bluuebunny/crossref_metadata_2025_split huggingface dataset:
Isoform-level discovery, quantification and fusion analysis from single-cell and spatial long-read RNA-seq data with Bambu-Clump
Authors: Sim Andre , Ling Min Hao , Chen Ying , Lu Han , See Yi Xiang , Perrin Arnaud , Leng Agnes Ong Bee , Cao Elaine Yiqun , Chia Burton , Liu Jinyue , Wüstefeld Torsten , Shin Jay W. , Göke Jonathan 
Published: January 2025

AbstractSingle cell and spatial transcriptomics have dramatically changed how we can profile RNA from heterogenous biological samples. Combining single cell and spatial profiling with long read RNA-Seq promises to enable the discovery and quantification of individual RNA isoforms at the single-cell level. However, highly multiplexed data such as from a single cell experiment only generates a limited number of reads for each cell, constituting a major challenge for transcript discovery and quantification with existing approaches that usually have limited power for samples with low sequencing depth.Here we present Bambu-Clump, a computational method that performs transcript discovery and quantification from single cell and spatial long read RNA-Seq data using information from both each cell and the cell cluster. Using this approach, Bambu-Clump provides the most accurate transcript discovery compared to other existing methods, and improves transcript quantification compared to methods that rely on estimates derived from single cells. We apply Bambu-Clump to identify fusion transcripts in single-cells, compare 5’ and 3’ selection protocols, and identify novel isoform cell-type markers in spatial mouse brain data. Together, Bambu-Clump provides an easy-to-use, efficient, and accurate method for analysing individual isoform expression for single cells and cell clusters across multiple datasets and replicates from long read RNA-Seq.
[11C]Carfentanil PET Whole-Body Imaging of Mu-Opioid Receptors: A First In-Human Study
Authors: Dubroff Jacob G. , Hsieh Chia-Ju , Wiers Corinde E. , Lee Hsiaoju , Li Elizabeth J. , Schubert Erin K. , Mach Robert H. , Kranzler Henry R. 
Published: January 2025

AbstractIntroductionMu-opioid receptors (MORs) are G-coupled protein receptors with a high affinity for both endogenous and exogenous opioids. MORs are widely expressed in the central nervous system (CNS), peripheral organs, and the immune system. They mediate pain and reward and have been implicated in the pathophysiology of opioid, cocaine, and other substance use disorders. Using the long axial field-of-view (LAFOV) PennPET Explorer instrument and the MOR selective radioligand [11C]carfentanil ([11C]CFN), we measured thewhole-bodydistribution of MORs in 13 healthy humans. We also examined sex differences in MOR distribution at baseline and after pretreatment with the MOR antagonist naloxone.MethodsSix female and seven male healthy subjects underwent two [11C]CFN PET imaging sessions—one at baseline and one immediately following pre-treatment with the MOR antagonist naloxone (13 mcg/kg). Whole-body PET imaging was performed on the PennPET Explorer, a 142-cm axial bore instrument. [11C]CFN brain distribution volume ratios (DVRs) were determined using the occipital cortex and the visual cortex within it as reference regions. For peripheral organ DVRs, the descending aorta and proximal extremity muscle (biceps/triceps) were used as reference regions.ResultsNaloxone blockade reduced MOR availability by 40-50% in the caudate, putamen, thalamus, amygdala, and ventral tegmentum, brain regions known to express high levels of MORs. Women showed greater receptor occupancy in the thalamus, amygdala, hippocampus and frontal and temporal lobes and a greater naloxone-induced reduction in thalamic MOR availability than men (p’s <0.05). For determining brain MOR availability, there was less variance in the visual cortex than the occipital cortex reference region. For peripheral MOR determination, the descending aorta reference region showed less variance than the extremity muscle, but both showed blocking effects of naloxone.Conclusions[11C]CFN whole- body PET scans are useful for understanding MOR physiology under both baseline and blocking conditions. Extra-CNS reference regions may be useful for quantifying radiotracers when a region devoid of binding in the CNS is unavailable. The LAFOV PET instrument was useful for measuring changes in the short-lived radiotracer [11C]CFN, with and without naloxone blocking. Further research is needed to evaluate the behavioral and clinical relevance of sex differences in naloxone-MOR interactions.
Integrating plasma, MRI, and cognitive biomarkers for personalized prediction of decline across cognitive domains
Authors: Moradi Elaheh , Dahnke Robert , Imani Vandad , Gaser Christian , Solomon Alina , Tohka Jussi ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: January 2025

