Distance maps to estimate cell volume from two-dimensional plankton images

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2012. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography: Methods 10 (2012): 278-288, doi:10.4319/lom.2012.10.278.We describe and evaluate an algorithm that uses a distance map to automatically calculate the biovolume of a planktonic organism from its two-dimensional boundary. Compared with existing approaches, this algorithm dramatically increases the speed and accuracy of biomass estimates from plankton images, and is thus especially suited for use with automated cell imaging technologies that produce large quantities of data. The algorithm operates on a two-dimensional image processed to identify organism boundaries. First, the distance of each interior pixel to the nearest boundary is calculated; next these same distances are assumed to apply for projection in the third dimension; and finally the resulting volume is adjusted by a multiplicative factor assuming locally circular cross-sections in the third dimension. Other cross-sectional shape factors can be applied as needed. In this way, the simple, computationally efficient, volume calculation can be refined to include taxon-specific shape information if available. We show that compared to traditional manual microscopic analysis, the distance map algorithm is unbiased and accurate (mean difference = -0.25%, standard deviation = 17%) for a range of cell morphologies, including those with concave boundaries that deviate from simple geometric shapes and whose volumes are not well represented by a solid of revolution around a single axis. Automated calculation of cell volumes can now be implemented with a combination of this new distance map algorithm for complex shapes and the solid of revolution approach for simple shapes, with an automated decision criterion to choose the appropriate approach for each image.This research was supported by grants (to HMS) from the Gordon and Betty Moore Foundation and NASA’s Ocean Biology and Biogeochemistry program, and a Woods Hole Oceanographic Institution Summer Student Fellow award (to EAM)

Identification of senescence and death in Emiliania huxleyi and Thalassiosira pseudonana: Cell staining, chlorophyll alterations, and dimethylsulfoniopropionate (DMSP) metabolism

We measured membrane permeability, hydrolytic enzyme, and caspase-like activities using fluorescent cell stains to document changes caused by nutrient exhaustion in the coccolithophore Emiliania huxleyi and the diatom Thalassiosira pseudonana, during batch-culture nutrient limitation. We related these changes to cell death, pigment alteration, and concentrations of dimethylsulfide (DMS) and dimethylsulfoniopropionate (DMSP) to assess the transformation of these compounds as cell physiological condition changes. E. huxleyi persisted for 1 month in stationary phase; in contrast, T. pseudonana cells rapidly declined within 10 d of nutrient depletion. T. pseudonana progressively lost membrane integrity and the ability to metabolize 5-chloromethylfluorescein diacetate (CMFDA; hydrolytic activity), whereas E. huxleyi developed two distinct CMFDA populations and retained membrane integrity (SYTOX Green). Caspase-like activity appeared higher in E. huxleyi than in T. pseudonana during the post-growth phase, despite a lack of apparent mortality and cell lysis. Photosynthetic pigment degradation and transformation occurred in both species after growth; chlorophyll a (Chl a) degradation was characterized by an increase in the ratio of methoxy Chl a : Chl a in T. pseudonana but not in E. huxleyi, and the increase in this ratio preceded loss of membrane integrity. Total DMSP declined in T. pseudonana during cell death and DMS increased. In contrast, and in the absence of cell death, total DMSP and DMS increased in E. huxleyi. Our data show a novel chlorophyll alteration product associated with T. pseudonana death, suggesting a promising approach to discriminate nonviable cells in nature

Candidatus Bartonella merieuxii, a potential new zoonotic Bartonella species in canids from Iraq.

