bluuebunny/crossref_metadata_2025 huggingface dataset:
A full-STAC remedy for global digital health transformation: open standards, technologies, architectures and content
Authors: Mehl Garrett L , Seneviratne Martin G , Berg Matt L , Bidani Suhel , Distler Rebecca L , Gorgens Marelize , Kallander Karin E , Labrique Alain B , Landry Mark S , Leitner Carl , Lubell-Doughtie Peter B , Marcelo Alvin B , Matias Yossi , Nelson Jennifer , Nguyen Von , Nsengimana Jean Philbert , Orton Maeghan , Otzoy Garcia Daniel R , Oyaole Daniel R , Ratanaprayul Natschja , Roth Susann , Schaefer Merrick P , Settle Dykki , Tang Jing , Tien-Wahser Barakissa , Wanyee Steven , Hersch Fred
Published: December 2023

The global digital health ecosystem is project-centric: point solutions are developed for vertical health programs and financed through vertical funding allocations. This results in data fragmentation and technology lock-in, compromising health care delivery. A convergence of trends enabled by interoperability and digital governance makes possible a shift towards person-focused health. Together, open Standards, open Technologies, open Architectures and open Content represent a next-generation ‘full-STAC’ remedy for digital health transformation. Local developers and implementers can avoid reinventing the wheel, and instead build digital tools suited to local needs—where data travels with an individual over time, evidence-based practice is easily integrated, and insights are gleaned from harmonized data. This is the culmination of the vision endorsed by 194 WHO Member States in the Global Strategy on Digital Health 2020 to 2025.
Combining wearable fNIRS and immersive virtual reality to study preschoolers’ social development: a proof-of-principle study on preschoolers’ social preference
Authors: Bulgarelli Chiara , Pinti Paola , Aburumman Nadine , Jones Emily J H
Published: December 2023

A child’s social world is complex and rich, but has traditionally been assessed with conventional experiments where children are presented with repeated stimuli on a screen. These assessments are impoverished relative to the dynamics of social interactions in real life, and can be challenging to implement with preschoolers, who struggle to comply with strict lab rules. The current work meets the need to develop new platforms to assess preschoolers’ social development, by presenting a unique virtual-reality set-up combined with wearable functional near-infrared spectroscopy (fNIRS). As a proof-of-principle, we validated this platform by measuring brain activity during self-guided social interaction in 3-to-5-year-olds, which is under-investigated, yet crucial to understand the basis of social interactions in preschoolers. 37 preschoolers chose an interaction partner from one of 4 human-like avatars of different gender and age. We recorded spontaneous brain fluctuations from the frontal and temporoparietal regions (notably engaged in social-categorization and preference) while children played a bubble-popping game with a preferred and an assigned avatar. 60% of the participants chose to play with the same-gender and same-age avatar. However, this result was driven by females (>80% vs. 50% in males). Different fronto-temporoparietal connectivity patterns when playing with the two avatars were observed, especially in females. We showed the feasibility of using a novel set-up to naturalistically assess social preference in preschoolers, which was assessed at the behavioural and functional connectivity level. This work provides a first proof-of-principle for using cutting-edge technologies and naturalistic experiments to study social development, opening new avenues of research.
OXIDOSQUALENE CYCLASE 1 and 2 influence triterpene biosynthesis and defense in Nicotiana attenuata
Authors: Yang Caiqiong , Halitschke Rayko , O'Connor Sarah E
Published: December 2023

Triterpenes are a class of bioactive compounds with diverse biological functions, playing pivotal roles in plant defense against biotic stressors. Oxidosqualene cyclases (OSCs) serve as gatekeepers in the biosynthesis of triterpenes. In this study, we utilized a Nicotiana benthamiana heterologous expression system to characterize NaOSC1 from Nicotiana attenuata as a multifunctional enzyme capable of synthesizing lupeol, dammarenediol II, 3-alpha,20-lupanediol, and 7 other triterpene scaffolds. We also demonstrated that NaOSC2 is, in contrast, a selective enzyme, producing only the β-amyrin scaffold. Through virus-induced gene silencing and in vitro toxicity assays, we elucidated the roles of NaOSC1 and NaOSC2 in the defense of N. attenuata against Manduca sexta larvae. Metabolomic and feature-based molecular network analyses of leaves with silenced NaOSC1 and NaOSC2 unveiled 3 potential triterpene glycoside metabolite clusters. Interestingly, features identified as triterpenes within these clusters displayed a significant negative correlation with larval mass. Our study highlights the pivotal roles of NaOSC1 and NaOSC2 from N. attenuata in the initial steps of triterpene biosynthesis, subsequently influencing defense against M. sexta through the modulation of downstream triterpene glycoside compounds.
Incorporating Functional Strength Integration Techniques During Total Hip Arthroplasty Rehabilitation: A Randomized Controlled Trial
Authors: Judd Dana L , Cheuy Victor , Peters Amy , Graber Jeremy , Hinrichs-Kinney Lauren , Forster Jeri E , Christiansen Cory L , Stevens-Lapsley Jennifer E
Published: December 2023

Objective

Total hip arthroplasty (THA) is a common orthopedic procedure that alleviates pain for millions of individuals. Yet, persistent physical function deficits, perhaps associated with movement compensations, are observed after THA. These deficits negatively affect quality of life and health for many individuals. Functional strength integration (FSI) techniques combine muscle strength training with specific movement retraining to improve physical function. This study aimed to determine if FSI would improve functional performance through remediation of movement compensations for individuals after THA.

