bluuebunny/crossref_metadata_2025 huggingface dataset:
Draft genome sequences of strains CBS6241 and CBS6242 of the basidiomycetous yeastFilobasidium floriforme
Authors: Guerreiro Marco Alexandre , Ahrendt Steven , Pangilinan Jasmyn , Chen Cindy , Yan Mi , Lipzen Anna , Barry Kerrie , Grigoriev Igor V , Begerow Dominik , Nowrousian Minou
Published: November 2021

The Tremellomycetes are a species-rich group within the basidiomycete fungi; however, most analyses of this group to date have focused on pathogenic Cryptococcus species within the order Tremellales. Recent genome-assisted studies of other Tremellomycetes have identified interesting features with respect to biotechnological applications as well as the evolution of genes involved in mating and sexual development. Here, we report genome sequences of two strains of Filobasidium floriforme, a species from the order Filobasidiales, which branches basally to the Tremellales, Trichosporonales, and Holtermanniales. The assembled genomes of strains CBS6241 and CBS6242 are 27.4 Mb and 26.4 Mb in size, respectively, with 8314 and 7695 predicted protein-coding genes. Overall sequence identity at nucleic acid level between the strains is 97%. Among the predicted genes are pheromone precursor and pheromone receptor genes as well as two genes encoding homedomain (HD) transcription factors, which are predicted to be part of the mating type (MAT) locus. Sequence analysis indicates that CBS6241 and CBS6242 carry different alleles for both the pheromone/receptor genes as well as the HD transcription factors. Orthology inference identified 1482 orthogroups exclusively found in F. floriforme, some of which were involved in carbohydrate transport and metabolism. Subsequent CAZyme repertoire characterization identified 267 and 247 enzymes for CBS6241 and CBS6242, respectively, the second highest number of CAZymes among the analyzed Tremellomycete species. In addition, F. floriforme contains five CAZymes absent in other species and several plant-cell-wall degrading CAZymes with the highest copy number in Tremellomycota, indicating the biotechnological potential of this species.
Genomic characterization of a wild diploid isolate of Saccharomyces cerevisiae reveals an extensive and dynamic landscape of structural variation
Authors: Heasley Lydia R , Argueso Juan Lucas
Published: November 2021

The budding yeast Saccharomyces cerevisiae has been extensively characterized for many decades and is a crucial resource for the study of numerous facets of eukaryotic biology. Recent whole genome sequence analysis of over 1000 natural isolates of S. cerevisiae has provided critical insights into the evolutionary landscape of this species by revealing a population structure comprised of numerous genomically diverse lineages. These survey-level analyses have been largely devoid of structural genomic information, mainly because short-read sequencing is not suitable for detailed characterization of genomic architecture. Consequently, we still lack a complete perspective of the genomic variation that exists within this species. Single molecule long-read sequencing technologies, such as Oxford Nanopore and PacBio, provide sequencing-based approaches with which to rigorously define the structure of a genome, and have empowered yeast geneticists to explore this poorly described realm of eukaryotic genomics. Here, we present the comprehensive genomic structural analysis of a wild diploid isolate of S. cerevisiae, YJM311. We used long-read sequence analysis to construct a haplotype-phased, telomere-to-telomere length assembly of the YJM311 genome and characterized the structural variations (SVs) therein. We discovered that the genome of YJM311 contains significant intragenomic structural variation, some of which imparts notable consequences to the genomic stability and developmental biology of the strain. Collectively, we outline a new methodology for creating accurate haplotype-phased genome assemblies and highlight how such genomic analyses can be used to define the structural architectures of natural S. cerevisiae isolates. It is our hope that continued structural characterization of S. cerevisiae genomes, such as we have reported here for YJM311, will comprehensively advance our understanding of eukaryotic genome structure-function relationships, structural genomic diversity, and evolution.
Single nucleotide substitutions effectively block Cas9 and allow for scarless genome editing inCaenorhabditis elegans
Authors: Medley Jeffrey C , Hebbar Shilpa , Sydzyik Joel T , Zinovyeva Anna Y
Published: November 2021

In Caenorhabditis elegans, germline injection of Cas9 complexes is reliably used to achieve genome editing through homology-directed repair of Cas9-generated DNA breaks. To prevent Cas9 from targeting repaired DNA, additional blocking mutations are often incorporated into homologous repair templates. Cas9 can be blocked either by mutating the PAM sequence that is essential for Cas9 activity or by mutating the guide sequence that targets Cas9 to a specific genomic location. However, it is unclear how many nucleotides within the guide sequence should be mutated, since Cas9 can recognize “off-target” sequences that are imperfectly paired to its guide. In this study, we examined whether single-nucleotide substitutions within the guide sequence are sufficient to block Cas9 and allow for efficient genome editing. We show that a single mismatch within the guide sequence effectively blocks Cas9 and allows for recovery of edited animals. Surprisingly, we found that a low rate of edited animals can be recovered without introducing any blocking mutations, suggesting a temporal block to Cas9 activity in C. elegans. Furthermore, we show that the maternal genome of hermaphrodite animals is preferentially edited over the paternal genome. We demonstrate that maternally provided haplotypes can be selected using balancer chromosomes and propose a method of mutant isolation that greatly reduces screening efforts postinjection. Collectively, our findings expand the repertoire of genome editing strategies in C. elegans and demonstrate that extraneous blocking mutations are not required to recover edited animals when the desired mutation is located within the guide sequence.
phiC31 integrase for recombination-mediated single-copy insertion and genome manipulation in Caenorhabditis elegans
Authors: Yang Fang-Jung , Chen Chiao-Nung , Chang Tiffany , Cheng Ting-Wei , Chang Ni-Chen , Kao Chia-Yi , Lee Chih-Chi , Huang Yu-Ching , Hsu Jung-Chen , Li Jengyi , Lu Meiyeh J , Chan Shih-Peng , Wang John
Published: November 2021

