bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic signatures of island colonization in highly diverse primates
Authors: Colmonero-Costeira I. , Guschanski K. , Djaló M.L. , Fernandes N. , Camará T. , Farh K.K.-H. , Kuderna L. , Rogers J. , Marques-Bonet T. , Bruford M.W. , Russo I-R.M. , Jensen A. , Ferreira da Silva M.J. 
Published: December 2024

AbstractUnderstanding how small populations cope with loss of genetic diversity and deleterious variation is crucial to address the current biodiversity crisis. Insular populations are particularly interesting as they have often persisted at low population sizes and higher inbreeding than their mainland counterparts. While the genome-wide consequences of inbreeding in threatened insular species have received some attention, comparative genomics between insular and mainland populations of wide-spread and genetically diverse species have rarely been performed. Yet, they are particularly well suited to inform about the consequences of drastic population declines from initially large populations - a phenomenon that is becoming increasingly common. The spot-nosed monkey (Cercopithecus petaurista), the Campbell’s monkey (Cercopithecus campbelli) and the green monkey (Chlorocebus sabaeus) are common and genetically diverse West African primates. Insular populations can be found at the Bijagós Archipelago, Guinea-Bissau. Here, we assessed the genome-wide diversity, inbreeding, genetic load and adaptive variation using whole genome sequencing data from insular and mainland populations. In the three species, island populations showed lower genome-wide diversity and higher inbreeding. Genetic drift has likely promoted the conversion of masked genetic load into realized load without increased purging of deleterious variation. Additionally, we found no evidence for accumulation of deleterious variation, suggesting that these populations are not yet at risk of extinction by genetic factors and may act as reservoirs of mainland genetic diversity. We highlight, however, that other anthropogenic factors are threatening these insular primates and therefore conservation management should target their immediate threats and safeguard against additional loss of diversity.
Expression screen of TNFR1R347A, MyD88, IRAK4 death domains in E. coli followed by purification and biophysical characterization of TNFR1R347Adeath domain
Authors: Przytulski Kamil , Podkówka Aleksandra , Tomczyk Tomasz , Gajewska Daria , Sypień Magdalena , Jeleń Agnieszka , Dahate Priyanka , Szlachcic Anna , Biśta Michał , Walczak Michał J. 
Published: December 2024

AbstractDeath domains play a crucial role in signaling pathways related to inflammation and programmed cell death, rendering them promising targets for therapeutic interventions. However, their expression as recombinant proteins often pose challenges. Here, we present expression screening of TNFR1, IRAK4, and MyD88 death domains inE. coli, followed by the biophysical characterization of TNFR1 death domain after subsequent construct optimization. The study also discusses the influence of pH and ionic strength on TNFR1R347Astability, providing statistical models to predict optimal conditions of the buffer to achieve the highest protein stability.HighlightsOptimization of expression conditions for TNFR1R347A, MyD88, IRAK4 death domains inE. coliBL21(DE3) cells.High-yield production of soluble monomeric TNFR1R347Adeath domain.
An age-specific burial practice reflected in ancient DNA preservation in Neolithic Çatalhöyük
Authors: Doğu Ayça Küçükakdağ , Baloğlu Fatma Küçük , Chyleński Maciej , Schotsmans Eline M.J. , Kılıç Muhammed Sıddık , Vural Kıvılcım Başak , Yüncü Eren , Kaptan Damla , Güler Merve N. , Yorulmaz Sevgi , Karabulut Nergis Bilge , Sağlıcan Ekin , Kazancı Duygu Deniz , Milella Marco , Marciniak Arkadiusz , Erdal Yılmaz Selim , Pilloud Marin , Larsen Clark Spencer , Götherström Anders , Hodder Ian , Özer Füsun , Haddow Scott D. , Knüsel Christopher J. , Somel Mehmet 
Published: December 2024

