bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial and temporal regulation of parent-of-origin allelic expression in the endosperm
Authors: van Ekelenburg Yuri S , Hornslien Karina S , Van Hautegem Tom , Fendrych Matyáš , Van Isterdael Gert , Bjerkan Katrine N , Miller Jason R , Nowack Moritz K , Grini Paul E 
Published: November 2022

Abstract
Genomic imprinting promotes differential expression of parental alleles in the endosperm of flowering plants and is regulated by epigenetic modification such as DNA methylation and histone tail modifications in chromatin. After fertilization, the endosperm develops through a syncytial stage before it cellularizes and becomes a nutrient source for the growing embryo. Regional compartmentalization has been shown both in early and late endosperm development, and different transcriptional domains suggest divergent spatial and temporal regional functions. The analysis of the role of parent-of-origin allelic expression in the endosperm as a whole and the investigation of domain-specific functions have been hampered by the inaccessibility of the tissue for high-throughput transcriptome analyses and contamination from surrounding tissue. Here, we used fluorescence-activated nuclear sorting (FANS) of nuclear targeted GFP fluorescent genetic markers to capture parental-specific allelic expression from different developmental stages and specific endosperm domains. This approach allowed us to successfully identify differential genomic imprinting with temporal and spatial resolution. We used a systematic approach to report temporal regulation of imprinted genes in the endosperm, as well as region-specific imprinting in endosperm domains. Analysis of our data identified loci that are spatially differentially imprinted in one domain of the endosperm, while biparentally expressed in other domains. These findings suggest that the regulation of genomic imprinting is dynamic and challenge the canonical mechanisms for genomic imprinting.
miRador: a fast and precise tool for the prediction of plant miRNAs
Authors: Hammond Reza K , Gupta Pallavi , Patel Parth , Meyers Blake C 
Published: November 2022

Abstract
Plant microRNAs (miRNAs) are short, noncoding RNA molecules that restrict gene expression via posttranscriptional regulation and function in several essential pathways, including development, growth, and stress responses. Accurately identifying miRNAs in populations of small RNA sequencing libraries is a computationally intensive process that has resulted in the misidentification of inaccurately annotated miRNA sequences. In recent years, criteria for miRNA annotation have been refined with the aim to reduce these misannotations. Here, we describe miRador, a miRNA identification tool that utilizes the most up-to-date, community-established criteria for accurate identification of miRNAs in plants. We combined target prediction and Parallel Analysis of RNA Ends (PARE) data to assess the precision of the miRNAs identified by miRador. We compared miRador to other commonly used miRNA prediction tools and found that miRador is at least as precise as other prediction tools while being substantially faster than other tools. miRador should be broadly useful for the plant community to identify and annotate miRNAs in plant genomes.
Dissection of the Pearl of Csaba pedigree identifies key genomic segments related to early ripening in grape
Authors: He Guang-Qi , Huang Xi-Xi , Pei Mao-Song , Jin Hui-Ying , Cheng Yi-Zhe , Wei Tong-Lu , Liu Hai-Nan , Yu Yi-He , Guo Da-Long 
Published: November 2022

Abstract
Pearl of Csaba (PC) is a valuable backbone parent for early-ripening grapevine (Vitis vinifera) breeding, from which many excellent early ripening varieties have been bred. However, the genetic basis of the stable inheritance of its early ripening trait remains largely unknown. Here, the pedigree, consisting of 40 varieties derived from PC, was re-sequenced for an average depth of ∼30×. Combined with the resequencing data of 24 other late-ripening varieties, 5,795,881 high-quality single nucleotide polymorphisms (SNPs) were identified following a strict filtering pipeline. The population genetic analysis showed that these varieties could be distinguished clearly, and the pedigree was characterized by lower nucleotide diversity and stronger linkage disequilibrium than the non-pedigree varieties. The conserved haplotypes (CHs) transmitted in the pedigree were obtained via identity-by-descent analysis. Subsequently, the key genomic segments were identified based on the combination analysis of haplotypes, selective signatures, known ripening-related quantitative trait loci (QTLs), and transcriptomic data. The results demonstrated that varieties with a superior haplotype, H1, significantly (one-way ANOVA, P &lt; 0.001) exhibited early grapevine berry development. Further analyses indicated that H1 encompassed VIT_16s0039g00720 encoding a folate/biopterin transporter protein (VvFBT) with a missense mutation. VvFBT was specifically and highly expressed during grapevine berry development, particularly at veraison. Exogenous folate treatment advanced the veraison of “Kyoho”. This work uncovered core haplotypes and genomic segments related to the early ripening trait of PC and provided an important reference for the molecular breeding of early-ripening grapevine varieties.
Ocular manifestations of ANCA-associated vasculitis
Authors: Junek Mats L , Zhao Lily , Garner Stephanie , Cuthbertson David , Pagnoux Christian , Koening Curry L , Langford Carol A , McAlear Carol A , Monach Paul A , Moreland Larry W , Rhee Rennie L , Seo Philip , Specks Ulrich , Sreih Antoine G , Warrington Kenneth , Wechsler Michael E , Merkel Peter A , Khalidi Nader A 
Published: November 2022

