bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pre-treatments of Ex vivo Vascularized Composite Allografts: A Scoping Review
Authors: Baker Caroline E , Stead Thor S , Shah Alay R , Pullmann Dominika , Chinta Sachin , Tran David L , Brydges Hilliard T , Laspro Matteo , Gelb Bruce E , Rodriguez Eduardo D , Rabbani Piul S 
Published: November 2024

AbstractPURPOSEThe various physiological profiles comprising vascularized composite allografts (VCAs) pose unique challenges to preservation. Minimizing ischemia, reperfusion injury, and rejection remains a primary focus of graft pre-treatments (PTs). Currently, the gold standard PT consists of flushing the graft and placing it in static cold storage in the University of Wisconsin solution. With this method, graft viability is limited to four to six hours. Prolonging this time limit will increase donor allocation radius, access to care, and positive patient outcomes. We aimed to evaluate novel PTs that could potentially enhance and lengthen VCA viability.METHODSFollowing PRISMA guidelines, we conducted a comprehensive literature search of Embase, Cochrane, and PubMed. Studies had to be published prior to June 15, 2022. PTs had to target cell physiology, rather than immunogenicity. We extracted data including study design, PT details, evaluation metrics, and outcomes.RESULTSWe identified thirteen studies, categorized into three groups: solution-based alterations to the gold standard, ex vivo perfusion, and other novel techniques. The incorporation of hydrogen sulfide and Perfadex as solutions in the gold standard protocol demonstrated a six-day delay in rejection and limited reperfusion injury markers, respectively. In one ex vivo perfusion study, after 24 hours of PT and 12 hours post-transplant, VCA muscle contractility remained close to normal. The gold standard PT did not demonstrate the same success. However, graft weight gain, up to 50% of baseline among the articles reviewed, is a prominent side effect of perfusion. Another technique, cryopreservation, displayed 90% graft failure by venous thrombosis, despite high free graft viability following two weeks of storage.CONCLUSIONSThis study of pre-treatment modalities found a variety of encouraging preservation techniques for grafts with high levels of tissue diversity. Ex vivo perfusion dominated PT innovation with promising results in preserving the viability and functionality of muscle, which is central to the restoration of movement. Future studies are necessary to evaluate long-term graft outcomes and to optimize PT protocols for extended preservation times to ensure clinical relevance.
Home range spillover in habitats with impassable boundaries: Causes, biases, and corrections using autocorrelated kernel density estimation
Authors: Hollins Jack P.W. , Fleming Christen H. , Calabrese Justin M. , Harris Les N. , Moore Jean Sebastien , Malley Brendan K. , Noonan Michael J. , Fagan William F. , Alston Jesse M. , Hussey Nigel E. 
Published: November 2024

AbstractAn animal’s home range plays a fundamental role in determining its resource use and overlap with conspecifics, competitors and predators, and is therefore a common focus of movement ecology studies. Autocorrelated kernel density estimation addresses many of the shortcomings of traditional home range estimators when animal tracking data is autocorrelated, but other challenges in home range estimation remain.One such issue is known as ‘spillover bias’, in which home range estimates do not respect impassable movement boundaries (e.g., shorelines, fences), and occurs in all forms of kernel density estimation. While several approaches to addressing spillover bias are used when estimating home ranges, these approaches introduce bias throughout the remaining home range area, depending on the amount of spillover removed, or are otherwise inaccessible to most ecologists. Here, we introduce local corrections to home range kernels to mitigate spillover bias in (autocorrelated) kernel density estimation in the continuous time movement model (ctmm) package, and demonstrate their performance using simulations with known home range extents and distributions, and a real world case study.Simulation results showed that local corrections minimised bias in bounded home range area estimates, and resulted in more accurate distributions when compared to commonly usedpost-hoccorrections, particularly at small-intermediate sample sizes.Comparison of the impacts of local vs post-hoc corrections to bounded home ranges estimated from lake trout (Salvelinus namaycush) demonstrated that local corrections constrained bias within the remaining home range area, resulting in proportionally smaller home range areas compared to when post-hoc corrections are used.
Effect of Western diet on body composition, locomotor performance and blood biochemical profile in the bank vole
Authors: Hseiky Alaa , Lipowska Małgorzata M. , Sadowska Edyta T. , Józkowicz Alicja , Nowak Witold N. , Koteja Paweł 
Published: November 2024

