bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical study of coorbital thermal torques on cold or hot satellites
Authors: Chametla Raúl O , Masset Frédéric S 
Published: November 2020

ABSTRACT
We evaluate the thermal torques exerted on low-mass planets embedded in gaseous protoplanetary discs with thermal diffusion, by means of high-resolution three-dimensional hydrodynamics simulations. We confirm that thermal torques essentially depend on the offset between the planet and its corotation, and find a good agreement with analytic estimates when this offset is small compared to the size of the thermal disturbance. For larger offsets that may be attained in discs with a large pressure gradient or a small thermal diffusivity, thermal torques tend towards an asymptotic value broadly compatible with results from a dynamical friction calculation in an unsheared medium. We perform a convergence study and find that the thermal disturbance must be resolved over typically 10 zones for a decent agreement with analytic predictions. We find that the luminosity at which the net thermal torque changes sign matches that predicted by linear theory within a few percents. Our study confirms that thermal torques usually supersede Lindblad and corotation torques by almost an order of magnitude for low-mass planets. As we increase the planetary mass, we find that the ratio of thermal torques to Lindblad and corotation torques is progressively reduced, and that the thermal disturbance is increasingly distorted by the horseshoe flow. Overall, we find that thermal torques are dominant for masses up to an order of magnitude larger than implemented in recent models of planetary population synthesis. We finally briefly discuss the case of stellar or intermediate-mass objects embedded in discs around active galactic nuclei.
Metabolic RNA labeling for probing RNA dynamics in bacteria
Authors: Meng Liying , Guo Yilan , Tang Qi , Huang Rongbing , Xie Yuchen , Chen Xing 
Published: November 2020

Abstract
Metabolic labeling of RNAs with noncanonical nucleosides that are chemically active, followed by chemoselective conjugation with imaging probes or enrichment tags, has emerged as a powerful method for studying RNA transcription and degradation in eukaryotes. However, metabolic RNA labeling is not applicable for prokaryotes, in which the complexity and distinctness of gene regulation largely remain to be explored. Here, we report 2′-deoxy-2′-azidoguanosine (AzG) as a noncanonical nucleoside compatible with metabolic labeling of bacterial RNAs. With AzG, we develop AIR-seq (azidonucleoside-incorporated RNA sequencing), which enables genome-wide analysis of transcription upon heat stress in Escherichia coli. Furthermore, AIR-seq coupled with pulse-chase labeling allows for global analysis of bacterial RNA degradation. Finally, we demonstrate that RNAs of mouse gut microbiotas can be metabolically labeled with AzG in living animals. The AzG-enabled metabolic RNA labeling should find broad applications in studying RNA biology in various bacterial species.
Structural basis of sequestration of the anti-Shine-Dalgarno sequence in the Bacteroidetes ribosome
Authors: Jha Vikash , Roy Bappaditya , Jahagirdar Dushyant , McNutt Zakkary A , Shatoff Elan A , Boleratz Bethany L , Watkins Dean E , Bundschuh Ralf , Basu Kaustuv , Ortega Joaquin , Fredrick Kurt 
Published: November 2020

Abstract
Genomic studies have indicated that certain bacterial lineages such as the Bacteroidetes lack Shine-Dalgarno (SD) sequences, and yet with few exceptions ribosomes of these organisms carry the canonical anti-SD (ASD) sequence. Here, we show that ribosomes purified from Flavobacterium johnsoniae, a representative of the Bacteroidetes, fail to recognize the SD sequence of mRNA in vitro. A cryo-electron microscopy structure of the complete 70S ribosome from F. johnsoniae at 2.8 Å resolution reveals that the ASD is sequestered by ribosomal proteins bS21, bS18 and bS6, explaining the basis of ASD inhibition. The structure also uncovers a novel ribosomal protein—bL38. Remarkably, in F. johnsoniae and many other Flavobacteriia, the gene encoding bS21 contains a strong SD, unlike virtually all other genes. A subset of Flavobacteriia have an alternative ASD, and in these organisms the fully complementary sequence lies upstream of the bS21 gene, indicative of natural covariation. In other Bacteroidetes classes, strong SDs are frequently found upstream of the genes for bS21 and/or bS18. We propose that these SDs are used as regulatory elements, enabling bS21 and bS18 to translationally control their own production.
Improved computational analysis of ribosome dynamics from 5′P degradome data using fivepseq
Authors: Nersisyan Lilit , Ropat Maria , Pelechano Vicent 
Published: November 2020

