bluuebunny/crossref_metadata_2025_split huggingface dataset:
Context-dependent choice and evaluation in real-world consumer behavior
Authors: Otto A. Ross , Devine Sean , Schulz Eric , Bornstein Aaron M. , Louie Kenway 
Published: April 2022

AbstractA body of work spanning neuroscience, economics, and psychology indicates that decisionmaking is context-dependent, which means that the value of an option depends not only on the option in question, but also on the other options in the choice set—or the ‘context’. While context effects have been observed primarily in small-scale laboratory studies with tightly constrained, artificially constructed choice sets, it remains to be determined whether these context effects take hold in real-world choice problems, where choice sets are large and decisions driven by rich histories of direct experience. Here, we investigate whether valuations are context-dependent in real-world choice by analyzing a large restaurant rating dataset (Yelp.com) as well as two independent replication datasets which provide complementary operationalizations of restaurant choice. We find that users make fewer ratings-maximizing choices in choice sets with higher-rated options—a hallmark of context-dependent choice— and that post-choice restaurant ratings also varied systematically with the ratings of unchosen restaurants. Furthermore, in a follow-up laboratory experiment using hypothetical choice sets matched to the real-world data, we find further support for the idea that subjective valuations of restaurants are scaled in accordance with the choice context, providing corroborating evidence for a general mechanistic-level account of these effects. Taken together, our results provide a potent demonstration of context-dependent choice in real-world choice settings, manifesting both in decisions and subjective valuation of options.
The E3/E4 ubiquitin ligase UFD-2 mediates negative feedback on Raf protein stability
Authors: Townley Robert , Deniaud Augustin , Stacy Kennedy S. , Rodriguez Torres Claudia S. , Cheraghi Fatemeh , de la Cova Claire C. 
Published: April 2022

AbstractSignaling by the kinase cascade comprised of Raf, MEK, and ERK is critical for animal development; moreover, its inappropriate activation is commonly found in human malignancies. In a genetic screen for factors that control signaling by the Caenorhabditis elegans Raf ortholog LIN-45, we found that it is negatively regulated by the E3/E4 ubiquitin ligase UFD-2. Both UFD-2 and its partner, the ATP-dependent unfoldase CDC-48, were required for degradation of LIN-45 protein. Our structure-function studies showed that disruption of LIN-45 domains that mediate protein interactions and complex formation, including the Ras binding domain, cysteine-rich domain, or C-terminus, allow for UFD-2-independent degradation. We propose a model whereby UFD-2 mediates a novel step of Raf degradation, by acting with the CDC-48 unfoldase machinery to extract Raf from multiprotein complexes.One-Sentence SummaryRaf kinase complexes are degraded by the UFD-2 ubiquitin ligase and CDC-48 unfoldase during Raf-MEK-ERK signal transduction.
Differential genetic strategies ofBurkholderia vietnamiensisandParaburkholderia kururiensisfor root colonization ofOryza sativassp.japonicaand ssp.indica, as revealed by Tn-seq
Authors: Wallner Adrian , Busset Nicolas , Lachat Joy , Guigard Ludivine , King Eoghan , Rimbault Isabelle , Mergaert Peter , Béna Gilles , Moulin Lionel 
Published: April 2022

