bluuebunny/crossref_metadata_2025_split huggingface dataset:
Citizens of the City: Undocumented Latinx Migrants Organising Politically in Post-Katrina New Orleans
Authors: Daser Deniz 
Published: March 2021

Abstract
Across the globe marginalised urban residents have organised for improved access to rights nominally afforded them as citizens. While studies of such insurgent citizenship movements mostly focus on formal citizens, I examine here how undocumented migrants have drawn upon past labour to organise for improved working conditions and the “right to the city” free of deportation. Based on ethnographic fieldwork with Latinx migrants who worked in post-Hurricane Katrina rebuilding in New Orleans, Louisiana, this study identified wage theft, work injury, and potential deportation as shaping their political activism. As reconstruction ended and immigration enforcement hardened throughout the 2010s, these workers framed their past labour as a moral and economic contribution worthy of rights and recognition. Key US industries such as construction rely on undocumented workers. These findings thus contribute to a growing literature on how undocumented migrants are also insurgent citizens by shifting analysis to labour’s importance in movement building.
Hollywood and the Myth of Criminal Convergence. The Case of Sicario: Day of the Soldado
Authors: Massari Alice 
Published: March 2021

Abstract
Narratives of drug cartels progressively assuming control of migration routes by smuggling and trafficking migrants and Islamic terrorists across borders is not only common in academic accounts and international organizations’ reports. It is also emerging in popular culture. This article sheds light on how the myth of criminal convergence can be created and conveyed to the public through crime-action films. I look at one of the most important places for mythmaking of any kind: Hollywood. Based on a visual social semiotic analysis of the film Sicario: Day of the Soldado, this article will show how the myth of convergence is conveyed throughout it, and what its implications are. It will argue that the rhetoric of criminal convergence fuels a simplistic account of the existence of a battle between good (law enforcement) and evil (criminals working on all sorts of interconnected cross-border crimes), thereby legitimizing every action in the fight against crime.
Intra-annual dynamics of cambial and xylem phenology in subalpine conifers at Deogyusan National Park in the Republic of Korea
Authors: Park Jun-Hui , Choi En-Bi , Park Hong-Chul , Lee Na-Yeon , Seo Jeong-Wook 
Published: March 2021

AbstractSubalpine conifers are highly sensitive to climatic changes. In these trees, the intra-annual dynamics of cambial activity and phenological process in xylem development are closely associated with climatic conditions. However, these scientific findings have not been verified for subalpine conifers in the Republic of Korea. Therefore, we initiated such a study with four subalpine conifers, viz. Abies koreana, Pinus koraiensis, Taxus cuspidata, and Picea jezoensis, growing between 1573 and 1594 m a.s.l. at Deogyusan National Park. Microcores (Ø 2 mm) of these trees were obtained using a mini borer, called as Trephor, every week between April 7 and September 25 in 2017 to monitor their growing seasons, the intra-annual dynamics of the cambial activity, and the number of cells during phenological phases of cell enlargement and cell-wall thickening. For the study, five trees were selected for each conifer species. Results showed that the cambial activity of A. koreana, P. koraiensis, and P. jezoensis required at least 73.8 heat-sum values, whereas the T. cuspidata needed 109.6 heat-sum. The durations of cambial activity of A. koreana, P. koraiensis, T. cuspidata, and P. jezoensis were 134 (127–144), 113 (92–128), 113 (106–120), and 100 (76–128) days, respectively. The intra-annual variations of the number of cells in the cambium, during the cell enlargement phase and cell-wall thickening phase showed predominantly a bell-shaped curve, with a delay of approximately 2–4 weeks between each other. On the other hand, the number of cumulated mature cells showed an S-shaped curve. Through this study, the first fundamental data on phenological process in xylem development of subalpine conifers in the Republic of Korea have been successfully presented.
Clinical and radiological outcomes of acetabular revision surgery with trabecular titanium cups in Paprosky type II and III bone defects
Authors: Perticarini Loris , Rossi Stefano Marco Paolo , Medetti Marta , Benazzo Francesco 
Published: March 2021

Abstract
Background
This prospective study aims to evaluate the mid-term clinical outcomes and radiographic stability of two different types of cementless trabecular titanium acetabular components in total hip revision surgery.

