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Results 1 through 20 out of 688

in category pathology

 

1: Pulmonary and Cardiac Pathology in Covid-19: The First Autopsy Series from New Orleans

Sharon E Fox, Aibek Akmatbekov et al.

88,581 downloads (posted 10 Apr 2020)

SARS-CoV-2 has rapidly spread across the United States, causing extensive morbidity and mortality, though the histopathologic basis of severe disease cases has yet to be studied in detail. Over the past century, autopsy has contributed significantly to our understanding of numerous disease processes, but for several reasons, autopsy reports following deaths related to SARS- CoV-2 have thus far been limited across the globe. We report on the relevant cardiopulmonary findings in the first series of autopsies in the United States, with the cause of death being due to SARS-CoV-2 infection. These cases identify key pathologic states potentially contributing to severe disease and decompensation in these patients.

https://rxivist.org/papers/108372
https://doi.org/10.1101/2020.04.06.20050575

2: ACE2 and TMPRSS2 are expressed on the human ocular surface, suggesting susceptibility to SARS-CoV-2 infection

Lingli Zhou, Zhenhua Xu et al.

15,471 downloads (posted 09 May 2020)

Purpose: Conjunctival signs and symptoms are observed in a subset of patients with COVID-19, and SARS-CoV-2 has been detected in tears, raising concerns regarding the eye both as a portal of entry and carrier of the virus. The purpose of this study was to determine whether ocular surface cells possess the key factors required for cellular susceptibility to SARS-CoV-2 entry/infection. Methods: We analyzed human post-mortem eyes as well as surgical specimens for the expression of ACE2 (the receptor for SARS-CoV-2) and TMP...

https://rxivist.org/papers/82851
https://doi.org/10.1101/2020.05.09.086165

3: Molecular Architecture of Early Disseminationand Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area

Scott Wesley Long, Randall J. Olsen et al.

13,399 downloads (posted 23 Sep 2020)

We sequenced the genomes of 5,085 SARS-CoV-2 strains causing two COVID-19 disease waves in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. The genomes were from viruses recovered in the earliest recognized phase of the pandemic in Houston, and an ongoing massive second wave of infections. The virus was originally introduced into Houston many times independently. Virtually all strains in the second wave have a Gly614 amino acid replacement in the spike protein, a polymorphism that ...

https://rxivist.org/papers/116981
https://doi.org/10.1101/2020.09.22.20199125

4: Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China

Fan Wu, Su Zhao et al.

12,875 downloads (posted 25 Jan 2020)

Emerging and re-emerging infectious diseases, such as SARS, MERS, Zika and highly pathogenic influenza present a major threat to public health[1][1]–[3][2]. Despite intense research effort, how, when and where novel diseases appear are still the source of considerable uncertainly. A severe respiratory disease was recently reported in the city of Wuhan, Hubei province, China. At the time of writing, at least 62 suspected cases have been reported since the first patient was hospitalized on December 12nd 2019. Epidemiologi...

https://rxivist.org/papers/71945
https://doi.org/10.1101/2020.01.24.919183

5: Pathophysiology of SARS-CoV-2: targeting of endothelial cells renders a complex disease with thrombotic microangiopathy and aberrant immune response. The Mount Sinai COVID-19 autopsy experience

Clare Bryce, Zachary Grimes et al.

11,014 downloads (posted 22 May 2020)

BACKGROUND Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) and its associated clinical syndrome COVID-19 are causing overwhelming morbidity and mortality around the globe, disproportionately affecting New York City. A comprehensive, integrative autopsy series that advances the mechanistic discussion surrounding this disease process is still lacking. METHODS Autopsies were performed at the Mount Sinai Hospital on 67 COVID-19 positive patients and data from the clinical records were obtained from the Mount Si...

https://rxivist.org/papers/111033
https://doi.org/10.1101/2020.05.18.20099960

6: Plasma Metabolomic and Lipidomic Alterations Associated with COVID-19

Di Wu, Ting Shu et al.

9,537 downloads (posted 07 Apr 2020)

The pandemic of the coronavirus disease 2019 (COVID-19) has become a global public health crisis. COVID-19 is marked by its rapid progression from mild to severe conditions, particularly in the absence of adequate medical care. However, the physiological changes associated with COVID-19 are barely understood. In this study, we performed untargeted metabolomic and lipidomic analyses of plasma from a cohort of COVID-19 patients who had experienced different symptoms. We found the metabolite and lipid alterations exhibit a...

https://rxivist.org/papers/108317
https://doi.org/10.1101/2020.04.05.20053819

7: H&E-stained Whole Slide Image Deep Learning Predicts SPOP Mutation State in Prostate Cancer

Andrew J. Schaumberg, Mark Rubin et al.

