bluuebunny/crossref_metadata_2025 huggingface dataset:
An evaluation of the i-gel Plus supraglottic airway device in elective patients: the interim results from a prospective international multicentre study
Authors: Werner Jakub , Klementova Olga , Bruthans Jan , Macoun Jaromir , Gaszynski Tomasz , Henlin Tomas , Donaldson Will , Lichnovsky Erik , Arava Shiva , Lopez Ana M , Berge Raquel , Michalek Pavel
Published: February 2024

The i-gel Plus supraglottic airway represents the next generation of the i-gel device. The aim of this international multicentre prospective cohort study was to evaluate its performance in adult patients during elective procedures in various surgical disciplines under general anaesthesia. The primary outcome of the study was the overall success rate of insertion allowing effective airway management, ventilation, and oxygenation. The secondary outcomes included perioperative performance of the device and the incidence of postoperative adverse events. The data of the first 1000 patients from our study (455 males and 545 females) are presented. These patients were mostly operated on in the supine position (83.3%) with a minority of them being in the lateral or lithotomy positions. The overall success rate was 98.6%, with a first-attempt success rate of insertion of 88.1%. A significant difference between males and females was seen for the overall success rate, 97.4% vs. 99.6% (p=0.002) but not for the successful insertion on the first attempt (p=0.97) The mean oropharyngeal seal pressure was 32 (7) cmH2O. The only independent factor increasing the risk of first-attempt failure was low experience of the operator (p<0.001). The insertion of the device was rated by 80.3% as being either very easy or easy. Fibreoptic assessment through the i-gel Plus showed a full view of the vocal cords in 67.8% of patients, a partial view in 21.9% and a downfolded epiglottis in 9.4% of patients. A gastric tube was inserted in 11.2% of patients with a 99.1% success rate. Perioperative complications included desaturation below 85% in 0.6%, traces of blood on the device in 7.4%, laryngospasm in 0.5% and gastric contents inside the cuff in 0.2% of patients. There were no clinical signs of aspiration and a 0.1% incidence of bronchospasm. Severe postoperative sore throat was recorded in 1.4%, and long-term hoarse voice in 0.2% of patients. All patients with moderate and serious postoperative complaints are being followed up by phone at 3 and 6 months. The i-gel Plus seems to be an effective supraglottic airway device providing a high success rate of insertion, sufficient oropharyngeal seal pressure, and a reasonably low incidence of complications.
Radiological signs supporting idiopathic intracranial hypertension in symptomatic patients with lumbar puncture opening pressure < 250 mm.
Authors: Horev Anat , Eliav Tal , Sherer Inbal , Biederko Ron , Ben-Arie Gal , Shelef Ilan , Zlotnik Yair , Regev Tamir , Tsumi Erez , Honig Asaf , Givaty Gili
Published: February 2024

Objective Lumbar puncture opening pressure (LPOP) exceeding 250mmH2O stands as a pivotal criterion in diagnosing idiopathic intracranial hypertension (IIH), according to the revised Friedman’s criteria. However, many studies discuss the variability of LPOP, while others highlight the accuracy of radiological findings as a credible diagnostic tool for IIH. We have encountered many symptomatic patients who did not meet the LPOP criteria (with or without papilledema), despite having IIH-related symptoms and neuroimaging findings. This study aimed to investigate the radiological findings and clinical symptoms in patients suspected of having IIH without meeting the LPOP criteria. Methods We retrospectively evaluated cerebral venous sinus stenosis using the conduit Farb score (CFS) as well as other radiological findings suggestive of IIH by computed tomography venography and magnetic resonance venography in female patients ≥18 years of age with chronic headaches and suspected IIH with an LPOP <250mm. Results Our cohort comprised eighty-eight women (56 with LPOP < 200 mm H2O and 32 with LPOP ranging between 200-250 mmH2O). Among patients with LPOP in the 200-250 mmH2O range, 40% (12 patients) exhibited three or more radiological findings supporting IIH, compared to 17% (8 patients) in the LPOP < 200 mmH2O group (p=0.048). Furthermore, cerebral venous stenosis, as measured by a Conduit Farb Score (CFS) of 5 or lower, was observed in 80% (24 patients) of the LPOP 200-250 mmH2O group, contrasting with 40% (19 patients) in the LPOP < 200 mmH2O group (p<0.001). Conclusion Cerebral venous stenosis, as well as other supportive radiological findings, were significantly more common in patients with LPOP 200-250 mmH2O than LPOP<200 mmH2O. These findings suggest that given supportive clinical and radiological evidence, patients with LPOP between 200-250 mmH2O, with or without papilledema, may benefit from treatment for IIH.
Development of a Marmoset Apparatus for Automated Pulling (MarmoAAP) to Study Cooperative Behaviors
Authors: Meisner Olivia C , Shi Weikang , Fagan Nicholas A , Greenwood Joel , Jadi Monika , Nandy Anirvan S. , Chang Steve W. C.
Published: February 2024