Abstract
In eukaryotes, 5′–3′ co-translation degradation machinery follows the last translating ribosome providing an in vivo footprint of its position. Thus, 5′ monophosphorylated (5′P) degradome sequencing, in addition to informing about RNA decay, also provides information regarding ribosome dynamics. Multiple experimental methods have been developed to investigate the mRNA degradome; however, computational tools for their reproducible analysis are lacking. Here, we present fivepseq: an easy-to-use application for analysis and interactive visualization of 5′P degradome data. This tool performs both metagene- and gene-specific analysis, and enables easy investigation of codon-specific ribosome pauses. To demonstrate its ability to provide new biological information, we investigate gene-specific ribosome pauses in Saccharomyces cerevisiae after eIF5A depletion. In addition to identifying pauses at expected codon motifs, we identify multiple genes with strain-specific degradation frameshifts. To show its wide applicability, we investigate 5′P degradome from Arabidopsis thaliana and discover both motif-specific ribosome protection associated with particular developmental stages and generally increased ribosome protection at termination level associated with age. Our work shows how the use of improved analysis tools for the study of 5′P degradome can significantly increase the biological information that can be derived from such datasets and facilitate its reproducible analysis.
Behavioral Economic Demand for Alcohol and Cigarettes in Heavy Drinking Smokers: Evidence of Asymmetric Cross-commodity Reinforcing Value
Authors: Green ReJoyce , MacKillop James , Hartwell Emily E , Lim Aaron C , Baskerville Wave-Ananda , Karno Mitchell , Ray Lara A 
Published: November 2020

AbstractIntroductionPrevious studies have highlighted a strong bidirectional relationship between cigarette and alcohol consumption. To advance our understanding of this relationship the present study uses a behavioral economic approach in a community sample (N = 383) of nontreatment seeking heavy drinking smokers.Aims and MethodsThe aims were to examine same-substance and cross-substance relationships between alcohol and cigarette use, and latent factors of demand. A community sample of nontreatment seeking heavy drinking smokers completed an in-person assessment battery including measures of alcohol and tobacco use as well as the Cigarette Purchase Task and the Alcohol Purchase Task. Latent factors of demand were derived from these hypothetical purchase tasks.ResultsResults revealed a positive correlation between paired alcohol and cigarette demand indices (eg, correlation between alcohol intensity and cigarette intensity) (rs = 0.18–0.46, p ≤ .003). Over and above alcohol factors, cigarette use variables (eg, Fagerström Test for Nicotine Dependence and cigarettes per smoking day) significantly predicted an additional 4.5% (p &lt; .01) of the variance in Persistence values but not Amplitude values for alcohol. Over and above cigarette factors, alcohol use variables predicted cigarette Persistence values (ΔR2 = .013, p = .05), however, did not predict Amplitude values.ConclusionsThese results advance our understanding of the overlap between cigarette and alcohol by demonstrating that involvement with one substance was associated with demand for the other substance. This asymmetric profile—from smoking to alcohol demand, but not vice versa—suggests that it is not simply tapping into a generally higher reward sensitivity and warrants further investigation.ImplicationsTo our knowledge, no study to date has examined alcohol and cigarette demand, via hypothetical purchase tasks, in a clinical sample of heavy drinking smokers. This study demonstrates that behavioral economic indices may be sensitive to cross-substance relationships and specifically that such relationships are asymmetrically stronger for smoking variables affecting alcohol demand, not the other way around.
Role of the Medial Orbitofrontal Cortex and Ventral Tegmental Area in Effort-Related Responding
Authors: Münster Alexandra , Votteler Angeline , Sommer Susanne , Hauber Wolfgang 
Published: November 2020

