bluuebunny/crossref_metadata_2025_split huggingface dataset:
Re-classification of archival Ovarian Carcinoma diagnostics using immunohistologic digital quantification and algorithmic prognosis
Authors: Vrabie Camelia D , Gangal Mihnea I. , Gangal Marius 
Published: August 2020

AbstractTwenty years of research improved the classification of ovarian carcinoma, making the diagnostic relevant from a scientific and clinical perspective. Our research question was to find out if old studies are still pertinent under new diagnostic criteria and how we can use machine learning techniques for re-classification purposes.The same main investigator re-classified 60 cases of ovarian carcinoma after 15 years, using 2014 WHO diagnostic criteria. Selected pathology data only (macro, micro information and immunohistochemistry images coming from a seven-stain panel) were provided for digital analysis. Biomarker images were digitalized and quantified using open source software and a validated methodology. 1080 attributes were classified using a random forest (open source) algorithm, using a supervised learning technique (the training dataset used 180 attributes). Human results were considered “ground truth” for the digital analysis.The human analysis maintained the initial histopathologic diagnostic in 61.5% of cases. The digital prediction shows 80% accuracy and 73% precision when compared with human reclassified data. Based on results, we concluded that “recycling” of old studies is possible. Limitation of the study are the low number of cases analyzed, the total absence of clinical, treatment and prognostic data and a possible human criteria selection bias. Even if technical difficulties related to biomarker selection and histological analysis exist, digital investigation of existing, large archival registries is feasible, reliable and it can be done at a low cost.
Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand
Authors: Geoghegan Jemma L , Ren Xiaoyun , Storey Matthew , Hadfield James , Jelley Lauren , Jefferies Sarah , Sherwood Jill , Paine Shevaun , Huang Sue , Douglas Jordan , Mendes Fábio K , Sporle Andrew , Baker Michael G , Murdoch David R , French Nigel , Simpson Colin R , Welch David , Drummond Alexei J , Holmes Edward C , Duchêne Sebastián , de Ligt Joep 
Published: August 2020

AbstractNew Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nation-wide lockdown of all non-essential services to curb the spread of COVID-19. New Zealand has now effectively eliminated the virus, with low numbers of new cases limited to new arrivals in managed quarantine facilities at the border. Here, we generated 649 SARS-CoV-2 genome sequences from infected patients in New Zealand with samples collected between 26 February and 22 May 2020, representing 56% of all confirmed cases in this time period. Despite its remoteness, the viruses imported into New Zealand represented nearly all of the genomic diversity sequenced from the global virus population. The proportion of D614G variants in the virus spike protein increased over time due to an increase in their importation frequency, rather than selection within New Zealand. These data also helped to quantify the effectiveness of public health interventions. For example, the effective reproductive number, Re, of New Zealand’s largest cluster decreased from 7 to 0.2 within the first week of lockdown. Similarly, only 19% of virus introductions into New Zealand resulted in a transmission lineage of more than one additional case. Most of the cases that resulted in a transmission lineage originated from North America, rather than from Asia where the virus first emerged or from the nearest geographical neighbour, Australia. Genomic data also helped link more infections to a major transmission cluster than through epidemiological data alone, providing probable sources of infections for cases in which the source was unclear. Overall, these results demonstrate the utility of genomic pathogen surveillance to inform public health and disease mitigation.
Repeat COVID-19 Molecular Testing: Correlation with Recovery of Infectious Virus, Molecular Assay Cycle Thresholds, and Analytical Sensitivity
Authors: Gniazdowski Victoria , Morris C. Paul , Wohl Shirlee , Mehoke Thomas , Ramakrishnan Srividya , Thielen Peter , Powell Harrison , Smith Brendan , Armstrong Derek T. , Herrera Monica , Reifsnyder Carolyn , Sevdali Maria , Carroll Karen C. , Pekosz Andrew , Mostafa Heba H. 
Published: August 2020

