bluuebunny/crossref_metadata_2025_split huggingface dataset:
The geometric influence on the Cys2His2 zinc finger domain and functional plasticity
Authors: Mueller April L , Corbi-Verge Carles , Giganti David O , Ichikawa David M , Spencer Jeffrey M , MacRae Mark , Garton Michael , Kim Philip M , Noyes Marcus B 
Published: April 2020

AbstractThe Cys2His2 zinc finger is the most common DNA-binding domain expanding in metazoans since the fungi human split. A proposed catalyst for this expansion is an arms race to silence transposable elements yet it remains poorly understood how this domain is able to evolve the required specificities. Likewise, models of its DNA binding specificity remain error prone due to a lack of understanding of how adjacent fingers influence each other's binding specificity. Here, we use a synthetic approach to exhaustively investigate binding geometry, one of the dominant influences on adjacent finger function. By screening over 28 billion protein–DNA interactions in various geometric contexts we find the plasticity of the most common natural geometry enables more functional amino acid combinations across all targets. Further, residues that define this geometry are enriched in genomes where zinc fingers are prevalent and specificity transitions would be limited in alternative geometries. Finally, these results demonstrate an exhaustive synthetic screen can produce an accurate model of domain function while providing mechanistic insight that may have assisted in the domains expansion.
Evolutionary selection of pestivirus variants with altered or no microRNA dependency
Authors: Kokkonos Konstantinos G , Fossat Nicolas , Nielsen Louise , Holm Christina , Hepkema Wytske M , Bukh Jens , Scheel Troels K H 
Published: April 2020

Abstract
Host microRNA (miRNA) dependency is a hallmark of the human pathogen hepatitis C virus (HCV) and was also described for the related pestiviruses, which are important livestock pathogens. The liver-specific miR-122 binds within the HCV 5′ untranslated region (UTR), whereas the broadly expressed let-7 and miR-17 families bind two sites (S1 and S2, respectively) in the pestiviral 3′ UTR. Here, we dissected the mechanism of miRNA dependency of the pestivirus bovine viral diarrhea virus (BVDV). Argonaute 2 (AGO2) and miR-17 binding were essential for viral replication, whereas let-7 binding was mainly required for full translational efficiency. Furthermore, using seed site randomized genomes and evolutionary selection experiments, we found that tropism could be redirected to different miRNAs. AGO cross-linking and immunoprecipitation (CLIP) experiments and miRNA antagonism demonstrated that these alternative variants bound and depended on the corresponding miRNAs. Interestingly, we also identified miRNA-independent variants that were obtained through acquisition of compensatory mutations near the genomic 3′ terminus. Rescue experiments demonstrated that miRNA binding and 3′ mutagenesis contribute to replication through mutually exclusive mechanisms. Altogether, our findings suggest that pestiviruses, although capable of miRNA-independent replication, took advantage of miRNAs as essential host factors, suggesting a favorable path during evolutionary adaptation.
Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds
Authors: Williamson Adele , Leiros Hanna-Kirsti S 
Published: April 2020

AbstractDNA ligases are diverse enzymes with essential functions in replication and repair of DNA; here we review recent advances in their structure and distribution and discuss how this contributes to understanding their biological roles and technological potential. Recent high-resolution crystal structures of DNA ligases from different organisms, including DNA-bound states and reaction intermediates, have provided considerable insight into their enzymatic mechanism and substrate interactions. All cellular organisms possess at least one DNA ligase, but many species encode multiple forms some of which are modular multifunctional enzymes. New experimental evidence for participation of DNA ligases in pathways with additional DNA modifying enzymes is defining their participation in non-redundant repair processes enabling elucidation of their biological functions. Coupled with identification of a wealth of DNA ligase sequences through genomic data, our increased appreciation of the structural diversity and phylogenetic distribution of DNA ligases has the potential to uncover new biotechnological tools and provide new treatment options for bacterial pathogens.
The Quest for Orthologs benchmark service and consensus calls in 2020
Authors: Altenhoff Adrian M , Garrayo-Ventas Javier , Cosentino Salvatore , Emms David , Glover Natasha M , Hernández-Plaza Ana , Nevers Yannis , Sundesha Vicky , Szklarczyk Damian , Fernández José M , Codó Laia , for Orthologs Consortium the Quest , Gelpi Josep Ll , Huerta-Cepas Jaime , Iwasaki Wataru , Kelly Steven , Lecompte Odile , Muffato Matthieu , Martin Maria J , Capella-Gutierrez Salvador , Thomas Paul D , Sonnhammer Erik , Dessimoz Christophe 
Published: April 2020