Methods

A double-blind randomized controlled trial was conducted. Ninety-five participants were randomized to either the FSI or control (CON) group for an 8-week intervention. The FSI protocol included exercise to improve muscular control and stability around the hip to minimize movement compensation during daily activity. The CON protocol included low-load resistance exercise, range-of-motion activities, and patient education. Functional performance, muscle strength, and self-reported outcomes were measured preoperatively, midway and after intervention, and 6 months after THA. Change from preoperative assessment to each time point was measured, and between-group differences were assessed.

Results

There were minimal differences in outcomes between groups at the first postoperative assessment. There were no statistically significant between-group differences in the later assessments, including the primary endpoint. Both groups improved functional outcomes throughout the study period.

Conclusion

The FSI intervention did not result in greater improvements in function after THA compared to the CON intervention. Future work should further investigate additional biomechanical outcomes, timing of the FSI protocol, effective dosing, and patient characteristics predictive of success with FSI.

Impact

Recovery after THA is complex, and individuals after THA are affected by persistent movement deficits that affect morbidity and quality of life. The present study suggests that either approach to THA rehabilitation could improve outcomes for patients, and that structured rehabilitation programs may benefit individuals after THA.
Development and psychometric evaluation of the sexual and reproductive health needs of incarcerated women scale: a methodological study
Authors: Ghareghozloo Mohadeseh , Moridi Maryam , Alimardi Masoud , Safari Kolsoom , Moghadam Zahra Behboodi
Published: December 2023

Background

This study aimed to develop and validate a comprehensive tool designed to assess the sexual and reproductive health (SRH) needs of incarcerated women.

Methods

A methodological study was conducted from January to March 2023 in two female prisons in Tehran and Hamedan, Iran. The participant pool consisted of women who had been incarcerated for a minimum of 6 months and were aged between 15 and 49 years. The instrument development involved two phases. Phase I involved a literature review and interviews with incarcerated women to understand their SRH needs. Phase II assessed psychometric properties to establish the scale’s validity and reliability.

Results

The SRH Needs of Incarcerated Women (SRH-NIW) scale was refined, comprising 37 items across six domains: pregnancy and childbirth services, parenting services, family planning and sexual health services, personal and medical care services, screening services and infection control services. Exploratory factor analysis explained 66.15% of variance. The Content Validity Ratio and Content Validity Index were 0.8 and 0.94, respectively, indicating high content validity. Average Variance Extracted values ranged from 0.592 to 0.698. The whole scale showed a Cronbach’s alpha of 0.823, and the Intra-class Correlation Coefficient was 0.879.

Conclusion

The SRH-NIW scale is a valid and reliable tool for assessing the SRH needs of incarcerated women. It can enhance healthcare services and interventions for incarcerated women, potentially leading to policy improvements within the prison system.
The speed of race
Authors: de Lissa Peter , Schaller Pauline , Caldara Roberto
Published: December 2023

When asked to categorize faces according to ‘race’, people typically categorize other-race faces faster than faces belonging to their own race. This ‘Other Race Categorization Advantage’ is thought to reflect enhanced sensitivity to early visual signals characteristic of other-race faces, and can manifest within 200 ms of face presentation. However, recent research has highlighted the importance of signal intensity in this effect, where visual-degradation of the face images significantly enhances the effect and exposes a behavioural threshold at very low levels of visual quality where other-race visual signals are able to be perceived while same-race signals are not. The current study investigated the effect of signal intensity in race categorization processes in the brain through electroencephalography and in accuracy/reaction times. While replicating the previously observed enhancement of the other-race categorization advantage, we also found enhanced sensitivity to other-race faces in early P1 peaks, as well as later N170 and N250 peaks. These effects, however, related to the varying levels of signal intensity in the face stimuli, suggesting that race categorization may involve different types of perceptual and neural processes rather than one discrete process. The speed at which race is perceived depends on the intensity of the face signal.
Toll-Like Receptor mRNA Levels in Schizophrenia: Association With Complement Factors and Cingulate Gyrus Cortical Thinning
Authors: Weickert Thomas W , Ji Ellen , Galletly Cherrie , Boerrigter Danny , Morishima Yosuke , Bruggemann Jason , Balzan Ryan , O’Donnell Maryanne , Liu Dennis , Lenroot Rhoshel , Weickert Cynthia Shannon , Kindler Jochen
Published: December 2023

Background and Hypotheses

Previous studies revealed innate immune system activation in people with schizophrenia (SZ), potentially mediated by endogenous pathogen recognition receptors, notably Toll-like receptors (TLR). TLRs are activated by pathogenic molecules like bacterial lipopolysaccharides (TLR1 and TLR4), viral RNA (TLR3), or both (TLR8). Furthermore, the complement system, another key component of innate immunity, has previously been linked to SZ.

Study Design

Peripheral mRNA levels of TLR1, TLR3, TLR4, and TLR8 were compared between SZ and healthy controls (HC). We investigated their relationship with immune activation through complement expression and cortical thickness of the cingulate gyrus, a region susceptible to immunological hits. TLR mRNA levels and peripheral complement receptor mRNA were extracted from 86 SZ and 77 HC white blood cells; structural MRI scans were conducted on a subset.

