bluuebunny/crossref_metadata_2025 huggingface dataset:
Harmonizing Definitions and Perspectives in Extreme Liver Surgery
Authors: Lopez-Lopez Victor , Lodge Peter , Oldhafer Karl , Hernandez-Alejandro Roberto , Akamatsu Nobuhisa , Honda Goro , Pinna Antonio , Balci Deniz , Govil Sanjay , Cillo Umberto , Schlegel Andrea , Nadalin Silvio , Di Benedetto Fabrizio , Pratschke Johann , Aldrighetti Luca , Soubrane Olivier , Scatton Olivier , Wakabayashi Go , Popescu Irinel , Ramia Jose Manuel , Ohtsuka Masayuki , Line Pål-Dag , Troisi Roberto Ivan , Machado Marcel A , Fusai Giuseppe Kito , Sapisochin Gonzalo , Pekolj Juan , Balzan Silvio , Fondevila Constantino , Han Ho-Seong , Lesurtel Mickaël , Pinto-Marques Hugo , Menon Krishna , Rotellar Fernando , Polak Wojciech G , Dopazo Cristina , Lopez-Ben Santiago , Torzilli Guido , de Vicente Emilio , de la Cruz Juan , Chavez-Villa Mariana , Ferreras David , Serrablo Alejandro , De Santibañez Eduardo , Clavien Pierre-Alain , Azoulay Daniel , Robles-Campos Ricardo
Published: June 2024

Objective:

To propose to our community a common language about extreme liver surgery.

Background:

The lack of a clear definition of extreme liver surgery prevents convincing comparisons of results among centers.

Methods:

We used a two-round Delphi methodology to quantify consensus among liver surgery experts. For inclusion in the final recommendations, we established a consensus when the positive responses (agree and totally agree) exceeded 70%. The study steering group summarized and reported the recommendations. In general, a five-point Likert scale with a neutral central value was used, and in a few cases multiple choices. Results are displayed as numbers and percentages.

Results:

A two-round Delphi study was completed by 38 expert surgeons in complex hepatobiliary surgery. The surgeon´s median age was 58 years old (52-63) and the median years of experience was 25 years (20-31). For the proposed definitions of total vascular occlusion, hepatic flow occlusion and inferior vein occlusion, the degree of agreement was 97%, 81% and 84%, respectively. In situ approach (64%) was the preferred, followed by ante situ (22%) and ex situ (14%). Autologous or cadaveric graft for hepatic artery or hepatic vein repair were the most recommended (89%). The use of veno-venous bypass or portocaval shunt revealed the divergence depending on the case. Overall, 75% of the experts agreed with the proposed definition for extreme liver surgery.

Conclusion:

Obtaining a consensus on the definition of extreme liver surgery is essential to guarantee the correct management of patients with highly complex hepatobiliary oncological disease. The management of candidates for extreme liver surgery involves comprehensive care ranging from adequate patient selection to the appropriate surgical strategy.
VIPER: A General Model for Prediction of Enzyme Substrates
Authors: Campbell Maxwell J.
Published: June 2024

Enzymes, nature’s catalysts, possess remarkable properties such as high stereo-, regio-, and chemo-specificity. These properties allow enzymes to greatly simplify complex synthetic processes, resulting in improved yields and reduced manufacturing costs compared to traditional chemical methods. However, the lack of experimental characterization of enzyme substrates, with only a few thousand out of tens of millions of known enzymes in Uniprot having annotated substrates, severely limits the ability of chemists to repurpose enzymes for industrial applications. Previous machine learning models aimed at predicting enzyme substrates have been hampered by poor generalization to new substrates. Here, we introduce VIPER (Virtual Interaction Predictor for Enzyme Reactivity), a model that achieves an average 30% improvement over the previous state-of-the-art model (ProSmith) in reaction prediction for unseen substrates. Furthermore, we reveal flaws in previous enzyme-substrate reaction datasets, and introduce a novel high-quality enzyme-substrate reaction dataset to alleviate these issues.
Phylogenetically-Preserved Multiscale Neuronal Activity: Iterative Coarse-Graining Reconciles Scale-Dependent Theories of Brain Function
Authors: Munn Brandon R. , Müller Eli , Favre-Bulle Itia , Scott Ethan , Breakspear Michael , Shine James M.
Published: June 2024

Brain recordings collected at different resolutions support statistically distinct signatures of information processing, leading to scale-dependent theories of brain function. Here, we demonstrate that these disparate neural-coding signatures emerge from the same multiscale functional organisation of neuronal activity across calcium-imaging recordings collected from the whole brains of zebrafish and nematode, as well as sensory regions of the fly, mouse, and macaque brain. Network simulations show that hierarchical-modular structural connectivity facilitates multiscale functional coordination, enhancing information processing benefits such as a maximal dynamic range. Finally, we demonstrate that this cross-scale organisation supports distinct behavioural states across species by reconfiguring functional affiliation and temporal dynamics at the mesoscale. Our findings suggest that self-similar scaling of neuronal activity is a universal principle that reconciles scale-dependent theories of brain function, facilitating both efficiency and resiliency while enabling significant reconfiguration of mesoscale cellular ensembles to accommodate behavioural demands.
Covid-19 vaccination decisions and impacts of vaccine mandates: A cross sectional survey of healthcare workers in Ontario, Canada
Authors: Chaufan Claudia , Hemsing Natalie , Moncrieffe Rachael
Published: June 2024

Background

Since vaccination policies were introduced in the healthcare sector in the province of Ontario, Canada, most establishments implemented vaccination or termination requirements, with most enforcing them to this day. Researchers have shown a strong interest in the perceived problem of vaccine hesitancy among healthcare workers, yet not in their lived experience of the policy or in their views on the policy’s impact on the quality of patient care in the province.

