bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergence of massless Froḧlich polarons in two-dimensional semi-metals on polar substrates
Authors: Banerjee Swapnonil 
Published: December 2020

Abstract
We consider the polaron dynamics driven by Froḧlich type, long wavelength dominated electron-phonon interaction at zero temperature, for three different semi-metals: single and bilayer graphene, and semi-Dirac, all grown on polar substrates such as, SiC. Single layer graphene (henceforth called SL graphene), bilayer graphene (henceforth called BL graphene), and semi-Dirac have two dimensional band-structures with point Fermi surfaces in their natural undoped conditions. When these materials are grown on polar substrates, their electrons can interact with the optical phonons (LO) at the surface of the substrates. That gives rise to the possibility of polaron formation in the context of these semi-metals, although they themselves are non-polar. Starting from the Froḧlich type electron-phonon interaction Hamiltonian, perturbation theory is employed to calculate the self energy of the electron due to polaron formation for the three aforementioned systems. The electron self energy, or the polaron energy, calculated analytically for BL graphene, is shown to vary linearly with the electron momentum for small electron momenta. Whereas for ordinary polar crystals (both two and three dimensional), for small electron momentum, the polaron energy is quadratic leading to the mass correction of the electron, for BL graphene the polaron energy disperses linearly, rendering the massive BL graphene electrons effectively massless. Energies for Froḧlich polarons in SL graphene and semi-Dirac on polar substrates, are numerically evaluated. Also, the electron relaxation rate, related to the imaginary part of the analytically continued electron self energy expression, is calculated for the three systems.
Identifying anti-coronavirus peptides by incorporating different negative datasets and imbalanced learning strategies
Authors: Pang Yuxuan , Wang Zhuo , Jhong Jhih-Hua , Lee Tzong-Yi 
Published: December 2020

Abstract
As the current worldwide outbreaks of the SARS-CoV-2, it is urgently needed to develop effective therapeutic agents for inhibiting the pathogens or treating the related diseases. Antimicrobial peptides (AMP) with functional activity against coronavirus could be a considerable solution, yet there is no research for identifying anti-coronavirus (anti-CoV) peptides with the computational approach. In this study, we first investigated the physiochemical and compositional properties of the collected anti-CoV peptides by comparing against three other negative sets: antivirus peptides without anti-CoV function (antivirus), regular AMP without antivirus functions (non-AVP) and peptides without antimicrobial functions (non-AMP). Then, we established classifiers for identifying anti-CoV peptides between different negative sets based on random forest. Imbalanced learning strategies were adopted due to the severe class-imbalance within the datasets. The geometric mean of the sensitivity and specificity (GMean) under the identification from antivirus, non-AVP and non-AMP reaches 83.07%, 85.51% and 98.82%, respectively. Then, to pursue identifying anti-CoV peptides from broad-spectrum peptides, we designed a double-stages classifier based on the collected datasets. In the first stage, the classifier characterizes AMPs from regular peptides. It achieves an area under the receiver operating curve (AUCROC) value of 97.31%. The second stage is to identify the anti-CoV peptides between the combined negatives of other AMPs. Here, the GMean of evaluation on the independent test set is 79.42%. The proposed approach is considered as an applicable scheme for assisting the development of novel anti-CoV peptides. The datasets and source codes used in this study are available at https://github.com/poncey/PreAntiCoV.
Introduction of user fee for language interpretation: effects on use of interpreters in Danish health care
Authors: Michaëlis Camilla , Krasnik Allan , Norredam Marie 
Published: December 2020

Abstract
Amendments to the Danish Health Act were introduced in 2018 that stated immigrant patients who have resided in Denmark for more than 3 years have to pay user fees for interpretation in health care. The aim of the study was to explore, how the use of interpreters was affected by the introduction of user fees for interpretation. Results showed a considerable decrease in interpretation services following the introduction of the fee. It is likely to assume that the reduced utilization of interpretation services is highly related to the fee. Further research is needed about the consequences of underutilization of interpretation services.
Federated learning improves site performance in multicenter deep learning without data sharing
Authors: Sarma Karthik V , Harmon Stephanie , Sanford Thomas , Roth Holger R , Xu Ziyue , Tetreault Jesse , Xu Daguang , Flores Mona G , Raman Alex G , Kulkarni Rushikesh , Wood Bradford J , Choyke Peter L , Priester Alan M , Marks Leonard S , Raman Steven S , Enzmann Dieter , Turkbey Baris , Speier William , Arnold Corey W 
Published: December 2020

Abstract

Objective
To demonstrate enabling multi-institutional training without centralizing or sharing the underlying physical data via federated learning (FL).