Methods
Between December 2008 and February 2017, 104 cup revisions were performed using trabecular titanium revision cups. Mean age of patients was 70 (range 29–90; SD 11) years. The majority of revisions were performed for aseptic loosening (86 cases, 82.69%), but in all the other diagnoses (18 cases), a significant bone loss (Paprosky type II or III) was registered preoperatively. Bone defects were classified according to Paprosky acetabular classification. We observed 53 type II defects and 42 type III defects. Cups were chosen according to the type of defect.

Results
Average follow-up was 91 (range 24–146) months. Mean Harris Hip Score (HHS) improved from 43.7 (range 25–70; SD 9) preoperatively to 84.4 (range 46–99; SD 7.56) at last follow-up. One (1.05%) cup showed radiographic radiolucent lines inferior to 2 mm and was clinically asymptomatic. One (1.05%) cup was loose and showed periacetabular allograft reabsorption. Kaplan–Meier survivorship was assessed to be 88.54% (95% CI 80.18–93.52%) at 71 months, with failure of the cup for any reason as the endpoint.

Conclusion
Trabecular titanium revision cups showed good clinical and radiographic results at mid-term follow-up in Paprosky type II and III bone defects.

Level of evidence
Level IV prospective case series
R.ROSETTA: an interpretable machine learning framework
Authors: Garbulowski Mateusz , Diamanti Klev , Smolińska Karolina , Baltzer Nicholas , Stoll Patricia , Bornelöv Susanne , Øhrn Aleksander , Feuk Lars , Komorowski Jan 
Published: March 2021

Abstract
Background
Machine learning involves strategies and algorithms that may assist bioinformatics analyses in terms of data mining and knowledge discovery. In several applications, viz. in Life Sciences, it is often more important to understand how a prediction was obtained rather than knowing what prediction was made. To this end so-called interpretable machine learning has been recently advocated. In this study, we implemented an interpretable machine learning package based on the rough set theory. An important aim of our work was provision of statistical properties of the models and their components.

Results
We present the R.ROSETTA package, which is an R wrapper of ROSETTA framework. The original ROSETTA functions have been improved and adapted to the R programming environment. The package allows for building and analyzing non-linear interpretable machine learning models. R.ROSETTA gathers combinatorial statistics via rule-based modelling for accessible and transparent results, well-suited for adoption within the greater scientific community. The package also provides statistics and visualization tools that facilitate minimization of analysis bias and noise. The R.ROSETTA package is freely available at https://github.com/komorowskilab/R.ROSETTA. To illustrate the usage of the package, we applied it to a transcriptome dataset from an autism case–control study. Our tool provided hypotheses for potential co-predictive mechanisms among features that discerned phenotype classes. These co-predictors represented neurodevelopmental and autism-related genes.

Conclusions
R.ROSETTA provides new insights for interpretable machine learning analyses and knowledge-based systems. We demonstrated that our package facilitated detection of dependencies for autism-related genes. Although the sample application of R.ROSETTA illustrates transcriptome data analysis, the package can be used to analyze any data organized in decision tables.
Whole genome de novo sequencing and comparative genomic analyses suggests that Chlamydia psittaci strain 84/2334 should be reclassified as Chlamydia abortus species
Authors: Longbottom David , Livingstone Morag , Ribeca Paolo , Beeckman Delphine Sylvie Anne , van der Ende Arie , Pannekoek Yvonne , Vanrompay Daisy 
Published: March 2021

Abstract
Background
Chlamydia abortus and Chlamydia psittaci are important pathogens of livestock and avian species, respectively. While C. abortus is recognized as descended from C. psittaci species, there is emerging evidence of strains that are intermediary between the two species, suggesting they are recent evolutionary ancestors of C. abortus. Such strains include C. psittaci strain 84/2334 that was isolated from a parrot. Our aim was to classify this strain by sequencing its genome and explore its evolutionary relationship to both C. abortus and C. psittaci.

