bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detection of self-harm and suicidal ideation in emergency department triage notes
Authors: Rozova Vlada , Witt Katrina , Robinson Jo , Li Yan , Verspoor Karin 
Published: November 2021

Abstract

Objective
Accurate identification of self-harm presentations to Emergency Departments (ED) can lead to more timely mental health support, aid in understanding the burden of suicidal intent in a population, and support impact evaluation of public health initiatives related to suicide prevention. Given lack of manual self-harm reporting in ED, we aim to develop an automated system for the detection of self-harm presentations directly from ED triage notes.

Materials and methods
We frame this as supervised classification using natural language processing (NLP), utilizing a large data set of 477 627 free-text triage notes from ED presentations in 2012–2018 to The Royal Melbourne Hospital, Australia. The data were highly imbalanced, with only 1.4% of triage notes relating to self-harm. We explored various preprocessing techniques, including spelling correction, negation detection, bigram replacement, and clinical concept recognition, and several machine learning methods.

Results
Our results show that machine learning methods dramatically outperform keyword-based methods. We achieved the best results with a calibrated Gradient Boosting model, showing 90% Precision and 90% Recall (PR-AUC 0.87) on blind test data. Prospective validation of the model achieves similar results (88% Precision; 89% Recall).

Discussion
ED notes are noisy texts, and simple token-based models work best. Negation detection and concept recognition did not change the results while bigram replacement significantly impaired model performance.

Conclusion
This first NLP-based classifier for self-harm in ED notes has practical value for identifying patients who would benefit from mental health follow-up in ED, and for supporting surveillance of self-harm and suicide prevention efforts in the population.
Determination of Gliadin as a Measure of Gluten in Food by R5 Sandwich ELISA RIDASCREEN® Gliadin Matrix Extension: Collaborative Study 2012.01
Authors: Lacorn Markus , Dubois Tina , Weiss Thomas , Zimmermann Lisa , Schinabeck Teresa-Maria , Loos-Theisen Simone , Scherf Katharina 
Published: November 2021

Abstract

Background
According to Codex Alimentarius, food products containing less than 20 mg/kg gluten can be labeled as “gluten-free.” Since 2002, the R5 antibody method allowed determination of gluten levels and led to a huge improvement of products available to celiac disease (CD) patients.

Method
The R5-containing test kit RIDASCREEN® Gliadin in combination with the cocktail solution was endorsed as Codex Type 1 Method in 2006 based on a collaborative study with corn-based bread, rice-based dough, wheat starches, rice, and corn flour. In 2012, the method was approved as First Action Official MethodSM2012.01 with an “in foods” claim. For Final Action in 2016, the matrix claim was reduced to rice- and corn-based matrixes.

Objective
Therefore, R-Biopharm decided to start a collaborative study to demonstrate the wide applicability of Official Method 2012.01 for the quantitative analysis of gliadin in soy, starches, pseudo cereals, legumes, spices, juice, nut nougat crème, cream cheese, pesto, meat, vegetarian meat alternative, cookies, dessert, cake, fish, bread, candies, and potatoes. Materials for incurring were the MoniQA wheat flour and the PWG gliadin preparation.

Results
Gliadin levels ranged from 3.4 up to 27.4 mg gliadin per kg. The results of the collaborative study with 14 participating laboratories showed recoveries ranging from 80 to 130%. Relative reproducibility standard deviations for contaminated samples were between 9.8 and 27.7%.

Conclusions
The collaborative study results confirmed that the method is accurate and suitable to measure gliadin in important gluten-free food matrixes.

Highlights
The title and applicability statement of Official Method 2012.01 were changed as proposed.
Prophylactic subtotal colectomy in a patient with an AXIN2 mutation
Authors: Vierra Benjamin M 
Published: November 2021

Abstract
A number of genetic syndromes that predispose patients to colon cancer have been well described, allowing for improved surveillance, diagnosis and treatment. However, other syndromes likely exist but have yet to be thoroughly characterized. I report the case of a 50-year-old woman who was found to have over 50 polyps on routine screening colonoscopy. Genetic sequencing revealed a mutation in Axin2, a rare gene implicated in oligodontia-colorectal cancer syndrome. It was later found that the patient lacks several permanent teeth, as does her mother, who also had a history of multiple colonic polyps. Given the rarity of Axin2 mutations, there are no guidelines for management of such patients. This highlights the importance of a thorough review of system when screening for colon cancer as well as documenting cases of Axin2 mutations to create management guidelines for these patients.
Mass, morphing, metallicities: the evolution of infalling high velocity clouds
Authors: Heitsch F , Marchal A , Miville-Deschênes M-A , Shull J M , Fox A J 
Published: November 2021

