tbuckley/cabot-search huggingface dataset:
Weakly supervised object detection with 2D and 3D regression neural networks
Authors: Florian Dubost, Hieab Adams, Pinar Yilmaz, Gerda Bortsova, Gijs van Tulder, M. Arfan Ikram, Wiro Niessen, Meike W. Vernooij, Marleen de Bruijne
Journal: Medical Image Analysis (2020)

Finding automatically multiple lesions in large images is a common problem in medical image analysis. Solving this problem can be challenging if, during optimization, the automated method cannot access information about the location of the lesions nor is given single examples of the lesions. We propose a new weakly supervised detection method using neural networks, that computes attention maps revealing the locations of brain lesions. These attention maps are computed using the last feature maps of a segmentation network optimized only with global image-level labels. The proposed method can generate attention maps at full input resolution without need for interpolation during preprocessing, which allows small lesions to appear in attention maps. For comparison, we modify state-of-the-art methods to compute attention maps for weakly supervised object detection, by using a global regression objective instead of the more conventional classification objective. This regression objective optimizes the number of occurrences of the target object in an image, e.g. the number of brain lesions in a scan, or the number of digits in an image. We study the behavior of the proposed method in MNIST-based detection datasets, and evaluate it for the challenging detection of enlarged perivascular spaces – a type of brain lesion – in a dataset of 2202 3D scans with point-wise annotations in the center of all lesions in four brain regions. In MNIST-based datasets, the proposed method outperforms the other methods. In the brain dataset, the weakly supervised detection methods come close to the human intrarater agreement in each region. The proposed method reaches the best area under the curve in two out of four regions, and has the lowest number of false positive detections in all regions, while its average sensitivity over all regions is similar to that of the other best methods. The proposed method can facilitate epidemiological and clinical studies of enlarged perivascular spaces and help advance research in the etiology of enlarged perivascular spaces and in their relationship with cerebrovascular diseases.
The SKI proto-oncogene restrains the resident CD103+CD8+ T cell response in viral clearance
Authors: Bing Wu, Ge Zhang, Zengli Guo, Gang Wang, Xiaojiang Xu, Jian-liang Li, Jason K. Whitmire, Junnian Zheng, Yisong Y. Wan
Journal: Cellular and Molecular Immunology (2020)
Elevated serum levels of S100A8/A9 and HMGB1 at hospital admission are correlated with inferior clinical outcomes in COVID-19 patients
Authors: Liting Chen, Xiaolu Long, Qian Xu, Jiaqi Tan, Gaoxiang Wang, Yang Cao, Jia Wei, Hui Luo, Hui Zhu, Liang Huang, Fankai Meng, Lifang Huang, Na Wang, Xiaoxi Zhou, Lei Zhao, Xing Chen, Zekai Mao, Caixia Chen, Zhen Li, Ziyong Sun, Jianping Zhao, Daowen Wang, Gang Huang, Wei Wang, Jianfeng Zhou
Journal: Cellular and Molecular Immunology (2020)

COVID-19 is a disease with heterogeneous clinical appearances.Most patients are asymptomatic or exhibit mild to moderate symptoms; approximately 15% progress to severe pneumonia and about 5% are eventually admitted to the intensive care unit (ICU) due to acute respiratory distress syndrome (ARDS), septic shock and/ or multiple organ failure.2][3] Inadequate identification of the determinants of fatal outcomes is one of the major obstacles to the improvement of the outcomes in severe COVID-19 patients.A previous study reported a scoring system (COVID-GRAM) which accurately predicted the occurrence of critical illness in hospitalized COVID-19 patients. 4Damage-associated molecular patterns (DAMPs), or alarmins, are a number of molecules, released by stressed cells undergoing microbial infection or sterile injury, that act as danger signals to promote and exacerbate the inflammatory response. 5,6Of note, the serum level of S100A8/A9 and HMGB1 was found to be correlated with both the severity of pathogen-associated tissue damage and excessive cytokine storm. 7espite the hypothesis that S100A8/A9 and HMGB1 are significantly involved in COVID-19, so far, no study has yet tried to substantiate the hypothesis.In this study, we aimed to define the role of S100A8/ A9 and HMGB1 in progression to a fatal outcome and develop clinically relevant risk strata for COVID-19 patients.A total of 121 patients were enrolled in this retrospective study, of which 40 patients were in ICU and 81 patients in general wards at enrollment (Table S1).ICU Patients had much higher COVID-GRAM risk scores in comparison to those in general wards.Complications, including ARDS, sepsis, septic shock, secondary infection, acute renal injury, acute cardiac injury or failure, were more frequent in CCOVID-19 patients admitted to ICU.As of the cutoff date of April 30, 2020, most of non-ICU patients (96.3%) had been discharged alive, while 82.5% of ICU patients had died in ICU.
Therapeutic potential of HERS spheroids in tooth regeneration
Authors: Yufeng Duan, Xuebing Li, Sicheng Zhang, Shikai Wang, Tao Wang, Hong Chen, Yan Yang, Sixun Jia, Guoqing Chen, Weidong Tian
Journal: Theranostics (2020)

