bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dual expression and anatomy lines allow simultaneous visualization of gene expression and anatomy
Authors: Kümpers Britta M C , Han Jingyi , Vaughan-Hirsch John , Redman Nicholas , Ware Alexander , Atkinson Jonathan A , Leftley Nicola , Janes George , Castiglione Giuseppe , Tarr Paul T , Pyke Kevin , Voß Ute , Wells Darren M , Bishopp Anthony 
Published: October 2021

Abstract
Studying the developmental genetics of plant organs requires following gene expression in specific tissues. To facilitate this, we have developed dual expression anatomy lines, which incorporate a red plasma membrane marker alongside a fluorescent reporter for a gene of interest in the same vector. Here, we adapted the GreenGate cloning vectors to create two destination vectors showing strong marking of cell membranes in either the whole root or specifically in the lateral roots. This system can also be used in both embryos and whole seedlings. As proof of concept, we follow both gene expression and anatomy in Arabidopsis (Arabidopsis thaliana) during lateral root organogenesis for a period of over 24 h. Coupled with the development of a flow cell and perfusion system, we follow changes in activity of the DII auxin sensor following application of auxin.
New-onset versus relapsing giant cell arteritis treated with tocilizumab: 3-year results from a randomized controlled trial and extension
Authors: Stone John H , Spotswood Helen , Unizony Sebastian H , Aringer Martin , Blockmans Daniel  , Brouwer Elisabeth , Cid Maria C , Dasgupta Bhaskar , Rech Juergen , Salvarani Carlo , Spiera Robert , Bao Min 
Published: October 2021

Abstract

Objective
Tocilizumab plus prednisone induces sustained glucocorticoid-free remission in patients with GCA. However, its long-term benefits in new-onset vs relapsing disease are uncertain, and the value of weekly vs every-other-week dosing has not been evaluated.

Methods
In Giant-Cell Arteritis Actemra (GiACTA) part 1, patients with new-onset or relapsing GCA received blinded tocilizumab weekly (TCZ QW), tocilizumab every-other-week (TCZ Q2W) or placebo for 52 weeks, with a prednisone taper. In part 2 (open-label), patients were treated at investigator discretion for 104 weeks. In this analysis, patients were evaluated according to their original treatment assignments, and outcomes beyond 52 weeks were assessed. Outcomes of interest included time to first flare and cumulative glucocorticoid exposure over 3 years according to baseline disease status.

Results
Part 1 enrolled 250 patients; 215 entered part 2. At baseline, 48% had new-onset disease and 52% had relapsing disease. In patients with new-onset and relapsing disease, the median time to first flare in the TCZ QW group was 577 and 575 days, respectively, vs 479 and 428 days with TCZ Q2W and 179 and 224 days with placebo; the median cumulative glucocorticoid dose was 3068 mg and 2191 mg with TCZ QW, 4080 mg and 2353 mg with TCZ Q2W, and 4639 mg and 6178 mg with placebo.

Conclusion
TCZ QW delayed the time to flare and reduced the cumulative glucocorticoid dose in patients with relapsing GCA and new-onset GCA. These data support initiating TCZ QW as part of first-line therapy in all patients with active GCA.

Trial registration
ClinicalTrials.gov, https://clinicaltrials.gov, NCT01791153.
Impact of the COVID-19 pandemic on juvenile idiopathic arthritis presentation and research recruitment: results from the CAPRI registry
Authors: Dushnicky Molly J , Campbell Catherine , Beattie Karen A , Berard Roberta , Cellucci Tania , Chan Mercedes , Gerschman Tommy , Johnson Nicole , Lim Lillian , Luca Nadia , Miettunen Paivi , Morishita Kimberly A , Proulx-Gauthier Jean-Philippe , Rumsey Dax G , Schmeling Heinrike , Scuccimarri Rosie , Tam Herman , Guzman Jaime , Batthish Michelle ,   for the CAPRI Registry Investigators, Cabral David , Chédeville Gaëlle , Duffy Ciarán , Gerhold Kerstin , Guzman Jaime , Hiraki Linda , Huber Adam , Schmeling Heinrike , Shiff Natalie , Tucker Lori 
Published: October 2021

Abstract

Objective
The COVID-19 pandemic has disrupted healthcare delivery and clinical research worldwide, with data from areas most affected demonstrating an impact on rheumatology care. This study aimed to characterize the impact of the pandemic on the initial presentation of JIA and JIA-related research in Canada.