AbstractRepeat molecular testing for SARS-CoV-2 may result in scenarios including multiple positive results, positive test results after negative tests, and repeated false negative results in symptomatic individuals. Consecutively collected specimens from a retrospective cohort of COVID-19 patients at the Johns Hopkins Hospital were assessed for RNA and infectious virus shedding. Whole genome sequencing confirmed the virus genotype in patients with prolonged viral RNA shedding and droplet digital PCR (ddPCR) was used to assess the rate of false negative standard of care PCR results. Recovery of infectious virus was associated with Ct values of 18.8 ± 3.4. Prolonged viral RNA shedding was associated with recovery of infectious virus in specimens collected up to 20 days after the first positive result in patients who were symptomatic at the time of specimen collection. The use of Ct values and clinical symptoms provides a more accurate assessment of the potential for infectious virus shedding.
Transient dynamics of SARS-CoV-2 as England exited national lockdown
Authors:   REACT Study Investigators, Riley Steven , Ainslie Kylie E. C. , Eales Oliver , Walters Caroline E. , Wang Haowei , Atchison Christina , Diggle Peter J. , Ashby Deborah , Donnelly Christl A. , Cooke Graham , Barclay Wendy , Ward Helen , Darzi Ara , Elliott Paul 
Published: August 2020

AbstractControl of the COVID-19 pandemic requires a detailed understanding of prevalence of SARS-CoV-2 virus in the population. Case-based surveillance is necessarily biased towards symptomatic individuals and sensitive to varying patterns of reporting in space and time. The real-time assessment of community transmission antigen study (REACT-1) is designed to overcome these limitations by obtaining prevalence data based on a nose and throat swab RT-PCR test among a representative community-based sample in England, including asymptomatic individuals. Here, we describe results comparing rounds 1 and 2 carried out during May and mid June / early July 2020 respectively across 315 lower tier local authority areas. In round 1 we found 159 positive samples from 120,620 tested swabs while round 2 there were 123 positive samples from 159,199 tested swabs, indicating a downwards trend in prevalence from 0.13% (95% CI, 0.11%, 0.15%) to 0.077% (0.065%, 0.092%), a halving time of 38 (28, 58) days, and an R of 0.89 (0.86, 0.93). The proportion of swab-positive participants who were asymptomatic at the time of sampling increased from 69% (61%, 76%) in round 1 to 81% (73%, 87%) in round 2. Although health care and care home workers were infected far more frequently than other workers in round 1, the odds were markedly reduced in round 2. Age patterns of infection changed between rounds, with a reduction by a factor of five in prevalence in 18 to 24 year olds. Our data were suggestive of increased risk of infection in Black and Asian (mainly South Asian) ethnicities. Using regional and detailed case location data, we detected increased infection intensity in and near London. Under multiple sensitivity analyses, our results were robust to the possibility of false positives. At the end of the initial lockdown in England, we found continued decline in prevalence and a shift in the pattern of infection by age and occupation. Community-based sampling, including asymptomatic individuals, is necessary to fully understand the nature of ongoing transmission.
Recapitulation of HIV-1 Env-Antibody Coevolution in Macaques Leading to Neutralization Breadth
Authors: Roark Ryan S. , Li Hui , Williams Wilton B. , Chug Hema , Mason Rosemarie D. , Gorman Jason , Wang Shuyi , Lee Fang-Hua , Rando Juliette , Bonsignori Mattia , Hwang Kwan-Ki , Saunders Kevin O. , Wiehe Kevin , Moody M. Anthony , Hraber Peter T. , Wagh Kshitij , Giorgi Elena E. , Russell Ronnie M. , Bibollet-Ruche Frederic , Liu Weimin , Connell Jesse , Smith Andrew G. , DeVoto Julia , Murphy Alexander I. , Smith Jessica , Ding Wenge , Zhao Chengyan , Chohan Neha , Okumura Maho , Rosario Christina , Ding Yu , Lindemuth Emily , Bauer Anya M. , Bar Katharine J. , Ambrozak David , Chao Cara W. , Chuang Gwo-Yu , Geng Hui , Lin Bob C. , Louder Mark K. , Nguyen Richard , Zhang Baoshan , Lewis Mark G. , Raymond Donald , Doria-Rose Nicole A. , Schramm Chaim A. , Douek Daniel C. , Roederer Mario , Kepler Thomas B. , Kelsoe Garnett , Mascola John R. , Kwong Peter D. , Korber Bette T. , Harrison Stephen C. , Haynes Barton F. , Hahn Beatrice H. , Shaw George M. 
Published: August 2020