Hertwig's epithelial root sheath (HERS) plays indispensable roles in tooth root development, including controlling the shape and number of roots, dentin formation, and helping generate the cementum.Based on these characteristics, HERS cell is a potential seed cell type for tooth-related tissue regeneration.However, the application is severely limited by a lack of appropriate culture methods and small cell numbers.Methods: Here, we constructed a 3D culture method to expand functional HERS cells into spheroids, and investigated characteristics and application of dental tissue regeneration of these spheroids.HERS spheroids and HERS cells (2D monolayer culture) were compared in terms of biological characteristics (such as proliferation, self-renewal capacity, and stemness) in vitro and functions (including differentiation potential and inductive ability of dentin formation) both in vitro and in vivo.Further, transcriptome analysis was utilized to reveal the molecular mechanisms of their obvious differences.Results: HERS spheroids showed obvious superiority in biological characteristics and functions compared to 2D monolayers of HERS cells in vitro.In vivo, HERS spheroids generated more mineralized tissue; when combined with dental papilla cells (DPCs), HERS spheroids contributed to dentin-like tissue formation.Moreover, the generation and expansion of HERS spheroids rely to some degree on the HIF-1 pathway.Conclusion: HERS spheroid generation is beneficial for functional HERS cell expansion and can provide a useful cell source for further tooth regeneration and mechanistic research.Notably, HIF-1 pathway plays a critical role in HERS spheroid formation and function.
Renin and Survival in Patients Given Angiotensin II for Catecholamine-Resistant Vasodilatory Shock. A Clinical Trial
Authors: Rinaldo Bellomo, Lui G. Forni, Laurence W. Busse, Michael T. McCurdy, Kealy R. Ham, David W. Boldt, Johanna Hästbacka, Ashish K. Khanna, Timothy E. Albertson, James Tumlin, Kristine Storey, Damian Handisides, George F. Tidmarsh, Lakhmir S. Chawla, Marlies Ostermann
Journal: American Journal of Respiratory and Critical Care Medicine (2020)

Rationale: Exogenous angiotensin II increases mean arterial pressure in patients with catecholamine-resistant vasodilatory shock (CRVS). We hypothesized that renin concentrations may identify patients most likely to benefit from such therapy.Objectives: To test the kinetic changes in renin concentrations and their prognostic value in patients with CRVS.Methods: We analyzed serum samples from patients enrolled in the ATHOS-3 (Angiotensin II for the Treatment of High-Output Shock) trial for renin, angiotensin I, and angiotensin II concentrations before the start of administration of angiotensin II or placebo and after 3 hours.Measurements and Main Results: Baseline serum renin concentration (normal range, 2.13-58.78 pg/ml) was above the upper limits of normal in 194 of 255 (76%) study patients with a median renin concentration of 172.7 pg/ml (interquartile range [IQR], 60.7 to 440.6 pg/ml), approximately threefold higher than the upper limit of normal. Renin concentrations correlated positively with angiotensin I/II ratios (r = 0.39; P < 0.001). At 3 hours after initiation of angiotensin II therapy, there was a 54.3% reduction (IQR, 37.9% to 66.5% reduction) in renin concentration compared with a 14.1% reduction (IQR, 37.6% reduction to 5.1% increase) with placebo (P < 0.0001). In patients with renin concentrations above the study population median, angiotensin II significantly reduced 28-day mortality to 28 of 55 (50.9%) patients compared with 51 of 73 patients (69.9%) treated with placebo (unstratified hazard ratio, 0.56; 95% confidence interval, 0.35 to 0.88; P = 0.012) (P = 0.048 for the interaction).Conclusions: The serum renin concentration is markedly elevated in CRVS and may identify patients for whom treatment with angiotensin II has a beneficial effect on clinical outcomes.Clinical trial registered with www.clinicaltrials.gov (NCT02338843).
A Case of Localized Malignant Peritoneal Mesothelioma Evaluated by 18F-FDG PET/CT
Authors: Tingting Xu, Jiajia Hu, Xinyi Zhang, Jianpeng Cao, Yue Chen
Journal: Clinical Nuclear Medicine (2020)

