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1. Eosinophil recovery in hospitalized COVID-19 patients is associated with lower rates of ICU admission and in-hospital mortality: An observational cohort analysis

Author

Yan, Peter D, Markovic, Daniela, Hixson, Roxana Y, Shover, Carolyn M, Buhr, Russell G, Salehi-Rad, Ramin, LeMaster, Blake, Tashkin, Donald P, Fulcher, Jennifer A, and Barjaktarevic, Igor Z

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Health Sciences, Coronaviruses, Infectious Diseases, Lung, Emerging Infectious Diseases, Good Health and Well Being, Humans, Eosinophils, COVID-19, Hospital Mortality, Hospitalization, Cohort Studies, Intensive Care Units, ARDS, Critical illness, Eosinophil, In flammation, Survival, Inflammation
Abstract

BackgroundAdmission eosinopenia (

Published
2023

2. Measuring the accuracy of cardiac output using POCUS: the introduction of artificial intelligence into routine care

Author

Shaikh, Faisal, Kenny, Jon-Emile, Awan, Omar, Markovic, Daniela, Friedman, Oren, He, Tao, Singh, Sidharth, Yan, Peter, Qadir, Nida, and Barjaktarevic, Igor

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Bioengineering, Clinical Research, Biomedical Imaging, 4.2 Evaluation of markers and technologies, Detection, screening and diagnosis, Velocity time integral, VTI, Point-of-care ultrasound, POCUS, Hemodynamic monitoring, Cardiac output, Artificial intelligence, Medical biotechnology
Abstract

BackgroundShock management requires quick and reliable means to monitor the hemodynamic effects of fluid resuscitation. Point-of-care ultrasound (POCUS) is a relatively quick and non-invasive imaging technique capable of capturing cardiac output (CO) variations in acute settings. However, POCUS is plagued by variable operator skill and interpretation. Artificial intelligence may assist healthcare professionals obtain more objective and precise measurements during ultrasound imaging, thus increasing usability among users with varying experience. In this feasibility study, we compared the performance of novice POCUS users in measuring CO with manual techniques to a novel automation-assisted technique that provides real-time feedback to correct image acquisition for optimal aortic outflow velocity measurement.Methods28 junior critical care trainees with limited experience in POCUS performed manual and automation-assisted CO measurements on a single healthy volunteer. CO measurements were obtained using left ventricular outflow tract (LVOT) velocity time integral (VTI) and LVOT diameter. Measurements obtained by study subjects were compared to those taken by board-certified echocardiographers. Comparative analyses were performed using Spearman's rank correlation and Bland-Altman matched-pairs analysis.ResultsAdequate image acquisition was 100% feasible. The correlation between manual and automated VTI values was not significant (p = 0.11) and means from both groups underestimated the mean values obtained by board-certified echocardiographers. Automated measurements of VTI in the trainee cohort were found to have more reproducibility, narrower measurement range (6.2 vs. 10.3 cm), and reduced standard deviation (1.98 vs. 2.33 cm) compared to manual measurements. The coefficient of variation across raters was 11.5%, 13.6% and 15.4% for board-certified echocardiographers, automated, and manual VTI tracing, respectively.ConclusionsOur study demonstrates that novel automation-assisted VTI is feasible and can decrease variability while increasing precision in CO measurement. These results support the use of artificial intelligence-augmented image acquisition in routine critical care ultrasound and may have a role for evaluating the response of CO to hemodynamic interventions. Further investigations into artificial intelligence-assisted ultrasound systems in clinical settings are warranted.

Published
2022

3. Chronic Obstructive Pulmonary Disease is Not Associated with In-Hospital Mortality in COVID-19: An Observational Cohort Analysis

Author

Toppen, William, Yan, Peter, Markovic, Daniela, Shover, Carolyn M, Buhr, Russell G, Fulcher, Jennifer A, Tashkin, Donald P, and Barjaktarevic, Igor

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Clinical Research, Coronaviruses, Emerging Infectious Diseases, Infectious Diseases, Chronic Obstructive Pulmonary Disease, Lung, Respiratory, Good Health and Well Being, Humans, Pulmonary Disease, Chronic Obstructive, COVID-19, Hospital Mortality, Cohort Studies, Aspirin, COPD, survival, critical illness, ARDS, Cardiorespiratory Medicine and Haematology, Respiratory System, Cardiovascular medicine and haematology
Abstract

BackgroundChronic obstructive pulmonary disease (COPD) is associated with worsened outcomes in COVID-19 (coronavirus disease 2019). However, data remain fraught with heterogeneity and bias from comorbid conditions. Additionally, data on the impact of COPD-specific factors, such as pre-hospital medications and pulmonologist involvement, remain sparse.ObjectiveWe report a single-center analysis of COPD patients hospitalized with COVID-19 compared to those without COPD. Primary outcomes include ICU admission, mechanical ventilation, and in-hospital mortality.MethodsWe evaluated all patients ≥40 years admitted with PCR-confirmed COVID-19 between February 2020 and February 2021. COPD was defined by documented ICD-10 diagnosis of COPD, confirmed smoking history, and active bronchodilator use. We compared outcomes between COPD patients and the remainder of the COVID-19 cohort. Multivariable analyses were adjusted for age, sex, smoking status, and comorbid conditions.ResultsOf 1537 hospitalized COVID-19 patients, 122 (7.9%) carried a diagnosis of COPD. The COPD cohort was older (74 ± 13 vs 66 ± 15 years, P < 0.001) and more often former smokers (P < 0.001). Comorbid conditions including diabetes, cardiovascular disease, and kidney disease were more prevalent in the COPD group (P < 0.001). After adjusting for comorbid conditions, the COPD cohort had higher severity scores and trended towards fewer hospital-free days. Among patients with COPD, pre-hospital use of aspirin was associated with decreased ICU admissions (aHR 0.56, P = 0.049) and mechanical ventilation (aHR 0.25, P = 0.008), while LAMAs (long-acting muscarinic antagonists) were associated with decreased in-hospital mortality (aHR 0.34, P = 0.047). Involvement of pulmonology in pre-hospital management of COPD was not found to significantly affect outcomes.ConclusionWhen corrected for comorbid illnesses, COPD was associated with more severe disease but not with increased ICU admission, mechanical ventilation, or in-hospital mortality rates. Among COPD patients, prehospital treatment with aspirin and COPD-directed therapies were associated with improved outcomes.