ABSTRACT
We revisit the reliability of metallicity estimates of high velocity clouds with the help of hydrodynamical simulations. We quantify the effect of accretion and viewing angle on metallicity estimates derived from absorption lines. Model parameters are chosen to provide strong lower limits on cloud contamination by ambient gas. Consistent with previous results, a cloud traveling through a stratified halo is contaminated by ambient material to the point that &lt;10 per cent of its mass in neutral hydrogen consists of original cloud material. Contamination progresses nearly linearly with time, and it increases from head to tail. Therefore, metallicity estimates will depend on the evolutionary state of the cloud, and on position. While metallicities change with time by more than a factor of 10, well beyond observational uncertainties, most lines-of-sight range only within those uncertainties at any given time over all positions. Metallicity estimates vary with the cloud’s inclination angle within observational uncertainties. The cloud survives the infall through the halo because ambient gas continuously condenses and cools in the cloud’s wake and thus appears in the neutral phase. Therefore, the cloud observed at any fixed time is not a well-defined structure across time, since material gets constantly replaced. The thermal phases of the cloud are largely determined by the ambient pressure. Internal cloud dynamics evolve from drag gradients caused by shear instabilities, to complex patterns due to ram-pressure shielding, leading to a peloton effect, in which initially lagging gas can catch up to and even overtake the head of the cloud.
Implications of spicule activity on coronal loop heating and catastrophic cooling
Authors: Nived V N , Scullion E , Doyle J G , Susino R , Antolin P , Spadaro D , Sasso C , Sahin S , Mathioudakis M 
Published: November 2021

ABSTRACT
We report on the properties of coronal loop foot-point heating with observations at the highest resolution, from the CRisp Imaging Spectro-Polarimeter located at the Swedish 1-m Solar Telescope and co-aligned NASA Solar Dynamics Observatory observations, of Type II spicules in the chromosphere and their signatures in the extreme ultraviolet (EUV) corona. Here, we address one important issue, as to why there is not always a one-to-one correspondence, between Type II spicules and hot coronal plasma signatures, i.e. beyond TR temperatures. We do not detect any difference in their spectral properties in a quiet Sun region compared to a region dominated by coronal loops. On the other hand, the number density close to the foot-points in the active region is found to be an order of magnitude higher than in the quiet Sun case. A differential emission measure analysis reveals a peak at ∼5 × 105 K of the order of 1022 cm−5 K−1. Using this result as a constraint, we conduct numerical simulations and show that with an energy input of 1.25 × 1024 erg (corresponding to ∼10 RBEs contributing to the burst) we manage to reproduce the observation very closely. However, simulation runs with lower thermal energy input do not reproduce the synthetic AIA 171 Å signatures, indicating that there is a critical number of spicules required in order to account for the AIA 171 Å signatures in the simulation. Furthermore, the higher energy (1.25 × 1024 erg) simulations reproduce catastrophic cooling with a cycle duration of ∼5 h, matching a periodicity we observe in the EUV observations.
Theoretical lifetimes and Stark broadening parameters for visible-infrared spectral lines of V i in Arcturus
Authors: Isidoro-García L , de Andrés-García I , Moreno-Conde D , Colón C 
Published: November 2021

ABSTRACT
In this work, the Stark broadening parameters (line widths and line shifts) of 114 visible-infrared spectral lines of neutral vanadium (V i) have been calculated. As in a previous work devoted to their spectral lines in the Ultraviolet (UV)-blue range, these parameters have been calculated using the Griem’s semi-empirical formula and the Cowan code for the calculation of the necessary matrix elements. In addition to their astrophysical interest (the majority of the analysed spectral lines have been detected in Arcturus, in the metal-poor star HD 84937 and in the Sun), these parameters are also relevant in the analysis of plasmas generated in industrial processes in Laser Shock Processes treatments of Ti-6Al-4V type samples.
Using a quadruplet codon to expand the genetic code of an animal
Authors: Xi Zhiyan , Davis Lloyd , Baxter Kieran , Tynan Ailish , Goutou Angeliki , Greiss Sebastian 
Published: November 2021

