bluuebunny/crossref_metadata_2025_split huggingface dataset:
An auto-release mechanism for HMCES-DNA-protein crosslinks
Authors: Donsbach Maximilian , Dürauer Sophie , Nguyen Kha T. , Grünert Florian , Yaneva Denitsa , Semlow Daniel R. , Stingele Julian 
Published: December 2022

SummaryThe conserved protein HMCES crosslinks to abasic (AP) sites in ssDNA to prevent strand scission and the formation of toxic dsDNA breaks during replication. Here, we report a non-proteolytic release mechanism for HMCES-DNA-protein crosslinks (DPCs), which is regulated by DNA context. In ssDNA and at ssDNA-dsDNA junctions, HMCES-DPCs are stable, which efficiently protects AP sites against spontaneous incisions and cleavage by APE1 endonuclease. In contrast, HMCES-DPCs are quickly released in dsDNA, allowing APE1 to initiate downstream repair. Mechanistically, we show that release is governed by two components. First, a conserved glutamate residue within HMCES’ active site catalyses reversal of the crosslink. Second, affinity to the underlying DNA structure determines whether HMCES re-crosslinks or dissociates. Our study reveals that the protective role of HMCES-DPCs involves their controlled release upon bypass by replication forks, which restricts DPC formation to a necessary minimum.
The YAP-TEAD complex promotes senescent cell survival by lowering endoplasmic reticulum stress
Authors: Anerillas Carlos , Mazan-Mamczarz Krystyna , Herman Allison B. , Munk Rachel , Lam Kwan-Wood Gabriel , Calvo-Rubio Miguel , Garrido Amanda , Tsitsipatis Dimitrios , Martindale Jennifer L. , Altés Gisela , Rossi Martina , Piao Yulan , Fan Jinshui , Cui Chang-Yi , De Supriyo , Abdelmohsen Kotb , de Cabo Rafael , Gorospe Myriam 
Published: December 2022

ABSTRACTSublethal cell damage can trigger a complex adaptive program known as senescence, characterized by growth arrest, resistance to apoptosis, and a senescence-associated secretory phenotype (SASP). As senescent cells accumulating in aging organs are linked to many age-associated diseases, senotherapeutic strategies are actively sought to eliminate them. Here, a whole-genome CRISPR knockout screen revealed that proteins in the YAP-TEAD pathway influenced senescent cell viability. Accordingly, treating senescent cells with a drug that inhibited this pathway, Verteporfin (VPF), selectively triggered apoptotic cell death and derepressed DDIT4, in turn inhibiting mTOR. Reducing mTOR function in senescent cells diminished endoplasmic reticulum (ER) biogenesis, causing ER stress and apoptosis due to high demands on ER function by the SASP. Importantly, VPF treatment decreased senescent cell numbers in the organs of old mice and mice exhibiting doxorubicin-induced senescence. We present a novel senolytic strategy that eliminates senescent cells by hindering ER activity required for SASP production.
Development of the Canadian Food Intake Screener to assess alignment of adults’ dietary intake with the 2019 Canada’s Food Guide healthy food choices recommendations
Authors: Hutchinson Joy M. , Williams Tabitha E. , Westaway Ailish M. , Bédard Alexandra , Pitre Camille , Lemieux Simone , Dodd Kevin W. , Lamarche Benoît , Guenther Patricia M. , Haines Jess , Wallace Angela , Martin Alicia , da Costa Louzada Maria Laura , Jessri Mahsa , Olstad Dana Lee , Prowse Rachel , Randall Simpson Janis , Vena Jennifer E. , Kirkpatrick Sharon I. 
Published: December 2022