Published
2022

4. Discovering dominant tumor immune archetypes in a pan-cancer census

Author

Combes, Alexis J, Samad, Bushra, Tsui, Jessica, Chew, Nayvin W, Yan, Peter, Reeder, Gabriella C, Kushnoor, Divyashree, Shen, Alan, Davidson, Brittany, Barczak, Andrea J, Adkisson, Michael, Edwards, Austin, Naser, Mohammad, Barry, Kevin C, Courau, Tristan, Hammoudi, Taymour, Argüello, Rafael J, Rao, Arjun Arkal, Olshen, Adam B, Consortium, The Immunoprofiler, Spitzer, Matthew, Fong, Lawrence, Nelson, Amanda, Kumar, Raj, Lee, Justin, Burra, Arun, Hsu, Joy, Hackett, Caroline, Tolentino, Karen, Sjarif, Jasmine, Johnson, Peter, Shao, Evans, Abrau, Darrell, Lupin, Leonard, Shaw, Cole, Collins, Zachary, Lea, Tasha, Corvera, Carlos, Nakakura, Eric, Carnevale, Julia, Alvarado, Michael, Loo, Kimberley, Chen, Lawrence, Chow, Melissa, Grandis, Jennifer, Ryan, Will, El-Sayed, Ivan, Jablons, David, Woodard, Gavitt, Meng, Maxwell W, Porten, Sima P, Okada, Hideho, Tempero, Margaret, Ko, Andrew, Kirkwood, Kim, Vandenberg, Scott, Guevarra, Denise, Oropeza, Erica, Cyr, Chris, Glenn, Pat, Bolen, Jennifer, Morton, Amanda, Eckalbar, Walter, Cai, Cathy, Zhan, Jenny, Davis, Katelyn C, Kelley, Robin K, Chapman, Jocelyn S, Atreya, Chloe E, Patel, Amar, Daud, Adil I, Ha, Patrick, Diaz, Aaron A, Kratz, Johannes R, Collisson, Eric A, Fragiadakis, Gabriela K, Erle, David J, Boissonnas, Alexandre, Asthana, Saurabh, Chan, Vincent, and Krummel, Matthew F

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Cancer Genomics, Cancer, Genetics, Human Genome, Biomarkers, Tumor, Censuses, Cluster Analysis, Cohort Studies, Computational Biology, Flow Cytometry, Gene Expression Regulation, Neoplastic, Humans, Neoplasms, RNA-Seq, San Francisco, Transcriptome, Tumor Microenvironment, Universities, Immunoprofiler Consortium, Pan Cancer analysis, immune profiling, solid tumor microenvironement, system immunology, tumor immunology, unsupervised clustering, Biological Sciences, Medical and Health Sciences, Developmental Biology, Biological sciences, Biomedical and clinical sciences
Abstract

Cancers display significant heterogeneity with respect to tissue of origin, driver mutations, and other features of the surrounding tissue. It is likely that individual tumors engage common patterns of the immune system-here "archetypes"-creating prototypical non-destructive tumor immune microenvironments (TMEs) and modulating tumor-targeting. To discover the dominant immune system archetypes, the University of California, San Francisco (UCSF) Immunoprofiler Initiative (IPI) processed 364 individual tumors across 12 cancer types using standardized protocols. Computational clustering of flow cytometry and transcriptomic data obtained from cell sub-compartments uncovered dominant patterns of immune composition across cancers. These archetypes were profound insofar as they also differentiated tumors based upon unique immune and tumor gene-expression patterns. They also partitioned well-established classifications of tumor biology. The IPI resource provides a template for understanding cancer immunity as a collection of dominant patterns of immune organization and provides a rational path forward to learn how to modulate these to improve therapy.

Published
2022

5. Cannabis consumption is associated with lower COVID-19 severity among hospitalized patients: a retrospective cohort analysis

Author

Shover, Carolyn M, Yan, Peter, Jackson, Nicholas J, Buhr, Russell G, Fulcher, Jennifer A, Tashkin, Donald P, and Barjaktarevic, Igor

Subjects
Health Sciences, Traditional, Complementary and Integrative Medicine, Drug Abuse (NIDA only), Clinical Research, Substance Misuse, Respiratory, Good Health and Well Being, COVID-19, Cannabis, Outcomes, Respiratory failure, ARDS, Traditional, complementary and integrative medicine
Abstract