Abstract Localized malignant mesothelioma is rare. The prognosis is generally more favorable for this condition than for diffuse malignant mesothelioma. An elderly woman recently complained of abdominal pain, fever, and weight loss. She had no history of asbestos exposure. Her serum CEA level was elevated. Plain CT revealed a mass under the left diaphragm, with liquefaction and necrosis. A contrast-enhanced scan showed circular enhancement of the mass. A subsequent biopsy of the mass revealed a poorly differentiated carcinoma. PET/CT showed a significant FDG-avid subphrenic mass without any indications of metastasis. Postoperative pathological and immunohistochemical examination confirmed a case of malignant mesothelioma.
Prevalence of SARS-CoV-2 in Spain (ENE-COVID): a nationwide, population-based seroepidemiological study
Authors: Marina Pollán, Beatriz Pérez-Gómez, Roberto Pastor-Barriuso, Jesús Oteo, Miguel A Hernán, Mayte Pérez-Olmeda, Jose L Sanmartín, Aurora Fernández-García, Israel Cruz, Nerea Fernández de Larrea, Marta Molina, Francisco Rodríguez-Cabrera, Mariano Martín, Paloma Merino-Amador, Jose León Paniagua, Juan F Muñoz-Montalvo, Faustino Blanco, Raquel Yotti, Faustino Blanco, Rodrigo Gutiérrez Fernández, Mariano Martín, Saturnino Mezcua Navarro, Marta Molina, Juan F. Muñoz-Montalvo, Matías Salinero Hernández, Jose L. Sanmartín, Manuel Cuenca-Estrella, Raquel Yotti, José León Paniagua, Nerea Fernández de Larrea, Pablo Fernández-Navarro, Roberto Pastor-Barriuso, Beatriz Pérez-Gómez, Marina Pollán, Ana Avellón, Giovanni Fedele, Aurora Fernández-García, Jesús Oteo Iglesias, María Teresa Pérez Olmeda, Israel Cruz, Maria Elena Fernandez Martinez, Francisco D. Rodríguez-Cabrera, Miguel A. Hernán, Susana Padrones Fernández, José Manuel Rumbao Aguirre, José M. Navarro Marí, Begoña Palop Borrás, Ana Belén Pérez Jiménez, Manuel Rodríguez-Iglesias, Ana María Calvo Gascón, María Luz Lou Alcaine, Ignacio Donate Suárez, Oscar Suárez Álvarez, Mercedes Rodríguez Pérez, Margarita Cases Sanchís, Carlos Javier Villafáfila Gomila, Lluis Carbo Saladrigas, Adoración Hurtado Fernández, Antonio Oliver, Elías Castro Feliciano, María Noemí González Quintana, José María Barrasa Fernández, María Araceli Hernández Betancor, Melisa Hernández Febles, Leopoldo Martín Martín, Luis-Mariano López López, Teresa Ugarte Miota, Inés De Benito Población, María Sagrario Celada Pérez, María Natalia Vallés Fernández, Tomás Maté Enríquez, Miguel Villa Arranz, Marta Domínguez-Gil González, Isabel Fernández-Natal, Gregoria Megías Lobón, Juan Luis Muñoz Bellido, Pilar Ciruela, Ariadna Mas i Casals, Maria Doladé Botías, M. Angeles Marcos Maeso, Dúnia Pérez del Campo, Antonio Félix de Castro, Ramón Limón Ramírez, Maria Francisca Elías Retamosa, Manuela Rubio González, María Sinda Blanco Lobeiras, Alberto Fuentes Losada, Antonio Aguilera, German Bou, Yolanda Caro, Noemí Marauri, Luis Miguel Soria Blanco, Isabel del Cura González, Montserrat Hernández Pascual, Roberto Alonso Fernández, Paloma Merino-Amador, Natalia Cabrera Castro, Aurora Tomás Lizcano, Cristóbal Ramírez Almagro, Manuel Segovia Hernández, Nieves Ascunce Elizaga, María Ederra Sanz, Carmen Ezpeleta Baquedano, Ana Bustinduy Bascaran, Susana Iglesias Tamayo, Luis Elorduy Otazua, Rebeca Benarroch Benarroch, Jesús Lopera Flores, Antonia Vázquez de la Villa
Journal: The Lancet (2020)
Advanced fabrication for electrospun three-dimensional nanofiber aerogels and scaffolds
Authors: Yujie Chen, Muhammad Shafiq, Mingyue Liu, Yosry Morsi, Xiumei Mo
Journal: Bioactive Materials (2020)