AbstractThe objective of this project was to develop a brief self-administered dietary screener, in English and French, to rapidly assess alignment of adults’ dietary intake with the 2019 Canada’ s Food Guide healthy food choices recommendations. In consultation with Health Canada and external advisors (n=15), foundational principles were defined. Existing screeners were scanned, and the healthy food choices recommendations were mapped to inform questions and response options. Cognitive interviews were conducted in English (n=17) and French (n=16) with adults aged 18-65 years from April to June 2021 to assess understanding of questions and face validity; recruitment emphasized variation in sociodemographic characteristics. Face and content validity were assessed with experts in nutrition, surveillance, and public health (n=13 English, 3 French) from April to May 2021. The testing indicated that the screener was well-understood overall but informed refinements to improve comprehension of the questions and their alignment with the healthy food choices recommendations. The resulting Canadian Food Intake Screener/Questionnaire court canadien sur les apports alimentaires includes 16 questions to rapidly assess alignment of intake with the 2019 Canada’ s Food Guide healthy food choices recommendations, including healthy foods and foods to limit, in situations in which comprehensive dietary assessment is not feasible.NoveltyThe Canadian Food Intake Screener was developed to rapidly assess alignment of adults’ dietary intake over the past month with the Food Guide’ s “healthy food choices” recommendations.The screener was developed and evaluated through an iterative process that included three rounds of cognitive interviews in each of English and French, along with ongoing feedback from external advisors and face and content validity testing with a separate panel of content experts.The 16-question screener is intended for use with adults, aged 18-65 years, with marginal and higher health literacy in research and surveillance contexts in which comprehensive dietary assessment is not possible.
Tracking the COVID-19 vaccine equity, distribution, and cases in the global south
Authors: Melesse Tigist Mekonnen , Nguyen Thuy D. , Kassa Getachew Mullu 
Published: December 2022

AbstractThe rapid development of vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has proved to make an important contribution in reducing both viral transmission and disease burden. In this study, we tracked the COVID-19 vaccine equity, distribution, and cases in global south countries using country-level data from Our World in Data using an event study analysis. We used data from 149 global south and 59 non-global south countries from January 2020 to May 2022. All non-global south and 90.32% of global south countries had universal availability of vaccines. The median time since the introduction of the first COVID-19 vaccine in the global south was almost eight weeks later than in non-global south countries. The median number of people fully vaccinated per hundred (68.8 vs 50.31), and the total number of boosters administered per hundred (45.7 vs. 13.02) were higher in non-global south countries compared to global south countries. Using the event study analysis, we found a significant reduction of COVID-19 new cases and deaths after the first COVID-19 vaccination rollout compared to the baseline in global south countries, average coefficient p-value <0.001. Programs aiming at improving vaccine access and distribution to global south countries are essential to effectively control COVID-19.
Outcomes in Patients with Acute Hypoxemic Respiratory Failure Secondary to COVID-19 Treated with Noninvasive Respiratory Support versus Invasive Mechanical Ventilation
Authors: Fisher Julia M , Subbian Vignesh , Essay Patrick , Pungitore Sarah , Bedrick Edward J , Mosier Jarrod M 
Published: December 2022

AbstractPurposeThe goal of this study was to compare noninvasive respiratory support to invasive mechanical ventilation as the initial respiratory support in COVID-19 patients with acute hypoxemic respiratory failure.MethodsAll patients admitted to a large healthcare network with acute hypoxemic respiratory failure associated with COVID-19 and requiring respiratory support were eligible for inclusion. We compared patients treated initially with noninvasive respiratory support (noninvasive positive pressure ventilation by facemask or high flow nasal oxygen) with patients treated initially with invasive mechanical ventilation. The primary outcome was time-to-in-hospital death analyzed using an inverse probability of treatment weighted Cox model adjusted for potential confounders. Secondary outcomes included unweighted and weighted assessments of mortality, lengths-of-stay (intensive care unit and hospital) and time-to-intubation.ResultsOver the study period, 2354 patients met inclusion criteria. Nearly half (47%) received invasive mechanical ventilation first and 53% received initial noninvasive respiratory support. There was an overall 38% in-hospital mortality (37% for invasive mechanical ventilation and 39% for noninvasive respiratory support). Initial noninvasive respiratory support was associated with an increased hazard of death compared to initial invasive mechanical ventilation (HR: 1.61, p < 0.0001, 95% CI: 1.33 - 1.94). However, patients on initial noninvasive respiratory support also experienced an increased hazard of leaving the hospital sooner, but the hazard ratio waned with time (HR: 0.97, p < 0.0001, 95% CI: 0.96 - 0.98).ConclusionThese data show that the COVID-19 patients with acute hypoxemic respiratory failure initially treated with noninvasive respiratory support had an increased hazard of in-hospital death.
A single mild juvenile TBI in mice leads to regional brain tissue abnormalities at 12 months of age that correlate with cognitive impairment at the middle age in male mice
Authors: Obenaus Andre , Rodriguez-Grande Beatriz , Bin Lee Jeong , Dubois Christophe J. , Fournier Marie-Line , Cador Martine , Caille Stéphanie , Badaut Jerome 
Published: December 2022

