bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is there a difference in the satisfaction levels between professionals who have participated and those who have not participated in the TeleUTIP telemedicine project regarding their engagement in tele-education activities?
Authors: Moleda Constant Hilda M. R. , Jacovas Vanessa Cristina , Vinadé Chagas Maria Eulália , Cotta Matte Maria Cristina , Klever Emanuele König , Cunha Luciane , Mafalda Krauzer João Ronaldo , de Campos Moreira Taís , Cabral Felipe Cezar 
Published: January 2024

ABSTRACTObjectiveThe aim of this study is to introduce a distance education program and assess the satisfaction of health professionals.MethodsA cross-sectional study was conducted in five public hospitals across different regions of Brazil. A total of 171 health professionals participated in a tele-education activity involving discussions of complex cases in a Case-Based Learning (CBL) format. Employee satisfaction was measured using the translated questionnaire Tele-Education Satisfaction Assessment Instrument (IAS-TE).ResultsThe mean satisfaction score for participants was 4.6 on a 5-point Likert-type scale. Participants engaged in the telemedicine project (35.5%) reported significantly higher satisfaction (p<0.001) compared to their non-participating peers (n = 149, 64.5%). The IAS-TE exhibited a Cronbach’s alpha of 0.73, indicating good reliability, and demonstrated good homogeneity (KMO = 0.76, Bartlett’s test of sphericity = p<0.00).ConclusionParticipants in the proposed activity expressed high levels of satisfaction. The findings suggest that satisfaction levels are elevated among professionals involved in the telemedicine project. The proposed satisfaction assessment instrument (IAS-TE) exhibits robust psychometric qualities and is suitable for evaluating other distance education activities. Future perspectives involve gaining a deeper understanding of strategies to enhance satisfaction for professionals who do not engage in activities using advanced technology.
WITHDRAWN: Impact of spatial clustering of cytotoxic and tumor infiltrating lymphocytes on overall survival in women with high grade serous ovarian cancer
Authors: Soupir Alex C. , Townsend Mary K. , Hathaway Cassandra A. , Nguyen Jonathan , Moran Segura Carlos , Saeed-Vafa Daryoush , Ospina Oscar E. , Peres Lauren C. , Conejo-Garcia Jose R. , Terry Kathryn L. , Tworoger Shelley S. , Fridley Brooke L. 
Published: January 2024

Withdrawal StatementThe authors have withdrawn their manuscript owing to incorrect handling of multiple measures in the survival analyses. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Mechanical hyperalgesia and neuropathic pain qualities impart risk for chronic postoperative pain after total knee replacement
Authors: Vigotsky Andrew D. , Cong Olivia , Pinto Camila B , Barroso Joana , Perez Jennifer , Petersen Kristian Kjaer , Arendt-Nielsen Lars , Hardt Kevin , Manning David , Apkarian A. Vania , Branco Paulo 
Published: January 2024

AbstractTotal knee replacement (TKR) is the gold-standard treatment for end-stage chronic osteoarthritis pain, yet many patients report chronic postoperative pain after TKR. The search for preoperative predictors for chronic postoperative pain following TKR has been studied with inconsistent findings. This study investigates the predictive value of quantitative sensory testing (QST) and PainDETECT for postoperative pain 3, 6, and 12 months post-TKR. We assessed baseline and postoperative (3- and 6-months) QST measures in 77 patients with knee OA (KOA) and 41 healthy controls, along with neuropathic pain scores in patients (PainDETECT). QST parameters included pressure pain pressure threshold (PPT), pain tolerance threshold (PTT), conditioned pain modulation (CPM), and temporal summation (TS) using cuff algometry, alongside mechanical hyperalgesia, and mechanical temporal summation to repeated pinprick stimulation. Compared to healthy controls, KOA patients at baseline demonstrated hyperalgesia to pinprick stimulation at the medial OA-affected knee and cuff pressure on the ipsilateral calf. Lower cuff algometry PTT and mechanical pinprick hyperalgesia were associated with baseline KOA pain intensity. Moreover, baseline pinprick pain hyperalgesia explained 25% of variance in pain intensity 12 months post-TKR and preoperative neuropathic pain scores also captured 30% and 20% of the variance in postoperative pain at 6- and 12-months, respectively. A decrease in mechanical pinprick hyperalgesia from before surgery to 3 months after TKR was associated with lower postoperative pain at the 12 months post-TKR follow-up, and vice-versa. Our findings suggest that preoperative pinprick hyperalgesia and PainDETECT neuropathic-like pain symptoms show predictive value for the development of chronic post-TKR pain.
Role of histone variants H2BC1 and H2AZ.2 in H2AK119ub nucleosome organization and Polycomb gene silencing
Authors: Shen Xiangyu , Chen Chunxu , Wang Yue , Zheng Wan , Zheng Jiahuan , Jones Amanda E. , Zhu Bing , Zhang Hao , Lyons Charles , Rijal Arjun , Moley James A. , Cao Gengsheng , Liu Kui , Winn Robert , Dickinson Amanda , Zhang Kai , Wang Hengbin 
Published: January 2024