Abstract
Genetic code expansion in multicellular organisms is currently limited to the use of repurposed amber stop codons. Here, we introduce a system for the use of quadruplet codons to direct incorporation of non-canonical amino acids in vivo in an animal, the nematode worm Caenorhabditis elegans. We develop hybrid pyrrolysyl tRNA variants to incorporate non-canonical amino acids in response to the quadruplet codon UAGA. We demonstrate the efficiency of the quadruplet decoding system by incorporating photocaged amino acids into two proteins widely used as genetic tools. We use photocaged lysine to express photocaged Cre recombinase for the optical control of gene expression and photocaged cysteine to express photo-activatable caspase for light inducible cell ablation. Our approach will facilitate the routine adoption of quadruplet decoding for genetic code expansion in eukaryotic cells and multicellular organisms.
Negative feedback forDARS2–Fis complex by ATP–DnaA supports the cell cycle-coordinated regulation for chromosome replication
Authors: Miyoshi Kenya , Tatsumoto Yuka , Ozaki Shogo , Katayama Tsutomu 
Published: November 2021

AbstractIn Escherichia coli, the replication initiator DnaA oscillates between an ATP- and an ADP-bound state in a cell cycle-dependent manner, supporting regulation for chromosome replication. ATP–DnaA cooperatively assembles on the replication origin using clusters of low-affinity DnaA-binding sites. After initiation, DnaA-bound ATP is hydrolyzed, producing initiation-inactive ADP–DnaA. For the next round of initiation, ADP–DnaA binds to the chromosomal locus DARS2, which promotes the release of ADP, yielding the apo-DnaA to regain the initiation activity through ATP binding. This DnaA reactivation by DARS2 depends on site-specific binding of IHF (integration host factor) and Fis proteins and IHF binding to DARS2 occurs specifically during pre-initiation. Here, we reveal that Fis binds to an essential region in DARS2 specifically during pre-initiation. Further analyses demonstrate that ATP–DnaA, but not ADP–DnaA, oligomerizes on a cluster of low-affinity DnaA-binding sites overlapping the Fis-binding region, which competitively inhibits Fis binding and hence the DARS2 activity. DiaA (DnaA initiator-associating protein) stimulating ATP–DnaA assembly enhances the dissociation of Fis. These observations lead to a negative feedback model where the activity of DARS2 is repressed around the time of initiation by the elevated ATP–DnaA level and is stimulated following initiation when the ATP–DnaA level is reduced.
Structure of CRL2Lrr1, the E3 ubiquitin ligase that promotes DNA replication termination in vertebrates
Authors: Zhou Haixia , Zaher Manal S , Walter Johannes C , Brown Alan 
Published: November 2021

Abstract
When vertebrate replisomes from neighboring origins converge, the Mcm7 subunit of the replicative helicase, CMG, is ubiquitylated by the E3 ubiquitin ligase, CRL2Lrr1. Polyubiquitylated CMG is then disassembled by the p97 ATPase, leading to replication termination. To avoid premature replisome disassembly, CRL2Lrr1 is only recruited to CMGs after they converge, but the underlying mechanism is unclear. Here, we use cryogenic electron microscopy to determine structures of recombinant Xenopus laevis CRL2Lrr1 with and without neddylation. The structures reveal that CRL2Lrr1 adopts an unusually open architecture, in which the putative substrate-recognition subunit, Lrr1, is located far from the catalytic module that catalyzes ubiquitin transfer. We further demonstrate that a predicted, flexible pleckstrin homology domain at the N-terminus of Lrr1 is essential to target CRL2Lrr1 to terminated CMGs. We propose a hypothetical model that explains how CRL2Lrr1’s catalytic module is positioned next to the ubiquitylation site on Mcm7, and why CRL2Lrr1 binds CMG only after replisomes converge.
Firm dynamics by age and size classes and the choice of size measure
Authors: Giannoulakis Stelios , Sakellaris Plutarchos 
Published: November 2021