AbstractThe identification of orthologs—genes in different species which descended from the same gene in their last common ancestor—is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous algorithms and resources have been conceived to address this problem, but benchmarking and interpreting them is fraught with difficulties (need to compare them on a common input dataset, absence of ground truth, computational cost of calling orthologs). To address this, the Quest for Orthologs consortium maintains a reference set of proteomes and provides a web server for continuous orthology benchmarking (http://orthology.benchmarkservice.org). Furthermore, consensus ortholog calls derived from public benchmark submissions are provided on the Alliance of Genome Resources website, the joint portal of NIH-funded model organism databases.
BREM-SC: a bayesian random effects mixture model for joint clustering single cell multi-omics data
Authors: Wang Xinjun , Sun Zhe , Zhang Yanfu , Xu Zhongli , Xin Hongyi , Huang Heng , Duerr Richard H , Chen Kong , Ding Ying , Chen Wei 
Published: April 2020

AbstractDroplet-based single cell transcriptome sequencing (scRNA-seq) technology, largely represented by the 10× Genomics Chromium system, is able to measure the gene expression from tens of thousands of single cells simultaneously. More recently, coupled with the cutting-edge Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), the droplet-based system has allowed for immunophenotyping of single cells based on cell surface expression of specific proteins together with simultaneous transcriptome profiling in the same cell. Despite the rapid advances in technologies, novel statistical methods and computational tools for analyzing multi-modal CITE-Seq data are lacking. In this study, we developed BREM-SC, a novel Bayesian Random Effects Mixture model that jointly clusters paired single cell transcriptomic and proteomic data. Through simulation studies and analysis of public and in-house real data sets, we successfully demonstrated the validity and advantages of this method in fully utilizing both types of data to accurately identify cell clusters. In addition, as a probabilistic model-based approach, BREM-SC is able to quantify the clustering uncertainty for each single cell. This new method will greatly facilitate researchers to jointly study transcriptome and surface proteins at the single cell level to make new biological discoveries, particularly in the area of immunology.
The ancillary N-terminal region of the yeast AP-1 transcription factor Yap8 contributes to its DNA binding specificity
Authors: Maciaszczyk-Dziubinska Ewa , Reymer Anna , Kumar Nallani Vijay , Białek Wojciech , Mizio Katarzyna , Tamás Markus J , Wysocki Robert 
Published: April 2020

Abstract
Activator protein 1 (AP-1) is one of the largest families of basic leucine zipper (bZIP) transcription factors in eukaryotic cells. How AP-1 proteins achieve target DNA binding specificity remains elusive. In Saccharomyces cerevisiae, the AP-1-like protein (Yap) family comprises eight members (Yap1 to Yap8) that display distinct genomic target sites despite high sequence homology of their DNA binding bZIP domains. In contrast to the other members of the Yap family, which preferentially bind to short (7–8 bp) DNA motifs, Yap8 binds to an unusually long DNA motif (13 bp). It has been unclear what determines this unique specificity of Yap8. In this work, we use molecular and biochemical analyses combined with computer-based structural design and molecular dynamics simulations of Yap8–DNA interactions to better understand the structural basis of DNA binding specificity determinants. We identify specific residues in the N-terminal tail preceding the basic region, which define stable association of Yap8 with its target promoter. We propose that the N-terminal tail directly interacts with DNA and stabilizes Yap8 binding to the 13 bp motif. Thus, beside the core basic region, the adjacent N-terminal region contributes to alternative DNA binding selectivity within the AP-1 family.
A method for unmasking incomplete astronomical signals: Application to the CO Multi-line Imaging of Nearby Galaxies project
Authors: Cooray Suchetha , Takeuchi Tsutomu T , Yoda Moe , Sorai Kazuo 
Published: April 2020