AbstractUbiquitination of histone H2A at lysine 119 residue (H2AK119ub) plays critical roles in a wide range of physiological processes, including Polycomb gene silencing1,2, replication3–5, DNA damage repair6–10,Xinactivation11,12, and heterochromatin organization13,14. However, the underlying mechanism and structural basis of H2AK119ub remains largely elusive. In this study, we report that H2AK119ub nucleosomes have a unique composition, containing histone variants H2BC1 and H2AZ.2, and importantly, this composition is required for H2AK119ub and Polycomb gene silencing. Using the UAB domain of RSF1, we purified H2AK119ub nucleosomes to a sufficient amount and purity. Mass spectrometry analyses revealed that H2AK119ub nucleosomes contain the histone variants H2BC1 and H2AZ.2. A cryo-EM study resolved the structure of native H2AK119ub nucleosomes to a 2.6A resolution, confirming H2BC1 in one subgroup of H2AK119ub nucleosomes. Tandem GST-UAB pulldown, Flag-H2AZ.2, and HA-H2BC1 immunoprecipitation revealed that H2AK119ub nucleosomes could be separated into distinct subgroups, suggesting their composition heterogeneity and potential dynamic organization. Knockout or knockdown of H2BC1 or H2AZ.2 reduced cellular H2AK119ub levels, establishing H2BC1 and H2AZ.2 as critical determinants of H2AK119ub. Furthermore, genomic binding profiles of H2BC1 and H2AZ.2 overlapped significantly with H2AK119ub binding, with the most significant overlapping in the gene body and intergenic regions. Finally, assays in developing embryos reveal an interaction of H2AZ.2, H2BC1, and RING1Ain vivo. Thus, this study revealed, for the first time, that the H2AK119ub nucleosome has a unique composition, and this composition is required for H2AK119ub and Polycomb gene silencing.
The impact of struvite and ash recycling-derived fertilizers on microbial phosphorus mobilization capabilities and community structure in aLolium perennefield trial
Authors: Deinert Lea , Ashekuzzaman SM , Forrestal Patrick , Schmalenberger Achim 
Published: January 2024

AbstractRock phosphate is a non-renewable primary source for mineral phosphorus (P) fertilizers that intensive agriculture is highly dependent on. To avoid P fertilizer shortages and limit negative environmental impacts, circular economy approaches are needed with recycling-derived fertilizer (RDF) applications such as struvites and ashese. Hence, a grassland field trial was conducted with four RDFs, two struvites (potato wastewater, municipal wastewater) and two ashes (poultry-litter ash, sewage-sludge ash) at a P application rate of 40 kg P ha-1(n=5). The impact of the RDFs on the soil microbial P cycling community was compared to conventional mineral P-fertiliser and a P-free control. Topsoil samples were taken directly afterLolium perennegrass cuts at months three, fife and 15. Cultivable phosphonate and phytate utilizing bacteria, potential acid and alkaline phosphomonoesterase activity, andphoCandphoDcopy numbers responded stronger to seasonal effects than treatment effects. No significant overall effect of the fertilizer application was detected in the beta diversity of the bacterial and fungal communities after 15 months, but individual phylogenetic groups were affected by the treatments. The ash treatments demonstrated some distinguishing results across the bacterial and fungal community, with significantly higher relative abundance of Firmicutes and Rokubacteria and lower relative abundance of Actinobacteriota. Sewage-sludge ash had significantly lowest abundances of generaBacillusandBradyrhizobium(month 15s) that are well known for their P cycling abilities. The struvite RDFs either positively influenced the P cycling microbial community or did not affect it at all, while demonstrating better tri-calcium phosphate solubilizing capabilities after the 3 months harvest. These findings indicate that struvites could be a suitable replacement for conventional P fertilizers in the future.
Anticipatory emotions and academic performance: The role of boredom in a preservice teachers’ lab experience
Authors: Gómez-Ochoa de Alda Jesús A. , Marcos-Merino José María , Valares-Masa Cristina , Esteban-Gallego María Rocío 
Published: January 2024