Study Results

We found significantly higher TLR4 and TLR8 mRNA levels and lower TLR3 mRNA levels in SZ compared to HC. TLRs and complemental factors were significantly associated in SZ and HC, with the strongest deviations of TLR mRNA levels in the SZ subgroup having elevated complement expression. Cortical thickness of the cingulate gyrus was inversely associated with TLR8 mRNA levels in SZ, and with TLR4 and TLR8 levels in HC.

Conclusions

The study underscores the role of innate immune activation in schizophrenia, indicating a coordinated immune response of TLRs and the complement system. Our results suggest there could be more bacterial influence (based on TLR 4 levels) as opposed to viral influence (based on TLR3 levels) in schizophrenia. Specific TLRs were associated with brain cortical thickness reductions of limbic brain structures.
Multivariate genome-wide association study of sleep health demonstrates unity and diversity
Authors: Morrison Claire L , Winiger Evan A , Wright Kenneth P , Friedman Naomi P
Published: December 2023

There has been a recent push to focus sleep research less on disordered sleep and more on the dimensional sleep health. Sleep health incorporates several dimensions of sleep: chronotype, efficiency, daytime alertness, duration, regularity, and satisfaction with sleep. A previous study demonstrated sleep health domains correlate only moderately with each other at the genomic level (|rGs| = 0.11–0.51) and show unique relationships with psychiatric domains (controlling for shared variances, duration, alertness, and non-insomnia independently related to a factor for internalizing psychopathology). Of the domains assessed, circadian preference was the least genetically correlated with all other facets of sleep health. This pattern is important because it suggests sleep health should be considered a multifaceted construct rather than a unitary construct. Prior genome-wide association studies (GWASs) have vastly increased our knowledge of the biological underpinnings of specific sleep traits but have only focused on univariate analyses. We present the first multivariate GWAS of sleep and circadian health (multivariate circadian preference, efficiency, and alertness factors, and three single-indicator factors of insomnia, duration, and regularity) using genomic structural equation modeling. We replicated loci found in prior sleep GWASs, but also discovered “novel” loci for each factor and found little evidence for genomic heterogeneity. While we saw overlapping genomic enrichment in subcortical brain regions and shared associations with external traits, much of the genetic architecture (loci, mapped genes, and enriched pathways) was diverse among sleep domains. These results confirm sleep health as a family of correlated but genetically distinct domains, which has important health implications.
Human Hepatocyte Transplantation: Three Decades of Clinical Experience and Future Perspective
Authors: Nulty Jessica , Anand Hanish , Dhawan Anil
Published: December 2023

Orthotopic liver transplantation (OLT) is the current standard of care for both chronic and acute terminal liver disease. However, a major limitation of this treatment is the shortage of healthy donor organs and the need for life-long immunosuppression to prevent graft rejection. Hepatocyte transplantation (HTx) has emerged as a promising, alternative therapeutic approach to either replace OLT or to act as a bridge until a donor liver becomes available thus reducing waiting list mortality. HTx involves the infusion and engraftment of human hepatocytes, typically isolated from organs unsuitable for OLT, into recipient liver parenchyma to carry out the missing hepatic function of the native cells. HTx is less invasive than OLT and can be performed repeatedly if required. The safety of clinical HTx has been shown and treatment results are promising, especially in patients with liver-based metabolic disorders. Nevertheless, HTx has failed to become the standard of care treatment for such disorders. This review aims to evaluate the progress that has been made within the field of HTx over the last 30 years and identify potential shortcomings within the approach which may be hindering its routine clinical application.
Establishment and Validation of a Model for Fetal Neural Ischemia Using Necrotic Core-Free Human Spinal Cord Organoids
Authors: Shin Aeri , Ryu Jae Ryun , Kim Byung Gon , Sun Woong
Published: December 2023

Fetal spinal cord ischemia is a serious medical condition that can result in significant neurological damage and adverse outcomes for the fetus. However, the lack of an appropriate experimental model has hindered the understanding of the pathology and the development of effective treatments. In our study, we established a system for screening drugs that affect fetal spinal cord ischemia using spinal cord organoids. Importantly, we produced necrotic core-free human spinal cord organoids (nf-hSCOs) by reducing the organoid size to avoid potential complications of spontaneous necrosis in large organoids. Exposing nf-hSCOs to CoCl2 as a hypoxia mimetic and hypoglycemic conditions resulted in significant neuronal damage, as assessed by multiple assay batteries. By utilizing this model, we tested chemicals that have been reported to exhibit beneficial effects in brain organoid-based ischemia models. Surprisingly, these chemicals did not provide sufficient benefit, and we discovered that rapamycin is a mild neuroprotective reagent for both axon degeneration and neuronal survival. We propose that nf-hSCO is suitable for large-scale screening of fetal neural ischemia due to its scalability, ease of ischemic induction, implementation of quantifiable assay batteries, and the absence of spontaneous necrosis.
Drought resistance in two populations of invasive Tamarix compared using multiple methods
Authors: Long Randall W , Pratt R Brandon , Jacobsen Anna L
Published: December 2023