AbstractObjectiveThe adverse effects of diets high in both fat and simple sugars (“Western diets”, WD), which are one of the causes of the epidemics of obesity and related disorders, have been extensively studied in laboratory rodents, but not in non-laboratory animals, which limits the scope of conclusions. For example, a few studies have shown that, unlike the laboratory mice or rats, non-laboratory rodents that reduce body mass for winter do not develop obesity when fed a high-fat diet. However, it is not known whether these rodents are also resistant to the adverse effects of WD. Here, we investigated the effects of WD on body composition, locomotor performance and blood biochemical profile in such a rodent, the bank vole (Clethrionomys = Myodes glareolus).MethodsYoung voles were fed either a standard diet or one of six versions of WD (varying in fat, sucrose, and cholesterol content) from the age of 21 days until adulthood (16 individuals per group), and then several morpho-physiological and biochemical traits were analyzed.ResultsNeither body mass, fat content nor blood glucose were elevated by WD (p≥0.11). Basal metabolic rate, sprint speed, endurance distance, and aerobic exercise capacity were also not significantly affected by the diet (p≥0.2). However, altered respiratory exchange rates indicated altered metabolic pathways, and the liver and spleen were enlarged in the groups fed WD with added cholesterol (p≤0.002). Similarly, concentrations of cholesterol, high-density lipoprotein (HDL), non-HDL, glutamic pyruvic transaminase, glutamic oxaloacetate transaminase (GOT), and lactate dehydrogenase (LDH) were elevated in the WD groups, especially the cholesterol-supplemented WD (p≤0.0001), indicating altered liver function.ConclusionsBank voles appeared to be resistant to diet-induced obesity and diabetes, but not to other adverse effects of WD, especially cholesterol-supplemented WD. Therefore, the bank vole is a promising model species to study diet-induced liver disease in lean individuals.
Transcriptional landscape of the archaeal cell cycle is broadly conserved in eukaryotes
Authors: Gomez-Raya-Vilanova Miguel V. , Teulière Jérôme , Medvedeva Sofia , Dai Yuping , Corel Eduardo , Lopez Philippe , Lapointe François-Joseph , Bhattacharya Debashish , Haraoui Louis-Patrick , Turc Elodie , Monot Marc , Cvirkaite-Krupovic Virginija , Bapteste Eric , Krupovic Mart 
Published: November 2024

ABSTRACTThe cell cycle is a series of events that occur from the moment of cell birth to cell division. In eukaryotes, cell growth, genome replication, genome segregation, and cytokinesis are strictly coordinated, defining discrete cell cycle phases. In contrast, these key processes may occur concurrently in bacteria. Thermoacidophilic archaea in the genusSaccharolobusfollow a defined cell cycle program, with the first pre-replicative growth (G1) phase, followed by the chromosome replication (S) phase, the second growth (G2) phase, and rapid genome segregation (M) and cytokinesis (D) phases. However, whether other processes, such as metabolism, catabolism, protein translation, and antiviral defense also occur at specific cell cycle phases, as in eukaryotes, or are active throughout the cell cycle, as in bacteria, remains unclear. To address this question, we synchronized cultures ofS. islandicusand performed an in-depth transcriptomic analysis of samples enriched in cells undergoing the M-G1, S, and G2 phases. Differential gene expression and consensus gene co-expression network analyses provided a holistic view of theS. islandicuscell cycle. In addition to the core transcriptome network, which is expressed throughout the cell cycle, we show that diverse metabolic pathways, protein synthesis, cell motility and even antiviral defense systems, are expressed in a cell cycle dependent fashion. Our data also refines understanding of the processes previously known to be linked to the cell cycle, such as DNA replication. We show that most DNA replication genes are expressed prior to the S phase, during the M-G1, whereas expression of the major chromatin genes, and accordingly, chromatinization are concomitant with replication. A statistical model was used to define sets of signature genes characteristic of each of the analyzed cell cycle phases, emphasizing transcriptional stratification of the phases. Signature genes are more conserved across Thermoproteota than non-signature genes and their peak expression, especially for the M-G1 and G2 specific genes, matches that of homologs in yeast. Collectively, our data elucidate the complexity of theS. islandicuscell cycle and suggest that it more closely resembles the cell cycle of eukaryotes than previously appreciated.
Cingulate and striatal hubs are linked to early skill learning
Authors: Sugata Hisato , Iwane Fumiaki , Hayward William , Azzollini Valentina , Dash Debadatta , Salamanca-Giron Roberto F , Bönstrup Marlene , Buch Ethan R , Cohen Leonardo G 
Published: November 2024