Abstract

Objectives
ANCA-associated vasculitis (AAV) is a group of multisystem diseases that can have several ocular manifestations. There are published data on ocular manifestations of granulomatosis with polyangiitis (GPA), but few for eosinophilic granulomatosis with polyangiitis (EGPA) or microscopic polyangiitis (MPA). There is little information concerning chronicity, complications, and association with other cranial manifestations of AAV.

Methods
This study retrospectively analysed longitudinal multicentre cohorts of individuals with AAV followed between 2006 and 2022. Data included diagnosis, demographics, cranial manifestations of disease, presence of manifestations at onset of disease and/or follow-up, and ocular complications of disease. Univariate and multivariable logistic regression analysis assessed associations across disease manifestations.

Results
Data from 1441 patients were analysed, including 395 with EGPA, 876 with GPA, and 170 with MPA. Ocular manifestations were seen within 23.1% of patients: 39 (9.9%) with EGPA, 287 (32.7%) with GPA, and 12 (7.1%) with MPA at any time in the disease course. There were more ocular manifestations at onset (n = 224) than during follow-up (n = 120). The most common disease-related manifestations were conjunctivitis/episcleritis and scleritis. In multivariable analysis, dacryocystitis, lacrimal duct obstruction, and retro-orbital disease were associated with sinonasal manifestations of GPA; ocular manifestations were associated with hearing loss in MPA. The most common ocular complications and/or damage seen were cataracts (n = 168) and visual impairment (n = 195).

Conclusion
Ocular manifestations occur in all forms of AAV, especially in GPA. Clinicians should be mindful of the wide spectrum of ocular disease in AAV, caused by active vasculitis, disease-associated damage, and toxicities of therapy.
Utility of nailfold capillary assessment for predicting psoriatic arthritis based on a prospective observational cohort study
Authors: Fukasawa Takemichi , Toyama Satoshi , Enomoto Atsushi , Yoshizaki-Ogawa Asako , Norimatsu Yuta , Tateishi Shoko , Kanda Hiroko , Miyagawa Kiyoshi , Sato Shinichi , Yoshizaki Ayumi 
Published: November 2022

Abstract

Objectives
PsA is one of the most serious comorbidities associated with psoriasis. While the early intervention in PsA is demanded, risk factors of PsA development are not well-known. This is the first prospective study to evaluate the clinical significance of nailfold capillary (NFC) changes in patients with psoriasis.

Methods
We conducted a prospective cohort study in a population of 449 psoriasis patients who had not been treated with systemic therapy or topical finger therapy. NFCs were observed by dermoscopy and capillaroscopy, and the correlation of NFC abnormalities, including nailfold bleeding (NFB) and enlarged capillaries, with the prevalence of PsA, incidence of new PsA, and serum levels of TNF-a, IL-17A and IL-23 were analysed.

Results
Detailed examination at the time of inclusion revealed that of 449 patients, 236 had Psoriasis vulgaris (PsV) and 213 had PsA. Both NFB and enlarged capillaries were significantly more frequent in patients with PsA (34.7% vs 84.5%, P &lt; 0.0001; 25.4% vs 100%, P &lt; 0.0001). In addition, PsV patients were prospectively observed before they developed PsA (mean 21 months, 95% CI 2, 77 months). Multivariate analysis suggested that the appearance of NFB and enlarged capillaries was a predictor of PsA development (HR 2.75, 95% CI 1.38, 5.47 and HR 4.49, 95% CI 2.25, 8.96, respectively). The degree of NFC abnormalities also correlated with the severity of PsA and serum cytokine levels.

Conclusions
NFC abnormalities were suggested to be a predictor of PsA in psoriasis patients, and at the same time, its degree could be an indicator of disease severity.
Symptomatic myopathies in sarcoidosis: disease spectrum and myxovirus resistance protein A expression
Authors: Chompoopong Pitcha , Skolka Michael P , Ernste Floranne C , Milone Margherita , Liewluck Teerin 
Published: November 2022

Abstract

Objectives
Symptomatic myopathy in sarcoidosis patients is not always due to sarcoid myopathy (ScM). We investigated the clinical and pathological spectrum including myxovirus resistance protein A (MxA) expression among sarcoidosis patients.