Results
In this study, methods based on multi-locus sequence typing (MLST) of seven housekeeping genes and on typing of five species discriminant proteins showed that strain 84/2334 clustered with C. abortus species. Furthermore, whole genome de novo sequencing of the strain revealed greater similarity to C. abortus in terms of GC content, while 16S rRNA and whole genome phylogenetic analysis, as well as network and recombination analysis showed that the strain clusters more closely with C. abortus strains. The analysis also suggested a closer evolutionary relationship between this strain and the major C. abortus clade, than to two other intermediary avian C. abortus strains or C. psittaci strains. Molecular analyses of genes (polymorphic membrane protein and transmembrane head protein genes) and loci (plasticity zone), found in key virulence-associated regions that exhibit greatest diversity within and between chlamydial species, reveal greater diversity than present in sequenced C. abortus genomes as well as similar features to both C. abortus and C. psittaci species. The strain also possesses an extrachromosomal plasmid, as found in most C. psittaci species but absent from all sequenced classical C. abortus strains.

Conclusion
Overall, the results show that C. psittaci strain 84/2334 clusters very closely with C. abortus strains, and are consistent with the strain being a recent C. abortus ancestral species. This suggests that the strain should be reclassified as C. abortus. Furthermore, the identification of a C. abortus strain bearing an extra-chromosomal plasmid has implications for plasmid-based transformation studies to investigate gene function as well as providing a potential route for the development of a next generation vaccine to protect livestock from C. abortus infection.
The complete chloroplast genome of Stauntonia chinensis and compared analysis revealed adaptive evolution of subfamily Lardizabaloideae species in China
Authors: Wen Feng , Wu Xiaozhu , Li Tongjian , Jia Mingliang , Liu Xinsheng , Liao Liang 
Published: March 2021

Abstract
Background
Stauntonia chinensis DC. belongs to subfamily Lardizabaloideae, which is widely grown throughout southern China. It has been used as a traditional herbal medicinal plant, which could synthesize a number of triterpenoid saponins with anticancer and anti-inflammatory activities. However, the wild resources of this species and its relatives were threatened by over-exploitation before the genetic diversity and evolutionary analysis were uncovered. Thus, the complete chloroplast genome sequences of Stauntonia chinensis and comparative analysis of chloroplast genomes of Lardizabaloideae species are necessary and crucial to understand the plastome evolution of this subfamily.

Results
A series of analyses including genome structure, GC content, repeat structure, SSR component, nucleotide diversity and codon usage were performed by comparing chloroplast genomes of Stauntonia chinensis and its relatives. Although the chloroplast genomes of eight Lardizabaloideae plants were evolutionary conserved, the comparative analysis also showed several variation hotspots, which were considered as highly variable regions. Additionally, pairwise Ka/Ks analysis showed that most of the chloroplast genes of Lardizabaloideae species underwent purifying selection, whereas 25 chloroplast protein coding genes were identified with positive selection in this subfamily species by using branch-site model. Bayesian and ML phylogeny on CCG (complete chloroplast genome) and CDs (coding DNA sequences) produced a well-resolved phylogeny of Lardizabaloideae plastid lineages.

Conclusions
This study enhanced the understanding of the evolution of Lardizabaloideae and its relatives. All the obtained genetic resources will facilitate future studies in DNA barcode, species discrimination, the intraspecific and interspecific variability and the phylogenetic relationships of subfamily Lardizabaloideae.
Minimal important difference and patient acceptable symptom state for pain, Constant-Murley score and Simple Shoulder Test in patients with subacromial pain syndrome
Authors: Kanto Kari , Lähdeoja Tuomas , Paavola Mika , Aronen Pasi , Järvinen Teppo L. N. , Jokihaara Jarkko , Ardern Clare L. , Karjalainen Teemu V. , Taimela Simo 
Published: March 2021

