bluuebunny/crossref_metadata_2025_split huggingface dataset:
WormSNAP: A software for fast, accurate, and unbiased detection of fluorescent puncta inC. elegans
Authors: Tiroumalechetty Araven , Frankel Elisa B. , Kurshan Peri T. 
Published: January 2025

ABSTRACTThe detection and characterization of fluorescent puncta are critical tasks in image analysis pipelines for fluorescence imaging. Existing methods for quantitative characterization of such puncta often suffer from biases and limitations, compromising the reliability and reproducibility of results. Moreover, the widespread adoption of many available analysis scripts is often hampered by over-optimization for specific samples, requiring extensive coding knowledge to repurpose for other datasets. We presentWormSNAP (Worm SyNapse Analysis Program), a freely available, no-code approach to automated unbiased detection and characterization of 2D fluorescent puncta, originally developed to characterize images of the synapses residing inC. elegansnerve cords but suitable for broader 2D fluorescence image analysis.WormSNAPincorporates a local means thresholding algorithm and a user-friendly Graphical User Interface (GUI) for efficient and accurate analysis of large datasets, with user control of thresholding and restriction parameters and visualization options for further refinement.WormSNAPalso calculates three types of correlation metrics for 2-channel images, enabling users to select the ideal metric for their dataset.WormSNAPprovides robust and accurate fluorescent puncta detection in a variety of conditions, accelerating the image analysis workflow from data acquisition to figure generation.
Translation and Validation of the Brazilian – Portuguese version of Quality of Life on Vascular Access Devices Specific Questionnaire in Chemotherapy patients
Authors: Ponte Bruno Jeronimo , Sorbello Carolina Carvalho Jansen , de Oliveira Ricardo Ferreira Mendes , Portugal Maria Fernanda Cassino , Louzada Andressa Cristina Sposato , da Silva Marcelo Fiorelli Alexandrino , Pinheiro Lucas Lembrança , de Almeida Mendes Cynthia , Wolosker Nelson 
Published: January 2025

1.AbstractBackgroundThe use of long-term devices for chemotherapy in neoplastic diseases is very common. The CAVA trial was an extensive study that prospectively evaluated more than a thousand patients undergoing chemotherapy and randomized them to three groups: patients using PICC, Port or Hickmann-type catheters. For this study, a specific questionnaire was elaborated, called theVenous access device quality of life questionnaire(QolVAD), the aim of which is to assess the impact of the device (Hickmann type, PICC or thoracic Port) on the patients’ routine. However, there is no Brazilian – Portuguese version available, blunting its use in Brazilian patients.ObjectiveThe objective of this study is to translate and validate de CAVA Trial QolVAD to the Brazilian – Portuguese, making possible its use in Brazilian population.MethodsOne hundred sixty-seven patients with long term vascular access devices for chemotherapy participated in the study. After translation and retranslation, construct validity was analyzed by identifying correlation between QolVAD and European Quality of Life Questionnaire (EuroQol). To determine the reliability, internal consistency and test-retest with at least 7 days interval between 2 questionnaire applications were calculated.ResultsThe results showed a good internal and external consistency of the QolVAD. When comparing to EuroQol, significant correlations were found after comparing both questionnaires (r −0,658 and p < 0,001).ConclusionThe Brazilian – Portuguese version of the Quality-of-Life Vascular Access Device has presented good clinimetric properties and has shown to be applicable to the Brazilian population.
Gut-on-Chip Methodology Based on 3D-Printed Molds: A Cost-Effective and Accessible Approach
Authors: Delannoy Elise , Burette Aurélie , Janel Sébastien , Daniel Catherine , Grassart Alexandre 
Published: January 2025