AbstractAffective experiences within academic contexts significantly influence educational outcomes. Despite this, the literature reveals a gap in generalising these effects to specific classroom activities, partly arising from the absence of suitable instruments to measure emotions in situational educational scenarios. Our study introduces an experience sampling method to measure sixteen discrete emotional states, deriving two scales for positive and negative activating emotions. Grounded in psychological and neuroscientific theories that integrate emotion with cognition, our research explores the interplay between prior knowledge, preservice teachers’ anticipatory situational emotions, and subsequent learning in an experimental science education context. Analysing data from 269 preservice teachers from diverse backgrounds (STEM and non-STEM) at the upper-secondary level, we found that negative activating emotions are often rooted in non-STEM backgrounds and exacerbated by limited prior science knowledge. These negative emotions impact achievement and learning primarily through the mediating role of boredom. Furthermore, our results indicate that the detrimental impact of boredom on achievement is significantly influenced by prior knowledge, with a more pronounced effect on students with lower levels. Given that emotions are amenable to intervention, our findings propose that specifically addressing boredom in students with low prior knowledge could amplify the benefits of educational strategies.
DUALISTIC SAHA DOSE-DEPENDENT EFFECTS ON GLIAL-INFLAMMATORY RESPONSE
Authors: Mancino S. , Boraso M. , Galmozzi A. , De Fabiani E. , Crestani  , Viviani B. 
Published: January 2024

ABSTRACTNeuroinflammation comprises biochemical and cellular responses of the nervous system to injury, emerging as a central process in many neurological conditions. Although beneficial in nature, over-activation of the immune response may result in the production of neurotoxic factors that exacerbate the disease state. Due to the relevant role of histone acetylation in transcriptional regulation, inhibition of histone deacetylase (HDAC) activity plays a central role in the pathogenesis of inflammation. Here, we investigated the impact of HDACs inhibition in the regulation of the inflammatory response elicited by lipopolysaccharide (LPS) in glia cells using trichostatin A (TSA) and suberoylanilide hydroxamic acid (SAHA). We observed that acute and prolonged exposure to low doses of TSA boosts the inflammatory response in glia cells. Conversely, TSA pre-treatment in cells exposed to LPS decreases inflammation. Additionally, we observed that low and high doses of SAHA exert opposite effects on LPS-induced inflammatory response. Low dose (100 nM) potentiates inflammatory response by increasing the production of pro-inflammatory cytokines tumour necrosis factor (TNF)-α and interleukin (IL) - 1β; and reducing the anti-inflammatory mediator IL-10. Nevertheless, 5 µM SAHA reverts the pro-towards anti-inflammatory profile.To better characterize SAHA dualistic effects in glia cells, we generated comparative genome-wide gene expression data. Simultaneous exposure to 5 µM SAHA and LPS (10 ng/ml) alters the expression of 1628 genes, while the combination of 100 nM SAHA and LPS regulates the expression of 97 transcripts. Both doses of SAHA differentially regulate important pathways involved in cellular function maintenance, homeostasis, and survival.Likewise, inhibition of the Janus Kinase - signal transducers and activators of the transcription (JAK/STAT) signalling pathway seems to mediate the anti-inflammatory effects of 5 µM SAHA. On the other hand, 100 nM SAHA increases pro-inflammatory cytokine levels possibly via modulation of the underlined feedback mechanisms triggered by IL-10 expression regulation.Together, these results contribute to outline a comprehensive picture of the involvement of HDACs inhibitors (HDACi) in the onset or prevention of neuroinflammation, showing that their effects depend on cell types, HDACi dosage and specificity, and protocol used.
HSV-1 ICP0 Dimer Domain Adopts a Novel β-barrel Fold
Authors: McCloskey Erick , Kashipathy Maithri , Cooper Anne , Gao Philip , Johnson David K. , Battaile Kevin P. , Lovell Scott , Davido David J. 
Published: January 2024