Materials and Methods
Deep learning models were trained at each participating institution using local clinical data, and an additional model was trained using FL across all of the institutions.

Results
We found that the FL model exhibited superior performance and generalizability to the models trained at single institutions, with an overall performance level that was significantly better than that of any of the institutional models alone when evaluated on held-out test sets from each institution and an outside challenge dataset.

Discussion
The power of FL was successfully demonstrated across 3 academic institutions while avoiding the privacy risk associated with the transfer and pooling of patient data.

Conclusion
Federated learning is an effective methodology that merits further study to enable accelerated development of models across institutions, enabling greater generalizability in clinical use.
Effects of Ascogregarina culicis (Eugregarinorida: Lecudinidae) on Mosquito Size and Dengue Virus Infection in Aedes aegypti (Diptera: Culicidae)
Authors: Thongsripong Panpim , Wesson Dawn M 
Published: December 2020

Abstract
Dengue virus infection, transmitted via mosquito bites, poses a substantial risk to global public health. Studies suggest that the mosquito’s microbial community can profoundly influence vector-borne pathogen transmissions, including dengue virus. Ascogregarina culicis (Ross) of the phylum Apicomplexa is among the most common parasites of Aedes aegypti (Linnaeus), the principal vector of dengue. Despite a high prevalence worldwide, including in the areas where dengue is endemic, the impact of A. culicis on Ae. aegypti vector competence for dengue virus is unknown. This study aimed to investigate the effects of A. culicis infection on mosquito size and fitness, as measured by wing length, and the susceptibility to dengue virus infection in Ae. aegypti. Our results showed that there was no statistically significant difference in wing lengths between Ae. aegypti infected and not infected with A. culicis. Furthermore, A. culicis infection did not significantly affect dengue virus infection or disseminated infection rate. However, there was a significant association between shorter wings and higher dengue virus infection rate, whereby a 0.1-mm increase in wing length decreased the odds of the mosquito being infected by 32%. Thus, based on our result, A. culicis infection does not influence the body size and dengue virus infection in Ae. aegypti. This study helps to shed light on a common but neglected eukaryotic mosquito parasite.
Zymosan enhances in vitro phagocyte function and the immune response of mice infected with Paracoccidioides brasiliensis
Authors: Silva G S , Silva D A , Guilhelmelli F , Jerônimo M S , Cardoso-Miguel M R D , Bürgel P H , Castro R J A , de Oliveira S A M , Silva-Pereira I , Bocca A L , Tavares A H 
Published: December 2020

Abstract

Paracoccidioides brasiliensis is the major etiologic agent of Paracoccidioidomycosis (PCM), the most frequent human deep mycosis in Latin America. It is proposed that masking of β-glucan in P. brasiliensis cell wall is a critical virulence factor that contributes to the development of a chronic disease characterized by a long period of treatment, which is usually toxic. In this context, the search for immunomodulatory agents for therapeutic purposes is highly desirable. One strategy is to use pattern recognition receptors (PRRs) ligands to stimulate the immune response mediated by phagocytes. Here, we sought to evaluate if Zymosan, a β-glucan-containing ligand of the PRRs Dectin-1/TLR-2, would enhance phagocyte function and the immune response of mice challenged with P. brasiliensis. Dendritic cells (DCs) infected with P. brasiliensis and treated with Zymosan showed improved secretion of several proinflammatory cytokines and expression of maturation markers. In addition, when cocultured with splenic lymphocytes, these cells induced the production of a potential protective type 1 and 17 cytokine patterns. In macrophages, Zymosan ensued a significant fungicidal activity associated with nitric oxide production and phagolysosome acidification. Importantly, we observed a protective effect of Zymosan-primed DCs delivered intranasally in experimental pulmonary PCM. Overall, our findings support the potential use of β-glucan-containing compounds such as Zymosan as an alternative or complementary antifungal therapy.