An on-going question in plant hydraulic research is whether there is intra-specific variability and/or plasticity in xylem traits. Plasticity could be important in taxa that colonize diverse habitats. We used Tamarix, a non-native woody plant, to investigate population differences in hydraulic conductivity (Ks), vulnerability-to-embolism curves and vessel anatomy. We also conducted a season-long drought experiment to determine water potentials associated with crown dieback of field-grown plants. We measured vessel length and diameter, and compared visual (micro-computed tomography; microCT) and hydraulic methods to quantify percentage loss in hydraulic conductivity (PLC). Among plants grown in a common environment, we did not find differences in our measured traits between two populations of Tamarix that differ in salinity at their source habitats. This taxon is relatively vulnerable to embolism. Within samples, large diameter vessels displayed increased vulnerability to embolism. We found that the microCT method overestimated theoretical conductivity and underestimated PLC compared with the hydraulic method. We found agreement for water potentials leading to crown dieback and results from the hydraulic method. Saplings, grown under common conditions in the present study, did not differ in their xylem traits, but prior research has found difference among source-site grown adults. This suggests that plasticity may be key in the success of Tamarix occurring across a range of habits in the arid southwest USA.
Parallel evolution and enhanced virulence upon in vivo passage of an RNA virus in Drosophila melanogaster
Authors: Lezcano Oscar M , Fuhrmann Lara , Ramakrishnan Gayatri , Beerenwinkel Niko , Huynen Martijn A , van Rij Ronald P
Published: December 2023

Virus evolution is strongly affected by antagonistic co-evolution of virus and host. Host immunity positively selects for viruses that evade the immune response, which in turn may drive counter-adaptations in host immune genes. We investigated how host immune pressure shapes virus populations, using the fruit fly Drosophila melanogaster and its natural pathogen Drosophila C virus (DCV), as a model. We performed an experimental evolution study in which DCV was serially passaged for ten generations in three fly genotypes differing in their antiviral RNAi response: wild-type flies and flies in which the endonuclease gene Dicer-2 was either overexpressed or inactivated. All evolved virus populations replicated more efficiently in vivo and were more virulent than the parental stock. The number of polymorphisms increased in all three host genotypes with passage number, which was most pronounced in Dicer-2 knockout flies. Mutational analysis showed strong parallel evolution, as mutations accumulated in a specific region of the VP3 capsid protein in every lineage in a host genotype-independent manner. The parental tyrosine at position ninety-five of VP3 was substituted with either one of five different amino acids in fourteen out of fifteen lineages. However, no consistent amino acid changes were observed in the viral RNAi suppressor gene 1A, nor elsewhere in the genome in any of the host backgrounds. Our study indicates that the RNAi response restricts the sequence space that can be explored by viral populations. Moreover, our study illustrates how evolution towards higher virulence can be a highly reproducible, yet unpredictable process.
Global value chains in EU law
Authors: Beckers Anna
Published: December 2023

There is a burgeoning legal literature about the legal underpinnings of global value chains (GVCs). This article contributes to this literature through the lens of European Union (EU) law and proposes a different conceptual way to read GVCs legally. To that end, the contribution proposes understanding the evolving EU law on GVCs as a process of institutionalization leading to at least three legal forms. In EU company law, GVCs manifest actor-centrically as corporate obligations to govern the value chain. This mostly happens in the policies related to sustainability, but also features in some digitalization policies. In EU consumer law, the value chain appears as a collective network of actors that also bears collective responsibility towards the consumer for the production process. Moreover, in EU market practices and trade law, the value chain is approached in a de-personified manner by, on the one hand, targeting products relating to the territory (import/internal market access) and, on the other hand, trading practices in relations characterised by power asymmetry. These findings suggests that, rather than identifying a uniform legal concept of GVCs in EU law, a fragmented picture emerges in which different sub-areas of EU law develop different, partly even opposing, legal understandings of GVCs.
An adeno‐associated viral labeling approach to visualize the meso‐ and microanatomy of mechanosensory afferents and autonomic innervation of the rat urinary bladder
Authors: Wiedmann Nicole M. , Fuller‐Jackson John‐Paul , Osborne Peregrine B. , Keast Janet R.
Published: December 2023

The urinary bladder is supplied by a rich network of sensory and autonomic axons, commonly visualized by immunolabeling for neural markers. This approach demonstrates overall network patterning but is less suited to understanding the structure of individual motor and sensory terminals within these complex plexuses. There is a further limitation visualizing the lightly myelinated (A‐delta) class of sensory axons that provides the primary mechanosensory drive for initiation of voiding. Whereas most unmyelinated sensory axons can be revealed by immunolabeling for specific neuropeptides, to date no unique neural marker has been identified to immunohistochemically label myelinated visceral afferents. We aimed to establish a non‐surgical method to visualize and map myelinated afferents in the bladder in rats. We found that in rats, the adeno‐associated virus (AAV), AAV‐PHP.S, which shows a high tropism for the peripheral nervous system, primarily transduced myelinated dorsal root ganglion neurons, enabling us to identify the structure and regional distribution of myelinated (mechanosensory) axon endings within the muscle and lamina propria of the bladder. We further identified the projection of myelinated afferents within the pelvic nerve and lumbosacral spinal cord. A minority of noradrenergic and cholinergic neurons in pelvic ganglia were transduced, enabling visualization and regional mapping of both autonomic and sensory axon endings within the bladder. Our study identified a sparse labeling approach for investigating myelinated sensory and autonomic axon endings within the bladder and provides new insights into the nerve‐bladder interface.
From biosynthesis and beyond—Loss or overexpression of the cytokinin synthesis gene, iptA, alters cytokinesis and mitochondrial and amino acid metabolism in Dictyostelium discoideum
Authors: Aoki Megan M. , Kisiala Anna B. , Mathavarajah Sabateeshan , Schincaglia Angela , Treverton Jared , Habib Elias , Dellaire Graham , Emery R. J. Neil , Brunetti Craig R. , Huber Robert J.
Published: December 2023