Goal

To document the experience and views on mandated vaccination of healthcare workers in the province of Ontario, Canada.

Methods

Between February and March 2024, we conducted a cross-sectional survey of Ontario healthcare workers, recruited through professional contacts, social media, and word-of-mouth.

Findings

Most respondents, most with 16 or more years of professional experience, were unvaccinated, and most had been terminated due to non-compliance with mandates. As well, and regardless of vaccination status, most respondents reported safety concerns with vaccination, yet did not request an exemption due to their experience of high rejection rates by employers. Nevertheless, most unvaccinated workers reported satisfaction with their vaccination choices, although they also reported significant, negative impacts of the policy on their finances, their mental health, their social and personal relationships, and to a lesser degree, their physical health. In contrast, most respondents within the minority of vaccinated respondents reported being dissatisfied with their vaccination decisions, as well as having experienced mild to serious post vaccine adverse events, with about one-quarter within this group reporting having been coerced into taking further doses, under threat of termination, despite these events. Further, a large minority of respondents reported having witnessed underreporting or dismissal by hospital management of adverse events post vaccination among patients, worse treatment of unvaccinated patients, and concerning changes in practice protocols. Close to half also reported their intention to leave the healthcare industry.

Discussion

Our findings indicate that in Ontario, Canada, mandated vaccination in the health sector had an overall negative impact on the well-being of the healthcare labour force, on patient care, on the sustainability of the health system, and on ethical medical practice. Our study should be reproduced in other provinces, as well as in other countries that adopted comparable policies. Findings from this and similar studies should be seriously considered when planning for future health emergencies, to protect health systems in crisis due to severe labour shortages, as well as the right to informed consent of healthcare workers and members of the public.
Binary Brains: How Excitable Dynamics Simplify Neural Connectomes
Authors: Messé Arnaud , Hütt Marc-Thorsten , Hilgetag Claus C.
Published: June 2024

Fiber networks connecting different brain regions are the structural foundation of brain dynamics and function. Recent studies have provided detailed characterizations of neural connectomes with weighted connections. However, the topological analysis of weighted networks still has conceptual and practical challenges. Consequently, many investigations of neural networks are performed on binarized networks, and the functional impact of unweighted versus weighted networks is unclear. Here we show, for the widespread case of excitable dynamics, that the excitation patterns observed in weighted and unweighted networks are nearly identical, if an appropriate network threshold is selected. We generalize this observation to different excitable models, and formally predict the network threshold from the intrinsic model features. The network-binarizing capacity of excitable dynamics suggests that neural activity patterns may primarily depend on the strongest structural connections. Our findings have practical advantages in terms of the computational cost of representing and analyzing complex networks. There are also fundamental implications for the computational simulation of connectivity-based brain dynamics and the computational function of diverse other systems governed by excitable dynamics such as artificial neural networks.
Effects of Centrally Acting Analgesics on Resting-State Electroencephalography Biomarker Candidates of Chronic Pain
Authors: Zebhauser Paul Theo , Bott Felix , Gil Avila Cristina , Heitmann Henrik , May Elisabeth S. , Tiemann Laura , Baki Enayatullah , Toelle Thomas R. , Ploner Markus
Published: June 2024

Resting-state electroencephalography (rsEEG) holds promise as a biomarker of chronic pain. However, the impact of centrally acting analgesics like opioids, antiepileptics, and antidepressants on rsEEG remains unclear. This confounds and limits the interpretability of previous studies and questions the validity of rsEEG biomarker candidates of chronic pain. We, therefore, aimed to elucidate the effects of opioids, antiepileptics, and antidepressants on common rsEEG biomarker candidates of chronic pain. To this end, we analyzed two large, independent rsEEG datasets, including 220 people with chronic pain. We performed preregistered multivariate Bayesian analyses and controlled for the potential confounds of age, pain intensity, and depression. The results predominantly provided evidence against effects of centrally acting analgesics on peak alpha frequency, oscillatory power in different frequency bands, and connectivity-based network measures. Although these findings do not rule out any effects of analgesics on rsEEG, they argue against medium to large effects of centrally acting analgesics on rsEEG. Thus, the findings strengthen the validity of rsEEG biomarker candidates of chronic pain and might thereby help to develop clinically valuable biomarkers of chronic pain.
Molecular underpinnings of hornwort carbon concentrating mechanisms: subcellular localization of putative key molecular components in the model hornwortAnthoceros agrestis
Authors: Ruaud Stephanie , Nötzold Svenja I , Waller Manuel , Galbier Florian , Mousavi Sabereh S. , Charran Mark , Zeeman Samuel , Bailly Aurélien , Baroux Celia , Hippler Michael , Wicke Susann , Szövényi Péter
Published: June 2024

Biophysical carbon concentrating mechanisms (CCMs) operating at the single-cell level have evolved independently in eukaryotic algae and a single land plant lineage, hornworts. An essential component for an efficient eukaryotic CCM is a pyrenoid whose biology is well-characterized in the unicellular green alga,Chlamydomonas reinhardtii. By contrast, pyrenoids and CCM are little understood in hornworts.