ABSTRACTPhotometric surveys have provided incredible amounts of astronomical information in the form of images. However, astronomical images often contain artifacts that can critically hinder scientific analysis by misrepresenting intensities or contaminating catalogs as artificial objects. These affected pixels need to be masked and dealt with in any data reduction pipeline. We present a flexible, iterative algorithm to recover (unmask) astronomical images where some pixels are lacking. We demonstrate the application of the method on some intensity calibration source images in the CO Multi-line Imaging of Nearby Galaxies (COMING) project conducted using the 45 m telescope at Nobeyama Radio Observatory. The proposed algorithm restored artifacts due to a detector error in the intensity calibration source images. The restored images were used to calibrate 11 out of 147 observed galaxy maps in the survey. The tests show that the algorithm can restore measured intensities at sub 1% error even for noisy images (S/N = 2.4), despite lacking a significant part of the image. We present the formulation of the reconstruction algorithm, discuss its possibilities and limitations for extensions to other astronomical signals, and examine the results of the COMING application.
Dissecting the statistical properties of the linear extrapolation method of determining protein stability
Authors: Lindorff-Larsen Kresten 
Published: April 2020

AbstractThe linear extrapolation method to determine protein stability from denaturant-induced unfolding experiments is based on the observation that the free energy of unfolding is often a linear function of the denaturant concentration. The value in the absence of denaturant is then estimated by extrapolation from this linear relationship. Parameters and their confidence intervals are typically estimated by nonlinear least-squares regression. We have compared different methods for calculating confidence intervals and found that a simple method based on linear theory gives accurate results. We have also compared three different parameterizations of the linear extrapolation method and show that the most commonly used form is problematic since the stability and m-value are correlated in the nonlinear least-squares analysis. Parameter correlation can in some cases causes problems in the estimation of confidence intervals and regions and should be avoided when possible. Two alternative parameterizations show much less correlation between parameters.
EP32 Seamless transition to a biosimilar
Authors: Wood Katherine , Pickersgill Gemma , Khoffash Mahmoud Al , Stevens Robert , Coote Annabel , Sekyrynskaya Helen , Mackenzie Felicity , Yee Chee-Seng 
Published: April 2020

Abstract

Background
As adalimumab biosimilars were about to be launched in the UK, our trust was looking for ways to simplify and streamline the process to make it an efficient and seamless transition from originator to biosimilar. Consultations took place between all the stakeholders (clinical commissioning groups, pharmacy department, rheumatology department, home-care provider and biosimilar manufacturer) and an agreement was reached as follows: letters were sent to patients explaining what a biosimilar is and the process of transition. A helpline was established whereby patients were advised to contact if they had any questions or concerns. The home-care provider provided pre-populated prescriptions for the biosimilar. Latex allergy was determined for each patient and transition was made at next delivery (patients with a latex allergy stayed on originator as biosimilar pen contains latex). There was no additional clinic visit required. This is a descriptive analysis of our experience using this seamless transition to the biosimilar adalimumab.

Methods
From our database, we collected demographic data on the rheumatology patients who were on the originator and those who transitioned to the biosimilar. The success of the transition was determined if patients remained on the biosimilar six months later. In patients who did not remain on the biosimilar at six months, we analysed if the patient had switched back to originator, to a different targeted therapy or no longer on a targeted therapy.

Results
There were 262 rheumatology patients on the originator and 2 patients had a latex allergy. Therefore 260 patients were transitioned during a two month period. They were 50.4% female with mean age of 54 years (range 22 to 86 years) and the majority were Caucasians (99%). The diagnoses for this population were axial spondyloarthropathy (45%), rheumatoid arthritis (33%), psoriatic arthritis (21%) and juvenile idiopathic arthritis (1%). At six months post transition, 18 patients (6.9%) were no longer on the biosimilar: 57.1% female, mean age 50 (range 23 to 73), 85.7% axial spondyloarthropathy and all Caucasian. Of these, 11 had switched back to the originator, 3 were switched to a different targeted therapy and 4 were no longer on targeted therapy. The reasons for switching back to the originator were worsening symptoms (6 patients), side effects (4 patients) and difficulty using the pen device (1 patient).

Conclusion
This seamless transition with minimal impact on clinical time was very successful (93.1% success). It will be the model to be used for the future transition of other biosimilars.

