bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inversions of landslide strength as a proxy for subsurface weathering
Authors: Alberti Stefano , Leshchinsky Ben , Roering Josh , Perkins Jonathan , Olsen Michael J. 
Published: October 2022

AbstractDistributions of landslide size are hypothesized to reflect hillslope strength, and consequently weathering patterns. However, the association of weathering and critical zone architecture with mechanical strength properties of parent rock and soil are poorly-constrained. Here we use three-dimensional stability to analyze 7330 landslides in western Oregon to infer combinations of strength - friction angles and cohesion - through analysis of both failed and reconstructed landslide terrain. Under a range of conditions, our results demonstrate that the failure envelope that relates shear strength and normal stress in landslide terrain is nonlinear owing to an exchange in strength with landslide thickness. Despite the variability in material strength at large scales, the observed gradient in proportional cohesive strength with landslide thickness may serve as a proxy for subsurface weathering. We posit that the observed relationships between strength and landslide thickness are associated with the coalescence of zones of low shear strength driven by fractures and weathering, which constitutes a first-order control on the mechanical behavior of underlying soil and rock mass.
Precision mitochondrial DNA editing with high-fidelity DddA-derived base editors
Authors: Lee Seonghyun , Lee Hyunji , Baek Gayoung , Kim Jin-Soo 
Published: October 2022

AbstractBacterial toxin DddA-derived cytosine base editors (DdCBEs)—composed of split DddAtox (a cytosine deaminase specific to double-stranded DNA), custom-designed TALE (transcription activator-like effector) DNA-binding proteins, and a uracil glycosylase inhibitor—enable mitochondrial DNA (mtDNA) editing in human cells, which may pave the way for therapeutic correction of pathogenic mtDNA mutations in patients. The utility of DdCBEs has been limited by off-target activity, which is probably caused by spontaneous assembly of the split DddAtox deaminase enzyme, independent of DNA-binding interactions. We engineered high-fidelity DddA-derived cytosine base editors (HiFi-DdCBEs) with minimal off-target activity by substituting alanine for amino acid residues at the interface between the split DddAtox halves. The resulting domains cannot form a functional deaminase without binding of their linked TALE proteins at adjacent sites on DNA. Whole mitochondrial genome sequencing shows that, unlike conventional DdCBEs, which induce hundreds of unwanted off-target C-to-T conversions in human mtDNA, HiFi-DdCBEs are highly efficient and precise, avoiding collateral off-target mutations, and as such, they will probably be desirable for therapeutic applications.
Loss of NECTIN1 triggers melanoma dissemination upon local IGF1 depletion
Authors: Ablain Julien , Al Mahi Amira , Rothschild Harriet , Prasad Meera , Aires Sophie , Yang Song , Dokukin Maxim E. , Xu Shuyun , Dang Michelle , Sokolov Igor , Lian Christine G. , Zon Leonard I. 
Published: October 2022

AbstractCancer genetics has uncovered many tumor-suppressor and oncogenic pathways, but few alterations have revealed mechanisms involved in tumor spreading. Here, we examined the role of the third most significant chromosomal deletion in human melanoma that inactivates the adherens junction gene NECTIN1 in 55% of cases. We found that NECTIN1 loss stimulates melanoma cell migration in vitro and spreading in vivo in both zebrafish and human tumors specifically in response to decreased IGF1 signaling. In human melanoma biopsy specimens, adherens junctions were seen exclusively in areas with low IGF1 levels, but not in NECTIN1-deficient tumors. Our study establishes NECTIN1 as a major determinant of melanoma dissemination and uncovers a genetic control of the response to microenvironmental signals.
Clinical and molecular response to tebentafusp in previously treated patients with metastatic uveal melanoma: a phase 2 trial
Authors: Carvajal Richard D. , Butler Marcus O. , Shoushtari Alexander N. , Hassel Jessica C. , Ikeguchi Alexandra , Hernandez-Aya Leonel , Nathan Paul , Hamid Omid , Piulats Josep M. , Rioth Matthew , Johnson Douglas B. , Luke Jason J. , Espinosa Enrique , Leyvraz Serge , Collins Laura , Goodall Howard M. , Ranade Koustubh , Holland Chris , Abdullah Shaad E. , Sacco Joseph J. , Sato Takami 
Published: October 2022

