bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining initial chest CT with clinical variables in differentiating coronavirus disease 2019 (COVID-19) pneumonia from influenza pneumonia
Authors: Zhao Shuang , Huang Zixing , Zeng Hanjiang , Chen Zhixia , Luo Fengming , Zhang Chongwei , Song Bin 
Published: March 2021

AbstractCoronavirus disease 2019 (COVID-19) has spread in more than 100 countries and regions around the world, raising grave global concerns. COVID-19 has a similar pattern of infection, clinical symptoms, and chest imaging findings to influenza pneumonia. In this retrospective study, we analysed clinical and chest CT data of 24 patients with COVID-19 and 79 patients with influenza pneumonia. Univariate analysis demonstrated that the temperature, systolic pressure, cough and sputum production could distinguish COVID-19 from influenza pneumonia. The diagnostic sensitivity and specificity for the clinical features are 0.783 and 0.747, and the AUC value is 0.819. Univariate analysis demonstrates that nine CT features, central–peripheral distribution, superior–inferior distribution, anterior–posterior distribution, patches of GGO, GGO nodule, vascular enlargement in GGO, air bronchogram, bronchiectasis within focus, interlobular septal thickening, could distinguish COVID-19 from influenza pneumonia. The diagnostic sensitivity and specificity for the CT features are 0.750 and 0.962, and the AUC value is 0.927. Finally, a multivariate logistic regression model combined the variables from the clinical variables and CT features models was made. The combined model contained six features: systolic blood pressure, sputum production, vascular enlargement in the GGO, GGO nodule, central–peripheral distribution and bronchiectasis within focus. The diagnostic sensitivity and specificity for the combined features are 0.87 and 0.96, and the AUC value is 0.961. In conclusion, some CT features or clinical variables can differentiate COVID-19 from influenza pneumonia. Moreover, CT features combined with clinical variables had higher diagnostic performance.
Terahertz refractive index-based morphological dilation for breast carcinoma delineation
Authors: Cassar Quentin , Caravera Samuel , MacGrogan Gaëtan , Bücher Thomas , Hillger Philipp , Pfeiffer Ullrich , Zimmer Thomas , Guillet Jean-Paul , Mounaix Patrick 
Published: March 2021

AbstractThis paper reports investigations led on the combination of the refractive index and morphological dilation to enhance performances towards breast tumour margin delineation during conserving surgeries. The refractive index map of invasive ductal and lobular carcinomas were constructed from an inverse electromagnetic problem. Morphological dilation combined with refractive index thresholding was conducted to classify the tissue regions as malignant or benign. A histology routine was conducted to evaluate the performances of various dilation geometries associated with different thresholds. It was found that the combination of a wide structuring element and high refractive index was improving the correctness of tissue classification in comparison to other configurations or without dilation. The method reports a sensitivity of around 80% and a specificity of 82% for the best case. These results indicate that combining the fundamental optical properties of tissues denoted by their refractive index with morphological dilation may open routes to define supporting procedures during breast-conserving surgeries.
Exploring the use of web searches for risk communication during COVID-19 in Germany
Authors: Kristensen Kaja , Lorenz Eva , May Jürgen , Strauss Ricardo 
Published: March 2021

AbstractRisk communication during pandemics is an element of utmost importance. Understanding the level of public attention—a prerequisite for effective communication—implicates expensive and time-consuming surveys. We hypothesise that the relative search volume from Google Trends could be used as an indicator of public attention of a disease and its prevention measures. The search terms ‘RKI’ (Robert Koch Institute, national public health authority in Germany), ‘corona’ and ‘protective mask’ in German language were shortlisted. Cross-correlations between these terms and the reported cases from 15 February to 27 April were conducted for each German federal state. The findings were contrasted against a timeline of official communications concerning COVID-19. The highest correlations of the term ‘RKI’ with reported COVID-19 cases were found between lags of − 2 and − 12 days, meaning web searches were already performed from 2 to 12 days before case numbers increased. A similar pattern was seen for the term ‘corona’. Cross-correlations indicated that most searches on ‘protective mask’ were performed from 6 to 12 days after the peak of cases. The results for the term ‘protective mask’ indicate a degree of confusion in the population. This is supported by conflicting recommendations to wear face masks during the first wave. The relative search volumes could be a useful tool to provide timely and location-specific information on public attention for risk communication.
Elucidation of Japanese pepper (Zanthoxylum piperitum De Candolle) domestication using RAD-Seq
Authors: Premarathne Maddumage Dona Ginushika Priyadarsh , Fukutome Nami , Yamasaki Kazuaki , Hayakawa Fumiyo , Nagano Atsushi J. , Mizuno Hisataka , Ibaragi Nobuo , Nagano Yukio 
Published: March 2021

