bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative effectiveness of oral prostacyclin pathway drugs on hospitalization in patients with pulmonary hypertension in the United States: a retrospective database analysis
Authors: McConnell John W. , Tsang Yuen , Pruett Janis , III William Drake 
Published: March 2020

Two oral medications targeting the prostacyclin pathway are available to treat pulmonary arterial hypertension in the United States: oral treprostinil and selexipag. We compared real‐world hospitalization in patients receiving these medications. A retrospective administrative claims study was conducted using the Optum® Clinformatics® Data Mart database. Patients with pulmonary hypertension were identified using diagnostic codes. Cohort inclusion required age ≥ 18 years, first oral treprostinil or selexipag prescription between 1 January 2015 and 30 September 2017 (index date), and continuous enrollment in the prior ≥6 months. Patients who switched index drug were excluded. Follow‐up was from index date until the first of end of index drug exposure, end of continuous enrollment, death, or 31 December 2017. Multivariable Cox proportional hazard and Poisson regression were used to compare risk and rate, respectively, of hospitalization associated with oral treprostinil vs. selexipag, adjusting for potential confounders. The study cohort included 99 patients receiving oral treprostinil and 123 receiving selexipag. Mean age was 61 years, and most patients were females (71%). Compared with oral treprostinil, selexipag was associated with a 46% lower risk of all‐cause hospitalization (hazard ratio 0.54, 95% confidence interval 0.31, 0.92; P = 0.02), a 47% lower risk of pulmonary hypertension‐related hospitalization (hazard ratio 0.53, 95% confidence interval 0.31, 0.93; P = 0.03), a 42% lower all‐cause hospitalization rate (rate ratio 0.58, 95% confidence interval 0.39, 0.87; P = 0.01), and a 46% lower pulmonary hypertension‐related hospitalization rate (rate ratio 0.54, 95% confidence interval 0.35, 0.82; P = 0.004). This study suggests that selexipag is associated with lower hospitalization risk and rate than oral treprostinil.
Surgical Outcomes In The Frequency, Etiology, Direction, Severity (feds) Classification System For Shoulder Instability
Authors: Magnuson Justin A. , Wolf Brian R. , Cronin Kevin J. , Jacobs Cale A. , Ortiz Shannon , Kuhn John E. , Group MOON Shoulder , Hettrich Carolyn M. 
Published: March 2020

Objectives: The Frequency, Etiology, Direction, Severity (FEDS) system is a reliable and reproducible classification of glenohumeral instability. Frequency is defined as Solitary (1), Occasional (2-5), or Frequent (>5) episodes per year; etiology as Traumatic or Atraumatic; direction as Anterior, Posterior, or Inferior; and severity as a Subluxation or Dislocation. 36 total combinations are possible, named by the first letter of each variable in order. The purpose of this descriptive study was to investigate epidemiology, surgical outcomes, and failure using FEDS in patients undergoing surgery in a large multicenter cohort of prospectively enrolled patients. Methods: 1204 patients undergoing surgery were assigned to FEDS categories. Two-year follow-up at time of analysis was available for 629 patients (85.7% of those eligible based on date of surgery). Those categories consisting of at least 5% of patients were further analyzed by patient reported outcomes (PROs) and failure rates for a total of 466 patients. PROs included American Shoulder and Elbow Surgeons score (ASES), Western Ontario Shoulder Instability index (WOSI), and Single Assessment Numeric Evaluation (SANE). Failure benchmarks included rates of recurrent subluxation, dislocation, and revision surgery. Results: Sixteen categories represented at least one percent of patients. Occasional Traumatic Anterior Dislocation (OTAD) was the most common category with 16.4% of patients. Five other anterior categories (STAS, OTAS, FTAS, STAD, FTAD) and one posterior category (STPS) represented at least 5%. PROs and failure rates for anterior categories are summarized in Figure 1. PROs improved significantly for each category. A downward trend in WOSI and ASES was noted in particular with increasing frequency of the dislocation groups. The highest rates of each type of failure occurred in the occasional and frequent groups for both dislocation and subluxation. Low rates of failure occurred in STPS, with 17.9% reporting subluxation, 3.6% dislocation, and no revisions. Conclusion: While overall success was good, different FEDS categories showed varying degrees of improvement and failure rates, indicating that the system can be used to provide prognostic insight for presurgical education. Overall, outcomes for traumatic anterior instability decreased with higher initial frequency, showing worse PROs and higher failure. Frequency appeared to have the greatest effect on outcomes. Early surgical intervention may be beneficial in preventing progression to more severe FEDS categories, with higher frequency having previously been associated with both higher rates of bone loss and greater time between initial event and surgical stabilization.
Does Intra-operative PRP Improve Patient Function & Complication Rates Following ACL Reconstruction With Meniscus Repair?
Authors: Weldon Matthew , Lowe Walter R. , Lauck Kyle , Kleihege Jacquelyn , Warth Ryan J. , Syed Mohammad , Pontes Ana C. , Hayes Matthew , Bailey Lane B. 
Published: March 2020