1ABSTRACTGut-on-chips (GoC) represent a disruptive technology with great potential to understand the underlying mechanisms of gut health and pathology. Researchers who want to implement this approach, can either use expensive commercial microfluidic chips or build them from scratch in their lab. However, the design of such devices demands specific technical skills and expertise in computer assisted design (CAD). Additionally, the fabrication of the master molds for the chip production is very costly, time consuming and requires dedicated microfabrication facilities. Thus, the diffusion of these models in biology and health research laboratories remains limited due to this technological complexity and lack of affordability. In order to break these two bottlenecks, we present here the 3DP-µGut with open access designs and a simple fabrication approach based on a commercial 3D printer intended for general users. To ensure a good reproducibility with a sufficient number of available replicates for biological experiments, the method has been optimized to allow the production of multiple GoC per batch. The chips were also improved for confocal live imaging microscopy analyses. The chips are designed to be compatible with different types of microfluidics pumps, from stand-alone to completely integrated instrumentation. As a proof of concept, Caco-2 cells were seeded inside the fabricated GoC to validate their biocompatibility and functionality. After 7 days of maturation, cells self-differentiated in a 3D epithelium resemblingin vivoexpected structures. In summary we proposed a low-cost and open access GoC design and fabrication method with medium throughput. These results demonstrate the advantage of using 3D SLA printing to accelerate GoC implementation for gut physiopathology research.
Strategies to decipher neuron identity from extracellular recordings in the cerebellum of behaving non-human primates
Authors: Herzfeld David J. , Hall Nathan J. , Lisberger Stephen G. 
Published: January 2025

AbstractIdentification of neuron type is critical to understand computation in neural circuits through extracellular recordings in awake, behaving animal subjects. Yet, modern recording probes have limited power to resolve neuron type. Here, we leverage the well-characterized architecture of the cerebellar circuit to perform expert identification of neuron type from extracellular recordings in behaving non-human primates. Using deep-learning classifiers we evaluate the information contained in readily accessible extracellular features for neuron identification. Waveform, discharge statistics, anatomical layer, and functional interactions each can inform neuron labels for a sizable fraction of cerebellar units. Together, as inputs to a deep-learning classifier, the features perform even better. Our tools and methodologies, validated during smooth pursuit eye movements in the cerebellar floccular complex of awake behaving monkeys, can guide expert identification of neuron type during cerebellar-dependent tasks in behaving animals across species. They lay the groundwork for characterization of information processing in the cerebellar cortex.Impact statementTo understand how the brain performs computations in the service of behavior, we develop methods to link neuron type to functional activity within well-characterized neural circuits. Here, we show how features derived from extracellular recordings provide complementary information to disambiguate neuron identity in the cerebellar cortex.
Engineering low pH-tolerantKomagataella phaffiifor industrial-ready itaconic acid production via methanol biorefinery
Authors: Wei Fangqing , Han Xiao , Tao Fei , Xu Ping 
Published: January 2025

AbstractMethanol biorefinery stands as a cornerstone strategy in the pursuit of sustainable biochemical production from non-food feedstocks. Despite its vast potential, bioconverting methanol into high titer biochemical production remains a formidable challenge. In this study, we have successfully engineeredKomagataella phaffiito efficiently produce itaconic acid (IA), one of the top 12 building block chemicals, utilizing methanol as the sole carbon source. Our approach involved strategic metabolic engineering interventions—such as enhancing the supply ofcis-aconitate and citrate precursors, minimizing isocitrate diversion, facilitating efficient formaldehyde assimilation, and optimizing IA export mechanisms—culminating in an unprecedented IA titer of 103.8 g/L in a 5-L bioreactor through fed-batch fermentation at pH 5.5. Remarkably, even at a reduced pH of 3.5, the strain still yielded 50.4 g/L of IA, highlighting the industrial viability of methanol biorefinery. This systematic work lays a robust foundation for high-titer production via methanol biorefinery, offering valuable insights for future research and applications.
Increased slow wave activity in response to sleep deprivation is highest immediately after micro-arousals
Authors: Hauglund Natalie L. , Krone Lukas B. , Kahn Martin , Blanco-Duque Cristina , Vyazovskiy Vladyslav V. 
Published: January 2025