AbstractIn patients with previously treated metastatic uveal melanoma, the historical 1 year overall survival rate is 37% with a median overall survival of 7.8 months. We conducted a multicenter, single-arm, open-label phase 2 study of tebentafusp, a soluble T cell receptor bispecific (gp100×CD3), in 127 patients with treatment-refractory metastatic uveal melanoma (NCT02570308). The primary endpoint was the estimation of objective response rate based on RECIST (Response Evaluation Criteria in Solid Tumours) v1.1. Secondary objectives included safety, overall survival, progression-free survival and disease control rate. All patients had at least one treatment-related adverse event, with rash (87%), pyrexia (80%) and pruritus (67%) being the most common. Toxicity was mostly mild to moderate in severity but was greatly reduced in incidence and intensity after the initial three doses. Despite a low overall response rate of 5% (95% CI: 2–10%), the 1 year overall survival rate was 62% (95% CI: 53–70%) with a median overall survival of 16.8 months (95% CI: 12.9–21.3), suggesting benefit beyond traditional radiographic-based response criteria. In an exploratory analysis, early on-treatment reduction in circulating tumour DNA was strongly associated with overall survival, even in patients with radiographic progression. Our findings indicate that tebentafusp has promising clinical activity with an acceptable safety profile in patients with previously treated metastatic uveal melanoma, and data suggesting ctDNA as an early indicator of clinical benefit from tebentafusp need confirmation in a randomized trial.
Brain de novo transcriptome assembly of a toad species showing polymorphic anti-predatory behavior
Authors: Chiocchio Andrea , Libro Pietro , Martino Giuseppe , Bisconti Roberta , Castrignanò Tiziana , Canestrelli Daniele 
Published: October 2022

AbstractUnderstanding the genomic underpinnings of antipredatory behaviors is a hot topic in eco-evolutionary research. Yellow-bellied toad of the genus Bombina are textbook examples of the deimatic display, a time-structured behavior aimed at startling predators. Here, we generated the first de novo brain transcriptome of the Apennine yellow-bellied toad Bombina pachypus, a species showing inter-individual variation in the deimatic display. Through Rna-Seq experiments on a set of individuals showing distinct behavioral phenotypes, we generated 316,329,573 reads, which were assembled and annotated. The high-quality assembly was confirmed by assembly validators and by aligning the contigs against the de novo transcriptome with a mapping percentage higher than 91.0%. The homology annotation with DIAMOND (blastx) led to 77,391 contigs annotated on Nr, Swiss Prot and TrEMBL, whereas the domain and site protein prediction made with InterProScan led to 4747 GO-annotated and 1025 KEGG-annotated contigs. The B. pachypus transcriptome described here will be a valuable resource for further studies on the genomic underpinnings of behavioral variation in amphibians.
First direct evidence of adult European eels migrating to their breeding place in the Sargasso Sea
Authors: Wright Rosalind M. , Piper Adam T. , Aarestrup Kim , Azevedo Jose M. N. , Cowan George , Don Andy , Gollock Matthew , Rodriguez Ramallo Sara , Velterop Randolph , Walker Alan , Westerberg Håkan , Righton David 
Published: October 2022

AbstractThe European eel (Anguilla anguilla) is critically endangered (according to the most recent IUCN assessment) and has suffered a 95% decline in recruitment since the 1980s, attributed in part to factors occurring during the marine phases of its life-cycle. As an adult, the European eel undertakes the longest spawning migration of all anguillid eels, a distance of 5000 to 10,000 km across the Atlantic Ocean to the Sargasso Sea. However, despite the passage of almost 100 years since Johannes Schmidt proposed the Sargasso Sea as the breeding place of European eels on the basis of larval surveys, no eggs or spawning adults have ever been sampled there to confirm this. Fundamental questions therefore remain about the oceanic migration of adult eels, including navigation mechanisms, the routes taken, timings of arrival, swimming speed and spawning locations. We attached satellite tags to 26 eels from rivers in the Azores archipelago and tracked them for periods between 40 and 366 days at speeds between 3 and 12 km day−1, and provide the first direct evidence of adult European eels reaching their presumed breeding place in the Sargasso Sea.
Birdsongs alleviate anxiety and paranoia in healthy participants
Authors: Stobbe E. , Sundermann J. , Ascone L. , Kühn S. 
Published: October 2022