Cytokinins (CKs) are a class of growth‐promoting signaling molecules that affect multiple cellular and developmental processes. These phytohormones are well studied in plants, but their presence continues to be uncovered in organisms spanning all kingdoms, which poses new questions about their roles and functions outside of plant systems. Cytokinin production can be initiated by one of two different biosynthetic enzymes, adenylate isopentenyltransfases (IPTs) or tRNA isopentenyltransferases (tRNA‐IPTs). In this study, the social amoeba, Dictyostelium discoideum, was used to study the role of CKs by generating deletion and overexpression strains of its single adenylate‐IPT gene, iptA. The life cycle of D. discoideum is unique and possesses both single‐ and multicellular stages. Vegetative amoebae grow and divide while food resources are plentiful, and multicellular development is initiated upon starvation, which includes distinct life cycle stages. CKs are produced in D. discoideum throughout its life cycle and their functions have been well studied during the later stages of multicellular development of D. discoideum. To investigate potential expanded roles of CKs, this study focused on vegetative growth and early developmental stages. We found that iptA‐deficiency results in cytokinesis defects, and both iptA‐deficiency and overexpression results in dysregulated tricarboxylic acid (TCA) cycle and amino acid metabolism, as well as increased levels of adenosine monophosphate (AMP). Collectively, these findings extend our understanding of CK function in amoebae, indicating that iptA loss and overexpression alter biological processes during vegetative growth that are distinct from those reported during later development.
An efficient plasmid-based system for the recovery of recombinant vesicular stomatitis virus encoding foreign glycoproteins
Authors: Marqués María-Carmen , Andreu-Moreno Iván , Sanjuán Rafael , Elena Santiago F. , Geller Ron
Published: December 2023

Viral glycoproteins mediate entry into host cells, thereby dictating host range and pathogenesis. In addition, they constitute the principal target of neutralizing antibody responses, making them important antigens in vaccine development. Recombinant vesicular stomatitis virus (VSV) encoding foreign glycoproteins can provide a convenient and safe surrogate system to interrogate the function, evolution, and antigenicity of viral glycoproteins from viruses that are difficult to manipulate or those requiring high biosafety levels containment. However, the production of recombinant VSV can be technically challenging. In this work, we present an efficient and robust plasmid-based system for the production of recombinant VSV encoding foreign glycoproteins. We validate the system using glycoproteins from different viral families, including arenaviruses, coronaviruses, and hantaviruses, as well as highlight their utility for studying the effects of mutations on viral fitness. Overall, the methods described herein can facilitate the study of both native and recombinant VSV encoding foreign glycoproteins and can serve as the basis for the production of VSV-based vaccines.
Fertilisation of agricultural soils with municipal biosoilds: Part 2- Site properties, environmental factors, and crop identify influence soil bacterial communities more than municipal biosolid application
Authors: Blakney Andrew J.C. , Morvan Simon , Lucotte Marc , Moingt Matthieu , Charbonneau Ariane , Bipfubusa Marie , Gonzalez Emmanuel , Pitre Frédéric E.
Published: December 2023

Reducing the environmental impact of Canadian field crop agriculture, including the reliance on conventional synthesised fertilisers, are key societal targets for establishing long-term sustainable practices. Municipal biosolids (MSB) are an abundant, residual organic material, rich in phosphate, nitrogen and other oligo-nutrients, that could be used in conjunction with conventional fertilisers to decrease their use. Though MBS have previously been shown to be an effective fertiliser substitute for different crops, including corn and soybean, there remain key knowledge gaps concerning the impact of MBS on the resident soil bacterial communities in agro-ecosystems. We hypothesised that the MBS fertiliser amendment would not significantly impact the structure or function of the soil bacterial communities, nor contribute to the spread of human pathogenic bacteria, in corn or soybean agricultural systems. In field experiments, fertiliser regimes for both crops were amended with MBS, and compared to corn and soybean plots with standard fertiliser treatments. We repeated this across four different agricultural sites in Quebec, over 2021 and 2022. We sampled MBS-treated, and untreated soils, and identified the composition of the soil bacterial communities via 16S rRNA metabarcoding. We found no indication that the MBS fertiliser amendment altered the structure of the soil bacterial communities, but rather that the soil type and crop identities were the most significant factors in structuring the bacterial communities. Moreover, there was no evidence that the MBS-treated soils experienced a shift in functions, nor contributed potential human bacterial pathogens over the two years of our study. Our analysis indicates that not only can MBS function as substitutes for conventional, synthesised fertilisers, but that they also do not disrupt the structure, or function, of the resident soil bacterial communities in the short term. Finally, we suggest that the use of MBS in agro-ecosystems poses no greater concern to the public than existing soil bacterial communities.