Bartonellae are emerging vector-borne pathogens infecting erythrocytes and endothelial cells of various domestic and wild mammals. Blood samples were collected from domestic and wild canids in Iraq under the United States Army zoonotic disease surveillance program. Serology was performed using an indirect immunofluorescent antibody test for B. henselae, B. clarridgeiae, B. vinsonii subsp. berkhoffii and B. bovis. Overall seroprevalence was 47.4% in dogs (n = 97), 40.4% in jackals (n = 57) and 12.8% in red foxes (n = 39). Bartonella species DNA was amplified from whole blood and representative strains were sequenced. DNA of a new Bartonella species similar to but distinct from B. bovis, was amplified from 37.1% of the dogs and 12.3% of the jackals. B. vinsonii subsp. berkhoffii was also amplified from one jackal and no Bartonella DNA was amplified from foxes. Adjusting for age, the odds of dogs being Bartonella PCR positive were 11.94 times higher than for wild canids (95% CI: 4.55-31.35), suggesting their role as reservoir for this new Bartonella species. This study reports on the prevalence of Bartonella species in domestic and wild canids of Iraq and provides the first detection of Bartonella in jackals. We propose Candidatus Bartonella merieuxii for this new Bartonella species. Most of the Bartonella species identified in sick dogs are also pathogenic for humans. Therefore, seroprevalence in Iraqi dog owners and bacteremia in Iraqi people with unexplained fever or culture negative endocarditis requires further investigation as well as in United States military personnel who were stationed in Iraq. Finally, it will also be essential to test any dog brought back from Iraq to the USA for presence of Bartonella bacteremia to prevent any accidental introduction of a new Bartonella species to the New World

Use of alternative energy sources to improve the efficiency of natural gas hydrate technology for gas offshore deposits transportation