AbstractSelective funerary practices can inform about social relationships in prehistoric societies but are often difficult to discern. Here we present evidence for an age-specific practice at the Neolithic site of Çatalhöyük in Anatolia, dating to the 7th millennium BCE. Among ancient DNA libraries produced from 362 petrous bone samples, those of subadults contained three times higher average human DNA than those of adults. This difference in organic preservation was also confirmed by FTIR analysis. Studying similar datasets from seven prehistoric and historical sites, we found a similar age-related difference in only one cemetery. We propose that the organic preservation difference with age was caused by the special treatment of chosen corpses before interment, such as defleshing or drying, which was more frequently applied to Çatalhöyük adults and promoted organic decay.
Single neuron diversity supports area functional specialization along the visual cortical pathways
Authors: Feyerabend M , Pommer S , Jimenez-Sosa MS , Rachel J , Sunstrum J , Preuss F , Mestern S , Hinkel R , Mietsch M , Viyajraghavan S , Everling S , Treue S , Arnsten AFT , Lewis DA , Wolf F , Murray J , McCarroll Steve , Muller Lyle , Krienen F , Datta D , Wang XJ , Tripathy SJ , Gonzalez-Burgos G , Inoue W , Neef A , Staiger JF , Martinez-Trujillo J 
Published: December 2024

AbstractHumans and other primates have specialized visual pathways composed of interconnected cortical areas. The input area V1 contains neurons that encode basic visual features, whereas downstream in the lateral prefrontal cortex (LPFC) neurons acquire tuning for novel complex feature associations. It has been assumed that each cortical area is composed of repeatable neuronal subtypes, and variations in synaptic strength and connectivity patterns underlie functional specialization. Here we test the hypothesis that diversity in the intrinsic make-up of single neurons contributes to area specialization along the visual pathways. We measured morphological and electrophysiological properties of single neurons in areas V1 and LPFC of marmosets. Excitatory neurons in LPFC were larger, less excitable, and fired broader spikes than V1 neurons. Some inhibitory fast spiking interneurons in the LPFC had longer axons and fired spikes with longer latencies and a more depolarized action potential trough than in V1. Intrinsic bursting was found in subpopulations of both excitatory and inhibitory LPFC but not V1 neurons. The latter may favour temporal summation of spikes and therefore enhanced synaptic plasticity in LPFC relative to V1. Our results show that specialization within the primate visual system permeates the most basic processing level, the single neuron.
Pleiotropic function ofDlx5/6in coordinating the development of mammalian vocal and auditory organs
Authors: Sánchez-Garrido Frida , Bouzerand Victoria , Kaiser Markéta , Chaumeton Chloé , Fontaine Anastasia , Zikmund Tomáš , Kaiser Jozef , Heude Églantine 
Published: December 2024

AbstractAcoustic communication, essential for mammalian social interactions, involves both effector (vocal) and receptor (auditory) organs that present a wide variety of morphologies between species. The molecular mechanisms supporting the harmonious diversification of effector and receptor systems along with the evolution of species-specific acoustic communication are still poorly understood. It is conceivable that common genetic pathways determine the parallel morphogenesis of vocal and auditory systems. Here, we investigated this question by generating mutant mice with targeted invalidation ofDlx5/6genes in the otic placode and cephalic neural crest cells, contributing to the formation of the ear and vocal tract components. We show thatDlx5/6inactivation provokes simultaneous defects of the outer, middle and inner ear and of the jaw, pharynx and larynx musculoskeletal systems. Our findings support the notion thatDlx5/6genes played a pleiotropic role in the co-adaptation of vocal and auditory systems in mammals.
Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP
Authors: Waldern Justin M. , Taylor Colin , Giannetti Catherine A. , Irving Patrick S. , Allen Scott R. , Zhu Mingyi , Backofen Rolf , Mathews Dave , Weeks Kevin M. , Laederach Alain 
Published: December 2024

AbstractBiogenesis of circular RNA usually involves a backsplicing reaction where the downstream donor site is ligated to the upstream acceptor site by the spliceosome. For this reaction to occur, it is hypothesized that these sites must be in proximity. Inverted repeat sequences, such as Alu elements, in the upstream and downstream introns are predicted to base-pair and represent one mechanism for inducing proximity. Here, we investigate the pre-mRNA structure of the humanHIPK3gene at exon 2, which forms a circular RNA via backsplicing. We leverage multiple chemical probing techniques, including the recently developed SHAPE- JuMP strategy, to characterize secondary and tertiary interactions in the pre- mRNA that govern backsplicing. Our data confirm that the antisense Alu elements, AluSz(-) and AluSq2(+) in the upstream and downstream introns, form a highly- paired interaction. Circularization requires formation of long-range Alu-mediated base pairs but does not require the full-length AluSq2(+). In addition to confirming long-range base pairs, our SHAPE-JuMP data identified multiple long-range interactions between non-pairing nucleotides. Genome-wide analysis of inverted repeats flanking circular RNAs confirm that their presence favors circularization, but the overall effect is modest. Together these results suggest that secondary structure considerations alone cannot fully explain backsplicing and additional interactions are key.
Zero valent sulfur is the product of assimilatory sulfite reductase and a substrate of cysteine synthase
Authors: Cao Qun , Liu Xuanyu , Zhang Xi , Wang Qingda , Xia Yongzhen , Xun Luying , Liu Huaiwei 
Published: December 2024