AbstractBurkholderia vietnamiensisLMG10929 (Bv) andParaburkholderia kururiensisM130 (Pk) are bacterial rice growth-promoting models. Besides this common ecological niche, species of theBurkholderiagenus are also found as opportunistic human pathogens whileParaburkholderiaare mostly environmental and plant-associated species. Here, we compared the genetic strategies used byBvandPkto colonize two subspecies of their common host,Oryza sativa ssp. japonica(cv. Nipponbare) andssp. indica(cv. IR64). We used high-throughput screening of transposon insertional mutant libraries (Tn-seq) to infer which genetic elements have the highest fitness contribution during root surface colonization at 7 days post inoculation. Overall, we detected twice more genes inBvinvolved in rice roots colonization compared toPk, including genes contributing to the tolerance of plant defenses, which suggests a stronger adverse reaction of rice towardsBvcompared toPk. For both strains, the bacterial fitness depends on a higher number of genes when colonizingindicarice compared tojaponica. These divergences in host pressure on bacterial adaptation could be partly linked to the cultivar’s differences in nitrogen assimilation. We detected several functions commonly enhancing root colonization in both bacterial strains e.g., Entner-Doudoroff (ED) glycolysis. Less frequently and more strain-specifically, we detected functions limiting root colonization such as biofilm production inBvand quorum sensing inPk.The involvement of genes identified through the Tn-seq procedure as contributing to root colonization i.e., ED pathway, c-di-GMP cycling and cobalamin synthesis, was validated by directed mutagenesis and competition with WT strains in rice root colonization assays.ImportanceBurkholderiaceae are frequent and abundant colonizers of the rice rhizosphere and interesting candidates to investigate for growth promotion. Species ofParaburkholderiahave repeatedly been described to stimulate plant growth. However, the closely relatedBurkholderiagenus hosts both beneficial and phytopathogenic species, as well as species able to colonize animal hosts and cause disease in humans. We need to understand to what extent the bacterial strategies used for the different biotic interactions differ depending on the host and if strains with agricultural potential could also pose a threat towards other plant hosts or humans. To start answering these questions, we used here transposon sequencing to identify genetic traits inBurkholderia vietnamiensisandParaburkholderia kururiensisthat contribute to the colonization of two different rice varieties. Our results revealed large differences in the fitness gene sets between the two strains and between the host plants, suggesting a strong specificity in each bacterium-plant interaction.
COVID-19 vaccine effectiveness against SARS-CoV-2 infection in the United States prior to the Delta and Omicron-associated surges: a retrospective cohort study of repeat blood donors
Authors: Grebe Eduard , Yu Elaine A. , Bravo Marjorie D. , Welte Alex , Bruhn Roberta L. , Stone Mars , Green Valerie , Williamson Phillip C. , Feldstein Leora R. , Jones Jefferson M. , Busch Michael P. , Custer Brian 
Published: April 2022

ABSTRACTTo inform public health policy, it is critical to monitor COVID-19 vaccine effectiveness (VE), including against acquiring infection. We estimated VE using a retrospective cohort study among repeat blood donors who donated during the first half of 2021, demonstrating a viable approach for monitoring of VE via serological surveillance. Using Poisson regression, we estimated overall VE was 88.8% (95% CI: 86.2–91.1), adjusted for demographic covariates and variable baseline risk. Time since first reporting vaccination, age, race-ethnicity, region, and calendar time were statistically significant predictors of incident infection. Studies of VE during periods of Delta and Omicron spread are underway.
Can We Really Trust the Findings of the COVID-19 Research? Quality Assessment of Randomized Controlled Trials Published on COVID-19
Authors: Joshy Athira S , Thomas Christy , Surendran Saphal , Undela Krishna 
Published: April 2022

AbstractObjectiveTo evaluate the quality of randomized controlled trials (RCTs) published on Coronavirus Disease-19 (COVID-19) and to investigate the reasons behind compromising the quality, if found.MethodsA systematic literature search was performed in PubMed, Google Scholar, and Cochrane CENTRAL to identify the Randomized Controlled Trails published on Coronavirus Disease-19 between 1st Dec 2019 to 31st Aug 2021. Research articles met with study criteria were included in the study. Assessment of quality of randomized controlled trials was done using modified Jadad scale.Results21,259 records of randomized controlled trials were identified through database searching, out of which 90 randomized controlled trials were included in the study and, 34 (37.8%) were of high-quality, 46 (51.1%) were of moderate quality, and 10 (11.1 %) were of low-quality studies. There were 40 (44.4%), 38 (42.2%), and 12 (13.3%) randomized controlled trials published in the early, middle, and late terms with Jadad score 5.12±1.67, 5.34±1.32, and 5.68±1.50 respectively (P=0.52). When comparing the blinding status, appropriate blinding, and methods to evaluate adverse events in randomized controlled trials with modified Jadad score, a significant difference was observed (P<0.001). A significant moderate positive correlation was found between the impact factor of the journal and the modified Jadad scale score (R2= 0.48, P<0.001).ConclusionFindings from our study indicate that accelerated publication of Coronavirus Disease-19 researches along with the fast-track review process has resulted in lowering study quality scores. With the emergence of stronger evidence, Coronavirus Disease-19 clinical studies with lower methodological quality should be revisited.Impacts on practiceThere have been numerous sacrifices and tragedies in the clinical response to covid-19. Revising the quality of randomized controlled trials published on COVID-19 as we enter the third wave of the pandemic and beyond, will improve the evidence-based practice of medications for clinical pharmacy services.COVID-19 Patients will benefit from evidence-based pharmaceutical care through reduced drug-related problems.
Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021
Authors: Vasylyeva Tetyana I. , Fang Courtney E. , Su Michelle , Havens Jennifer L. , Parker Edyth , Wang Jade C. , Zeller Mark , Yakovleva Anna , Hassler Gabriel W. , Chowdhury Moinuddin A. , Andersen Kristian G. , Hughes Scott , Wertheim Joel O. 
Published: April 2022