Caenorhabditis elegans benefits from a large set of tools for genome manipulation. Yet, the precise single-copy insertion of very large DNA constructs (>10 kb) and the generation of inversions are still challenging. Here, we adapted the phiC31 integrase system for C. elegans. We generated an integrated phiC31 integrase expressing strain flanked by attP sites that serves as a landing pad for integration of transgenes by recombination-mediated cassette exchange (RCME). This strain is unc-119(−) so RMCE integrants can be produced simply by injection of a plasmid carrying attB sites flanking unc-119(+) and the gene(s) of interest. Additionally, phiC31 integrase is removed concomitantly with integration, eliminating the need to outcross away the integrase. Integrations were obtained for insert sizes up to ∼33.4 kb. Taking advantage of this integration method we establish a dual-color fluorescent operon reporter system able to study post-transcriptional regulation of mRNA. Last, we show that large chromosomal segments can be inverted using phiC31 integrase. Thus, the phiC31 integrase system should be a useful addition to the C. elegans toolkit.
Population biology of accessory gland-expressed de novo genes in Drosophila melanogaster
Authors: Cridland Julie M , Majane Alex C , Zhao Li , Begun David J
Published: November 2021

Early work on de novo gene discovery in Drosophila was consistent with the idea that many such genes have male-biased patterns of expression, including a large number expressed in the testis. However, there has been little formal analysis of variation in the abundance and properties of de novo genes expressed in different tissues. Here, we investigate the population biology of recently evolved de novo genes expressed in the Drosophila melanogaster accessory gland, a somatic male tissue that plays an important role in male and female fertility and the post mating response of females, using the same collection of inbred lines used previously to identify testis-expressed de novo genes, thus allowing for direct cross tissue comparisons of these genes in two tissues of male reproduction. Using RNA-seq data, we identify candidate de novo genes located in annotated intergenic and intronic sequence and determine the properties of these genes including chromosomal location, expression, abundance, and coding capacity. Generally, we find major differences between the tissues in terms of gene abundance and expression, though other properties such as transcript length and chromosomal distribution are more similar. We also explore differences between regulatory mechanisms of de novo genes in the two tissues and how such differences may interact with selection to produce differences in D. melanogaster de novo genes expressed in the two tissues.
Eight-Year Changes in Multimorbidity and Frailty in Adults With Type 2 Diabetes Mellitus: Associations With Cognitive and Physical Function and Mortality
Authors: Espeland Mark A , Justice Jamie Nicole , Bahnson Judy , Evans Joni K , Munshi Medha , Hayden Kathleen M , Simpson Felicia R , Johnson Karen C , Johnston Craig , Kritchevsky Stephen R
Published: November 2021

Background

Indices of multimorbidity and deficit accumulation (ie, frailty indices) have been proposed as markers of biological aging. If true, changes in these indices over time should predict downstream changes in cognition and physical function, and mortality.

Methods

We examined associations that 8-year changes in (i) a multimorbidity index comprised of 9 chronic diseases and (ii) a frailty index (FI) based on deficit accumulation in functional, behavioral, and clinical characteristics had with subsequent measures of cognitive and physical function over 10 years. We drew data from 3 842 participants in the Action for Health in Diabetes clinical trial. They were aged 45–76 years at baseline and at risk for accelerated biological aging due to overweight/obesity and type 2 diabetes mellitus.

Results

A total of 1 501 (39%) of the cohort had 8-year increases of 1 among the 9 diseases tracked in the multimorbidity index and 868 (23%) had increases of ≥2. Those with greatest increases in multimorbidity tended to be older individuals, males, and non-Hispanic Whites. Greater FI increases tended to occur among individuals who were older, non-Hispanic White, heavier, and who had more baseline morbidities. Changes in multimorbidity and FI were moderately correlated (r = 0.26; p < .001). Increases in both multimorbidity and FI were associated with subsequently poorer composite cognitive function and 400-m walk speed and increased risk for death (all p < .001).

Conclusions

Accelerated biological aging, as captured by multimorbidity and frailty indices, predicts subsequent reduced function and mortality. Whether intensive lifestyle interventions generally targeting multimorbidity and FI reduce risks for downstream outcomes remains to be seen.

Clinical Trials Registration Number: NCT00017953
Is Wrist Accelerometry Suitable for Threshold Scoring? A Comparison of Hip-Worn and Wrist-Worn ActiGraph Data in Low-Active Older Adults With Obesity
Authors: Fanning Jason , Miller Michael E , Chen Shyh-Huei , Davids Carlo , Kershner Kyle , Rejeski W Jack
Published: November 2021

Background

Hip- and wrist-worn ActiGraph accelerometers are widely used in research on physical activity as they offer an objective assessment of movement intensity across the day. Herein we characterize and contrast key structured physical activities and common activities of daily living via accelerometry data collected at the hip and wrist from a sample of community-dwelling older adults.

