bluuebunny/crossref_metadata_2025_split huggingface dataset:
A generalizable data-driven multicellular model of pancreatic ductal adenocarcinoma
Authors: Aguilar Boris , Gibbs David L , Reiss David J , McConnell Mark , Danziger Samuel A , Dervan Andrew , Trotter Matthew , Bassett Douglas , Hershberg Robert , Ratushny Alexander V , Shmulevich Ilya 
Published: July 2020

Abstract

Background
Mechanistic models, when combined with pertinent data, can improve our knowledge regarding important molecular and cellular mechanisms found in cancer. These models make the prediction of tissue-level response to drug treatment possible, which can lead to new therapies and improved patient outcomes. Here we present a data-driven multiscale modeling framework to study molecular interactions between cancer, stromal, and immune cells found in the tumor microenvironment. We also develop methods to use molecular data available in The Cancer Genome Atlas to generate sample-specific models of cancer.

Results
By combining published models of different cells relevant to pancreatic ductal adenocarcinoma (PDAC), we built an agent-based model of the multicellular pancreatic tumor microenvironment, formally describing cell type–specific molecular interactions and cytokine-mediated cell-cell communications. We used an ensemble-based modeling approach to systematically explore how variations in the tumor microenvironment affect the viability of cancer cells. The results suggest that the autocrine loop involving EGF signaling is a key interaction modulator between pancreatic cancer and stellate cells. EGF is also found to be associated with previously described subtypes of PDAC. Moreover, the model allows a systematic exploration of the effect of possible therapeutic perturbations; our simulations suggest that reducing bFGF secretion by stellate cells will have, on average, a positive impact on cancer apoptosis.

Conclusions
The developed framework allows model-driven hypotheses to be generated regarding therapeutically relevant PDAC states with potential molecular and cellular drivers indicating specific intervention strategies.
Efficacy of extracorporeal membrane oxygenation before surgery of a post-infarction ventricular septal rupture in cardiogenic shock
Authors: Takaki Hidenobu , Hashizume Kenichi , Matsuoka Tadashi , Ikebata Koki 
Published: July 2020

Abstract
A 73-year-old man with an acute myocardial infarction experienced severe cardiogenic shock due to an inferior ventricular septal rupture with a massive left-to-right shunt. Emergency surgery was considered a too high mortality risk. The patient was implanted with an extracorporeal membrane oxygenation system as a bridge to surgery. On the seventh day after admission, the ventricular septal defect was successfully repaired. Our case study demonstrates that extracorporeal membrane oxygenation could be an option in cases of ventricular septal rupture as a bridge for stabilizing patients.
Can synthetic controls improve causal inference in interrupted time series evaluations of public health interventions?
Authors: Degli Esposti Michelle , Spreckelsen Thees , Gasparrini Antonio , Wiebe Douglas J , Bonander Carl , Yakubovich Alexa R , Humphreys David K 
Published: July 2020

Abstract
Interrupted time series designs are a valuable quasi-experimental approach for evaluating public health interventions. Interrupted time series extends a single group pre-post comparison by using multiple time points to control for underlying trends. But history bias—confounding by unexpected events occurring at the same time of the intervention—threatens the validity of this design and limits causal inference. Synthetic control methodology, a popular data-driven technique for deriving a control series from a pool of unexposed populations, is increasingly recommended. In this paper, we evaluate if and when synthetic controls can strengthen an interrupted time series design. First, we summarize the main observational study designs used in evaluative research, highlighting their respective uses, strengths, biases and design extensions for addressing these biases. Second, we outline when the use of synthetic controls can strengthen interrupted time series studies and when their combined use may be problematic. Third, we provide recommendations for using synthetic controls in interrupted time series and, using a real-world example, we illustrate the potential pitfalls of using a data-driven approach to identify a suitable control series. Finally, we emphasize the importance of theoretical approaches for informing study design and argue that synthetic control methods are not always well suited for generating a counterfactual that minimizes critical threats to interrupted time series studies. Advances in synthetic control methods bring new opportunities to conduct rigorous research in evaluating public health interventions. However, incorporating synthetic controls in interrupted time series studies may not always nullify important threats to validity nor improve causal inference.
Using UMLS for electronic health data standardization and database design
Authors: Reimer Andrew P , Milinovich Alex 
Published: July 2020