In recent years, the field of neuroscience has increasingly recognized the importance of studying animal behaviors in naturalistic environments to gain deeper insights into ethologically relevant behavioral processes and neural mechanisms. The common marmoset (Callithrix jacchus), due to its small size, prosocial nature, and genetic proximity to humans, has emerged as a pivotal model toward this effort. However, traditional research methodologies often fail to fully capture the nuances of marmoset social interactions and cooperative behaviors. To address this critical gap, we developed the Marmoset Apparatus for Automated Pulling (MarmoAAP), a novel behavioral apparatus designed for studying cooperative behaviors in common marmosets. MarmoAAP addresses the limitations of traditional behavioral research methods by enabling high-throughput, detailed behavior outputs that can be integrated with video and audio recordings, allowing for more nuanced and comprehensive analyses even in a naturalistic setting. We also highlight the flexibility of MarmoAAP in task parameter manipulation which accommodates a wide range of behaviors and individual animal capabilities. Furthermore, MarmoAAP provides a platform to perform investigations of neural activity underlying naturalistic social behaviors. MarmoAAP is a versatile and robust tool for advancing our understanding of primate behavior and related cognitive processes. This new apparatus bridges the gap between ethologically relevant animal behavior studies and neural investigations, paving the way for future research in cognitive and social neuroscience using marmosets as a model organism.
InSilicoSeq 2.0: Simulating realistic amplicon-based sequence reads
Authors: Lelieveld Stefan H. , Maas Thijs , Duk Tessa C. X. , Gourlé Hadrien , van den Ham Henk-Jan
Published: February 2024

Motivation

Simulating high-throughput sequencing reads that mimic empirical sequence data is of major importance for designing and validating sequencing experiments, as well as for benchmarking bioinformatic workflows and tools.

Results

Here, we present InSilicoSeq 2.0, a software package that can simulate realistic Illumina-like sequencing reads for a variety of sequencing machines and assay types. InSilicoSeq now supports amplicon-based sequencing and comes with premade error models of various quality levels for Illumina MiSeq, HiSeq, NovaSeq and NextSeq platforms. It provides the flexibility to generate custom error models for any short-read sequencing platform from a BAM-file. We demonstrated the novel amplicon sequencing algorithm by simulating Adaptive Immune Receptor Repertoire (AIRR) reads. Our benchmark revealed that the simulated reads by InSilicoSeq 2.0 closely resemble the Phred-scores of actual Illumina MiSeq, HiSeq, NovaSeq and NextSeq sequencing data. InSilicoSeq 2.0 generated 15 million amplicon based paired-end reads in under an hour at a total cost of €4.3e-05per million bases advocating for testing experimental designs through simulations prior to actual sequencing.

Availability and implementation

InSilicoSeq 2.0 is implemented in Python and is freely available under the MIT licence athttps://github.com/HadrienG/InSilicoSeq
Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
Authors: Chen Li-Ting , Jager Myrthe , Rebergen Dàmi , Brink Geertruid J. , van den Ende Tom , Vanderlinden Willem , Kolbeck Pauline , Pagès-Gallego Marc , van der Pol Ymke , Besselink Nicolle , Moldovan Norbert , Hami Nizar , Kloosterman Wigard , van Laarhoven Hanneke , Mouliere Florent , Zweemer Ronald , Lipfert Jan , Derks Sarah , Marcozzi Alessio , de Ridder Jeroen
Published: February 2024

Shallow genome-wide cell-free DNA (cfDNA) sequencing holds great promise for non-invasive cancer monitoring by providing reliable copy number alteration (CNA) and fragmentomic profiles. Single nucleotide variations (SNVs) are, however, much harder to identify with low sequencing depth due to sequencing errors. Here we present Nanopore Rolling Circle Amplification (RCA)-enhanced Consensus Sequencing (NanoRCS), which leverages RCA and consensus calling based on genome-wide long-read nanopore sequencing to enable simultaneous multimodal tumor fraction estimation through SNVs, CNAs, and fragmentomics. Efficacy of NanoRCS is tested on 18 cancer patient samples and 3 healthy controls, demonstrating its ability to reliably detect tumor fractions as low as 0.24%. In vitro experiments confirm that SNV measurements are essential for detecting tumor fractions below 2%. NanoRCS provides the opportunity for cost-effective and rapid processing, which aligns well with clinical needs, particularly in settings where quick and accurate cancer monitoring is essential for personalized treatment strategies.
The budding yeast Fkh1 Forkhead associated (FHA) domain promoted a G1-chromatin state and the activity of chromosomal DNA replication origins
Authors: Hoggard Timothy , Chacin Erika , Hollatz Allison J. , Kurat Christoph F. , Fox Catherine A.
Published: February 2024