Methods

Low-active, older adults with obesity (age 60+ years) were fit with an ActiGraph GT3X+ accelerometer on their nondominant wrist and hip before completing a series of tasks in a randomized order, including sitting/standing, sweeping, folding laundry, stair climbing, ambulation at different intensities, and cycling at different intensities. Participants returned a week later and completed the tasks once again. Vector magnitude counts/second were time-matched during each task and then summarized into counts/minute (CPM).

Results

Monitors at both wear locations similarly characterized standing, sitting, and ambulatory tasks. A key finding was that light home chores (sweeping, folding laundry) produced higher and more variable CPM values than fast walking via wrist ActiGraph. Regression analyses revealed wrist CPM values were poor predictors of hip CPM values, with devices aligning best during fast walking (R2 = 0.25) and stair climbing (R2 = 0.35).

Conclusions

As older adults spend a considerable portion of their day in nonexercise activities of daily living, researchers should be cautious in the use of simply acceleration thresholds for scoring wrist-worn accelerometer data. Methods for better classifying wrist-worn activity monitor data in older adults are needed.
How Do Individuals in a Radical Echo Chamber React to Opposing Views? Evidence from a Content Analysis of Stormfront
Authors: Bright Jonathan , Marchal Nahema , Ganesh Bharath , Rudinac Stevan
Published: November 2021

Calls to “break up” radical echo chambers by injecting them with alternative viewpoints are common. Yet, thus far there is little evidence about the impact of such counter-messaging. To what extent and how do individuals who inhabit a radical echo chamber engage with messages that challenge their core beliefs? Drawing on data from the radical right forum Stormfront we address this question with a large-scale content and longitudinal analysis of users’ posting behavior, which analyses more than 35,000 English language contributions to the forum spanning 2011 through 2013. Our findings show that engaging with oppositional views is actually a core practice among Stromfront users which invites active participation and encourages engagement. Indeed, many “echoes” in the echo chamber we studied were not core beliefs being restated, but the sound of opposing viewpoints being undermined and marginalized. These findings underscore the limited potential for counter-messages to undermine radical echo chambers.
Current Trends in IBD—Development of Mucosal-Based Biomarkers and a Novel Minimally Invasive Recoverable Sampling System
Authors: Yau Yunki Y , Wasinger Valerie C , Hirten Robert P , Chuang Emil , Huntsman Merodean , Stylli Jack , Shimizu Jeff , Yajnik Vijay , Smith Jeffrey , Lee Shaoying N , Singh Sharat , Wahl Christopher , Leong Rupert W , Sands Bruce E
Published: November 2021

Despite recent developments in therapy for inflammatory bowel diseases (IBDs), there have been limited advances in diagnostic tools available to aid in disease management. A growing body of evidence suggests that there are important host-microbe interactions at the mucosal interface that modulate the inflammatory response in patients with IBD. Additionally, the importance of mucosal integrity and its disruption appears to be important in the pathophysiology and perpetuation of the disease. The ability to characterize this interface may provide valuable information for both disease monitoring and identification of new treatment targets. Endoscopy remains the primary tool for disease monitoring, and mucosal healing is the primary therapeutic target in IBD treatment. However, establishing mucosal healing requires repetitive endoscopic procedures, and endoscopy is limited by factors such as invasiveness, cost, and risk of adverse events. Moreover, the use of a bowel preparation for colonoscopies alters the mucus layer and thus perturbs evaluation of the host-microbe interaction. Stool sampling may also be inaccurate because it reflects the end state of metabolites and proteins, failing to take into account the degradation or alteration of substrates of interest by bacterial proteases and other enzymes during passage through the colon.

A novel sampling capsule, called the Recoverable Sampling System (RSS), is being developed as a complementary tool to colonoscopy. The RSS is intended to be a platform for noninvasive autonomous sampling, preservation, handling, and storage of analytes of interest found in the gastrointestinal fluids. A proprietary preservative contained within the chambers of the capsule has been developed to stabilize DNA and proteins for ex vivo microbiome and metabolomics analyses.

Surrogate markers such as SPP24 and GUCA2a have been identified to correlate with gut health, intestinal permeability, and inflammation and could be locally sampled by the RSS. The potential clinical utility of an RSS device is broad and would likely be able to guide therapy by allowing for more frequent disease monitoring, aiding in disease characterization, and facilitating in the identification of novel therapeutic targets.
Colon Capsule Endoscopy in the Assessment of Mucosal Healing in Crohn’s Disease
Authors: Papalia Isabella , Tjandra Douglas , Quah Stephanie , Tan Christina , Gorelik Alexandra , Sivanesan Suresh , Macrae Finlay
Published: November 2021

Background

Patients with Crohn’s disease (CD) undergo frequent endoscopic procedures, with visualization of the gastrointestinal mucosa central to treatment decision-making. Subsequently, a noninvasive alternative to optical colonoscopy (OC) would be welcomed. One such technology is capsule endoscopy, including the PillCam COLON 2 (PCC2), though research validating its use in ileocolonic CD is limited. This study aims to compare PCC2 with ileocolonoscopy (OC) in assessing mucosal CD through use of a standardized scoring system.