AbstractNon-rapid eye movement (NREM) sleep is not uniform but characterized by brief intrusions of wake-like brain activity, known as micro-arousals or brief awakenings. Although micro-arousals are an inherent feature of both human and animal sleep, knowledge about the neural correlates of micro-arousals across the cortical column is sparse. We here developed an algorithm for automatic detection of micro-arousals based on EMG activity and used it to explore how micro-arousals modulate laminar neural activity in the motor cortex, and how this relationship is affected by sleep pressure in mice. Our analysis showed that micro-arousals were associated with a general suppression of local field potential (LFP) power across the cortical column. Slow wave activity (SWA, 1-4 Hz) immediately after micro-arousals was tightly correlated with sleep pressure and even surpassed average SWA levels during NREM sleep in sleep deprived animals. In addition, analysis of single-channel firing showed that some channels exhibited increased activity immediately prior to micro-arousals, while others exhibited decreased activity. This study provides new insights into the neural mechanisms underlying micro-arousals and identifies a new link between micro-arousals and sleep homeostasis.
Assessing Human Liver Spheroids as a Model for Antiviral Drug Evaluation Against BSL-3 Haemorrhagic Fever viruses
Authors: Chaput Sarah , Driouich Jean-Sélim , de Lamballerie Xavier , Nougairède Antoine , Touret Franck 
Published: January 2025

AbstractHaemorrhagic fever viruses (HFVs) cause highly lethal syndromes with limited therapeutic options. Increasingly, 3D cell culture models are becoming an important tool in the field of virology. Since the liver is an important target for many HFVs, we evaluated a ready-to-use 96-well liver spheroid model composed of human primary cells for antiviral assessment. We worked with four biosafety level 3 (BSL-3) HFVs in this study: two orthoflaviviruses, Alkhumra haemorrhagic fever virus (AHFV) and yellow fever virus (YFV), and two viruses belonging toHareaviralesorder, Pirital virus (PIRV), a surrogate for new-world BSL-4 mammarenaviruses, and Rift Valley fever virus (RVFV). We found that RVFV and PIRV were able of replicating in this model, whereas the orthoflaviviruses were not. A high viral dose was required for robust replication, and infectivity of RVFV in spheroids was low. We successfully demonstrated the antiviral activity of known broad-spectrum antiviral compounds— favipiravir, nitazoxanide, ribavirin, and galidesivir—despite some variability. However, except for ribavirin, higher doses were required in spheroids to detect antiviral effect compared to the 2D cell culture model. Overall, we conclude that while this model can provide valuable complementary information to traditional models, it should not be considered a critical selection step for antiviral compounds. More broadly, this model could be useful to study viral pathogenicity and host-pathogen interactions.
Neuropathological changes in the nucleus basalis of Meynert in people with type 1 or type 2 diabetes mellitus
Authors: Jiang Wei , Kalsbeek Martin J. , Correa-da-Silva Felipe , Kalsbeek Andries , Swaab Dick F. , Siegelaar Sarah E. , Yi Chun-Xia 
Published: January 2025

AbstractPeople with type 1 or type 2 diabetes mellitus (T1DM or T2DM) often experience cognitive impairment. We profiled cells in the nucleus basalis of Meynert (NBM) in postmortem human brain tissues to investigate neuropathological changes. 71 postmortem NBM samples were grouped by T1DM, T2DM and non-diabetic controls, with Braak stage 0-2 or 3-6. T1DM subjects had only Braak stage 0-2 and were thus compared only to controls with a similar Braak stage and not subjects with Braak stage 3-6. We analysed neurons expressing choline acetyltransferase (ChAT), phosphorylated-Tau, glial cells and vasculature with respective markers. We found significantly less neuronal expression of ChAT in T1DM compared to controls and T2DM with Braak stage 0-2. Later-stage hyperphosphorylated-Tau levels were higher in T2DM compared to controls with Braak stages 3-6. Our results suggest that reduced acetylcholine production by NBM neurons might underlie the cognitive complains of people with T1DM. In contrast, T2DM may exacerbate neuropathological changes associated with Alzheimer’s disease-like alterations.
Characterization of a virulent bacteriophage consortium targeting Enterobacteriaceae from inflamed preterm gut mucosa
Authors: Spiegelhauer Malene Roed , Offersen Simone Margaard , Krych Lukasz , Nielsen Dennis Sandris , Gambino Michela , Brunse Anders , Nguyen Duc Ninh 
Published: January 2025