Abstract

Objective
Patients that undergo medical transfer represent 1 patient population that remains infrequently studied due to challenges in aggregating data across multiple domains and sources that are necessary to capture the entire episode of patient care. To facilitate access to and secondary use of transport patient data, we developed the Transport Data Repository that combines data from 3 separate domains and many sources within our health system.

Methods
The repository is a relational database anchored by the Unified Medical Language System unique concept identifiers to integrate, map, and standardize the data into a common data model. Primary data domains included sending and receiving hospital encounters, medical transport record, and custom hospital transport log data. A 4-step mapping process was developed: 1) automatic source code match, 2) exact text match, 3) fuzzy matching, and 4) manual matching.

Results
431 090 total mappings were generated in the Transport Data Repository, consisting of 69 010 unique concepts with 77% of the data being mapped automatically. Transport Source Data yielded significantly lower mapping results with only 8% of data entities automatically mapped and a significant amount (43%) remaining unmapped.

Discussion
The multistep mapping process resulted in a majority of data been automatically mapped. Poor matching of transport medical record data is due to the third-party vendor data being generated and stored in a nonstandardized format.

Conclusion
The multistep mapping process developed and implemented is necessary to normalize electronic health data from multiple domains and sources into a common data model to support secondary use of data.
The Efficacy of Five Different Wound Dressings on Some Histological Parameters in Children With Partial-Thickness Burns
Authors: Harma Birsen , Gül Mehmet , Demircan Mehmet 
Published: July 2020

Abstract
An ideal dressing should ensure that the wound remains moist with exudates but not macerated. Currently, there is no dressing available to suit all wounds, at all stages of the healing process. Although silver-containing dressings are the gold standard for burn wound care, few high-level trials have been completed comparing the clinical utilities of these dressings. In our study, five different types of wound dressings: carboxymethyl cellulose hydrofiber dressing with ionized silver (CMCH-Ag), polyethylene-polyethylene terephthalate aqua fiber dressing with elementary silver (PPAF-Ag), calcium alginate (CA), calcium + zinc alginate (CZA), and 0.2% nitrofurazone-embedded (NF) gauze dressings were compared in regard to histopathological parameters. Children aged between 0 and 18 years with small or middle-sized partial-thickness burns that affected less than 30% of the total body surface area were included in this study. The study groups (CMCH-Ag, PPAF-Ag, CA, and CZA) and the control group (NF) were randomly attained. Wound healing was evaluated by punch biopsies on the 21st day. The thickness of the stratum corneum and the epithelium, the number of papillae, and the papillary length were calculated and compared. The histological parameters of healing, except the stratum corneum thickness, did not show any statistical significance among the groups (P &gt; .05). The dressings that included silver, calcium, or zinc showed useful and similar effects in noninfective burn wounds when compared with nitrofurazone-only dressings. Thus, it may be concluded that silver-containing wound dressings should not be considered as the gold standard in noninfective partial-thickness burn wounds in children.
‘Fitting In’ and ‘Giving Back’: Constructions of Australia’s ‘Ideal’ Refugee Through Discourses of Assimilation and Market Citizenship
Authors: Haw Ashleigh L 
Published: July 2020