AbstractBackgroundPlasma biomarkers are associated with cognitive performance and decline in Alzheimer’s disease, making them promising for early detection. This study investigates their predictive value, combined with non-invasive measures, for cognitive decline in non-demented individuals.MethodsWe developed a machine-learning approach incorporating plasma biomarkers (Aβ42/40, p-tau181, NfL), MRI, demographics, APOE4, and cognitive assessments. Various models were designed to predict decline rates across cognitive domains and assess their relevance in predicting dementia progression.ResultsCross-validated correlations between predicted and actual cognitive decline rates were 0.50 for memory, 0.49 for language, 0.42 for executive function, and 0.44 for visuospatial ability. MRI showed greater predictive importance than plasma biomarkers. Among plasma biomarkers, NfL and p-tau181 outperformed Aβ42/40.ConclusionPlasma biomarkers, especially when combined with MRI, APOE4, and cognitive measures, have the potential to predict memory decline and assess conversion risk, even in cognitively unimpaired individuals.
MaiZaic: a robust end-to-end pipeline for mosaicking freely flown aerial video of agricultural fields
Authors: Kharismawati Dewi Endah , Kazic Toni 
Published: January 2025

ABSTRACTUnmanned aerial vehicles (UAVs) are increasingly used for high throughput phenotyping. In principle, freely flown vehicles would permit real-time flexibility in identifying and scouting regions of interest. Mosaicking multiple images provides a high resolution global image and consumer-grade UAVs offer low cost, ease of flying, and excellent RGB cameras. The vehicles’ inaccurate telemetry complicates estimating the homographies between pairs of frames, the standard mosaicking approach. Moreover, errors accumulate during computation, distorting later portions of the mosaic. Finally, crop fields are particularly challenging to mosaic because their planting is so regular and the plants are so similar, eliminating distinctive features that could guide mosaicking. We proposeMaiZaic, an end-to-end pipeline that dynamically samples video frames using optical flow, automates camera and gimbal calibration, estimates homographies with an unsupervised convolutional neural network, detects shots among frames, and generates mini-mosaics. Together, these techniques significantly reduce errors in the output mosaics. Our deep learning model is trained on a comprehensive video dataset comprising different flight trajectories, maize lines, growth stages, and augmented illumination data.MaiZaicis more accurate and faster than ASIFT and more robust than our earlierCorNetandCorNetv2. We demonstrateMaiZaic’s effectiveness in generating accurate mosaics of imagery captured by freely-flown UAVs and explore its generalizability.Core ideasMaiZaicis an end-to-end pipeline to mosaic freely flown agricultural imagery captured with consumer-grade UAVs.MaiZaicintroduces novel algorithms that efficiently choose video frames, calibrate, and mosaic the imagery.Our unsupervised deep homography estimator,CorNetv3, is 14 times faster and 8.59% more accurare than ASIFT.MaiZaicgeneralizes well and mosaicks maize at different growth stages, objects, trajectories, cameras, and pilots.The mini-mosaicking algorithm improves mosaic accuracy by interrupting error accumulation.
A generative framework for enhanced cell-type specificity in rationally designed mRNAs
Authors: Khoroshkin Matvei , Zinkevich Arsenii , Aristova Elizaveta , Yousefi Hassan , Lee Sean B. , Mittmann Tabea , Manegold Karoline , Penzar Dmitry , Raleigh David R. , Kulakovskiy Ivan V. , Goodarzi Hani 
Published: January 2025

