bluuebunny/crossref_metadata_2025_split huggingface dataset:
Suppressing simulation bias in multi-modal data using transfer learning
Authors: Kustowski Bogdan , Gaffney Jim A , Spears Brian K , Anderson Gemma J , Anirudh Rushil , Bremer Peer-Timo , Thiagarajan Jayaraman J , G Kruse Michael K , Nora Ryan C 
Published: March 2022

AbstractMany problems in science and engineering require making predictions based on few observations. To build a robust predictive model, these sparse data may need to be augmented with simulated data, especially when the design space is multi-dimensional. Simulations, however, often suffer from an inherent bias. Estimation of this bias may be poorly constrained not only because of data sparsity, but also because traditional predictive models fit only one type of observed outputs, such as scalars or images, instead of all available output data modalities, which might have been acquired and simulated at great cost. To break this limitation and open up the path for multi-modal calibration, we propose to combine a novel, transfer learning technique for suppressing the bias with recent developments in deep learning, which allow building predictive models with multi-modal outputs. First, we train an initial neural network model on simulated data to learn important correlations between different output modalities and between simulation inputs and outputs. Then, the model is partially retrained, or transfer learned, to fit the experiments; a method that has never been implemented in this type of architecture. Using fewer than 10 inertial confinement fusion experiments for training, transfer learning systematically improves the simulation predictions while a simple output calibration, which we design as a baseline, makes the predictions worse. We also offer extensive cross-validation with real and carefully designed synthetic data. The method described in this paper can be applied to a wide range of problems that require transferring knowledge from simulations to the domain of experiments.
Impact of an electronic health record alert on inappropriate prescribing of high-risk medications to patients with concurrent “do not give” orders
Authors: Smith Kirsten , Durant Karin M , Zimmerman Chris 
Published: March 2022

AbstractPurposeTo evaluate the effectiveness of clinical decision support (CDS) alerts tied to high-risk medications at a Michigan health system by determining the true prescriber action rate in response to select “do not give” (DNG) alerts.MethodsA retrospective review of prescriber actions in response to CDS alerts was conducted to evaluate the effectiveness of alerts designed to prevent prescribing of high-risk medications to patients with concurrent DNG orders. The primary endpoint was the overall action rate, determined by totaling orders cancelled within the alert display and orders modified shortly after an alert. The overall action rate was hypothesized to significantly exceed the action rate estimated on the basis of alert overrides alone. Following the initial review, changes were made to the alert format and preset documentation choices (“acknowledgement comments”), and it was hypothesized that these changes would increase the overall action rate. A repeat analysis was conducted to evaluate the impact of these changes.ResultsAcross a total of 506 CDS alerts over 14 months, 78% resulted in prescribers modifying orders to comply with alert recommendations. Prescribers cancelled orders in response to only 26% of alerts, often overriding alerts prior to modifying orders. Documentation of rationale or approval for overrides was inconsistent, and while requiring acknowledgement comments facilitated documentation of prescriber rationale, it did not consistently improve overall action rates.ConclusionThese findings demonstrate that override rates alone are not good markers for the true effectiveness of CDS alerts and support the need for frequent evaluation of alerts at the institutional level. CDS alerts remain a valuable tool to prevent inappropriate prescribing of high-risk medications and for promoting patient safety.
Memory Perfectionism is Associated with Persistent Memory Complaints after Concussion
Authors: Picon Edwina L , Todorova Evgenia V , Palombo Daniela J , Perez David L , Howard Andrew K , Silverberg Noah D 
Published: March 2022

Abstract

Objective
The etiology of persistent memory complaints after concussion is poorly understood. Memory perfectionism (highly valuing memory ability and intolerance of minor memory lapses) may help explain why some people report persistent subjective memory problems in the absence of corresponding objective memory impairment. This study investigated the relationship between memory perfectionism and persistent memory complaints after concussion.