AbstractEarly skill learning develops in the context of activity changes in distributed cortico-subcortical regions. Here, we investigated network hubs—centers of information integration and transmission—within the brain network supporting early skill learning. We recorded magnetoencephalographic (MEG) brain activity in healthy human subjects who learned a moderately difficult sequence skill with their non-dominant left hand. We then computed network hub strength by summing top 10% functional connectivity over 86 parcellated brain regions (AAL3 atlas) and five brain oscillatory frequency bands (alpha, low-, high-beta, low- and high-gamma). Virtually all skill gains developed during rest intervals of early learning (micro-offline gains). MEG hub strength in the alpha band (8-13Hz) in bilateral anterior cingulate (ACC) and caudate and in the low-beta band (13-16Hz) in bilateral caudate and right putamen correlated with micro-offline gains. These regions linked strongly with the hippocampus, parahippocampal cortex, and lingual and fusiform gyri. Thus, alpha and low-beta brain oscillatory activity in cingulate and striatal regions appear to contribute as hubs of information integration and transmission during early skill learning.Significance StatementEarly learning of moderately difficult skill sequences develops over periods of rest interspersed with practice (micro-offline gains). We demonstrate here a link between alpha and low-beta oscillatory activity in a cingulate-hippocampo-striato network hubs and rest intervals of early learning.
Syntopic call diversity among morphologically similar calling morphs of the paleotropical katydid of genusMecopoda(Tettigoniidae) from an Indo-Burma biodiversity hotspot
Authors: Ghosh Aarini , Dasoju Vivek , Borgohain Jishnu , Rahman Ashique , Rajaraman Bittu Kaveri 
Published: November 2024

AbstractThe acoustically diverse family of Tettigoniidae (Ensifera, Orthoptera) (commonly called bushcrickets or katydids), constitutes an excellent system to study the evolution of calling songs.Mecopodais a genus that is particularly interesting because of the many morphologically cryptic calling morphs that have been described across South, East, and Southeast Asia, some of which are considered endemic to India. We describe five new syntopic and sympatric calling morphs of the genusMecopodathat are morphologically similar but acoustically diverse from a sub-tropical forest in Meghalaya, in the Indo-Burma biodiversity hotspot. We report the morphological and acoustic characterization of these five call types, finding morphological overlap but well-separated acoustic clusters based on a PCA analysis of call temporal and spectral features. We also sequenced the COI gene mitochondrial gene of these five call types as well as other call types previously reported from India and performed a phylogenetic analysis of this gene relative to previously reported COI gene sequences from genusMecopoda.Phylogenetic results suggest our five call types are not mutually monophyletic and relate from different subspecies ofMecopoda, of which three call types are genetically well separated from other calling morphs. This broadens our understanding of the evolution of acoustic diversity among paleotropical katydids.
Characterization of the Kaposi’s sarcoma-associated herpesvirus terminase complex component ORF29
Authors: Iwaisako Yuki , Suzuki Youichi , Nakano Takashi , Fujimuro Masahiro 
Published: November 2024