AbstractmRNA delivery offers new opportunities for disease treatment by directing cells to produce therapeutic proteins. However, designing highly stable mRNAs with programmable cell type-specificity remains a challenge. To address this, we measured the regulatory activity of 60,000 5’ and 3’ untranslated regions (UTRs) across six cell types and developed PARADE (Prediction And RAtional DEsign of mRNA UTRs), a generative AI framework to engineer untranslated RNA regions with tailored cell type-specific activity. We validated PARADE by testing 15,800 de novo-designed sequences across these cell lines and identified many sequences that demonstrated superior specificity and activity compared to existing RNA therapeutics. mRNAs with PARADE-engineered UTRs also exhibited robust tissue-specific activity in animal models, achieving selective expression in the liver and spleen. We also leveraged PARADE to enhance mRNA stability, significantly increasing protein output and therapeutic durability in vivo. These advancements translated to notable increases in therapeutic efficacy, as PARADE-designed UTRs in oncosuppressor mRNAs, namely PTEN and P16, effectively reduced tumor growth in patient-derived neuroglioma xenograft models and orthotopic mouse models. Collectively, these findings establish PARADE as a versatile platform for designing safer, more precise, and highly stable mRNA therapies.
Brain activation for language and its relationship to cognitive and linguistic measures
Authors: Balboni Irene , Rampinini Alessandra , Kepinska Olga , Berthele Raphael , Golestani Narly 
Published: January 2025

ABSTRACTLanguage learning and use are complex cognitive skills requiring domain-general cognition and sensori-motor skills, these also being important for numerical and music processing. Previous studies have explored behavioural associations across domains and neural underpinnings of specific abilities, yet less work has examined these questions together in the same participants. We collected data from 152 participants on behavioural measures of language, reading, multilingual experience, cognition, musicality, arithmetic, and motor skills, along with fMRI data during L1 story listening. Participants varied in multilingual language experience and reading aptitudes, including both typical (TRs) and dyslexic readers (DRs). Using multivariate Partial Least Squares correlation, we identified a main component linking cognitive, linguistic, and phonological measures to brain areas underlying lexico/semantics, combinatorial processing, and amodal semantic processing. A second analysis excluding DRs showed closer associations between cognitive/linguistic, literacy, phonological and memory processes within the same brain network as in the full sample. Here, we also isolated additional, complementary components, including one involving speed, automatization and lexical access, linked to auditory and motor brain areas. This suggests greater coherence and more integrated, ‘expert’ processing in TRs. This work is a first step in exploring complex relationships between language and non-linguistic functions that are important to it.
Argonaute proteins regulate the timing of the spermatogenic transcriptional program
Authors: Carro Maria de las Mercedes , Dziubek Alexis , Touey Amanda , Popkowski Elizabeth A. , Abdelmassih Mark , Simon Leah , Tanis Stephanie , Ahmed Faraz , Grenier Jen K. , Grimson Andrew , Cohen Paula E. 
Published: January 2025

ABSTRACTArgonaute proteins are best known for their role in microRNA-mediated post-transcriptional gene silencing. Here, we show that AGO3 and AGO4, but not AGO2, localize to the sex chromatin of pachytene spermatocytes where they are required for transcriptional silencing of XY-linked genes, known as Meiotic Sex Chromosome Inactivation (MSCI). Using anAgo413-/-mouse, we show that AGO3 and AGO4 are key regulators of spermatogenesis, orchestrating expression of meiosis-related genes during prophase I while maintaining silencing of spermiogenesis genes. Premature overexpression of spermiogenesis genes during prophase I inAgo413-/-mice results in subfertility, altered sperm morphology and reduced fertilization capability. We also identify BRG1, a BAF complex subunit, as an AGO3 interactor. Loss of AGO3 and AGO4 results in increased BRG1 in spermatocytes, suggesting that AGO3 aids in removing BRG1 from the XY chromatin to achieve MSCI and demonstrating a meiotic role for AGO3 in transcriptional control through the chromatin remodeling machinery.
Slimnastics School of Ballet: entrepreneurial decision-making “En Pointe”
Authors: Barsoum Miray Rashad 
Published: January 2025

Learning outcomes
Students studying this case study will critically evaluate business scenarios to develop strategic decisions, incorporating ethics, stakeholder impacts and long-term outcomes; assess managerial competencies and offer recommendations for growth, stability and employee engagement; identify entrepreneurial traits and characteristics, analyzing their impact on strategic planning and growth; evaluate leadership styles and their influence on organizational culture, motivation and success; and apply theoretical frameworks to assess Slimnastics’ challenges and propose data-driven growth strategies.