Methods
Data collected from the Canadian Alliance of Pediatric Rheumatology Investigators JIA Registry from the year pre-pandemic (11 March 2019 to 10 March 2020) was compared with data collected during the first year of the pandemic (11 March 2020 to 10 March 2021). Outcomes included time from symptom onset to first assessment, disease severity at presentation and registry recruitment. Proportions and medians were used to describe categorical and continuous variables, respectively.

Results
The median time from symptom onset to first assessment was 138 (IQR 64–365) days pre-pandemic vs 146 (IQR 83–359) days during the pandemic. The JIA category frequencies remained overall stable (44% oligoarticular JIA pre-pandemic, 46.8% pandemic), except for systemic JIA (12 cases pre-pandemic, 1 pandemic). Clinical features, disease activity (cJADAS10), disability (CHAQ) and quality of life (JAQQ) scores were similar between the two cohorts. Pre-pandemic, 225 patients were enrolled, compared with 111 in the pandemic year, with the greatest decrease from March to June 2020.

Conclusions
We did not observe the anticipated delay in time to presentation or increased severity at presentation, suggesting that, within Canada, care adapted well to provide support to new patient consults without negative impacts. The COVID-19 pandemic was associated with an initial 50% decrease in registry enrolment but has since improved.
Getting under the Skin: The Impact of Terrorist Attacks on Native and Immigrant Sentiment
Authors: Frey Arun 
Published: October 2021

Abstract
There is growing academic interest in examining how terrorist attacks shape the majority’s attitudes towards minority groups. Yet, little is known of how these minority groups react to the backlash such events provoke. This paper leverages the exogenous occurrence of a series of terrorist attacks during the fieldwork period of two surveys to estimate how such events affect the sentiment of both citizens and asylum seekers in Germany. Results of the natural experiment reveal that the 2016 terror attacks in Nice, Würzburg, and Ansbach substantially increased anti-refugee sentiment among German respondents. In line with this increase in hostility, refugees experienced more discrimination, felt less welcome in Germany, and suffered clinically relevant declines in mental health in the aftermath of the attacks. These results provide a more holistic understanding of how terrorism corrodes intergroup relations and how it affects those that are blamed for the events and thus suffer the brunt of the backlash following their occurrence.
Joint-Venture Ambulatory Surgery Centers: The Perfect Partnership
Authors: Tanna Neil , Gibstein Alexander R. , Boll Adam , Coppa Gene F. , Kasabian Armen K. , Bello Stephen , Solazzo Mark 
Published: October 2021

Background:
Ambulatory surgery growth has increased in the last few decades as ambulatory surgery centers have been shown to succeed in cost efficiencies through their smaller size and breadth, specialization of care, and ability to quickly participate in perioperative process improvement and education.

Methods:
A 5-year retrospective fiscal review was performed for all Northwell Health–physician ambulatory surgery center joint ventures. The outcome measures studied included model of ownership, specialty types, and gross revenue. Additional facility characteristics were studied, including growth trajectory, facility size, and cost to build a de novo facility.

Results:
Eleven free-standing ambulatory surgery centers were identified at Northwell Health during the 5-year study period. The total gross revenue for all Northwell clinical joint ventures for 2019 alone was $102,854,000. Northwell Health is a majority stakeholder in eight of their joint venture ambulatory surgery centers, with an average Northwell ownership of 53 percent and an average number of physician owners per facility of 11. The number of hospital-physician joint-venture ambulatory surgery centers grew from two to 11 facilities during the study period (450 percent). Surgical volume followed a similar trajectory, increasing 295 percent over the same time period.

Conclusions:
The ambulatory surgery center setting provides a vast number of possibilities for key stakeholders, including patients themselves, to benefit from financial and clinical efficiencies. Ambulatory surgery centers have been popular, as they meet patient expectations for convenience of elective surgery, reduce payer and clinical pressures to minimize length of stay in hospitals, and achieve similar or higher quality care with less intense resources.
The Relationship of Psychiatric Comorbidities and Their Impact on Trigger Site Deactivation Surgery for Headaches
Authors: Amador Ricardo O. , Gfrerer Lisa , Hansdorfer Marek A. , Colona Mia R. , Tsui Jane M. , Austen William G. 
Published: October 2021

Background:
Patients seeking trigger site deactivation surgery for headaches often have debilitating symptoms that can affect their functional and mental health. Although prior studies have shown a strong correlation between psychiatric variables and chronic headaches, their associations in patients undergoing surgery have not been fully elucidated. This study aims to analyze psychiatric comorbidities and their impact on patients undergoing trigger site deactivation surgery for headaches.