Here, we investigate the molecular underpinnings and dynamics of hornwort pyrenoids. We do so by studying the subcellular localization of candidate proteins homologous to essential CCM genes inC. reinhardtiiand assessing their mobility kinetics in the hornwort modelAnthoceros agrestis.

We provide evidence that an EPYC1 analog and the RuBisCO co-localize in the pyrenoid but pyrenoids seem less dynamic inA. agrestisthan inC. reinhardtii. We further found that a carbon anhydrase homolog (CAH3) localizes to the pyrenoid, while an LCIB-like homolog is less intimately linked to the pyrenoid than inC. reinhardtii.

Our results imply that the pyrenoid-based CCM of hornworts is characterized by a mixture ofChlamydomonas-like as well as hornwort-specific features which is in line with its independent evolutionary origin. Using these observations, we provide a first mechanistic model of hornwort CCM.
A highly contiguous reference genome for the Alpine ibex (Capra ibex)
Authors: Çilingir F. Gözde , Landuzzi Fabio , Brambilla Alice , Charrance Debora , Furia Federica , Trova Sara , Peracino Alberto , Camenisch Glauco , Waldvogel Dominique , Howard-McCombe Jo , Castillo De Spelorzi Yeraldin Chiquinquira , Henzen Edoardo , Bernagozzi Andrea , Coppe Alessandro , Christille Jean Marc , Vecchi Manuela , Vozzi Diego , Cavalli Andrea , Bassano Bruno , Gustincich Stefano , Croll Daniel , Pandolfini Luca , Grossen Christine
Published: June 2024

Anthropogenic hybridization, the unintentional hybridization with a non-native or domestic species in human-dominated environments, is a major concern for species conservation and a challenge for conservation management decisions. Genetically depleted species are expected to be particularly vulnerable to hybridization and introgression since hybridization can restore or introduce new adaptive genetic variation and alleviate the effects of inbreeding through hybrid vigour. However, defining the precise sets of deleterious or beneficial mutations resulting from anthropogenic hybridization is complex and limited by the quality of genomic resources. The Alpine ibex (Capra ibex), a species native to the Alps, faced near-extinction two centuries ago, but conservation programs have successfully restored its populations. Alpine ibex are known to hybridize with the domestic goat (Capra hircus) occasionally leading to hybrid swarm formation. Past introgression has been observed at immune-related genes and was suggested to have had an adaptive effect. Alpine ibex also carry deleterious mutation load from the reintroduction bottlenecks, which could be alleviated through admixture. Here, we produced a chromosome-level reference genome for Alpine ibex based on Oxford Nanopore sequencing coupled with high-throughput chromosome conformation capture. The highly contiguous assembly of 2.66 Gbp reveals 30 chromosomes and is augmented by a 98.8% complete RNAseq-assisted gene model prediction. The Alpine ibex genome presents overall a high degree of synteny compared to the domestic goat, with a number of structural variants spanning 38 Mb of insertion and deletions, as well as 49 Mb of inversions. We also identified structural variants near but not within the major histocompatibility complex (MHC), an immune-relevant gene complex, where previous studies found signals of introgression. The high degree of synteny between the Alpine ibex and domestic goat chromosomes likely facilitates recombination between haplotypes of the two species and is, therefore, in accordance with the observation of hybrid swarms. To determine the precise impact of recent admixture, we resequenced eight hybrid individuals sampled from two hybrid swarms in Northern Italy. Swarm individuals carried between 18-80% goat genome representing up to 3rd generation hybrids, including one F1 hybrid. The reference genome will facilitate quantifying maladaptive variation introduced from domestic goats and guide management efforts.
Evolving a High-Performance Terminal Deoxynucleotidyl Transferase for Enzymatic DNA Synthesis
Authors: Forget Stephanie , Krawczyk Mikayla , Knight Anders , Ching Charlene , Copeland Rachelle , Mahmoodi Niusha , Mayo Melissa , Nguyen James , Tan Amanda , Miller Matt , Vroom Jonathan , Lutz Stefan
Published: June 2024

Enzymatic DNA synthesis, using stepwise nucleotide addition catalyzed by template-independent polymerases, promises higher efficiency, quality, and sustainability than today’s industry standard phosphoramidite-based processes. We report on the directed evolution of a terminal deoxynucleotidyl transferase that uses 3’-phosphate blocked dNTPs to control the polymerization reaction and demonstrates high activity for these modified substrates and improved template promiscuity and thermostability.
Genomic evolution reshapes cell type diversification in the amniote brain
Authors: Chen Duoyuan , Zhuang Zhenkun , Huang Maolin , Huang Yunqi , Yan Yuting , Zhang Yanru , Lin Youning , Jin Xiaoying , Wang Yuanmei , Huang Jinfeng , Xu Wenbo , Pan Jingfang , Wang Hong , Huang Fubaoqian , Liao Kuo , Cheng Mengnan , Zhu Zhiyong , Bai Yinqi , Niu Zhiwei , Zhang Ze , Xiang Ya , Wei Xiaofeng , Yang Tao , Zeng Tao , Dong Yuliang , Lei Ying , Sun Yangang , Wang Jian , Yang Huanming , Sun Yidi , Cao Gang , Poo Muming , Liu Longqi , Naumann Robert K. , Xu Chun , Wang Zhenlong , Xu Xun , Liu Shiping
Published: June 2024