Lay Summary
We report for the first time that Paracoccidioides brasiliensis-infected phagocytes treated with Zymosan (cell wall extract from bakers' yeast) show enhanced cytokine production, maturation, and fungal killing. Also, Zymosan-primed phagocytes induce a protective immune response in infected mice.
Humanizing the Morbidity and Mortality Conference
Authors: Pang Sharon , Warraich Haider J. 
Published: December 2020

Morbidity and mortality conferences (MMCs) are a long-held legacy institution in academic medicine that enable medical providers and hospital administrators to learn from systemic and individual errors, thereby leading to improved medical care. Originally, this forum had 1 major role—education. The MMC evolved and a second key role was added: quality improvement. In the wake of the 2020 COVID-19 pandemic, a second evolution—one that will humanize the MMC—is required. The pandemic emphasizes the need to use MMCs not only as a place to discuss errors but also as a place for medical providers to reflect on lives lost. The authors’ review of the literature regarding MMCs indicates that most studies focus on enabling MMCs to become a forum for quality improvement, while none have emphasized the need to humanize MMCs to decrease medical provider burnout and improve patient satisfaction. Permitting clinicians to be human on the job requires restructuring the MMC to provide a space for reflection and, ultimately, defining a new purpose and charge for the MMC.
The authors have 3 main recommendations. First, principles of humanism such as compassion, empathy, and respect, in particular, should be incorporated into traditional MMCs. Second, shorter gatherings devoted to giving clinicians the opportunity to focus on their humanity should be arranged. Third, an MMC focused entirely on the human aspects of medical care should be periodically arranged to provide an outlet for storytelling, artistic expression, and reflection.
Humanizing the MMC—a core symposium in clinical medicine worldwide—could be the first step in revitalizing the spirit at the heart of medicine, one dedicated to health and healing. This spirit, which has been eroding as the field of medicine becomes increasingly corporate in structure and mission, is as essential during peaceful times in health care as during a pandemic.
The Impact of Biopsy Tool Choice and Rapid On-Site Evaluation on Diagnostic Accuracy for Malignant Lesions in the Prospective
Authors: Gildea Thomas R. , Folch Erik E. , Khandhar Sandeep J. , Pritchett Michael A. , LeMense Gregory P. , Linden Philip A. , Arenberg Douglas A. , Rickman Otis B. , Mahajan Amit K. , Singh Jaspal , Cicenia Joseph , Mehta Atul C. , Lin Haiying , Mattingley Jennifer S. 
Published: December 2020

Background:
The diagnostic yield of electromagnetic navigation bronchoscopy (ENB) is impacted by biopsy tool strategy and rapid on-site evaluation (ROSE) use. This analysis evaluates usage patterns, accuracy, and safety of tool strategy and ROSE in a multicenter study.

Methods:
NAVIGATE (NCT02410837) evaluates ENB using the superDimension navigation system (versions 6.3 to 7.1). The 1-year analysis included 1215 prospectively enrolled subjects at 29 United States sites. Included herein are 416 subjects who underwent ENB-aided biopsy of a single lung lesion positive for malignancy at 1 year. Use of a restricted number of tools (only biopsy forceps, standard cytology brush, and/or bronchoalveolar lavage) was compared with an extensive multimodal strategy (biopsy forceps, cytology brush, aspirating needle, triple needle cytology brush, needle-tipped cytology brush, core biopsy system, and bronchoalveolar lavage).

Results:
Of malignant cases, 86.8% (361/416) of true positive diagnoses were obtained using extensive multimodal strategies. ROSE was used in 300/416 cases. The finding of malignancy by ROSE reduced the total number of tools used. A malignant ROSE call was obtained in 71% (212/300), most (88.7%; 188/212) by the first tool used (49.5% with aspirating needle, 20.2% with cytology brush, 17.0% with forceps). True positive rates were highest for the biopsy forceps (86.9%) and aspirating needle (86.6%). Use of extensive tool strategies did not increase the rates of pneumothorax (5.5% restricted, 2.8% extensive) or bronchopulmonary hemorrhage (3.6% restricted, 1.1% extensive).

Conclusion:
These results suggest that extensive biopsy tool strategies, including the aspirating needle, may provide higher true positive rates for detecting lung cancer without increasing complications.
Impact of a Dedicated Education Unit Experience on Critical Thinking Development in Nursing Students
Authors: Bittner Nancy Phoenix , Campbell Elizabeth , Gunning Thomas 
Published: December 2020

Aim
The purpose of this study was to identify the impact of the dedicated education unit (DEU) on nursing students' critical thinking ability.

