bluuebunny/crossref_metadata_2025_split huggingface dataset:
The rapid expansion of offshore wind farms challenges the reliability of ICES-coordinated fish surveys—insights from the Baltic Sea
Authors: Haase S , von Dorrien C , Kaljuste O , Plantener N , Sepp E , Stelzenmüller V , Velasco A , Oesterwind D 
Published: August 2023

Abstract
Fish stock assessment and sustainable management requires that the whole distribution area of the managed fish stocks is representatively sampled. Along with an increasing demand for renewable energy in Europe, a growing number of areas are allocated for current and future offshore wind farms (OWF). Besides various unknown environmental effects, impacts on different stakeholder activities, such as fisheries, are considered during the implementation process. Scientific interests and tasks are, however, often marginalized. The current ban of commercial fisheries and fisheries monitoring in OWFs, in combination with an increase of OWF areas and habitat alteration within OWFs, might therefore bias the time series of scientific surveys and, thus, fisheries stock assessments. The expected increase in the overlap between OWFs and scientific fish surveys coordinated by the International Council for the Exploration of the Sea (ICES) in the Baltic Sea could result in, depending on the survey, up to 6.6–11.5% of the stations and transects being unavailable for sampling. We discuss the potential consequences for survey time series and stock assessments. Further, we aim to stimulate the discussion about the future of current standard surveys in the context of rapid expansions of OWFs, including the need for adaptations in survey design.
SARS-CoV-2 Reinfection Cases in a Household-Based Prospective Cohort in Rio de Janeiro
Authors: Penetra Stephanie L S , Santos Heloisa F P , Resende Paola Cristina , Bastos Leonardo Soares , da Silva Michele F B , Pina-Costa Anielle , Lopes Renata Serrano , Saboia-Vahia Leonardo , de Oliveira Any Caroline Alves , Pereira Elisa Cavalcante , Filho Fernando Medeiros , Wakimoto Mayumi D , Calvet Guilherme A , Fuller Trevon L , Whitworth Jimmy , Smith Christopher , Nielsen-Saines Karin , Carvalho Marilia Sá , Espíndola Otávio M , Guaraldo Lusiele , Siqueira Marilda M , Brasil Patricia 
Published: August 2023

Abstract
This was a household-based prospective cohort study conducted in Rio de Janeiro, in which people with laboratory-confirmed coronavirus disease 2019 (COVID-19) and their household contacts were followed from April 2020 through June 2022. Ninety-eight reinfections were identified, with 71 (72.5%) confirmed by genomic analyses and lineage definition in both infections. During the pre-Omicron period, 1 dose of any COVID-19 vaccine was associated with a reduced risk of reinfection, but during the Omicron period not even booster vaccines had this effect. Most reinfections were asymptomatic or milder in comparison with primary infections, a justification for continuing active surveillance to detect infections in vaccinated individuals. Our findings demonstrated that vaccination may not prevent infection or reinfection with severe acute respiratory syndrome coronavirus 2 (SARS CoV-2). Therefore we highlight the need to continuously update the antigenic target of SARS CoV-2 vaccines and administer booster doses to the population regularly, a strategy well established in the development of vaccines for influenza immunization programs.
Risk factors for carbapenem-resistant Acinetobacter baumannii (CRAB) bloodstream infections and related mortality in critically ill patients with CRAB colonization
Authors: Cogliati Dezza Francesco , Covino Sara , Petrucci Flavia , Sacco Federica , Viscido Agnese , Gavaruzzi Francesca , Ceccarelli Giancarlo , Raponi Gianmarco , Borrazzo Cristian , Alessandri Francesco , Mastroianni Claudio Maria , Venditti Mario , Oliva Alessandra 
Published: August 2023

Abstract

Background
Among MDR bacteria, carbapenem-resistant Acinetobacter baumannii (CRAB) is a major concern due to the limited therapeutic options. During the COVID-19 pandemic, a worrying increase in the spread of CRAB infections was reported.

Objectives
The study assessed the risk factors for CRAB bloodstream infection (BSI) in patients admitted to the ICU with CRAB colonization, and the related mortality risk factors.

Methods
We conducted a single-centre, observational, prospective study; all consecutive patients with CRAB colonization admitted to the ICU of a tertiary hospital in Rome from January 2021 to September 2022 were included in the study. Univariate and multivariate analyses were performed to investigate BSI and mortality risk factors.