Methods

At an Australian tertiary hospital, same-day PCC2 and ileocolonoscopy results of 47 CD patients, with known nonstricturing disease, were prospectively collected and analyzed for correlation and agreement. Deidentified recordings were reported by a single expert gastroenterologist. Mucosal disease was quantified using the Simple Endoscopic Score for Crohn’s Disease (SES-CD). The SES-CD results of paired endoscopic modalities were compared in total per bowel segment and per SES-CD variable.

Results

Of 47 PCC2 recordings, 68% were complete, fully assessing terminal ileum to rectum, and OC was complete in 89%. Correlation (r) between total SES-CD scores was strongest in the terminal ileum (r = 0.77, P < .001), with the SES-CD variable of “ulcer detection” showing the strongest agreement. The PCC2 (vs OC) identified additional ulcers in the terminal ileum; ascending, transverse, and descending colon; and rectum; scores were 5 (1), 5 (3), 1 (1), 2 (1), and 2 (2), respectively.

Conclusions

The PCC2 shows promise in assessing ileocolonic mucosa, especially in proximal bowel segments, with greater reach of visualization in the small bowel. Given the resource and safety considerations raised by the Coronavirus disease 2019 pandemic, capsule endoscopy has particular significance.

This article aims to contribute to the limited body of research surrounding the validity of capsule endoscopy technology in assessing ileocolonic mucosa in Crohn’s Disease patients. In doing so, an alternative option for patients enduring frequent endoscopies is given potential.
Research-Based Product Innovation to Address Critical Unmet Needs of Patients with Inflammatory Bowel Diseases
Authors: Honig Gerard , Larkin Paul B , Heller Caren , Hurtado-Lorenzo Andrés
Published: November 2021

Despite progress in recent decades, patients with inflammatory bowel diseases face many critical unmet needs, demonstrating the limitations of available treatment options. Addressing these unmet needs will require interventions targeting multiple aspects of inflammatory bowel disease pathology, including disease drivers that are not targeted by available therapies. The vast majority of late-stage investigational therapies also focus primarily on a narrow range of fundamental mechanisms. Thus, there is a pressing need to advance to clinical stage differentiated investigational therapies directly targeting a broader range of key mechanistic drivers of inflammatory bowel diseases. In addition, innovations are critically needed to enable treatments to be tailored to the specific underlying abnormal biological pathways of patients; interventions with improved safety profiles; biomarkers to develop prognostic, predictive, and monitoring tests; novel devices for nonpharmacological approaches such as minimally invasive monitoring; and digital health technologies. To address these needs, the Crohn’s & Colitis Foundation launched IBD Ventures, a venture philanthropy–funding mechanism, and IBD Innovate®, an innovative, product-focused scientific conference. This special IBD Innovate® supplement is a collection of articles reflecting the diverse and exciting research and development that is currently ongoing in the inflammatory bowel disease field to deliver innovative and differentiated products addressing critical unmet needs of patients. Here, we highlight the pipeline of new product opportunities currently advancing at the preclinical and early clinical development stages. We categorize and describe novel and differentiated potential product opportunities based on their potential to address the following critical unmet patient needs: (1) biomarkers for prognosis of disease course and prediction/monitoring of treatment response; (2) restoration of eubiosis; (3) restoration of barrier function and mucosal healing; (4) more effective and safer anti-inflammatories; (5) neuromodulatory and behavioral therapies; (6) management of disease complications; and (7) targeted drug delivery.
Recommendations for Standardizing Clinical Trial Design and Endoscopic Assessment in Postoperative Crohn’s Disease
Authors: Hanzel Jurij , Jairath Vipul , De Cruz Peter , Guizzetti Leonardo , Shackelton Lisa M , Bossuyt Peter , Duijvestein Marjolijn , Dulai Parambir S , Grossmann Johannes , Hirten Robert P , Khanna Reena , Panes Julian , Peyrin-Biroulet Laurent , Regueiro Miguel , Rubin David T , Singh Siddharth , Stidham Ryan W , Sandborn William J , Feagan Brian G , D’Haens Geert R , Ma Christopher
Published: November 2021

Background

The lack of standardized methods for clinical trial design and disease activity assessment has contributed to an absence of approved medical therapies for the prevention of postoperative Crohn’s disease (CD). We developed recommendations for regulatory trial design for this indication and for endoscopic assessment of postoperative CD activity.

Methods

An international panel of 19 gastroenterologists was assembled. Modified Research and Development/University of California Los Angeles methodology was used to rate the appropriateness of 196 statements using a 9-point Likert scale in 2 rounds of voting. Results were reviewed and discussed between rounds.

Results

Inclusion of patients with a history of completely resected ileocolonic CD in regulatory clinical trials for the prevention of postoperative recurrence was appropriate. Given the absence of approved medical therapies, a placebo-controlled design with a primary end point of endoscopic remission at 52 weeks was appropriate for drug development for this indication; however, there was uncertainty regarding the appropriateness of a coprimary end point of symptomatic and endoscopic remission and the use of currently available patient-reported outcome measures. The modified Rutgeerts Score, endoscopic assessment of the anastomosis, and a minimum of 5cm of neoterminal ileum were also appropriate; although the appropriateness of other indices including the Simple Endoscopic Score for CD for endoscopic assessment of postoperative CD activity was uncertain.