Methods:
One hundred forty-two patients were prospectively enrolled. Patients were asked to complete the Patient Health Questionnaire-2 and Migraine Headache Index surveys preoperatively and at 12 months postoperatively. Data on psychiatric comorbidities were collected by means of both survey and retrospective chart review.

Results:
Preoperatively, 38 percent of patients self-reported a diagnosis of depression, and 45 percent of patients met Patient Health Questionnaire-2 criteria for likely major depressive disorder (Patient Health Questionnaire-2 score of ≥3). Twenty-seven percent of patients reported a diagnosis of generalized anxiety disorder. Patients with depression and anxiety reported more severe headache symptoms at baseline. At 1 year postoperatively, patients with these conditions had successful surgical outcomes comparable to those of patients without these conditions. Patients also reported a significant decrease in their Patient Health Questionnaire-2 score, with 22 percent of patients meeting criteria suggestive of depression, compared to 45 percent preoperatively.

Conclusions:
There is a high prevalence of depression and anxiety in patients undergoing trigger site deactivation surgery. Patients with these comorbid conditions achieve successful surgical outcomes comparable to those of the general surgical headache population. Furthermore, trigger site deactivation surgery is associated with a significant decrease in depressive symptoms.
A Novel Alaska Pollock Gelatin Sealant Shows Higher Bonding Strength and Nerve Regeneration Comparable to That of Fibrin Sealant in a Cadaveric Model and a Rat Model
Authors: Masuda Shusuke , Suzuki Taku , Shibata Shinsuke , Moritoki Nobuko , Abe Yoshifumi , Chen Xi , Mizuno Yosuke , Nishiguchi Akihiro , Kimura Hiroo , Matsumura Noboru , Iwamoto Takuji , Taguchi Tetsushi , Matsumoto Morio , Nakamura Masaya 
Published: October 2021

Background:
A novel biocompatible sealant composed of Alaska pollock–derived gelatin (ApGltn) has recently shown good burst strength and biocompatibility in a porcine aorta. The purpose of this study was to investigate the bonding strength and biocompatibility of the ApGltn sealant in transected digital nerves of fresh frozen cadavers and in the sciatic nerves of a rat model.

Methods:
Eighty human digital nerves of fresh frozen cadavers were transected for biomechanical traction testing. They were treated with four surgical interventions: (1) suture plus ApGltn sealant; (2) suture; (3) ApGltn sealant; and (4) fibrin sealant. Forty-three sciatic nerves of male Wistar rats were used for functional and histopathologic evaluation. They were treated with six surgical interventions: (1) suture plus ApGltn sealant; (2) suture; (3) ApGltn sealant; (4) fibrin sealant; (5) resection with a 5-mm gap (10 rats per group); and (6) sham operation (three rats). Macroscopic confirmation, muscle weight measurement, and histopathologic findings including G-ratio were examined 8 weeks after the procedure.

Results:
The maximum failure load of the ApGltn sealant was significantly higher than that of a fibrin sealant (0.22 ± 0.05 N versus 0.06 ± 0.04 N). The maximum failure load of the ApGltn sealant was significantly lower that of suture plus ApGltn sealant (1.37 N) and suture (1.27 N). Functional evaluation and histologic examination showed that sciatic nerves repaired with ApGltn sealant showed similar nerve recovery compared to repair with the suture and fibrin sealant.

Conclusion:
The ApGltn sealant showed higher bonding strength and equal effect of nerve regeneration when compared with the fibrin sealant.
Genome-wide association study of liver fat, iron, and extracellular fluid fraction in the UK Biobank
Authors: O’Dushlaine Colm , Germino Mary , Verweij Niek , Nielsen Jonas B. , Yadav Ashish , Benner Christian , Backman Joshua D. , Lin Nan , R. Abecasis Gonçalo , Baras Aris , Ferreira Manuel A. , Lotta Luca A. , Walls Johnathon R. , Parasoglou Prodromos , Marchini Jonathan L. 
Published: October 2021

