Ecology of Juvenile Walleye Pollock, Theragra chalcogramma: Papers from the workshop "The Importance of Prerecruit Walleye Pollock to the Bering Sea and North Pacific Ecosystems" Seattle, Washington, 28-30 October 1993

The Alaska Fisheries Science Center (AFSC), National Marine Fisheries Service (NMFS), hosted an international workshop, 'The Importance of Prerecruit Walleye Pollock to the Bering Sea and North Pacific Ecosystems," from 28 to 30 October 1993. This workshop was held in conjunction with the annual International North Pacific Marine Science Organization (PICES) meeting held in Seattle. Nearly 100 representatives from government agencies, universities, and the fishing industry in Canada, Japan, the People's Republic of China, Russia, and the United States took part in the workshop to review and discuss current knowledge on juvenile pollock from the postlarval period to the time they recruit to the fisheries. In addition to its importance to humans as a major commercial species, pollock also serves as a major forage species for many marine fishes, birds, and mammals in the North Pacific region. (PDF file contains 236 pages.

Effect of Phosphorus Amendments on Present Day Plankton Communities in Pelagic Lake Erie

To address questions regarding the potential impact of elevated total phosphorus (TP) inputs (due to relaxed regulations of TP loading), a series of TP enrichment experiments were conducted at pelagic stations in the 3 hydrologically distinct basins of Lake Erie. Results of nutrient assimilation measurements and assays for nutrient bioavailability suggest that the chemical speciation, and not concentration, of nitrogenous compounds may influence phytoplankton community structure; this in turn may lead to the selective proliferation of cyanobacteria in the eastern basin of the lake. Assays with cyanobacterial bioluminescent reporter systems for P and N availability as well as N-tot:P-tot assimilation ratios from on-deck incubation experiments support this work. Considered in the context of a microbial food web relative to a grazing food web, the results imply that alterations in current TP loading controls may lead to alterations in the phytoplankton community structure in the different basins of the Lake Erie system

Clear-Column Radiative Closure During ACE-Asia: Comparison of Multiwavelength Extinction Derived from Particle Size and Composition with Results from Sun Photometry

From March to May 2001, aerosol size distributions and chemical compositions were measured using differential mobility analyzers (DMA), an aerodynamic particle sizer (APS), Micro-Orifice Uniform Deposit Impactors (MOUDI), and denuder samplers onboard the Twin Otter aircraft as part of the Aerosol Characterization Experiment (ACE)-Asia campaign. Of the 19 research flights, measurements on four flights that represented different aerosol characteristics are analyzed in detail. Clear-column radiative closure is studied by comparing aerosol extinctions predicted using in situ aerosol size distribution and chemical composition measurements to those derived from the 14-wavelength NASA Ames Airborne Tracking Sun photometer (AATS-14). In the boundary layer, pollution layers, and free troposphere with no significant mineral dust present, aerosol extinction closure was achieved within the estimated uncertainties over the full range of wavelengths of AATS-14. Aerosol extinctions predicted based on measured size distributions also reproduce the wavelength dependence derived from AATS-14 data. Considering all four flights, the best fit lines yield Predicted/Observed ratios in boundary and pollution layers of 0.97 ± 0.24 and 1.07 ± 0.08 at λ = 525 nm and 0.96 ± 0.21 and 1.08 ± 0.08 at λ = 1059 nm, respectively. In free troposphere dust layers, aerosol extinctions predicted from the measured size distributions were generally smaller than those derived from the AATS-14 data, with Predicted/Observed ratios of 0.65 ± 0.06 and 0.66 ± 0.05 at 525 and 1059 nm, respectively. A detailed analysis suggests that the discrepancy is likely a result of the lack of the knowledge of mineral dust shape as well as variations in aerosol extinction derived from AATS-14 data when viewing through horizontally inhomogeneous layers

Dissociation Protocols Used for Sarcoma Tissues Bias the Transcriptome Observed in Single-Cell and Single-Nucleus RNA Sequencing