ABSTRACTBackgroundMonitoring the emergence and spread of SARS-CoV-2 variants is an important public health objective. Travel restrictions, aimed to prevent viral spread, have major economic consequences and unclear effectiveness despite considerable research. We investigated the introduction and establishment of the Gamma variant in New York City (NYC) in 2021.MethodsWe performed phylogeographic analysis on 15,967 Gamma sequences available on GISAID and sampled between March 10th through May 1st, 2021, to identify geographic sources of Gamma lineages introduced into NYC. We identified locally circulating Gamma transmission clusters and inferred the timing of their establishment in NYC.FindingsWe identified 16 phylogenetically-distinct Gamma clusters established in NYC (cluster sizes ranged 2-108 genomes). Most of the NYC clusters were introduced from Florida and Illinois; only one was introduced from outside the United States (US). By the time the first Gamma case was reported by genomic surveillance in NYC on March 10th, the majority (57%) of circulating Gamma lineages had already been established in the city for at least two weeks.InterpretationDespite the expansion of SARS-CoV-2 genomic surveillance in NYC, there was a substantial gap between Gamma variant introduction and establishment in January/February 2021, and its identification by genomic surveillance in March 2021. Although travel from Brazil to the US was restricted from May 2020 through the end of the study period, this restriction did not prevent Gamma from becoming established in NYC as most introductions occurred from domestic locations.
The Validity of the Parsley Symptom Index: an e-PROM designed for Telehealth
Authors: Williams Hants , Steinberg Sarah , Leon Kendall , O’Shea Catherine , Berzin Robin , Hagg Heather 
Published: April 2022

AbstractBackground / PurposeThe Parsley Symptom Index (PSI) is a recently developed symptom assessment for adults with chronic disease in telehealth settings. The purpose of this study was to validate the PSI against the Self-Rated Health (SRH) item.Materials and MethodsThis prospective cohort study took place from January 15, 2021 to December 15, 2021 among a sample of 10,519 adult patients at Parsley Health, a subscription based holistic medical practice. The PSI and the SRH were completed by patients via an online portal. The association between the PSI and SRH was assessed via polyserial and polychoric correlations, while weighted kappa scores provided information related to agreement between the PSI and SRH.ResultsFrom 22,748 responses, there were moderate levels of association (polyserial r=0.51; polychoric r=0.52) and agreement (weighted □ = 0.46) between the PSI and SRH. In total 74.2% (16865) of responses between the PSI and SRH were relatively congruent while 36.2% (8229) were literally congruent.ConclusionsThe PSI demonstrates validity with the SRH for adults with chronic disease in a telehealth setting.
Linking Genotype to Phenotype: Further Exploration of Mutations in SARS-CoV-2 Associated with Mild or Severe Outcomes
Authors: Agarwal Roshna , Leblond Tyler , McAuley Erin M , Maier Ezekiel J , Skarzynski Martin , Voss Jameson D , Sozhamannan Shanmuga 
Published: April 2022