Abstract
The posterior subdivision of the medial orbitofrontal cortex (mOFC-p) mediates the willingness to expend effort to reach a selected goal. However, the neural circuitry through which the mOFC-p modulates effort-related function is as yet unknown. The mOFC-p projects prominently to the posterior ventral tegmental area (pVTA). Therefore, we analyzed the role of the mOFC-p and interactions with the pVTA in effort-related responding using a combination of behavioral, pharmacological, and neural circuit analysis methods in rats. Pharmacological inhibition of the mOFC-p was found to increase lever pressing for food under a progressive ratio (PR) schedule of reinforcement. These findings provide further support for a modulation of effort-related function by the mOFC-p. Then, we investigated effects of disconnecting the mOFC-p and pVTA on PR responding using unilateral pharmacological inhibition of both areas. This asymmetric intervention was also found to increase PR responding suggesting that the mOFC-p controls effort-related function through interactions with the pVTA. Possibly, a reduced excitatory mOFC-p drive on pVTA gamma-aminobutyric acid (GABA)ergic relays disinhibits VTA dopamine neurons which are known to support PR responding. Collectively, our findings suggest that the mOFC-p and pVTA are key components of a neural circuit mediating the willingness to expend effort to reach a goal.
Tranexamic acid and traumatic brain injuries
Authors: Sanford Katarina , Garcia Sarah 
Published: November 2020

ABSTRACT
The CRASH-3 trial examined the use of tranexamic acid (TXA) in patients with intracranial bleeding secondary to traumatic brain injury. The trial demonstrated that TXA, an antifibrinolytic medication, reduces mortality in patients with mild to moderate head injuries. However, because of the trial's multiple limitations, TXA cannot yet be called the gold standard.
Medical Students’ Perspectives on Entrustment Decision Making in an Entrustable Professional Activity Assessment Framework: A Secondary Data Analysis
Authors: Caro Monroig Angeliz M. , Chen H. Carrie , Carraccio Carol , Richards Boyd F. , ten Cate Olle , Balmer Dorene F. 
Published: November 2020

Purpose
Research on how entrustment decisions are made identifies 5 influential factors (supervisor, trainee, supervisor–trainee relationship, context, task). However, this literature primarily represents the perspective of supervisors in graduate medical education and is conducted outside of an assessment framework where entrustment decisions have consequences for trainees and for patients. To complement the literature, the authors explored how medical students in a pilot program that used an entrustable professional activity (EPA) assessment framework perceived factors influencing entrustment decisions.

Method
The authors conducted a secondary analysis of qualitative data from program evaluation of a pilot project using an EPA assessment framework to advance students through their curriculum and into residency. Data were derived from 8 focus groups conducted over 4 years (2015–2018) with 27 students who shared their experience of learning and supervision in the project. Sensitized by the entrustment literature, the authors coded and analyzed focus group transcripts according to principles of thematic analysis.

Results
Components of the trainee and supervisor–trainee relationship factors predominated students’ perceptions of entrustment decisions. Students directed their own learning by asking for feedback, seeking opportunities to engage in learning, sharing limitations of their knowledge with supervisors, and pushing supervisors to recalibrate assessments when appropriate. Students’ agentic actions were facilitated by longitudinal supervisor–trainee relationships wherein they felt comfortable asking for help and built confidence in patient care. Students mentioned components of other factors that influenced entrustment decisions (supervisor, clinical task, clinical context), but did so less frequently and from a nonagentic vantage point.

Conclusions
Students’ perspectives on entrustment decisions can be derived from their views on learning and supervision in an EPA assessment framework. Their perspectives complement the literature by highlighting students’ agentic actions to influence entrustment decisions and promotion of agentic action through practices incorporating longitudinal supervisor–trainee relationships.
Does Community College Attendance Affect Matriculation to a Physician Assistant Program? A Pathway to Increase Diversity in the Health Professions
Authors: Luo Qian , Erikson Clese E. , Chitwood Ryan , Yuen Cynthia X. 
Published: November 2020

Purpose
To explore whether community college (CC) applicants were a significant contributor to the diversity of matriculants to physician assistant (PA) programs and whether CC applicants were less likely to matriculate to PA programs than non-CC applicants.

Method
The authors used national data from the 2016–2017 application cycle. They categorized applicants to PA programs into 5 pathways: HS-CC (applicant attended CC while in high school), first-CC (applicant attended CC before a 4-year university), 4Y-CC (applicant attended CC while at a 4-year university), post-CC (applicant attended CC after graduating from a 4-year university), and no-CC (applicant never attended CC). The authors used Pearson chi-square and Kruskal-Wallis H tests and the appropriate post hoc tests to assess whether applicants in the 4 CC pathways were more diverse in terms of their race, ethnicity, gender, rurality, and socioeconomic status than those in the no-CC pathway. They used logistic regressions to assess associations between the CC pathways and matriculation to a PA program.