InSaccharomyces cerevisiae, the forkhead (Fkh) transcription factor Fkh1 (forkhead homolog) enhances the activity of many DNA replication origins that act in early S-phase (early origins). Current models posit that Fkh1 acts directly to promote these origins’ activity by binding to origin-adjacent Fkh1 binding sites (FKH sites). However, the post-DNA binding functions that Fkh1 uses to promote early origin activity are poorly understood. Fkh1 contains a conserved FHA (forkhead associated) domain, a protein-binding module with specificity for phosphothreonine (pT)-containing partner proteins. At a small subset of yeast origins, the Fkh1-FHA domain enhances the ORC (origin recognition complex)-origin binding step, the G1-phase event that initiates the origin cycle. However, the importance of the Fkh1-FHA domain to either chromosomal replication or ORC-origin interactions at genome scale is unclear. Here, S-phase SortSeq experiments were used to compare genome replication in proliferatingFKH1andfkh1-R80Amutant cells. The Fkh1-FHA domain promoted the activity of 100 origins that act in early to mid-S-phase, including the majority of centromere-associated origins, while simultaneously inhibiting 100 late origins. Thus, in the absence of a functional Fkh1-FHA domain, the temporal landscape of the yeast genome was flattened. Origins are associated with a positioned nucleosome array that frames a nucleosome depleted region (NDR) over the origin, and ORC-origin binding is necessary but not sufficient for this chromatin organization. To ask whether the Fkh1-FHA domain had an impact on this chromatin architecture at origins, ORC ChIPSeq data generated from proliferating cells and MNaseSeq data generated from G1-arrested and proliferating cell populations were assessed. Origin groups that were differentially regulated by the Fkh1-FHA domain were characterized by distinct effects of this domain on ORC-origin binding and G1-phase chromatin. Thus, the Fkh1-FHA domain controlled the distinct chromatin architecture at early origins in G1-phase and regulated origin activity in S-phase.
A new chromosome-level genome assembly and annotation ofCryptosporidium meleagridis
Authors: Penumarthi Lasya R , de Paula Baptista Rodrigo C , Beaudry Megan S , Glenn Travis , Kissinger Jessica C
Published: February 2024

Cryptosporidiumspp. are medically and scientifically relevant protozoan parasites that cause severe diarrheal illness in infants and immunosuppressed populations as well as animals. Although most humanCryptosporidiuminfections are caused byC. parvumandC. hominis, there are several other human-infecting species includingC. meleagridis, which is commonly observed in developing countries. Here, we polished and annotated a long-read genome sequence assembly forC. meleagridisTU1867, a species which infects birds and humans. The genome sequence was generated using a combination of whole genome amplification (WGA) and long-read Oxford Nanopore Technologies sequencing. The assembly was then polished with Illumina data. The chromosome-level genome assembly is 9.2 Mbp with a contig N50 of 1.1 Mb. Annotation revealed 3,923 protein-coding genes. A BUSCO analysis indicates a completeness of 96.6% (n=446), including 430 (96.4%) single-copy and 1 (0.224%) duplicated apicomplexan conserved gene(s). The newC. meleagridisgenome assembly is nearly gap-free and provides a valuable new resource for theCryptosporidiumcommunity and future studies on evolution and host-specificity.
Sex-Specific Associations of the Plasma-Proteome with incident Coronary Artery Disease
Authors: Sier Vincent Q. , Willems van Dijk Ko , van Heemst Diana , Quax Paul H.A. , Jukema J. Wouter , Noordam Raymond , de Vries Margreet R.
Published: February 2024

Background and Aims The aetiology of coronary artery disease (CAD) is different for men and women, yet insights into underlying sex-specific biological and pathophysiological mechanisms are limited. We investigated the sex-specific associations of the plasma-proteome with incident CAD. Methods In 40,829 participants from UK Biobank free-of-CAD from baseline to 365 days thereafter (55% women, mean 56.9, standard deviation 8.1 years), we analysed associations between 2,922 plasma-proteins and CAD incidence. Baseline plasma samples (2006-2010), were analysed in relation to incident CAD over a median follow-up of 13.7 (IQR: 13.1,14.4) years. Combined and sex-specific analyses were performed using Cox-proportional hazard models, adjusting for considered confounders, and causal inference using Mendelian Randomisation (MR). Results Multivariable-adjusted Cox-proportional hazard models identified 1,138 proteins associated with incident CAD (false-discovery-rate-corrected p-value<0.05), of which 219 showed evidence for potential causality using MR. Overrepresentation analyses identified involvement of cytokine-cytokine receptor interactions (p<0.0001), matrix remodelling (p<0.0001), regulation of innate and adaptive immune cells (p<0.0001), and angiogenesis (p<0.0001) pathways associated with incident CAD. Sex-specific analyses revealed additional 412 female-exclusive and 37 male-exclusive proteins and distinct CAD-risk pathways were identified for women (e.g., innate immune response) and men (e.g., tube morphogenesis (angiogenesis)). Translation toward druggability on targets with causal evidence revealed sex-specific clinical drug candidates such as C1S (men) and FOXO1 (women). Conclusions Although the majority of proteins showed consistent associations with incident CAD in both sexes, multiple proteins and biological pathways were either more strongly associated with incident CAD in men or in women, potentially indicating sex-specific pathogenesis and opening new alleys for prevention and clinical strategies.
mgPGPT: Metagenomic analysis of plant growth-promoting traits
Authors: Patz Sascha , Rauh Mario , Gautam Anupam , Huson Daniel H.
Published: February 2024