Methods
We reviewed the Mayo Clinic database (May 1980–December 2020) to identify sarcoidosis patients with myopathic symptoms and pathological evidence of myopathy.

Results
Among 5885 sarcoidosis patients, 21 had symptomatic myopathy. Eight carried a diagnosis of sarcoidosis 5.5 years (median) prior to myopathy onset. Eleven patients had ScM. The remaining had non-sarcoid myopathies (five IBM, one immune-mediated necrotizing myopathy, one non-specific myositis, two non-specific myopathy and one steroid myopathy). Estimated frequency of IBM is 85 per 100 000 sarcoidosis patients. The following features were associated with non-sarcoid myopathies (P &lt; 0.05): (i) predominant finger flexor and quadriceps weakness, (ii) modified Rankin scale (mRS) &gt;2 at time of diagnosis, (iii) creatine kinase &gt;500 U/l, and (iv) absence of intramuscular granulomas. Sarcoplasmic MxA expression was observed in scattered myofibres in three patients, two of whom were tested for DM-specific autoantibodies and were negative. Immunosuppressive therapy led to improvement in mRS ≥1 in 5/10 ScM, none of the five IBM, and 3/3 remaining patients with non-sarcoid myopathies.

Discussion
Symptomatic myopathy occurred in 0.36% of sarcoidosis. IBM was the second most common cause of myopathies after ScM. Frequency of IBM in sarcoidosis is higher than in the general population. Recognition of features suggestive of alternative aetiologies can guide proper treatment. Our findings of abnormal MxA expression warrant a larger study.
Prevalence and predictors of atlanto-axial subluxation in rheumatoid arthritis after 12-years’ follow-up (ESPOIR Cohort)
Authors: Le Quellec Aurore , Guyard Thibaut , Carvajal Alegria Guillermo , Ruyssen-Witrand Adeline , Fautrel Bruno , Flipo René Marc , Garrigues Florent , Saraux Alain 
Published: November 2022

Abstract

Objectives
Anterior atlanto-axial subluxation (AAS), defined as an anterior atlanto-dental interval ≥3 mm, can occur in RA and carries a risk of severe neurological impairments. Our objective was to determine the prevalence and predictors of radiographic aAAS after 12 years’ follow-up of patients with early polyarthritis.

Methods
We studied patients enrolled in the early polyarthritis cohort ESPOIR (Study and Monitoring of Early Undifferentiated Arthritis) between 2002 and 2005 (at least two swollen joints for &gt;6 weeks and &lt;6 months, no other diagnosis than RA, and no previous exposure to glucocorticoids or DMARDs). All patients still in the cohort after 12 years had dynamic cervical-spine radiographs taken then read by two blinded observers. To evaluate how well combinations of tests performed at baseline and 10 years predicted aAAS after 12 years, univariate analysis and multiple logistic regression procedure were applied.

Results
Of 323 patients followed for 12 years, 15 (4.6%; 95% CI 2.8, 6.4) had aAAS. Among baseline variables, only IgA RFs were associated (P &lt; 0.05) with aAAS (sensitivity 60%, specificity 75%). Among data collected after 10 years, oral CS therapy during the 10-year interval, treatment by DMARDs, CRP (mg/dl) and positive tests for RFs were associated with aAAS after 12 years, but only CRP and RFs remained in a model of logistic regression (combination predicted aAAS with a sensitivity of 60% for a specificity of 90%).

Conclusion
In conclusion, the prevalence of aAAS after 12 years was 4.6% in the ESPOIR cohort, with no patients having severe aAAS. Although some factors were found to be statistically associated to AAS, the event is too rare to allow a clinical relevance.
Impact of COVID-19 on urology services at a quaternary referral center in Johannesburg, South Africa
Authors: Christofides Chris , Carides Michaela , Masa Martha , Zamparini Jarrod , Adam Ahmed 
Published: November 2022

Abstract

Background
South Africa was placed into a nationwide lockdown on March 26, 2020, to limit the transmission of severe acute respiratory syndrome coronavirus 2. Medical facilities were overwhelmed, and the redeployment of medical staff to deal with coronavirus disease 2019 (COVID-19) cases resulted in the disruption of typical urology services. This has led to the reprioritization of care for urology patients with delays in all elective cases.