BackgroundWhile cannabis is known to have immunomodulatory properties, the clinical consequences of its use on outcomes in COVID-19 have not been extensively evaluated. We aimed to assess whether cannabis users hospitalized for COVID-19 had improved outcomes compared to non-users.MethodsWe conducted a retrospective analysis of 1831 patients admitted to two medical centers in Southern California with a diagnosis of COVID-19. We evaluated outcomes including NIH COVID-19 Severity Score, need for supplemental oxygen, ICU (intensive care unit) admission, mechanical ventilation, length of hospitalization, and in-hospital death for cannabis users and non-users. Cannabis use was reported in the patient's social history. Propensity matching was used to account for differences in age, body-mass index, sex, race, tobacco smoking history, and comorbidities known to be risk factors for COVID-19 mortality between cannabis users and non-users.ResultsOf 1831 patients admitted with COVID-19, 69 patients reported active cannabis use (4% of the cohort). Active users were younger (44 years vs. 62 years, p < 0.001), less often diabetic (23.2% vs 37.2%, p < 0.021), and more frequently active tobacco smokers (20.3% vs. 4.1%, p < 0.001) compared to non-users. Notably, active users had lower levels of inflammatory markers upon admission than non-users-CRP (C-reactive protein) (3.7 mg/L vs 7.6 mg/L, p < 0.001), ferritin (282 μg/L vs 622 μg/L, p < 0.001), D-dimer (468 ng/mL vs 1140 ng/mL, p = 0.017), and procalcitonin (0.10 ng/mL vs 0.15 ng/mL, p = 0.001). Based on univariate analysis, cannabis users had significantly better outcomes compared to non-users as reflected in lower NIH scores (5.1 vs 6.0, p < 0.001), shorter hospitalization (4 days vs 6 days, p < 0.001), lower ICU admission rates (12% vs 31%, p < 0.001), and less need for mechanical ventilation (6% vs 17%, p = 0.027). Using propensity matching, differences in overall survival were not statistically significant between cannabis users and non-users, nevertheless ICU admission was 12 percentage points lower (p = 0.018) and intubation rates were 6 percentage points lower (p = 0.017) in cannabis users.ConclusionsThis retrospective cohort study suggests that active cannabis users hospitalized with COVID-19 had better clinical outcomes compared with non-users, including decreased need for ICU admission or mechanical ventilation. However, our results need to be interpreted with caution given the limitations of a retrospective analysis. Prospective and observational studies will better elucidate the effects cannabis use in COVID-19 patients.

Published
2022

6. SCENITH: A Flow Cytometry-Based Method to Functionally Profile Energy Metabolism with Single-Cell Resolution

Author

Argüello, Rafael J, Combes, Alexis J, Char, Remy, Gigan, Julien-Paul, Baaziz, Ania I, Bousiquot, Evens, Camosseto, Voahirana, Samad, Bushra, Tsui, Jessica, Yan, Peter, Boissonneau, Sebastien, Figarella-Branger, Dominique, Gatti, Evelina, Tabouret, Emeline, Krummel, Matthew F, and Pierre, Philippe

Subjects
Biomedical and Clinical Sciences, Immunology, Clinical Research, Genetics, Hematology, Pediatric Research Initiative, 2.1 Biological and endogenous factors, Aetiology, Inflammatory and immune system, Cancer, Adult, Animals, Cells, Cultured, Energy Metabolism, Female, Fibroblasts, Humans, Male, Metabolome, Mice, Inbred C57BL, Middle Aged, Neoplasms, Single-Cell Analysis, cell culture media and metabolism, functional assay metabolism single cells, metabolic function by flow cytometry, metabolic gene signatures, metabolic profiling of blood samples, metabolism analysis in samples from patients, protein synthesis and metabolism, translation and metabolism, tumor immunometabolism, Biochemistry and Cell Biology, Medical Biochemistry and Metabolomics, Endocrinology & Metabolism, Biochemistry and cell biology, Medical biochemistry and metabolomics
Abstract

Energetic metabolism reprogramming is critical for cancer and immune responses. Current methods to functionally profile the global metabolic capacities and dependencies of cells are performed in bulk. We designed a simple method for complex metabolic profiling called SCENITH, for single-cell energetic metabolism by profiling translation inhibition. SCENITH allows for the study of metabolic responses in multiple cell types in parallel by flow cytometry. SCENITH is designed to perform metabolic studies ex vivo, particularly for rare cells in whole blood samples, avoiding metabolic biases introduced by culture media. We analyzed myeloid cells in solid tumors from patients and identified variable metabolic profiles, in ways that are not linked to their lineage or their activation phenotype. SCENITH's ability to reveal global metabolic functions and determine complex and linked immune-phenotypes in rare cell subpopulations will contribute to the information needed for evaluating therapeutic responses or patient stratification.

Published
2020

7. Discovering dominant tumor immune archetypes in a pan-cancer census

Author

Spitzer, Matthew, Fong, Lawrence, Nelson, Amanda, Kumar, Raj, Lee, Justin, Burra, Arun, Hsu, Joy, Hackett, Caroline, Tolentino, Karen, Sjarif, Jasmine, Johnson, Peter, Shao, Evans, Abrau, Darrell, Lupin, Leonard, Shaw, Cole, Collins, Zachary, Lea, Tasha, Corvera, Carlos, Nakakura, Eric, Carnevale, Julia, Alvarado, Michael, Loo, Kimberley, Chen, Lawrence, Chow, Melissa, Grandis, Jennifer, Ryan, Will, El-Sayed, Ivan, Jablons, David, Woodard, Gavitt, Meng, Maxwell W., Porten, Sima P., Okada, Hideho, Tempero, Margaret, Ko, Andrew, Kirkwood, Kim, Vandenberg, Scott, Guevarra, Denise, Oropeza, Erica, Cyr, Chris, Glenn, Pat, Bolen, Jennifer, Morton, Amanda, Eckalbar, Walter, Combes, Alexis J., Samad, Bushra, Tsui, Jessica, Chew, Nayvin W., Yan, Peter, Reeder, Gabriella C., Kushnoor, Divyashree, Shen, Alan, Davidson, Brittany, Barczak, Andrea J., Adkisson, Michael, Edwards, Austin, Naser, Mohammad, Barry, Kevin C., Courau, Tristan, Hammoudi, Taymour, Argüello, Rafael J., Rao, Arjun Arkal, Olshen, Adam B., Cai, Cathy, Zhan, Jenny, Davis, Katelyn C., Kelley, Robin K., Chapman, Jocelyn S., Atreya, Chloe E., Patel, Amar, Daud, Adil I., Ha, Patrick, Diaz, Aaron A., Kratz, Johannes R., Collisson, Eric A., Fragiadakis, Gabriela K., Erle, David J., Boissonnas, Alexandre, Asthana, Saurabh, Chan, Vincent, and Krummel, Matthew F.