Disclosures
K. Wood None. G. Pickersgill None. M. Al Khoffash None. R. Stevens None. A. Coote None. H. Sekyrynskaya None. F. Mackenzie None. C. Yee None.
EP43 Biologic retention in psoriatic arthritis: a real world study
Authors: Jawad Issrah , Nisar Muhammad K 
Published: April 2020

Abstract

Background
Biologics have led to a sea change in the management of psoriatic arthritis (PsA) with unprecedented improvement in the signs, symptoms and radiographic damage, resulting in improvement in functionality and quality of life. However longitudinal data for their retention and tolerability is sparse. Our objective was to evaluate real-world biologic therapy duration and reasons for discontinuing treatment.

Methods
We conducted a retrospective analysis of our PsA electronic register from 1994 up to and including April 2019 at our university teaching hospital. We had access to full patient records including details on co-morbidities, drugs and disease management.

Results
335 patients were identified with PsA. 58% were female with mean age 46 yr (13-81). 113 (33.7%) patients had been treated with a biologic with 105 (93%) continuing at the time of analysis. 60 individuals were prescribed combination therapy with DMARDs. Mean age was 43.3 (13-81) with 56% women. The biologics sample was ethnically diverse including 80% White Caucasian patients, 17% Asian and others (3%). Significant co-morbidities included cardiovascular disease (18.6%) and diabetes (4.4%). Eight different biologics were in use with adalimumab being the most prescribed (67%). 35 (30.9%) patients had stopped biologics at some point with 76 episodes of cessation. 6% of our sample had discontinued two or more biologic treatments. The mean duration before biologic therapy was discontinued was 18.2 months (8 days to 9.5 years), which was almost twice as long as the average period before discontinuing a DMARD (9.9 months). Main reasons for stopping treatment included 23% each due to GI symptoms, neurological causes, cutaneous symptoms and other side effects. The remaining 8% reported fatigue as the reason for stopping therapy.

Conclusion
To our knowledge this is the first dedicated retrospective review of a large real world PsA cohort comparing drug survival and tolerability of biologics against DMARDs. Biologic therapies are well tolerated in psoriatic arthritis. There is no significant difference amongst various modes of action. Over a quarter of the patients discontinue the drug owing to intolerance with mean drug survival of 18 months. In contrast nearly two-thirds were intolerant of DMARDs and stopped within ten months. Thus both the rate and duration of biologic retention is significantly better than conventional DMARDs. This has significant economic impact as NICE guidelines require an adequate trial of two DMARDs for six months prior to advanced therapy. However, this approach is unlikely to be cost effective as the disease progresses whilst patients struggle with DMARDs prescription and thus delay biologics which are more likely to be tolerated and retained longer. Hence there is an urgent need to review NICE guidelines to allow earlier employment of biologics in the treatment paradigm with significant benefits to both patients and the health economy.
Disclosures: I. Jawad: None. M.K. Nisar: None.
O35 Efficacy & safety of tocilizumab in GCA: a multi-centre experience of NHS clinical practice
Authors: Sebastian Alwin , Kayani Abdul , Ranasinghe Chavini , Hall Frances , Ransom Colin , Jayne David , Quick Vanessa , Hughes Mark , Stack John , Mukhtyar Chetan , Coath Fiona , Bharadwaj Anurag , Hajela Vijay , Butler Stephanie , Lwin May , Edwards Christopher , Whitlock Madeline , Dasgupta Bhaskar 
Published: April 2020

Abstract

Background
Giant cell arteritis (GCA) has a relapsing, remitting course with ischemic/vascular damage in a number of cases. Glucocorticoids (GC) remain mainstay of treatment with SAEs e.g. diabetes and fractures commonly seen. The GiACTA trial of tocilizumab (TCZ) in GCA led to NICE approval for 12 month’s therapy in relapsing/ refractory disease. We report real life experience in 51 cases.

Methods
Multicentre retrospective data collected through ENRAD and individual centres across England (Table 1). Outcomes were as assessed by supervising clinicians.