Conclusions

A framework for regulatory trial design for the prevention of postoperative CD recurrence and endoscopic assessment of disease activity has been developed. Research to empirically validate end points for these trials is needed.
Strategies to Distinguish Perianal Fistulas Related to Crohn’s Disease From Cryptoglandular Disease: Systematic Review With Meta-Analysis
Authors: Chin Koon Siw Kevin , Engel Jake , Visva Samantha , Mallick Ranjeeta , Hart Ailsa , de Buck van Overstraeten Anthony , McCurdy Jeffrey D
Published: November 2021

Background

Management of perianal fistulas differs based on fistula type. We aimed to assess the ability of diagnostic strategies to differentiate between Crohn’s disease (CD) and cryptoglandular disease (CGD) in patients with perianal fistulas.

Methods

We performed a diagnostic accuracy systematic review and meta-analysis. A systematic search of electronic databases was performed from inception through February 2021 for studies assessing a diagnostic test’s ability to distinguish fistula types. We calculated weighted summary estimates with 95% confidence intervals for sensitivity and specificity by bivariate analysis, using fixed effects models when data were available from 2 or more studies. The Quality Assessment of Diagnostic Accuracy Studies tool was used to assess study quality.

Results

Twenty-one studies were identified and included clinical symptoms (2 studies; n=154), magnetic resonance imaging (MRI) characteristics (3 studies; n=296), ultrasound characteristics (7 studies; n=1003), video capsule endoscopy (2 studies; n=44), fecal calprotectin (1 study; n=56), and various biomarkers (8 studies; n=440). MRI and ultrasound characteristics had the most robust data. Rectal inflammation, multiple-branched fistula tracts, and abscesses on pelvic MRI and the Crohn’s ultrasound fistula sign, fistula debris, and bifurcated fistulas on pelvic ultrasonography had high specificity (range, 80%-95% vs 89%-96%) but poor sensitivity (range, 17%-37% vs 31%-63%), respectively. Fourteen of 21 studies had risk of bias on at least 1 of the Quality Assessment of Diagnostic Accuracy Studies domains.

Conclusions

Limited high-quality evidence suggest that imaging characteristics may help discriminate CD from CGD in patients with perianal fistulas. Larger, prospective studies are needed to confirm these findings and to evaluate if combining multiple diagnostic tests can improve diagnostic sensitivity.
Epidemiology and Natural History of Perianal Crohn’s Disease: A Systematic Review and Meta-Analysis of Population-Based Cohorts
Authors: Tsai Lester , McCurdy Jeffrey D , Ma Christopher , Jairath Vipul , Singh Siddharth
Published: November 2021

Background and Aims

Perianal Crohn’s disease (pCD) is a potentially severe phenotype of CD. We conducted a systematic review with meta-analysis to estimate cumulative incidence, risk factors, and outcomes of pCD in population-based cohort studies.

Methods

Through a systematic literature review through March 1, 2021, we identified population-based inception cohort studies reporting cumulative incidence of perianal disease (primarily abscess and/or fistula) in patients with CD. We estimated the cumulative incidence of pCD at presentation and 1-, 5-, and 10-year follow-up, and risk factors for perianal disease and outcomes including risk of major (bowel resection, proctectomy, ostomy) and minor perianal (incision and drainage, seton placement, etc.) surgery.

Results

In 12 population-based studies, prevalence of pCD was 18.7% (95% confidence interval [CI], 12.5%-27.0%) with 1-, 5-, and 10-year risk of perianal disease being 14.3% (95% CI, 7.9%-24.6%), 17.6% (95% CI, 11.3%-26.5%), and 18.9% (95% CI, 15.0%-23.4%), respectively. Approximately 11.5% of patients (95% CI, 6.7%-19.0%) had perianal disease at or before CD diagnosis. Colonic disease location and rectal involvement were associated with higher risk of pCD. Overall, 63.3% of patients (95% CI, 53.3-72.3) required minor perianal surgery and 6.4% of patients (95% CI, 1.8%-20.6%) required major abdominal surgery for pCD. Use of biologic therapy for pCD is common and has steadily increased throughout the years.

Conclusions

Approximately 1 in 5 patients with CD develops perianal disease within 10 years of CD diagnosis, including 11.5% who have perianal disease at presentation. Approximately two-thirds of patients require perianal surgery, with a smaller fraction requiring major abdominal surgery.
Behind a Digital Mask: Users’ Subjective Experience of Animated Characters and Its Effect on Source Credibility
Authors: Di Natale Anna Flavia , Triberti Stefano , Sibilla Federica , Imperato Chiara , Villani Daniela , Mancini Tiziana , Riva Giuseppe
Published: November 2021

Recently, computer-mediated communication has incorporated animated characters (ACs) as interface technologies. These digital entities are animated by mimicry and can be used either to deliver pre-recorded messages or to live communicate with others. The interlocutors can choose the physical appearance of the character and decide to use a character that may or may not represent their actual self. In this respect, it is important to investigate the psychological mechanisms describing how the user responds to ACs and the resulting effects on communication. To do this, a 2 × 2 experiment was conducted (n = 85) to evaluate the effects of human-likeness (human-like vs. non-human-like) and self-representation (actual self vs. ideal self) on users’ subjective experience, in terms of para-social relationship, identification and emotions, and its effect on communication-related variables such as source credibility. Results showed that, unlike self-representation, human-likeness had a significant effect on the interaction between the user and an AC, with non-human-like ACs stimulating a more engaging and positive interaction compared with human-like ACs. Data also confirmed the importance of para-social relationship and identification in fostering source credibility. Theoretical and practical implications are discussed.
Rapid Screening of β-Agonists in Animal Hair by Thermal Desorption Electrospray Ionization Mass Spectrometry
Authors: Zhang Hongyan , Chang Qiaoying , Wu Xingqiang , Qiu Guoyu , Li Jian , Wu Fuxiang
Published: November 2021

Background

Even though the use of β-agonists in livestock has been banned in many countries, β-agonists abuse is still out of control owing to time-consuming and complicated determination techniques.

