bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simulation-Based Up-Training in Response to the COVID-19 Pandemic
Authors: Nair Sunil S. , Kaufman Brian 
Published: September 2020

Summary Statement
The dramatic outbreak of COVID-19 placed unprecedented strain on the critical care workforce of New York City. The enhanced precautions required to safely care for COVID-19 patients impacted the performance of even routine critical care procedures. Meanwhile, staff were stretched to care for exponentially rising case volume as COVID intensive care units (ICUs) expanded. Simulation was used to bridge these gaps—first to familiarize personnel within the Division of Pulmonary and Critical Care with revised COVID-19 care procedures, then to orient noncritical care clinicians volunteering from other specialties for COVID ICU deployment to general critical care and COVID-19 care principles. Using mannequin-based simulation scenarios followed by comprehensive debriefing sessions, simulation participants received high-intensity, high-fidelity training in respiratory failure, circulatory failure, bedside ultrasound, bedside ICU procedures, and elements of COVID-19–specific care. More than 200 physicians and advanced practice practitioners completed simulation training in preparation for deployment, supplementing and enhancing the ICU workforce at a decisive time during the outbreak.
Readmission for venous thromboembolism after emergency general surgery is underreported and influenced by insurance status
Authors: Rattan Rishi , Cioci Alessia C. , Urréchaga Eva M. , Chatoor Matthew S. , Krocker Joseph D. , Johnson Deanna L. , Curcio Gary J. , Namias Nicholas , Yeh Daniel D. , Ginzburg Enrique , Parreco Joshua P. 
Published: October 2020

BACKGROUND
Prior studies of venous thromboembolism (VTE) after emergency general surgery (EGS) are not nationally representative nor do they fully capture readmissions to different hospitals. We hypothesized that different-hospital readmission accounted for a significant number of readmissions with VTE after EGS and that predictive factors would be different for same- and different-hospital readmissions.

METHODS
The 2014 Nationwide Readmissions Database was queried for nonelective EGS hospitalizations. The outcomes were readmission to the index or different hospitals within 180 days with VTE. Multivariate logistic regressions identified risk factors for readmission to index and different hospitals with VTE, reported as odds ratios with their 95% confidence intervals. Patients were excluded if during the index admission they expired, developed a VTE, had a vena cava filter placed, or did not have at least 180 days of follow-up.

RESULTS
Of 1,584,605 patients meeting inclusion criteria, 1.3% (n = 20,963) of patients were readmitted within 180 days with a VTE. Of these, 28% (n = 5,866) were readmitted to a different hospital. Predictors overall for readmission with VTE were malignancy, prolonged hospitalization, age, and being publicly insured. However, predictors for readmission to a different hospital are based on hospital characteristics, including for-profit status, or procedure type.

CONCLUSIONS
Nearly one in three readmissions with VTE after EGS occurs at a different hospital and may be missed by current quality metrics that only capture same-hospital readmission. Such metrics may underestimate for-profit hospital postoperative VTE rates relative to public and nonprofit hospitals, potentially affecting benchmarking and reimbursement. Postdischarge VTE rate is associated with insurance status. These findings have implications for policy and prevention programming design.

LEVEL OF EVIDENCE
Epidemiological study, level III.
Inference of malaria transmission dynamics under varying assumptions about the spatial scale of transmission: a modelling study in three elimination settings
Authors: Routledge Isobel , Bhatt Samir 
Published: September 2020