Highlights

Municipal biosolids may represent a sustainable fertiliser substitute

But, the impact of biosolids on soil bacteria in agricultural fields is unknown

Using 16S rRNA metabarcoding we analysed community structure and functions

We found no disruption of soil bacterial communities fertilised with biosolids

Biosolids are safe, sustainable fertilisers with little impact on soil bacteria

Graphical Abstract
miR-519a-3p, found to regulate cellular prion protein during Alzheimer’s disease pathogenesis, as a biomarker of asymptomatic stages
Authors: Jácome Dayaneth , Cotrufo Tiziana , Andrés-Benito Pol , Martí Eulàlia , Ferrer Isidre , del Río José Antonio , Gavín Rosalina
Published: December 2023

MiRNAs induce post-transcriptional gene silencing by binding to the 3’-UTR of complementary messenger RNAs and causing either degradation or inhibition of translation.

The clinical relevance of miRNAs as biomarkers is growing due to their stability and detection in biofluids. In this sense, diagnosis at asymptomatic stages of Alzheimer’s disease (AD) remains a challenge since it can only be made at autopsy according to Braak NFT staging. Achieving the objective of detecting AD at early stages would allow possible therapies to be addressed before the onset of cognitive impairment.

Many studies have determined that the expression pattern of some miRNAs is deregulated in AD patients, but to date, none has been correlated with downregulated expression of cellular prion protein (PrPC) during disease progression. That is why, by means of cross studies of miRNAs up-regulated in AD within silicoidentification of potential miRNAs-binding to 3’UTR of humanPRNPgene, we selected miR-519a-3p for our study.

Other family members of miR-519 have been shown to bind to the 3’UTR region ofPRNP in vitroand presumably degradePRNPmRNA. In addition, up-regulation of some of them has been reported in various tissues from AD patients, including cerebrospinal fluid, plasma, and blood serum. In fact, miR-519d-3p is marked as a bridge regulator between mild cognitive impairment and severe AD. However, none of the studies address the prodromal stages of the disease or the expression profile of miR-519 in other neurodegenerative diseases that also may present dementia. Therefore, in this study we analyzed miR-519a-3p expression in cerebral samples of AD at different stages of evolution as well as other neurodegenerative diseases such as other tauopathies and synucleinopathies. Our results show the specific and early upregulation of miR-519a-3p starting from Braak stage I of AD, suggesting its potential use as a biomarker of preclinical stages of the disease.
Benchmarking the identification of a single degraded protein to explore optimal search strategies for ancient proteins
Authors: Rodriguez Palomo Ismael , Nair Bharath , Chiang Yun , Dekker Joannes , Dartigues Benjamin , Mackie Meaghan , Evans Miranda , Macleod Ruairidh , Olsen Jesper V. , Collins Matthew J.
Published: December 2023

Palaeoproteomics is a rapidly evolving discipline, and practitioners are constantly developing novel strategies for the analyses and interpretations of complex, degraded protein mixtures. The community has also established standards of good practice to interrogate our data. However, there is a lack of a systematic exploration of how these affect the identification of peptides, post-translational modifications (PTMs), proteins and their significance (through the False Discovery Rate) and correctness. We systematically investigated the performance of a wide range of sequencing tools and search engines in a controlled system: the experimental degradation of the single purified bovine β-lactoglobulin (BLG), heated at 95 °C and pH 7 for 0, 4 and 128 days. We target BLG since it is one of the most robust and ubiquitous proteins in the archaeological record. We tested different reference database choices, a targeted dairy protein one, and the whole bovine proteome and the three digestion options (tryptic-, semi-tryptic- and non-specific searches), in order to evaluate the effects of search space and the identification of peptides. We also explored alternative strategies, including open search that allows for the global identification of PTMs based upon wide precursor mass tolerance andde novosequencing to boost sequence coverage. We analysed the samples using Mascot, MaxQuant, Metamorpheus, pFind, Fragpipe and DeNovoGUI (pepNovo+, DirecTag, Novor), benchmarked these tools and discuss the optimal strategy for the characterisation of ancient proteins. We also studied physicochemical properties of the BLG that correlate with bias in the identification coverage.
Refinement of Cryo-EM 3D Maps with Self-Supervised Denoising Model: crefDenoiser
Authors: Agarwal Ishaant , Kaczmar-Michalska Joanna , Nørrelykke Simon F. , Rzepiela Andrzej J.
Published: December 2023