Results
Overall, 129 patients were included in the study; 57 (44%) out of these developed BSI. In our study population, at the multivariable analysis the Charlson comorbidity index (CCI) (P = 0.026), COVID-19 (P &lt; 0.001), multisite colonization (P = 0.016) and the need for mechanical ventilation (P = 0.024) were risk factors independently associated with BSI development. Furthermore, age (P = 0.026), CCI (P &lt; 0.001), septic shock (P = 0.001) and Pitt score (P &lt; 0.001) were independently associated with mortality in the BSI patients. Instead, early appropriate therapy (P = 0.002) and clinical improvement within 72 h (P = 0.011) were shown to be protective factors.

Conclusions
In critically ill patients colonized by CRAB, higher CCI, multisite colonization and the need for mechanical ventilation were identified as risk factors for BSI onset. These predictors could be useful to identify patients at highest risk of BSI.
Artificial intelligence suppression as a strategy to mitigate artificial intelligence automation bias
Authors: Wang Ding-Yu , Ding Jia , Sun An-Lan , Liu Shang-Gui , Jiang Dong , Li Nan , Yu Jia-Kuo 
Published: August 2023

Abstract

Background
Incorporating artificial intelligence (AI) into clinics brings the risk of automation bias, which potentially misleads the clinician’s decision-making. The purpose of this study was to propose a potential strategy to mitigate automation bias.

Methods
This was a laboratory study with a randomized cross-over design. The diagnosis of anterior cruciate ligament (ACL) rupture, a common injury, on magnetic resonance imaging (MRI) was used as an example. Forty clinicians were invited to diagnose 200 ACLs with and without AI assistance. The AI’s correcting and misleading (automation bias) effects on the clinicians’ decision-making processes were analyzed. An ordinal logistic regression model was employed to predict the correcting and misleading probabilities of the AI. We further proposed an AI suppression strategy that retracted AI diagnoses with a higher misleading probability and provided AI diagnoses with a higher correcting probability.

Results
The AI significantly increased clinicians’ accuracy from 87.2%±13.1% to 96.4%±1.9% (P &lt; .001). However, the clinicians’ errors in the AI-assisted round were associated with automation bias, accounting for 45.5% of the total mistakes. The automation bias was found to affect clinicians of all levels of expertise. Using a logistic regression model, we identified an AI output zone with higher probability to generate misleading diagnoses. The proposed AI suppression strategy was estimated to decrease clinicians’ automation bias by 41.7%.

Conclusion
Although AI improved clinicians’ diagnostic performance, automation bias was a serious problem that should be addressed in clinical practice. The proposed AI suppression strategy is a practical method for decreasing automation bias.
Fir (Abies balsamea) (Pinales: Pinaceae) needle essential oil enhances the knockdown activity of select insecticides
Authors: Norris Edmund J , Bloomquist Jeffrey R 
Published: August 2023

Abstract
Because of the increased interest in plant essential oils (PEO) for both home pest control and personal bite protection, the ability of fir needle (Abies balsamea) oil to synergize the 1-h knockdown and 24-h toxicity of 9 different synthetic insecticides was evaluated. Fir needle oil strongly synergized knockdown of the neonicotinoids, clothianidin, and thiamethoxam (between 16- and 24-fold), as well as natural pyrethrins (12-fold), but had less effect with organophosphates and fipronil. For 24-h mortality, only pirimiphos-methyl was strongly synergized by fir needle oil pretreatment (18-fold). Chemical analysis and testing identified delta-3-carene is the most bioactive constituent, producing synergism similar to that of the whole oil. In fact, this constituent synergized the 24-h mortality of clothianidin to a higher degree than fir needle oil itself (4.9-fold vs. 2.4-fold). Synergism is unlikely to be mediated by effects on the nervous system, as fir needle oil caused no change in mosquito central nervous system firing at 100 ppm and did not synergize an inactive concentration of natural pyrethrins (10 nM). To better understand fir needle oil effects, we evaluated the ability of pretreatment with this oil to impact Aedes aegypti monooxygenase degradation of a model substrate, 7-ethoxycoumarin. Interestingly, both fir needle oil and delta-3-carene caused a significant increase in metabolic degradation of 7-ethoxycoumarin, perhaps indicating they upregulate oxidative metabolic processes. Such an action would explain why fir needle oil enhances knockdown, but not 24-h mortality for most of the insecticides studied here, whereas increased bioactivation would explain the synergism of pirimiphos-methyl toxicity.
Inter-rater Agreement in Classifying Music According to a Guided Imagery and Music Taxonomy
Authors: Bemman Brian , Bertelsen Lars Rye , Wärja Margareta , Bonde Lars Ole 
Published: August 2023