AbstractJapanese pepper, Zanthoxylum piperitum, is native to Japan and has four well-known lineages (Asakura, Takahara, Budou, and Arima), which are named after their production area or morphology. Restriction-site associated DNA sequencing (RAD-Seq) was used to analyse 93 accessions from various areas, including these four lineages. Single nucleotide variant analysis was used to classify the plants into eight groups: the Asakura and Arima lineages each had two groups, the Takahara and Budou lineages each had one group, and two additional groups were present. In one Asakura group and two Arima groups, the plants were present in agricultural fields and mountains, thus representing the early stage of domestication of the Japanese pepper. The second Asakura lineage group was closely related to plants present in various areas, and this represents the second stage of domestication of this plant because, after early domestication, genetically related lineages with desirable traits spread to the periphery. These results demonstrate that domestication of Japanese pepper is ongoing. In addition, this study shows that spineless plants are polyphyletic, despite the spineless lineage being considered a subspecies of Japanese pepper.
A chain mediation model on COVID-19 symptoms and mental health outcomes in Americans, Asians and Europeans
Authors: Wang Cuiyan , Chudzicka-Czupała Agata , Tee Michael L. , Núñez María Inmaculada López , Tripp Connor , Fardin Mohammad A. , Habib Hina A. , Tran Bach X. , Adamus Katarzyna , Anlacan Joseph , García Marta E. Aparicio , Grabowski Damian , Hussain Shahzad , Hoang Men T. , Hetnał Mateusz , Le Xuan T. , Ma Wenfang , Pham Hai Q. , Reyes Patrick Wincy C. , Shirazi Mahmoud , Tan Yilin , Tee Cherica A. , Xu Linkang , Xu Ziqi , Vu Giang T. , Zhou Danqing , Chan Natalie A. , Kuruchittham Vipat , McIntyre Roger S. , Ho Cyrus S. H. , Ho Roger , Sears Samuel F. 
Published: March 2021

AbstractThe novel Coronavirus-2019 (COVID-19) was declared a pandemic by the World Health Organization (WHO) in March 2020, impacting the lifestyles, economy, physical and mental health of individuals globally. This study aimed to test the model triggered by physical symptoms resembling COVID-19 infection, in which the need for health information and perceived impact of the pandemic mediated the path sequentially, leading to adverse mental health outcomes. A cross-sectional research design with chain mediation model involving 4612 participants from participating 8 countries selected via a respondent-driven sampling strategy was used. Participants completed online questionnaires on physical symptoms, the need for health information, the Impact of Event Scale-Revised (IES-R) questionnaire and Depression, Anxiety and Stress Scale (DASS-21). The results showed that Poland and the Philippines were the two countries with the highest levels of anxiety, depression and stress; conversely, Vietnam had the lowest mean scores in these areas. Chain mediation model showed the need for health information, and the perceived impact of the pandemic were sequential mediators between physical symptoms resembling COVID-19 infection (predictor) and consequent mental health status (outcome). Excessive and contradictory health information might increase the perceived impact of the pandemic. Rapid COVID-19 testing should be implemented to minimize the psychological burden associated with physical symptoms, whilst public mental health interventions could target adverse mental outcomes associated with the pandemic.
Enlarged periventricular space and periventricular lesion extension on baseline brain MRI predicts poor neurological outcomes in cryptococcus meningoencephalitis
Authors: Lee Woo-Jin , Ryu Young Jin , Moon Jangsup , Lee Soon-Tae , Jung Keun-Hwa , Park Kyung-Il , Kim Manho , Lee Sang Kun , Chu Kon 
Published: March 2021