AbstractBackgroundIndividual-level geographic information about malaria cases, such as the GPS coordinates of residence or health facility, is often collected as part of surveillance in near-elimination settings, but could be more effectively utilised to infer transmission dynamics, in conjunction with additional information such as symptom onset time and genetic distance. However, in the absence of data about the flow of parasites between populations, the spatial scale of malaria transmission is often not clear. As a result, it is important to understand the impact of varying assumptions about the spatial scale of transmission on key metrics of malaria transmission, such as reproduction numbers.MethodsWe developed a method which allows the flexible integration of distance metrics (such as Euclidian distance, genetic distance or accessibility matrices) with temporal information into a single inference framework to infer malaria reproduction numbers. Twelve scenarios were defined, representing different assumptions about the likelihood of transmission occurring over different geographic distances and likelihood of missing infections (as well as high and low amounts of uncertainty in this estimate). These scenarios were applied to four individual level datasets from malaria eliminating contexts to estimate individual reproduction numbers and how they varied over space and time.ResultsModel comparison suggested that including spatial information improved models as measured by ΔAICc, compared to time only results. Across scenarios and across datasets, including spatial information tended to increase the seasonality of temporal patterns in reproduction numbers and reduced noise in the temporal distribution of reproduction numbers. The best performing parameterisations assumed long-range transmission (>200km) was possible.ConclusionsOur approach is flexible and provides the potential to incorporate other sources of information which can be converted into distance or adjacency matrices such as travel times or molecular markers.
Inhibition of SHP2 ameliorates psoriasis by decreasing TLR7 endosome localization
Authors: Zhu Yuyu , Shao Fenli , Yan Wei , Chen Zhen Bouman , Ke Bowen , Jiang Xian , Cheng Haibo , Sun Dongdong , Song Chenglin , Kong Lingdong , Guo Wenjie , Lai Yuping , Feng Gen-Sheng , Xu Qiang , Sun Yang 
Published: October 2020

SUMMARYPsoriasis is a complex chronic inflammatory skin disease with unclear molecular mechanisms. Here, we identify Src homology-2 domain containing protein tyrosine phosphatase-2 (SHP2) as a novel accelerator of psoriasis development. Both genetic ablation of SHP2 in macrophages and pharmacological inhibition of SHP2 prevents the development of psoriasis-like skin inflammation in an imiquimod-induced murine model of psoriasis. Mechanistically, SHP2 promotes the trafficking of Toll-like receptor 7 (TLR7) from Golgi to endosome through its interaction with and dephosphorylation of TLR7 at Tyr1024, which promotes the ubiquitination of TLR7 and psoriasis-like skin inflammation. Importantly, SHP2 allosteric inhibitor SHP099 reduces the expression of pro-inflammatory cytokines in peripheral blood mononuclear cells from human patients with psoriasis. Collectively, our findings identify SHP2 as a novel regulator of psoriasis and suggest that SHP2 inhibition may be a promising therapeutic approach for psoriatic patients.
Impact of visual impairment on balance and visual processing functions in students with special educational needs
Authors: Choi KY , Wong HY , Cheung HN , Tseng JK , Chen CC , Wu CL , Eng H , Woo GC , Cheong AMY 
Published: October 2020

AbstractIntroductionVision is a critical factor for children’s development. However, prevalence of visual impairment (VI) is high in students with special educational needs (SEN). Other than vision disability, this group of students is prone to having functional deficits. It is unclear whether visual problems relate to these compromised functional deficits. This study aimed to assess the impact of vision on visual processing functions and balance performance in SEN students through a community service in special schools.MethodsA total of 104 (chronological age 14.3 ± 4.3 years, 43 females) SEN students in Taiwan were assessed and classified as having normal vision (NV) or vision impairment (VI). Visual acuity (distance and near) and contrast sensitivity (CS) were measured as the visual outcomes. Visual processing function assessment included facial expression recognition by Heidi expression test, in terms of card matching (FEC), and examiner’s facial expression matching (FEE), and visual orientation recognition (by mailbox game, VO). Dynamic balance was assessed with Timed Up and Go (TUG) test, while static standing balance was assessed using a force plate to measure the postural sway in double-legged feet-together and tandem stance with eyes open and closed conditions. Static balance was presented in terms of the change in the centre of pressure in maximal medial-lateral (ML) and antero-posterior (AP) sways, sway variability (V), and sway path length (L).ResultsAlthough visual acuity was significantly worse in VI than NV (p < 0.001), CS was similar in the two groups (p = 0.08). VO, FEC, and FEE also did not differ significantly between groups (p > 0.05). NV performed better in the TUG than VI (p = 0.03). There was a significant interaction between eye condition and the vision group (p < 0.05) for static balance. Pairwise comparisons showed that NV swayed significantly less in ML than VI under tandem stance-open eye condition (p = 0.04), but significantly more in closed eye condition (p = 0.03). Conversely, VI had less V and shorter L than NV under tandem stance-closed eye condition (p = 0.03).ConclusionThis study is the first to our knowledge to examine the effect of vision on visual processing functions and balance performance in SEN students. Vision did not appear to be the major reason for impairment in visual processing. However, vision plays an important role in maintaining dynamic and static balance in SEN students.
The potential contribution of face coverings to the control of SARS-CoV-2 transmission in schools and broader society in the UK: a modelling study
Authors: Panovska-Griffiths J. , Kerr C.C. , Waites W. , Stuart R.M. , Mistry D. , Foster D. , Klein D.J. , Viner R.M. , Bonell C. 
Published: September 2020