AbstractPreterm infants have a high risk of intestinal inflammation which can progress to necrotizing enterocolitis (NEC). The gut microbial colonization commencing at birth is essential for proper intestinal maturation, but this process is often disrupted in preterm infants, leading to dysbiosis and increased risk of developing NEC. Bacteriophages (phages), viruses that specifically infect bacteria, are an important constituent of the gut microbiome and protects the gut epithelium against invading bacteria. This study aimed to isolate and characterize phages for use as a preventive measure against NEC-associated bacteria. We initially culturedEnterobacteriaceaefrom ileal mucosa of preterm piglets that exhibited severe NEC-like pathology. We then screened 23 donor fecal samples for inhibition of bacterial growth and isolated a collection of unique phages to use further. The phages were characterized by whole genome sequencing, host receptor binding determination, and immune cell activationin vitro. The final phage collection consisted of ten virulent phages within five genera, representing myovirus, podovirus and siphovirus morphologies. All phages in the collection induced expression of both pro-and anti-inflammatory genes in co-culture with macrophage-like THP-1 cells, but to different extents thanEscherichia coli. Ultimately, we selected one phage for a high-dose oral administration to newborn piglets and assessed its infectivity and presence in different gut segments. This intervention did not result in any direct side effects, while both infective phages and signatures of phage DNA were detected in the intestinal content and mucosa. Having characterized a set of rationally selected virulent phages, we support the advancement of phage therapy as a potential protection against NEC.
Identifying and treating CLN3 disease outside the central nervous system
Authors: Ziółkowska Ewa A. , Jablonka-Shariff Albina , Williams Letitia L. , Jansen Matthew J. , Wang Sophie H , Eultgen Elizabeth M. , Wood Matthew D. , Hunter Daniel A. , Sharma Jaiprakash , Sardiello Marco , Bradley Rebecca P. , Whiteman Ineka T. , Reese Robyn , Pestronk Alan , Sands Mark S. , Heuckeroth Robert O. , Snyder-Warwick Alison K. , Cooper Jonathan D. 
Published: January 2025

AbstractCLN3 disease causes profound neurological deficits in affected children, but less well recognized are a variety of peripheral neuromuscular and gastrointestinal problems. We hypothesized that in addition to central nervous system (CNS) degeneration, CLN3 deficiency may also directly affect neuronal and/or glial cell populations in the rest of the body. Therefore, we examined the neuromuscular and enteric nervous system inCln3Δex7/8mice. There was no overt sciatic nerve axon loss or demyelination inCln3Δex7/8mice, but significant loss of terminal Schwann cells (tSCs) at lower limb neuromuscular junctions (NMJ), and progressive NMJ denervation. This was accompanied by pronounced myofiber atrophy, with fewer and displaced myofibril nuclei, with similar pathology seen in a human CLN3 muscle biopsy. Atrophy was also evident in bowel smooth muscle withCln3Δex7/8mice displaying slow bowel transit, and significant loss of both enteric neurons and glial cells throughout the bowel. Similar enteric pathology was evident at autopsy in the small intestine and colon of a human CLN3 case. Neonatal administration of intravenous gene therapy toCln3Δex7/8mice using an AAV9-hCLN3 vector completely prevented tSCs and NMJ pathology, atrophy of both skeletal and smooth muscle, positively impacted bowel transit and largely prevented the loss of enteric neurons and glia. These findings reveal an underappreciated, but profound, impact of CLN3 disease outside the CNS and suggest these novel aspects of disease may be treatable using gene therapy.Graphical abstract
How leader–subordinate (In)congruence in narcissism influences leaders’ effectiveness: the mediating role of relationship conflict
Authors: Liu Dege , Lan Yuanmei , Li Chaoping 
Published: January 2025

Purpose
Previous research on narcissism and leadership seldom takes into account the leader–subordinate dyadic relationship and ignores the role of subordinate. Drawing on the contextual reinforcement model of narcissism, the purpose of this study is to explore the joint effects of both leaders’ and their subordinates’ narcissism on the former’s effectiveness through the latter’s perceived relationship conflict with them (RCWL).