Methods
Secondary analysis of baseline data from a randomized controlled trial. Adults (N = 77; 61% women) with persistent symptoms following concussion were recruited from outpatient specialty clinics. Participants completed the National Institutes of Health Toolbox Cognition Battery, Test of Memory Malingering-Trial 1, and questionnaires measuring memory perfectionism (Metamemory in Adulthood-Achievement subscale), forgetfulness and other postconcussion symptoms (Rivermead Postconcussion Symptoms Questionnaire; RPQ), and depression (Patient Health Questionnaire-2) at M = 17.8 weeks postinjury. Patients with versus without severe memory complaints (based on the RPQ) were compared.

Results
Memory perfectionism was associated cross-sectionally with severe memory complaint, after controlling for objective memory ability, overall cognitive ability, and depression (95% confidence interval for odds ratio = 1.11–1.40). Sensitivity analyses showed that this relationship did not depend on use of specific objective memory tests nor on inclusion of participants who failed performance validity testing. In a control comparison to test the specificity of identified relationships, memory perfectionism was not associated with severe fatigue (95% confidence interval for odds ratio = 0.91–1.07).

Conclusions
Memory perfectionism may be a risk factor for persistent memory symptoms after concussion, with potential relevance to the spectrum of functional cognitive disorders more broadly.
IL10 Secretion Endows Intestinal Human iNKT Cells with Regulatory Functions Towards Pathogenic T Lymphocytes
Authors: Burrello Claudia , Strati Francesco , Lattanzi Georgia , Diaz-Basabe Angelica , Mileti Erika , Giuffrè Maria Rita , Lopez Gianluca , Cribiù Fulvia Milena , Trombetta Elena , Kallikourdis Marinos , Cremonesi Marco , Conforti Francesco , Botti Fiorenzo , Porretti Laura , Rescigno Maria , Vecchi Maurizio , Fantini Massimo C , Caprioli Flavio , Facciotti Federica 
Published: March 2022

Abstract

Background and Aims
Invariant natural killer T [iNKT] cells perform pleiotropic functions in different tissues by secreting a vast array of pro-inflammatory and cytotoxic molecules. However, the presence and function of human intestinal iNKT cells capable of secreting immunomodulatory molecules such as IL-10 has never been reported so far. Here we describe for the first time the presence of IL10-producing iNKT cells [NKT10 cells] in the intestinal lamina propria of healthy individuals and of Crohn’s disease [CD] patients.

Methods
Frequency and phenotype of NKT10 cells were analysed ex vivo from intestinal specimens of Crohn’s disease [n = 17] and controls [n = 7]. Stable CD-derived intestinal NKT10 cell lines were used to perform in vitro suppression assays and co-cultures with patient-derived mucosa-associated microbiota. Experimental colitis models were performed by adoptive cell transfer of splenic naïve CD4+ T cells in the presence or absence of IL10-sufficient or -deficient iNKT cells. In vivo induction of NKT10 cells was performed by administration of short chain fatty acids [SCFA] by oral gavage.

Results
Patient-derived intestinal NKT10 cells demonstrated suppressive capabilities towards pathogenic CD4+ T cells. The presence of increased proportions of mucosal NKT10 cells associated with better clinical outcomes in CD patients. Moreover, an intestinal microbial community enriched in SCFA-producing bacteria sustained the production of IL10 by iNKT cells. Finally, IL10-deficient iNKT cells failed to control the pathogenic activity of adoptively transferred CD4+ T cells in an experimental colitis model.

Conclusions
These results describe an unprecedentd IL10-mediated immunoregulatory role of intestinal iNKT cells in controlling the pathogenic functions of mucosal T helper subsets and in maintaining the intestinal immune homeostasis.
Association between stressful life events and non-optimal lipid levels among women with hyperlipidaemia
Authors: Kuo Wan-chin , Ersig Anne L , Johnson Heather M , Brown Roger L , Oakley Linda D , Hagen Erika W , Barnet Jodi H , Peppard Paul E 
Published: March 2022