ABSTRACTInfected cell protein 0 (ICP0) is an immediate-early regulatory protein of herpes simplex virus 1 (HSV-1) that possesses E3 ubiquitin ligase activity. ICP0 transactivates viral genes, in part, through its C-terminal dimer domain (residues 555-767). Deletion of this dimer domain results in reduced viral gene expression, lytic infection, and reactivation from latency. Since ICP0’s dimer domain is associated with its transactivation activity and efficient viral replication, we wanted to determine the structure of this specific domain. The C-terminus of ICP0 was purified from bacteria and analyzed by X-ray crystallography to solve its structure. Each subunit or monomer in the ICP0 dimer is composed of nine β-strands and two α-helices. Interestingly, two adjacent β-strands from one monomer “reach” into the adjacent subunit during dimer formation, generating two β-barrel-like structures. Additionally, crystallographic analyses indicate a tetramer structure is formed from two β-strands of each dimer, creating a “stacking” of the β-barrels. The structural protein database searches indicate the fold or structure adopted by the ICP0 dimer is novel. The dimer is held together by an extensive network of hydrogen bonds. Computational analyses reveal that ICP0 can either form a dimer or bind to SUMO1 via its C-terminal SUMO-interacting motifs but not both. Understanding the structure of the dimer domain will provide insights into the activities of ICP0 and, ultimately, the HSV-1 life cycle.
Quantitative assessment of Newcastle disease virus proteins interactions with all known mucin types of Chicken and Quail
Authors: Almhanna Hazem , Kumar Arun HS 
Published: January 2024

AbstractBackgroundNewcastle Disease (ND), caused by the Newcastle Disease Virus (NDV) poses a significant threat to poultry, leading to severe economic losses. Understanding the molecular interactions between NDV proteins and avian mucins is crucial for developing targeted interventions.Material and MethodsIn this study, twelve NDV proteins were systematically assessed for their interactions with sixteen quail and eight chicken mucin types, revealing diverse and species-specific binding patterns.ResultsHigh-affinity interactions between mucins (Muc5A, Muc5B, and Muc6) and NDV hemagglutinin-neuraminidase, was observed in addition to significant interactions with NDV fusion glycoprotein. Notably, chicken Muc4 displayed mid-range interactions exclusively with NDV fusion glycoprotein, highlighting potential species-specific differences in viral entry mechanisms between quails and chickens. Furthermore, the study investigated the number of binding sites on NDV proteins and chicken/quail mucins. Chicken Muc5B emerged as a standout with the highest number (20) of binding sites, suggesting its crucial role in NDV infection. The binding site analysis identified key regions in NDV fusion glycoprotein and hemagglutinin-neuraminidase, indicating potential targets for vaccine development.ConclusionThis study provides a foundation for future research into optimizing diagnostic approaches and therapeutic strategies for NDV infections. Validation of these interactions with real-world clinical data, coupled with an exploration of tissue-specific mucin expression patterns, could further enhance our understanding of host-virus dynamics. The identified interactions offer promising avenues for developing vaccines that target specific binding sites, thereby contributing to the effective control and prevention of Newcastle Disease in poultry populations.
Rapid and reversible dissolution of biomolecular condensates using light-controlled recruitment of a solubility tag
Authors: Brumbaugh-Reed Ellen H. , Aoki Kazuhiro , Toettcher Jared E. 
Published: January 2024

AbstractBiomolecular condensates are broadly implicated in both normal cellular regulation and disease. Consequently, several chemical biology and optogenetic approaches have been developed to induce phase separation of a protein of interest. However, few tools are available to perform the converse function—dissolving a condensate of interest on demand. Such a tool would aid in testing whether the condensate plays specific functional roles, a major question in cell biology and drug development. Here we report an optogenetic approach to selectively dissolve a condensate of interest in a reversible and spatially controlled manner. We show that light-gated recruitment of maltose-binding protein (MBP), a commonly used solubilizing domain in protein purification, results in rapid and controlled dissolution of condensates formed from proteins of interest. Our optogenetic MBP-based dissolution strategy (OptoMBP) is rapid, reversible, and can be spatially controlled with subcellular precision. We also provide a proof-of-principle application of OptoMBP, showing that disrupting condensation of the oncogenic fusion protein FUS-CHOP results in reversion of FUS-CHOP driven transcriptional changes. We envision that the OptoMBP system could be broadly useful for disrupting constitutive protein condensates to probe their biological functions.
G-quadruplexes inHaloferax volcanii
Authors: Aktary Zackie , Cucchiarini Anne , Vesco Guglielmo , Noury Dorian , Jourdain Thomas , Verga Daniela , Mahou Pierre , Olivier Nicolas , Valková Natalia , Porubiaková Otilia , Brázda Václav , Bouvier Marie , Kwapisz Marta , Clouet-d’Orval Béatrice , Allers Thorsten , Lestini Roxane , Mergny Jean-Louis , Guittat Lionel 
Published: January 2024

