bluuebunny/crossref_metadata_2025_split huggingface dataset:
SEAweb: the small RNA Expression Atlas web application
Authors: Rahman Raza-Ur , Liebhoff Anna-Maria , Bansal Vikas , Fiosins Maksims , Rajput Ashish , Sattar Abdul , Magruder Daniel S , Madan Sumit , Sun Ting , Gautam Abhivyakti , Heins Sven , Liwinski Timur , Bethune Jörn , Trenkwalder Claudia , Fluck Juliane , Mollenhauer Brit , Bonn Stefan 
Published: October 2019

AbstractWe present the Small RNA Expression Atlas (SEAweb), a web application that allows for the interactive querying, visualization and analysis of known and novel small RNAs across 10 organisms. It contains sRNA and pathogen expression information for over 4200 published samples with standardized search terms and ontologies. In addition, SEAweb allows for the interactive visualization and re-analysis of 879 differential expression and 514 classification comparisons. SEAweb's user model enables sRNA researchers to compare and re-analyze user-specific and published datasets, highlighting common and distinct sRNA expression patterns. We provide evidence for SEAweb's fidelity by (i) generating a set of 591 tissue specific miRNAs across 29 tissues, (ii) finding known and novel bacterial and viral infections across diseases and (iii) determining a Parkinson's disease-specific blood biomarker signature using novel data. We believe that SEAweb's simple semantic search interface, the flexible interactive reports and the user model with rich analysis capabilities will enable researchers to better understand the potential function and diagnostic value of sRNAs or pathogens across tissues, diseases and organisms.
VDJbase: an adaptive immune receptor genotype and haplotype database
Authors: Omer Aviv , Shemesh Or , Peres Ayelet , Polak Pazit , Shepherd Adrian J , Watson Corey T , Boyd Scott D , Collins Andrew M , Lees William , Yaari Gur 
Published: October 2019

Abstract
VDJbase is a publicly available database that offers easy searching of data describing the complete sets of gene sequences (genotypes and haplotypes) inferred from adaptive immune receptor repertoire sequencing datasets. VDJbase is designed to act as a resource that will allow the scientific community to explore the genetic variability of the immunoglobulin (Ig) and T cell receptor (TR) gene loci. It can also assist in the investigation of Ig- and TR-related genetic predispositions to diseases. Our database includes web-based query and online tools to assist in visualization and analysis of the genotype and haplotype data. It enables users to detect those alleles and genes that are significantly over-represented in a particular population, in terms of genotype, haplotype and gene expression. The database website can be freely accessed at https://www.vdjbase.org/, and no login is required. The data and code use creative common licenses and are freely downloadable from https://bitbucket.org/account/user/yaarilab/projects/GPHP.
APAatlas: decoding alternative polyadenylation across human tissues
Authors: Hong Wei , Ruan Hang , Zhang Zhao , Ye Youqiong , Liu Yaoming , Li Shengli , Jing Ying , Zhang Huiwen , Diao Lixia , Liang Han , Han Leng 
Published: September 2019

AbstractAlternative polyadenylation (APA) is an RNA-processing mechanism on the 3′ terminus that generates distinct isoforms of mRNAs and/or other RNA polymerase II transcripts with different 3′UTR lengths. Widespread APA affects post-transcriptional gene regulation in mRNA translation, stability, and localization, and exhibits strong tissue specificity. However, no existing database provides comprehensive information about APA events in a large number of human normal tissues. Using the RNA-seq data from the Genotype-Tissue Expression project, we systematically identified APA events from 9475 samples across 53 human tissues and examined their associations with multiple traits and gene expression across tissues. We further developed APAatlas, a user-friendly database (https://hanlab.uth.edu/apa/) for searching, browsing and downloading related information. APAatlas will help the biomedical research community elucidate the functions and mechanisms of APA events in human tissues.
DNAproDB: an expanded database and web-based tool for structural analysis of DNA–protein complexes
Authors: Sagendorf Jared M , Markarian Nicholas , Berman Helen M , Rohs Remo 
Published: October 2019