ABSTRACTKaposi’s sarcoma-associated herpesvirus (KSHV) belongs to the gammaherpesvirinae subfamily. In the lytic phase of herpesviruses, viral capsids are formed in the nucleus of the host cell and the replicated viral genome is packaged into capsids. The herpesviral genome is replicated as a precursor head-to-tail concatemer consisting of tandemly repeated genomic units, and each genomic unit is flanked by terminal repeats (TRs). The herpesvirus terminase complex packages one genomic unit into a capsid, by cleavage of the TRs in a precursor genome. Although the terminase complexes of alpha- and beta-herpesviruses are well characterized, in KSHV, the terminase complex is poorly understood. KSHV ORF7, ORF67.5, and ORF29 are thought to be components of the terminase complex. We previously reported that ORF7- or ORF67.5-deficient KSHV formed immature soccer ball-like capsids and failed to cleave the TRs, resulting in decreased virion production. Moreover, ORF7 interacted with ORF29 and ORF67.5. However, ORF29 and ORF67.5 did not interact with each other. Thus, although ORF7 and ORF67.5 are important for KSHV terminase function, the function of ORF29 remains largely unknown. Here, we constructed ORF29-deficient BAC16 and analyzed its virological properties. ORF29 was essential for virion production and TR cleavage. Numerous immature soccer ball-like capsids were observed in ORF29-deficient KSHV-harboring cells. The N-terminal region of ORF29 was important for its interaction with ORF7, although full-length ORF29 was required for effective complexation of the KSHV terminase. Furthermore, ORF29 preferentially interacted with itself rather than with ORF7. Thus, our data shows that ORF29 functions as a fundamental terminase component.IMPORTANCESince the role of ORF29 in the KSHV terminase complex remains unknown, we constructed ORF29-deficient KSHV. Our results demonstrated that ORF29 functions as a component of the KSHV terminase and is critical for capsid formation, TR cleavage, and terminase complexation. Moreover, ORF29 robustly interacted with itself. In HSV-1, a terminase complex containing UL15, UL28, and UL33 forms a trimer, and six trimers assemble into a hexameric ring. The HSV-1 genome passes through this ring and undergoes TR cleavage and genome packaging into a capsid. The self-interaction of ORF29 may be involved in the multimerization of a terminase complex or formation of the KSHV terminase ring. In addition, a novel KSHV protein, which we refer to as ORF29.5, was expressed during the lytic state. ORF29.5 mRNA shares the same stop codon with the ORF29 mRNA. Moreover, a part of the ORF29.5 coding region may overlap with the C-terminal ORF29 coding region.
ReachUHC - A randomized controlled trial study protocol of mobile phone-based reminder and automatic renewal interventions to increase health insurance renewal rates in Kumasi, Ghana
Authors: Nübler Laura , Kwawukume Mawumenyo Aku , Ibrahim Fati , Neumann Anne , Okoe-Boye Bernard , Addo-Cobbiah Vivian , Owusu-Dabo Ellis , Mensah Kofi Akohene , Struckmann Verena , Knauss Samuel , Emmrich Julius Valentin , Waitzberg Ruth , Affanyi Enoch , Afflu Orison , Annor-Darkwah Joe , Blankson Daniel , Asenso-Boadi Francis , Cazier Juliette , Bencivenga Jennifer , Pioch Carolina , Siegel Martin , Quentin Wilm , Opoku Daniel 
Published: November 2024