Over 320 million years of evolution, amniotes have developed complex brains and cognition through largely unexplored genetic and gene expression mechanisms. We created a comprehensive single-cell atlas of over 1.3 million cells from the telencephalon and cerebellum of turtles, zebra finches, pigeons, mice, and macaques, employing single-cell resolution spatial transcriptomics to validate gene expression patterns across species. Our study revealed significant species-specific variations in cell types, highlighting their conservation and diversification in evolution. We found pronounced differences in telencephalon excitatory neurons (EX) and cerebellar cell types between birds and mammals. Birds predominantly expressSLC17A6in EX, whereas mammals expressedSLC17A7in neocortex andSLC17A6elsewhere, possibly due to loss ofSLC17A7function loss in birds. Additionally, we identified a novel bird-specific Purkinje cell subtype (SVIL+), implicating the LSD11/KDM1A pathway in learning and circadian rhythms, and related numerous positively selected genes in birds, suggesting an evolutionary optimization of cerebellar functions for ecological and behavioral adaptation. Our findings elucidate the complex interplay between genetic evolution and environmental adaptation, underscoring the role of genetic diversification in the development of specialized cell types across amniotes.
GelMA as scaffold material for epithelial cells to emulate the small intestinal microenvironment
Authors: Roegiers Inez , Gheysens Tom , Vanbeversluys Kim , Rać Nikoletta , Stroka Grzegorz , de Croock Jana , Van de Wiele Tom , Dubruel Peter , Arroyo Marta Calatayud
Published: June 2024

Host-microbe interactions in the intestine play a significant role in health and disease. Novel scaffolds for host cells, capable of potentially supporting ese intricate interactions, are necessary to improve our current systems for mimicking host-microbiota interplayin vitro/ex vivo. In this research paper, we study the application of gelatin methacrylamide (GelMA) as scaffold material for intestinal epithelial cells in terms of permeability, mechanical strength, and biocompatibility. We investigated whether the degree of substitution (DS) of GelMA influences the permeability and found that both high and low DS GelMA show sufficient permeability of biorelevant transport markers. Additionally, we researched epithelial cell adherence and viability, as well as mechanical characteristics of different concentrations of GelMA. All concentrations of hydrogel show long-term biocompatibility for the mono- and co-cultures, despite the goblet-like cells (LS174T) showing lower performance than enterocyte-like cells (Caco-2). The mechanical strength of all hydrogel concentrations was in a physiologically relevant range to be used as scaffold material for intestinal cells. Based on these results, we conclude that GelMA is a suitable material as a scaffold for intestinal cell types in terms of permeability, mechanical strength and biocompatibility. These findings contribute to the growing field ofin vitromodeling of the gut and moves the field further to ensuring more translatable research on host-microbe interactions.
Distinct pathway for evolution of enhanced receptor binding and cell entry in SARS-like bat coronaviruses
Authors: Tse Alexandra L. , Acreman Cory M. , Ricardo-Lax Inna , Berrigan Jacob , Lasso Gorka , Balogun Toheeb , Kearns Fiona L. , Casalino Lorenzo , McClain Georgia L. , Chandran Amartya Mudry , Lemeunier Charlotte , Amaro Rommie E. , Rice Charles M. , Jangra Rohit K. , McLellan Jason S. , Chandran Kartik , Miller Emily Happy
Published: June 2024

Understanding the zoonotic risks posed by bat coronaviruses (CoVs) is critical for pandemic preparedness. Herein, we generated recombinant vesicular stomatitis viruses (rVSVs) bearing spikes from divergent bat CoVs to investigate their cell entry mechanisms. Unexpectedly, the successful recovery of rVSVs bearing the spike from SHC014, a SARS-like bat CoV, was associated with the acquisition of a novel substitution in the S2 fusion peptide-proximal region (FPPR). This substitution enhanced viral entry in both VSV and coronavirus contexts by increasing the availability of the spike receptor-binding domain to recognize its cellular receptor, ACE2. A second substitution in the spike N–terminal domain, uncovered through forward-genetic selection, interacted epistatically with the FPPR substitution to synergistically enhance spike:ACE2 interaction and viral entry. Our findings identify genetic pathways for adaptation by bat CoVs during spillover and host-to-host transmission, fitness trade-offs inherent to these pathways, and potential Achilles’ heels that could be targeted with countermeasures.
A Zero-Inflated Hierarchical Generalized Transformation Model to Address Non-Normality in Spatially-Informed Cell-Type Deconvolution
Authors: Melton Hunter J. , Bradley Jonathan R. , Wu Chong
Published: June 2024