ABSTRACTThe archaeal domain is a taxonomically rich component of microbial communities that inhabit a wide range of habitats on Earth, including the human body. Phylogenomic analyses have indicated that archaea represent the closest known relatives of eukaryotes, thus suggesting that eukaryotes may have evolved from an archaeal ancestor. G-quadruplex structures (G4), formed by guanine rich sequences, are among the most intensively studied local DNA/RNA structures and regulate key biological processes such as replication and gene expression. A bioinformatics analysis of the genome of the salt-loving archaeaH. volcaniirevealed a large number of potential G4 sequences (PQS). Biophysical analyses showed that a representative panel of these sequences form stable G4 structures under physiological conditionsin vitro. In addition, immunofluorescence experiments using the G4-specific antibody, BG4, detected G4sin vivoat the single-cell level with super-resolution microscopy. Moreover, we directly visualized G4 in exponentially growing or stationary cells both at the DNA and RNA levels. G4s were also observed in the RNA and DNA of the hyperthermophile archaeonT. barophilus. Finally, we identified helicases potentially involved in G4 unfolding. Together, withH. volcaniias a new model, our work helps to fill the gap between bacteria and eukaryotic organisms for G4 studies and will aid in uncovering the evolutionary history of G4 structures in the tree of life.
Annotation-free prediction of microbial dioxygen utilization
Authors: Flamholz Avi I. , Goldford Joshua E. , Larsson Elin M. , Jinich Adrian , Fischer Woodward W. , Newman Dianne K. 
Published: January 2024

AbstractAerobes require dioxygen (O2) to grow; anaerobes do not. But nearly all microbes — aerobes, anaerobes, and facultative organisms alike — express enzymes whose substrates include O2, if only for detoxification. This presents a challenge when trying to assess which organisms are aerobic from genomic data alone. This challenge can be overcome by noting that O2utilization has wide-ranging effects on microbes: aerobes typically have larger genomes, encode more O2-utilizing enzymes, and tend to use different amino acids in their proteins. Here we show that these effects permit high-quality prediction of O2utilization from genome sequences, with several models displaying >70% balanced accuracy on a ternary classification task wherein blind guessing is only 33.3% accurate. Since genome annotation is compute-intensive and relies on many assumptions, we asked if annotation-free methods also perform well. We discovered that simple and efficient models based entirely on genome sequence content — e.g. triplets of amino acids — perform about as well as intensive annotation-based algorithms, enabling the rapid processing of global-scale sequence data to predict aerobic physiology. To demonstrate the utility of efficient physiological predictions we estimated the prevalence of aerobes and anaerobes along a well-studied O2gradient in the Black Sea, finding strong quantitative correspondence between local chemistry (O2:sulfide concentration ratio) and the composition of microbial communities. We therefore suggest that statistical methods like ours can be used to estimate, or “sense,” pivotal features of the environment from DNA sequencing data.ImportanceWe now have access to sequence data from a wide variety of natural environments. These data document a bewildering diversity of microbes, many known only from their genomes. Physiology — an organism’s capacity to engage metabolically with its environment — may provide a more useful lens than taxonomy for understanding microbial communities. As an example of this broader principle, we developed algorithms that accurately predict microbial dioxygen utilization directly from genome sequences without first annotating genes, e.g. by considering only the amino acids in protein sequences. Annotation-free algorithms enabled rapid characterization of natural samples, demonstrating a quantitative correspondence between sequences and local O2levels. These results suggest that DNA sequencing can be repurposed as a multi-pronged chemical sensor, estimating concentrations of O2and other key facets of complex natural settings.