In a recent publication, we introduce the PGPT ontology and PGPT-db of bacterial plant growth-promotion traits and associated database of protein sequences, and provide several tools for bacterial genome analysis on the PLaBAse server. Here, we extend the scope of the PGPT ontology to perform PGPT analysis of metagenomic datasets. First, we introduce mgPGPT-db, an extended database of 39, 582, 183 protein sequences obtained computationally by including proteins from AnnoTree. With this, we have integrated the PGPT ontology into our metagenome analysis tool MEGAN and provide mapping files to identify PGPT-related genes using the results of a DIAMOND alignment of reads against either the new mgPGPT-db database, the NCBI-nr protein database, or the AnnoTree protein database. We demonstrate and compare these different approaches in detail on an example data set and evince the improvement compared to the PGPT-db. We also compare the inferred PGPT content of several samples taken from different environments and reveal plant specific PGPT clustering. IMPORTANCE: A deeper understanding of plant growth-promoting traits of bacteria is important to enlight and enhance the native plant-beneficial bacterial functional diversity regarding the environmental stress adaption or the ability to suppress even food-borne pathogens by strain inoculation dedicated to agriculture and other plant production systems. The work presented here extends recent work beyond the analysis of individual to allow the assessment of the PGPT potential of metagenomes obtained from environmental samples.
Microscopic Origin of the Entropy of Black Holes in General Relativity
Authors: Balasubramanian Vijay , Lawrence Albion , Magán Javier M. , Sasieta Martin
Published: February 2024

We construct an infinite family of microstates with geometric interiors for eternal black holes in general relativity with a negative cosmological constant in any dimension. Wormholes in the Euclidean path integral for gravity cause these states to have small, but nonzero, quantum mechanical overlaps that have a universal form. The overlaps have a dramatic consequence: The microstates span a Hilbert space of log dimension equal to the Bekenstein-Hawking entropy. The semiclassical microstates we construct contain Einstein-Rosen bridges of arbitrary size behind their horizons. Our results imply that all these bridges can be interpreted as quantum superpositions of wormholes of size at most exponential in the entropy.

Published by the American Physical Society
2024
Stability Criterion for Electrodeposition in Solid-State Batteries with Metallic Anodes
Authors: Liu Yuanpeng , Zhang Jiawei , Zhang Bowen , Gao Haowen , Chen Dongjiang , Wang Mingsheng , Wang Changguo
Published: February 2024

We establish an analytical criterion for stable electrodeposition by combining electrochemistry and mechanics. experiments combined with molecular simulations are performed to validate the robustness of the theoretical predictions. Our analysis shows that stable electrodeposition is intimately linked with the interfacial defect size, fracture toughness, and molar volume of solid electrolytes. We find an exponential scaling law between the critical current density and the interfacial defect size, and the inherent softening in strength of grain boundaries lowers the critical current density in polycrystalline solid electrolytes. Modeling and analyses provide roadmaps to design solid electrolytes with metallic anodes for achieving stable electrodeposition.

Published by the American Physical Society
2024
Short-sale constraints and stock returns: a systematic review
Authors: Khan Mostafa Saidur Rahim
Published: February 2024

Purpose

This study delves into the nuanced implications of short-sale constraints on stock prices within the context of stock market efficiency. While existing research has explored this relationship, inconsistencies persist in their findings. The purpose of this study is to conduct a comprehensive review of literature to elucidate the reasons behind these disparities.

Design/methodology/approach

A systematic review of existing theoretical and empirical studies was conducted following the PRISMA method. The analysis centered on discerning the factors contributing to the divergence in projected stock prices due to these constraints. Key areas explored included assumptions related to expectations homogeneity, revisions, information uncertainty, trading motivations and fluctuations in supply and demand of risky assets.

Findings

The review uncovered multifaceted reasons for the disparities in findings regarding the influence of short-sale constraints on stock prices. Variations in assumptions related to market expectations, coupled with fluctuations in perceived information uncertainty and trading motivations, were identified as pivotal factors contributing to differing projections. Empirical evidence disparities stemmed from the use of proxies for short-sale constraints, varied sample periods, market structure nuances, regulatory changes and the presence of option trading.

Originality/value

This study emphasizes the significance of not oversimplifying the impact of short-sale constraints on stock prices. It highlights the need to understand these effects within the broader context of market structure and methodological considerations. By delineating the intricate interplay of factors affecting stock prices under short-sale constraints, this review provides a nuanced perspective, contributing to a more comprehensive understanding in the field.
AI and the metaverse in the workplace: DEI opportunities and challenges
Authors: Marabelli Marco , Lirio Pamela
Published: February 2024

Purpose

The metaverse, through artificial intelligence (AI) systems and capabilities, allows considerable data analysis in the workplace, largely exceeding traditional people analytics data collection. While concerns over surveillance and issues associated with privacy and discrimination have been raised, the metaverse has the potential to offer opportunities associated with fairer assessment of employee performance and enhancement of the employee experience, especially with respect to gender and race, inclusiveness and workplace equity. This paper aims at shedding light on the diversity, equity and inclusion (DEI) opportunities and challenges of implementing the metaverse in the workplace, and the role played by AI.

Design/methodology/approach

This paper draws on our past research on AI and the metaverse and provides insights addressed to human resources (HR) scholars and practitioners.

Findings

Our analysis of AI applications to the metaverse in the workplace sheds light on the ambivalent role of and potential trade-offs that may arise with this emerging technology. If used responsibly, the metaverse can enable positive changes concerning the future of work, which can promote DEI. Yet, the same technology can lead to negative DEI outcomes if implementations occur quickly, unsupervised and with a sole focus on efficiencies and productivity (i.e. collecting metrics, models etc.).

Practical implications

Managers and HR leaders should try to be first movers rather than followers when deciding if (or, better, when) to implement metaverse capabilities in their organizations. But how the metaverse is implemented will be strategic. This involves choices concerning the degree of invasive/pervasive monitoring (internal) as well as make or buy decisions concerning outsourcing AI capabilities.