AbstractThe present study investigated the effect of urban (traffic noise) vs. natural (birdsongs) soundscapes on mood, state paranoia, and cognitive performance, hypothesizing that birdsongs lead to significant improvements in these outcomes. An additional goal was to explore the differential impact of lower vs. higher diversity of the soundscapes by manipulating the number of different typical traffic sounds or songs of different bird species within the respective soundscapes. In a randomized online experiment, N = 295 participants were exposed to one out of four conditions for 6 min: traffic noise low, traffic noise high, birdsong low, and birdsong high diversity soundscapes. Before and after the exposure, participants performed a digit-span and dual n-back task, and filled out depression, anxiety, and paranoia questionnaires. The traffic noise soundscapes were associated with a significant increase in depression (small effect size in low, medium effect size in high diversity condition). Concerning the birdsong conditions, depression exclusively decreased after exposure to the high diversity soundscape (small effect size). Anxiety and paranoia significantly decreased in both birdsong conditions (medium effect sizes). For cognition, no effects were observed. In sum, the present study suggests that listening to birdsongs regardless of diversity improves anxiety, while traffic noise, also regardless of diversity, is related to higher depressiveness. Moreover, for the first time, beneficial, medium-sized effects of birdsong soundscapes were demonstrated, reducing paranoia. Overall, the results bear interesting implications for further research, such as actively manipulating soundscapes in different environments or settings (e.g., psychiatric wards) and testing their effect on subclinical or even clinical manifestations of anxiety and paranoia.
Constrained quantum optimization for extractive summarization on a trapped-ion quantum computer
Authors: Niroula Pradeep , Shaydulin Ruslan , Yalovetzky Romina , Minssen Pierre , Herman Dylan , Hu Shaohan , Pistoia Marco 
Published: October 2022

AbstractRealizing the potential of near-term quantum computers to solve industry-relevant constrained-optimization problems is a promising path to quantum advantage. In this work, we consider the extractive summarization constrained-optimization problem and demonstrate the largest-to-date execution of a quantum optimization algorithm that natively preserves constraints on quantum hardware. We report results with the Quantum Alternating Operator Ansatz algorithm with a Hamming-weight-preserving XY mixer (XY-QAOA) on trapped-ion quantum computer. We successfully execute XY-QAOA circuits that restrict the quantum evolution to the in-constraint subspace, using up to 20 qubits and a two-qubit gate depth of up to 159. We demonstrate the necessity of directly encoding the constraints into the quantum circuit by showing the trade-off between the in-constraint probability and the quality of the solution that is implicit if unconstrained quantum optimization methods are used. We show that this trade-off makes choosing good parameters difficult in general. We compare XY-QAOA to the Layer Variational Quantum Eigensolver algorithm, which has a highly expressive constant-depth circuit, and the Quantum Approximate Optimization Algorithm. We discuss the respective trade-offs of the algorithms and implications for their execution on near-term quantum hardware.
Whole farm planning raises profit despite burgeoning climate crisis
Authors: Muleke Albert , Harrison Matthew Tom , Eisner Rowan , de Voil Peter , Yanotti Maria , Liu Ke , Yin Xiaogang , Wang Weilu , Monjardino Marta , Zhao Jin , Zhang Feng , Fahad Shah , Zhang Yunbo 
Published: October 2022

AbstractThe climate crisis challenges farmer livelihoods as increasingly frequent extreme weather events impact the quantum and consistency of crop production. Here, we develop a novel paradigm to raise whole farm profit by optimising manifold variables that drive the profitability of irrigated grain farms. We build then invoke a new decision support tool—WaterCan Profit—to optimise crop type and areas that collectively maximise farm profit. We showcase four regions across a climate gradient in the Australian cropping zone. The principles developed can be applied to cropping regions or production systems anywhere in the world. We show that the number of profitable crop types fell from 35 to 10 under future climates, reflecting the interplay between commodity price, yield, crop water requirements and variable costs. Effects of climate change on profit were not related to long-term rainfall, with future climates depressing profit by 11–23% relative to historical climates. Impacts of future climates were closely related to crop type and maturity duration; indeed, many crop types that were traditionally profitable under historical climates were no longer profitable in future. We demonstrate that strategic whole farm planning of crop types and areas can yield significant economic benefits. We suggest that future work on drought adaptation consider genetic selection criteria more diverse than phenology and yield alone. Crop types with (1) higher value per unit grain weight, (2) lower water requirements and (3) higher water-use efficiency are more likely to ensure the sustainability and prosperity of irrigated grain production systems under future climates.
Low functional vulnerability of fish assemblages to coral loss in Southwestern Atlantic marginal reefs
Authors: Luza André L. , Quimbayo Juan P. , Ferreira Carlos E. L. , Floeter Sergio R. , Francini-Filho Ronaldo B. , Bender Mariana G. , Longo Guilherme O. 
Published: October 2022