Cryogenic electron microscopy (cryo-EM) is a pivotal technique for imaging macromolecular structures. Despite extensive processing of large image sets collected in a cryo-EM experiment to amplify the signal-to-noise ratio, the reconstructed 3D protein density maps are often limited in quality due to residual noise, which in turn affects the accuracy of the macromolecular representation. In this paper, we introduce crefDenoiser, a denoising neural network model designed to enhance the signal in 3D cryo-EM maps produced with standard processing pipelines, beyond the current state of the art. crefDenoiser is trained without the need for ‘clean’, ground-truth target maps. Instead, we employ a custom dataset composed of real noisy protein half-maps sourced from the Electron Microscopy Data Bank repository. Strong model performance is achieved by optimizing for the theoretical noise-free map during self-supervised training. We demonstrate that our model successfully amplifies the signal across a wide variety of protein maps, outperforming a classical map denoiser and a network-based sharpening model. Without biasing the map, the proposed denoising method often leads to improved visibility of protein structural features, including protein domains, secondary structure elements, and amino-acid side chains.
Structural and mechanistic views of enzymatic, heme-dependent nitrogen-nitrogen bond formation
Authors: Higgins Melanie A. , Shi Xinjie , Soler Jordi , Harland Jill B. , Parkkila Taylor , Lehnert Nicolai , Garcia-Borràs Marc , Du Yi-Ling , Ryan Katherine S.
Published: December 2023

Molecules with nitrogen-nitrogen (N-N) bonds constitute a large group of clinically important drugs, and various synthetic approaches have been developed to construct functional groups like hydrazines, diazos, pyrazoles, and N-nitrosos. While hundreds of N-N-containing specialized natural metabolites have also been discovered, little is known about the underlying enzymatic mechanisms that have evolved for N-N bond formation. In order to directly form a single N(sp3)-N(sp3) bond, enzymes must reverse the typical nucleophilicity of one nitrogen. Here, we report structural and mechanistic interrogations of the piperazate synthase PipS, a heme-dependent enzyme that catalyzes an N-N bond forming cyclization ofN5-OH-L-ornithine to give the non-proteinogenic amino acid L-piperazic acid. We show that PipS can process a variety ofN-substituted hydroxylamines, to give either an imine or an N-N bond, in a substrate-specific manner. Using a combination of structural and biochemical experiments, computational studies, and spectroscopic characterization, we propose that heme-dependent dehydration and N-N bond formation in PipS proceed through divergent pathways, which may stem from a shared nitrenoid intermediate that effectively reverses the nucleophilicity of the hydroxylamine nitrogen. Our work expands the current knowledge of enzymatic N-N bond formation, and delineates the catalytic versatility of a heme cofactor, paving the way for future development of genetically encoded biocatalysts for N-N bond formation.
Synergistic insulation of regulatory domains by developmental genes and clusters of CTCF sites
Authors: Ealo Thais , Sanchez-Gaya Victor , Respuela Patricia , Martín María Muñoz-San , Martin-Batista Elva , Haro Endika , Rada-Iglesias Alvaro
Published: December 2023

The specificity of gene expression during development requires the insulation of regulatory domains to avoid inappropriate enhancer-gene interactions. In vertebrates, this insulator function is mostly attributed to clusters of CTCF sites located at topologically associating domain (TAD) boundaries. However, TAD boundaries allow a certain level of physical crosstalk across regulatory domains, which is at odds with the highly specific and precise expression of developmental genes. Here we show that developmental genes and nearby clusters of CTCF sites synergistically foster the robust insulation of regulatory domains. Firstly, we found that the TADs containing developmental genes have distinctive features, including the sequential organization of developmental genes and CTCF clusters near TAD boundaries. Most importantly, by genetically dissecting representative loci in mouse embryonic stem cells, we showed that developmental genes and CTCF sites synergistically strengthened the insulation capacity of nearby boundaries through different mechanisms. Namely, while CTCF sites prevent undesirable enhancer-gene contacts (i.e.physical insulation), developmental genes preferentially contribute to regulatory insulation through non-structural mechanisms involving promoter competition rather than enhancer blocking. Overall, our work provides important insights into the specificity of gene regulation, which in turn might help interpreting the pathological consequences of certain structural variants.
Recent evolution of large offspring size and post-fertilization nutrient provisioning in swordtails
Authors: Payne Cheyenne Y. , Ly Derek , Rodriguez-Soto Rebecca A. , Powell Daniel L. , Robles Nim D. , Gunn Theresa , Bazcenas John J , Bergman Abby J. , Pollock Alexa , Moran Ben M. , Baker Julie C. , Reznick David , Schumer Molly
Published: December 2023

Organisms have evolved diverse reproductive strategies that impact the probability that their offspring survive to adulthood. Here, we describe divergence in reproductive strategy between two closely related species of swordtail fish (Xiphophorus). Swordtail fish and their relatives have evolved viviparity: they have internal fertilization and give birth to fully developed fry. We find that one species,X. malinche, which lives in high-elevation environments, has evolved larger offspring than its closest relativeX. birchmanniand dwarfs the offspring size of other species in the genus. The larger fry ofX. malincheare more resilient to starvation than theirX. birchmannirelatives, hinting that the evolution of large offspring size may be an adaptation to the particularly challenging environments in whichX. malincheare born. We find evidence thatX. malincheachieves larger offspring size in part by continuing to provision their offspring over the course of embryonic development after fertilization, the first time this process has been documented in theXiphophorusgenus. Moreover, we observe differential regulation in the ovary of genes associated with maternal nutrient provisioning in other species that use this reproductive strategy. Intriguingly, these reproductive differences may drive an asymmetric hybrid incompatibility, sinceX. birchmannimothers pregnant with F1embryos give birth to premature and stillborn fry at an exceptionally high rate.
Contributions of tactile information to the sense of agency and its metacognitive representations
Authors: Charalampaki Angeliki , Ciston Anthony Buck , Filevich Elisa
Published: December 2023

We compared the contribution of tactile information to other sources of information in our representations of agency. Participants (N = 40) reached with their right hand toward a ridged plate with a specific orientation and saw online feedback that could match or differ from their action in one of three ways: the physical plate’s orientation, the action’s timing, or the hand’s position in space. Absolute subjective ratings revealed that an increased mismatch in tactile information led to a diminished sense of agency, similar to what has been reported for spatial and temporal mismatches. Further, estimations of metacognitive efficiency revealed similar M-ratios in the identification of tactile violation predictions as compared to temporal violations (but lower than spatial). These findings emphasize the importance of tactile information in shaping our experience of acting voluntarily, and show how this important component can be experimentally probed.