AbstractAimsPsychological stress has been linked to lipid dysregulation with noticeable gender differences, but it remains unclear whether women are more susceptible to non-optimal lipid levels than men, when experiencing stressful life events. This study aims to examine the association between stressful life events and non-optimal lipid levels among persons with hyperlipidaemia and whether the association differs between men and women.Methods and resultsA nested case–control study was performed using data from the Wisconsin Sleep Cohort (WSC) Study from 2011 to 2015, including 224 participants with hyperlipidaemia and without a history of myocardial infarction or heart failure. Among them, 63 participants with non-optimal LDL cholesterol or triglyceride levels were identified as cases, and 161 participants with optimal LDL cholesterol and triglyceride levels were identified as controls. Cases and controls were traced back to their self-reported life events collected through the Retirement and Sleep Trajectories study during 2010–11. The association between stressful life events and non-optimal lipid levels was examined using multivariable logistic regression; confounding effects were addressed using propensity score weighting and Mahalanobis distance matching; gender differences were examined using subgroup analysis. Results showed that a higher number of stressful life events during 2010–11 was associated with greater odds of non-optimal lipid levels during 2011–15 (odds ratio = 1.45, P = 0.03) among women with hyperlipidaemia, whereas the association was not significant among men with hyperlipidaemia (P = 0.910).ConclusionFuture studies are needed to examine the underlying mechanisms that explain gender differences in the association between stressful life events and non-optimal lipid levels.RegistrationClinicalTrials.gov NCT00005557
Chromosome-Level Genome Assembly of the Bioluminescent Cardinalfish Siphamia tubifer: An Emerging Model for Symbiosis Research
Authors: Gould A. L. , Henderson J. B. , Lam A. W. 
Published: March 2022

Abstract
The bioluminescent symbiosis involving the sea urchin cardinalfish Siphamia tubifer and the luminous bacterium Photobacterium mandapamensis is an emerging vertebrate model for the study of microbial symbiosis. However, little genetic data are available for the host, limiting the scope of research that can be implemented with this association. We present a chromosome-level genome assembly for S. tubifer using a combination of PacBio HiFi sequencing and Hi–C technologies. The final assembly was 1.2 Gb distributed on 23 chromosomes and contained 32,365 protein coding genes with a BUSCO score of 99%. A comparison of the S. tubifer genome to that of another nonluminous species of cardinalfish revealed a high degree of synteny, whereas a comparison to a more distant relative in the sister order Gobiiformes revealed the fusion of two chromosomes in the cardinalfish genomes. The complete mitogenome of S. tubifer was also assembled, and an inversion in the vertebrate WANCY tRNA genes as well as heteroplasmy in the length of the control region were discovered. A phylogenetic analysis based on whole the mitochondrial genome indicated that S. tubifer is divergent from the rest of the cardinalfish family, highlighting the potential role of the bioluminescent symbiosis in the initial divergence of Siphamia. This high-quality reference genome will provide novel opportunities for the bioluminescent S. tubifer–P. mandapamensis association to be used as a model for symbiosis research.
The Mnn10/Anp1-dependent N-linked outer chain glycan is dispensable for Candida albicans cell wall integrity
Authors: Dean Neta , Jones Rachel , DaSilva Justin , Chionchio Gregory , Ng Henry 
Published: March 2022

Abstract
Candida albicans cell wall glycoproteins, and in particular their mannose-rich glycans, are important for maintaining cellular integrity as well as host recognition, adhesion, and immunomodulation. The asparagine (N)-linked mannose outer chain of these glycoproteins is produced by Golgi mannosyltransferases (MTases). The outer chain is composed of a linear backbone of ∼50 α1,6-linked mannoses, which acts as a scaffold for addition of ∼150 or more mannoses in other linkages. Here, we describe the characterization of C. albicans OCH1, MNN9, VAN1, ANP1, MNN10, and MNN11, which encode the conserved Golgi MTases that sequentially catalyze the α1,6 mannose outer chain backbone. Candida albicans och1Δ/Δ, mnn9Δ/Δ, and van1Δ/Δ mutants block the earliest steps of backbone synthesis and like their Saccharomyces cerevisiae counterparts, have severe cell wall and growth phenotypes. Unexpectedly, and in stark contrast to S. cerevisiae, loss of Anp1, Mnn10, or Mnn11, which together synthesize most of the backbone, have no obvious deleterious phenotypes. These mutants were unaffected in cell morphology, growth, drug sensitivities, hyphal formation, and macrophage recognition. Analyses of secreted glycosylation reporters demonstrated that anp1Δ/Δ, mnn10Δ/Δ, and mnn11Δ/Δ strains accumulate glycoproteins with severely truncated N-glycan chains. This hypo-mannosylation did not elicit increased chitin deposition in the cell wall, which in other yeast and fungi is a key compensatory response to cell wall integrity breaches. Thus, C. albicans has evolved an alternate mechanism to adapt to cell wall weakness when N-linked mannan levels are reduced.
Evaluating the Working With Older Adults Scale With Clinical Psychology Doctoral Students
Authors: Graham Kirsten L , King Katherine D 
Published: March 2022