Oral squamous cell carcinomas (OSCC), the predominant head and neck cancer, pose significant challenges due to late-stage diagnoses and low five-year survival rates. Spatial transcriptomics offers a promising avenue to decipher the genetic intricacies of OSCC tumor microenvironments. In spatial transcriptomics, Cell-type deconvolution is a crucial inferential goal; however, current methods fail to consider the high zero-inflation present in OSCC data. To address this, we develop a novel zero-inflated version of the hierarchical generalized transformation model (ZI-HGT) and apply it to the Conditional AutoRegressive Deconvolution (CARD) for cell-type deconvolution. The ZI-HGT serves as an auxiliary Bayesian technique for CARD, reconciling the highly zero-inflated OSCC spatial transcriptomics data with CARD’s normality assumption. The combined ZI-HGT + CARD framework achieves enhanced cell-type deconvolution accuracy and quantifies uncertainty in the estimated cell-type proportions. We demonstrate the superior performance through simulations and analysis of the OSCC data. Furthermore, our approach enables the determination of the locations of the diverse fibroblast population in the tumor microenvironment, critical for understanding tumor growth and immunosuppression in OSCC.
Semi-Automatic Detection of Errors in Genome-Scale Metabolic Models
Authors: Moyer Devlin C. , Reimertz Justin , Segrè Daniel , Fuxman Bass Juan I.
Published: June 2024

Background

Genome-Scale Metabolic Models (GSMMs) are used for numerous tasks requiring computational estimates of metabolic fluxes, from predicting novel drug targets to engineering microbes to produce valuable compounds. A key limiting step in most applications of GSMMs is ensuring their representation of the target organism’s metabolism is complete and accurate. Identifying and visualizing errors in GSMMs is complicated by the fact that they contain thousands of densely interconnected reactions. Furthermore, many errors in GSMMs only become apparent when considering pathways of connected reactions collectively, as opposed to examining reactions individually.

Results

We present Metabolic Accuracy Check and Analysis Workflow (MACAW), a collection of algorithms for detecting errors in GSMMs. The relative frequencies of errors we detect in manually curated GSMMs appear to reflect the different approaches used to curate them. Changing the method used to automatically create a GSMM from a particular organism’s genome can have a larger impact on the kinds of errors in the resulting GSMM than using the same method with a different organism’s genome. Our algorithms are particularly capable of identifying errors that are only apparent at the pathway level, including loops, and nontrivial cases of dead ends.

Conclusions

MACAW is capable of identifying inaccuracies of varying severity in a wide range of GSMMs. Correcting these errors can measurably improve the predictive capacity of a GSMM. The relative prevalence of each type of error we identify in a large collection of GSMMs could help shape future efforts for further automation of error correction and GSMM creation.
Surveillance and molecular characterization of banana viruses and their association with Musa germplasm in Malawi.
Authors: Masangwa Johnny Isaac Gregorio , Pareta Nuria Fontdevila , Moses Philemon , Hřibová Eva , Doležel Jaroslav , Fandika Isaac , Massart Sebastien
Published: June 2024

Malawi has local banana germplasm preferred by its population. However, the epidemics of banana bunchy top disease, caused by the banana bunchy top virus (BBTV), is wiping out the most preferred germplasm and limiting its plantation. On the other hand, there needs to be more knowledge on viruses present in Malawi on banana crops. Therefore, a survey was conducted country-wide to characterize banana germplasm and evaluate the presence, incidence and prevalence of banana viruses. The survey covered four country zones, combined farmer's structured questionnaire and plant sampling. PCR products from infected germplasm were sequenced and aligned for each detected virus to build a phylogenetic tree. BBTV, BanMMV and BSV species were detected in Malawi. Malawi's BBTV isolates belonged to the Pacific Indian Ocean group only and BanMMV isolates clustered to three sub-branches. All the BSV species present in Malawi belonged to clade 1. Among the genetic groups of Musa, the identified banana germplasm belonged to AA, AAA, AB, AAB, and ABB groups with some germplasms unique compared to already genotyped germplasms. The ABB group was dominant in Malawi and was often infected by BSV species (probably originating from endogenous viral sequences), while BBTV more often infected the AAA group. Banana propagule sharing was the primary source of banana planting materials with a higher risk of spreading virus diseases. The survey underlined the need to set up a banana seed industry and policies that promote farmers' access to virus-tested planting materials, which will consequently prevent future virus epidemics.
HyDRA: a pipeline for integrating long- and short-read RNAseq data for custom transcriptome assembly
Authors: Almeida Isabela , Lu Xue , Edwards Stacey L. , French Juliet D. , Bitar Mainá
Published: June 2024

Background

Short-read RNA sequencing (RNAseq) has widely been used to sequence RNA from a wide range of different tissues, developmental stages and species. However, the technology is limited by inherent biases and its inability to capture full-length transcripts. Long-read RNAseq overcomes these issues by providing reads that can span multiple exons, resolve complex repetitive regions and the capability to cover entire transcripts. Unfortunately, this technology is still prone to higher error rates. Noncoding RNA transcripts are highly specific to different cell types and tissues and remain underrepresented in current reference annotations. This problem is exacerbated by the dismissal of sequenced reads that align to genomic regions that do not contain annotated transcripts, resulting in approximately half of the expressed transcripts being overlooked in transcriptional studies.