Originality/value

Our paper is one among few (to date) that discusses AI capabilities in the metaverse at the intersection of the HR and information systems(IS) literature and that specifically tackles DEI issues. Also, we take a “balanced” approach when evaluating the metaverse from a DEI perspective. While most studies either demonize or celebrate these technologies from an ethical and DEI standpoint, we aim to highlight challenges and opportunities, with the goal to guide scholars and practitioners towards a responsible use of the metaverse in organizations.
Approximating personal exposure to ambient air pollution
Authors: Younger Ashley
Published: February 2024

Linked article: This is a mini commentary on Hammer et al. To view this article visit https://doi.org/10.1111/1471-0528.17696.
Wrong Kind of Transparency? Mutual Funds’ Higher Reporting Frequency, Window Dressing, and Performance
Authors: XIN XIANGANG , YEUNG P. ERIC , ZHANG ZILONG
Published: February 2024

This study examines whether mandatory increase in reporting frequency exacerbates agency problems. Utilizing the setting of the 2004 SEC mandate on increased reporting frequency of mutual fund holdings, we show that increased reporting frequency elevates window dressing (buying winners or selling losers shortly before the end of the reporting period). This effect is driven by low‐skill fund managers’ incentives to generate mixed signals. Funds managed by low‐skill managers experience lower returns, more outflows, and a higher collapse rate when their window dressing is elevated after the 2004 rule change. These results suggest that, although higher reporting frequency on agents’ actions can exacerbate signal manipulations, the related manipulation costs improve sorting among agents in the longer term.
VAT do you eat? Green consumption taxes and firms' market share
Authors: Zerwer Kira
Published: February 2024

This paper examines the role of a ‘green’ value‐added tax in the competitive environment of firms. Using data on firms in Romania and leveraging the introduction of a tax reduction on organic products in 2019, I show that although the overall market for organic goods grows and potential to generate windfall profit exists, the market share of incumbent firms decreases because of intensified competition post‐reform driven by new entrants competing for profits in the market. The market share decreases by about 2 percentage points after the reform. The effect depends on the relative elasticity of demand vis‐à‐vis supply in the market and the ability of a firm to protect its sales from new market entrants. Firms operating geographically further from the main consumer (i.e., more rural firms) and further upstream from the retail sector are more vulnerable to losing market share because urban demand is less elastic than rural demand and retail demand is less elastic than primary demand. Firms that are in markets where it is easier to switch from non‐organic to organic and that are less capital intensive (i.e., have fewer fixed costs) are more vulnerable to losing market share to new market entrants.
Right to counsel? A mixed‐methods evaluation of the St. Louis County initial appearance program
Authors: Morgan Lauren A. , Shamserad Faraneh , Huebner Beth M.
Published: February 2024

Research summary

Legal representation is a critical right in the criminal legal process, yet it is unclear when representation is guaranteed. Further, many individuals find obtaining legal representation difficult and expensive. The current study is an evaluation of an initial appearance program implemented in St. Louis County, Missouri. This mixed‐methods study focuses on understanding if and how providing counsel at initial appearance affects the bond amount, release type, and length of pretrial detention. Data from official court records and interviews with project staff and stakeholders suggest that early, free representation at arraignment can facilitate release on recognizance and lowered bail amounts. Results from a series of interaction models suggest that this type of programming may be able to help reduce some racial disparities. Our thematic analysis indicates that courtroom stakeholders see value in the program for the defendants, the criminal process, and the courtroom workgroup dynamics during pretrial stages.

Policy implications

The results reflect the need for early representation in the legal process. Representation can potentially reduce some of the racial and ethnic disparities in case processing, which are relatively stark and can lead to downstream effects like a greater likelihood of recidivism and conviction. Currently, most funding for public defenders is inequitable to that of the prosecutor's office, and this work speaks to the necessity of providing representation that begins with the initial appearance and continues throughout the life of the case. This work also highlights how outside funding can be used to support more equitable and fair case processing in the criminal legal system.
Probing efficient microbial CO2 utilisation through metabolic and process modelling
Authors: Gorter de Vries Philip J. , Mol Viviënne , Sonnenschein Nikolaus , Jensen Torbjørn Ølshøj , Nielsen Alex Toftgaard
Published: February 2024

Acetogenic gas fermentation is increasingly studied as a promising technology to upcycle carbon‐rich waste gasses. Currently the product range is limited, and production yields, rates and titres for a number of interesting products do not allow for economically viable processes. By pairing process modelling and host‐agnostic metabolic modelling, we compare fermentation conditions and various products to optimise the processes. The models were then used in a simulation of an industrial‐scale bubble column reactor. We find that increased temperatures favour gas transfer rates, particularly for the valuable and limiting H2, while furthermore predicting an optimal feed composition of 9:1 mol H2 to mol CO2. Metabolically, the increased non‐growth associated maintenance requirements of thermophiles favours the formation of catabolic products. To assess the expansion of the product portfolio beyond acetate, both a product volatility analysis and a metabolic pathway model were implemented. In‐situ recovery of volatile products is shown to be within range for acetone but challenging due to the extensive evaporation of water, while the direct production of more valuable compounds by acetogens is metabolically unfavourable compared to acetate and ethanol. We discuss alternative approaches to overcome these challenges to utilise acetogenic CO2 fixation to produce a wider range of carbon negative chemicals.
Microbial metabolism of diosgenin by a novel isolated Mycolicibacterium sp. HK‐90: A promising biosynthetic platform to produce 19‐carbon and 21‐carbon steroids
Authors: Wang Zhikuan , Qiu Hailiang , Chen Yulong , Chen Xuemin , Fu Chunhua , Yu Longjiang
Published: February 2024