Materials and methods
In this retrospective study, we compared the numbers and types of patients seen in our urology outpatient clinics, ward admissions, and theater cases 90 days before and after the first COVID-19 lockdown. The changes in numbers were calculated as percentages, and Fisher exact test was used to determine p values.

Results
The number of patients in urology outpatient clinics significantly declined (26.4%) after the lockdown started. Outpatient procedures, which were mostly diagnostic, decreased by 28.6%, with no change observed in therapeutic procedures. A decrease in the total number of theater cases (37.4%) and ward admissions (45.0%) was also observed after the lockdown because of a decrease in elective cases, although the number of emergency and oncology patients was relatively stable.

Conclusions
Coronavirus disease 2019 and the lockdown forced the urology department to shift the focus to only emergency and oncology cases. This resulted in delays in the treatment of benign elective conditions and a subsequent increase in the backlog of pending surgeries for these conditions, which could potentially lead to future complications. Although COVID-19 is a major problem requiring many resources, ensuring that urological patients still receive adequate care and management is also important.
A Prognostic Score To Predict Atrial fibrillation Recurrence After External Electrical Cardioversion—SLAC Score
Authors: Thangjui Sittinun , Yodsuwan Ratdanai , Thyagaturu Harshith , Navaravong Leenhapong , Zoltick Jerel 
Published: November 2022

Introduction:
Atrial fibrillation (AF) recurrence after a successful external electrical cardioversion (ECV) is common. Assessing an individual’s risk of AF recurrence is a critical part of the treatment plan. We aimed to develop a prognostic prediction score to predict AF recurrence in AF patients who underwent successful ECV.

Methods:
A retrospective cohort study that included AF patients who underwent successful ECV was conducted with a primary outcome of AF recurrence at 6 months. Logistic regression analysis was done to identify variables, and a prognostic prediction score was created and internally validated.

Results:
Four prognostic predictors were identified, including the type of AF, persistent AF (1 point) and long-standing persistent AF (4 points), previous cardioversion (1 point), stroke/transient ischemic attack (3 points), and left atrial volume index ≥40 mL/m2 (6 points). The total score of 14 was further divided into 3 risk groups; low-risk (0–2 points), moderate-risk (3–7 points), and high-risk (8–14 points). The positive likelihood ratio for a moderate-risk patient was 2.08 (95% CI, 1.64-2.63) and for a high-risk patient was 7.90 (95% CI, 2.48-25.17). The score showed good discrimination power with the c-statistic of 0.74 (95% CI, 0.69-0.79).

Conclusions:
A simple prognostic prediction score for AF recurrence after successful ECV was created with a promising internally validated discrimination power. An external assessment of its usefulness as a tool to identify patients with low, moderate, and high risk for AF recurrence is warranted.
Evaluation of the Practice Guideline Used for Rule-Out of Myocardial Infarction at a Tertiary Cardiology Center
Authors: Sheikh Sharbafan Reza , Farrokhpour Hossein , Keykhaei Mohammad , Rashedi Sina , Foroumadi Roham , Mehrani Mehdi , Tajdini Masih 
Published: November 2022

Introduction:
With the current high burden on the healthcare system and limited resources, the efficient utilization of facilities is of utmost importance. We sought to present the practice guideline used at a high prevalence tertiary cardiology center and compare its safety and efficacy performance with the single high-sensitivity cardiac troponin T strategy, conventional and modified HEART score.

Methods:
In this prospective cohort study, consecutive patients presenting to the emergency department with chest pain or an angina equivalent were recruited. The primary endpoints consisted of major adverse cardiac events at index visits and 30-day follow-up. Patients were managed according to the practice guideline, and sensitivity and negative predictive values were compared.

Results:
Of the total 1548 patients, the mean age was 50.4 ± 15.7 years. Ninety-nine (10.9%) patients were admitted at the index visit, and 89 patients were consequently diagnosed with acute coronary symptoms. Six (0.007%) patients experienced major adverse cardiac events within the 30-day follow-up among discharged patients. Among 911 patients with at least 1 troponin, using single high-sensitivity cardiac troponin T, HEART score, and modified HEART score would have further admitted 805, 450, and 609 patients, respectively. The negative predictive value for all 4 algorithms did not significantly differ (99.2% vs. 100% vs. 99.3% vs. 99.6%, respectively).