Objective

This study applied ambient thermal desorption electrospray ionization mass spectrometry (TD-ESI/MS) as a new strategy for rapidly screening seven β-agonists. As it does not require pretreatment, this method allows on-site and real-time detection.

Method

Samples were collected directly using a simple metal probe. Analytes on the probe were desorbed and ionized by TD-ESI, after which analyte ions were detected using a triple quadrupole mass analyser.

Results

The results showed that a thermal desorption temperature of 320°C and nebulizer pressure of 3 psi demonstrated the highest sensitivity. Excellent linear relationships were obtained in concentrations ranging from 10 to 400 μg/kg. The limit of detection of the method was 1–10 μg/kg with RSDs of 7.2–14.6%. A positive sample was verified using HPLC coupled with triple quadrupole tandem mass spectrometry, consistent with the results from TD-ESI/MS.

Conclusion

This method was the first to apply TD-ESI/MS to rapid analyse β-agonists in livestock hair and was proven to be accurate, fast, and environmentally friendly. Because qualitative screening for each analysis was completed within approximately 1 min, the method could contribute to preventing non-compliance in the flow of animal-derived food to the market.

Highlights

This method was a promising method for the rapid screening of β-agonists in livestock hair at any time of breeding without imposing any harm to animal which proven to be a rapid, in situ, and non-destructive detection technique without any pretreatment.
Early Transcriptomic Response to Burn Injury: Severe Burns Are Associated With Immune Pathway Shutdown
Authors: Keyloun John W , Campbell Ross , Carney Bonnie C , Yang Ruoting , Miller Stacy-Ann , Detwiler Leanne , Gautam Aarti , Moffatt Lauren T , Hammamieh Rasha , Jett Marti , Shupp Jeffrey W ,   SYSCOT study group, McLawhorn Melissa M , Callcut Rachael A , Cohen Mitchell J , Petzold Linda R , Varner Jeffrey D , Bravo Maria Cristina , Brummel-Ziedins Kathleen E , Freeman Kalev , Mann Kenneth G , Orfeo Thomas , Pusateri Anthony E
Published: November 2021

Burn injury induces a systemic hyperinflammatory response with detrimental side effects. Studies have described the biochemical changes induced by severe burns, but the transcriptome response is not well characterized. The goal of this work is to characterize the blood transcriptome after burn injury. Burn patients presenting to a regional center between 2012 and 2017 were prospectively enrolled. Blood was collected on admission and at predetermined time points (hours 2, 4, 8, 12, and 24). RNA was isolated and transcript levels were measured with a gene expression microarray. To identify differentially regulated genes (false-discovery rate ≤0.1) by burn injury severity, patients were grouped by TBSA above or below 20% and statistically enriched pathways were identified. Sixty-eight patients were analyzed, most patients were male with a median age of 41 (interquartile range, 30.5–58.5) years, and TBSA of 20% (11%–34%). Thirty-five patients had % TBSA injury ≥20%, and this group experienced greater mortality (26% vs 3%, P = .008). Comparative analysis of genes from patients with </≥20% TBSA revealed 1505, 613, 380, 63, 1357, and 954 differentially expressed genes at hours 0, 2, 4, 8, 12, and 24, respectively. Pathway analysis revealed an initial up-regulation in several immune/inflammatory pathways within the ≥20% TBSA groups followed by shutdown. Severe burn injury is associated with an early proinflammatory immune response followed by shutdown of these pathways. Examination of the immunoinflammatory response to burn injury through differential gene regulation and associated immune pathways by injury severity may identify mechanistic targets for future intervention.
Repair, Consumption, and Sustainability: Fixing Fragile Objects and Maintaining Consumer Practices
Authors: Godfrey D Matthew , Price Linda L , Lusch Robert F
Published: November 2021

Repair is an overlooked but important aspect of consumer behavior with implications for the social and environmental sustainability of consumption. This ethnographic study examines the interplay of repair and consumption by analyzing when and how consumers repair the objects they use. The analysis examines how conflicting and complementary practice elements can lead to object replacement and disposal or, alternatively, facilitate object repair and extended use. Results unfold how consumers calibrate their routine activities around the continually changing material capacities of objects. Consumers engage in repair as a response to worn or damaged objects that misalign from and often disrupt ongoing practices. Repairers, including consumers and professional service providers, attempt to adjust object capacities in ways that realign disrupted practices with the routinized ways that consumers do them. When successful, repair sustains consumer practices by avoiding prolonged disruption and unnecessary waste. However, conflicts between production, consumption, and repair can hinder the efficacy of repair interventions and shape whether and how consumers repair the objects they use. The article explains these challenges and concludes by discussing their implications for studies of repair, consumer practices, and sustainable consumption.
Three Decades of the Nakajima Doctrine in EU Law: Where Are We Now?
Authors: Stoyanov Kristiyan
Published: November 2021