AbstractTraumatic brain injury (TBI) has the highest incidence amongst the pediatric population and its mild severity represents the most frequent cases. Moderate and severe injuries as well as repetitive mild TBI result in lasting morbidity. However, whether a single mild TBI sustained during childhood can produce long-lasting modifications within the brain is still debated. We aimed to assess the consequences of a single juvenile mild TBI (jmTBI) at 12 months post-injury in a mouse model.Non-invasive diffusion tensor imaging (DTI) revealed significant microstructural alterations in the hippocampus and the in the substantia innominata/nucleus basalis (SI/NB), structures known to be involved in spatial learning and memory. DTI changes paralled neuronal loss, increased astrocytic AQP4 and microglial activation in the hippocampus. In contrast, decreased astrocytic AQP4 expression and microglia activation were observed in SI/NB. Spatial learning and memory were impaired and correlated with alterations in DTI-derived derived fractional ansiotropy (FA) and axial diffusivity (AD).This study found that a single juvenile mild TBI leads to significant region-specific DTI microstructural alterations, distant from the site of impact, that correlated with cognitive discriminative novel object testing and spatial memory impairments at 12 months after a single concussive injury. Our findings suggest that exposure to jmTBI leads to a chronic abnormality, which confirms the need for continued monitoring of symptoms and the development of long-term treatment strategies to intervene in children with concussions.
BUSZ: Compressed BUS files
Authors: Einarsson Pétur Helgi , Melsted Páll 
Published: December 2022

AbstractSummaryWe describe a compression scheme for BUS files and an implementation of the algorithm in the bustools software. Our compression algorithm yields smaller file sizes than gzip, at significantly faster compression and decompression speeds. We evaluated our algorithm on 533 BUS files from scRNA-seq experiments with a total size of 1Tb. Our compression is more than 2x faster than the fastest gzip option and results in 1.5x smaller files than the best gzip compression. This amounts to an 8.3x reduction in the file size, resulting in a compressed size of 122Gb for the dataset.Availability and ImplementationA complete description of the format is available athttps://github.com/BUStools/BUSZ-formatand an implementation athttps://github.com/BUStools/bustoolsContactpmelsted@hi.isonline.
Single-subject EEG measurement of interhemispheric transfer-time for the in-vivo estimation of axonal morphology
Authors: Oliveira Rita , De Lucia Marzia , Lutti Antoine 
Published: December 2022

AbstractAssessing axonal morphology in-vivo opens new avenues for the combined study of brain structure and function. A novel approach has recently been introduced to estimate the morphology of axonal fibers from the combination of MRI data and EEG measures of the interhemispheric transfer time (IHTT). In the original study, the IHTT measures were computed from EEG data averaged across a group, leading to bias of the axonal morphology estimates.Here, we seek to estimate axonal morphology from individual measures of IHTT, obtained from EEG data acquired in a visual evoked potential experiment. Subject-specific IHTTs are computed in a data-driven framework with minimala prioriconstraints, based on the maximal peak of neural responses to visual stimuli within periods of statistically significant evoked activity in the inverse solution space. The subject-specific IHTT estimates ranged from 8 to 29 ms except for one participant and the between-session variability was comparable to the differences in IHTT between subjects. The scale parameter of the axonal radius distribution, computed from the IHTT estimates and the MRI data, ranged from 0 to 0.79μm. The change in axonal g-ratio with axonal radius ranged from 0.62 to 0.81μm−α.The single-subject measurement of the IHTT yields estimates of axonal morphology that are consistent with histological values. However, improvement of the repeatability of the IHTT estimates is required to improve the specificity of the single-subject axonal morphology estimates.
Unique functional responses differentially map onto genetic subtypes of dopamine neurons
Authors: Azcorra Maite , Gaertner Zachary , Davidson Connor , Hayes Cooper K. , Ramakrishnan Charu , Fenno Lief , Kim Yoon Seok , Deisseroth Karl , Longnecker Richard , Awatramani Rajeshwar , Dombeck Daniel A. 
Published: December 2022