AbstractThe relationship of firm size and age to its growth and survival differs depending on whether the size is measured by sales or employment. Using a large dataset of Greek firms over the period 1999–2014, we find the following patterns. Controlling for age, there is a strong negative growth–size relationship when measuring size with sales, but a strong positive one when measuring size with employment. Controlling for size, there is a positive monotonic survival–age relationship when measuring size with sales, whereas survival is negatively related with age for young firms when we measure size with employment. Our results indicate that public policies aimed at supporting SMEs should be specialized to the employment scale and the sales scale of enterprises, separately.
La prise en charge des exacerbations aiguës de l’asthme chez les enfants
Authors: Trottier Evelyne D , Chan Kevin , Allain Dominic , Chauvin-Kimoff Laurel 
Published: November 2021

Abstract
Les enfants et les adolescents atteints d’exacerbations aiguës de l’asthme se rendent souvent à l’urgence à cause de signes de détresse respiratoire. Les épisodes les plus graves ont un potentiel mortel. Pour que les traitements soient efficaces, le patient doit faire l’objet d’une évaluation exacte et rapide de la gravité de la crise d’asthme. Le présent document de principes traite de l’évaluation, de la prise en charge et de la disposition des patients pédiatriques ayant un diagnostic connu d’asthme qui consultent à cause d’une exacerbation aiguë. Les directives portent sur l’évaluation de la gravité de l’asthme, les considérations thérapeutiques, le plan de congé approprié, le suivi et la prescription de corticostéroïdes inhalés pour éviter de nouvelles exacerbations et limiter la morbidité chronique.
Piriformospora indica recruits host-derived putrescine for growth promotion in plants
Authors: Kundu Anish , Mishra Shruti , Kundu Pritha , Jogawat Abhimanyu , Vadassery Jyothilakshmi 
Published: November 2021

Abstract
Growth promotion induced by the endosymbiont Piriformospora indica has been observed in various plants; however, except growth phytohormones, specific functional metabolites involved in P. indica-mediated growth promotion are unknown. Here, we used a gas chromatography-mass spectrometry-based untargeted metabolite analysis to identify tomato (Solanum lycopersicum) metabolites whose levels were altered during P. indica-mediated growth promotion. Metabolomic multivariate analysis revealed several primary metabolites with altered levels, with putrescine (Put) induced most significantly in roots during the interaction. Further, our results indicated that P. indica modulates the arginine decarboxylase (ADC)-mediated Put biosynthesis pathway via induction of SlADC1 in tomato. Piriformospora indica did not promote growth in Sladc1-(virus-induced gene silencing of SlADC1) lines of tomato and showed less colonization. Furthermore, using LC–MS/MS we showed that Put promoted growth by elevation of auxin (indole-3-acetic acid) and gibberellin (GA4 and GA7) levels in tomato. In Arabidopsis (Arabidopsis thaliana) adc knockout mutants, P. indica colonization also decreased and showed no plant growth promotion, and this response was rescued upon exogenous application of Put. Put is also important for hyphal growth of P. indica, indicating that it is co-adapted by both host and microbe. Taken together, we conclude that Put is an essential metabolite and its biosynthesis in plants is crucial for P. indica-mediated plant growth promotion and fungal growth.
P009 Osteoporosis is a frequent complication in enthesitis related arthritis patients
Authors: Ferjani Hanene , Bettaieb Hiba , Maatallah Kaouther , Ben Nessib Dorra , Triki Wafa , Kaffal Dhia , Hamdi Wafa 
Published: November 2021

Abstract

Background
Enthesitis related arthritis (ERA) represents a clinical entity of juvenile idiopathic arthritis. This chronic rheumatic disease may lead to early bone mass loss and increase risk fracture. The aims of this study were to evaluate the prevalence of clinical osteoporosis in patients with ERA and to identify what factors are associated with increased occurrence of osteoporosis.

Methods
We reviewed the medical records of patients with confirmed ERA. We analyzed their demographic data and the clinical characteristics. Dual-energy X-ray absorptiometry (DEXA) was used to determine bone status. Osteoporosis was defined as Z score &lt;-2.5DS. Disease activity was evaluated by: erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) and Bath Ankylosing Spondylitis Disease Activity Index (BASDAI). Data were analyzed using the SPSS statistical package. A P-value &lt; 0.05 was considered significant.