Green manufacture of steroid precursors from diosgenin by microbial replacing multistep chemical synthesis has been elusive. It is currently limited by the lack of strain and degradation mechanisms. Here, we demonstrated the feasibility of this process using a novel strain Mycolicibacterium sp. HK‐90 with efficiency in diosgenin degradation. Diosgenin degradation by strain HK‐90 involves the selective removal of 5,6‐spiroketal structure, followed by the oxygenolytic cleavage of steroid nuclei. Bioinformatic analyses revealed the presence of two complete steroid catabolic gene clusters, SCG‐1 and SCG‐2, in the genome of strain HK‐90. SCG‐1 cluster was found to be involved in classic phytosterols or cholesterol catabolic pathway through the deletion of key kstD1 gene, which promoted the mutant m‐∆kstD1 converting phytosterols to intermediate 9α‐hydroxyandrostenedione (9‐OHAD). Most impressively, global transcriptomics and characterization of key genes suggested SCG‐2 as a potential gene cluster encoding diosgenin degradation. The gene inactivation of kstD2 in SCG‐2 resulted in the conversion of diosgenin to 9‐OHAD and 9,16‐dihydroxy‐pregn‐4‐ene‐3,20‐dione (9,16‐(OH)2‐PG) in mutant m‐ΔkstD2. Moreover, the engineered strain mHust‐ΔkstD1,2,3 with a triple deletion of kstDs was constructed, which can stably accumulate 9‐OHAD by metabolizing phytosterols, and accumulate 9‐OHAD and 9,16‐(OH)2‐PG from diosgenin. Diosgenin catabolism in strain mHust‐ΔkstD1,2,3 was revealed as a progression through diosgenone, 9,16‐(OH)2‐PG, and 9‐OHAD to 9α‐hydroxytestosterone (9‐OHTS). So far, this work is the first report on genetically engineered strain metabolizing diosgenin to produce 21‐carbon and 19‐carbon steroids. This study presents a promising biosynthetic platform for the green production of steroid precursors, and provide insights into the complex biochemical mechanism of diosgenin catabolism.
Rapid detection of six Oceanobacillus species in Daqu starter using single‐cell Raman spectroscopy combined with machine learning
Authors: Xu Lei , Liang Yuan , Huang Wei E , Shang Lin‐Dong , Chai Li‐Juan , Zhang Xiao‐Juan , Shi Jin‐Song , Li Bei , Wang Yun , Xu Zheng‐Hong , Lu Zhen‐Ming
Published: February 2024

Many traditional fermented foods and beverages industries around the world request the addition of multi‐species starter cultures. However, the microbial community in starter cultures is subject to fluctuations due to their exposure to an open environment during fermentation. A rapid detection approach to identify the microbial composition of starter culture is essential to ensure the quality of the final products. Here, we applied single‐cell Raman spectroscopy (SCRS) combined with machine learning to monitor Oceanobacillus species in Daqu starter, which plays crucial roles in the process of Chinese baijiu. First, a total of six Oceanobacillus species (O. caeni, O. kimchii, O. iheyensis, O. sojae, O. oncorhynchi subsp. Oncorhynchi and O. profundus) were detected in 44 Daqu samples by amplicon sequencing and isolated by pure culture. Then, we created a reference database of these Oceanobacillus strains which correlated their taxonomic data and single‐cell Raman spectra (SCRS). Based on the SCRS dataset, five machine‐learning algorithms were used to classify Oceanobacillus strains, among which support vector machine (SVM) showed the highest rate of accuracy. For validation of SVM‐based model, we employed a synthetic microbial community composed of varying proportions of Oceanobacillus species and demonstrated a remarkable accuracy, with a mean error was less than 1% between the predicted result and the expected value. The relative abundance of six different Oceanobacillus species during Daqu fermentation was predicted within 60 min using this method, and the reliability of the method was proved by correlating the Raman spectrum with the amplicon sequencing profiles by partial least squares regression. Our study provides a rapid, non‐destructive and label‐free approach for rapid identification of Oceanobacillus species in Daqu starter culture, contributing to real‐time monitoring of fermentation process and ensuring high‐quality products.
Bacterially enhanced plant‐growing media for controlled environment agriculture
Authors: Van Gerrewey Thijs , Navarrete Oscar , Vandecruys Maarten , Perneel Maaike , Boon Nico , Geelen Danny
Published: February 2024