ABSTRACTNeutralizing antibodies elicited by HIV-1 coevolve with viral Envs in distinctive patterns, in some cases acquiring substantial breadth. Here we show that primary HIV-1 Envs, when expressed by simian-human immunodeficiency viruses in rhesus macaques, elicited patterns of Env-antibody coevolution strikingly similar to those in humans. This included conserved immunogenetic, structural and chemical solutions to epitope recognition and precise Env-amino acid substitutions, insertions and deletions leading to virus persistence. The structure of one rhesus antibody, capable of neutralizing 49% of a 208-strain panel, revealed a V2-apex mode of recognition like that of human bNAbs PGT145/PCT64-35M. Another rhesus antibody bound the CD4-binding site by CD4 mimicry mirroring human bNAbs 8ANC131/CH235/VRC01. Virus-antibody coevolution in macaques can thus recapitulate developmental features of human bNAbs, thereby guiding HIV-1 immunogen design.One sentence summaryVirus-antibody coevolution in rhesus macaques recapitulates developmental features of human antibodies.
Clump sequencing exposes the spatial expression programs of intestinal secretory cells
Authors: Manco Rita , Averbukh Inna , Porat Ziv , Halpern Keren Bahar , Amit Ido , Itzkovitz Shalev 
Published: August 2020

AbstractSingle-cell RNA sequencing combined with spatial information on landmark genes enables reconstruction of spatially-resolved tissue cell atlases. However, such approaches are challenging for rare cell types, since their mRNA contents are diluted in the spatial transcriptomics bulk measurements used for landmark gene detection. In the small intestine, enterocytes, the most common cell type, exhibit zonated expression programs along the crypt-villus axis, but zonation patterns of rare cell types such as goblet and tuft cells remain uncharacterized. Here, we present ClumpSeq, an approach for sequencing small clumps of attached cells. By inferring the crypt-villus location of each clump from enterocyte landmark genes, we establish spatial atlases for all epithelial cell types in the small intestine. We uncover immune-modulatory programs in villus tip goblet and tuft cells and heterogeneous migration patterns of enteroendocrine cells. ClumpSeq can be applied for reconstructing spatial atlases of rare cell types in other tissues and tumors.
CFD simulation of empty fuel tanks separation from a trainer jet
Authors: Olejnik Aleksander , Dziubiński Adam , Kiszkowiak Łukasz 
Published: August 2020

Purpose
This study aims to create 6-degree of freedom (SDOF) for computational fluid dynamics (CFD) simulations of body movement, and to validate using the experimental data for empty tank separation from I-22 Iryda jet trainer. The procedure has an ability to be modified or extended, to simulate, for example, a sequential release from the joints.

Design/methodology/approach
A set of CFD simulations are calculated. Both the SDOF procedure and the CFD simulation settings are validated using the wind tunnel data available for the aircraft.

Findings
The simulation using designed procedure gives predictable results, but offers availability to be modified to represent external forces, i.e. from body interaction or control system without necessity to model the control surfaces.

Practical implications
The procedure could be used to model the separation of external stores and design the deployment of anti-radar chaff, flares or ejection seats.

Originality/value
The work presents original work, caused by insufficient abilities of original SDOF procedure in ANSYS code. Additional value is the ability of the procedure to be easily modified.
China’s AI Strike Force on COVID-19
Authors: Wong Wilson Kia Onn 
Published: August 2020

PurposeThis paper examines the methodical and highly efficacious manner in which China deployed its comprehensive AI (artificial intelligence) strategy to significantly stymie the spread of COVID-19 across the country.Design/methodology/approachThis study deploys a case-study approach, supported by the literature on existing and emerging AI and related technologies.FindingsThe onset of the COVID-19 pandemic has revealed to the world the remarkable progress China has made in AI and its accompanying ecosystem. More importantly, this outlier event demonstrates the surgical, hybridised manner in which China has utilised these emerging technologies in containing its spread (i.e. “AI Epidemiological Targeting”) and set itself on the path to unleashing their full potential (i.e. “AI Symbiosis Paradigm”). Nonetheless, China still needs to harness its rapidly advancing AI prowess in identifying COVID-19's pathogenesis and developing a proven vaccine.Originality/valueThis study presents a pioneering effort to analyse the deployment of AI and its ecosystem in the “war” against COVID-19.
Dynamic stress analysis on nonlinear vibration of a stiffened plate with initial stresses and geometric imperfections considering different resonance conditions
Authors: Ma Niu-Jing , Gu Li-Xiong , Piao Long , Zhang Xing-Zhi 
Published: August 2020