Results
Thirty-three patients (27 male and 7 female) with a mean age at of 23.8 ± 7.5 years were enrolled. The mean age at disease onset was 12 ± 2.6 years. Median disease duration was 108 months [12–408]. The median ESR and CRP levels were 35 mm/h [8–90] and 20 mg/l [1–70] respectively. Median BASDAI score was 4.7 [1–9.7]. At bone densitometry, osteoporosis and osteopenia were found in 44.1% and 23.5% cases respectively. None of the patients had a history of osteoporotic fractures. Long term corticosteroid therapy and sedentarily were noted in 18.2% and 47.1% of patients respectively. On statistical analysis, osteoporosis was associated with these parameters: age at ERA onset (P = 0.035), disease duration (P = 0.04), CRP (P = 0.009), BASDAI score (P = 0.05) and sedentarily (P = 0.031). Neither corticosteroid therapy (P = 0.68) nor high ESR level (P = 0.73) were associated with osteoporosis.

Conclusion
In this study, osteoporosis was a common extra articular feature during ERA. As adult spondyloarthritis, disease activity, duration and sedentarily seem to be associated with the bone loss.
P046 A review and retrospective case series of paediatric Sjögren’s syndrome from Southern Africa
Authors: Akhalwaya S Y , Webb K , Scott C 
Published: November 2021

Abstract

Background
Paediatric Sjögren’s syndrome (pSS) is an uncommon autoimmune paediatric disease, rarely reported in children in Africa. It remains an important consideration in a child with parotid swelling. Here, we present a retrospective case-series of four patients from a paediatric rheumatology clinic in South Africa and discuss some of the difficulties of diagnosis in our context.

Methods
We performed a retrospective analysis of patients who attend the Red Cross War Memorial Hospital Paediatric Rheumatology clinic between 2010 and 2019.

Result
The four patients diagnosed with Sjögren’s all had varied presentations and disease courses. There were 3 females and 1 male and the ages at diagnosis ranged from 6 to 19 years old. The time to diagnosis was prolonged and ranged from 1 month to 10 years. Two patients with primary pSS presented with extra-articular manifestations of arthritis, abdominal pain and fatigue, followed by dry mouth, dry eyes, parotid swelling and and suggestive histopathology. The remaining 2 patients had a secondary pSS due to juvenile onset SLE and tuberculosis respectively.

Conclusion
In less resourced settings the diagnosis of pSS is often delayed. Both patients with primary pSS had preceding extra-glandular manifestations. In less resourced settings, infectious diseases may present as pSS and associated rheumatic diseases causing secondary pSS must be considered.
P049 Comparison between the ACR 1997, SLICC 2012 and EULAR/ACR 2019 classification criteria in juvenile systemic lupus erythematosus
Authors: Faid T , Menjel I , Sakhi A , Bouayed K 
Published: November 2021

Abstract

Background
Juvenile systemic lupus erythematosus is a multisystem inflammatory autoimmune disease affecting patients under 16 years old. Diagnosis may be difficult because of the large clinical heterogeneity. Classification criteria are important to ensure a clear definition and consistent inclusion of patients in clinical trials. The objective of the work: is to Compare the performance of the classification criteria of the American College of Rheumatology (ACR 1997), those of the Systemic Lupus International Collaborating Clinics (SLICC 2012) and the new classification criteria together with the European League Against Rheumatism “EULAR” and the American College of Rheumatology “ACR” (EULAR/ACR 2019).

Methods
This is a cross-sectional retrospective study carried out in a tertiary care service over a period of one year, from January 1, 2020 to December 31, 2020. The patients were subjected to the different classification criteria ACR 1997, SLICC 2012 and EULAR/ACR 2019. All our patients were matched in age and sex with control cases followed for inflammatory disease (12 control cases).

Results
Six patients were diagnosed with juvenile systemic lupus erythematosus (JSL) over the period of our study. A clear predominance of women was noted with a sex ratio of 5 girls/1 boy. The mean age at the time of diagnosis was 9 years (extremes: 3 –12 years). The diagnosis was made after an average delay of 5 months (extremes: 1–12 months). All of our patients met the three classification criteria. Sensitivity to all criteria was noted at diagnosis and during the first months of follow-up with higher sensitivity for SLICC criteria. Regarding the control cases, 3 patients met the ACR 1997 criteria.

Conclusion
In this population of Juvenile systemic lupus erythematosus, the SLICC criteria gave the best results in terms of sensitivity and precision at the time of diagnosis and during the first months of follow-up, while the ACR 1997 criteria were less specific.