Conclusions:
The Tehran Herat Center protocol was a relatively safe protocol with high efficacy. Despite the high safety of the other diagnostic pathways, the high volume of patients needing additional evaluation could impose a high burden on the health care system.
Distal Trans-radial Access Compared to Conventional Trans-radial Access in Coronary Interventions: A Meta-analysis
Authors: Talha Khawaja M. , Waqar Eisha , Ashley Kellan E. , Cohen Mauricio G. , Lemor Alejandro , McMullan Michael R. , Winscott John G. , Hernandez Gabriel A. 
Published: November 2022

Background:
Distal trans-radial access (dTRA) is a novel technique of arterial cannulation in coronary interventions. The comparative efficacy of dTRA and conventional trans-radial access (TRA) in attenuating peri-procedural complications is unknown.

Methods:
Embase and PubMed/MEDLINE were searched from their inception until June 25, 2022, for randomized clinical trials. Outcomes included were radial artery occlusion (RAO), radial artery spasm, hemostasis time, access time, unsuccessful cannulation, crossover rate, and early discharge after trans-radial stenting of coronary arteries (EASY) type I-III hematomas. Statistical analysis was conducted using the random effects model to derive risk ratios (RRs) and mean differences (MDs) with their corresponding 95% confidence intervals (CIs).

Results:
A total of 6 randomized clinical trials comprising 3240 patients were included. Subjects were predominantly male (73%) and had a mean age of 66 years. The dTRA group had a lower risk of RAO [RR 0.43 (95% CI, 0.26-0.69); P = 0.0005; I2 = 0%] and had a shorter hemostasis time [MD −22.85 min (95% CI, −39.06 to −6.65); P = 0.006; I2 = 99%]. The dTRA group had a higher crossover rate [RR 3.04 (95% CI, 1.88-4.91); P = 0.00001; I2 = 56%] and a longer access time [MD 0.68 min (95% CI, 0.17-1.18); P = 0.009; I2 = 99%]. The TRA group had a lower rate of unsuccessful cannulation [RR 0.81 (95% CI, 0.70-0.95); P = 0.01; I2 = 92%]. There was no significant difference between the groups for radial artery spasm and EASY type I-III hematomas.

Conclusion:
dTRA is a safe alternative to conventional TRA for coronary interventions with a lower risk of RAO. Future trials are required to further compare both approaches.
Comparison of Artificial Intelligence With Other Interventions to Improve Adenoma Detection Rate for Colonoscopy
Authors: Aziz Muhammad , Haghbin Hossein , Sayeh Wasef , Alfatlawi Halah , Gangwani Manesh K. , Sohail Amir H. , Zahdeh Tamer , Weissman Simcha , Kamal Faisal , Lee-Smith Wade , Nawras Ali , Sharma Prateek , Shaukat Aasma 
Published: November 2022

Introduction:
Recent randomized controlled trials (RCTs) and meta-analysis have demonstrated improved adenoma detection rate (ADR) for colonoscopy with artificial intelligence (AI) compared with high-definition (HD) colonoscopy without AI. We aimed to perform a systematic review and network meta-analysis of all RCTs to assess the impact of AI compared with other endoscopic interventions aimed at increasing ADR such as distal attachment devices, dye-based/virtual chromoendoscopy, water-based techniques, and balloon-assisted devices.

Methods:
A comprehensive literature search of PubMed/Medline, Embase, and Cochrane was performed through May 6, 2022, to include RCTs comparing ADR for any endoscopic intervention mentioned above. Network meta-analysis was conducted using a frequentist approach and random effects model. Relative risk (RR) and 95% CI were calculated for proportional outcome.

Results:
A total of 94 RCTs with 61,172 patients (mean age 59.1±5.2 y, females 45.8%) and 20 discrete study interventions were included. Network meta-analysis demonstrated significantly improved ADR for AI compared with autofluorescence imaging (RR: 1.33, CI: 1.06 to 1.66), dye-based chromoendoscopy (RR: 1.22, CI: 1.06 to 1.40), endocap (RR: 1.32, CI: 1.17 to 1.50), endocuff (RR: 1.19, CI: 1.04 to 1.35), endocuff vision (RR: 1.26, CI: 1.13 to 1.41), endoring (RR: 1.30, CI: 1.10 to 1.52), flexible spectral imaging color enhancement (RR: 1.26, CI: 1.09 to 1.46), full-spectrum endoscopy (RR: 1.40, CI: 1.19 to 1.65), HD (RR: 1.41, CI: 1.28 to 1.54), linked color imaging (RR: 1.21, CI: 1.08 to 1.36), narrow band imaging (RR: 1.33, CI: 1.18 to 1.48), water exchange (RR: 1.22, CI: 1.06 to 1.42), and water immersion (RR: 1.47, CI: 1.19 to 1.82).

Conclusions:
AI demonstrated significantly improved ADR when compared with most endoscopic interventions. Future RCTs directly assessing these associations are encouraged.