Published
2022
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8. Statin-centric versus low-density lipoprotein-centric approach for atherosclerotic cardiovascular disease prevention: a Singapore perspective.

Author

Yan, Peter, Tan, Eng Kiat Kevin, Choo, Jason Chon Jun, Liew, Choon Fong Stanley, Lau, Titus, and Waters, David D

Subjects
Humans, Cardiovascular Diseases, Lipoproteins, LDL, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Risk Assessment, Risk Factors, Life Style, Cardiology, Aging, Singapore, Atherosclerosis, Practice Guidelines as Topic, atherosclerosis, cardiovascular disease, lipids, Lipoproteins, LDL, Medical and Health Sciences, General & Internal Medicine
Abstract

The link between cholesterol levels and atherosclerotic cardiovascular disease (ASCVD) is well-established. In Singapore, there is an increasing prevalence of risk factors for ASCVD. Like many Asian countries, Singapore's population is rapidly ageing and increasingly sedentary, which predisposes individuals to chronic health problems. Current international and local guidelines recommend statin therapy for the primary and secondary prevention of ASCVD. However, despite the effectiveness of statin therapy, some studies have highlighted that Asian patients with cardiovascular disease are not achieving target lipid goals. Furthermore, it is widely believed that the responses of Asians (both patients and physicians) to statin therapy are different from those of their Western counterparts. Experts convened in 2014 to determine the impact of current guidelines on clinical practice in Singapore. This review summarises the key findings and recommendations of these guidelines, and presents key principles to aid clinicians to manage the cardiovascular risk of their patients more effectively.

Published
2016

10. Clinical and neurocognitive outcomes after transcatheter aortic valve implantation (TAVI) with cerebral protection: initial experience with a novel dual-filter device in Southeast Asia

Author

Chiam, Paul Toon Lim, Chan, Nien Shen, Lim, Yean Teng, Lim, Choon Pin, Nair, Dinesh, Lim, Tai Tian, Soon, Chao Yang, Khoo, Brian Chung Hoe, Lim, Jimmy, Tan, Kok Soon, Lam, Leslie, Yan, Peter, Ooi, Yau Wei, and Chong, Mei Sian

Subjects
Aged, 80 and over, Male, Aortic Valve Stenosis, General Medicine, Prosthesis Design, Stroke, Transcatheter Aortic Valve Replacement, Treatment Outcome, Aortic Valve, Heart Valve Prosthesis, Humans, Original Article, Female, Asia, Southeastern, Aged
Abstract

INTRODUCTION Transcatheter aortic valve implantation (TAVI) is increasingly performed in patients with severe aortic stenosis. A novel dual-filter system to reduce cerebral embolism during TAVI recently became available. We aimed to assess the feasibility, safety, and clinical and neurocognitive outcomes of TAVI with cerebral protection in Asian patients. METHODS 40 consecutive patients undergoing TAVI with cerebral protection were enrolled. All procedures were performed via femoral access using the self-expanding Evolut R/PRO or Portico, or the balloon-expandable SAPIEN 3 bioprostheses. Baseline characteristics, procedural and clinical outcomes were recorded. Cognition was assessed at baseline and 30 days using the abbreviated mental test (AMT). RESULTS The mean age of the patients (75% male) was 76.4 ± 8.4 years. TAVI was uncomplicated in all patients. The filter device was successfully deployed in 38 (95.0%) patients without safety issues. There was no stroke or death at 30 days, and the survival rate at nine months was 95.0%. There was no overall cognitive change (baseline vs. 30-day AMT: 9.2 ± 1.1 vs. 9.0 ± 1.5, p = 0.12), and only 1 (2.5%) patient developed impaired cognition at 30 days. Patients with a decreased AMT score at 30 days were significantly older than those without (82.1 ± 4.5 vs. 74.4 ± 7.7 years, p = 0.019). All patients with decreased AMT scores were aged ≥ 76 years. CONCLUSION In this early Asian experience of TAVI under cerebral protection, the filter device was successfully deployed in 95% of patients, with 100% procedural success. There were no filter-related complications and no stroke or mortality at 30 days. Overall cognition was preserved, although increased age was associated with a decline in AMT score.