Design/methodology/approach
Self-report data were collected from 315 full-time employees using a three-wave survey. Polynomial regression and response surface analysis were used to test the hypotheses.

Findings
The results of this study reveal that although RCWL is higher when leaders’ narcissism is higher along both congruence and incongruence line, RCWL is lower when leaders’ narcissism exceeds that of their subordinates than it falls short of subordinates’ narcissism when both leader’s and subordinate’s narcissism are low. Furthermore, the results of this study also demonstrate that leader–subordinate (in)congruence in narcissism has an indirect influence on the leaders’ effectiveness because of the resulting relationship conflict, and that the response surface of the total effect of joint narcissism on leader effectiveness possesses a convex surface, which demonstrates that leader effectiveness is lower at the median point when compared to the low- and high-level congruence points.

Originality/value
This study not only contributes to fit theory, vertical relational conflict and research on narcissistic leader by simultaneously investigating both leaders’ and subordinates’ narcissism and their joint influence on leader–subordinate relational conflict and leaders’ effectiveness but also offers several practical recommendations for companies to enhance leaders’ effectiveness.
Navigating trauma: mental well-being after Kiteezi landfill collapse and residential displacement in Uganda
Authors: Kyambade Mahadih , Namatovu Afulah 
Published: January 2025

PurposeThis study aims to investigate the mental health impacts of this disaster, focusing on the psychological resilience and vulnerability of displaced individuals. The study explores the mental health outcomes, including anxiety, depression and post-traumatic stress disorder (PTSD) that have emerged as a result of the sudden loss of homes, livelihoods and social networks.Design/methodology/approachThe research employed a phenomenological approach, conducting 20 in-depth interviews with adult residents of Kiteezi who were displaced by the landslide. The interviews, conducted in English and transcribed for analysis, focused on three primary phenomena: landslides, displacement and mental well-being.FindingsFindings reveal that the collapse of the Kiteezi landfill had profound mental health impacts on the displaced residents, with widespread reports of anxiety, depression and PTSD. The loss of homes and livelihoods, coupled with the uncertainty surrounding resettlement, exacerbated these mental health challenges.Research limitations/implicationsThe study’s implications are significant for disaster response and mental health intervention strategies. The findings underscore the need for comprehensive mental health support for displaced individuals, emphasizing the importance of addressing both immediate psychological needs and long-term resilience-building.Originality/valueThis study is original in its focus on the specific context of the Kiteezi landfill collapse, contributing to the limited literature on the mental health impacts of environmental disasters in Uganda. It provides valuable insights into the complex interplay between environmental disasters, displacement and mental well-being, offering practical recommendations for improving disaster response and recovery efforts in similar settings.
Effect of IFRS on foreign shareholdings and corporate investments in Saudi Arabia
Authors: Donker Han , Jermakowicz Eva K. , Nurunnabi Mohammad 
Published: January 2025

Purpose
Prior research has shown that implementing International Financial Reporting Standards (IFRS) increases foreign direct investments at the macroeconomic (country) level. This study aims to demonstrate that the implementation of mandatory adoption of IFRS positively influences foreign shareholdings at the company level in Saudi Arabia.

Design/methodology/approach
The fixed effects regression model is used to estimate the impact of the adoption of IFRS on foreign ownership in a panel data set for Saudi Arabia over the period 2010 through 2021.

Findings
This study finds that IFRS adoption reduces information asymmetry and increases comparability, which attracts foreign investors. It also finds that firms with high foreign ownership have greater capital expenditures post-IFRS adoption, suggesting that foreign investors encourage firms to align their interests with those of shareholders and make more long-term investments. This paper demonstrates that firms increased their long-term investments and garnered greater free cash flows after adopting IFRS. Finally, this paper observes a positive association between IFRS employment and market liquidity.

Originality/value
To the best of the authors’ knowledge, this is the first research to reveal that, following the compulsory adoption of IFRS, foreign shareholdings have a favorable effect on corporate investments (capital expenditures and property, plant and equipment) at the micro (firm) level. It has been motivated by the assertion that a lack of portfolio investments results primarily from an asymmetry of information, which can be mitigated by providing high quality comparable financial information based on IFRS.