Case overview/synopsis
This case study focuses on a critical dilemma faced by Passant Esmail, founder of Slimnastics School of Ballet in Egypt. With the business recovering from the effects of the global pandemic and Esmail considering a personal relocation, she faces a key strategic decision: whether to sell Slimnastics for a profit, risking its legacy or to distribute equity among the management team, ensuring continuity but potentially compromising operational growth and future scalability. This dilemma forces her to weigh the sustainability of the business, ethical concerns and the impact of her decision on employees, students and the broader community.

Complexity academic level
This case study is designed for both undergraduate and postgraduate level students and is ideal for courses in entrepreneurship, strategic management and leadership in sports management.

Supplementary materials
Teaching notes are available for educators only.

Subject code
CSS3: Entrepreneurship.
Summer-time performance of Finnish housing: POE of five apartments
Authors: Elsayed Mohamed Ahmed Abdelfattah , Lastovets Natalia , Pistore Lorenza , Pelsmakers Sofie 
Published: January 2025

PurposeDespite the increased retrofitting of Finnish residential buildings, there are limited post-retrofit studies on the actual measured indoor environmental quality (IEQ) and occupant satisfaction during summer-time. This paper provides a better understanding of the actual performance of retrofitted residential apartment buildings in Finland, focusing on some aspects of and the risk of summer overheating through post-occupancy evaluation (POE).Design/methodology/approachThe study used both qualitative and quantitative data collection methods, including satisfaction surveys, indoor air temperature and relative humidity measurements, self-reported behaviour forms, open-ended discussions, and site visits in five apartments in different residential buildings in Tampere city, monitored during the summer-time, for at least 2 weeks at a time.FindingsWhile occupants were positive regarding most aspects of IEQ, concerns about indoor air quality (IAQ), summer overheating and acoustic comfort were raised. The summer-time monitoring highlighted that indoor air temperatures could reach as high as 27 °C for 2–9 days depending on the monitored apartment. Little cloud cover and warmer outdoor temperatures directly influenced indoor air temperature overheating. For some aspects of the investigated IEQ parameters, it was noted that while occupants’ satisfaction was influenced by the length of their residence, their acceptance of the same conditions remained positive over time (i.e. more than one year) as they adapted over time.Research limitations/implicationsThe number of participants and case studies was relatively small due to the well-known difficulty in gaining access to private homes, so the results do not allow generalisation but do provide interesting insights of these specific cases to be validated with future additional research. The short sequential rather than long-term parallel monitoring of the case study apartments was another limitation making comparison between cases and understanding reasons for differences difficult.Practical implicationsFindings highlight the need to maintain the performance of housing in Finland during summer-time. The highlighted subjective issues emphasised in this study underscore the necessity for enhanced pre- and post-retrofit quality processes and the prompt resolution of issues as they arise. The integration of POE studies into all residential construction practices becomes pivotal for the advancement of sustainable homes now, but also in the future, especially when subjected to a warming climate.Originality/valueThis study is among the few POE studies conducted in Finland, offering insights into post-retrofit performance and occupant satisfaction during the summer-time. The study highlights the potential of POE to understand the performance of retrofitted Finnish apartments from a user-centric perspective.
Influence of ChatGPT in professional communication – moderating role of perceived innovativeness
Authors: Mathur Smriti , Anand Vandana , Sharma Durgansh , Vishnoi Sushant Kr. 
Published: January 2025

PurposeChatGPT, a cutting-edge language model, stands as an unparalleled, unmatched conversational ally, showcasing novel versatility and intelligence in its responses. This research delves into the incorporation of ChatGPT, a powerful generative AI tool, into professional communication. This study utilizes the information system success model (ISSM) to examine the role of ChatGPTs in strengthening information quality (IQ), system quality (SQ) and service quality (SEQ) for improving customer usage intention (UI) and satisfaction (SAT). The study also investigates the moderating impact of perceived innovativeness between these relationships.Design/methodology/approachThe research collected data from a sample of 400 customers through an online survey and validated the hypothesized relationships using structural equation modelling (SEM). Process Macros 4.1 in SPSS 22.0 is used to test the moderating role of perceived innovation between IQ, SQ and SEQ and UI and SAT.FindingsThe results of SEM analysis indicate that IQ, SQ and SEQ all positively support UI to use ChatGPT for professional communication with SAT. The result also establishes that perceived innovativeness positively moderates the relationship between IQ, SQ and SEQ and UI and SAT.Originality/valueThis research study offers novel contributions to the literature and body of knowledge by establishing the moderating role of perceived innovativeness in strengthening the relationship between IQ, SQ and SEQ and UI and SAT. Further, this study also proposes a 2*2 matrix to segment the UI and SAT of ChatGPT users in professional communication with varying degrees of perceived innovativeness.
Societal spirits in the silver streak: Unraveling complexity in drinking habits of the mature adult population
Authors: van den Ende Maarten W. J. , Freichel René , van der Maas Han L. J. , Wiers Reinout W. , Epskamp Sacha 
Published: January 2025