Published
2022
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12. Chronic Obstructive Pulmonary Disease is Not Associated with In-Hospital Mortality in COVID-19: An Observational Cohort Analysis

Author

Toppen,William, Yan,Peter, Markovic,Daniela, Shover,Carolyn M, Buhr,Russell G, Fulcher,Jennifer A, Tashkin,Donald P, Barjaktarevic,Igor, Toppen,William, Yan,Peter, Markovic,Daniela, Shover,Carolyn M, Buhr,Russell G, Fulcher,Jennifer A, Tashkin,Donald P, and Barjaktarevic,Igor

Abstract

William Toppen,1,&ast; Peter Yan,2,&ast; Daniela Markovic,3 Carolyn M Shover,4,5 Russell G Buhr,4,6 Jennifer A Fulcher,6,7 Donald P Tashkin,4 Igor Barjaktarevic4 1Section of Hospital Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; 2David Geffen School of Medicine, University of California, Los Angeles, CA, USA; 3Department of Medicine Statistics Core, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; 4Division of Pulmonary, Critical Care and Sleep Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA; 5Offsite Care, Santa Rosa, CA, USA; 6Department of Medicine, Greater Los Angeles Veterans Affairs Health Care System, Los Angeles, CA, USA; 7Division of Infectious Diseases, David Geffen School of Medicine, University of California, Los Angeles, CA, USA&ast;These authors contributed equally to this workCorrespondence: Igor Barjaktarevic, 10833 Le Conte Avenue, 43118 CHS, Los Angeles, CA, 90095, Email ibarjaktarevic@mednet.ucla.eduBackground: Chronic obstructive pulmonary disease (COPD) is associated with worsened outcomes in COVID-19 (coronavirus disease 2019). However, data remain fraught with heterogeneity and bias from comorbid conditions. Additionally, data on the impact of COPD-specific factors, such as pre-hospital medications and pulmonologist involvement, remain sparse.Objective: We report a single-center analysis of COPD patients hospitalized with COVID-19 compared to those without COPD. Primary outcomes include ICU admission, mechanical ventilation, and in-hospital mortality.Methods: We evaluated all patients ≥ 40 years admitted with PCR-confirmed COVID-19 between February 2020 and February 2021. COPD was defined by documented ICD-10 diagnosis of COPD, confirmed smoking history, and active bronchodilator use. We compared outcomes between COPD patients and the remainder of the COVID-19 cohort. Multivariable analyses were adjusted for age

Published
2022

14. Fossil traces of Thalassinoides from serov suite gaizes (Middle Trans-Urals, Upper Paleocene)

Author

Trubin, Yaroslav Sergeevich and Yan, Peter Alexandrovich

Subjects
Materials Science (miscellaneous), опоки, Management, Monitoring, Policy and Law, Structural basin, fossil traces, Sedimentary depositional environment, Paleontology, Stage (stratigraphy), Serov Formation, Glossifungites, Зауралье, палеоцен, серовская свита, Западная Сибирь, Waste Management and Disposal, Thalassinoides, ихнофоссилии, gaizes, biology, Western Siberia, Geotechnical Engineering and Engineering Geology, biology.organism_classification, Transuralian, Diagenesis, Fuel Technology, Period (geology), кремнистые отложения, полевые исследования, Paleocene, Economic Geology, Sedimentary rock, Paleogene, Geology
Abstract

Актуальность исследования. В северных районах Западной Сибири в отложениях танетского яруса отмечаются перерывы осадконакопления, масштабность проявления и диапазон которых остаются неясными. В частности, для доказательства их существования на южных окраинах бассейна требуется привлечение дополнительных палеонтологических и седиментологических данных, которые могут фиксировать кризис привноса осадочного материала. Одним из наиболее надежных источников информации о перерывах в осадконакоплении и других седиментационных событиях могут являться ископаемые ходы. Цель: ихнофациальный анализ кремнистых отложений верхнего палеоцена Западной Сибири. Объект: ископаемые норы Thalassinoides серовской свиты (среднее Зауралье, верхний палеоцен), вмещающие ходы породы (темные опоки с афанитовой структурой), заполняющие ходы породы (светлые опоки с тонкоглобулярной структурой). Методика: полевые исследования, растровая электронная микроскопия, литолого-петрографический, ихнотекстурный, ихнофациальный и седиментологический анализы Результаты. Приведены данные о находках ископаемых следов Thalassinoides в кремнистых породах серовской свиты (верхний палеоцен, среднее Зауралье), и дана характеристика особенностей их морфологии. Рассматриваются вопросы возможных условий, при которых происходило формирование нор и их сохранение в ископаемом состоянии. Микроскопические исследования кремнистых пород серовской свиты позволяют определить особенности и различия в постседиментационных изменениях вмещающих и выполняющих норы отложений. В качестве наиболее вероятных продуцентов ходов Thalassinoides в танетском бассейне определены десятиногие ракообразные. Ископаемые следы в кремнистых формациях палеогена ранее не изучались и приводятся в научной литературе впервые. The relevance of the research. In the northern margins of Western Siberia, depositional breaks are indicated in the sediments of Tanetian stage. Global nature of such hiatuses and possibility of their existence in the southern margins remain debatable. This requires the use of additional paleontological and sedimentological data that capture the crisis of the introduction of sedimentary material. One of the most reliable source of information about interruptions to introduction of sedimentary material and other events in sedimentation can be fossil burrows. The aim of the research is the ichnofacial analysis of siliceous sediments of the Upper Paleocene of Western Siberia. Objects: fossil traces of Thalassinoides from silica rocks Serov suite (Middle Trans-Urals, Upper Paleocene), burrow-filling rock (light gaize with a thin-globular structure), burrow-containing rock (dark gaize, represented by a structureless mass of silica) Methods: field work, scanning electron microscopy, lithologic-petrographic, ichno-structure, ichno-facies and sedimentological analyzes. Results. Information on fossil traces of Thalassinoides from Serov suite gaizes and fossil traces morphology are given. The paper considers the issues of possible environmental conditions, under which the burrow marks were formed and preserved in fossil state. Microscopic studies of Serov suite gaizes allow identifying the features of changes in rocks, that contain and fill burrows, during further diagenetic transformation. Also the article highlights the most likely producers for Thalassinoides burrows of Tanetian time in the West Siberian basin. The study of fossil traces in siliceous rocks of the Paleogene period has not been undertaken before and has not been noted in scientific literature.