AbstractIn Cryptococcus neoformans meningoencephalitis, brain MRI findings might reflect the phathomechanism of disease progression that is fungal accumulation in the peri-venular space and consequent invasion into the parenchyma. This study analyzed serial brain MRI findings of 76 patients with cryptococcus meningoencephalitis in association with the disease progression and outcomes. MRI parameters included the enlarged periventricular space (ePVS) score (range 0–8), periventricular lesion extension, cryptococcoma, and hydrocephalus. Clinical outcomes at 2-week, 10-week, and 6-month were evaluated using modified Rankin scale (mRS). At 6 months, 15 (19.7%) patients died and 34 (44.1%) had poor neurological outcomes (mRS scores > 2). At baseline, an ePVS score of ≥ 5 (Odds-ratio [OR]: 94.173, 95% confidence-interval [95%CI]: 7.507–1181.295, P < .001), periventricular lesion extension (OR: 51.965, 95%CI: 2.592–1041.673, P = .010), and presence of encephalitis feature (OR: 44.487, 95%CI: 1.689–1172.082, P = .023) were associated with 6-month poor outcomes. Presence of two or more risk factors among encephalitis feature, ePVS score ≥ 5, and periventricular lesion extension at baseline, was associated with 6-month poor outcomes (area under the curve [AUC]: 0.978, P < .001) and mortality (AUC: 0.836, P < .001). Disease progression was associated with interval development of cryptococcoma and hydrocephalus. Brain MRI findings might be useful in predicting outcomes and monitoring the progression of cryptococcus meningoencephalitis.
Presence of interplate channel layer controls of slip during and after the 2011 Tohoku-Oki earthquake through the frictional characteristics
Authors: Nakata Ryoko , Hori Takane , Miura Seiichi , Hino Ryota 
Published: March 2021

AbstractThere are significant differences between the middle and southern segments of the Japan Trench in terms of the seismic and aseismic slips on the plate interface and seismic velocity structures. Although the large coseismic slip of the 2011 Tohoku-Oki earthquake was limited to the middle segment, the observed negative residual gravity anomaly area in the southern segment corresponds to the postseismic slip area of the Tohoku-Oki earthquake. A density distribution model can explain the different slip behaviours of the two segments by considering their structural differences. The model indicates that the plate interface in the south was covered with a thick channel layer, as indicated by seismic survey imaging, and this layer resulted in a residual gravity anomaly. Numerical simulations which assumed evident frictional heterogeneity caused by the layer in the south efficiently reproduced M9 earthquakes recurring only in the middle, followed by evident postseismic slips in the south. This study proposes that although the layer makes the megathrust less compliant to seismic slip, it promotes aseismic slips following the growth of seismic slips on the fault in an adjacent region.
Development of PUFF–Gaussian dispersion model for the prediction of atmospheric distribution of particle concentration
Authors: Lee Jooyong , Lee Sungsu , Son HyunA , Yi Waon-ho 
Published: March 2021

AbstractMt. Baekdu’s eruption precursors are continuously observed and have become a global social issue. Volcanic activities in neighboring Japan are also active. There are no direct risks of proximity-related disasters in South Korea from the volcanic eruptions at Japan or Mt. Baekdu; however, severe impacts are expected from the spread of volcanic ash. Numerical analysis models are generally used to predict and analyze the diffusion of volcanic ash, and each numerical analysis model has its own limitations caused by the computational algorithm it employs. In this study, we analyzed the PUFF–UAF model, an ash dispersion model based on the Lagrangian approach, and observed that the number of particles used in tracking substantially affected the results. Even with the presence of millions of particles, the concentration of ash predicted by the PUFF–UAF model does not accurately represent the dispersion. To overcome this deficit and utilize the computational efficiency of the Lagrangian model, we developed a PUFF–Gaussian model to consider the dispersive nature of ash by applying the Gaussian dispersion theory to the results of the PUFF–UAF model. The results of the proposed method were compared with the field measurements from actual volcanic eruptions, and the comparison showed that the proposed method can produce reasonably accurate predictions for ash dispersion.
Automatic lumen detection and magnetic alignment control for magnetic-assisted capsule colonoscope system optimization
Authors: Yen Sheng-Yang , Huang Hao-En , Lien Gi-Shih , Liu Chih-Wen , Chu Chia-Feng , Huang Wei-Ming , Suk Fat-Moon 
Published: March 2021