AbstractAbdominal magnetic resonance imaging (MRI) represents a non-invasive approach allowing the extraction of clinically informative phenotypes. We developed an automated pipeline to segment liver pixels from abdominal MRI images and apply published models to approximate fat fraction, extracellular fluid fraction and iron content in 40,058 MRIs from the UK Biobank. We then conducted a genome-wide association of these traits using imputed variants (N=37,250 individuals, 11,914,698 variants) and exome sequence data (N=35,274 individuals, 8,287,315 variants). For liver fat we identified 8 novel loci in or near genes MARC1, GCKR, ADH1B, MTTP, TRIB1, GPAM, PNPLA2 and APOH. For liver iron we identified 1 novel locus between the genes ASNSD1 and SLC40A1, an iron transporter involved in hemochromatosis. For extracellular fluid fraction we identified 6 novel loci in or near genes AGMAT, NAT2, MRPL4-S1PR2, FADS1, ABO and HFE, with almost all having prior associations to obesity, liver, iron, or lipid traits.
Limited impact of Delta variant’s mutations in the effectiveness of neutralization conferred by natural infection or COVID-19 vaccines in a Latino population
Authors: Sariol Carlos A. , Serrano-Collazo Crisanta , Ortiz Edwin J. , Pantoja Petraleigh , Cruz Lorna , Arana Teresa , Atehortua Dianne , Pabon-Carrero Christina , Espino Ana M. 
Published: October 2021

AbstractThe SARS-CoV-2 pandemic has impacted public health systems all over the world. The Delta variant seems to possess enhanced transmissibility, but no clear evidence suggests it has increased virulence. Our data shows that pre-exposed individuals had similar neutralizing activity against the authentic COVID-19 strain and the Delta and Epsilon variants. After one vaccine dose, the neutralization capacity expands to all tested variants. Healthy vaccinated individuals showed a limited breadth of neutralization. One vaccine dose induced similar neutralizing antibodies against the Delta compared to the authentic strain. However, even after two doses, this capacity only expanded to the Epsilon variant.
A scalable serology solution for profiling humoral immune responses to SARS-CoV-2 infection and vaccination
Authors: Colwill Karen , Galipeau Yannick , Stuible Matthew , Gervais Christian , Arnold Corey , Rathod Bhavisha , Abe Kento T , Wang Jenny H , Pasculescu Adrian , Maltseva Mariam , Rocheleau Lynda , Pelchat Martin , Fazel-Zarandi Mahya , Iskilova Mariam , Barrios-Rodiles Miriam , Bennett Linda , Yau Kevin , Cholette François , Mesa Christine , Li Angel X , Paterson Aimee , Hladunewich Michelle A , Goodwin Pamela J , Wrana Jeffrey L , Drews Steven J , Mubareka Samira , McGeer Allison J , Kim John , Langlois Marc-André , Gingras Anne-Claude , Durocher Yves 
Published: October 2021

AbstractOBJECTIVESAntibody testing against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been instrumental in detecting previous exposures and analyzing vaccine-elicited immune responses. Here, we describe a scalable solution to detect and quantify SARS-CoV-2 antibodies, discriminate between natural infection- and vaccination-induced responses, and assess antibody-mediated inhibition of the spike-angiotensin converting enzyme 2 (ACE2) interaction.METHODSWe developed methods and reagents to detect SARS-CoV-2 antibodies by enzyme-linked immunosorbent assay (ELISA). The main assays focus on the parallel detection of immunoglobulin (Ig)Gs against the spike trimer, its receptor binding domain (RBD), and nucleocapsid (N). We automated a surrogate neutralization (sn)ELISA that measures inhibition of ACE2-spike or -RBD interactions by antibodies. The assays were calibrated to a World Health Organization reference standard.RESULTSOur single-point IgG-based ELISAs accurately distinguished non-infected and infected individuals. For seroprevalence assessment (in a non-vaccinated cohort), classifying a sample as positive if antibodies were detected for ≥ 2 of the 3 antigens provided the highest specificity. In vaccinated cohorts, increases in anti-spike and -RBD (but not -N) antibodies are observed. We present detailed protocols for serum/plasma or dried blood spots analysis performed manually and on automated platforms. The snELISA can be performed automatically at single points, increasing its scalability.CONCLUSIONSMeasuring antibodies to three viral antigens and identify neutralizing antibodies capable of disrupting spike-ACE2 interactions in high-throughput enables large-scale analyses of humoral immune responses to SARS-CoV-2 infection and vaccination. The reagents are available to enable scaling up of standardized serological assays, permitting inter-laboratory data comparison and aggregation.
Open chromatin analysis inTrypanosoma cruzilife forms highlights critical differences in genomic compartments and developmental regulation at tDNA loci
Authors: Lima Alex Ranieri Jerônimo , Poubel Saloe Bispo , Rosón Juliana Nunes , de Lima Loyze Paola Oliveira , Costa-Silva Héllida Marina , de Sousa Silva Herbert Guimarães , Gonçalves Camila Silva , Galante Pedro A. F. , Holetz Fabiola , Motta Maria Cristina Machado M. , Silber Ariel M. , Elias M. Carolina , da Cunha Julia Pinheiro Chagas 
Published: October 2021