BACKGROUND: Single-cell RNA-seq has emerged as an innovative technology used to study complex tissues and characterize cell types, states, and lineages at a single-cell level. Classification of bulk tumors by their individual cellular constituents has also created new opportunities to generate single-cell atlases for many organs, cancers, and developmental models. Despite the tremendous promise of this technology, recent evidence studying epithelial tissues and diverse carcinomas suggests the methods used for tissue processing, cell disaggregation, and preservation can significantly bias gene expression and alter the observed cell types. To determine whether sarcomas - tumors of mesenchymal origin - are subject to the same technical artifacts, we profiled patient-derived tumor explants (PDXs) propagated from three aggressive subtypes: osteosarcoma (OS), Ewing sarcoma (ES), desmoplastic small round cell tumor (DSRCT). Given the rarity of these sarcoma subtypes, we explored whether single-nuclei RNA-seq from more widely available archival frozen specimens could accurately be identified by gene expression signatures linked to tissue phenotype or pathognomonic fusion proteins. RESULTS: We systematically assessed dissociation methods across different sarcoma subtypes. We compared gene expression from single-cell and single-nucleus RNA-sequencing of 125,831 whole-cells and nuclei from ES, DSRCT, and OS PDXs. We detected warm dissociation artifacts in single-cell samples and gene length bias in single-nucleus samples. Classic sarcoma gene signatures were observed regardless of the dissociation method. In addition, we showed that dissociation method biases could be computationally corrected. CONCLUSIONS: We highlighted transcriptional biases, including warm dissociation and gene-length biases, introduced by the dissociation method for various sarcoma subtypes. This work is the first to characterize how the dissociation methods used for sc/snRNA-seq may affect the interpretation of the molecular features in sarcoma PDXs

Clear-sky closure studies of lower tropospheric aerosol and water vapor during ACE-2 using airborne sunphotometer, airborne in-situ, space-borne, and ground-based measurements

We report on clear-sky column closure experiments (CLEARCOLUMN) performed in the Canary Islands during the second Aerosol Characterization Experiment (ACE-2) in June/July 1997. We present CLEARCOLUMN results obtained by combining airborne sunphotometer and in-situ (optical particle counter, nephelometer, and absorption photometer) measurements taken aboard the Pelican aircraft, space-borne NOAA/AVHRR data and ground-based lidar and sunphotometer measurements. During both days discussed here, vertical profiles flown in cloud-free air masses revealed 3 distinctly different layers: a marine boundary layer (MBL) with varying pollution levels, an elevated dust layer, and a very clean layer between the MBL and the dust layer. A key result of this study is the achievement of closure between extinction or layer aerosol optical depth (AOD) computed from continuous in-situ aerosol size-distributions and composition and those measured with the airborne sunphotometer. In the dust, the agreement in layer AOD (λ=380–1060 nm) is 3–8%. In the MBL there is a tendency for the in-situ results to be slightly lower than the sunphotometer measurements (10–17% at λ=525 nm), but these differences are within the combined error bars of the measurements and computations

Use of Medicare claims to rank hospitals by surgical site infection risk following coronary artery bypass graft surgery

ObjectiveTo evaluate whether longitudinal insurer claims data allow reliable identification of elevated hospital surgical site infection (SSI) rates.DesignWe conducted a retrospective cohort study of Medicare beneficiaries who underwent coronary artery bypass grafting (CABG) in US hospitals performing at least 80 procedures in 2005. Hospitals were assigned to deciles by using case mix-adjusted probabilities of having an SSI-related inpatient or outpatient claim code within 60 days of surgery. We then reviewed medical records of randomly selected patients to assess whether chart-confirmed SSI risk was higher in hospitals in the worst deciles compared with the best deciles.ParticipantsFee-for-service Medicare beneficiaries who underwent CABG in these hospitals in 2005.ResultsWe evaluated 114,673 patients who underwent CABG in 671 hospitals. In the best decile, 7.8% (958/12,307) of patients had an SSI-related code, compared with 24.8% (2,747/11,068) in the worst decile ([Formula: see text]). Medical record review confirmed SSI in 40% (388/980) of those with SSI-related codes. In the best decile, the chart-confirmed annual SSI rate was 3.2%, compared with 9.4% in the worst decile, with an adjusted odds ratio of SSI of 2.7 (confidence interval, 2.2-3.3; [Formula: see text]) for CABG performed in a worst-decile hospital compared with a best-decile hospital.ConclusionsClaims data can identify groups of hospitals with unusually high or low post-CABG SSI rates. Assessment of claims is more reproducible and efficient than current surveillance methods. This example of secondary use of routinely recorded electronic health information to assess quality of care can identify hospitals that may benefit from prevention programs

Bi-allelic JAM2 Variants Lead to Early-Onset Recessive Primary Familial Brain Calcification.