AbstractMarginal reefs sustain coral assemblages under conditions considered suboptimal for most corals, resulting in low coral abundance. These reefs are inhabited by numerous fishes with a generally unknown degree of association with corals that might lead to the assumption that corals play minor roles in determining fish occurrence, when corals could be actually sustaining diverse and resilient assemblages. Using site-occupancy models fitted to data of 113 reef fish species of different life stages (adults and juveniles) from 36 reefs distributed across the Southwestern Atlantic (0.87–27.6°S) we first assessed fish assemblage’s response to coral and turf algal cover, and identified coral-associated fish. Then, we simulated the loss of coral-associated fishes and contrasted it with random losses, providing inferences on the resilience of fish assemblage’s functional trait space to species loss. The entire fish assemblage responded more positively to coral than to turf algae, with 42 (37%) species being identified as coral-associated fish. The simulated loss of coral-associated fish reduced up to 5% the functional trait space and was not different from the random loss. These results reveal that marginal reefs of Southwestern Atlantic reefs host resilient fish assemblages that might preserve fundamental ecological functions and ecosystem services even with coral declines.
Protein delivery to living cells by thermal stimulation for biophysical investigation
Authors: Torricella Francesco , Barbieri Letizia , Bazzurro Virginia , Diaspro Alberto , Banci Lucia 
Published: October 2022

AbstractStudying biomolecules in their native environment represents the ideal sample condition for structural biology investigations. Here we present a novel protocol which allows to delivery proteins into eukaryotic cells through a mild thermal stimulation. The data presented herein show the efficacy of this approach for delivering proteins in the intracellular environment of mammalian cells reaching a concentration range suitable for successfully applying biophysical methods, such as double electron electron resonance (DEER) measurements for characterising protein conformations.
Applicability of modified weibull extension distribution in modeling censored medical datasets: a bayesian perspective
Authors: Feroze Navid , Tahir Uroosa , Noor-ul-Amin Muhammad , Nisar Kottakkaran Sooppy , Alqahtani Mohammed S. , Abbas Mohamed , Ali Rashid , Jirawattanapanit Anuwat 
Published: October 2022

AbstractThere are some contributions analyzing the censored medical datasets using modifications of the conventional lifetime distribution; however most of the said contributions did not considered the modification of the Weibull distribution (WD). The WD is an important lifetime model. Due to its prime importance in modeling life data, many researchers have proposed different modifications of WD. One of the most recent modifications of WD is Modified Weibull Extension distribution (MWED). However, the ability of MWED to model the censored medical data has not yet been explored in the literature. We have explored the suitability of the model in modeling censored medical datasets. The analysis has been carried out using Bayesian methods under different loss functions and informative priors. The approximate Bayes estimates have been computed using Lindley’s approximation. Based on detailed simulation study and real life analysis, it has been concluded that Bayesian methods performed better as compared to maximum likelihood estimates. In case of small samples, the performance of Bayes estimates under ELF and informative prior was the best. However, in case of large samples, the choice of prior and loss function did not affect the efficiency of the results to a large extend. The MWED performed efficiently in modeling real censored datasets relating to survival times of the leukemia and bile duct cancer patients. The MWED was explored to be a very promising candidate model for modeling censored medical datasets.
Effects of odors on sleep quality in 139 healthy participants
Authors: Sabiniewicz Agnieszka , Zimmermann Pia , Ozturk Guliz Akin , Warr Jonathan , Hummel Thomas 
Published: October 2022