Purpose. Justification of the principal schemes acceptable for the existing level of technology, methods of extraction and transportation of offshore natural gas deposits. Increase in their efficiency by maximum reduction of energy consumption resulting from complex considerations of thermal and physical properties and parameters of the system components interaction. The work is focused on the improvement of borehole products preparation system according to the gas hydrate technology during the development of offshore gas fields. The research objects were thermodynamic parameters of the system “gas – water – gas hydrate” in a vertical pipeline under nonadiabatic conditions. Methods. Analysis and generalization of the results obtained from the complex experimental research. Mathematical modeling and software development. Findings. The technology of gas transfer into a gas hydrate form without energy consumption for phase transition was proposed. The expediency of gas deposits development by its binding into the gas hydrate form during passage through the sea layer in the appropriate thermobaric conditions was substantiated. Mechanism of the alternative energy sources use for the production of gas hydrates, as the most energy-consuming process in technology of transporting gases in the form of gas hydrates, was grounded. Originality. The principle possibility of binding the extracted gas into the gas hydrate form due to the energy of the productive layer and salt water was estimated. A mathematical model and software product for the description of the hydrate formation process in the presence of excess water in a vertical pipe under non-adiabatic conditions were developed. Practical implications. The proposed gas hydrate technology creates important prerequisites for the development of small and medium remote gas deposits, improves the efficiency and competitiveness of technology for marine transportation of natural gas in hydrate form.Мета. Підвищення ефективності технології транспорту газу морських родовищ шляхом максимального зниження енерговитрат на основі дослідження термодинамічних параметрів системи “газ – вода – газовий гідрат” у вертикальному трубопроводі за неадіабатних умов. Методика. В роботі використано комплексний науково-методичний підхід, що включає аналіз літературних та інформаційних джерел, що стосуються енерговитрат при газогідратних технологіях, основні положення термодинаміки, аналітичні та експериментальні дослідження. Експериментальні дослідження проведені на ділянці вертикального трубопроводу, що моделює з’єднання морської газової свердловини із видобувною платформою, в якому рухається видобутий зі свердловини газ. Ділянка трубопровода розглядалась як реактор гідратоутворення, де досліджувались термобаричні умови формування гідрату. Для встановлення формули газогідрату використано метод Форкрана. Для чисельного розв’язання процесу утворення газових гідратів застосовано метод кінцевих різниць, а розрахунок процесу гідратоутворення виконано у середовищі Matlab. Результати. Запропоновано технологію переведення газу у газогідратну форму без витрати енергії на фазовий перехід. Доведено доцільність розробки газових родовищ шляхом зв’язування газу в газогідрат за рахунок наявності необхідних термобаричних умов при його проходженні крізь морську товщу. Обґрунтовано передумови і механізм використання альтернативних джерел низькопотенційної енергії для виробництва газогідрату як найбільш енерговитратного процесу технології транспортування газів у газогідратній формі. Наукова новизна. Надана наукова оцінка принципової можливості зв’язування видобутого газу у газогідратну форму за рахунок енергії продуктивного пласта і низькопотенційної енергії морської води. Розроблено нову математичну модель та алгоритм у програмному продукті для опису процесу гідратоутворення при надлишку води за неадіабатних умов у вертикальній трубі, що омивається водою. Практична значимість. Запропонована газогідратна технологія створює важливі передумови розробки малих та середніх віддалених родовищ газу, підвищення ефективності й конкурентоздатності технології морського транспортування природного газу у газогідратній формі.Цель. Повышение эффективности технологии транспорта газа морских месторождений путем максимального снижения энергозатрат на основе исследования термодинамических параметров системы “газ – вода – газовый гидрат” в вертикальном трубопроводе при неадиабатных условиях. Методика. В работе использован комплексный научно-методический подход, включающий анализ литературных и информационных источников, касающихся энергозатрат при газогидратных технологиях, основные положения термодинамики, аналитические и экспериментальные исследования. Экспериментальные исследования проведены на участке вертикального трубопровода, моделирующего соединение морской газовой скважины с добывающей платформой, в котором движется добытый из скважины газ. Участок трубопровода рассматривался как реактор гидратообразования, где исследовались термобарические условия процесса формирования гидрата. Для получения формулы газогидратов использован метод Форкрана. Для численного решения процесса образования газовых гидратов применен метод конечных элементов, а расчет процесса гидратообразования выполнен в среде Matlab. Результаты. Предложена технология перевода газа в газогидратную форму без затрат энергии на фазовый переход. Доказана целесообразность разработки газовых месторождений путем связывания газа в газогидрат за счет наличия необходимых термобарических условий при его прохождении через морскую толщу. Обоснованно предпосылки и механизм использования альтернативных источников низкопотенциальной энергии для производства газогидратов как наиболее энергозатратного процесса технологии транспортировки газов в газогидратной форме. Научная новизна. Дана научная оценка принципиальной возможности связывания добытого газа в газогидратную форму за счет энергии продуктивного пласта и низкопотенциальной энергии морской воды. Разработана новая математическая модель и алгоритм в программном продукте для описания процесса гидратообразования при избытке воды в неадиабатных условиях в вертикальной трубе, омываемой водой. Практическая значимость. Предложенная газогидратная технология создает важные предпосылки разработки малых и средне удаленных месторождений газа, повышение эффективности и конкурентоспособности технологии морской транспортировки природного газа в газогидратной форме.This work has become possible due to financial and organizational support within the frames of the state budget research project under the auspices of the Ministry of Education and Science of Ukraine “Application of gas hydrate technology in the development of traditionaland gas hydrate gas deposits” No.0113U00857, “Research of influence of thermodynamic parameters of phase transitions in systems with gas hydrates on the efficiency of gas hydrate technology” No.0115U002420

Associations of NINJ2 sequence variants with incident ischemic stroke in the Cohorts for Heart and Aging in Genomic Epidemiology (CHARGE) consortium