AbstractBackgroundThe results of clinical trials should be assessed for both statistical significance and importance of observed effects to patients. Minimal important difference (MID) is a threshold denoting a difference that is important to patients. Patient acceptable symptom state (PASS) is a threshold above which patients feel well.ObjectiveTo determine MID and PASS for common outcome instruments in patients with subacromial pain syndrome (SAPS).MethodsWe used data from the FIMPACT trial, a randomised controlled trial of treatment for SAPS that included 193 patients. The outcomes were shoulder pain at rest and on arm activity, both measured with the 0–100 mm visual analogue scale (VAS), the Constant-Murley score (CS), and the Simple Shoulder Test (SST). The transition question was a five-point global rating of change. We used three anchor-based methods to determine the MID for improvement: the receiver operating characteristic (ROC) curve, the mean difference of change and the mean change methods. For the PASS, we used the ROC and 75th percentile methods and calculated estimates using two different anchor question thresholds.ResultsDifferent MID methods yielded different estimates. The ROC method yielded the smallest estimates for MID: 20 mm for shoulder pain on arm activity, 10 points for CS and 1.5 points for SST, with good to excellent discrimination (areas under curve (AUCs) from 0.86 to 0.94). We could not establish a reliable MID for pain at rest. The PASS estimates were consistent between methods. The ROC method PASS thresholds using a conservative anchor question threshold were 2 mm for pain at rest, 9 mm for pain on activity, 80 points for CS and 11 points for SST, with AUCs from 0.74 to 0.83.ConclusionWe recommend the smallest estimate from different methods as the MID, because it is very unlikely that changes smaller than the smallest MID estimate are important to patients: 20 mm for pain VAS on arm activity, 10 points for CS and 1.5 points for SST. We recommend PASS estimates of 9 mm for pain on arm activity, 80 points for CS, and 11 points for SST.Trial registrationClinicalTrials.govNCT00428870 (first registered January 29, 2007).
Onset of acid-neutralizing action of a calcium/magnesium carbonate-based antacid using an artificial stomach model: an in vitro evaluation
Authors: Voropaiev Maxim , Nock Deborah 
Published: March 2021

Abstract
Background
Calcium carbonate antacids are potent over-the-counter antacids, made more effective by adding magnesium carbonate (as in Rennie, Bayer). However, published studies on their onset of action are scarce. Therefore, we carried out an in vitro study comparing Rennie and placebo under simulated conditions of the human stomach (artificial stomach model) to reconfirm the onset of action of Rennie.

Methods
The validated Simulator of the Human Intestinal Microbial Ecosystem apparatus (SHIME, ProDigest, Belgium) was used, comprising five reactors simulating different parts of the human gastrointestinal tract. Both Rennie and placebo were dosed at two tablets per incubation over six independent, 2-h stomach incubations each. Primary objectives: to evaluate the time required to achieve pH 3.0, 3.5, 4.0 and 4.5, as well as the maximum pH reached. Secondary objective: to evaluate pepsin activity over the entire 2-h gastric incubation.

Results
After addition of Rennie, the gastric medium reached a pH of 3.0 within 40 s. The maximum pH of 5.24 was maintained for almost 10 min. In contrast, the maximum pH with placebo was 1.28 during the entire gastric simulation. Furthermore, Rennie strongly reduced the activity of mucosa-damaging pepsin during the period of increased pH. With placebo, the lower pH resulted in consistently high loads of digested peptides, reflecting the high cumulative and instantaneous pepsin activity.

Conclusions
New data is a critical component in informed decision making. Our data confirm the high efficacy and fast onset of acid-neutralizing action of Rennie, which begins to work within seconds.
Patient factors associated with new prescribing of potentially inappropriate medications in multimorbid US older adults using multiple medications
Authors: Jungo Katharina Tabea , Streit Sven , Lauffenburger Julie C. 
Published: March 2021