AbstractRecent findings suggest that an adequate test-trace-isolate (TTI) strategy is needed to prevent a secondary COVID-19 wave with the reopening of society in the UK. Here we assess the potential importance of mandatory masks in the parts of community and in secondary schools. We show that, assuming current TTI levels, adoption of masks in secondary schools in addition to community settings can reduce the size of a second wave, but will not prevent it; more testing of symptomatic people, tracing and isolating of their contacts is also needed. To avoid a second wave, with masks mandatory in secondary schools and in certain community settings, under current tracing levels, 68% or 46% of those with symptomatic infection would need to be tested if masks’ effective coverage were 15% or 30% respectively, compared to 76% and 57% if masks are mandated in community settings but not secondary schools.
Conditional Generative Adversarial Networks for Individualized Treatment Effect Estimation and Treatment Selection
Authors: Ge Qiyang , Huang Xuelin , Fang Shenying , Guo Shicheng , Liu Yuanyuan , Lin Wei , Xiong Momiao 
Published: September 2020

AbstractTreatment response is heterogeneous. However the classical methods treat the treatment response as homogeneous and estimate the average treatment effects. The traditional methods are difficult to apply to precision oncology. The artificial intelligence (AI) is a powerful tool for precision oncology. It can accurately estimate the individualized treatment effects and learn optimal treatment choices. Therefore, the AI approach can substantially improve progress and treatment outcomes of patients. As one of AI approach, conditional generative adversarial nets for inference of individualized treatment effects (GANITE) have been developed. However, the GANITE can only deal with binary treatment and does not provide a tool for optimal treatment selection. To overcome these limitations, we modify conditional generative adversarial networks (MCGANs) to allow estimation of individualized effects of any types of treatments including binary, categorical and continuous treatments. We propose to use sparse techniques for selection of biomarkers that predict the best treatment for each patient. Simulations show that the CGANs outperform seven other state-of-the-art methods: linear regression (LR), Bayesian linear ridge regression (BLR), KNN, random forest classification (RF (C)), random forest regression (RF (R)), logistic regression (LogR) and support vector machine (SVM). To illustrate their applications, the proposed CGANs were applied to 256 patients with newly diagnosed acute myeloid leukemia (AML) who were treated with high dose ara-C (HDAC), Idarubicin (IDA) and both of these two treatments (HDAC+IDA) at M. D. Anderson Cancer Center. Our results showed that the MCGAN can more accurately and robustly estimate the individualized treatment effects than other state-of-the art methods. Several biomarkers such as GSK3, BILIRUBIN, SMAC are identified and a total of 30 biomarkers can explain 36.8% of treatment effect variation.
Parameters for assessment of talar neck geometry: a protocol for scoping literature review
Authors: Sharma Siddhartha , Jindal Karan , Patel Sandeep , Prabhakar Sharad , Dhillon Mandeep S. 
Published: September 2020