Background
The DEU is an innovative approach to clinical education, which uses clinical nurses with expert practice consistently in a competency-based experience.

Method
Participants (intervention and control groups) completed the Nursing Executive Center's Critical Thinking Diagnostic Assessment tool before and after clinical experience.

Results
Participants included 243 students with 179 non-DEU and 64 DEU students. There were significant increases in total pretest and posttest score means (P < .05) for the DEU (intervention) group. A significant change (P < .0001) was seen in critical thinking scores by category for both groups and in the intervention group on pretest and posttest scores, even after controlling for pretest scores (P < .0001).

Conclusions
Results support the efficacy of the DEU model in developing critical thinking. Prior DEU studies have focused on implementation and satisfaction with the model.
Content Evidence for Validity of Time-to-Task Initiation
Authors: Nichols Blake E. , McMichael Ali B. V. , Ambardekar Aditee P. 
Published: December 2020

Introduction
Educators require validated tools to assess learner competency in simulation-based mastery learning. We previously created a simulation to incorporate crisis resource management skills after a needs assessment of our pediatric residency program. We present the development of and content evidence for validity of a task list with time-to-task initiation designed to aid in rapid cycle deliberate practice (RCDP) debriefing and assessment of pediatrics resident learners.

Methods
Five board-certified pediatricians developed the initial task list with 30 tasks. We used the Delphi technique to seek content evidence for validity of the initial task list using 17 board-certified pediatricians at 7 institutions across the United States. After finalizing the task list, we video recorded 3 pediatric experts performing the tasks in a simulation. We then used the Delphi technique to establish and to attain agreement on time-to-task initiation. We calculated Cronbach α coefficient to measure internal consistency of the expert responses. After finalizing the task list, we divided it into 3 stages with 5 separate cycles per stage to direct the educator in performance of RCDP debriefing.

Results
The group reached 80% agreement after 2 Delphi rounds with a Cronbach α coefficient of 0.95. The resultant list included 25 tasks. The group subsequently achieved 80% agreement on the time-to-task initiation in 2 Delphi rounds.

Conclusions
We present content evidence for validity of a task list with associated time-to-task initiation for a simulation scenario that incorporates crisis resource management skills and is designed to aid educators in RCDP debriefing. This task list may decrease intereducator inconsistencies in delivery of RCDP for a common pediatric resuscitation scenario.
High Rate of Positive Circumferential Resection Margin in Colon Cancer
Authors: Healy Mark A. , Peacock Oliver , Hu Chung-Yuan , Bednarski Brian K. , Tillman Matthew M. , Messick Craig , Kaur Harmeet , Chang George J. 
Published: December 2020

Objective:
To identify rates of positive circumferential resection margin (CRM) for colon cancer surgery in the US.

Summary Background Data:
CRM is one of the most important determinants of local control in colorectal cancers. The extent to which CRM involvement exists after colon cancer surgery is unknown.

Methods:
Colon cancer cases with resection 2010 to 2015 were identified from the National Cancer Data Base. Adjusting for patient and tumor characteristics, comparisons were made between cases with CRM > 1 mm (negative margin) and those with margin involved with tumor or ≤ 1 mm (positive margin, CRM+). Hospital-level analysis was performed, examining observed-to-expected CRM+ rates.

Results:
In total, 170,022 cases were identified: 150,291 CRM- and 19,731 CRM+ (11.6%). Pathologic T-category was the greatest predictor of CRM+, with higher rates in pT4(25.8%), pT4A(24.7%), and pT4B(31.5%) versus pT1(4.5%), pT2(6.3%) and pT3 (10.9%, P < 0.001). Within pT4 patients, predictors of CRM+ included signet-ring histology (38.1% vs 26.7% nonmucinous, and 26.9% mucinous adenocarcinoma, P < 0.001), removing < 12 lymph nodes (36.5% vs 26.1% >12, P < 0.001), community facilities (32.7%) versus academic/research (23.6%, P < 0.001), year (30.1% 2010 vs 22.6% 2015, P < 0.001), and hospital volume (24.5% highest quartile vs 32.7% lowest, P < 0.001). Across 1288 hospitals, observed-to-expected ratios for CRM+ ranged from 0 to 7.899; 429 facilities had higher than expected rates.