7,329 downloads (posted 17 Jul 2016)

A quantitative model to genetically interpret the histology in whole microscopy slide images is desirable to guide downstream immunohistochemistry, genomics, and precision medicine. We constructed a statistical model that predicts whether or not SPOP is mutated in prostate cancer, given only the digital whole slide after standard hematoxylin and eosin [H&E] staining. Using a TCGA cohort of 177 prostate cancer patients where 20 had mutant SPOP, we trained multiple ensembles of residual networks, accurately distinguishing...

https://rxivist.org/papers/20150
https://doi.org/10.1101/064279

8: High multiplex, digital spatial profiling of proteins and RNA in fixed tissue using genomic detection methods

Christopher R. Merritt, Giang T Ong et al.

6,814 downloads (posted 22 Feb 2019)

We have developed Digital Spatial Profiling (DSP), a non-destructive method for high-plex spatial profiling of proteins and RNA, using oligonucleotide detection technologies with unlimited multiplexing capability. The key breakthroughs underlying DSP are threefold: (1) multiplexed readout of proteins/RNA using oligo-tags; (2) oligo-tags attached to affinity reagents (antibodies/RNA probes) through a photocleavable (PC) linker; (3) photocleaving light projected onto the tissue sample to release PC-oligos in any spatial p...

https://rxivist.org/papers/44619
https://doi.org/10.1101/559021

9: Histopathology and Ultrastructural Findings of Fatal COVID-19 Infections

Benjamin T. Bradley, Heather Maioli et al.

6,266 downloads (posted 21 Apr 2020)

Background SARS-CoV-2 is the cause of an ongoing pandemic with a projected 100,000 to 240,000 U.S. deaths. To date, documentation of histopathologic features in fatal cases of COVID-19 has been limited due to small sample size and incomplete organ sampling. Methods Post-mortem examinations were performed on 12 fatal COVID-19 cases in Washington State during February-March 2020. Clinical and laboratory data were reviewed. Tissue examination of all major organs was performed by light microscopy and electron microscopy. Th...

https://rxivist.org/papers/108994
https://doi.org/10.1101/2020.04.17.20058545

10: Are pangolins the intermediate host of the 2019 novel coronavirus (2019-nCoV) ?

Ping Liu, Jing-Zhe Jiang et al.

5,741 downloads (posted 20 Feb 2020)

The outbreak of 2019-nCoV pneumonia (COVID-19) in the city of Wuhan, China has resulted in more than 60,000 laboratory confirmed cases, and recent studies showed that 2019-nCoV (SARS-CoV-2) could be of bat origin but involve other potential intermediate hosts. In this study, we assembled the genomes of coronaviruses identified in sick pangolins. The molecular and phylogenetic analyses showed that pangolin Coronaviruses (pangolin-CoV) are genetically related to both the 2019-nCoV and bat Coronaviruses but do not support ...

https://rxivist.org/papers/74486
https://doi.org/10.1101/2020.02.18.954628

11: Diabetic Retinopathy detection through integration of Deep Learning classification framework

Alexander Rakhlin

5,539 downloads (posted 27 Nov 2017)

This document represents a brief account of ongoing project for Diabetic Retinopathy Detection (DRD) through integration of state-of the art Deep Learning methods. We make use of deep Convolutional Neural Networks (CNNs), which have proven revolutionary in multiple fields of computer vision including medical imaging, and we bring their power to the diagnosis of eye fundus images. For training our models we used publicly available Kaggle data set. For testing we used portion of Kaggle data withheld from training and Mess...

https://rxivist.org/papers/20078
https://doi.org/10.1101/225508

12: Calcium channel blocker amlodipine besylate is associated with reduced case fatality rate of COVID-19 patients with hypertension

Lei-Ke Zhang, Yuan Sun et al.

5,518 downloads (posted 14 Apr 2020)

The coronavirus disease (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now spread to more than 100 countries posing as a serious threat to the public health on a global scale. Patients with comorbidity such as hypertension suffer more severe infection with elevated case fatality rate. Development of effective anti-viral drug is in urgent need to treat COVID-19 patients. Here we report that calcium channel blockers (CCBs), a type of anti-hypertension drugs that are widely ...

https://rxivist.org/papers/108609
https://doi.org/10.1101/2020.04.08.20047134

13: Pangolin homology associated with 2019-nCoV

Tao Zhang, Qunfu Wu et al.

5,363 downloads (posted 20 Feb 2020)

To explore potential intermediate host of a novel coronavirus is vital to rapidly control continuous COVID-19 spread. We found genomic and evolutionary evidences of the occurrence of 2019-nCoV-like coronavirus (named as Pangolin-CoV) from dead Malayan Pangolins. Pangolin-CoV is 91.02% and 90.55% identical at the whole genome level to 2019-nCoV and BatCoV RaTG13, respectively. Pangolin-CoV is the lowest common ancestor of 2019-nCoV and RaTG13. The S1 protein of Pangolin-CoV is much more closely related to 2019-nCoV than ...

https://rxivist.org/papers/74468
https://doi.org/10.1101/2020.02.19.950253

14: Pericyte-specific vascular expression of SARS-CoV-2 receptor ACE2 – implications for microvascular inflammation and hypercoagulopathy in COVID-19

Liqun He, Maarja Andaloussi Mäe et al.