AbstractThis paper examines how the ‘ideal’ refugee is conceptualized in discussions about Australia’s humanitarian policies. Critical Discourse Analysis of semi-structured interviews with 24 Western Australians revealed strong themes of assimilation alongside the neoliberal concept of ‘market citizenship’, where the ‘ideal’ refugee is positioned as achieving economic success through contributions to Australia’s labour market. These discourses served competing ends—they were voiced both in support of, and opposition to, Australia’s acceptance of refugees. I argue that by constructing refugees’ deservingness of protection along market citizenship lines, their belonging becomes contingent upon their adherence to a narrowly defined ideal. Consequently, refugees who do not fit within this ideal face continued exclusion, with their ‘human capital’ prioritized over their safety and human rights. This article calls for a reconsideration of arguments that focus on refugees’ capacity to ‘fit in’ and ‘give back’ as these narratives may exacerbate their experiences of exclusion and stigmatization.
Aircraft disinsection: what is the usefulness as a public health measure?
Authors: Grout Andrea , Russell Richard C 
Published: July 2020

Abstract

Rationale for review
Insecticide treatments in aircraft (termed ‘aircraft disinsection’) aim to support the containment of potentially disease-carrying vector insects. The introduction of non-endemic mosquito species is of concern as some mosquitoes can act as vectors of many serious human diseases. Expansion of vectors to previously non-endemic regions, extended flight networks and mosquito resistance to insecticides pose challenges to contemporary vector-control approaches. Despite established efficacy of aircraft disinsection in trials, there is increasing concern over its effectiveness and feasibility in flight operations, and its usefulness as a public health measure.

Key findings
We explored the literature on disinsection through a narrative approach to obtain a pragmatic assessment of existing and future implementation challenges. We describe the shortcomings that hinder evaluation of the success of aircraft disinsection. These shortcomings include operational constraints that may impact effective treatment outcomes, lack of longitudinal data on pesticide exposure scenarios, lack of compliance mechanisms, pesticide resistance in mosquitoes, and limited evidence of the extent and type of mosquito species potentially transported via aircraft.

Conclusions and recommendations
Concerns about the introduction of non-endemic mosquito vectors reinforce the need for effective preventive measures. Import of disease vectors is likely to occur in the future under changing environmental and operational conditions. Optimal impact from disinsection requires appropriate deployment, commitment and use. The current system of evaluation is inadequate for producing the evidence needed for informed policy decisions. While utilizing the results of research into environmentally sustainable vector-control methods for use in aircraft, future approaches to aircraft disinsection require improved evidence of anticipated benefits and harms, reliable monitoring data on insecticide resistance, and must be supported by strong vector control at airports.
Change is Hard: Leadership is Harder
Authors: Roberts Teresa 
Published: July 2020

Abstract
The transformation of the Military Health System to the Defense Health Agency under the National Defense Authorization Act of 2017 is a change of historical proportion. Change can be seen as hard, yet change is always happening. What is actually hard is providing leadership to accomplish the mission and goals for ourselves and our organizations within constant change. Those of us selected for leadership positions often receive standardized preparation and experiences to help us with this challenge. The hard part, though, is not what we often think it is. Leadership is not hard because of the amount of change or the people we are leading. Leadership is hard because, as we increase our rank and responsibilities, there are more people we need to see as people, having an outward mindset toward them, to have a positive influence and impact. In this article, I share the challenge I experienced with an outward mindset in leading the transition of our military treatment facility under the transformation to Defense Health Agency.
Distribution and kinematics of 26Al in the Galactic disc
Authors: Fujimoto Yusuke , Krumholz Mark R , Inutsuka Shu-ichiro 
Published: July 2020