Conclusions:
Overall rate of CRM+ in US colon cancer cases is high. Variation exists across hospitals, with higher than expected rates in many facilities. Although biology is a major influencing factor, CRM+ rates represent an area for multidisciplinary improvement in quality of colon cancer care.
Adaptive immunity to SARS-CoV-2 in cancer patients: The CAPTURE study
Authors: Fendler Annika , Au Lewis , Boos Laura Amanda , Byrne Fiona , Shepherd Scott T.C. , Shum Ben , Gerard Camille L. , Ward Barry , Xie Wenyi , Cerrone Maddalena , Cornish Georgina H. , Pule Martin , Mekkaoui Leila , Ng Kevin W. , Stone Richard , Gomes Camila , Flynn Helen R. , Agua-Doce Ana , Hobson Phillip , Caidan Simon , Howell Mike , Goldstone Robert , Gavrielides Mike , Nye Emma , Snijders Bram , Macrae James , Nicod Jerome , Hayday Adrian , Gronthoud Firza , Messiou Christina , Cunningham David , Chau Ian , Starling Naureen , Turner Nicholas , Rusby Jennifer , Welsh Liam , van As Nicholas , Jones Robin , Droney Joanne , Banerjee Susana , Tatham Kate , Jhanji Shaman , O’Brien Mary , Curtis Olivia , Harrington Kevin , Bhide Shreerang , Slattery Tim , Khan Yasir , Tippu Zayd , Leslie Isla , Gennatas Spyridon , Okines Alicia , Reid Alison , Young Kate , Furness Andrew , Pickering Lisa , Ghandi Sonia , Gamblin Steve , Swanton Charles , Nicholson Emma , Kumar Sacheen , Yousaf Nadia , Wilkinson Katalin , Swerdlow Anthony , Harvey Ruth , Kassiotis George , Wilkinson Robert , Larkin James , Turajlic Samra 
Published: December 2020

SUMMARYThere is a pressing need to characterise the nature, extent and duration of immune response to SARS-CoV-2 in cancer patients and inform risk-reduction strategies and preserve cancer outcomes. CAPTURE is a prospective, longitudinal cohort study of cancer patients and healthcare workers (HCWs) integrating longitudinal immune profiling and clinical annotation. We evaluated 529 blood samples and 1051 oronasopharyngeal swabs from 144 cancer patients and 73 HCWs and correlated with >200 clinical variables. In patients with solid cancers and HCWs, S1-reactive and neutralising antibodies to SARS-CoV-2 were detectable five months post-infection. SARS-CoV-2-specific T-cell responses were detected, and CD4+T-cell responses correlated with S1 antibody levels. Patients with haematological malignancies had impaired but partially compensated immune responses. Overall, cancer stage, disease status, and therapies did not correlate with immune responses. These findings have implications for understanding individual risks and potential effectiveness of SARS-CoV-2 vaccination in the cancer population.
Discovery of Cyclic Peptide Ligands to the SARS-CoV-2 Spike Protein using mRNA Display
Authors: Norman Alexander , Franck Charlotte , Christie Mary , Hawkins Paige M. E. , Patel Karishma , Ashhurst Anneliese S. , Aggarwal Anupriya , Low Jason K. K. , Siddiquee Rezwan , Ashley Caroline L. , Steain Megan , Triccas James A. , Turville Stuart , Mackay Joel P. , Passioura Toby , Payne Richard J. 
Published: December 2020

ABSTRACTThe COVID-19 pandemic, caused by SARS-CoV-2, has led to substantial morbidity, mortality and disruption globally. Cellular entry of SARS-CoV-2 is mediated by the viral spike protein and affinity ligands to this surface protein have the potential for applications as antivirals and diagnostic reagents. Here, we describe the affinity selection of cyclic peptide ligands to the SARS-CoV-2 spike protein receptor binding domain (RBD) from three distinct libraries (in excess of a trillion molecules each) by mRNA display. We identified six high affinity molecules with dissociation constants (KD) in the nanomolar range (15-550 nM) to the RBD. The highest affinity ligand could be used as an affinity reagent to detect spike protein in solution by ELISA, and the co-crystal structure of this molecule bound to the RBD demonstrated that it binds to a cryptic binding site, displacing a β-strand near the C-terminus. Our findings provide key mechanistic insight into the binding of peptide ligands to the SARS-CoV-2 spike RBD and the ligands discovered in this work may find future use as reagents for diagnostic applications.