Abstract

Background and Objectives
The ongoing workforce shortage in geropsychology requires continued efforts to understand the factors that influence whether or not students choose to enter this field. The current study builds on prior research by replicating the Working with Older Adults Scale (WOAS) model. Further, the scale was expanded to add professional attitudes, adultist concerns, and number of known professionals in the field of aging.

Research Design and Methods
Graduate students in clinical psychology (n = 117) completed the WOAS and new items as part of a larger survey of graduate students in an American Psychological Association-accredited doctoral program. Structural equation modeling was used to first replicate the existing WOAS model and then expanded to include new antecedents in a second model.

Results
Results were largely similar to past research validating the WOAS, with the exception that Perceived Behavioral Control was not a significant predictor of Intention in this population. In the expanded model, new items improved the overall model fit and exhibited significant indirect paths to predict intention to work with older adults.

Discussion and Implications
These findings further validate use of the WOAS and expand scholarly understanding of the factors influencing the choice of a career in aging. Individuals positioned to encourage careers in aging may wish to address adultist concerns, explore attitudes about such careers, challenge unhelpful assumptions, and provide greater exposure and access to mentors in the field as part of recruitment efforts.
Autophagic pathway contributes to low-nitrogen tolerance by optimizing nitrogen uptake and utilization in tomato
Authors: Cao Jiajian , Zheng Xuelian , Xie Dongling , Zhou Hui , Shao Shujun , Zhou Jie 
Published: March 2022

Abstract
Autophagy is a primary process involved in the degradation and reuse of redundant or damaged cytoplasmic components in eukaryotes. Autophagy has been demonstrated to facilitate nutrient recycling and remobilization by delivering intracellular materials to the vacuole for degradation in plants under nutrient starvation. However, the role of autophagy in nitrogen (N) uptake and utilization remains unknown. Here, we report that the ATG6-dependent autophagic pathway regulates N utilization in tomato (Solanum lycopersicum) under low-nitrogen (LN) conditions. Autophagy-disrupted mutants exhibited weakened biomass production and N accumulation compared with wild-type (WT), while ATG6 overexpression promoted autophagy and biomass production under LN stress. The N content in atg6 mutants decreased while that in ATG6-overexpressing lines increased due to the control of N transporter gene expression in roots under LN conditions. Furthermore, ATG6-dependent autophagy enhanced N assimilation efficiency and protein production in leaves. Nitrate reductase and nitrite reductase activities and expression were compromised in atg6 mutants but were enhanced in ATG6-overexpressing plants under LN stress. Moreover, ATG6-dependent autophagy increased plant carbon fixation and photosynthetic capacity. The quantum yield of photosystem II, photosynthetic N use efficiency and photosynthetic protein accumulation were compromised in atg6 mutants but were restored in ATG6-overexpressing plants. A WT scion grafted onto atg6 mutant rootstock and an atg6 scion grafted onto WT rootstock both exhibited inhibited LN-induced autophagy and N uptake and utilization. Thus, ATG6-dependent autophagy regulates not only N uptake and utilization as well as carbon assimilation but also nutrient recycling and remobilization in tomato plants experiencing LN stress.
Construction of a collection of introgression lines of “Texas” almond DNA fragments in the “Earlygold” peach genetic background
Authors: Kalluri Naveen , Serra Octávio , Donoso José Manuel , Picañol Roger , Howad Werner , Eduardo Iban , Arús Pere 
Published: March 2022