Under the Nakajima doctrine, the Court of Justice of the European Union (CJEU) can review the legality of a European Union (EU) measure in the light of the World Trade Organization (WTO) agreements if the EU legislature intended to implement a particular obligation assumed in the context of those agreements. This article argues that Nakajima remains a valid exception to the lack of direct effect of WTO law in the EU. Section II highlights the CJEU’s restrictive interpretation of Nakajima. Section III shows that in recent case law the CJEU continues to take a narrow interpretation of Nakajima, although the CJEU has been reluctant to abolish it altogether. This section also analyses the feasibility of establishing the intention to implement WTO law based on external circumstances (Section III.B) and demonstrates Nakajima’s significance beyond EU law (Section III.C). Section IV criticizes the CJEU’s combination of Nakajima and the principle of interpreting EU law in consistency with international law. Section V concludes.
Utilization of West Virginia Pediatric Medicaid Claims Data to Guide Outpatient Antimicrobial Stewardship Interventions
Authors: Kilgore Jacob T , Lanata Mariana M , Willis Jonathan M , McCarthy Michael J , Becker James B , Evans Joseph E , Smith Michael J
Published: November 2021

West Virginia consistently ranks in the top two nationally for per capita antibiotic prescription rates in both pediatric and adult outpatient populations. We present the first descriptive analysis evaluating outpatient prescription rates within the WV pediatric Medicaid population, which demonstrated significant antibiotic prescribing variability by provider type, specialty, and geography.
The updated basti stellar evolution models and isochrones – III. White dwarfs
Authors: Salaris Maurizio , Cassisi Santi , Pietrinferni Adriano , Hidalgo Sebastian
Published: November 2021

We present new cooling models for carbon–oxygen white dwarfs (WDs) with both H- and He-atmospheres, covering the whole relevant mass range, to extend our updated basti (a Bag of Stellar Tracks and Isochrones) stellar evolution archive. They have been computed using core chemical stratifications obtained from new progenitor calculations, adopting a semi-empirical initial–final mass relation. The physics inputs have been updated compared to our previous basti calculations: 22Ne diffusion in the core is now included, together with an updated CO phase diagram, and updated electron conduction opacities. We have calculated models with various different neon abundances in the core, suitable to study WDs in populations with metallicities ranging from supersolar to metal poor, and have performed various tests/comparisons of the chemical stratification and cooling times of our models. Two complete sets of calculations are provided, for two different choices of the electron conduction opacities, to reflect the current uncertainty in the evaluation of the electron thermal conductivity in the transition regime between moderate and strong degeneracy, crucial for the H- and He-envelopes. We have also made a first, preliminary estimate of the effect – that turns out to be generally small – of Fe sedimentation on the cooling times of WD models, following recent calculations of the phase diagrams of carbon–oxygen-iron mixtures. We make publicly available the evolutionary tracks from both sets of calculations, including cooling times and magnitudes in the Johnson-Cousins, Sloan, Pan-STARSS, GALEX, Gaia-DR2, Gaia-eDR3, HST-ACS, HST-WFC3, and JWST photometric systems.
A 6D view of stellar shells
Authors: Dong-Páez C A , Vasiliev E , Evans N W
Published: November 2021

Stellar shells are low surface brightness features, created during nearly head-on galaxy mergers from the debris of the tidally disrupted satellite. Here, we investigate the formation and evolution mechanism of shells in six dimensions (3D positions and velocities). We propose a new description in action-angle coordinates which condenses the seemingly complex behaviour of an expanding shell system into a simple picture, and stresses the crucial role of the existence of different stripping episodes in the properties of shells. Based on our findings, we construct a method for constraining the potential of the host galaxy and the average epoch of stripping. The method is applicable even if the shells cannot be identified or isolated from the data, or if the data are heavily contaminated with additional foreground stars. These results open up a new possibility to study the ancient merger that built the Milky Way Galaxy’s stellar halo.
The second decametre pulsar census at the UTR-2
Authors: Kravtsov Ihor P , Zakharenko Vyacheslav V , Ulyanov Oleg M , Shevtsova Alisa I , Yerin Serge M , Konovalenko Oleksandr O
Published: November 2021

In this paper, we present the results of the second census of pulsars in the decametre wave range at the Ukrainian T-shaped Radio telescope, second modification (UTR-2). Over the past 10 yr, the worldwide number of discovered nearby pulsars has doubled, which means that there is some urgency to search for a low-frequency radio emission from these newly discovered sources. To increase the sensitivity of this census, the integration time was doubled compared with the first census of 2010–2013. As a result, the decametre radio emission of 20 pulsars was detected, and their flux densities and the shape of their pulses were obtained. The dispersion measures for 10 pulsars and the rotation periods for eight pulsars were refined. For several pulsars, the scattering time constant and FWHM were estimated in the decametre wave range. The upper limits of flux densities for 102 pulsars that have not yet been detected were also estimated.
Monte Carlo simulations of evolving rotational distributions of low-mass stars in young open clusters. Testing the influence of initial conditions
Authors: Vasconcelos M J , Bouvier J , Gallet F , Luz Filho E A
Published: November 2021