Abstract
Guided Imagery and Music (GIM) is a range of therapeutic practices in which clients listen to music selected by a trained practitioner with the aim of gaining cognitive insight through evoked imagery that may be beneficial in working through various inner experiences, pain, or trauma. It is crucial to this process that the chosen music is tailored to the client’s therapeutic goals and receptiveness. Wärja and Bonde [(2014). Music as co-therapist: Towards a taxonomy of music in therapeutic Music and Imagery work. Music and Medicine, 6(2), 16–27.] developed a taxonomy consisting of nine categories of musical-psychological characteristics and constructs (e.g., tempo, instrumentation, and mood) aligning with various therapeutic contexts (e.g., supporting and exploring) for helping GIM practitioners select appropriate music; however, its reliability has never before been assessed. In this paper, we present a listening study carried out with 63 GIM therapists and trainees, in order to measure the inter-rater agreement in (1) classifying 10 randomly selected pieces from 30 into one or more categories of the Wärja and Bonde [(2014). Music as co-therapist: Towards a taxonomy of music in therapeutic Music and Imagery work. Music and Medicine, 6(2), 16–27.] taxonomy, and (2) identifying for each piece heard one or more adjectives from the Hevner mood wheel that best characterize it. Our results indicate participants who utilized all categories but with slight to fair overall agreement; however, largely moderate agreement was reported for less musically complex pieces as well as across all pieces when considering only the three primary categories. Our findings not only support the continued use of the taxonomy and mood for helping select GIM music but also suggest the possible need for clearer descriptions in its subcategories and further training of practitioners who employ it in practice.
Comparative Genomic Analysis Identifies Great–Ape–Specific Structural Variants and Their Evolutionary Relevance
Authors: Zhou Bin , He Yaoxi , Chen Yongjie , Su Bing 
Published: August 2023

Abstract
During the origin of great apes about 14 million years ago, a series of phenotypic innovations emerged, such as the increased body size, the enlarged brain volume, the improved cognitive skill, and the diversified diet. Yet, the genomic basis of these evolutionary changes remains unclear. Utilizing the high-quality genome assemblies of great apes (including human), gibbon, and macaque, we conducted comparative genome analyses and identified 15,885 great ape-specific structural variants (GSSVs), including eight coding GSSVs resulting in the creation of novel proteins (e.g., ACAN and CMYA5). Functional annotations of the GSSV-related genes revealed the enrichment of genes involved in development and morphogenesis, especially neurogenesis and neural network formation, suggesting the potential role of GSSVs in shaping the great ape-shared traits. Further dissection of the brain-related GSSVs shows great ape-specific changes of enhancer activities and gene expression in the brain, involving a group of GSSV-regulated genes (such as NOL3) that potentially contribute to the altered brain development and function in great apes. The presented data highlight the evolutionary role of structural variants in the phenotypic innovations during the origin of the great ape lineage.
Identification of G-quadruplex structures in MALAT1 lncRNA that interact with nucleolin and nucleophosmin
Authors: Ghosh Arpita , Pandey Satya Prakash , Joshi Dheeraj Chandra , Rana Priya , Ansari Asgar Hussain , Sundar Jennifer Seematti , Singh Praveen , Khan Yasmeen , Ekka Mary Krishna , Chakraborty Debojyoti , Maiti Souvik 
Published: August 2023