Abstract
DNAproDB (https://dnaprodb.usc.edu) is a web-based database and structural analysis tool that offers a combination of data visualization, data processing and search functionality that improves the speed and ease with which researchers can analyze, access and visualize structural data of DNA–protein complexes. In this paper, we report significant improvements made to DNAproDB since its initial release. DNAproDB now supports any DNA secondary structure from typical B-form DNA to single-stranded DNA to G-quadruplexes. We have updated the structure of our data files to support complex DNA conformations, multiple DNA–protein complexes within a DNAproDB entry and model indexing for analysis of ensemble data. Support for chemically modified residues and nucleotides has been significantly improved along with the addition of new structural features, improved structural moiety assignment and use of more sequence-based annotations. We have redesigned our report pages and search forms to support these enhancements, and the DNAproDB website has been improved to be more responsive and user-friendly. DNAproDB is now integrated with the Nucleic Acid Database, and we have increased our coverage of available Protein Data Bank entries. Our database now contains 95% of all available DNA–protein complexes, making our tools for analysis of these structures accessible to a broad community.
A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes
Authors: Mostajo Nelly F , Lataretu Marie , Krautwurst Sebastian , Mock Florian , Desirò Daniel , Lamkiewicz Kevin , Collatz Maximilian , Schoen Andreas , Weber Friedemann , Marz Manja , Hölzer Martin 
Published: October 2019

Abstract
Although bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies, we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (rna.uni-jena.de/supplements/bats) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology and important host–virus interactions.
Charitable giving when donors are constrained to give a minimum amount
Authors: Cartwright Edward J , Mirza Zarak 
Published: October 2019

Abstract
In some instances charities insist on donors giving more than a minimum amount. In other instances charities frame appeals for funds in a way that suggests there is a minimum donation. So, what are the effects on charitable giving if a minimum donation is required? We first provide a simple theoretical model that shows the effects are ambiguous. We then report the results of two lab experiments that consider very different settings. In the first experiment the only incentive to give is intrinsic motivation. Here we find that a minimum constraint lowers giving. The second experiment involves group interaction with extrinsic incentives to give. Here we find that a minimum constraint increases giving. Our results suggest that the effects of a minimum constraint may depend critically on the mix of intrinsic and extrinsic incentives.
Establishment of xenografts of urological cancers on chicken chorioallantoic membrane (CAM) to study metastasis
Authors: Hu Junhui , Ishihara Moe , Chin Arnold I , Wu Lily 
Published: October 2019

Abstract
Cancer of the urological system commonly occurs in the kidney, bladder, and prostate gland. The clear cell subtype of renal cell carcinoma (ccRCC) constitutes the great majority of kidney cancer. Metastatic ccRCC portends a very poor outcome with no effective treatment available. Prostate cancer is the most common cancer in males in the US. Despite recent advances in selective kinase inhibitors and immunotherapies, the rate of developing new treatment from bench to bedside is slow. A time-consuming step is at the animal drug testing stage, in which the mouse model is the gold standard. In the pursuit to streamline the in vivo cancer biology research and drug development, we explored the feasibility of the chicken chorioallantoic membrane (CAM) model to establish xenografts. The CAM model greatly shortens the time of tumor growth and lowers the cost comparing to immunocompromised mice. We generated CAM xenografts from ccRCC, bladder and prostate cancer, with established cancer cell lines and freshly isolated patient-derived tissues, either as primary tumor cells or small pieces of tumors. The successful CAM engraftment rate from the different tumor sources is 70% or above. Using our previously established metastatic ccRCC mouse model, we showed that the CAM xenograft maintains the same tumor growth pattern and metastatic behavior as observed in mice. Taken together, CAM can serve as a valuable platform to establish new patient-derived xenografts (PDXs) to study tumor biology, thus accelerating the development of individualized treatment to halt the deadly metastatic stage of cancer.
Interaction among inflammasome, autophagy and non-coding RNAs: new horizons for drug
Authors: Pu Qinqin , Lin Ping , Wang Zhihan , Gao Pan , Qin Shugang , Cui Luqing , Wu Min 
Published: October 2019