AbstractBackgroundThe use of potentially inappropriate medications (PIMs) is common in older adults and is associated with potential negative consequences, such as falls and cognitive decline. Our objective was to investigate measurable patient factors associated with new outpatient prescribing of potentially inappropriate medications in older multimorbid adults already using multiple medications.MethodsIn this retrospective US cohort study, we used linked Medicare pharmacy and medical claims and electronic health record data from a large healthcare system in Massachusetts between 2007 and 2014. We identified patients aged ≥65 years with an office visit who had not been prescribed or used a PIM in the prior 180 days. PIMs were defined using 2019 Beers criteria of the American Geriatrics Society. To specifically evaluate factors in patients with polypharmacy and multimorbidity, we selected those who filled medications for ≥90 days (i.e., chronic use) from ≥5 pharmaceutical classes in the prior 180 days and had ≥2 chronic conditions. Multivariable Cox regression analysis was used to estimate the association between baseline demographic and clinical characteristics on the probability of being prescribed a PIM in the 90-day follow-up period.ResultsIn total, we identified 17,912 patients aged ≥65 years with multimorbidity and polypharmacy who were naïve to a PIM in the prior 180 days. Of those, 10,497 (58.6%) were female, and mean age was 78 (SD = 7.5). On average, patients had 5.1 (SD = 2.3) chronic conditions and previously filled 6.1 (SD = 1.4) chronic medications. In total, 447 patients (2.5%) were prescribed a PIM during the 90-day follow-up. Male sex (adjusted hazard ratio (HR) = 1.29; 95%CI: 1.06–1.57), age (≥85 years: HR = 0.75, 95%CI: 0.56–0.99, 75–84 years: HR = 0.87, 95%CI: 0.71–1.07; reference: 65–74 years), ambulatory visits (18–29 visits: HR = 1.42, 95%CI: 1.06–1.92; ≥30 visits: HR = 2.12, 95%CI: 1.53–2.95; reference: ≤9 visits), number of prescribing orders (HR = 1.02, 95%CI: 1.01–1.02 per 1-unit increase), and heart failure (HR = 1.38, 95%CI: 1.07–1.78) were independently associated with being newly prescribed a PIM.ConclusionSeveral demographic and clinical characteristics, including factors suggesting lack of care coordination and increased clinical complexity, were found to be associated with the new prescribing of potentially inappropriate medications. This knowledge could inform the design of interventions and policies to optimize pharmacotherapy for these patients.
Adverse outcomes associated with rapid linear and non-linear patterns of chronic kidney disease progression
Authors: Ali Ibrahim , Chinnadurai Rajkumar , Ibrahim Sara T. , Kalra Philip A. 
Published: March 2021

Abstract
Background
Patients with rapidly declining renal function face the dual threat of end-stage renal disease (ESRD) and mortality prior to ESRD. What is less well characterised is whether the pattern of the renal trajectory, linear or non-linear, unmasks subgroups of rapidly progressing patients that face adverse outcomes in a differential manner.

Methods
An individual eGFR slope was applied to all outpatient estimated glomerular filtration rate (eGFR) values for each patient in the Salford Kidney Study from 2002 to 2018 who had at least 2 years follow-up, ≥4 eGFR values and baseline eGFR 15 to < 60 ml/min/1.73m2. Rapid progression was defined as an annual eGFR slope of ≤ − 3 ml/min/1.73m2/yr and patients were categorised as linear or non-linear progressors based on the nature of their eGFR-time graphs. A Fine-Gray competing risk hazard model was used to determine factors associated with progression to ESRD and with mortality prior to ESRD. Cumulative incidence function curves highlighted differences in outcomes between linear and non-linear patients.

Results
There were 211 rapidly deteriorating patients with linear eGFR trajectories and 61 rapid non-linear patients in the study cohort. Factors associated with ESRD included younger age, male gender, lower baseline eGFR and higher serum phosphate, whilst older age, history of myocardial infarction and anaemia predicted mortality prior to ESRD. Over a median follow-up of 3.7 years, linear progressors reached ESRD sooner whilst those with non-linear progression faced significantly higher rates of mortality prior to ESRD.

Conclusions
Patients with rapid eGFR decline have high rates of adverse outcomes that are differentially expressed in those progressing linearly and non-linearly as a result of differing phenotypic profiles. Consequently, addressing individual risk factor profiles is important to deliver optimal personalised patient care.