Abstract
Nuclear-retained long non-coding RNAs (lncRNAs) including MALAT1 have emerged as critical regulators of many molecular processes including transcription, alternative splicing and chromatin organization. Here, we report the presence of three conserved and thermodynamically stable RNA G-quadruplexes (rG4s) located in the 3′ region of MALAT1. Using rG4 domain-specific RNA pull-down followed by mass spectrometry and RNA immunoprecipitation, we demonstrated that the MALAT1 rG4 structures are specifically bound by two nucleolar proteins, Nucleolin (NCL) and Nucleophosmin (NPM). Using imaging, we found that the MALAT1 rG4s facilitate the localization of both NCL and NPM to nuclear speckles, and specific G-to-A mutations that disrupt the rG4 structures compromised the localization of both NCL and NPM in speckles. In vitro biophysical studies established that a truncated version of NCL (ΔNCL) binds tightly to all three rG4s. Overall, our study revealed new rG4s within MALAT1, established that they are specifically recognized by NCL and NPM, and showed that disrupting the rG4s abolished localization of these proteins to nuclear speckles
Pot1b
−/− tumors activate G-quadruplex-induced DNA damage to promote telomere hyper-elongation
Authors: Takasugi Taylor , Gu Peili , Liang Fengshan , Staco Isabelle , Chang Sandy 
Published: August 2023

Abstract
Malignant cancers must activate telomere maintenance mechanisms to achieve replicative immortality. Mutations in the human Protection of Telomeres 1 (POT1) gene are frequently detected in cancers with abnormally long telomeres, suggesting that the loss of POT1 function disrupts the regulation of telomere length homeostasis to promote telomere elongation. However, our understanding of the mechanisms leading to elongated telomeres remains incomplete. The mouse genome encodes two POT1 proteins, POT1a and POT1b possessing separation of hPOT1 functions. We performed serial transplantation of Pot1b−/− sarcomas to better understand the role of POT1b in regulating telomere length maintenance. While early-generation Pot1b−/− sarcomas initially possessed shortened telomeres, late-generation Pot1b−/− cells display markedly hyper-elongated telomeres that were recognized as damaged DNA by the Replication Protein A (RPA) complex. The RPA-ATR-dependent DNA damage response at telomeres promotes telomerase recruitment to facilitate telomere hyper-elongation. POT1b, but not POT1a, was able to unfold G-quadruplex present in hyper-elongated telomeres to repress the DNA damage response. Our findings demonstrate that the repression of the RPA-ATR DDR is conserved between POT1b and human POT1, suggesting that similar mechanisms may underly the phenotypes observed in human cancers harboring human POT1 mutations.
Observing inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution
Authors: Marx Sinduja K , Mickolajczyk Keith J , Craig Jonathan M , Thomas Christopher A , Pfeffer Akira M , Abell Sarah J , Carrasco Jessica D , Franzi Michaela C , Huang Jesse R , Kim Hwanhee C , Brinkerhoff Henry , Kapoor Tarun M , Gundlach Jens H , Laszlo Andrew H 
Published: August 2023

Abstract
The genome of SARS-CoV-2 encodes for a helicase (nsp13) that is essential for viral replication and highly conserved across related viruses, making it an attractive antiviral target. Here we use nanopore tweezers, a high-resolution single-molecule technique, to gain detailed insight into how nsp13 turns ATP-hydrolysis into directed motion along nucleic acid strands. We measured nsp13 both as it translocates along single-stranded DNA or unwinds double-stranded DNA. Our data reveal nsp13’s single-nucleotide steps, translocating at ∼1000 nt/s or unwinding at ∼100 bp/s. Nanopore tweezers’ high spatiotemporal resolution enables detailed kinetic analysis of nsp13 motion. As a proof-of-principle for inhibition studies, we observed nsp13’s motion in the presence of the ATPase inhibitor ATPγS. We construct a detailed picture of inhibition in which ATPγS has multiple mechanisms of inhibition. The dominant mechanism of inhibition depends on the application of assisting force. This lays the groundwork for future single-molecule inhibition studies with viral helicases.
Temporal patterns in taste sensitivity
Authors: Costanzo Andrew 
Published: August 2023