Abstract
Autophagy and inflammasomes are shown to interact in various situations including infectious disease, cancer, diabetes and neurodegeneration. Since multiple layers of molecular regulators contribute to the interplay between autophagy and inflammasome activation, the detail of such interplay remains largely unknown. Non-coding RNAs (ncRNAs), which have been implicated in regulating an expanding list of cellular processes including immune defense against pathogens and inflammatory response in cancer and metabolic diseases, may join in the crosstalk between inflammasomes and autophagy in physiological or disease conditions. In this review, we summarize the latest research on the interlink among ncRNAs, inflammasomes and autophagy and discuss the emerging role of these three in multiple signaling transduction pathways involved in clinical conditions. By analyzing these intriguing interconnections, we hope to unveil the mechanism inter-regulating these multiple processes and ultimately discover potential drug targets for some refractory diseases.
Opioid Exposure Negatively Affects Antidepressant Response to Venlafaxine in Older Adults with Chronic Low Back Pain and Depression
Authors: Stahl Sarah T , Jung Changgi , Weiner Debra K , Peciña Marta , Karp Jordan F 
Published: October 2019

Abstract

Objective
Serotonin norepinephrine reuptake inhibitors (SNRIs) are commonly co-prescribed with opioids for chronic pain. The purpose of this study was to describe pain and mood response to venlafaxine among older adults with chronic low back pain (CLBP) and depression relative to opioid exposure.

Design
Secondary analyses were collected from a randomized clinical trial testing a stepped-care approach to comorbid pain and depression in older patients: the Addressing Depression and Pain Together study (ADAPT: 2010–2016).

Setting
University-based late-life mental health research clinic.

Subjects
Two hundred twenty-seven adults aged 65+ years with CLBP and depression.

Methods
Participants received six weeks of lower-dose venlafaxine (≤150 mg/d). Pain and depression were measured each week. Response for both pain and depression at the end of six weeks was defined by a ≥30% improvement on a 0–20 numeric rating scale for low back pain and a Patient Health Questionnaire-9 score ≤5. Opioid exposure was analyzed as prescribed (yes or no) and by morphine equivalent dosing (MED).

Results
Patients co-prescribed an opioid were less likely to report a pain response to venlafaxine. MED was negatively correlated with pain response. Depression response was not impacted.

Conclusions
Opioids are negatively associated with older adults’ early analgesic response to lower-dose venlafaxine. These findings suggest that clinicians may wish to consider either nonopioid or alternative antidepressant approaches to pain management in these complex patients. It is reassuring that opioids do not prevent depression response. Future research should examine both longer duration of treatment and a wider range of doses.
NICE UpdateNICE public health guidance update
Authors: Winchester Sarah , Haynes Charlotte , Owen Lesley , Leng Gillian 
Published: October 2019

Abstract
This article covers recent National Institute for Health and Care Excellence guidance and standards relevant to public health with a focus on behaviour change. The article summarizes recommendations for local commissioners and providers to help them tackle a range of behaviours including smoking, poor eating patterns, lack of physical activity and alcohol misuse.
P35 Prevalence of chronic kidney disease in patients with juvenile systemic lupus erythematosus: a single centre study
Authors: Mahfouz Yasmin , Madenidou Anastasia-Vasiliki , Ciurtin Coziana 
Published: September 2019

Abstract

Background
Systemic lupus erythematosus (SLE) is a systemic autoimmune/inflammatory disorder that can affect any organ system. An estimated 10- 20% of all patients with SLE develop clinical disease before the age of 16 years and are therefore classified as juvenile-onset SLE (JSLE). JSLE is characterised by more severe clinical manifestations, such as lupus nephritis, more complications and less favourable outcomes compared to adult-onset SLE. Chronic kidney disease (CKD) refers to a state of irreversible kidney damage and/or reduction of kidney function that is associated with progressive loss of function over time. Lupus nephritis does not always lead to CKD. However, when it does it is associated with increased morbidity and mortality. It is important to identify clinical and laboratory predictors of CKD development in JSLE patients, as a more aggressive treatment approach could be advocated for these patients. In this study we compared the baseline characteristics of JSLE patients with and without chronic kidney disease to ascertain if there are any significant differences between the two groups.