AbstractWe developed a magnetic-assisted capsule colonoscope system with integration of computer vision-based object detection and an alignment control scheme. Two convolutional neural network models A and B for lumen identification were trained on an endoscopic dataset of 9080 images. In the lumen alignment experiment, models C and D used a simulated dataset of 8414 images. The models were evaluated using validation indexes for recall (R), precision (P), mean average precision (mAP), and F1 score. Predictive performance was evaluated with the area under the P-R curve. Adjustments of pitch and yaw angles and alignment control time were analyzed in the alignment experiment. Model D had the best predictive performance. Its R, P, mAP, and F1 score were 0.964, 0.961, 0.961, and 0.963, respectively, when the area of overlap/area of union was at 0.3. In the lumen alignment experiment, the mean degrees of adjustment for yaw and pitch in 160 trials were 21.70° and 13.78°, respectively. Mean alignment control time was 0.902 s. Finally, we compared the cecal intubation time between semi-automated and manual navigation in 20 trials. The average cecal intubation time of manual navigation and semi-automated navigation were 9 min 28.41 s and 7 min 23.61 s, respectively. The automatic lumen detection model, which was trained using a deep learning algorithm, demonstrated high performance in each validation index.
Inflation of tumor mutation burden by tumor-only sequencing in under-represented groups
Authors: Asmann Yan W. , Parikh Kaushal , Bergsagel P. Leif , Dong Haidong , Adjei Alex A. , Borad Mitesh J. , Mansfield Aaron S. 
Published: March 2021

AbstractWith the recent FDA approval of tumor mutational burden-high (TMB-H) status as a biomarker for treatment with a PD-1 inhibitor regardless of tumor type, accurate assessment of patient-specific TMB is more critical now more than ever. Using paired tumor and germline exome sequencing data from 701 patients newly diagnosed with multiple myeloma, including 575 self-reported White patients and 126 self-reported Black patients, we observed that compared to the gold standard of filtering germline variants with patient-paired germline sequencing data, TMB estimates were significantly higher in both Black and White patients when using public databases for filtering non-somatic mutations; however, TMB was more significantly inflated in Black patients compared to White patients. TMB as a biomarker for patient selection to receive immune checkpoint inhibitors (ICIs) therapy without patient-paired germline sequencing may introduce racial bias due to the under-representation of minority groups in public databases.
Quantitative investigation reveals distinct phases in Drosophila sleep
Authors: Xu Xiaochan , Yang Wei , Tian Binghui , Sui Xiuwen , Chi Weilai , Rao Yi , Tang Chao 
Published: March 2021

AbstractThe fruit fly, Drosophila melanogaster, has been used as a model organism for the molecular and genetic dissection of sleeping behaviors. However, most previous studies were based on qualitative or semi-quantitative characterizations. Here we quantified sleep in flies. We set up an assay to continuously track the activity of flies using infrared camera, which monitored the movement of tens of flies simultaneously with high spatial and temporal resolution. We obtained accurate statistics regarding the rest and sleep patterns of single flies. Analysis of our data has revealed a general pattern of rest and sleep: the rest statistics obeyed a power law distribution and the sleep statistics obeyed an exponential distribution. Thus, a resting fly would start to move again with a probability that decreased with the time it has rested, whereas a sleeping fly would wake up with a probability independent of how long it had slept. Resting transits to sleeping at time scales of minutes. Our method allows quantitative investigations of resting and sleeping behaviors and our results provide insights for mechanisms of falling into and waking up from sleep.
Fluorescence-detection size-exclusion chromatography utilizing nanobody technology for expression screening of membrane proteins
Authors: Jin Fei , Shen Cheng , Wang Yao , Wang Mengqi , Sun Minxuan , Hattori Motoyuki 
Published: March 2021

AbstractGFP fusion-based fluorescence-detection size-exclusion chromatography (FSEC) has been widely employed for membrane protein expression screening. However, fused GFP itself may occasionally affect the expression and/or stability of the targeted membrane protein, leading to both false-positive and false-negative results in expression screening. Furthermore, GFP fusion technology is not well suited for some membrane proteins, depending on their membrane topology. Here, we developed an FSEC assay utilizing nanobody (Nb) technology, named FSEC-Nb, in which targeted membrane proteins are fused to a small peptide tag and recombinantly expressed. The whole-cell extracts are solubilized, mixed with anti-peptide Nb fused to GFP for FSEC analysis. FSEC-Nb enables the evaluation of the expression, monodispersity and thermostability of membrane proteins without the need for purification but does not require direct GFP fusion to targeted proteins. Our results show FSEC-Nb as a powerful tool for expression screening of membrane proteins for structural and functional studies.
TagBiFC technique allows long-term single-molecule tracking of protein-protein interactions in living cells
Authors: Shao Shipeng , Zhang Hongchen , Zeng Yong , Li Yongliang , Sun Chaoying , Sun Yujie 
Published: March 2021

