mandatory to deploy innovation successfully. The ratio can vary based on the characteristics and requirements of construction firms.

Practical implications
This paper shall motivate construction practitioners to adopt radical–incremental innovation ambidexterity in firms and ultimately enhance the productivity and efficiency of the construction industry.

Originality/value
Previous construction innovation research has frequently explored firm or project-level innovation separately. This study identified a multi-level focus on innovation. Through the lens of exploratory–exploitative theory, different forms of innovation ambidexterity for different levels are suggested rather than one specific ambidexterity.
Not all innovation is prioritized: economic policy uncertainty, industry environmental, and firms' relative exploitative innovation emphasis
Authors: Zhong Xi , Ren Ge , Wu Xiaojie 
Published: June 2023

PurposeEconomic policy uncertainty has increased around the world since the financial crisis of 2007–2008. While scholars have devoted a lot of time and energy to investigating the impact of economic policy uncertainty (EPU) on firm innovation, they have not reached consistent research conclusions. This study aimed to clarify the above research differences by exploring the impact of EPU on firms' relative exploitative innovation emphasis, so as to provide a more comprehensive and granular understanding of the relationship between EPU and firm innovation.Design/methodology/approachThis study obtained 17,165 firm-year data points from 3,107 listed companies in China. It analyzed the above data with a fixed effects model. In addition, this study used an instrumental variables method to solve potential endogeneity problems.FindingsBased on real options theory and contingency theory, the authors proposed and found that EPU has a significant positive effect on relative exploitative innovation emphasis. In addition, the authors proposed and found that this effect is more pronounced in industries with high technological uncertainty, low competitive intensity, and low state monopolization.Originality/valueThis study is the first to explore why firms prefer exploitative innovation over exploratory innovation from the perspective of EPU. In doing so, this study expands and enriches the EPU literature and the innovation literature. Furthermore, by introducing the moderating role of industry environment, this study deepens the authors' understanding of how complex interactions between industry and institutional environments work together to shape firm strategic choices, and especially firm innovation. Finally, the conclusions of this study have important practical implications for shareholders to take measures to balance exploitative innovation and exploratory innovation to achieve better development.
Exploring (r)evolutionary college-going literacies with immigrant youth in a youth participatory action research (YPAR) seminar
Authors: Filipiak Danielle , Caraballo Limarys 
Published: June 2023

PurposeThis paper aims to examine critical, college-going identities and literacies of first-generation immigrant youth within a dual enrollment, youth participatory action research seminar.Design/methodology/approachThis study is a qualitative case study drawn from a larger, critical ethnographic study.FindingsFindings illustrate that youth’s multiple literacies, forged in a deliberately intergenerational and relational space, served as a powerful site of analysis as well as a means to disrupt restrictive definitions of success, supporting youth’s worldmaking amidst the construction and negotiation of new and critical “academic” identities grounded in the familial, cultural and historical knowledges that their inquiries surfaced.Originality/valueThis research attends to the transformative power afforded by humanizing collectives that center youth voices and perspectives, specifically those of first-generation immigrant students.
The status of open access repositories in the field of technology: insights from OpenDOAR
Authors: Wani Javaid Ahmad , Sofi Taseef Ayub , Sofi Ishrat Ayub , Ganaie Shabir Ahmad 
Published: June 2023

Purpose
Open-access repositories (OARs) are essential for openly disseminating intellectual knowledge on the internet and providing free access to it. The current study aims to evaluate the growth and development of OARs in the field of technology by investigating several characteristics such as coverage, OA policies, software type, content type, yearly growth, repository type and geographic contribution.

Design/methodology/approach
The directory of OARs acts as the source for data harvesting, which provides a quality-assured list of OARs across the globe.

Findings
The study found that 125 nations contributed a total of 4,045 repositories in the field of research, with the USA leading the list with the most repositories. Maximum repositories were operated by institutions having multidisciplinary approaches. The DSpace and Eprints were the preferred software types for repositories. The preferred upload content by contributors was “research articles” and “electronic thesis and dissertations”.

Research limitations/implications
The study is limited to the subject area technology as listed in OpenDOAR; therefore, the results may differ in other subject areas.

Practical implications
The work can benefit researchers across disciplines and, interested researchers can take this study as a base for evaluating online repositories. Moreover, policymakers and repository managers could also get benefitted from this study.

Originality/value
The study is the first of its kind, to the best of the authors’ knowledge, to investigate the repositories of subject technology in the open-access platform.
Accessible heritage cities
Authors: Doan Tin , Nguyen Hai 
Published: June 2023

Purpose
This viewpoint note aims to discuss the challenges and the suggestions of using assistive technologies to improve the accessibility for travellers with disabilities and their companions at heritage cities.

Design/methodology/approach
The viewpoint note used the narrative approach which conceptualised accessible tourism, challenges and solutions of using assistive technologies for improving the heritage cities visit experience of travellers with disabilities.

Findings
The viewpoint note discussed three challenges (physical, informational and attitudinal) and three approaches of accessible platform, navigation system, and accessible and interactive heritage interpretation solutions for accessible heritage cities.

Originality/value
The viewpoint note presents the expert opinion of authors who investigated the accessibility issue in heritage cities. The first author of this note is a person with disabilities who has been living and studying about experience of travellers with disabilities at many heritage cities. The other author is an expert in heritage tourism.