AbstractThe present study aimed to systematically examine whether laurinal, orange odor, and a specifically designed “perfume” influence sleep quality. During sleep, healthy participants (n = 139) were presented with odor or no odor through nose clips for fourteen consecutive nights (phase one). We collected physiological parameters together with subjective reports. Later on, longer lasting effects of this manipulation were examined for the following fourteen nights (phase two) without exposition to odors. Additionally, olfactory, cognitive and non-cognitive measures were conducted before phase one, between both phases and after phase two. One-way analyses of variance for repeated measures with nights and condition (1 vs 2) as the within-subject factor and odor condition (0, 1, 2 or 3) together with odor pleasantness rating as between-subject factor, was employed to analyse data. Overall, the present results demonstrated that the odor condition in comparison to control had no consistent effect on sleep in healthy participants which can be possibly explained by exposure to odors via nose clips. However, the analyses indicated that the individual pleasantness of odors enhanced the positive assessment of sleep quality. Altogether, the present results indicate that the subjective perception of an odor’s hedonic value appears to be crucial for sleep quality, not the odors themselves.
Using the Baidu index to understand Chinese interest in thyroid related diseases
Authors: Hu Qian , Mou Yuan-lin , Yin Ruo-yun , Tang Lei , Zhang Fan 
Published: October 2022

AbstractCommon thyroid diseases are hyperthyroidism, hypothyroidism, thyroiditis, thyroid tumor and so on. Baidu is currently the most widely used online search tool in China, has developed an internet search trends collection and analysis tool called the Baidu Index. The aim of the present study was to understand the trend and characteristics of public’s online attention to thyroid diseases, and to explore the value of Baidu Index in monitoring online retrieval behavior of thyroid-related information. Taking the period from January 1, 2011 to December 31, 2019 as the time range into consideration, we used the big data analysis tool of Baidu Index and took “thyroid nodules”, “thyroid cancer”, “thyroiditis” “hyperthyroidism” and “hypothyroidism” as the keywords, the data of “search index” and “media index” were recorded on a weekly basis, and all information were aggregated into quarterly and annual to generate the final data which was carried out for secondary analysis. Pearson correlation analysis was used to analyze the correlation between the search index of keywords and the year. One-way Analysis of Variance was used to analyze the differences between search index and media index. Among the five keywords, thyroid nodule search index had the highest growth rate (640%), followed by thyroid cancer (298%). The media’s attention to thyroid diseases had been declining year by year. Unlike the public’s attention, the media index of hyperthyroidism was significantly higher than other keywords. Over the past nine years, the public's attention to thyroid-related diseases has been increasing gradually. Baidu Index is an effective tool to track the health information query behavior of Chinese internet users, which can provide a cost-effective supplement to traditional monitoring system.
Severity of underweight affects the development of nontuberculous mycobacterial pulmonary disease; a nationwide longitudinal study
Authors: Kang Ji Young , Han Kyungdo , Kim Mee Kyoung 
Published: October 2022

AbstractRegarding to known association between underweight and non-tuberculous mycobacterial pulmonary disease (NTM-PD), the underweight was simply categorized as body mass index (BMI) less than 18.5 kg/m2, mainly because of its low prevalence. We aimed to better define the impact of BMI severity on NTM-PD development. We analysed health data from 4,332,529 individuals examined in 2009 and followed up until December 2017 to determine the incidence of NTM-PD. Based on the BMI in kg/m2, the population was categorized into mild (17.00–18.49), moderate (16.00–16.99), and severe underweight (< 16.00) groups. Using Cox proportional-hazards analyses, hazard ratios for NTM-PD were calculated according to the severity of underweight in reference to normal BMI (18.50–22.99). Over a median follow-up of 5.6 ± 1.2 years, 6223 participants developed NTM-PD. Risk of NTM-PD increased significantly with the severity of underweight: multivariate adjusted hazard ratios (95% confidence intervals) for mild, moderate, and severe underweight were 2.34 (2.17–2.52), 3.50 (3.07–3.99), and 4.35 (3.63–5.21), respectively. In subgroup analysis, being younger (< 65 years old) or male exacerbated the effect of severe underweight on the risk of NTM-PD. This study proved that as underweight categories became more severe, the risk of NTM-PD increased proportionally.