Purpose
Stiffened plates have been widely used in civil, marine, aerospace engineering. As a kind of thin-walled structure operating in complex environment, stiffened plates mostly undergo a variety of dynamic loads, which may sometimes result in large-amplitude vibration. Additionally, initial stresses and geometric imperfections are widespread in this type of structure. Furthermore, it is universally known that initial stresses and geometric imperfections may affect mechanical behavior of structures severely, particularly in dynamic analysis. Thus, the purpose of this paper is to study the stress variation rule of a stiffened plate during large-amplitude vibration considering initial stresses and geometric imperfections.

Design/methodology/approach
The initial stresses are represented in the form of initial bending moments applying to the stiffened plate, while the initial geometric imperfections are considered by means of trigonometric series, and they are assumed existing in the plate along the z-direction exclusively. Then, the dynamic equilibrium equations of the stiffened plate are established using Lagrange’s equation as well as aforementioned conditions. The nonlinear differential equations of motion are simplified as a two-degree-of-freedom system by considering 1:2 and 1:3 internal resonances, respectively, and the multiscale method is applied to solve the equations.

Findings
The influence of initial stresses on the plate, stresses during internal resonance is remarkable, while that is moderate for initial geometric imperfections. (Upon considering the existence of initial stresses or geometric imperfections, the stresses of motivated modes are less than the primary mode for both and internal resonances). The influence of bidirectional initial stresses on the plate’s stresses during internal resonance is more remarkable than that of unidirectional initial stresses. The coupled vibration in 1%3A2 internal resonance is fiercer than that in internal resonance.

Originality/value
Stiffened plates are widely used in engineering structures. However, as a type of thin-walled structure, stiffened plates vibrate with large amplitude in most cases owning to their complicated operation circumstance. In addition, stiffened plates usually contain initial stresses and geometric imperfections, which may result in the variation of their mechanical behavior, especially dynamical behavior. Based on the above consideration, this paper studies the nonlinear dynamical behavior of stiffened plates with initial stresses and geometrical imperfections under different internal resonances, which is the originality of this work. Furthermore, the research findings can provide references for engineering design and application.
A robust numerical method for a coupled system of singularly perturbed parabolic delay problems
Authors: Kumar Mukesh , Singh Joginder , Kumar Sunil , Aakansha Aakansha 
Published: August 2020

Purpose
The purpose of this paper is to design and analyze a robust numerical method for a coupled system of singularly perturbed parabolic delay partial differential equations (PDEs).

Design/methodology/approach
Some a priori bounds on the regular and layer parts of the solution and their derivatives are derived. Based on these a priori bounds, appropriate layer adapted meshes of Shishkin and generalized Shishkin types are defined in the spatial direction. After that, the problem is discretized using an implicit Euler scheme on a uniform mesh in the time direction and the central difference scheme on layer adapted meshes of Shishkin and generalized Shishkin types in the spatial direction.

Findings
The method is proved to be robust convergent of almost second-order in space and first-order in time. Numerical results are presented to support the theoretical error bounds.

Originality/value
A coupled system of singularly perturbed parabolic delay PDEs is considered and some a priori bounds are derived. A numerical method is developed for the problem, where appropriate layer adapted Shishkin and generalized Shishkin meshes are considered. Error analysis of the method is given for both Shishkin and generalized Shishkin meshes.
The creative minds of extraordinary pastry chefs: an integrated theory of aesthetic expressions – a portraiture study
Authors: Lee Kai-Sean , Blum Denise , Miao Li , Tomas Stacy R. 
Published: August 2020

Purpose
This paper aims to demystify the creative experiences of an extraordinary group of pastry chefs – The Malaysian World Pastry Team, champions of the 2019 World Pastry Cup. The authors adopted an expressionist theoretical lens informed by two aesthetic philosophers – John Dewey and Wassily Kandinsky.