Electrospinning is a versatile strategy for creating nanofiber materials with various structures, which has broad application for a myriad of areas ranging from tissue engineering, energy harvesting, filtration and has become one of the most important academic and technical activities in the field of material science in recent years. In addition to playing a significant role in the construction of two-dimensional (2D) nanomaterials, electrospinning holds great promise as a robust method for producing three-dimensional (3D) aerogels and scaffolds. This article reviews and summarizes the recent advanced methods for fabricating electrospun three-dimensional nanofiber aerogels and scaffolds, including gas foaming, direct electrospinning of 3D nanofibrous scaffold, short nanofibers assembling into 3D aerogels/scaffolds, 3D printing, electrospray, origami and cell sheet engineering, centrifugal electrospinning, and other methods. Besides, intriguing formation process, crosslinking pathway, properties, and applications of 3D aerogels and scaffolds are also introduced. Taken together, these aerogels and scaffolds with various excellent features present tremendous potential in various fields.
How the coronavirus pandemic has affected the clinical management of Philadelphia-negative chronic myeloproliferative neoplasms in Italy—a GIMEMA MPN WP survey
Authors: Francesca Palandri, Alfonso Piciocchi, Valerio De Stefano, Massimo Breccia, Guido Finazzi, Alessandra Iurlo, Paola Fazi, Stefano Soddu, Bruno Martino, Sergio Siragusa, Francesco Albano, Francesco Passamonti, Marco Vignetti, Alessandro M. Vannucchi
Journal: Leukemia (2020)
SARS-CoV-2 Transmission and the Risk of Aerosol-Generating Procedures
Authors: Susan Pasnick, W. Graham Carlos, Charles S. Dela Cruz, Jane E. Gross, Garth Garrison, Shazia Jamil
Journal: American Journal of Respiratory and Critical Care Medicine (2020)

"SARS-CoV-2 Transmission and the Risk of Aerosol-Generating Procedures." American Journal of Respiratory and Critical Care Medicine, 202(4), pp. P13–P14
Tumour-reprogrammed stromal BCAT1 fuels branched-chain ketoacid dependency in stromal-rich PDAC tumours
Authors: Ziwen Zhu, Abhinav Achreja, Noah Meurs, Olamide Animasahun, Sarah Owen, Anjali Mittal, Pooja Parikh, Ting-Wen Lo, Janusz Franco-Barraza, Jiaqi Shi, Valerie Gunchick, Mara H. Sherman, Edna Cukierman, Andrew M. Pickering, Anirban Maitra, Vaibhav Sahai, Meredith A. Morgan, Sunitha Nagrath, Theodore S. Lawrence, Deepak Nagrath
Journal: Nature Metabolism (2020)
Use of Molecular Epidemiology to Inform Response to a Hepatitis A Outbreak — Los Angeles County, California, October 2018–April 2019
Authors: Meredith Haddix, Rachel Civen, Jill K. Hacker, Will Probert, Sarah New, Nicole Green, Peera Hemarajata, Prabhu Gounder
Journal: MMWR Morbidity and Mortality Weekly Report (2020)

Los Angeles County comprises 4,058 square miles and is home to approximately 10 million residents (1), an estimated 59,000 (0.6%) of whom experience homelessness on a given night (2). In late 2018, Los Angeles County Department of Public Health (LAC DPH) was notified of a case of hepatitis A virus (HAV) infection in a person experiencing homelessness. LAC DPH conducted an investigation to determine the source of infection, identify additional cases, and identify contacts for postexposure prophylaxis (PEP). Over the next week, LAC DPH identified two additional hepatitis A cases in persons experiencing homelessness who knew one another socially and were known to congregate at a specific street intersection. To identify and respond rapidly to additional outbreak-associated cases, LAC DPH implemented enhanced surveillance procedures, including immediately obtaining specimens for molecular testing from all patients with suspected hepatitis A in the same geographic area. Enhanced surveillance identified four additional cases in persons linked to a senior living campus within two blocks of the intersection where the initial three patients reported congregating. These four cases were linked to the cluster in persons experiencing homelessness through HAV genotyping. Overall, DPH identified seven outbreak-associated hepatitis A cases during October 2018-January 2019. The DPH response to this community hepatitis A outbreak included conducting vaccination outreach to persons at risk, conducting environmental health outreach to restaurants in the outbreak area, and issuing health care provider alerts about the increased occurrence of hepatitis A. Implementation of near real-time molecular testing can improve hepatitis A outbreak responses by confirming HAV infections, linking additional cases to the outbreak, and informing the targeting of prevention efforts.
Abstract 14018: Platelet Phenotype and Function are Fundamentally Different in STEMI and NSTEMI Patients
Authors: Rachel Schmidt, Preya Simlote, Frederick S Ling, Genaro Fernandez, Craig N Morrell, David Q Rich, David H Adler, Joe W Gervase, Scott J Cameron
Journal: Circulation (2017)