SummaryWe previously interrogated the relationship between SARS-CoV-2 genetic mutations and associated patient outcomes using publicly available data downloaded from GISAID in October 2020 [1]. Using high-level patient data included in some GISAID submissions, we were able to aggregate patient status values and differentiate between severe and mild COVID-19 outcomes. In our previous publication, we utilized a logistic regression model with an L1 penalty (Lasso regularization) and found several statistically significant associations between genetic mutations and COVID-19 severity. In this work, we explore the applicability of our October 2020 findings to a more current phase of the COVID-19 pandemic.Here we first test our previous models on newer GISAID data downloaded in October 2021 to evaluate the classification ability of each model on expanded datasets. The October 2021 dataset (n=53,787 samples) is approximately 15 times larger than our October 2020 dataset (n=3,637 samples). We show limitations in using a supervised learning approach and a need for expansion of the feature sets based on progression of the COVID-19 pandemic, such as vaccination status. We then re-train on the newer GISAID data and compare the performance of our two logistic regression models. Based on accuracy and Area Under the Curve (AUC) metrics, we find that the AUC of the re-trained October 2021 model is modestly decreased as compared to the October 2020 model. These results are consistent with the increased emergence of multiple mutations, each with a potentially smaller impact on COVID-19 patient outcomes. Bioinformatics scripts used in this study are available at https://github.com/JPEO-CBRND/opendata-variant-analysis. As described in Voss et al. 2021, machine learning scripts are available at https://github.com/Digital-Biobank/covid_variant_severity.
Sustained morphine delivery suppresses bone formation and alters metabolic and circulating miRNA profiles in male C57BL/6J mice
Authors: Carvalho Adriana Lelis , Brooks Daniel J , Barlow Deborah , Langlais Audrie L. , Morrill Breanna , Houseknecht Karen L. , Bouxsein Mary L. , Lian Jane B , King Tamara , Farina Nicholas H , Motyl Katherine J 
Published: April 2022

ABSTRACTOpioid use is detrimental to bone health, causing both indirect and direct effects on bone turnover. While the mechanisms of these effects are not entirely clear, recent studies have linked chronic opioid use to alterations in circulating miRNAs. Our aim was to develop a model of opioid-induced bone loss to understand bone turnover and identify candidate miRNA-mediated regulatory mechanisms. We evaluated the effects of sustained morphine treatment on the skeleton, metabolism, and body composition of male and female C57BL/6J mice by treating with vehicle (0.9% saline) or morphine (18 mg/kg) using subcutaneous osmotic minipumps for 25 days. Morphine-treated mice had higher energy expenditure and respiratory quotient, indicating a shift toward carbohydrate metabolism. Microcomputed tomography (µCT) analysis indicated that male mice treated with morphine had reduced trabecular bone volume fraction (Tb.BV/TV) (15%) and Tb. bone mineral density (BMD) (14%) in the distal femur compared to vehicle. Conversely, bone microarchitecture was not changed in females after morphine treatment. Histomorphometric analysis demonstrated that in males, morphine reduced bone formation rate compared to vehicle, but osteoclast parameters were not different. Furthermore, morphine reduced bone formation marker gene expression in the tibia of males (Bglap and Dmp1). Circulating miRNA profile changes were evident in males, with 14 differentially expressed miRNAs associated with morphine treatment. Target analysis indicated hypoxia inducible factor (HIF) signaling pathway was targeted by miR-223-3p and fatty acid metabolism by miR-484, - 223-3p, and -328-3p. In summary, we have established a model where morphine leads to a lower trabecular bone formation in males. Further, understanding the mechanisms of bone loss from opioid treatment will be important for improving management of the adverse effects of opioids on the skeleton.
A Genome-Scale Metabolic Model of Marine HeterotrophVibrio splendidussp. 1A01
Authors: Iffland-Stettner Arion , Okano Hiroyuki , Gralka Matti , Guessous Ghita , Amarnath Kapil , Cordero Otto X. , Hwa Terence , Bonhoeffer Sebastian 
Published: April 2022