Abstract
Individuals vary in their ability to taste, and some individuals are more sensitive to certain tastes than others. Taste sensitivity is a predictor of various factors, such as diet, eating behavior, appetite regulation, and overall health. Furthermore, taste sensitivity can fluctuate within an individual over short to long periods of time: for example, in daily (diurnal) cycles, monthly (menstrual) cycles (in females), and yearly (seasonal) cycles. Understanding these temporal patterns is important for understanding individual eating habits and food preferences, particularly in the context of personalized and precision nutrition. This review provides a summary of the literature on taste sensitivity patterns across 3 temporal dimensions: daily, monthly, and yearly. Good evidence for diurnal patterns has been observed for sweet taste and fat taste, although the evidence is limited to rodent studies for the latter. Obese populations showed limited variation to sweet and fat taste sensitivities over a day, with limited variation in sweet taste sensitivity being linked to insulin resistance. There were mixed observations of temporal variation in sensitivity to sour and umami tastes, and there were no patterns in sensitivity to bitter taste. Menstrual patterns in sweet taste sensitivity were consistent with patterns in food intake. Other taste modality investigations had mixed findings that had little agreement across studies. Hormonal changes in females influence taste sensitivity to some degree, although the overall patterns are unclear. Seasonal patterns have been less well studied, but there is weak evidence that sweet, salty, and bitter taste sensitivities change across seasons. Differences in seasonal taste patterns have been observed in subgroups susceptible to mental health disorders, requiring further investigation. Patterns of taste sensitivity are evident across multiple temporal dimensions, and more research is needed to determine the influence of these patterns on food intake. Dysregulation of these patterns may also be a marker of certain diseases or health conditions, warranting further investigation. Notably, the alimentary tastes (umami, fat, and carbohydrate) are underrepresented in this research area and require additional investigation.
Marital sorting, family output, and wealth inequality
Authors: Gahramanov Emin , Tang Xueli , Yang Zhenhai , Zhu Shenghao 
Published: August 2023

Abstract
In this article, we analytically model marital sorting, intergenerational transfers, and inequality in a household optimization model with uncertainty. We modify and apply a ‘sorting, reverse sorting’ numerical approach by Demirtas in the context of marriage market mating, illustrating the robustness of our analytical results. We show that the parameters of the family production function play an important role in driving the path of an economy’s inequality. One finding is that, under assortative mating, factor shares in the family production function positively affect inequality, while under disassortative mating, the relationship between the factor shares and inequality is U-shaped. This and other results that we obtain can stimulate further empirical research, holding potentially important policy implications.
Delayed and Attenuated Antibody Responses to Coronavirus Disease 2019 Vaccination With Poor Cross-Variant Neutralization in Solid-Organ Transplant Recipients—A Prospective Longitudinal Study
Authors: Liew May Y , Mathews Josh I , Li Amy , Singh Rohan , Jaramillo Salvador A , Weiss Zoe F , Bowman Kathryn , Ankomah Pierre O , Ghantous Fadi , Lewis Gregory D , Neuringer Isabel , Bitar Natasha , Lipiner Taryn , Dighe Anand S , Kotton Camille N , Seaman Michael S , Lemieux Jacob E , Goldberg Marcia B 
Published: August 2023

Abstract

Background
Therapeutically immunosuppressed transplant recipients exhibit attenuated responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines. To elucidate the kinetics and variant cross-protection of vaccine-induced antibodies in this population, we conducted a prospective longitudinal study in heart and lung transplant recipients receiving the SARS-CoV-2 messenger RNA (mRNA) 3-dose vaccination series.

Methods
We measured longitudinal serum antibody and neutralization responses against the ancestral and major variants of SARS-CoV-2 in SARS-CoV-2-uninfected lung (n = 18) and heart (n = 17) transplant recipients, non–lung-transplanted patients with cystic fibrosis (n = 7), and healthy controls (n = 12) before, during, and after the primary mRNA vaccination series.

Results
Among healthy controls, strong anti-spike responses arose immediately following vaccination and displayed cross-neutralization against all variants. In contrast, among transplant recipients, after the first 2 vaccine doses, increases in antibody concentrations occurred gradually, and cross-neutralization was completely absent against the Omicron B.1.1.529 variant. However, most (73%) of the transplant recipients had a significant response to the third vaccine dose, reaching levels comparable to those of healthy controls, with improved but attenuated neutralization of immune evasive variants, particularly Beta, Gamma, and Omicron. Responses in non–lung-transplanted patients with cystic fibrosis paralleled those in healthy controls.

Conclusions
In this prospective, longitudinal analysis of variant-specific antibody responses, lung and heart transplant recipients display delayed and defective responses to the first 2 SARS-CoV-2 vaccine doses but significantly augmented responses to a third dose. Gaps in antibody-mediated immunity among transplant recipients are compounded by decreased neutralization against Omicron variants, leaving many patients with substantially weakened immunity against currently circulating variants.