Microbe–plant interactions in the root zone not only shape crop performance in soil but also in hydroponic cultivation systems. The biological and physicochemical properties of the plant‐growing medium determine the root‐associated microbial community and influence bacterial inoculation effectiveness, which affects plant growth. This study investigated the combined impact of plant‐growing media composition and bacterial community inoculation on the root‐associated bacterial community of hydroponically grown lettuce (Lactuca sativa L.). Ten plant‐growing media were composed of varying raw materials, including black peat, white peat, coir pith, wood fibre, composted bark, green waste compost, perlite and sand. In addition, five different bacterial community inocula (BCI S1–5) were collected from the roots of lettuce obtained at different farms. After inoculation and cultivation inside a vertical farm, lettuce root‐associated bacterial community structures, diversity and compositions were determined by evaluating 16S rRNA gene sequences. The study revealed distinct bacterial community structures among experimental replicates, highlighting the influence of raw material variations on root‐associated bacterial communities, even at the batch level. However, bacterial community inoculation allowed modulation of the root‐associated bacterial communities independently from the plant‐growing medium composition. Bacterial diversity was identified as a key determinant of plant growth performance with green waste compost introducing Bacilli and Actinobacteria, and bacterial community inoculum S3 introducing Pseudomonas, which positively correlated with plant growth. These findings challenge the prevailing notion of hydroponic cultivation systems as sterile environments and highlight the significance of proper plant‐growing media raw material selection and bacterial community inoculation in shaping root‐associated microbiomes that provide stability through microbial diversity. This study supports the concept of creating bacterially enhanced plant‐growing media to promote plant growth in controlled environment agriculture.
Neotropical songbird chick predation by an invasive wasp, the German yellowjacket (Vespula germanica)
Authors: Gorosito Cristian Andrés , Cueto Victor Rodolfo
Published: February 2024

Social wasps (Family: Vespidae) are opportunistic and generalist feeders, which can occasionally feed on live vertebrates. The German yellowjacket (Vespula germanica) is native to Eurasia and Northern Africa, and has invaded many countries around the world, producing several environmental, economic and social impacts. Here we report the first video‐recorded evidence that this wasp species preys on chicks. Over six breeding seasons, we studied the parental care behaviour of the Chilean Elaenia (Elaenia chilensis), a long‐distance migratory bird that breeds in the Andean‐Patagonian Forest. We filmed 59 nests when chicks were 2–3 and 10–11 days old, and recorded in a nest containing two 10‐day‐old nestlings the predation of one of them by German yellowjackets. The other chick was found alive on the ground, indicating that it escaped from the wasps. Parents did not defend offspring against wasp attacks. The rarity of this observation may suggest either that this insect is not yet a significant nest predator or that it is difficult to obtain a record of predation by wasps, because birds may remove dead nestlings from the nests (i.e. nest sanitation). Although Chilean Elaenia is not threatened, 41% of bird species in the Andean‐Patagonian Forest are endemic, and this new nest predator may potentially become a threat to the conservation of any of those species, which deserves further research. Hence, to evaluate the German yellowjacket impact on bird populations, it is imperative to conduct videotaped nest monitoring in order to remove the masking effect of nest sanitation on predator identity, which will allow to determine how much this wasp contributes to nest failure in the invaded zone of the Neotropical region.
Clinical utility of maternal TORCH screening in fetal growth restriction: A retrospective two‐centre study
Authors: Wade Christine A. , Atkinson Naomi , Holmes Natasha E. , Hui Lisa
Published: February 2024

Objective

The aim of this study was to evaluate the indications for maternal TORCH (Toxoplasma gondii, rubella, cytomegalovirus (CMV), and herpes simplex virus (HSV)) serology, with a focus on the yield in isolated fetal growth restriction (FGR).

Materials and Methods

A retrospective review of antenatal TORCH testing between January 2014 and December 2018 was carried out at two hospitals in Melbourne, Australia. TORCH testing ordered for pregnancy losses and stillbirth was excluded.

Results

Medical records of 718 pregnancies were reviewed, representing 760 fetuses. Isolated FGR was the indication for TORCH screening in 71.2% of pregnancies. Screens ordered for isolated FGR were positive in 7.4% (95% CI 5.5–10.0%). There were 49 positive maternal immunoglobulin M (CMV = 34, Toxoplasma = 15). Two acute maternal infections during pregnancy were diagnosed (CMV = 1, Toxoplasma = 1), with both screens ordered to assess symptomatic maternal illness. There was one neonatal CMV infection, born to a woman with symptomatic primary CMV. No maternal or neonatal rubella or HSV infections were identified. We found a diagnostic yield of TORCH screening for isolated FGR of 0.0% (95% CI 0.00–0.8%). An estimated AUD$64 269.75 was expended on maternal TORCH screens in this study.

Conclusion

Maternal TORCH testing for isolated FGR is of no diagnostic yield and should be abandoned.
The effect of ultrasound‐assisted thrombolysis studied in blood‐on‐a‐chip
Authors: Li Yan , Li Yongjian , Chen Haosheng
Published: February 2024

Background

Thromboembolism, which leads to pulmonary embolism and ischemic stroke, remains one of the main causes of death. Ultrasound‐assisted thrombolysis (UAT) is an effective thrombolytic method. However, further studies are required to elucidate the mechanism of ultrasound on arterial and venous thrombi.

Methods

We employed the blood‐on‐a‐chip technology to simulate thrombus formation in coronary stenosis and deep vein valves. Subsequently, UAT was conducted on the chip to assess the impact of ultrasound on thrombolysis under varying flow conditions. Real‐time fluorescence was used to assess thrombolysis and drug penetration. Finally, scanning electron microscopy and immunofluorescence were used to determine the effect of ultrasound on fibrinolysis.