Objectives: The frequent injury and compromised healing of intra-articular structures (i.e. cruciate ligaments and menisci) has led to an intense interest among surgeons and scientists for discovering new methods of enhancing the biological healing response of these tissues. Platelet-rich-plasma (PRP) contains various growth factors that positively effect biological healing, unfortunately few existing clinical studies are available to determine the risks and benefits of these therapies. Therefore, the purpose of this study was to determine the influence of intraoperative PRP on postoperative knee function and complications out to 2-years following ACL reconstruction with meniscus repair. Methods: A matched case-control study was conducted using a single surgeon database of 673 patients undergoing ACL reconstruction with concomitant meniscus repair (Figure 1) resulting in 324 patients [PRP (n = 162) vs matched-control (n = 162)] who met the study criteria. Patients were matched on age, gender, graft type, and meniscus tear size and location. The single assessment numeric evaluation (SANE) was administered at 2-years and served as the primary outcome measure. Secondary outcomes included the time to return-to-activity (mo), self-reported knee function [International Knee Disability Committee (IKDC)], objective functional testing (knee ROM, single-leg balance, single leg-hopping, agility testing), and postoperative complications (graft failure, infection, loss of motion, venous thrombosis, etc). Univariate models were used for between groups comparisons and alpha was set at .05 for all analyses. Results: There were no differences in SANE knee function scores between the PRP and matched-control groups at 2-years, respectively (91.6 ±11.2 vs 92.4 ±10.6, P = .599). Additionally, no differences were observed between groups for self-reported function (IKDC score; 87.6 ±13.3 vs 88.1 ±12.6, P = .952), objective functional testing (P > .05), and timing of return-to-activity (7.8 ±1.9 vs 8.0 ±1.9, P = .765). The PRP group demonstrated a higher rate of postoperative knee motion loss complications when compared to the control group (13.5% vs 4.9%, P < .001). No other differences were observed in postoperative complications (P > .05). Conclusion: The added use of intraoperative PRP did not improve self-reported knee function, objective functional testing, and timing of return-to-activity for patients undergoing ACL reconstruction with concomitant meniscus repair. Furthermore, the use of PRP may have negative consequences for regaining knee ROM after surgery. Based on these data, surgeons should cautiously consider the application of PRP when surgical planning for intra-articular injuries of the knee.
The Effect Of Playing Surface On Anterior Cruciate Ligament Injury In NCAA Soccer
Authors: Howard Mark , Kang Hyunwoo Paco , Solaru Samantha , Weber Alexander E. , Rick C Mark F. 
Published: March 2020