Design/methodology/approach
A two-year portraiture was conducted – a qualitative methodology that draws features from phenomenology and narrative inquiry, rendering artistically and empirically written “portraits” that reflect themes and patterns of participants’ experiences. In-depth interviews, observations and material artifacts were collected amid a journey alongside nine extraordinary Malaysian pastry chefs.

Findings
Presented in story structures, the authors offer three “portraits” of culinary creativity, each representing a core essence of the creative phenomenon: creative harmony in the form of sensorial and symbolic poetry; imaginative episodes as a hypnotic state of inspiration and incubation; and the creative duality of scientific rationalism and artistic fashion. The authors delineated the intricacies of each theme by presenting them as individual narratives.

Research limitations/implications
The portraits indicated that culinary creativity reflects an organic and emancipating aesthetic experience that is unbounded by formative structures or sequential processes. This provides a novel theoretical view that moves beyond conventional studies’ capitalistic frameworks, and toward the intimate viewpoints of the chef-creators. Specific contributions are discussed.

Originality/value
Through a unique qualitative approach and an aesthetic theoretical framework, this study provided a novel perspective on the culinary creative process. The aesthetic view captures culinary creativity through the eyes of the creator, a viewpoint less considered, yet imperative to the culinary profession.
International reserves: self-insurance and monetary policy in crisis
Authors: Silva Junior Antonio Francisco de Almeida da 
Published: August 2020

PurposeThis work presents a model of a two-period economy to discuss the link between the precautionary motivation for holding international reserves and the country's monetary policy concerns due to a crisis.Design/methodology/approachThere are two possible states of nature in the second period of the economy: a normal state and a crisis state. These states of nature represent uncertainty to the policy maker and he can insure against a crisis. The household has a constant-elasticity-of-substitution (CES) utility function, where utility depends on consumption and money.FindingsBy allowing money in the utility function and in the household financial constraint and considering that the objective of the central bank is to smooth inflation, it is concluded that monetary policy plays a role in the precautionary motivation of holding international reserves.Practical implicationsThe model can be used to calculate optimal reserves holdings in its complete or even in its simplified version. Furthermore, it is possible to evaluate the impact of the intra-temporal substitution elasticity between consumption and real money in the decision of accumulating international reserves.Originality/valueHigher intra-temporal substitution elasticities implies in more insurance via international reserves, and this discussion is not found in the existent literature on international reserves.
Relational flexibility norms and relationship-building capabilities as a mediating mechanism in export performance: insights from exporting SMEs in an emerging economy, Peru
Authors: Malca Oscar , Bolaños Jean Pierre , Acedo Francisco J. , Rubio Donet Jorge Luis , Peña-Vinces Jesus 
Published: August 2020

PurposeThe purpose of this study is to analyse the mediating and moderating effects of relational flexibility norms on relationship building capacities and export performance.Design/methodology/approachThe study followed a quantitative and cross-sectional approach. The analysis was applied to 95 Peruvian Exporting SMEs which were examined through structural equation modelling (SEM) using AMOS 24.0 statistical package. The responses were gathered through telephone and personal interviews which were tested using the Mann–WhitneyUtest, finding no statistically significant differences.FindingsThe main finding of the study is to demonstrate the indirect effect of relational flexibility norms on the export performance of SMEs through relationship-building capabilities. In this way, these capabilities become very important variables in the export management of SMEs, since they directly affect the relationship of the Exporter–Importer dyad.Research limitations/implicationsOne of the limitations is the cross-sectional type study that applies to the short-term effects of relational norms. Organizational characteristics and other factors that may affect export performance should also be considered in future research, as well as longitudinal studies should be developed.Practical implicationsThe study allows SMEs to focus management efforts on strengthening the relationship – building capabilities, which are very important given SMEs' resource constraints. Therefore, an adequate management of relations with importers can contribute to the reduction of control and coordination costs; and have a positive impact on export performance. Similarly, the study contributes to the management of export promotion by suggesting that one area to be prioritized is the strengthening of the relationship capacities of exporting SMEs.Originality/valueThe study provides the analysis of the mediating effect of the relationship-building capability between relational flexibility and export performance. In this way, it enriches the theoretical analysis and contributes with the empirical evidence of an emerging country like the case of Peru.