ABSTRACTThe long process of the assimilatory sulfate-reduction consists of sulfate reduction to H2S and then H2S assimilation for cysteine synthesis. The concept has not been challenged for a long time until now. Herein, phylogenetic analysis grouped assimilatory sulfite reductases into five clusters and we re-examined four representatives from two major clusters. These enzymes produced both zero valent sulfur (S0) and H2S from sulfite. However, S0was more like a direct product, while H2S was just a derivative of S0via chemical reduction. Phylogenetic analysis of cysteine synthases grouped them into six clusters, and we re-examined six representatives from two major clusters. These enzymes used both glutathione persulfide (GSSH, a common intracellular compounds containing a S0atom) and H2S as substrates to synthesize cysteine, but preferred to use GSSH. These findings challenged the long standing concept and supported that S0, other than H2S, is the key intermediate during the process of inorganic sulfur converting to organic sulfur.IMPORTANCEFirst, this study provides new insights into the sulfate reduction process. Representative sulfite reductases were investigated and bothin vitro&in vivotests proved they produce more zero valent sulfur (S0) than H2S from sulfite. S0is the direct product while H2S is derivative of S0. Second, this study provides new insights into cysteine synthesis pathway. Screening and analyses revealed that most cysteine synthases prefer S0-containing compounds (e.g., GSSH) as substrate for cysteine synthesis. Together, the two findings indicate that S0is the key knot connecting sulfate reduction and cysteine synthesis, not the long believed H2S.
Encephalomyocarditis virus non-structural protein 2C degrades NDP52 autophagy protein to promote its own survival
Authors: Mo Rongqian , Cheng Rongrong , Dong Pingan , Ma Tingting , Zhang Yaxin , Xie Jingying , Li Shasha , Li Huixia , Idris Adi , Li Xiangrong , Feng Ruofei 
Published: December 2024

AbstractEncephalomyocarditis virus (EMCV) is an important zoonotic pathogen that causes encephalitis and myocarditis, primarily in pigs and in some mammals. Nuclear dot protein (NDP) 52 is an important autophagy adaptor protein that is known to target microbial pathogens, including viruses into autophagosomes to facilitate the selective autophagy process. Here, we wanted to investigate how an important zoonotic virus such as EMCV interacts with NDP52. We found that NDP52 negatively regulates the entry and replication phases of EMCV and interacts with EMCV VP1/VP2 proteins to mediate its autophagic degradation. EMCV counteracts this by exerting autophagy induction through its encoded 2C protein. The autophagy machinery then hijacks NDP52 and transports it to lysosomes for subsequent degradation via late endosomal molecules Rab7 and Rab9. Our study describes a novel mechanism by which EMCV escapes the host’s antiviral response to promote its survival by hijacking the autophagy pathway using the non-structural protein 2C of EMCV.ImportanceEMCV is an important zoonotic pathogen that can induce autophagy, but the regulatory role of autophagy receptors in EMCV infection has been rarely reported. Herein, we show that NDP52 is a novel host limiting factor for EMCV, which not only inhibits early EMCV endocytosis, but also restricts EMCV replication in vitro by controlling autophagic degradation of EMCV structural proteins VP1 and VP2. In order to counteract this, EMCV uses the N-terminal region of its non-structural protein 2C to interact with NDP52, and hijacks the autophagy machine to transport NDP52 to lysosomes for degradation, which weakens NDP52-mediated degradation of VP1 and VP2. Importantly, we reveal a novel mechanism by which EMCV evades the host antiviral response, contributing to a deeper understanding of the infectious mechanism of EMCV and providing new ideas for the design of antiviral drug targets.
Regulation of Fungal Morphology, Conidiogenesis and Violet Pigment Synthesis by the Betalain Biosynthesis Pathway Genes inAspergillus sydowiiH-1
Authors: Ran Yulu , Cao Yu , Guo Yihan , Zeng Jie , Wang Jiale , Xiang Dongyou , Xu Hui , Cao Yi 
Published: December 2024

