bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validity of a novel excessive daytime sleepiness’ screening stool : the Yaoundé Sleepiness Score.
Authors: MASSONGO MASSONGO , Duthoit Louise , Balkissou Adamou Dodo , Ngah Komo Marie Elisabeth , Kuaban Alain , Fry Stéphanie , Pefura Yone Eric Walter , Mallart Anne 
Published: February 2024

Background The subjective assessment of excessive daytime sleepiness (EDS) using Epworth sleepiness scale (ESS) has shown some limits. This study aimed to assess the validity of the Yaoundé Sleepiness Scale (YSS), a new tool for EDS screening, using ESS as reference. Methodology A 6-item questionnaire was assessed for validity features. The content validity was based on sleep physiology. Four sleep specialists approved the initial draft for face validity. A cross-sectional study was led in Lille University Hospital to assess the criterion and construct validity. Baseline data, full night recording, and sleepiness scales (YSS, ESS) were recorded. The criterion validity was assessed using the Pearson correlation between YSS and ESS and the area under the receiver operator characteristics (AUROC) curve. A graphical method was used to find the YSS threshold. We used a simple linear regression to seek the association between YSS and EDS predictors for construct validity. Results A total of 566 patients (mean age ± standard deviation = 53.1 ± 14.6 years, female = 47%) were enrolled. The mean ± standard deviation YSS and ESS were 9.8 ± 4.7 and 9.1 ± 5.3, respectively. The Pearson correlation between YSS and ESS was 0.74% (p<0.0001). The AUROC curves (95% confidence interval, 95CI) for ESS-based EDS and severe EDS prediction were 0.856 (0.829 – 0.889) and 0.871 (0.829 – 0.913), respectively. The YSS thresholds for EDS and severe EDS were 9 and 15, respectively. Using ESS as gold standard, the sensitivity and specificity for EDS and severe EDS were 92.3 (88.7 - 95.9)% and 60.6 (55.3 - 65.9)%, and 60.3 (49.0 - 71.5)% and 90.2 (87.5 - 92.9)%. The YSS significantly increased with the use of psychotropic drugs and psychiatric conditions, and significantly decreased with age. Conclusion We found a good criterion validity and an acceptable construct validity of the YSS compared with ESS. This questionnaire could be proposed as an alternative to ESS. However, these data should be confirmed by other studies, notably based on objective sleepiness tests.
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

AbstractMotivationSimulating 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.ResultsHere, 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 implementationInSilicoSeq 2.0 is implemented in Python and is freely available under the MIT licence athttps://github.com/HadrienG/InSilicoSeq
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

AbstractInSaccharomyces 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.
Short-sale constraints and stock returns: a systematic review
Authors: Khan Mostafa Saidur Rahim 
Published: February 2024

PurposeThis 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/approachA 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.FindingsThe 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/valueThis 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

PurposeThe 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/approachThis paper draws on our past research on AI and the metaverse and provides insights addressed to human resources (HR) scholars and practitioners.FindingsOur 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 implicationsManagers 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/valueOur 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.
Wrong Kind of Transparency? Mutual Funds’ Higher Reporting Frequency, Window Dressing, and Performance
Authors: XIN XIANGANG , YEUNG P. ERIC , ZHANG ZILONG 
Published: February 2024

ABSTRACTThis 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

AbstractThis 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

AbstractResearch summaryLegal 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 implicationsThe 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

AbstractAcetogenic 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

AbstractGreen 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

AbstractMany 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

AbstractMicrobe–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.