Introduction: We recently identified ERK5 in normal human platelets and in a murine myocardial infarction (MI) model as a mediator of dysregulated platelet activity and infarct expansion via matrix...
Social stigma in the time of coronavirus disease 2019
Authors: Giovanni Sotgiu, Claudia C. Dobler
Journal: European Respiratory Journal (2020)

The coronavirus disease 2019 (COVID-19) pandemic has dramatically changed the lives of people around the globe since it appeared in Wuhan, China, at the beginning of December 2019. The burden of disease and its death toll have had an unprecedented impact on the healthcare, economic and financial systems of low-, middle- and high-income countries [1–3]. Peoples' lives have been disrupted and negatively impacted by COVID-19-related suffering and lockdowns at community and household level. Addressing COVID-19-related stigma <https://bit.ly/2CPuxO1>
VWF maturation and release are controlled by 2 regulators of Weibel-Palade body biogenesis: exocyst and BLOC-2
Authors: Anish V. Sharda, Alexandra M. Barr, Joshua A. Harrison, Adrian R. Wilkie, Chao Fang, Lourdes M. Mendez, Ionita C. Ghiran, Joseph E. Italiano, Robert Flaumenhaft
Journal: Blood (2020)
Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples
Authors: Minfeng Xiao, Xiaoqing Liu, Jingkai Ji, Min Li, Jiandong Li, Lin Yang, Wanying Sun, Peidi Ren, Guifang Yang, Jincun Zhao, Tianzhu Liang, Huahui Ren, Tian Chen, Huanzi Zhong, Wenchen Song, Yanqun Wang, Ziqing Deng, Yanping Zhao, Zhihua Ou, Daxi Wang, Jielun Cai, Xinyi Cheng, Taiqing Feng, Honglong Wu, Yanping Gong, Huanming Yang, Jian Wang, Xun Xu, Shida Zhu, Fang Chen, Yanyan Zhang, Weijun Chen, Yimin Li, Junhua Li
Journal: Genome Medicine (2020)

Abstract Background COVID-19 (coronavirus disease 2019) has caused a major epidemic worldwide; however, much is yet to be known about the epidemiology and evolution of the virus partly due to the scarcity of full-length SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) genomes reported. One reason is that the challenges underneath sequencing SARS-CoV-2 directly from clinical samples have not been completely tackled, i.e., sequencing samples with low viral load often results in insufficient viral reads for analyses. Methods We applied a novel multiplex PCR amplicon (amplicon)-based and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of SARS-CoV-2 from serials dilutions of a cultured isolate, and eight clinical samples covering a range of sample types and viral loads. We also examined and compared the sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. Results We demonstrated that both amplicon and capture methods efficiently enriched SARS-CoV-2 content from clinical samples, while the enrichment efficiency of amplicon outran that of capture in more challenging samples. We found that capture was not as accurate as meta and amplicon in identifying between-sample variations, whereas amplicon method was not as accurate as the other two in investigating within-sample variations, suggesting amplicon sequencing was not suitable for studying virus-host interactions and viral transmission that heavily rely on intra-host dynamics. We illustrated that meta uncovered rich genetic information in the clinical samples besides SARS-CoV-2, providing references for clinical diagnostics and therapeutics. Taken all factors above and cost-effectiveness into consideration, we proposed guidance for how to choose sequencing strategy for SARS-CoV-2 under different situations. Conclusions This is, to the best of our knowledge, the first work systematically investigating inter- and intra-individual variations of SARS-CoV-2 using amplicon- and capture-based whole-genome sequencing, as well as the first comparative study among multiple approaches. Our work offers practical solutions for genome sequencing and analyses of SARS-CoV-2 and other emerging viruses.