Published
2020

15. First isotope-hydrogeochemical data on the natural waters of the south-east slope of the Chekanovsky ridge (Arctic areas of the Siberian platform)

Author

Novikov, Dmitry Anatolyevich, Maksimova, Anastasia Alekseevna, Pyrayev, Alexander Nikolaevich, and Yan, Peter Alexandrovich

Subjects
Siberian platform, Materials Science (miscellaneous), изотопно-геохимические исследования, Арктика, геохимические особенности, intensity of water migration of elements, природные воды, химический состав, Management, Monitoring, Policy and Law, Geotechnical Engineering and Engineering Geology, интенсивность, permafrost rocks, стабильные изотопы, Fuel Technology, Arctic, natural waters, chemical composition, Economic Geology, south-east slope of the Chekanovsky ridge, элементы, многолетнемерзлые породы, Waste Management and Disposal, водная миграция, Сибирская платформа, кряжи
Abstract

Актуальность исследования обусловлена получением материалов по неизученным ранее природным водам юго-восточного склона кряжа Чекановского (арктические районы Сибирской платформы). Исследуемый район относится к труднодоступным, со сплошным распространением многолетнемерзлых пород. Цель: выявить геохимические особенности природных вод юго-восточного склона кряжа Чекановского. Методы. Полевое опробование проведено в соответствии с общепринятыми методиками. Химико-аналитические исследования выполнены методами титриметрии, ионной хроматографии и масс-спектрометрии с индуктивно связанной плазмой. Анализ изотопных отношений [sigma]D, [sigma]18O, [sigma]13С проводился на приборе Isotope Ratio Mass Spectrometer FinniganTM MAT 253, снабженном приставками пробоподготовки H/Device (для анализа отношений [sigma]D) и GasBench II (для анализа отношений [sigma]18O и [sigma]13СDIC). При анализе гидрогеохимической информации использовались коэффициенты: геохимические (Ca/Na, Ca/Mg, Ca/Si, Mg/Si, Na/Si, Si/Na, rNa/rCl и SO4/Cl), концентрации и водной миграции по А. И. Перельману. Результаты. Представлены первые результаты изотопно-геохимических исследований природных вод юго-восточного склона кряжа Чекановского, расположенного в низовьях реки Лены, в арктических районах Сибирской платформы. Изучены реки и временные водотоки, образующиеся в период таяния многолетнемерзлых пород. Установлено, что воды ультрапресные с величиной общей минерализации от 63 до 100 мг/дм3, по показателю pH (6,9-7,9) нейтральные и слабощелочные. Характеризуются показателем химического потребления кислорода от 1,6 до 9,7 мгО/дм3. Речные воды имеют преимущественно гидрокарбонатный кальциевый состав. Временные водотоки отличаются преобладанием сульфат-иона, а также низкими значениями ХПК от 1,6 до 3,1 мгO/дм3. Рассчитанные коэффициенты водной миграции распределились следующим образом: очень сильная интенсивность миграции I, Se, Br; сильная Sr, B, Sb; средняя As, P, Ni, Cu, Li, Ba, Zn, U, Sn, Mo; слабая (инертная) Sc, Y, Be, Mn, Pb, Si, Ge, Cr, Rb, Co, V, Fe, Ga, Th, Al, Zr, Ti. Изотопные отношения кислорода и водорода изучаемых вод варьируют в широком диапазоне для [sigma]18O: от -24,2 до -19,5 ‰, и для [sigma]D - от -183,0 до -149,3 ‰. По изотопному составу воды имеют метеорное происхождение. Наблюдается смещение акцента питания вод от зимнего к летнему для рек, в то время как для временных водотоков в большей степени проявляются зимние (снеговые) источники. Изотопные отношения [sigma]13CDIC варьируют от -9,7 до -7,2 ‰. В речных водах наблюдаются как положительные (до -7,2 ‰), так и отрицательные (до -9,7 ‰) отклонения [sigma]13CDIC относительно проб, отобранных из временных водотоков. Для них характерны значения от -8,0 до -7,7 ‰. Можно предположить, что обогащение углекислотой и изотопом 13CDIC происходит, в первую очередь, за счет карбонатных пород и углекислоты, образованной в ходе вегетации растений типа C4.The relevance of the study is caused by the obtaining of the previously unexplored isotope-hydrogeochemical data on the natural waters of the south-east slope of the Chekanovsky ridge (Arctic regions of the Siberian Platform). The study area is difficult due to the access continuous distribution of permafrost. The aim of the research is to identify the geochemical features of the natural waters of the south-east slope of the Chekanovsky ridge. Methods. Field sampling was carried out in accordance with generally accepted methods. Chemical analytical studies were performed by titrimetry, ion chromatography and inductively coupled plasma mass spectrometry. The analysis of the isotope ratios ([sigma]D, [sigma]18O, and [sigma]13СDIC) was carried out on an Isotope Ratio Mass Spectrometer FinniganTM MAT 253 equipped with H/Device (for analyzing [sigma]D ratios) and GasBench II (for analyzing [sigma]18O and [sigma]13СDIC ratios) sample preparation attachments. In the study of hydrogeochemical data, we used geochemical coefficients (Ca/Na, Ca/Mg, Ca/Si, Mg/Si, Na/Si, Si/Na, rNa/rCl and SO4/Cl), coefficients of concentration and water migration according to A. I. Perelman. Results. The paper presents the first results of isotope-geochemical studies of the natural waters of the south-east slope of the Chekanovsky ridge, located in the downstream of the Lena river, in the Arctic regions of the Siberian Platform. The rivers and temporary streams formed during the period of thawing of permafrost have been studied. It was established that the waters are ultra-fresh with a total salinity of 63 to 100 mg/dm3, neutral and slightly alkaline in terms of pH (6,9-7,9), characterized by chemical oxygen demand (COD) from 1,6 to 9,7 mgO/dm3. River waters have a predominantly bicarbonate calcium composition. Temporary streams are characterized by the predominance of sulfate ion, as well as low COD values - from 1,6 to 3,1 mgO/dm3. The calculated coefficients of water migration were distributed as follows: very high intensity of migration of I, Se, Br; high Sr, B, Sb; average As, P, Ni, Cu, Li, Ba, Zn, U, Sn, Mo; low Sc, Y, Be, Mn, Pb, Si, Ge, Cr, Rb, Co, V, Fe, Ga, Th, Al, Zr, Ti. The isotopic ratios of oxygen and hydrogen were studied in a wide range for [sigma]18O - from -24,2 to -19,5 ‰, and for [sigma]D - from -183,0 to -149,3 ‰. According to the isotopic composition the waters has a meteor origin. A shift in the water supply from winter to summer is observed for rivers, while winter (snow) sources are more pronounced for temporary streams. The [sigma]13CDIC isotopic ratios range from -9,7 to -7,2 ‰. In river waters, both positive (up to -7,2 ‰) and negative (up to -9,7 ‰) deviations of [sigma]13C relative to samples taken from temporary streams (characterized by values from -8,0 to -7 ‰), are observed. It supposed enrichment of water with carbon dioxide and heavy isotope 13C firstly due to material and isotopic exchange with the carbonate rocks weathered by soil CO2 formed from plants of type C4.