Methods
This is a single-centre retrospective study, who included patients reviewed in our young adult and adolescent clinics. All data were analysed descriptively. Mann-Whitney U or Chi-Square tests were performed to compare the characteristics between the patients with and without CKD. We used the Pearson’s (r) or Kendall’s τ (tau) correlation to examine if there is any association between the CKD and the baseline characteristics.

Results
We identified 44 JSLE patients, out of which 17 (39%) fulfilled the diagnostic criteria for CKD at their last clinical review. The stages of CKD varied from 2 to 5. All patients with CKD also had lupus nephritis, while 5/44 patients (11%) had lupus nephritis without CKD. There were statistical significant differences in the treatments used for patients with and without CKD. As expected, the highest dsDNAlevels were higher in patients with CKD (p = 0.03). There was also a positive moderate correlation (ρ = 0.32) between raised levels of dsDNAand the development of CKD (p = 0.008). We also found a negative moderate correlation (τ= -0.439) between the presence of RF and CKD (p = 0.04).

Conclusion
We found a negative moderate correlation between the presence of RF and CKD, which has also been reported in the literature before. Further research using a large JSLE cohort is suggested to explore further if RF exerts a protective effect against renal disease in SLE. dsDNA is a serological marker of lupus nephritis and it is reasonable that the highest dsDNA correlates with CKD.

Conflicts of Interest
The authors declare no conflicts of interest.
P62 Getting to know you: a quality improvement project designed to enhance paediatric inpatient rehabilitation for those with non-inflammatory musculoskeletal pain
Authors: McKenna Dearbhla , Rooney Madeline , Jackson Paul , Harkness Cathyrn 
Published: October 2019

Abstract

Background
In November 2018 the paediatric rheumatology team in Belfast attended the Bridges self-management course. Bridges reflects on what works well as a team and how you can build upon current practice, with an emphasis upon a self-management approach. There are eleven Bridges principles aiming to help interdisciplinary team’s co-ordinate their service around the patient. Bridges believes that the language we use can improve our clinical practice, especially with regards to problem solving, encouraging self-discovery, encouraging patients to reflect and enabling them to take action.
Our team felt that we should use this approach to enhance our inpatient rehabilitation service. We chose this group of patients as we felt that this can be a challenging group to treat and it can take a long time to build supportive and trusting relationships.

Methods
Prior to commencing this project each member of the multidisciplinary team assessed the patient individually on the first day of admission. In retrospect we discovered that this led to repetition for the patient and this assessment was very clinician led. It also focused on clinician led (SMART) goals and achieving these. We furthermore realised we did not separately ask patients and parents what they wanted to gain from our service.
Our method of improvement was to devise three questionnaires. One for a parent, one for a child under fourteen and over fourteen. These are distributed prior to being assessed by the team, allowing us to gather information and negating the need for repetition. The questionnaire gathers information regarding family members, education, school attendance, additional educational assistance, past medical history. For the patient we ask, what are their main concerns, what has helped so far, what support the patient has, what activities they enjoy as a family and what they hope to gain from their inpatient stay. The patient must fill out a description of their typical day, including their mood. Questions specifically for the parents are asking why their child has been referred, what their main concerns are, to outline their typical day, what do they feel has helped and what do they aim to gain from our team.

Results
We have utilised the questionnaires for every inpatient since January 2019. All team members feel that this new approach allows us to gain valuable information from patients and their parents thus encouraging them to adopt a self-management approach and to prioritise the patient’s story. As a team we feel that we learn a lot about our patients using this method and that it is more time effective. It allows us to identify unrealistic hopes and discuss these.