Statement of Relevance

The sense of agency is the feeling that we are the authors of our actions. It is essential not only for the control we assert over our bodies but also for how we interact with interfaces like a computer or a mobile phone. Despite the central role of touch in our daily activities, the role of tactile information in forming our sense of agency is often overlooked. In this project, we used a novel experimental design that allowed us to compare the role of tactile information relative to two other sources of information that have been previously reported to affect our agency, namely temporal and spatial information of the action. We provide evidence for the first time that tactile information is crucial for our subjective experience of agency and a tool to study this role further.
AAV-mediated expression of mouse or human GLDC normalises metabolic biomarkers in a GLDC-deficient mouse model of Non-Ketotic Hyperglycinemia
Authors: Leung Kit-Yi , Santos Chloe , De Castro Sandra C.P. , Diaz Diana Gold , Copp Andrew J. , Waddington Simon , Greene Nicholas DE
Published: December 2023

Non-Ketotic Hyperglycinemia (NKH) is a rare inborn error of metabolism caused by impaired function of the glycine cleavage system (GCS) and characterised by accumulation of glycine in body fluids and tissues. NKH is an autosomal recessive condition and the majority of affected individuals carry mutations inGLDC(glycine decarboxylase). Current treatments for NKH are not effective or curative. As a monogenic condition with known genetic causation, NKH is potentially amenable to gene therapy. An AAV9-based expression vector was designed to target sites of GCS activity. Using an ubiquitous promoter to drive expression of a GFP reporter, transduction of liver and brain was confirmed following intra-venous and/or intra-cerebroventricular administration to neonatal mice. Using the same capsid and promoter with transgenes to express mouse or human GLDC, vectors were then tested in a GLDC-deficient mice that provide a model of NKH. GLDC-deficient mice exhibited elevated plasma glycine concentration and accumulation of glycine in liver and brain tissues as previously observed. Moreover, the folate profile indicated suppression of folate one carbon metabolism (FOCM) in brain tissue, as found at embryonic stages, and reduced abundance of FOCM metabolites including betaine and choline. Neonatal administration of vector achieved reinstatement ofGLDCmRNA and protein expression in GLDC-deficient mice. Treated GLDC-deficient mice showed significant lowering of plasma glycine, confirming functionality of vector expressed protein. AAV9-GLDC treatment also led to lowering of brain tissue glycine, and normalisation of the folate profile indicating restoration of glycine-derived one-carbon supply. These findings support the hypothesis that AAV-mediated gene therapy may offer potential in treatment of NKH.
Production of single-cell-protein (SCP) / poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) matrices through fermentation of archaeaHaloferax mediterranei
Authors: Unis Razan , Gnaim Rima , Kashyap Mrinal , Shamis Olga , Gnayem Nabeel , Gozin Michael , Liberzon Alexander , Gnaim Jallal , Golberg Alexander
Published: December 2023

The idea ofin-situintegrating poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) sieves in a single-cell protein (SCP) represents a promising approach to enhance the properties of microbial biomass as protein alternatives. Archaea SCP/PHBV matrix was successfully produced with a concentration of 8.0 ± 0.1 g L-1and a productivity of 11.1 mg L-1h-1usingHaloferax mediterranei. This was achieved by employing 30 g L-1of enzymatically hydrolyzed bread waste (BW) and 200 g L-1of red sea salt at 42 °C and with shaking at 150 rpm for 3 days. The amino acid profile of the SCP/PHBV matrix revealed a total amino acid content of 358 g kg-1, including 147 g kg-1of essential amino acids. The protein quality of theH. mediterraneiSCP/PHBV matrix was assessed using thein-vitroenzyme digestion method, indicating a high-quality protein with anin-vitrodigestibility value of 0.91 and a protein digestibility-corrected amino acid score (PDCAAS) of 0.78. The PHBV component (36.0 ± 6.3% w/w) in the SCP/PHBV matrix consisted of a copolymer of 3-hydroxybutyrate and 3- hydroxyvalerate in a 91:9 mol% ratio, respectively. The simultaneous production of PHBV polymeric sieves within theH. mediterraneiSCP/PHBV matrix provides an alternative protein source with enhanced physicochemical and thermal properties.

Highlights

SCP/PHBV matrices were produced from wasted bread by archaeaH. mediterranei.

This is the first report that explored the production and properties of SCP/PHBV.

The presence of PHBV in SCP affected its physicochemical and thermal properties.

SCP/PHBV with high-quality protein was achieved with a PDCAAS value of 0.78.

Graphical abstract