Primary familial brain calcification (PFBC) is a rare neurodegenerative disorder characterized by a combination of neurological, psychiatric, and cognitive decline associated with calcium deposition on brain imaging. To date, mutations in five genes have been linked to PFBC. However, more than 50% of individuals affected by PFBC have no molecular diagnosis. We report four unrelated families presenting with initial learning difficulties and seizures and later psychiatric symptoms, cerebellar ataxia, extrapyramidal signs, and extensive calcifications on brain imaging. Through a combination of homozygosity mapping and exome sequencing, we mapped this phenotype to chromosome 21q21.3 and identified bi-allelic variants in JAM2. JAM2 encodes for the junctional-adhesion-molecule-2, a key tight-junction protein in blood-brain-barrier permeability. We show that JAM2 variants lead to reduction of JAM2 mRNA expression and absence of JAM2 protein in patient's fibroblasts, consistent with a loss-of-function mechanism. We show that the human phenotype is replicated in the jam2 complete knockout mouse (jam2 KO). Furthermore, neuropathology of jam2 KO mouse showed prominent vacuolation in the cerebral cortex, thalamus, and cerebellum and particularly widespread vacuolation in the midbrain with reactive astrogliosis and neuronal density reduction. The regions of the human brain affected on neuroimaging are similar to the affected brain areas in the myorg PFBC null mouse. Along with JAM3 and OCLN, JAM2 is the third tight-junction gene in which bi-allelic variants are associated with brain calcification, suggesting that defective cell-to-cell adhesion and dysfunction of the movement of solutes through the paracellular spaces in the neurovascular unit is a key mechanism in CNS calcification

Applying refinement to the use of mice and rats in rheumatoid arthritis research

Rheumatoid arthritis (RA) is a painful, chronic disorder and there is currently an unmet need for effective therapies that will benefit a wide range of patients. The research and development process for therapies and treatments currently involves in vivo studies, which have the potential to cause discomfort, pain or distress. This Working Group report focuses on identifying causes of suffering within commonly used mouse and rat ‘models’ of RA, describing practical refinements to help reduce suffering and improve welfare without compromising the scientific objectives. The report also discusses other, relevant topics including identifying and minimising sources of variation within in vivo RA studies, the potential to provide pain relief including analgesia, welfare assessment, humane endpoints, reporting standards and the potential to replace animals in RA research

Cerebral hypomyelination associated with biallelic variants of FIG4

The lipid phosphatase gene FIG4 is responsible for Yunisâ Varón syndrome and Charcotâ Marieâ Tooth disease Type 4J, a peripheral neuropathy. We now describe four families with FIG4 variants and prominent abnormalities of central nervous system (CNS) white matter (leukoencephalopathy), with onset in early childhood, ranging from severe hypomyelination to mild undermyelination, in addition to peripheral neuropathy. Affected individuals inherited biallelic FIG4 variants from heterozygous parents. Cultured fibroblasts exhibit enlarged vacuoles characteristic of FIG4 dysfunction. Two unrelated families segregate the same Gâ >â A variant in the +1 position of intron 21 in the homozygous state in one family and compound heterozygous in the other. This mutation in the splice donor site of exon 21 results in readâ through from exon 20 into intron 20 and truncation of the final 115 Câ terminal amino acids of FIG4, with retention of partial function. The observed CNS white matter disorder in these families is consistent with the myelination defects in the FIG4 null mouse and the known role of FIG4 in oligodendrocyte maturation. The families described here the expanded clinical spectrum of FIG4 deficiency to include leukoencephalopathy.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/149294/1/humu23720-sup-0001-Supp_Mat_Lenk_2018.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149294/2/humu23720.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/149294/3/humu23720_am.pd