Results

We have developed a pipeline, named HyDRA (Hybridde novoRNAassembly), which combines the precision of short reads with the structural resolution of long reads, enhancing the accuracy and reliability of custom transcriptome assemblies. Deep, short- and long-read RNAseq data derived from ovarian and fallopian tube samples were used to develop, validate and assess the efficacy of HyDRA. We identified more than 50,000 high-confidence long noncoding RNAs, most of which have not been previously detected using traditional methods.

Conclusions

HyDRA’s assembly performed more than 40% better than a similar assembly obtained with the top-ranked stand-alonede novotranscriptome short-read-only assembly tool and over 30% better than one obtained with the best-in-class multistep short-read-only approach. Although long-read sequencing is rapidly advancing, the vast availability of short-read RNAseq data will ensure that hybrid approaches like the one implemented in HyDRA continue to be relevant, allowing the discovery of high-confidence transcripts within specific cell types and tissues. As the practice of performing hybridde novotranscriptome assemblies becomes commonplace, HyDRA will advance the annotation of coding and noncoding transcripts and expand our knowledge of the noncoding genome.
Detecting Data Embedding Spatial Patterns and Identifying Biomarkers with BioRSP
Authors: Yao Zeyu , Chen Jake Y.
Published: June 2024

Motivation

High-dimensional data embedding has become an essential tool in bioinformatics, particularly for single-cell data analysis, as it aids in characterizing cells with complex gene expression patterns based on projected low-dimensional data point spatial distributions. However, traditional methods often fall short in distinguishing subtle changes within cell populations. To address this, we developed BioRSP (BiologicalRadarScanningPlots), an innovative open-source software designed to enhance the characterization of single-cell gene expression patterns by simulating radar beam scanning across defined clusters from a fixed coordinate, referred to as the “vantage point.”

Results

BioRSP enables users to analyze the distribution of each gene within and across cell clusters using a quantitative measure known as the RSP plot. These plots categorize genes and spatial embedding patterns into four distinct groups based on combinations of gene coverage (high/low) and RSP values (high/low), reflecting spatial distribution regularities in the embedding space. This novel approach allows BioRSP to distinguish subtle differences between background cells and those expressing specific markers above a preset threshold, significantly improving upon traditional gene-to-gene correlation analyses. A case study utilizing a neonatal mouse heart tissue dataset from the Mouse Cell Atlas demonstrates BioRSP’s capability to identify spatially distinct and functionally significant gene expression patterns.

Availability

The Python package and its comprehensive documentation are publicly available athttps://github.com/cytronicoder/biorsp.

Contact

cytronicoder@gmail.com
Drivers of spatio-temporal variability in a marine foundation species
Authors: Giraldo-Ospina Anita , Bell Tom , Carr Mark H. , Caselle Jennifer E.
Published: June 2024

Marine foundation species are critical for the structure and functioning of ecosystems and constitute the pillar of trophic chains while also providing a variety of ecosystem services. In recent decades many foundation species have declined in abundance, sometimes threatening their current geographical distribution. Kelps (Laminariales) are the primary foundation species in temperate coastal systems worldwide. Kelp ecosystems are notoriously variable and identifying the key factors that control the dynamics of kelp abundance is key to predicting the fate of kelp ecosystems under climatic change and informing management and conservation decisions such as forest restoration. Here, we usedin situdata from long-term monitoring programs across 1,350 km of coast spanning multiple biogeographic regions in the state of California (USA) to identify the major regional drivers of density of two dominant canopy-forming kelp species and to elucidate the spatial and temporal scales over which they operate. We used generalized additive models to identify the key drivers of density of two dominant kelp species (Nereocystis luetkeanaandMacrocystis pyrifera) across four ecological regions of the state of California (north, central, south-west and south-east) and for the past two decades (2004-2021). Our study identified that the dominant drivers of kelp density varied between regions and species but always included some combination of nitrate availability, wave energy and exposure, density of purple sea urchins, and temperature as the most important predictors explaining 63% of the variability of bull kelp in the north and central regions, and 45% and 51.4% of the variability in giant kelp for the central/south-west and south-east regions, respectively. These large-scale analyses infer that a combination of lower nutrient availability, changes in wave energy and exposure, and increases in temperature and purple sea urchin counts have contributed to the decline of kelp observed in the last decade. Understanding the drivers of kelp dynamics can be used to identify regions and periods of significant change and historical stability, ultimately informing resource management and conservation decisions such as site selection for kelp protection and restoration.

Open research statement

Data (Giraldo-Ospina et al. 2023) are available in DataOne at doi:10.25494/P6/When_where_and_how_kelp_restoration_guidebook_2.
Guidelines for evaluating the success of large carnivore reintroductions
Authors: Briers-Louw Willem D. , Lindsey Peter , Gaylard Angela , Cristescu Bogdan , Verschueren Stijn , Plessis Cole du , Drouilly Marine , Bantlin Drew , Kendon Tamar A. , Evers Emma E.M. , Curry Caitlin J. , Almeida João , Gaynor David , Leslie Alison J. , Naude Vincent N.
Published: June 2024