AbstractThe biosynthesis of antioxidant pigments, namely, betalains, has predominantly been found in Caryophyllales. The potential betalains biosynthesis was firstly explored inAspergillus sydowiiH-1 under controlled culture conditions. This study identified, knocked out, and overexpressed genes involved in the betanin biosynthesis and assessed the activities of tyrosinase, 4’5-DOPA dioxygenase and LigB. The results indicated these betanin biosynthesis pathway was crucial for colony morphology, conidiogenesis, stress response, and violet pigment synthesis. Moreover, AsDODA and AsLigB catalyzed the conversion of L-DOPA into 4’5-seco-DOPA, a key intermediate in the formation of betalamic acid in vitro. Additionally, transcription factors such as AsbHLH, AsMYB1R, and AsWD40 positively regulated the expression of betalain biosynthesis genes. This research provides new insights into the evolutionary origins of betalain-producing species, expanding the scope of betalain biosynthesis to includeAspergillusspecies.ImportanceTo date, betalains were restricted to plants of the order Caryophyllales, fungi of Basidiomycota and several types of bacteria. This study is the first to demonstrate the potential of AscomycetesA. sydowiiH-1 to synthesize betalains under controlled culture conditions, providing a detailed genetic and biological characterization of the associated genes and metabolic pathways. This finding demonstrates that betalain biosynthesis can be expanded to otherAspergillus.
Differentiation and co-occurrence of obsessive-compulsive disorder and autism spectrum disorder in people with intellectual developmental disorder: a case series on symptoms specificities
Authors: Andreini Nicole , Boniotti Veronica , Scuticchio Daniela , Bianco Annamaria , Bertelli Marco O. 
Published: December 2024

Purpose
In persons with an intellectual developmental disorder, obsessive-compulsive disorder (OCD) and autism spectrum disorder (ASD) are often difficult to differentiate, particularly when patients present major communication difficulties and low accessibility to subjective symptoms and clinicians are poorly trained in the specific psychopathological phenomenology. OCD and ASD share some important symptoms such as repetitiveness of behaviours, low flexibility to contextual variations or a narrow range of interests. The purpose of this study is to identify and describe symptomatological specificities, including how they manifest at behavioural level.

Design/methodology/approach
The present study is a retrospective case series study (n = 3) focusing on in-depth assessment, detection and comprehension of symptomatological specificities as well as on the direct observation of behavioural symptoms.

Findings
Some symptoms such as signs of sudden autonomous nervous system activation or behavioural equivalents of obsessive thoughts are crucial in achieving an effective differential or comorbidity diagnosis. These symptoms can be identified through a multidisciplinary and comprehensive evaluation, integrating present clinical and test findings with a thorough developmental and medical history. Symptoms should also be interpreted in the light of antecedent, contextual and personal factors.

Originality/value
Differential diagnosis between OCD and ASD in persons with major cognitive and communication issues is a rather neglected research area, although it has significant implications for treatment planning and implementation.
Driving resiliency and digitalization in the sourcing process: integration of blockchain technology and smart contracts
Authors: Meafa Azz-Eddine , Chaouni Benabdellah Abla , Zekhnini Kamar , Belhadi Amine , Kamble Sachin 
Published: December 2024