Background<p></p> Stroke, the leading neurologic cause of death and disability, has a substantial genetic component. We previously conducted a genome-wide association study (GWAS) in four prospective studies from the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium and demonstrated that sequence variants near the NINJ2 gene are associated with incident ischemic stroke. Here, we sought to fine-map functional variants in the region and evaluate the contribution of rare variants to ischemic stroke risk.<p></p> Methods and Results<p></p> We sequenced 196 kb around NINJ2 on chromosome 12p13 among 3,986 European ancestry participants, including 475 ischemic stroke cases, from the Atherosclerosis Risk in Communities Study, Cardiovascular Health Study, and Framingham Heart Study. Meta-analyses of single-variant tests for 425 common variants (minor allele frequency [MAF] ≥ 1%) confirmed the original GWAS results and identified an independent intronic variant, rs34166160 (MAF = 0.012), most significantly associated with incident ischemic stroke (HR = 1.80, p = 0.0003). Aggregating 278 putatively-functional variants with MAF≤ 1% using count statistics, we observed a nominally statistically significant association, with the burden of rare NINJ2 variants contributing to decreased ischemic stroke incidence (HR = 0.81; p = 0.026).<p></p> Conclusion<p></p> Common and rare variants in the NINJ2 region were nominally associated with incident ischemic stroke among a subset of CHARGE participants. Allelic heterogeneity at this locus, caused by multiple rare, low frequency, and common variants with disparate effects on risk, may explain the difficulties in replicating the original GWAS results. Additional studies that take into account the complex allelic architecture at this locus are needed to confirm these findings

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 355)

This bibliography lists 147 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during October, 1991. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance

Is there an association between leukoaraiosis volume and diabetes?

Objectives: The relation between white matter loss (WML) and diabetes is still debated. The aim of this study was to investigate the correlation between typical WML— and diabetesrelated magnetic resonance imaging (MRI) findings in a cohort of patients scheduled for carotid endarterectomy (CEA). Materials and methods: Ninety-three consecutive patients (mean age 71 ± 9 years; male 71) were included in a single-centre retrospective study. All the patients underwent MRI as baseline evaluation prior to CEA. A neuroradiologist blinded to the presence of risk factors calculated WML volume and number of lesions on FLAIR images using a semi-automated segmentation technique. Receiver operating characteristics analysis was performed to search for any association between WML volume and the number of WML lesions. The Mann—Whitney tests were used to determine significant WML differences between diabetic and non-diabetic patients. Logistic regression analysis was performed to evaluate the potential association of other variables. Results: The prevalence of diabetes was 20.4% (n = 19). WML volume and number of WML lesions were significantly associated with diabetes (P = 0.001). A statistically significant difference in WML volume was found between diabetic and non-diabetic patients (P < 0.0001). Only diabetes, among all the investigated variables (WML volume, CAD status, age, smoking status, gender, hypertension, hyperlipidemia, diabetes) was significantly associated with WML (P = 0.0001)

Layton, Thomas N.

University of California, Davis, B.A. 1965 University of California, Davis, M.A. 1966 Harvard University, Anthropology, Ph.D. 1971https://scholarworks.sjsu.edu/erfa_bios/1276/thumbnail.jp

Prevalence and Antimicrobial Susceptibility of Methicillin-resistant Staphylococcus aureus in Pregnant Women and Their Newborns in Las Vegas, Nevada

Colonization and infection by resistant strains of Staphylococcus aureus are being reported in epidemic proportions. The goal of this study was to determine the local prevalence of methicillin-resistant Staphylococcus aureus (MRSA) colonization in pregnant women in southern Nevada and how it correlates with colonization and infection of their neonates. Signed consent was obtained, and a brief questionnaire was administered by the medical staff to each pregnant woman to collect demographic data and pertinent medical, family and social history. Nasal and vaginal specimens were obtained from pregnant women at ≥35 weeks gestation, and nasal and umbilicus specimens were obtained from their newborns. Specimens were cultured onto two selective media for S. aureus and MRSA. Potential MRSA isolates were further evaluated for susceptibility to antibiotics. Specimens from 307 pregnant women and 174 neonates were collected, resulting in 172 mother-neonate paired specimens. A total of 278 questionnaires were received from study participants. MRSA prevalence in pregnant women was 1.0% and 0.3% for nasal and vaginal specimens, respectively. The MRSA prevalence in neonates was 0% and 0.6% for nasal and umbilical specimens, respectively. Four different antimicrobial susceptibility profiles were observed among the MRSA isolates. The results did not show transmission of MRSA from pregnant women to their newborns, or infections of newborns with MRSA. It is expected that the results of this study will inform future decisions on surveillance, treatment and prevention of MRSA infections in Nevada