Results
Among the 8,577 matriculants in the 2016–2017 application cycle, more than 75% attended a CC at some point. First-CC and post-CC matriculants were more likely to be Black (P < .001) or Hispanic (P < .001) and come from a disadvantaged background (P < .001) than no-CC matriculants. After adjusting for applicant demographics, academic performance, rurality and socioeconomic status, and application strategy, first-CC applicants had 17% lower odds of matriculating to a PA program than no-CC applicants (P < .001).

Conclusions
CCs are an important pathway to the PA profession, with 3 of 4 matriculants having a CC background. However, lower matriculation rates among similarly qualified applicants who transferred from a CC to a 4-year university than among applicants with no-CC background suggest that PA programs are missing important opportunities for increasing student diversity and thereby the profession.
Differentiating gastric cancer and gastric lymphoma using texture analysis (TA) of positron emission tomography (PET)
Authors: Sun Yi-Wen , Ji Chang-Feng , Wang Han , He Jian , Liu Song , Ge Yun , Zhou Zheng-Yang 
Published: November 2020

Abstract

Background:
Texture analysis (TA) can quantify intra-tumor heterogeneity using standard medical images. The present study aimed to assess the application of positron emission tomography (PET) TA in the differential diagnosis of gastric cancer and gastric lymphoma.

Methods:
The pre-treatment PET images of 79 patients (45 gastric cancer, 34 gastric lymphoma) between January 2013 and February 2018 were retrospectively reviewed. Standard uptake values (SUVs), first-order texture features, and second-order texture features of the grey-level co-occurrence matrix (GLCM) were analyzed. The differences in features among different groups were analyzed by the two-way Mann-Whitney test, and receiver operating characteristic (ROC) analysis was used to estimate the diagnostic efficacy.

Results:
InertiaGLCM was significantly lower in gastric cancer than that in gastric lymphoma (4975.61 vs. 11,425.30, z = −3.238, P = 0.001), and it was found to be the most discriminating texture feature in differentiating gastric lymphoma and gastric cancer. The area under the curve (AUC) of inertiaGLCM was higher than the AUCs of SUVmax and SUVmean (0.714 vs. 0.649 and 0.666, respectively). SUVmax and SUVmean were significantly lower in low-grade gastric lymphoma than those in high grade gastric lymphoma (3.30 vs. 11.80, 2.40 vs. 7.50, z = −2.792 and −3.007, P = 0.005 and 0.003, respectively). SUVs and first-order grey-level intensity features were not significantly different between low-grade gastric lymphoma and gastric cancer. EntropyGLCM12 was significantly lower in low-grade gastric lymphoma than that in gastric cancer (6.95 vs. 9.14, z = −2.542, P = 0.011) and had an AUC of 0.770 in the ROC analysis of differentiating low-grade gastric lymphoma and gastric cancer.

Conclusions:
InertiaGLCM and entropyGLCM were the most discriminating features in differentiating gastric lymphoma from gastric cancer and low-grade gastric lymphoma from gastric cancer, respectively. PET TA can improve the differential diagnosis of gastric neoplasms, especially in tumors with similar degrees of fluorodeoxyglucose uptake.
Clinical presentation of vertebrobasilar stroke
Authors: Carvalho Vanessa , Cruz Vitor Tedim 
Published: November 2020

Abstract
Vertebrobasilar (VB) stroke is responsible for 20% of all strokes and transient ischemic attacks. Due to the vast cerebral territory it supplies, VB ischemia can present with a wide range of symptoms and signs, sometimes even overlapping with carotid circulation stroke. Furthermore, brain computed tomography, usually performed as initial imaging modality, has a suboptimal visualization of the posterior fossa, making VB stroke an even more challenging diagnosis to any physician. Hence, awareness of the vertebrobasilar anatomy and the clinical presentation of VB ischemia is crucial to promote early recognition of this disorder.
A Chemotactic Functional Scaffold with VEGF-Releasing Peptide Amphiphiles Facilitates Bone Regeneration by BMP-2 in a Large-Scale Rodent Cranial Defect Model
Authors: Bakshi Reena , Hokugo Akishige , Khalil Daniel , Wang Lixin , Shibuya Yoichiro , Zhou Situo , Zhang Zheyu , Rezzadeh Kameron , McClendon Mark , Stupp Samuel I. , Jarrahy Reza 
Published: November 2020