AbstractPeach [Prunus persica L. Batsch] is one of the major temperate fruit tree species, the commercial materials of which have a low level of genetic variability. Almond [P. dulcis (Mill) DA Webb], a close relative of peach cultivated for its kernels, has a much higher level of diversity. The species are inter-compatible and often produce fertile hybrids, almond being a possible source of new genes for peach that could provide biotic and abiotic stress tolerance traits. In this paper we describe the development of a collection of peach-almond introgression lines (ILs) having a single fragment of almond (cv. Texas) in the peach background (cv. Earlygold). Lines with few introgressions were selected with markers from successive generations from a “Texas” × “Earlygold” F1 hybrid, initially using a set of SSRs and later with the 18 k peach SNP chip, allowing for the final extraction of 67 lines, 39 with almond heterozygous introgressions covering 99% of the genome, and 28 with homozygous introgressions covering 83% of the genome. As a proof of concept, four major genes and four quantitative characters were examined in the selected ILs giving results generally consistent with previous information on the genetics of these characters. This collection is the first of its kind produced in a woody perennial species and promises to be a valuable tool for genetic analyses, including dissection of quantitative traits, positional cloning, epistasis and as prebreeding material to introgress almond genes of interest into the peach commercial gene pool.
Clinical challenges treatingStenotrophomonas maltophiliainfections: an update
Authors: Mojica Maria F. , Humphries Romney , Lipuma John J. , Mathers Amy J. , Rao Gauri G. , Shelburne Samuel A. , Fouts Derrick E. , Van Duin David , Bonomo Robert A. 
Published: March 2022

AbstractStenotrophomonas maltophilia is a non-fermenting, Gram-negative bacillus that has emerged as an opportunistic nosocomial pathogen. Its intrinsic multidrug resistance makes treating infections caused by S. maltophilia a great clinical challenge. Clinical management is further complicated by its molecular heterogeneity that is reflected in the uneven distribution of antibiotic resistance and virulence determinants among different strains, the shortcomings of available antimicrobial susceptibility tests and the lack of standardized breakpoints for the handful of antibiotics with in vitro activity against this microorganism. Herein, we provide an update on the most recent literature concerning these issues, emphasizing the impact they have on clinical management of S. maltophilia infections.
Usability of HIV-1 Assay Using DBS for Early Infant Diagnosis in Field Settings in Kenya
Authors: Wandera Gloria , Bwana Priska , Mwau Matilu 
Published: March 2022

Abstract

Background
The Xpert HIV-1 Qualitative assay has been in use in Kenya since 2016 for infant diagnosis of HIV. Recently, the assay has been improved and its impact of this on ease of use is yet to be determined. We sought to determine the usability of Xpert® HIV-1 Qual XC assay using dried blood spots (DBS) for early infant diagnosis following this improvement.

Methods
This was a cross-sectional usability study undertaken in 2 selected health facilities in Kenya from October 2020 to February 2021. The laboratory technicians were retrained for this study. HIV-exposed infants were recruited with the consent of their parents. Patient data were recorded, and DBS samples were collected from the infants and tested for HIV on the improved assay. Each laboratory technician performing the assay documented usability characteristics on the provided questionnaire. Data on test errors were collected from the machine logs and analyzed using STATA for Windows.

Results
Of 313 test cartridges, 265 (84.66%) were successfully tested on the GeneXpert platform, and 263 valid outcomes were used for comparison with the Roche CAP/CTM HIV-1 Qualitative assay. The sensitivity, specificity, and accuracy of the Xpert HIV-1 Qualitative assay on DBS was 100%. Overall, 48 (15.34%) errors were recorded; 40 (83.33%) were user related and 8 (16.67%) were hardware related. All 4 (4/4, 100%) participating laboratory technicians said the assay had a simple workflow, was easy to use, the tests results were easy to interpret, and the assay throughput was sufficient for their workload.

Conclusions
The improved Xpert HIV-1 Qual XC assay is highly accurate, has a simple workflow, and is easy to use and easy to interpret. Both hardware- and user- related errors are common.