AbstractBackgroundGenomic organization and gene expression regulation in trypanosomes are remarkable because protein-coding genes are organized into codirectional gene clusters with unrelated functions. Moreover, there is no dedicated promoter for each gene, resulting in polycistronic gene transcription, with posttranscriptional control playing a major role. Nonetheless, these parasites harbor epigenetic modifications at critical regulatory genome features that dynamically change among parasite stages, which are not fully understood.ResultsHere, we investigated the impact of chromatin changes in a scenario commanded by posttranscriptional control exploring the parasiteTrypanosoma cruziand its differentiation program using genome-wide approaches supported by transmission electron microscopy. The integration of FAIRE and MNase-seq data, two complementary epigenomic approaches, enabled us to identify differences inT. cruzigenome compartments, putative transcriptional start regions and virulence factors. In addition, we also detected developmental chromatin regulation at tRNA loci (tDNA), which seems to be linked to the translation regulatory mechanism required for parasite differentiation. Strikingly, a positive correlation was observed between active chromatin and steady-state transcription levels.ConclusionTaken together, our results indicate that chromatin changes reflect the unusual gene expression regulation of trypanosomes and the differences among parasite developmental stages, even in the context of a lack of canonical transcriptional control of protein-coding genes.
Anatomic development of the upper airway during the first five years of life: A three-dimensional imaging study
Authors: Chuang Ying Ji , Hwang Seong Jae , Buhr Kevin A. , Miller Courtney A. , Avey Gregory D. , Story Brad H. , Vorperian Houri K. 
Published: October 2021

AbstractPurposeNormative data on the growth and development of the upper airway across the sexes is needed for the diagnosis and treatment of congenital and acquired respiratory anomalies and to gain insight on developmental changes in speech acoustics and disorders with craniofacial anomalies.MethodsThe growth of the upper airway in children ages birth-to-five years, as compared to adults, was quantified using an imaging database with computed tomography studies from typically developing individuals. Methodological criteria for scan inclusion and airway measurements included: head position, histogram-based airway segmentation, anatomic landmark placement, and development of a semi-automatic centerline for data extraction. A comprehensive set of 2D and 3D supra- and sub-glottal measurements from the choanae to tracheal opening were obtained including: naso-oro-laryngo-pharynx subregion volume and length, each subregion’s superior and inferior cross-sectional-area, and antero-posterior and transverse/width distances.ResultsGrowth of the upper airway during the first five years of life was more pronounced in the vertical and transverse/lateral dimensions than in the antero-posterior dimension. By age five years, females have larger pharyngeal measurement than males. Prepubertal sex-differences were identified in the subglottal region.ConclusionsOur findings demonstrate the importance of studying the growth of the upper airway in 3D. As the lumen length increases, its shape changes, becoming increasingly elliptical during the first five years of life. This study also emphasizes the importance of methodological considerations for both image acquisition and data extraction, as well as the use of consistent anatomic structures in defining pharyngeal regions.
Value creation through omnichannel practices for multi-actor customers: an evolutionary view
Authors: Costa Climent Ricardo , Haftor Darek M. , Chowdhury Soumitra 
Published: October 2021

Purpose
The purpose of this paper is to investigate the omnichannel practices to porpose a conceptual overview to offer guidance on how to handle their inherent complexities.

Design/methodology/approach
This study is based on a literature review of more than 100 academics papers about the multichannel practices and omnichannel practices in the global market.

Findings
To this end, this paper identifies and addresses three limitations of the contemporary omnichannel literature: the failure to articulate the sources of value creation generated by omnichannel practices, the conception of omnichannel as targeting a single customer actor only and the static conception of omnichannel practices. In response to these limitations, this study offers the following: four sources of value creation based on the business model concept, a multi-actor customer conception, where several actors partake in the overall purchase decision and an evolutionary notion of omnichannel practices in terms of their constitution and use as part of the overall evolution of a marketplace

Originality/value
The framework presented in this paper provides a map to take new research beyond its current boundaries and an audit tool to help managers identify their firm’s current omnichannel situation, including limitations and opportunities for further development.