5,286 downloads (posted 12 May 2020)

Accumulating clinical observations implicate vascular inflammation as an underlying cause of coagulopathy in severely ill COVID-19 patients and it was recently suggested that SARS-CoV-2 virus particles infect endothelial cells. Here, we show that endothelial cells do not express angiotensin-converting enzyme-2 (ACE2), the SARS-CoV-2 receptor. Instead, pericytes and microvascular smooth muscle cells express ACE2 in an organotypic manner. Pericyte deficiency leads to increased endothelial expression and release of Von Wil...

https://rxivist.org/papers/83119
https://doi.org/10.1101/2020.05.11.088500

15: Analytical Validation of a COVID-19 qRT-PCR Detection Assay Using a 384-well Format and Three Extraction Methods

Andrew C. Nelson, Benjamin Auch et al.

5,109 downloads (posted 05 Apr 2020)

The COVID-19 global pandemic is an unprecedented health emergency. Insufficient access to testing has hampered effective public health interventions and patient care management in a number of countries. Furthermore, the availability of regulatory-cleared reagents has challenged widespread implementation of testing. We rapidly developed a qRT-PCR SARS-CoV-2 detection assay using a 384-well format and tested its analytic performance across multiple nucleic acid extraction kits. Our data shows robust analytic accuracy on r...

https://rxivist.org/papers/78989
https://doi.org/10.1101/2020.04.02.022186

16: Deep Convolutional Neural Networks for Breast Cancer Histology Image Analysis

Alexander Rakhlin, Alexey A. Shvets et al.

4,672 downloads (posted 05 Feb 2018)

Breast cancer is one of the main causes of cancer death worldwide. Early diagnostics significantly increases the chances of correct treatment and survival, but this process is tedious and often leads to a disagreement between pathologists. Computer-aided diagnosis systems showed potential for improving the diagnostic accuracy. In this work, we develop the computational approach based on deep convolution neural networks for breast cancer histology image classification. Hematoxylin and eosin stained breast histology micro...

https://rxivist.org/papers/20102
https://doi.org/10.1101/259911

17: Treatment of COVID-19 Patients with Convalescent Plasma in Houston, Texas

Eric Salazar, Katherine K. Perez et al.

4,339 downloads (posted 13 May 2020)

Background: COVID-19 disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread globally, and no proven treatments are available. Convalescent plasma therapy has been used with varying degrees of success to treat severe microbial infections for more than 100 years. Methods: Patients (n=25) with severe and/or life-threatening COVID-19 disease were enrolled at the Houston Methodist hospitals from March 28 to April 14, 2020. Patients were transfused with convalescent plasma obtained from do...

https://rxivist.org/papers/110459
https://doi.org/10.1101/2020.05.08.20095471

18: EXCEPTIONALLY LOW LIKELIHOOD OF ALZHEIMER'S DEMENTIA IN APOE2 HOMOZYGOTES

Eric M. Reiman, Joseph F. Arboleda-Velasquez et al.

3,923 downloads (posted 02 Nov 2019)

Each additional copy of the apolipoprotein E4 (APOE4) allele is associated with a higher risk of Alzheimers dementia, such that APOE4 homozygotes have a particularly high risk. While the APOE2 allele is associated with a lower risk of Alzheimers dementia, it is not yet known whether APOE2 homozygotes have a particularly low risk. We generated Alzheimers dementia odds ratios and other findings in more than 5,000 clinically characterized and neuropathologically characterized Alzheimers dementia cases and controls. APOE2/2...

https://rxivist.org/papers/106170
https://doi.org/10.1101/19011015

19: Prognostic biomarkers in oral squamous cell carcinoma: a systematic review

César Rivera, Ana Karina de Oliveira et al.

3,568 downloads (posted 16 Jul 2017)

Over the years, several tumor biomarkers have been suggested to foresee the prognosis of oral squamous cell carcinoma (OSCC) patients. Here, we present a systematic review to identify, evaluate and summarize the evidence for OSCC reported markers. Eligible studies were identified through a literature search of MEDLINE/PubMed until January 2016. We included primary articles reporting overall survival, disease-free survival and cause-specific survival as outcomes. Our findings were analysed using REporting recommendations...

https://rxivist.org/papers/20140
https://doi.org/10.1101/164111

20: Adversarial childhood events are associated with Sudden Infant Death Syndrome (SIDS): an ecological study

Eran Elhaik

3,351 downloads (posted 07 Jun 2018)

Sudden Infant Death Syndrome (SIDS) is the most common cause of postneonatal infant death. The allostatic load hypothesis posits that SIDS is the result of perinatal cumulative painful, stressful, or traumatic exposures that tax neonatal regulatory systems. To test it, we explored the relationships between SIDS and two common stressors, male neonatal circumcision (MNC) and prematurity, using latitudinal data from 15 countries and over 40 US states during the years 1999-2016. We used linear regression analyses and likeli...

https://rxivist.org/papers/20086
https://doi.org/10.1101/339465