The rotational evolution of a young stellar population can give informations about the rotation pattern of more evolved clusters. Combined with rotational period values of thousands of young stars and theoretical propositions about the redistribution and loss of stellar angular momentum, it allows us to trace the rotational history of stars according to their mass. We want to investigate how internal and environmental changes on single stars can change the rotational evolution of a young stellar population. We run Monte Carlo simulations of a young cluster composed by solar mass stars of 0.5, 0.8 and 1.0 M⊙ from 1 to 550 Myr taking into account observational and theoretical parameters. In order to compare our results with the observations we run Kolmogorov-Smirnov tests. Our standard model is able to reproduce some clusters younger than h Per and marginally M37, which is 550 Myr old. Varying the disk fraction or the initial period distribution did not improve the results. However, when we run a model with a finer mass grid the Pleiades can be also reproduced. Changing the initial mass distribution to be similar to the empirical ONC mass function also gives good results. Modeling the evolution of a young synthetic cluster from pre-main sequence to early main sequence considering physical mechanisms of extraction and exchange of angular momentum can not be achieved successfully for all clusters for which we have enough rotational data. Clusters of about the same age present different rotational behaviors due perhaps to differences in their initial conditions.
The ZTF-BTS Type Ia supernovae luminosity function is consistent with a single progenitor channel for the explosions
Authors: Sharon Amir , Kushnir Doron
Published: November 2021

We construct the Type Ia supernovae (SNe Ia) luminosity function (LF) using the Zwicky Transient Facility Bright Transient Survey (BTS) catalogue. While this magnitude-limited survey has an unprecedented number of objects, it suffers from large distance uncertainties and lacks an estimation of host extinction. We bypass these issues by calculating the intrinsic luminosities from the shape parameters of the light curve’s g and r bands, with the luminosities calibrated from the well observed SNe Ia sample of the Carnegie Supernova Project, allowing us to construct, for the first time, the intrinsic LF of SNe Ia. We then use a novel tight relation between the colour stretch and the synthesized 56Ni mass, MNi56, to determine the MNi56 distribution of SNe Ia. We find that the LFs are unimodal, with their peaks in line with previous results, but have a much lower rate of dim events and luminous events. We show that the features on top of the unimodal LF-derived distributions are all compatible with statistical noise, consistent with a single progenitor channel for the explosions. We further derive, for the first time, the SNe Ia distribution of host galaxy extinction, and find a mean selective extinction of E(B − V) ≈ 0.1 and a non-negligible fraction with large, $\gt 1\, \text{mag}$, extinction in the optical bands. The high extinction is typical for luminous SNe, supporting their young population origin.
A Deep-Learning Approach for Inference of Selective Sweeps from the Ancestral Recombination Graph
Authors: Hejase Hussein A , Mo Ziyi , Campagna Leonardo , Siepel Adam
Published: November 2021

Detecting signals of selection from genomic data is a central problem in population genetics. Coupling the rich information in the ancestral recombination graph (ARG) with a powerful and scalable deep-learning framework, we developed a novel method to detect and quantify positive selection: Selection Inference using the Ancestral recombination graph (SIA). Built on a Long Short-Term Memory (LSTM) architecture, a particular type of a Recurrent Neural Network (RNN), SIA can be trained to explicitly infer a full range of selection coefficients, as well as the allele frequency trajectory and time of selection onset. We benchmarked SIA extensively on simulations under a European human demographic model, and found that it performs as well or better as some of the best available methods, including state-of-the-art machine-learning and ARG-based methods. In addition, we used SIA to estimate selection coefficients at several loci associated with human phenotypes of interest. SIA detected novel signals of selection particular to the European (CEU) population at the MC1R and ABCC11 loci. In addition, it recapitulated signals of selection at the LCT locus and several pigmentation-related genes. Finally, we reanalyzed polymorphism data of a collection of recently radiated southern capuchino seedeater taxa in the genus Sporophila to quantify the strength of selection and improved the power of our previous methods to detect partial soft sweeps. Overall, SIA uses deep learning to leverage the ARG and thereby provides new insight into how selective sweeps shape genomic diversity.
Interstitial lung disease in a woman with rheumatoid arthritis treated with denosumab: A case report
Authors: Mori Yu , Izumiyama Takuya , Mori Naoko , Aizawa Toshimi
Published: November 2021

The present report describes the case of an 84 year old female Japanese patient with rheumatoid arthritis (RA) who experienced exacerbation of interstitial lung disease (ILD) after denosumab (Dmab) treatment. The onset of RA occurred in 2008, and the patient had been treated with intravenous or subcutaneous injection of tocilizumab since 2009. In July 2013, she experienced a lumbar vertebral fracture and began treatment with 60 mg Dmab injection every 6 months in January 2014. The patient had a history of mild ILD and was evaluated for ILD by chest computed tomography (CT) imaging prior to the start of Dmab use. The vertebral fracture did not recur after the initiation of Dmab treatment, and her osteoporosis was successfully treated. However, she expressed a concern of exacerbations of cough and respiratory discomfort that had occurred since September 2019. The chest CT image in November 2015 showed minor ILD progression, whereas the image in September 2019 showed severe exacerbation of ILD. To treat this exacerbation, 10 mg of methylprednisolone and 2.5 mg of tacrolimus were administered, and Dmab was discontinued. The patient was subsequently switched to oral bisphosphonate. The patient’s respiratory discomfort and the finding of interstitial lung lesion in CT imaging improved after Dmab discontinuation. This case showed that exacerbation of ILD may occur after Dmab treatment, and physicians should consider the risks of Dmab-related ILD in patients with RA complicated by ILD.