AbstractBackgroundUnderstanding the three-dimensional anatomy of the talar neck is essential in assessing reduction of talar neck fractures, as well as in planning surgical correction for talar malunions. However, the geometrical parameters that describe this anatomy are sparsely reported in the literature.ObjectivesThis review aims to identify from the existing literature, those geometrical parameters that describe the three-dimensional anatomy of the talar neck.MethodsA scoping literature review will be conducted in accordance with the PRISMA-ScR guidelines. The primary searches will be conducted on the PubMed, EMBASE and Scopus databases, using a pre-defined search strategy. Any original research study (whether clinical or cadaveric, prospective or retrospective, comparative or noncomparative), looking at the human talus neck geometry or morphology will be included. Studies that do not describe the talar neck geometry, animal studies, review articles, conference abstracts and case reports will be excluded. Geometrical parameters (including techniques to measure these) that describe the three-dimensional anatomy of the talar neck will be identified. Qualitative analysis will be done by means of appropriate tables and diagrams. If feasible, quantitative analysis to determine pooled estimated of geometrical parameters identified in the review will be conducted by a random-effects meta-analysis model. No formal risk-of-bias assessment has been planned, as this is a scoping literature review.
Comparative transcriptomics and host-specific parasite gene expression profiles inform on drivers of proliferative kidney disease
Authors: Faber Marc , Yoon Sohye , Shaw Sophie , de Paiva Alves Eduardo , Wang Bei , Qi Zhitao , Okamura Beth , Hartikainen Hanna , Secombes Christopher J. , Holland Jason W. 
Published: September 2020

AbstractThe myxozoan parasite,Tetracapsuloides bryosalmonaehas a two-host life cycle alternating between freshwater bryozoans and salmonid fish. Infected fish can develop Proliferative Kidney Disease (PKD), characterised by a gross lymphoid-driven kidney pathology in wild and farmed salmonids. To facilitate an in-depth understanding ofT. bryosalmonae-host interactions, we have adopted a two-host parasite transcriptome sequencing approach to minimize host contamination in the absence of a completeT. bryosalmonaegenome. Parasite contigs common to both infected hosts (the intersect transcriptome; 7,362 contigs) were typically AT-rich (60-75% AT). 5,432 contigs within the intersect were annotated with 1,930 unannotatde contigs encoding for unknown transcripts. We have focused on transcripts encoding proteins involved in; nutrient acquisition, host-parasite interactions, development, and cell-to-cell communication or proteins of unknown function, establishing their potential importance in each host by RT-qPCR. Host-specific expression profiles were evident, particularly in transcripts encoding proteases and proteins involved in lipid metabolism, cell adhesion, and development. We confirm for the first time the presence of homeobox proteins and a frizzled homologue in myxozoan parasites.The novel insights into myxozoan biology that this study reveals will help to focus research in developing future disease control strategies.
Temporal emergence of age-associated changes in cognitive and physical function in vervets (Chlorocebus aethiops sabaeus)
Authors: Frye Brett M. , Valure Payton M. , Craft Suzanne , Baxter Mark G. , Scott Christie , Wise-Walden Shanna , Bissinger David , Register Hannah M. , Copeland Carson , Jorgensen Matthew J. , Justice Jamie N. , Kritchevsky Stephen B. , Register Thomas C. , Shively Carol A. 
Published: September 2020

ABSTRACTDual declines in gait speed and cognitive performance are associated with increased risk of developing dementia. Characterizing the patterns of such impairments therefore is paramount to distinguishing healthy from pathological aging. Nonhuman primates such as vervet/African green monkeys (Chlorocebus aethiops sabaeus) are important models of human neurocognitive aging, yet the trajectory of dual decline has not been characterized. We therefore 1) assessed whether cognitive and physical performance (i.e., gait speed) are lower in older aged animals; 2) explored the relationship between performance in a novel task of executive function (Wake Forest Maze Task – WFMT) and a well-established assessment of working memory (Delayed Response Task – DR Task); and 3) examined the association between baseline gait speed with executive function and working memory at one-year follow-up. We found 1) physical and cognitive declines with age; 2) strong agreement between performance in the novel WFMT and DR task; and 3) that slow gait predicted poor cognitive performance in both domains. Our results suggest that older-aged vervets exhibit a coordinated suite of traits consistent with human aging and that slow gait may be a risk factor for cognitive decline. This integrative approach provides evidence that gait speed and cognitive function differ across the lifespan in female vervet monkeys, which advances them as a model that could be used to evaluate the trajectory of dual decline over time.
On-site eDNA detection of species using ultra-rapid mobile PCR
Authors: Doi Hideyuki , Watanabe Takeshi , Nishizawa Naofumi , Saito Tatsuya , Nagata Hisao , Kameda Yuichi , Maki Nobutaka , Ikeda Kousuke , Fukuzawa Takashi 
Published: September 2020