Published
2020

16. An Anti–CD22-seco-CBI-Dimer Antibody–Drug Conjugate (ADC) for the Treatment of Non-Hodgkin Lymphoma That Provides a Longer Duration of Response than Auristatin-Based ADCs in Preclinical Models

Author

Yu, Shang-Fan, primary, Lee, Donna W., additional, Zheng, Bing, additional, del Rosario, Geoffrey, additional, Leipold, Douglas, additional, Booler, Helen, additional, Zhong, Fiona, additional, Carrasco-Triguero, Montserrat, additional, Hong, Kyu, additional, Yan, Peter, additional, Rowntree, Rebecca K., additional, Schutten, Melissa M., additional, Pillow, Thomas, additional, Sadowsky, Jack D., additional, Dragovich, Peter S., additional, and Polson, Andrew G., additional

Published
2021
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17. Yasco Horsman. Theaters of Justice: Judging, Staging, and Working Through in Arendt, Brecht, and Delbo

Author

Yan, Peter

Subjects
Literature/writing
Abstract

Review of Yasco Horsman. Theaters of Justice: Judging, Staging, and Working Through in Arendt, Brecht, and Delbo. Stanford UP, 2010. 232 pp. Keywords theater, Hannah Arendt, Charlotte Delbo, Bertolt Brecht, Yasco Horsman. Theaters of Justice: Judging, Staging, and Working Through in Arendt, Brecht, and Delbo. Stanford UP, 2010. 232 pp. This volume investigates how the theatrical structure of legal trials [...]

Published
2014
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18. Optimal Dataflow Scheduling on a Heterogeneous Multiprocessor With Reduced Response Time Bounds

Author

Dong, Zheng, Liu, Cong, Gatherer, Alan, McFearin, Lee, Yan, Peter, Anderson, James H., Dong, Zheng, Liu, Cong, Gatherer, Alan, McFearin, Lee, Yan, Peter, and Anderson, James H.

Abstract

Heterogeneous computing platforms with multiple types of computing resources have been widely used in many industrial systems to process dataflow tasks with pre-defined affinity of tasks to subgroups of resources. For many dataflow workloads with soft real-time requirements, guaranteeing fast and bounded response times is often the objective. This paper presents a new set of analysis techniques showing that a classical real-time scheduler, namely earliest-deadline first (EDF), is able to support dataflow tasks scheduled on such heterogeneous platforms with provably bounded response times while incurring no resource capacity loss, thus proving EDF to be an optimal solution for this scheduling problem. Experiments using synthetic workloads with widely varied parameters also demonstrate that the magnitude of the response time bounds yielded under the proposed analysis is reasonably small under all scenarios. Compared to the state-of-the-art soft real-time analysis techniques, our test yields a 68% reduction on response time bounds on average. This work demonstrates the potential of applying EDF into practical industrial systems containing dataflow-based workloads that desire guaranteed bounded response times.

Published
2017
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19. Optimal Dataflow Scheduling on a Heterogeneous Multiprocessor With Reduced Response Time Bounds

Author

Zheng Dong and Cong Liu and Alan Gatherer and Lee McFearin and Peter Yan and James H. Anderson, Dong, Zheng, Liu, Cong, Gatherer, Alan, McFearin, Lee, Yan, Peter, Anderson, James H., Zheng Dong and Cong Liu and Alan Gatherer and Lee McFearin and Peter Yan and James H. Anderson, Dong, Zheng, Liu, Cong, Gatherer, Alan, McFearin, Lee, Yan, Peter, and Anderson, James H.

Abstract

Heterogeneous computing platforms with multiple types of computing resources have been widely used in many industrial systems to process dataflow tasks with pre-defined affinity of tasks to subgroups of resources. For many dataflow workloads with soft real-time requirements, guaranteeing fast and bounded response times is often the objective. This paper presents a new set of analysis techniques showing that a classical real-time scheduler, namely earliest-deadline first (EDF), is able to support dataflow tasks scheduled on such heterogeneous platforms with provably bounded response times while incurring no resource capacity loss, thus proving EDF to be an optimal solution for this scheduling problem. Experiments using synthetic workloads with widely varied parameters also demonstrate that the magnitude of the response time bounds yielded under the proposed analysis is reasonably small under all scenarios. Compared to the state-of-the-art soft real-time analysis techniques, our test yields a 68% reduction on response time bounds on average. This work demonstrates the potential of applying EDF into practical industrial systems containing dataflow-based workloads that desire guaranteed bounded response times.