ABSTRACT
26Al is a short-lived radioactive isotope thought to be injected into the interstellar medium (ISM) by massive stellar winds and supernovae (SNe). However, all-sky maps of 26Al emission show a distribution with a much larger scale height and faster rotation speed than either massive stars or the cold ISM. We investigate the origin of this discrepancy using an N-body + hydrodynamics simulation of a Milky-Way-like galaxy, self-consistently including self-gravity, star formation, stellar feedback, and 26Al production. We find no evidence that the Milky Way’s spiral structure explains the 26Al anomaly. Stars and the 26Al bubbles they produce form along spiral arms, but, because our simulation produces material arms that arise spontaneously rather than propagating arms forced by an external potential, star formation occurs at arm centres rather than leading edges. As a result, we find a scale height and rotation speed for 26Al similar to that of the cold ISM. However, we also show that a synthetic 26Al emission map produced for a possible Solar position at the edge of a large 26Al bubble recovers many of the major qualitative features of the observed 26Al sky. This suggests that the observed anomalous 26Al distribution is the product of foreground emission from the 26Al produced by a nearby, recent SN.
The PDR structure and kinematics around the compact H ii regions S235 A and S235 C with [C ii], [13C ii], [O i], and HCO+ line profiles
Authors: Kirsanova M S , Ossenkopf-Okada V , Anderson L D , Boley P A , Bieging J H , Pavlyuchenkov Ya N , Luisi M , Schneider N , Andersen M , Samal M R , Sobolev A M , Buchbender C , Aladro R , Okada Y 
Published: July 2020

ABSTRACT
The aim of this work is to study structure and gas kinematics in the photodissociation regions (PDRs) around the compact H ii regions S235 A and S235 C. We observe the [C ii], [13C ii], and [O i] line emission, using SOFIA/upGREAT, and complement them by data of HCO+ and CO. We use the [13C ii] line to measure the optical depth of the [C ii] emission, and find that the [C ii] line profiles are influenced by self-absorption, while the [13C ii] line remains unaffected by these effects. Hence, for dense PDRs, [13C ii] emission is a better tracer of gas kinematics. The optical depth of the [C ii] line is up to 10 in S235 A. We find an expanding motion of the [C ii]-emitting layer of the PDRs into the front molecular layer in both regions. Comparison of the gas and dust columns shows that gas components visible neither in the [C ii] nor in low-J CO lines may contribute to the total column across S235 A. We test whether the observed properties of the PDRs match the predictions of spherical models of expanding H ii region + PDR + molecular cloud. Integrated intensities of the [13C ii], [C ii], and [O i] lines are well represented by the model, but the models do not reproduce the double-peaked [C ii] line profiles due to an insufficient column density of C+. The model predicts that the [O i] line could be a more reliable tracer of gas kinematics, but the foreground self-absorbing material does not allow using it in the considered regions.
Ultracompact H ii regions with extended emission: the case of G43.89–0.78 and its molecular environment
Authors: de la Fuente Eduardo , Tafoya Daniel , Trinidad Miguel A , Porras Alicia , Nigoche-Netro Alberto , Kemp Simon N , Kurtz Stanley E , Franco José , Rodríguez-Rico Carlos A 
Published: July 2020

ABSTRACT
The Karl Jansky Very Large Array (VLA), Owens Valley Radio Observatory (OVRO), Atacama Large Millimetric Array (ALMA), and the infrared Spitzer observatories are powerful facilities to study massive star formation regions and related objects such as ultra-compact (UC) H ii regions, molecular clumps, and cores. We used these telescopes to study the UC H ii region G43.89–0.78. The morphological study at arcminute scales using NVSS and Spitzer data shows that this region is similar to those observed in the bubble-like structures revealed by Spitzer observations. With this result, and including a physical characterization based on 3.6 cm data, we suggest G43.89–0.78 be classified as an UC H ii region with Extended Emission because it meets the operational definition given in this paper comparing radio continuum data at 3.6 and 20 cm. For the ultra-compact component, we use VLA data to obtain physical parameters at 3.6 cm confirming this region as an UC H ii region. Using ALMA observations, we detect the presence of a dense (2.6 × 107 cm−3) and small (∼ 2.0 arcsec; 0.08 pc) molecular clump with a mass of 220 M⊙ and average kinetic temperature of 21 K, located near to the UC H ii region. In this clump, catalogued as G43.890–0.784, water masers also exist, possibly tracing a bipolar outflow. We discover in this vicinity two additional clumps which we label as G43.899–0.786 (Td = 50 K; M = 11 M⊙) and G43.888–0.787 (Td = 50 K; M = 15 M⊙).
Orbital period cut-off of W UMa-type contact binaries
Authors: Zhang Xu-Dong , Qian Sheng-Bang 
Published: July 2020