Results

The study revealed that UAT enhanced the thrombolytic rate by 40% in the coronary stenosis chip and by 10% in the deep venous valves chip. This enhancement is attributed to the disruption of crosslinked fibrin fibers by ultrasound, leading to increased urokinase diffusion within the thrombus and accumulation of plasminogen on the fibrinogen α chain. Moreover, the acceleration of the dissolution rate of thrombi in the venous valve chip by ultrasound was not as significant as that in the coronary stenosis chip.

Conclusion

These findings highlight the differential impact of ultrasound on thrombolysis under various flow conditions and emphasize the valuable role of the blood‐on‐a‐chip technology in exploring thrombolysis mechanisms.
Immigrant's death at the border: Do they influence White and Latinx Americans’ belief in the American dream?
Authors: Vega Rivas Alexa , Ben Hagai Ella , Starr Christine
Published: February 2024

In this study, we test a clashing narrative approach to conflict, which argues that political conflict is based on opposing narratives that negate one another. We focus on the role of two master narratives central to political schism in the United States. The first is the American dream narrative, which posits that anyone who works hard can become successful in the United States. The opposing narrative, the systemic racism narrative, argues that the United States is a racist country where minorities are systemically held back. A survey study of 189 participants demonstrated that these two master narratives predict support for the presidential candidacy of Donald Trump or Joe Biden above and beyond more traditional ideological dispositions such as right‐wing authoritarianism and social dominance orientation. In a follow‐up experiment (n = 157), we examined how the Trump's administration policies of increased surveillance and policing of Latino immigrants crossing the border influenced White and Latinx participants’ agreement with the narrative of the American dream and the United States as a systemically racist country. Findings suggest that when confronted with news clips of immigrant death at the border, Latinx participants, compared to White participants, increased their endorsement of the American dream narrative. Conversely, White participants, increased their endorsement of the United States as a systemically racist country compared to Latinx participants. The results of this study help us understand support for the Republican party among Latinx voters.
Parental cigarette smoking before and during pregnancy in a cohort of 21 472 pregnancies
Authors: Voutilainen Taija , Keski‐Nisula Leea , Rysä Jaana , Kärkkäinen Olli
Published: February 2024

Smoking during pregnancy is one of the leading causes for adverse pregnancy outcomes. We studied parental smoking both before and during pregnancy in a retrospective cohort of 21 472 singleton pregnancies. Although most smoking women (74%) ceased tobacco use, there was possible gestational exposure to maternal cigarette smoking in every fifth pregnancy. Continued smoking throughout pregnancy was more prevalent in the partners (22%) than in the pregnant women (7%). The smoking behaviour of the women, especially the number of cigarettes smoked per day (CPD), before and in early pregnancy predicted the continuation of smoking throughout the pregnancy and could be used in identifying high risk groups. In addition, their partner's smoking habits both before and during pregnancy, were associated with the likelihood that the woman would continue to smoke during her pregnancy (rs ≈ 0.4). Furthermore, continued smoking of both parents were associated with decreased birth weight, head circumference and Apgar score, and increased duration of hospital stay and need for special care after birth. Consequently, addressing the lifestyles of both parents in the health care and maternity clinics could help in reducing maternal cigarette smoking during pregnancy and the adverse pregnancy outcomes associated with smoking.
HLA peptide‐binding pocket diversity modulates immunological complications after cord blood transplant in acute leukaemia
Authors: Boukouaci Wahid , Rivera‐Franco Monica M. , Volt Fernanda , Lajnef Mohamed , Wu Ching‐Lien , Rafii Hanadi , Cappelli Barbara , Scigliuolo Graziana Maria , Kenzey Chantal , Ruggeri Annalisa , Rocha Vanderson , Gluckman Eliane , Tamouza Ryad
Published: February 2024

Pocket motifs and their amino acid positions of HLA molecules are known to govern antigen presentation to effector cells. Our objective was to analyse their influence on the risk of graft‐versus‐host disease (GVHD) and relapse after umbilical cord blood transplant (UCBT). The transplant characteristics of 849 patients with acute leukaemia were obtained from the Eurocord/EBMT database. Higher acute (a) GVHD was associated with homozygosity of UCB HLA‐C amino acid positions 77 and 80 (NN/KK) (p = 0.008). Severe aGVHD was associated with HLA‐A pocket B YSAVMENVHY motif (p = 0.002) and NN and RR genotypes of the HLA‐C amino acid positions 77 and 156 (p = 0.006 and p = 0.002). Such risk was also increased in case of recipient and UCB mismatches in P4 (p < 0.0001) and P9 (p = 0.003) pockets of HLA‐DQB1 alleles. For chronic GVHD, the pocket B YYAVMEISNY motif of the HLA‐B*15:01 allele and the absence of mismatch between recipient and UCB in the P6 pocket of HLA‐DRB1 were associated with a lower risk (p = 0.0007 and p = 0.0004). In relapse, both UCB pocket B YFAVMENVHY belonging to HLA‐A*32:01 and recipient pocket B YDSVGENYQY motif of the HLA‐C*07:01 allele were associated with higher risk (p = 0.0026 and p = 0.015). We provide clues on HLA‐mediated cellular interactions and their role in the development of GVHD and relapse.