SummaryDopamine neurons are characterized by their response to unexpected rewards, but they also fire during movement and aversive stimuli. Dopamine neuron diversity has been observed based on molecular expression profiles; however, whether different functions map onto such genetic subtypes remains unclear. Here, we establish that three genetic dopamine subtypes within the substantia nigra pars compacta each have a unique set of responses to rewards, aversive stimuli, accelerations and decelerations, and these signaling patterns are highly-correlated between somas and axons within subtypes. Remarkably, reward responses were not detected in one subtype, which instead displayed acceleration-correlated signaling. Our findings establish a connection between functional and genetic dopamine subtypes and demonstrate that molecular expression patterns can serve as a common framework to dissect dopaminergic functions.
Is there an accurate and generalisable way to use soundscapes to monitor biodiversity?
Authors: Sethi Sarab S. , Bick Avery , Ewers Robert M. , Klinck Holger , Ramesh Vijay , Tuanmu Mao-Ning , Coomes David A. 
Published: December 2022

AbstractAcoustic monitoring has the potential to deliver biodiversity insight on vast scales. Whilst autonomous recording networks are being deployed across the world, existing analytical techniques struggle with generalisability. This limits the insight that can be derived from audio recordings in regions without ground-truth calibration data. By calculating 128 learned features and 60 soundscape indices of audio recorded during 8,023 avifaunal point counts from diverse ecosystems, we investigated the generalisability of soundscape approaches to biodiversity monitoring. Within each dataset, we found univariate correlations between several acoustic features and avian species richness, but features behaved unpredictably across datasets. Training a machine learning model on compound indices, we could predict species richness within datasets. However, models were uninformative when applied to datasets not used for training. We found that changes in soundscape features were correlated with changes in avian communities across all datasets. However, there were cases where avian communities changed without an associated shift in soundscapes. Our results suggest that there are no common hallmarks of biodiverse soundscapes across ecosystems. Therefore, soundscape monitoring should only be used when high quality ground-truth data exists for the region of interest, and in conjunction with more targeted and accurate in-person ecological surveys. By better understanding how to use interpret data reliably, we hope to unlock the scale at which acoustic monitoring can be used to deliver true impact for land managers and scientists monitoring biodiversity around the world.SummaryWhilst eco-acoustic monitoring has the potential to deliver biodiversity insight on vast scales, existing analytical approaches behave unpredictably across studies. We collated 8,023 audio recordings with paired manual avifaunal point counts to investigate whether soundscapes could be used to monitor biodiversity across diverse ecosystems. We found that neither univariate indices nor machine learning models were predictive of species richness across datasets, but soundscape change was consistently indicative of community change. Our findings indicate that there are no common features of biodiverse soundscapes, and that soundscape monitoring should be used cautiously and in conjunction with more reliable in-person ecological surveys.
Anti-Biofilm Potential of Nanonized Eugenol againstPseudomonas aeruginosa
Authors: Ghosh Sourav , Sett Upasana , Pal Anabadya , Nandy Sanchita , Nandy Susmita , Chakrabarty Soumajit , Das Abhijit , Bandopadhyay Pathikrit , Basu Tarakdas 
Published: December 2022