ABSTRACT
Period cut-off and period–colour relation are two special characters of W UMa-type contact binaries. In the past, many authors noted these two properties, however, a comprehensive study was still lacking. In order to reveal a theoretical mechanism behind these two peculiarities, we collected 365 contact binaries whose orbital periods, mass ratios, masses, and radii are compiled and attempted to make this idea come true by statistical means. Then, we obtained a lower limit (0.15 d) of orbital period by studying the correlation among four physical parameters (orbital period P, mass ratio q, mass of primary star M1, and separation between two components a). Furthermore, we used the most reliable parameters (P and q) to check our result, fortunately, all evidence indicated that our predicted value is credible. In the end, the reason why the period–colour relation exists was also discussed.
A comprehensive rat transcriptome built from large scale RNA-seq-based annotation
Authors: Ji Xiangjun , Li Peng , Fuscoe James C , Chen Geng , Xiao Wenzhong , Shi Leming , Ning Baitang , Liu Zhichao , Hong Huixiao , Wu Jun , Liu Jinghua , Guo Lei , Kreil David P , Łabaj Paweł P , Zhong Liping , Bao Wenjun , Huang Yong , He Jian , Zhao Yongxiang , Tong Weida , Shi Tieliu 
Published: July 2020

AbstractThe rat is an important model organism in biomedical research for studying human disease mechanisms and treatments, but its annotated transcriptome is far from complete. We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium. Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for ∼42% and ∼6.5% of the genome, respectively. Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 728 as high confident long noncoding transcripts. Different tissues rather than different stages have a significant influence on the expression patterns of transcripts. We also found that 11 715 genes and 15 852 transcripts were expressed in all 11 tissues and that 849 house-keeping genes expressed different isoforms among tissues. This comprehensive transcriptome is freely available at http://www.unimd.org/rtr/. Our new rat transcriptome provides essential reference for genetics and gene expression studies in rat disease and toxicity models.
The Relationship Between Stimulation Current and Functional Site Localization During Brain Mapping
Authors: Muster Rachel H , Young Jacob S , Woo Peter Y M , Morshed Ramin A , Warrier Gayathri , Kakaizada Sofia , Molinaro Annette M , Berger Mitchel S , Hervey-Jumper Shawn L 
Published: July 2020

Abstract

BACKGROUND
Gliomas are often in close proximity to functional regions of the brain; therefore, electrocortical stimulation (ECS) mapping is a common technique utilized during glioma resection to identify functional areas. Stimulation-induced seizure (SIS) remains the most common reason for aborted procedures. Few studies have focused on oncological factors impacting cortical stimulation thresholds.

OBJECTIVE
To examine oncological factors thought to impact stimulation threshold in order to understand whether a linear relationship exists between stimulation current and number of functional cortical sites identified.

METHODS
We retrospectively reviewed single-institution prospectively collected brain mapping data of patients with dominant hemisphere gliomas. Comparisons of stimulation threshold were made using t-tests and ANOVAs. Associations between oncologic factors and stimulation threshold were made using multivariate regressions. The association between stimulation current and number of positive sites was made using a Poisson model.

RESULTS
Of the 586 patients included in the study, SIS occurred in 3.92% and the rate of SIS events differed by cortical location (frontal 8.5%, insular 1.6%, parietal 1.3%, and temporal 2.8%; P = .009). Stimulation current was lower when mapping frontal cortex (P = .002). Stimulation current was not associated with tumor plus peritumor edema volume, world health organization) (WHO grade, histology, or isocitrate dehydrogenase (IDH) mutation status but was associated with tumor volume within the frontal lobe (P = .018). Stimulation current was not associated with number of positive sites identified during ECS mapping (P = .118).

CONCLUSION
SISs are rare but serious events during ECS mapping. SISs are most common when mapping the frontal lobe. Greater stimulation current is not associated with the identification of more cortical functional sites during glioma surgery.