Objectives: Previous orthopaedic literature has examined the effect of synthetic playing surfaces on the risk of anterior cruciate ligament (ACL) injury in athletes and produced varying and inconclusive results. The objective of this study was to examine the role of playing surface on the incidence and risk of ACL injury in collegiate soccer athletes. Methods: The NCAA Injury Surveillance Program (ISP) database was queried for ACL injuries for male and female soccer players from the 2004-05 through the 2013-14 seasons at all levels of competition. The number of athlete exposures (AEs), defined as 1 athlete participating in 1 practice or competition in which they were exposed to the possibility of athletic injury, were recorded for grass and synthetic playing surfaces. Both the reported injuries and exposures provided were weighted in order to represent the entire NCAA collegiate soccer population. Normalized ACL incidence rates were calculated as well as 95% confidence intervals (95%CI). Rate ratios comparing competition type amongst both competition and practice were calculated. Results: ACL injuries were more common on grass surfaces (1.16 per 10,000 AEs, 95%CI 1.12-1.20) than artificial turf (0.92 per 10,000 AEs, 95%CI 0.84-1.04). This difference was statistically significant (IRR 1.26, p<0.0001), and driven primarily by the difference in injury incidence during practice. The injury incidence during practice on natural grass (1.18 per 10,000 AEs, 95% CI 1.11-1.26) was significantly greater than the injury incidence rate during practice on artificial turf (0.067 per 10,000 AEs, 95%CI 0.043-0.096). Players were 17.7 times more likely (95%CI 10.6678-27.2187, p<0.0001) to sustain an ACL injury during practice on natural grass when compared to practice on artificial turf. However, there was no significant difference in injury incidence during matches (IRR 0.96, p=0.44), with matches on natural grass (3.35 per 10,000 AEs, 95% CI 3.21-3.51) equivalent to matches on artificial surfaces (3.49 per 10,000 AEs, 95%CI 3.18-3.81). When comparing exposure type, the injury rate was significantly greater during matches (3.38 per 10,000 AEs, 95% CI 3.25-3.52) compared to practices (0.82 per 10,000 AEs, 95%CI 0.77-0.88), with a 4.10-fold increase in ACL injury incidence during matches compared to practice (p<0.0001). Conclusion: Between 2004 and 2014, NCAA soccer players experienced a greater number of ACL injuries on natural grass playing surfaces compared with artificial turf playing surfaces. This difference is driven by injuries during practice, where athletes were nearly 18 times more likely to suffer an ACL injury on grass versus artificial turf. While ACL injuries were more likely during matches compared to practices, no difference in incidence was noted between playing surfaces. Additional study is warranted investigating potential causes for this observed increased risk with soccer practice on grass fields.
Knee Scooter–Related Injuries: A Survey of Foot and Ankle Orthopedic Surgeons
Authors: Rahman Rafa , Shannon Brett A. , Ficke James R. 
Published: March 2020

Background: Knee scooters (“scooters”) are a commonly used device to facilitate postoperative adherence to weightbearing restrictions. Although high rates of falls have been reported, little is known about injuries related to scooter use. Methods: We analyzed survey responses from 316 of 2046 members (15%) of the American Orthopaedic Foot & Ankle Society in May-June 2019 describing (1) frequency of scooter recommendation; (2) indications for which they recommended scooters; (3) characteristics of patients for whom they recommended scooters; (4) prevalence, anatomic locations, mechanisms, and sequelae of scooter-related injuries; and (5) characteristics of patients with scooter-related injuries. Descriptive statistics and χ2 goodness-of-fit tests were performed (alpha = .05). Results: Mean frequency with which respondents recommended scooters in particular was 69%. Respondents most often recommended scooters after hindfoot arthrodesis (97% [305/316]), ankle arthrodesis (96% [302/316]), and for total nonweightbearing (64% [202/316]) and to patients who were overweight (vs obese) or aged 45-75 years. Mean prevalence of scooter-related injuries was 2.5%. The most common injury mechanism was making a sharp turn (reported by 62% [103/166]). Thirty-four percent (56/166) of respondents with injured patients said patients underwent surgery to treat scooter-related injuries. Patients with scooter-related injuries were more often women, >44 years old, obese, and sedentary. Conclusion: Scooters were commonly recommended postoperatively, most often for total nonweightbearing after hindfoot or ankle arthrodesis, and most often in overweight adults or those aged 45-75 years. Mean reported prevalence of scooter-related injuries was 2.5%. Female sex, older age, obesity, and sedentary lifestyle were associated with scooter-related injury. Level of Evidence: Level IV, retrospective case series.
Phase dependent hypothalamic activation following trigeminal input in cluster headache
Authors: Schulte Laura H. , Haji Ame Abdu , May Arne 
Published: March 2020

Abstract
Background
Task-free imaging approaches using PET have shown the posterior hypothalamus to be specifically activated during but not outside cluster headache attacks. Evidence from task related functional imaging approaches however is scarce.