AbstractThis study dealt with nanonization of eugenol, a major phytochemical present in basil leaf, which has pharmacological potential as an anti-bacterial agent. Eugenol nanoparticle (ENP) was synthesized by simple ultrasonic cavitation method through emulsification of hydrophobic eugenol into hydrophilic gelatin. Thus, the nanonization process made the water-insoluble eugenol to water-soluble nano-eugenol, making the nano-form bioavailable. The average size of the ENPs was 20-30 nm. Entrapment efficiency of eugenol within gelatin cap was about 80% of the eugenol, that was used as precursor in the nanonization reaction.In vitrorelease of eugenol from gelatin cap was slow and sustained over a period of five days. The ENP had higher anti-biofilm potency than eugenol for both formation and eradication of biofilm, formed by clinically relevant pathogenPseudomonas aeruginosa. Minimal biofilm inhibitory concentration and minimal biofilm eradication concentration of ENPs were 2.0 and 4.0 mM respectively. In addition, the measurement ofP. aeruginosabiofilm biomass, biofilm pellicle formation, biofilm thickness, amount of biofilm-forming extra-polymeric substance, cell surface hydrophobicity, cell swarming and twitching efficiencies, cellular morphology and biofilm formation in catheter demonstrated that the anti-biofilm efficacy of nano-eugenol was 30-40% higher than that of bulk eugenol. Thus, ENP can be used as a potential drug against pneumonia, a chronic infection in lung caused byP. aeruginosa, which is difficult to treat with antibiotics, due to natural intrinsic resistance of biofilm-formed cells to most antibiotics. The overall actions of ENP have been presented in the figure 1.HighlightsNano-formulation of eugenol, an important phytochemical, by ultrasonic cavitation method, which was simple, time-saving, low-cost and eco-friendly.Nanonization made water-insoluble eugenol into water-soluble form with enhanced therapeutic efficacy.The eugenol nanoparticle (ENP) could inhibit formation of biofilm as well as facilitate eradication of pre-formed biofilm ofP. aeruginosa.Biofilm formation was found to be prevented significantly on ENP-coated catheter.Nano-eugenol may be used as a potential drug against bacterial diseases, caused by pseudomonal biofilm, which are difficult to treat by antibiotics.Nano-formulated eugenol may also be used as an effective anti-fouling agent for biomedical devices like contact lens, pace-maker, materials for organ transplantation etc. to prevent bacterial colonization.
Humoral responses against BQ.1.1 elicited after breakthrough infection and SARS-CoV-2 mRNA vaccination
Authors: Tauzin Alexandra , Benlarbi Mehdi , Medjahed Halima , Grégoire Yves , Perreault Josée , Gendron-Lepage Gabrielle , Gokool Laurie , Morisseau Chantal , Arlotto Pascale , Tremblay Cécile , Kaufmann Daniel E. , Valérie-Martel-Laferrière  , Levade Inès , Côté Marceline , de Serres Gaston , Bazin Renée , Finzi Andrés 
Published: December 2022

AbstractThe Omicron BQ.1.1 variant is now the major SARS-CoV-2 circulating strain in many countries. Because of the many mutations present in its Spike glycoprotein, this variant is resistant to humoral responses elicited by monovalent mRNA vaccines. With the goal to improve immune responses against Omicron subvariants, bivalent mRNA vaccines have recently been approved in several countries. In this study, we measure the capacity of plasma from vaccinated individuals, before and after a fourth dose of mono-or bivalent mRNA vaccine, to recognize and neutralize the ancestral (D614G) and the BQ.1.1 Spikes. Before and after the fourth dose, we observe a significantly better recognition and neutralization of the ancestral Spike. We also observe that fourth-dose vaccinated individuals who have been recently infected recognize and neutralize better the BQ.1.1 Spike, independently of the mRNA vaccine used, than donors who have never been infected or have an older infection. Our study supports that hybrid immunity, generated by vaccination and a recent infection, induces higher humoral responses than vaccination alone, independently of the mRNA vaccine used.
Exploring the determinants of wine export performance. Analyzing the importance of noneconomic performance
Authors: Santos Filipe , Dias Álvaro , Pereira Leandro , Costa Renato , Gonçalves Rui 
Published: December 2022

PurposeThe wine sector is a growing industry with an important share of the revenue resulting from export markets. Due to its cultural nature, wine exporting requires specific firm and managerial capabilities. As such, traditional approaches to the factors influencing export performance must integrate the specificities of wine as a product.Design/methodology/approachThis study, based on a sample of 93 wine producers, develops and tests, using structural equation modeling, specifically the partial least squares method, a conceptual model of the influence of internal factors, external factors and partner relationship capabilities in export performance.FindingsResults reveal that internal factors and partner relationships have an impact on the firm’s noneconomic performance which influences economic performance. It is also shown by the results that external factors do not affect the noneconomic performance or economic performance. Moreover, the results show the moderation effect of the noneconomic variable. Internal factors and relationship capabilities have an impact on economic performance considering the mediation effect of the noneconomic performance. Overall, firms’ internal factors and relationship capabilities are crucial to achieve better export performance for Portuguese wine companies.Originality/valueThis study combines the theories of SCP, resource-based view and relational or behavior perspective to present a novel approach to export performance by analyzing the external and internal dimensions of the firm in relation to both financial and nonfinancial performances.