AbstractMolecular methods, including environmental DNA (eDNA) methods, provide essential information for biological and conservation sciences. Molecular measurements are often performed in the laboratory, which limits their scope, especially for rapid on-site analysis. eDNA methods for species detection provide essential information for the management and conservation of species and communities in various environments. We developed an innovative novel method for on-site eDNA measurements using an ultra-rapid mobile PCR platform. We tested the ability of our method to detect the distribution of silver carp, Hypophthalmichthys molitrix, an invasive fish in Japanese rivers and lakes. Our method reduced the measurement time to 30 min and provided high detectability of aquatic organisms compared to the national observation surveys using multiple fishing nets and laboratory extraction/detection using a benchtop qPCR platform. Our on-site eDNA method can be immediately applied to various taxa and environments.
Making sense of the linear genome, gene function and TADs
Authors: Long Helen S , Greenaway Simon , Powell George , Mallon Ann-Marie , Lindgren Cecilia M , Simon Michelle M 
Published: October 2020

ABSTRACTBackgroundTopologically associating domains (TADs) are thought to act as functional units in the genome. TADs co-localise genes and their regulatory elements as well as forming the unit of genome switching between active and inactive compartments. This has led to the speculation that genes which are required for similar processes may fall within the same TADs, allowing them to share regulatory programs and efficiently switch between chromatin compartments. However, evidence to link genes within TADs to the same regulatory program is limited.ResultsWe investigated the functional similarity of genes which fall within the same TAD. To do this we developed a TAD randomisation algorithm to generate sets of “random TADs” to act as null distributions. We found that while pairs of paralogous genes are enriched in TADs overall, they are depleted in TADs with CCCTC-binding factor (CTCF) ChIP-seq peaks at both boundaries. By assessing gene constraint as a proxy for functional importance we found that genes which singly occupy a TAD have greater functional importance than genes which share a TAD, and these genes are enriched for developmental processes. We found little evidence that pairs of genes in CTCF bound TADs are more likely to be co-expressed or share functional annotations than can be explained by their linear proximity alone.ConclusionsThese results suggest that algorithmically defined TADs consist of two functionally different groups, those which are bound by CTCF and those which are not. We detected no association between genes sharing the same CTCF TADs and increased co- expression or functional similarity, other than that explained by linear genome proximity. We do however find that functionally important genes are more likely to fall within a TAD on their own suggesting that TADs play an important role in the insulation of these genes.
Dincta: Data Integration and Cell Type Annotation of Single Cell Transcriptomes
Authors: Shi Songting 
Published: October 2020

AbstractWe proposed a method for data integration and cell type annotation (Dincta) of single cell transcriptomes in a unify framework. The Dincta can handle three cases. In the first case, the data has been annotated the cell type for all cells, Dincta can integrate the the data into a common low dimension embedding space such that cells with different cell types separate while cells from the different batches but in the same cell type cluster together. In the second case, the data was only annotated for part of cells, such as one sample, Dincta can integrate the data into a common low dimension embedding space such that cells with different cell types separate while cells from the different batches but in the same cell type cluster together. Moreover, it can infer the known or novel cell type of the cells with unknown cell type initially. In the third case, there are no cell type information of cells, we can run Dincta in an unsupervised way. It can infer the number of new cell types and annotate the cells into its correspond cell type, and do data integration keeping cells from different cell type separate while removing the batch effects to mix cells in the same cell type. Dincta is simple, accurate and efficient to integrate data, which keeps the cell type information preserved while removes the batch effects, and infers the known or novel cell types of cells.