AbstractWhile theVibrio splendidusspecies is best known as an opportunistic pathogen in oysters, theVibrio splendidussp. 1A01 strain was first identified as an early colonizer of synthetic chitin particles incubated in seawater. To gain a better understanding of its metabolism, a genome-scale metabolic model (GSMM) ofV. splendidussp. 1A01 was reconstructed. GSMMs enable us to simulate all metabolic reactions in a bacterial cell using Flux Balance Analysis. A draft model was built using an automated pipeline from BioCyc. Manual curation was then performed based on experimental data, in part by gap-filling metabolic pathways and tailoring the model’s biomass reaction toV. splendidussp. 1A01. The challenges of building a metabolic model for a marine microorganism likeV. splendidussp. 1A01 are described.
Probing neuronal functions with precise and targeted laser ablation in the living cortex: reply
Authors: Cheng Zongyue , Lin Jianian , Han Yiyong , Wei Bowen , Lai Baoling , Li Baoming , Cui Meng , Gan Wen-Biao 
Published: April 2022

AbstractIn the comment on the article [Optica 8, 12 (2021)], the authors performed theoretical calculation to show that with a 1.1 NA objective and 140 fs laser pulses with single pulse energy of 2.2 nJ, and 80 MHz repetition rate, the focal point temperature rises 0.3 K and reaches equilibrium after 100 μs in water. They suggest that the damage to brain tissue by laser could not be caused by thermal effects but rather by plasma-mediated chemical effects. To quantify the thermal accumulation due to the fs laser illumination in living animals, we used a thermocouple sensor to measure the temperature change in the vicinity of the laser focus at a depth of 300 μm in the adult mouse cortex. Our results show that at 930 nm wavelength, 25 μm from the laser focus, 19-300 mW laser can all lead to a brain tissue temperature rise of more than 0.3 K at 1 second and the maximum equilibrium temperature rise of more than 28 K. These experimental measurements are significantly higher than theoretically calculated values in the comment. These results suggest that the thermal accumulation effect of focused low-energy pulses from fs laser oscillators could contribute significantly to the collateral damage in the living brain.
rox: A statistical model for regression with missing values
Authors: Buyukozkan Mustafa , Benedetti Elisa , Krumsiek Jan 
Published: April 2022

AbstractHigh-dimensional omics datasets frequently contain missing data points, which typically occur due to concentrations below the limit of detection (LOD) of the profiling platform. The presence of such missing values significantly limits downstream statistical analysis and result interpretation. Two common techniques to deal with this issue include the removal of samples with missing values, and imputation approaches which substitute the missing measurements with reasonable estimates. Both approaches, however, suffer from various shortcomings and pitfalls. In this paper, we present “rox”, a novel statistical model for the analysis of omics data with missing values without the need for imputation. The model directly incorporates missing values as “low” concentrations into the calculation. We show the superiority of rox over common approaches on simulated data and on six metabolomics datasets. Fully leveraging the information contained in LOD-based missing values, rox provides a powerful tool for the statistical analysis of omics data.
Cross-activation of the FGF, TGF-β and WNT pathways constrains BMP4-mediated induction of the Totipotent state in mouse embryonic stem cells
Authors: Meharwade Thulaj , Joumier Loïck , Parisotto Maxime , Huynh Vivian , da Rocha Edroaldo Lummertz , Malleshaiah Mohan 
Published: April 2022

SUMMARYCell signaling induced cell fate determination is central to stem cell and developmental biology. Embryonic stem cells (ESC) are an attractive model for understanding the relationship between cell signaling and cell fates. Cultured mouse ESCs can exist in multiple cell states resembling distinct stages of early embryogenesis, such as Totipotent, Pluripotent, Primed and Primitive Endoderm. The signaling mechanisms regulating the Totipotent state acquisition and coexistence of these states are poorly understood. Here we identify BMP4 as an inducer of the Totipotent state. However, we discovered that BMP4-mediated induction of the Totipotent state is constrained by the cross-activation of FGF, TGF-β and WNT pathways. We exploited this finding to enhance the proportion of Totipotent cells in ESCs by rationally inhibiting these cross-activated pathways using small molecules. Single-cell mRNA-sequencing further revealed that induction of the Totipotent state is accompanied by the suppression of both the Primed and Primitive Endoderm states. Furthermore, the reprogrammed Totipotent cells generated in culture have a molecular and functional resemblance to Totipotent cell stages of preimplantation embryos. Our findings reveal a novel BMP4 signaling mechanism in ESCs to regulate multiple cell states, potentially significant for managing stem cell heterogeneity in differentiation and reprogramming.