Published
2017
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22. Greasing bearings

Author

Yan, Peter

Subjects
Bearings (Machinery) -- Maintenance and repair, Business, Engineering and manufacturing industries
Abstract

Problem: Hand packing ball or roller bearings is a messy job. And what happens if you don't have an expensive bearing packer? Is there a cheap, easy way to do [...]

Published
2001

23. Botched but not forgotten

Author

Yan, Peter

Subjects
Stauffenberg, a Family History, 1905-1944 (Book) -- Book reviews, Books -- Book reviews, Literature/writing
Published
2005

25. Reply

Author

Williams, Bryan, primary, Lacy, Peter, additional, Yan, Peter, additional, Chua, Ngak Hwee, additional, Liang, Chen, additional, and Ting, Choon Meng, additional

Published
2011
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27. Children's Books

Author

Yan, Peter

Subjects
The Report Card (Book) -- Book reviews, Books -- Book reviews, Literature/writing
Published
2005

28. A tame, tame west

Author

Yan, Peter

Subjects
Lightning (Book) -- Book reviews, Books -- Book reviews, Literature/writing
Published
2004

29. The Report Card.

Author

Yan, Peter

Abstract

Reviews the book "The Report Card," by Andrew Clements.

Published
2005

30. Structural Alphabet: From a Local Point of View to a Global Description of Protein 3D Structures

Author

de Brevern, Alexandre, Benros, Cristina, Hazout, Serge, de Brevern, Alexandre G., and Yan, Peter V

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology
Abstract

The study of protein structures' local conformations has a long history principally based on the analysis of the classical repetitive structures (i.e. alpha-helix and beta-sheet), and also on the characterization of some particular structures in the coil state (e.g. turns). The secondary structures are interesting for describing the global protein fold but miss all the orientations of the connecting regions and so neglect many particularities of the coil state. In order to take these structural features into account, we have identified a local structural alphabet composed of 16 folding patterns of five consecutive residues, called Protein Blocks (PBs). Conversely to the secondary structures, the PBs are able to approximate every part of the protein structures. These PBs have been used both to describe precisely the 3D protein backbones with an average rmsd of 0.42 A, and to perform a local structure prediction with a rate of correct prediction of 48.7%. In this chapter, we present the interest of the Protein Blocks by comparing the secondary structure assignment with the assignment in terms of PBs. We highlight the discrepancies between different secondary structure assignment methods and show some interesting correspondence between particular local folds and the Protein Blocks. Then, we use the Protein Block prediction to classify proteins into the classical structural classes, namely all , all and mixed. The prediction rate of theses different classes is good, i.e. 71.5%, with no confusion between all and all classes. Finally, we present a new approach named TopKAPi that stands for "Triangular Kohonen Map for Analyzing Proteins". It enables to classify and analyze proteins according to their Protein Block frequencies using for this purpose a novel unsupervised clustering method: a triangular self-organizing Kohonen map. This method enables to determine new relationships between local structures and amino acid distributions. This new methodology could be of great interest in proteomics and sequence alignment.

Published
2005

31. Guiding Principles for a Pediatric Neurology ICU (neuroPICU) Bedside Multimodal Monitor: Findings from an International Working Group.

Author

Grinspan ZM, Eldar YC, Gopher D, Gottlieb A, Lammfromm R, Mangat HS, Peleg N, Pon S, Rozenberg I, Schiff ND, Stark DE, Yan P, Pratt H, and Kosofsky BE

Subjects
Child, Electroencephalography, Humans, Needs Assessment, Patient Care Team, Signal Processing, Computer-Assisted, Surveys and Questionnaires, Intensive Care Units, Pediatric, Internationality, Neurology methods
Abstract

Background: Physicians caring for children with serious acute neurologic disease must process overwhelming amounts of physiological and medical information. Strategies to optimize real time display of this information are understudied., Objectives: Our goal was to engage clinical and engineering experts to develop guiding principles for creating a pediatric neurology intensive care unit (neuroPICU) monitor that integrates and displays data from multiple sources in an intuitive and informative manner., Methods: To accomplish this goal, an international group of physicians and engineers communicated regularly for one year. We integrated findings from clinical observations, interviews, a survey, signal processing, and visualization exercises to develop a concept for a neuroPICU display., Results: Key conclusions from our efforts include: (1) A neuroPICU display should support (a) rapid review of retrospective time series (i.e. cardiac, pulmonary, and neurologic physiology data), (b) rapidly modifiable formats for viewing that data according to the specialty of the reviewer, and (c) communication of the degree of risk of clinical decline. (2) Specialized visualizations of physiologic parameters can highlight abnormalities in multivariable temporal data. Examples include 3-D stacked spider plots and color coded time series plots. (3) Visual summaries of EEG with spectral tools (i.e. hemispheric asymmetry and median power) can highlight seizures via patient-specific "fingerprints." (4) Intuitive displays should emphasize subsets of physiology and processed EEG data to provide a rapid gestalt of the current status and medical stability of a patient., Conclusions: A well-designed neuroPICU display must present multiple datasets in dynamic, flexible, and informative views to accommodate clinicians from multiple disciplines in a variety of clinical scenarios.

Published
2016
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