Methods
Twenty-one inactive cluster headache patients (episodic cluster headache out of bout), 16 active cluster headache patients (10 episodic cluster headache in bout, 6 chronic cluster headache) and 18 control participants underwent high resolution brainstem functional magnetic resonance imaging of trigeminal nociception using gaseous ammonia as a painful stimulus.

Results
Following trigeminonociceptive stimulation with ammonia there was a significantly stronger activation within the posterior hypothalamus in episodic cluster headache patients out of bout when compared to controls. When contrasting estimates of the pain contrast, active cluster headache patients where in between the two other groups but did not differ significantly from either.

Conclusion
The posterior hypothalamus might thus be hyperexcitable in cluster headache patients outside the bout while excitability to external nociceptive stimuli decreases during in bout periods, probably due to frequent hypothalamic activation and possible neurotransmitter exhaustion during cluster attacks.
Reducing the effective dose of cisplatin using gold nanoparticles as carriers
Authors: González-López M. A. , Gutiérrez-Cárdenas E. M. , Sánchez-Cruz C. , Hernández-Paz J. F. , Pérez I. , Olivares-Trejo J. J. , Hernández-González O. 
Published: March 2020

AbstractNanotechnology is a frequent treatment for cancer. Nanomaterials are the vehicles which deliver drugs in smaller but equally effective quantities. The aim of this investigation is to synthesize gold nanoparticles, functionalize them for the transportation of cisplatin and release them to the cancer-affected area. They have the same cytotoxicity as conventional treatments but with the smallest effective quantity of cisplatin. We synthesized spherical gold nanoparticles using the Turkevich method. We functionalized them with polyethylene glycol and cisplatin, adapting the method used by Sun. Using electronic transmission microscopy, Dynamic Light Scattering and potential Z, we analyzed the size, hydrodynamic size, shape and stability of the synthesized nanoparticles. We analyzed their composition using images from scanning electronic microscopy to carry out energy dispersive spectroscopy measurements, ultraviolet/visible light spectroscopy and Fourier transform infrared spectroscopy. We used MTT tests to find cell viability and obtained the IC50 of the different cancer cell lines. The synthesized nanoparticles were spherical in shape and, after functionalization, were of the core–shell type. They contain approximately 7% cisplatin. The IC50 obtained diminished approximately 7 times (compared to the IC50 of cisplatin used alone) when using the gold nanoparticles. Therefore, this study opens up the possibility of an alternative way of transporting the cisplatin anticancer drug, using gold nanoparticles. It decreases the dose and has the same effect as the cisplatin, so that the undesired side effects decrease.
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly
Authors: Wcisel Dustin J. , Howard J. Thomas , Yoder Jeffrey A. , Dornburg Alex 
Published: March 2020

Abstract
Background
Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towards phylogeneticists to efficiently identify orthologous sequences currently hinders effective harnessing of this resource.

Results
We introduce TOAST, an open source R software package that can utilize the ortholog searches based on the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to assemble multiple sequence alignments of orthologous loci from transcriptomes for any group of organisms. By streamlining search, query, and alignment, TOAST automates the generation of locus and concatenated alignments, and also presents a series of outputs from which users can not only explore missing data patterns across their alignments, but also reassemble alignments based on user-defined acceptable missing data levels for a given research question.

Conclusions
TOAST provides a comprehensive set of tools for assembly of sequence alignments of orthologs for comparative transcriptomic and phylogenomic studies. This software empowers easy assembly of public and novel sequences for any target database of candidate orthologs, and fills a critically needed niche for tools that enable quantification and testing of the impact of missing data. As open-source software, TOAST is fully customizable for integration into existing or novel custom informatic pipelines for phylogenomic inference.
Software, a detailed manual, and example data files are available through github carolinafishes.github.io
A large-scale comparative study of isoform expressions measured on four platforms
Authors: Zhang Wei , Petegrosso Raphael , Chang Jae-Woong , Sun Jiao , Yong Jeongsik , Chien Jeremy , Kuang Rui 
Published: March 2020

Abstract
Background
Most eukaryotic genes produce different transcripts of multiple isoforms by inclusion or exclusion of particular exons. The isoforms of a gene often play diverse functional roles, and thus it is necessary to accurately measure isoform expressions as well as gene expressions. While previous studies have demonstrated the strong agreement between mRNA sequencing (RNA-seq) and array-based gene and/or isoform quantification platforms (Microarray gene expression and Exon-array), the more recently developed NanoString platform has not been systematically evaluated and compared, especially in large-scale studies across different cancer domains.