AbstractBackgroundThe complex interactions between an individual's drinking behavior and their social environment is crucial but understudied, particularly in mature adult populations. Our aim is to unravel these complexities by investigating how personal drinking patterns are related to those of one's social environment over time, and what the interplay is with personal factors such as occupational prestige and smoking behavior.MethodThe present study adopts an innovative graphical autoregressive (GVAR) panel network modeling approach to investigate the dynamics between personal drinking habits and social environmental factors, utilizing a comprehensive longitudinal dataset from the Framingham Heart Study with a large sample of predominantly mature adults (N = 1719–5718) connected within a social network. We explored both temporal and contemporaneous associations between individuals' drinking habits (self‐reported), smoking behavior (self‐reported), perceived job prestige (Treiman prestige score), and the drinking behaviors of their social environment. The latter consists of the proportion of abstaining, moderate drinking, and heavy drinking social connections of each subject.ResultsOur findings reveal significant associations between participants' behavior and that of their peers, with reciprocal interactions, substantiating the importance of the influence of one's social network for mature individuals. We found dynamic, reciprocal associations between an individual's drinking behavior and that of their peers, with periods of increased or decreased drinking correlating with increased connections to heavy drinkers or abstainers, respectively. In addition, when individuals drink more than usual, they also tend to consume more cigarettes, and vice versa.ConclusionsThe reciprocal feedback loops identified between an individual's drinking behavior and their social environment highlight the crucial role of social influences in shaping drinking behavior, including among older people. This emphasizes the need to consider social elements in the development of future theories, models, and interventions aimed at addressing problematic alcohol consumption in this vulnerable population.
Mucilage of Pereskia aculeata Miller as Cryoprotectant of Frozen Strawberries: Preservation of Bioactive Compounds and Microstructure
Authors: Piva Samella Fabiane , de Oliveira Meira Ana Cristina Freitas , de Morais Larissa Carolina , Alexandre Ana Claúdia Silveira , de Resende Jaime Vilela 
Published: January 2025

ABSTRACTWhole strawberries were frozen after being impregnated with solutions of ora‐pro‐nóbis mucilage (MOPN) or pectin at concentrations of 0%, 0.5%, and 1.0% (w/v), CaCl2 at concentrations of 0.5% and 1.0% (w/v), and sucrose at concentrations of 5.0% and 10% (w/v). The strawberries were vacuum impregnated for 2 h with a controlled pressure of 64.3 kPa, and the rheological behavior of the solutions was evaluated before and after vacuum impregnation. In the strawberries, the texture and cell fluid losses, total soluble solids, pH, titratable acidity, and bioactive compounds were analyzed before and after processing. The microstructures of the frozen samples were evaluated by low‐vacuum electron microscopy. The impregnation process influenced the rheological parameters, and the solutions showed Newtonian or non‐Newtonian (n < 1) behavior. The treatment with MOPN efficiently reduced the cell fluid loss and texture loss in the thawed strawberries. Compared with pectin, these samples more effectively preserved the anthocyanin content and showed less reduction and oxidation of β‐carotene from the β‐carotene/linoleic acid system. For the treatments with MOPN or pectin combined with sucrose and CaCl2, the values for the milligrams ascorbic acid/100 g of strawberry and 1,1‐diphenyl‐2‐picrylhydrazyl (DPPH) were statistically similar to those of the fresh fruit. Microstructural analysis by low‐vacuum SEM confirmed that the vacuum impregnation process was able to incorporate the solutions inside the microstructure of whole strawberries. Compared to pectin solutions, MOPN solutions have potential for use as cryoprotectants of fruits.