Anthropogenic impacts have led to widespread species decline and extirpation, thereby compelling a global movement to protect and regenerate biodiversity through holistic ecosystem restoration including reintroductions. Yet, despite the increasing practice of conservation-driven reintroduction efforts over the past century, peer-reviewed literature and policy providing criteria with which to evaluate reintroduction stages and efficacy remain limited. Without these comprehensive and quantifiable metrics of relative success, such drastic conservation intervention strategies cannot be objectively evaluated nor compared, hindering the advancement of restoration as a discipline. Herein, we systematically reviewed 227 large carnivore reintroductions of 14 terrestrial mammal species across 23 countries since 1930 to contextualize global efforts to date, and from these, have developed a standardized framework to evaluate reintroduction success. We further retrospectively determined the extent to which existing studies met these criteria towards identifying current knowledge gaps and guide future reintroduction efforts. Most large carnivore records were of Felidae (70%) reintroduced into ‘closed’ systems (69%) across southern Africa (70%). Our proposed framework provides a full suite of stages, indicators, and targets for reintroduction evaluation, which, when retrospectively applied to reviewed studies, indicated that at least one-third lacked sufficient information to effectively evaluate and compare reintroduction outcomes. This comprehensive and prioritized framework provides novel transparency and scalability to large carnivore reintroduction programs, which is increasingly required to secure the sustained support of impacted communities and stakeholder networks. Moreover, the incorporation of this framework into future practice and policy as an applied tool may directly benefit the recovery of at least 30 large carnivore species, while its principles may be applied more broadly across taxonomic groups for faunal rewilding and global ecosystem restoration.
Creating a genetic toolbox for the carbon-fixing, nitrogen-fixing and dehalogenating bacteriumXanthobacter autotrophicus
Authors: Van Voorhis Alexa F. , Sherbo Rebecca S.
Published: June 2024

X. autotrophicusis a metabolically flexible microorganism with two key features: 1) The organism has adapted to grow on a wide variety of carbon sources including CO2, methanol, formate, propylene, haloalkanes and haloacids; and 2)X. autotrophicuswas the first chemoautotroph identified that could also simultaneously fix N2, meaning the organism can utilize CO2, N2, and H2for growth. This metabolic flexibility has enabled use ofX. autotrophicusfor gas fixation, the creation of fertilizers and foods from gases, and the dehalogenation of environmental contaminants. Despite the wide variety of applications that have already been demonstrated for this organism, there are few genetic tools available to explore and exploit its metabolism. Here, we report a genetic toolbox for use inX. autotrophicus. We first identified suitable origins of replication and quantified their copy number, and identified antibiotic resistance cassettes that could be used as selectable markers. We then tested several constitutive and inducible promoters and terminators and quantified their promoter strengths and termination efficiencies. Finally, we demonstrated that gene expression tools remain effective under both autotrophic and dehalogenative metabolic conditions to show that these tools can be used in the environments that makeX. autotrophicusunique. Our extensive characterization of these tools inX. autotrophicuswill enable genetic and metabolic engineering to optimize production of fertilizers and foods from gases, and enable bioremediation of halogenated environmental contaminants.
Genomic Convergence in Hibernating Mammals Elucidates the Genetics of Metabolic Regulation in the Hypothalamus
Authors: Ferris Elliott , Murcia Josue D. Gonzalez , Rodriguez Adriana Cristina , Steinwand Susan , Hörndli Cornelia Stacher , Traenkner Dimitri , Maldonado-Catala Pablo J , Gregg Christopher
Published: June 2024

Elucidating the genetic basis of mammalian metabolism could help define mechanisms central to health and disease. Here, we define conservedcis-regulatory elements (CREs) and programs for mammalian metabolic control. We delineate gene expression and chromatin responses in the mouse hypothalamus for 7 steps of the Fed-to-Fasted-to-Refed (FFR) response process. Comparative genomics of hibernating versus non-hibernating lineages then illuminatescis-elements showing convergent changes in hibernators. Hibernators accumulated loss-of-function effects for specific CREs regulating hypothalamic FFR responses. Multi-omics approaches pinpoint key CREs, genes, regulatory programs, and cell types in the divergence of hibernating and homeothermic lineages. The refeeding period after extended fasting is revealed as one critical period of chromatin remodeling with convergent genomic changes. This genetic framework is a step toward harnessing hibernator adaptations in medicine.

One sentence summary

Convergent signals definecis-regulatory mechanisms behind food scarcity responses and hibernator-homeotherm divergence.
Computational Mechanisms Underlying Multi-Step Planning Deficits in Methamphetamine Use Disorder
Authors: Lavalley Claire A. , Mehta Marishka M. , Taylor Samuel , Chuning Anne E. , Stewart Jennifer L. , Huys Quentin J. M. , Khalsa Sahib S. , Paulus Martin P. , Smith Ryan
Published: June 2024

Current theories suggest individuals with methamphetamine use disorder (iMUDs) have difficulty considering long-term outcomes in decision-making, which could contribute to risk of relapse. Aversive interoceptive states (e.g., stress, withdrawal) are also known to increase this risk. The present study analyzed computational mechanisms of planning in iMUDs, and examined the potential impact of an aversive interoceptive state induction. A group of 40 iMUDs and 49 healthy participants completed two runs of a multi-step planning task, with and without an anxiogenic breathing resistance manipulation. Computational modeling revealed that iMUDs had selective difficulty identifying the best overall plan when this required enduring negative short-term outcomes – a mechanism referred to as aversive pruning. Increases in reported craving before and after the induction also predicted greater aversive pruning in iMUDs. These results highlight a novel mechanism that could promote poor choice in recovering iMUDs and create vulnerability to relapse.
Dosimetry of [64Cu]FBP8: a fibrin-binding PET probe
Authors: Izquierdo-Garcia David , Désogère Pauline , Philip Anne L. , Sosnovik David E. , Catana Ciprian , Caravan Peter
Published: June 2024

Purpose

This study presents the biodistribution, clearance and dosimetry estimates of [64Cu]Fibrin Binding Probe #8 ([64Cu]FBP8) in healthy subjects.