Background:
Current common techniques for repairing calvarial defects by autologous bone grafting and alloplastic implants have significant limitations. In this study, the authors investigated a novel alternative approach to bone repair based on peptide amphiphile nanofiber gels that are engineered to control the release of vascular endothelial growth factor (VEGF) to recruit circulating stem cells to a site of bone regeneration and facilitate bone healing by bone morphogenetic protein-2 (BMP-2).

Methods:
VEGF release kinetics from peptide amphiphile gels were evaluated. Chemotactic functional scaffolds were fabricated by combining collagen sponges with peptide amphiphile gels containing VEGF. The in vitro and in vivo chemotactic activities of the scaffolds were evaluated by measuring mesenchymal stem cell migration, and angiogenic capability of the scaffolds was also evaluated. Large-scale rodent cranial bone defects were created to evaluate bone regeneration after implanting the scaffolds and other control materials.

Results:
VEGF was released from peptide amphiphile in a controlled-release manner. In vitro migration of mesenchymal stem cells was significantly greater when exposed to chemotactic functional scaffolds compared to control scaffolds. In vivo chemotaxis was evidenced by migration of tracer-labeled mesenchymal stem cells to the chemotactic functional scaffolds. Chemotactic functional scaffolds showed significantly increased angiogenesis in vivo. Successful bone regeneration was noted in the defects treated with chemotactic functional scaffolds and BMP-2.

Conclusions:
The authors’ observations suggest that this bioengineered construct successfully acts as a chemoattractant for circulating mesenchymal stem cells because of controlled release of VEGF from the peptide amphiphile gels. The chemotactic functional scaffolds may play a role in the future design of clinically relevant bone graft substitutes for large-scale bone defects.
Strategies for Mesh Fixation in Abdominal Wall Reconstruction: Concepts and Techniques
Authors: Rangwani Shiva M. , Kraft Casey T. , Schneeberger Steven J. , Khansa Ibrahim , Janis Jeffrey E. 
Published: November 2020

Summary:
Ventral hernias have numerous causes, ranging from sequelae of surgical procedures to congenital deformities. Patients suffering from these hernias experience a reduced quality of life through pain, associated complications, and physical disfigurement. Therefore, it is important to provide these patients with a steadfast repair that restores functionality and native anatomy. To do this, techniques and materials for abdominal wall reconstruction have advanced throughout the decades, leading to durable surgical repairs. At the cornerstone of this lies the use of mesh. When providing abdominal wall reconstruction, a surgeon must make many decisions with regard to mesh use. Along with the type of mesh and plane of placement of mesh, a surgeon must decide on the method of mesh fixation. Fixation of mesh provides an equal distribution of tension and a more robust tissue-mesh interface, which promotes integration. There exist numerous modalities for mesh fixation, each with its own benefits and drawbacks. This Special Topic article aims to compare and contrast methods of mesh fixation in terms of strength of fixation, clinical outcomes, and cost-effectiveness. Methods included in this review are suture, tack, fibrin glue, mesh strip, and self-adhering modes of fixation.
A bibliography of Canadian Inuit periodicals: a case study in Omeka.net migration
Authors: Rankin Sharon 
Published: November 2020

Purpose
This paper aims to describe the migration steps taken by a humanities librarian to create a new searchable website for an indigenous bibliography on the Omeka.net cloud-based service.

Design/methodology/approach
Using CSV files and Excel, the bibliography entries were moved from the old website to the new one, carefully mapping the descriptive information into Qualified Dublin Core metadata elements.

Findings
After resolving diacritic and other data normalization issues, the new site was created in Omeka.net with ease. The plugins available for Omeka.net allowed the editor to geolocate the site of publications. Using TimelineJS, the editor was able to create several timelines and link them to the new CanInuit website as an exhibition.

Originality/value
This is a unique application of the Omeka.net cloud-based service.