AbstractProtein-protein interactions (PPIs) are critical for cellular activity regulation. Visualization of PPIs using bimolecular fluorescence complementation (BiFC) techniques helps to understand how PPIs implement their functions. However, current BiFC is based on fluorescent proteins and the brightness and photostability are suboptimal for single molecule tracking experiments, resulting in either low spatiotemporal resolution or incapability of tracking for extended time course. Here, we developed the TagBiFC technique based on split HaloTag, a self-labeling tag that could conjugate an organic dye molecule and thus offered better brightness and photostability than fluorescent proteins for PPI visualization inside living cells. Through screening and optimization, we demonstrated that the reconstituted HaloTag exhibited higher localization precision and longer tracking length than previous methods. Using TagBiFC, we reveal that the dynamic interactions of transcription factor dimers with chromatin DNA are distinct and closely related to their dimeric states, indicating a general regulatory mechanism for these kinds of transcription factors. In addition, we also demonstrated the advantageous applications of TagBiFC in single nucleosome imaging, light-burden imaging of single mRNA, low background imaging of cellular structures. We believe these superior properties of our TagBiFC system will have broad applications in the studies of single molecule imaging inside living cells.
Cooperation between oncogenic Ras and wild-type p53 stimulates STAT non-cell autonomously to promote tumor radioresistance
Authors: Dong Yong-Li , Vadla Gangadhara P. , Lu Jin-Yu , Ahmad Vakil , Klein Thomas J. , Liu Lu-Fang , Glazer Peter M. , Xu Tian , Chabu Chiswili-Yves 
Published: March 2021

AbstractOncogenic RAS mutations are associated with tumor resistance to radiation therapy. Cell-cell interactions in the tumor microenvironment (TME) profoundly influence therapy outcomes. However, the nature of these interactions and their role in Ras tumor radioresistance remain unclear. Here we use Drosophila oncogenic Ras tissues and human Ras cancer cell radiation models to address these questions. We discover that cellular response to genotoxic stress cooperates with oncogenic Ras to activate JAK/STAT non-cell autonomously in the TME. Specifically, p53 is heterogeneously activated in Ras tumor tissues in response to irradiation. This mosaicism allows high p53-expressing Ras clones to stimulate JAK/STAT cytokines, which activate JAK/STAT in the nearby low p53-expressing surviving Ras clones, leading to robust tumor re-establishment. Blocking any part of this cell-cell communication loop re-sensitizes Ras tumor cells to irradiation. These findings suggest that coupling STAT inhibitors to radiotherapy might improve clinical outcomes for Ras cancer patients.
Architectural control of metabolic plasticity in epithelial cancer cells
Authors: Al-Masri Maia , Paliotti Karina , Tran Raymond , Halaoui Ruba , Lelarge Virginie , Chatterjee Sudipa , Wang Li-Ting , Moraes Christopher , McCaffrey Luke 
Published: March 2021

AbstractMetabolic plasticity enables cancer cells to switch between glycolysis and oxidative phosphorylation to adapt to changing conditions during cancer progression, whereas metabolic dependencies limit plasticity. To understand a role for the architectural environment in these processes we examined metabolic dependencies of cancer cells cultured in flat (2D) and organotypic (3D) environments. Here we show that cancer cells in flat cultures exist in a high energy state (oxidative phosphorylation), are glycolytic, and depend on glucose and glutamine for growth. In contrast, cells in organotypic culture exhibit lower energy and glycolysis, with extensive metabolic plasticity to maintain growth during glucose or amino acid deprivation. Expression of KRASG12V in organotypic cells drives glucose dependence, however cells retain metabolic plasticity to glutamine deprivation. Finally, our data reveal that mechanical properties control metabolic plasticity, which correlates with canonical Wnt signaling. In summary, our work highlights that the architectural and mechanical properties influence cells to permit or restrict metabolic plasticity.