Results
In this paper, we present a large-scale comparative study among RNA-seq, NanoString, array-based, and RT-qPCR platforms using 46 cancer cell lines across different cancer types. The goal is to understand and evaluate the calibers of the platforms for measuring gene and isoform expressions in cancer studies. We first performed NanoString experiments on 59 cancer cell lines with 404 custom-designed probes for measuring the expressions of 478 isoforms in 155 genes, and additional RT-qPCR experiments for a subset of the measured isoforms in 13 cell lines. We then combined the data with the matched RNA-seq, Exon-array, and Microarray data of 46 of the 59 cell lines for the comparative analysis.

Conclusion
In the comparisons of the platforms for measuring the expressions at both isoform and gene levels, we found that (1) the agreement on isoform expressions is lower than the agreement on gene expressions across the four platforms; (2) NanoString and Exon-array are not consistent on isoform quantification even though both techniques are based on hybridization reactions; (3) RT-qPCR experiments are more consistent with RNA-seq and Exon-array than NanoString in isoform quantification; (4) different RNA-seq isoform quantification methods show varying estimation results, and among the methods, Net-RSTQ and eXpress are more consistent across the platforms; and (5) RNA-seq has the best overall consistency with the other platforms on gene expression quantification.
Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA
Authors: Takahashi Hiro , Hayashi Noriya , Hiragori Yuta , Sasaki Shun , Motomura Taichiro , Yamashita Yui , Naito Satoshi , Takahashi Anna , Fuse Kazuyuki , Satou Kenji , Endo Toshinori , Kojima Shoko , Onouchi Hitoshi 
Published: March 2020

AbstractBackgroundUpstream open reading frames (uORFs) in the 5′-untranslated regions (5′-UTRs) of certain eukaryotic mRNAs encode evolutionarily conserved functional peptides, such as cis-acting regulatory peptides that control translation of downstream main ORFs (mORFs). For genome-wide searches for uORFs with conserved peptide sequences (CPuORFs), comparative genomic studies have been conducted, in which uORF sequences were compared between selected species. To increase chances of identifying CPuORFs, we previously developed an approach in which uORF sequences were compared using BLAST betweenArabidopsisand any other plant species with available transcript sequence databases. If this approach is applied to multiple plant species belonging to phylogenetically distant clades, it is expected to further comprehensively identify CPuORFs conserved in various plant lineages, including those conserved among relatively small taxonomic groups.ResultsTo efficiently compare uORF sequences among many species and efficiently identify CPuORFs conserved in various taxonomic lineages, we developed a novel pipeline, ESUCA. We applied ESUCA to the genomes of five angiosperm species, which belong to phylogenetically distant clades, and selected CPuORFs conserved among at least three different orders. Through these analyses, we identified 89 novel CPuORF families. As expected, ESUCA analysis of each of the five angiosperm genomes identified many CPuORFs that were not identified from ESUCA analyses of the other four species. However, unexpectedly, these CPuORFs include those conserved across wide taxonomic ranges, indicating that the approach used here is useful not only for comprehensive identification of narrowly conserved CPuORFs but also for that of widely conserved CPuORFs. Examination of the effects of 11 selected CPuORFs on mORF translation revealed that CPuORFs conserved only in relatively narrow taxonomic ranges can have sequence-dependent regulatory effects, suggesting that most of the identified CPuORFs are conserved because of functional constraints of their encoded peptides.ConclusionsThis study demonstrates that ESUCA is capable of efficiently identifying CPuORFs likely to be conserved because of the functional importance of their encoded peptides. Furthermore, our data show that the approach in which uORF sequences from multiple species are compared with those of many other species, using ESUCA, is highly effective in comprehensively identifying CPuORFs conserved in various taxonomic ranges.