Conclusion
We believe that using the Bridges approach and by mainly adapting our language skills and organisation we have improved this service.

Conflicts of Interest
The authors declare no conflicts of interest.
Racial differences in systemic sclerosis disease presentation: a European Scleroderma Trials and Research group study
Authors: Jaeger Veronika K , Tikly Mohammed , Xu Dong , Siegert Elise , Hachulla Eric , Airò Paolo , Valentini Gabriele , Matucci Cerinic Marco , Distler Oliver , Cozzi Franco , Carreira Patricia , Allanore Yannick , Müller-Ladner Ulf , Ananieva Lidia P , Balbir-Gurman Alexandra , Distler Jörg H W , Czirják Laszlo , Li Mengtao , Henes Jörg , Jimenez Sergio A , Smith Vanessa , Damjanov Nemanja , Denton Christopher P , DelGaldo Francesco , Saketkoo Lesley Ann , Walker Ulrich A ,   and EUSTAR co-authors
Published: October 2019

AbstractObjectivesRacial factors play a significant role in SSc. We evaluated differences in SSc presentations between white patients (WP), Asian patients (AP) and black patients (BP) and analysed the effects of geographical locations.MethodsSSc characteristics of patients from the EUSTAR cohort were cross-sectionally compared across racial groups using survival and multiple logistic regression analyses.ResultsThe study included 9162 WP, 341 AP and 181 BP. AP developed the first non-RP feature faster than WP but slower than BP. AP were less frequently anti-centromere (ACA; odds ratio (OR) = 0.4, P &lt; 0.001) and more frequently anti-topoisomerase-I autoantibodies (ATA) positive (OR = 1.2, P = 0.068), while BP were less likely to be ACA and ATA positive than were WP [OR(ACA) = 0.3, P &lt; 0.001; OR(ATA) = 0.5, P = 0.020]. AP had less often (OR = 0.7, P = 0.06) and BP more often (OR = 2.7, P &lt; 0.001) diffuse skin involvement than had WP. AP and BP were more likely to have pulmonary hypertension [OR(AP) = 2.6, P &lt; 0.001; OR(BP) = 2.7, P = 0.03 vs WP] and a reduced forced vital capacity [OR(AP) = 2.5, P &lt; 0.001; OR(BP) = 2.4, P &lt; 0.004] than were WP. AP more often had an impaired diffusing capacity of the lung than had BP and WP [OR(AP vs BP) = 1.9, P = 0.038; OR(AP vs WP) = 2.4, P &lt; 0.001]. After RP onset, AP and BP had a higher hazard to die than had WP [hazard ratio (HR) (AP) = 1.6, P = 0.011; HR(BP) = 2.1, P &lt; 0.001].ConclusionCompared with WP, and mostly independent of geographical location, AP have a faster and earlier disease onset with high prevalences of ATA, pulmonary hypertension and forced vital capacity impairment and higher mortality. BP had the fastest disease onset, a high prevalence of diffuse skin involvement and nominally the highest mortality.
HUMAN EXPOSURE TO BACKGROUND RADIATION IN ORTUM, KENYA
Authors: Wanjala F O , Hashim N O , Otwoma D , Nyambura C , Kebwaro J , Mauring A , Bartilol J , Chege M 
Published: October 2019

Abstract
The activity concentration of radionuclides 238U, 232Th and 40K in soil and the absorbed dose rate (ADRA) at 1 m above the ground in Ortum was determined. The activity concentration in soils ranged from 33 to 85, 20 to 67 and 148–1019 Bq kg–1, respectively with an average of 40 ± 1.43, 56 ± 1.46 and 425 ± 19.24 Bq kg–1, respectively. The activity concentration of 232Th and 238U was found to reduce with increasing depth while that of 40K increased with increasing depth. The average activity concentration in soil was higher than the world average values. The average ADRA in air at 1 m above the ground was found to be 112 ± 29.6 nGy h–1. The soil and rocks in Ortum are recommended for use because the activity concentration of the terrestrial radionuclides is lower than the recommended threshold values.