PurposeUnder the current untrusted business environment, digital technologies, such as blockchain technology (BT), show the potential to digitally transform SC processes particularly the sourcing process (SP). Indeed, this process suffers from a lack of digitalization, a lack of trust and a high workload in the automotive supply chain (ASC). Therefore, BT coupled with smart contracts can deal with such issues by fostering trust, transparency, reliability and traceability as a digital solution.Design/methodology/approachThis paper conducts multiple case studies in the automotive sector and interviews 11 managers from two firms. It follows the managers’ perspective to identify and analyze the main issues that occurred while conducting this process using the existing technology.FindingsIt proposes a new architecture for the smart sourcing process (SSP) that uses BT & smart contracts to mitigate the identified issues, enable traceability, improve resilience, eliminate intermediaries, automate tasks, and enhance trust and data management. Also, the paper provides a decision tree to help determine which blockchain platform is needed for adopting the SSP solution.Practical implicationsThis study is useful for both academics and practitioners as it demonstrates the digitalization of one of the SC processes using BT and smart contracts, as well as develops a roadmap for digitalizing the SP of the ASC, and solves its vulnerabilities.Originality/valueBT has been used by researchers to digitalize the sourcing process only in the public procurement area. Considering all the faced challenges by the private procurement area, this paper aims to present a new architecture for the digitalization of the SP using BT and smart contracts in the ASC as a private SC.
Are developmental performance management systems inclusive? An intersectional analysis for age and gender
Authors: Nepoti Francesca , Curzi Ylenia , Ferrarini Filippo 
Published: December 2024

Purpose
Rooted in Joan Acker’s “gendered organisations” framework, this paper aims to explore the impact of employee’s developmental performance management systems (DPMSs) on occupational wellbeing, highlighting gender and age-based intersectional disparities within organisations.

Design/methodology/approach
This study uses data from a sample of more than 600 Italian employees and investigates with a three-way interaction, the effect that DPMS have on employee’s occupational wellbeing by considering the intersectionality between gender and ages’ categories.

Findings
The findings dismiss the idea that DPMS can be regarded as a practice for inclusion. Moreover, the analysis discloses the need for intersectional perspective as the authors do reveal different effects of developmental performance system adoption on occupational wellbeing for people in diverse intersections of genders and ages.

Originality/value
This paper expands on Acker’s tradition with a focus on age, dismissing the possible inclusive outcome of competency based employee performance systems.
The effects of the different dimensions of social capital on situated learning processes in projects
Authors: Guribie Francis Lanme , Owusu-Manu Dr. De-Graft , Badu Edward , Edwards David John 
Published: December 2024

Purpose
The purpose of the study is to demonstrate the influences of three dimensions of social capital (the structural, relational and cognitive dimensions) on five situated learning processes (institutionalization, socialization, knowledge articulation, experience accumulation and knowledge reuse) in projects.

Design/methodology/approach
Drawing on a cross sectional survey, data were drawn from 203 construction professionals in Ghana who have hands-on experience in managing projects. Partial least square structural equation modeling was used to conduct both confirmatory factor analysis and path analysis of the structural model of the relationship between these two constructs.

Findings
In relation to the research questions, all three dimensions of social capital have effects of the situating learning processes. However, the research’s key finding is that the relational dimension of social capital exerts much influence on the situated learning processes in projects, with the structural and cognitive dimensions of social capital exerting medium and small effects, respectively.

Practical implications
The study’s key finding implies that – addressing the “relational” conditioners that moderate project participants’ behaviour in social relationships is critical for increasing situated learning activity in projects. These must, however, be complemented by both structural and cognitive factors.

Originality/value
The research findings expand existing frontiers of knowledge by addressing the gap in the literature on the lack of practical demonstration of the influences exerted by the various dimensions of social capital on a situated learning activity in projects.
Digitalization and bank performance: the mediator effect of financial stability and moderator effect of nonperforming loans
Authors: Saadaoui Amir , Chouchene Issam 
Published: December 2024

Purpose
Digitalization is a keyword not only mentioned in recent years but also strongly applied by financial institutions. However, the benefits of digitalization for banks remain an issue that needs to be investigated.

Design/methodology/approach
Therefore, this study is conducted to determine the role of digitalization in improving the financial performance of banks in the presence of financial stability as a mediating variable and nonperforming loans (NPLs) as a moderating variable. The research was conducted by African banks between 2000 and 2021.

Findings
Using panel data, the results showed that digitalization has a positive and significant effect on the performance of African banks. Similarly, the results showed that the financial stability of African banks plays a mediating role between digitalization and performance.

Originality/value
However, the effect of digitalization on the performance of African banks goes through their financial stability, which verifies its mediating role. Similarly, this study’s results showed that NPLs have a moderating role between digitalization and bank performance. Indeed, this paper found that NPLs play a braking role that minimizes the effect of digitalization on improving the financial performance of banks.