Results
Fifty-one patients were treated with TCZ (26 cranial, 13 LVV, 11 both). 11 (22.0%) had prior permanent sight loss due to AION, CRAO or both. One died prior to TCZ, from recurrent cerebral infarcts. Mean age was 71 years with 66.7% females. Ultrasound (US) was used for diagnosis in 28 (56.0%), exclusively or in combination with other tests such as biopsy, PET-CT or CTA. 70% had prior DMARD (LEF/MTX/AZT/MMF/CYC, mean duration 58 weeks). MTX was used in 50% alone or combination. Initial TCZ was given as subcutaneous or intravenous (85.4% and 14.6%). TCZ indication in 89.8% was relapsing, refractory or ischemic disease. Steroid AEs that prevented optimal GC dosing constituted 10% of TCZ indication. Mean follow up was 31 weeks, 30 (58.8%) continuing TCZ uninterrupted, 4 completed 12 months, 4 discontinued due to SAEs. Ten had brief interruptions due to minor AEs. One restarted after 12 months due to flare but died 12 weeks later from abdominal aortic aneurysm rupture. At follow up, 37(74%) were in remission with a mean GC dose of 6.97 mg (mean GC dose pre-TCZ 33.2 mg), Thirty-two (65.3%) ≤ 5mg. In 4 (8%) outcome could not be assessed as either they started TCZ recently or about to start. In 53% lipids were not checked after commencing TCZ. AEs seen were 37.0%.

Conclusion
In clinical practice, TCZ is efficacious and safe in relapsing/refractory/ischemic GCA. I.V. route is an option awaiting NHSE approval in refractory visual symptoms. Infections and other AEs do occur but overall safety profile is acceptable. US is excellent in identifying patients at need and is a useful disease activity monitoring tool.

Disclosures
A. Sebastian: None. A. Kayani: None. C. Ranasinghe: None. F. Hall: Consultancies; Sobi, S. Grants/research support; Actelion. C. Ransom: None. D. Jayne: None. V. Quick: Honoraria; Roche. M. Hughes: None. J. Stack: Member of speakers’ bureau; Roche. C. Mukhtyar: None. F. Coath: None. A. Bharadwaj: None. V. Hajela: None. S. Butler: Consultancies; Lily. M. Lwin: None. C. Edwards: Consultancies; Roche, Chugai. Grants/research support; Roche, Chugai. M. Whitlock: None. B. Dasgupta: Consultancies; Roche, Sanofi, GSK. Grants/research support; Roche.
O41 Percentage body fat as a predictor for fragility fracture: an observational study
Authors: Beith Dominic T , Bukhari Marwan 
Published: April 2020

Abstract

Background
A body mass index (BMI) of less than 19 is a known risk factor for the development of osteoporosis and thus increases the propensity of one having a fragility fracture. Bone mineral density (BMD) referrals are aided by the FRAX™ tool, which contains BMI in order to calculate the ten-year fracture risk. We aimed to investigate the effect of percentage body fat on risk of fracture referred for BMD estimation.

Methods
Between June 2004 and October 2015, patients were referred for bone mineral density (BMD) estimation in a scanner in the North West of England. All patients were referred with all FRAX™ indications including rheumatoid arthritis, excess alcohol, steroids, family history of fracture and secondary osteoporosis. The cohort was divided into quintiles of ascending body mass percentage. Logistical regression was then applied before adjusting for age at scan, gender and total left BMD comparing patients with a fracture and those that had not.

Results
35,759 patients were referred for scanning during the period. 22,765 (63.66%) were referred for BMD estimation and had body fat percentage measured. Mean age at scan was 63.16 (SD 12.86) and 18,961 (88.29%) of the cohort were females. 8,072 (35.46%) had a fracture. More fractures were seen in higher quintiles of percentage body fat, 1,693 (20.97%) compared to 1,580 (19.57%) in females (p = &lt;0.05). Predictors shown in the Table 1 below adjusted for age at scan, gender and total left BMD. Logistical regression of the quintiles after adjustment shows statistical significance in quintiles 3, 4 and 5 as well as for age at scan and total left BMD. Other predictors did not shows statistical significance p &gt; 0.05.

Conclusion
Our study of 22,765 patients referred for BMD estimations opposes current literature on the effect of BMI on fragility fractures. The data shows that increasing percentage body fat in associated with an increased propensity of fragility fractures in those with BMI as a FRAX™ indicator. Currently percentage body fact is not featured in the FRAX™ tool and further work needs to be done to show the relationship between fracture risk and percentage body fat.

Disclosures
D.T. Beith: None. M. Bukhari: None.