Procedures

This prospective study included 8 healthy subjects to evaluate biodistribution, safety and dosimetry estimates of [64Cu]FBP8, a fibrin-binding positron emission tomography (PET) probe. All subjects underwent up to 3 sessions of PET/Magnetic Resonance Imaging (PET/MRI) 0-2 hours, 4h and 24h post injection. Dosimetry estimates were obtained using OLINDA 2.2 software.

Results

Subjects were injected with ∼400 MBq of [64Cu]FBP8. Subjects did not experience adverse effects due to the injection of the probe. [64Cu]FBP8 PET images demonstrated fast blood clearance (half-life = 67 min) and renal excretion of the probe, showing low background signal across the body. The organs with the higher doses were: the urinary bladder (0.075 vs. 0.091 mGy/MBq for males and females, respectively); the kidneys (0.050 vs. 0.056 mGy/MBq respectively); and the liver (0.027 vs. 0.035 mGy/MBq respectively). The combined mean effective dose for males and females was 0.016 ± 0.0029 mSv/MBq, lower than the widely used [18F]fluorodeoxyglucose ([18F]FDG, 0.020mSv/MBq).

Conclusions

This study demonstrates the following properties of the [64Cu]FBP8 probe: low dosimetry estimates; fast blood clearance and renal excretion; low background signal; and whole-body acquisition within 20 minutes in a single session. These properties provide the basis for [64Cu]FBP8 to be an excellent candidate for whole-body non-invasive imaging of fibrin, an important driver/feature in many cardiovascular, oncological and neurological conditions
Quantitative detection of plant signaling peptides utilizing ELISA
Authors: König Maurice , Sorger Zarah , Doehlemann Gunther , Misas Villamil Johana C.
Published: June 2024

Plant signaling peptides, also known as phytocytokines, are involved in a number of signaling mechanisms, including cell-to-cell communication during plant development and immunity. The detection of small peptides in plant tissues is challenging and often relies on time-consuming and cost-intensive approaches. Here, we present an ELISA-based assay as a rapid and cost-effective method for the detection of naturally released peptides in plant tissues. Our ELISA-based method was developed to detect Zip1, a 17-amino-acid phytocytokine derived fromZea maysthat elicits salicylic acid signaling in maize leaves. Using a custom peptide-antibody, we designed an experimental pipeline to achieve peptide specificity, selectivity and sensitivity allowing the detection of the Zip1 peptide in complex biological samples. As a proof of concept, we transfected maize protoplasts to overexpress the precursor molecule PROZIP1 and treated maize leaves with salicylic acid to induce native PROZIP1 expression and Zip1 release. Using ELISA, we were able to quantify native Zip1 signals with a detection limit in the nanogram range, which allowed us to detect different Zip1-containing peptides in plant material. This method can be adapted for the detection and quantification of a variety of plant signaling peptides.
Convergent evolution of sex chromosomes in palms
Authors: Tessarotto H. , Beulé T. , Cherif E. , Orjuela J. , Lindstrom A. , Lemansour A. , Dahme M. , Santoni S. , Käfer J. , Aberlenc F.
Published: June 2024

While sex chromosomes often evolve in species with separate sexes through similar processes, there are also many differences in their evolutionary dynamics. In palms, a clade with 8-10 independent evolutionary origins of dioecy, sex chromosomes have hitherto been well characterized only in the date palm genusPhoenix. Using genome-wide target capture sequencing, we found that the same region independently became sex-linked both inPhoenixand in the rather distantly related speciesKerriodoxa elegans. Investigating the gene content of this region revealed it contains many genes involved in flower sex differentiation which might be the reason for this case of convergent evolution. This region, which could function as a “genetic toolbox” for the production of unisexual flowers or individuals, may have an ancestral functional importance in palm genomes.
Cryo-electron tomography pipeline for plasma membranes
Authors: Sun Willy W. , Michalak Dennis J. , Sochacki Kem A. , Kunamaneni Prasanthi , Alfonzo-Méndez Marco A. , Arnold Andreas M. , Strub Marie-Paule , Hinshaw Jenny E. , Taraska Justin W.
Published: June 2024

Cryo-electron tomography (cryoET) provides sub-nanometer protein structure within the dense cellular environment. Existing sample preparation methods are insufficient at accessing the plasma membrane and its associated proteins. Here, we present a correlative cryo-electron tomography pipeline optimally suited to image large ultra-thin areas of isolated basal and apical plasma membranes. The pipeline allows for angstrom-scale structure determination with sub-tomogram averaging and employs a genetically-encodable rapid chemically-induced electron microscopy visible tag for marking specific proteins within the complex cell environment. The pipeline provides fast, efficient, distributable, low-cost sample preparation and enables targeted structural studies of identified proteins at the plasma membrane of cells.