AbstractBackgroundSince the Ghanaian National Health Insurance Scheme (NHIS) was introduced in 2004, coverage rates have remained low, despite affordable premiums and payment exemptions for minor, senior, poor and pregnant individuals. While 82% of the population have registered with the NHIS, many fail to complete the annual renewal and thus lose their coverage. A mobile renewal service introduced in 2018 simplified the previously cumbersome renewal procedure. Still, 40% of active member experience gaps in coverage in a given year, and 19% fail to renew at all. Baseline research suggests that forgetfulness is a major barrier to renewal.Methods342,818 NHIS members from Kumasi will be randomized into the reminder, autorenewal or control groups. The reminder arm receives SMS prompts to complete the mobile renewal process and payment before expiration. The autorenewal arm is eligible to sign up for automatic renewal and give the NHIS permission to deduct the premium from their mobile money account, and will receive SMS prompt to do so. The intervention lasts 6 months. NHIS routine data will be used to evaluate the effect of the interventions on renewals. A follow-up survey household survey in Kumasi will evaluate additional aspects user experience.DiscussionImproving insurance retention has the potential to substantially increase health insurance coverage rates, as 45% of the Ghanaians currently have expired insurance. Assessing these tools will identify enabling factors and barriers of the intervention and inform the transferability of the intervention to other health insurance systems in sub-Saharan African countries.Trial registrationPan African Clinical Trials Registry (PACTR)
Horizontal transfer of accessory chromosomes in fungi – a regulated process for exchange of genetic material?
Authors: Habig Michael , Patneedi Satish Kumar , Stam Remco , De Fine Licht Henrik Hjarvard 
Published: November 2024

AbstractHorizontal transfer of entire chromosomes has been reported in several fungal pathogens, often significantly impacting the fitness of the recipient fungus. All documented instances of horizontal chromosome transfers (HCTs) showed a marked propensity for accessory chromosomes, consistently involving the transfer of an accessory chromosome while other chromosomes were seldom, if ever, co-transferred. The mechanisms underlying HCTs, as well as the factors regulating the specificity of HCTs for accessory chromosomes, remain unclear. In this perspective, we provide an overview of the observed propensity in reported cases of horizontal chromosome transfers. We hypothesize the existence of a signal that distinguishes mobile, i.e., horizontally transferred, accessory chromosomes from the rest of the donor genome. Recent findings inMetarhizium robertsiiandMagnaporthe oryzae, suggest that a mobile accessory chromosome may contain putative histones and/or histone modifiers, which could generate such a signal. Based on this, we propose that mobile accessory chromosomes may encode the machinery required for their own horizontal transmission, implying that HCT could be a regulated process. Finally, we present evidence of substantial differences in codon usage bias between core and accessory chromosomes in 14 out of 19 analysed fungal species and strains. Such differences in codon usage bias could indicate past horizontal transfers of these accessory chromosomes. Interestingly, HCT was previously unknown for many of these species, suggesting that the horizontal transfer of accessory chromosomes may be more widespread than previously thought and, therefore, an important factor in fungal genome evolution.
Unravelling the molecular activation of the reparative cardiac fibroblasts after myocardial infarction
Authors: Hernández Silvia C , Ainciburu Marina , Sudupe Laura , Planell Nuria , Vilas-Zornoza Amaia , López-Moreno María , Sarvide Sarai , Diaz-Martinez Luis , Cobos-Figueroa Jorge , Martin-Uriz Patxi San , Muinos-López Emma , Abizanda Gloria , Ripalda-Cemboráin Purificación , Lagani Vincenzo , Romero Juan P. , Tegner Jesper , Pérez-Pomares José Mª , Wu Ming , Janssens Stefan , Prósper Felipe , Ruiz-Villalba Adrián , Gómez-Cabrero David 
Published: November 2024

AbstractActivated cardiac fibroblasts (Postn+CFs) are responsible for the healing of the heart tissue after a myocardial infarction (MI). However, so far little is known about the moment that CFs are activated, and the genes involved in this process. This is especially relevant in the context of CF heterogeneity and their role in the response to the damage. In this context, we have described a subpopulation of activated CFs responsible for the healing scar and for preventing the rupture of the ventricle after the damage: the Reparative Cardiac Fibroblasts (RCFs). Our new data indicate that RCFs directly derived from activated CFs, and this transcriptional shift happens in a close window after damage. Interestingly, our results exhibited two different molecular dynamics that would give rise to this activation and, consequently, the appearance of definitive RCFs. Using bulk RNA-Seq, RNAScope and Spatial Transcriptomics, we anatomically localized some of the genes related to both dynamics in the infarcted heart and highlight the potential role ofAspnas a new marker of this transcriptional transition in mice, pigs and patients.