MAGIC-DR: An interpretable machine-learning guided approach for acute myeloid leukemia measurable residual disease analysis

Multiparameter flow cytometry is widely used for acute myeloid leukemia minimal residual disease testing (AML MRD) but is time consuming and demands substantial expertise. Machine learning offers potential advancements in accuracy and efficiency, but has yet to be widely adopted for this application. To explore this, we trained single cell XGBoost classifiers from 98 diagnostic AML cell populations and 30 MRD negative samples. Performance was assessed by cross-validation. Predictions were integrated with UMAP as a heatmap parameter for an augmented/interactive AML MRD analysis framework, which was benchmarked against traditional MRD analysis for 25 test cases. The results showed that XGBoost achieved a median AUC of 0.97, effectively distinguishing diverse AML cell populations from normal cells. When integrated with UMAP, the classifiers highlighted MRD populations against the background of normal events. Our pipeline, MAGIC-DR, incorporated classifier predictions and UMAP into flow cytometry standard (FCS) files. This enabled a human-in-the-loop machine learning guided MRD workflow. Validation against conventional analysis for 25 MRD samples showed 100% concordance in myeloid blast detection, with MAGIC-DR also identifying several immature monocytic populations not readily found by conventional analysis. In conclusion, Integrating a supervised classifier with unsupervised dimension reduction offers a robust method for AML MRD analysis that can be seamlessly integrated into conventional workflows. Our approach can support and augment human analysis by highlighting abnormal populations that can be gated on for quantification and further assessment. This has the potential to speed up MRD analysis, and potentially improve detection sensitivity for certain AML immunophenotypes.

Data File Standard for Flow Cytometry, Version FCS 3.2

FCS 3.2 is a revision of the flow cytometry data standard based on a decade of suggested improvements from the community as well as industry needs to capture instrument conditions and measurement features more precisely. The unchanged goal of the standard is to provide a uniform file format that allows files created by one type of acquisition hardware and software to be analyzed by any other type. The standard retains the overall FCS file structure and most features of previous versions, but also contains a few changes that were required to support new types of data and use cases efficiently. These changes are incompatible with existing FCS file readers. Notably, FCS 3.2 supports mixed data types to, for example, allow FCS measurements that are intrinsically integers (e.g., indices or class assignments) or measurements that are commonly captured as integers (e.g., time ticks) to be more represented as integer values, while capturing other measurements as floating-point values in the same FCS data set. In addition, keywords explicitly specifying dyes, detectors, and analytes were added to avoid having to extract those heuristically and unreliably from measurement names. Types of measurements were formalized, several keywords added, others removed, or deprecated, and various aspects of the specification were clarified. A reference implementation of the cyclic redundancy check (CRC) calculation is provided in two programming languages since a correct CRC implementation was problematic for many vendors. © 2020 International Society for Advancement of Cytometry.

ISAC Probe Tag Dictionary: Standardized Nomenclature for Detection and Visualization Labels Used in Cytometry and Microscopy Imaging

Since the advent of microscopy imaging and flow cytometry, there has been an explosion in the number of probes, consisting of a component binding to an analyte and a detectable tag, to mark areas of interest in or on cells and tissue. Probe tags have been created to detect and/or visualize probes. Over time, these probe tags have increased in number. The expansion has resulted in arbitrarily created synonyms of probe tags used in publications and software. The synonyms are problematic for readability of publications, accuracy of text/data mining, and bridging data from multiple platforms, protocols, and databases for Big Data analysis. Development and implementation of a universal language for probe tags will ensure equivalent quality and level of data being reported or extracted for clinical/scientific evaluation as well as help connect data from many platforms. The International Society for Advancement of Cytometry Data Standards Task Force composed of academic scientists and industry hardware/software/reagent manufactures have developed recommendations for a standardized nomenclature for probe tags used in cytometry and microscopy imaging. These recommendations are shared in this technical note in the form of a Probe Tag Dictionary. © 2020 International Society for Advancement of Cytometry.

High-throughput phenotyping reveals expansive genetic and structural underpinnings of immune variation

By developing a high-density murine immunophenotyping platform compatible with high-throughput genetic screening, we have established profound contributions of genetics and structure to immune variation (http://www.immunophenotype.org). Specifically, high-throughput phenotyping of 530 unique mouse gene knockouts identified 140 monogenic 'hits', of which most had no previous immunologic association. Furthermore, hits were collectively enriched in genes for which humans show poor tolerance to loss of function. The immunophenotyping platform also exposed dense correlation networks linking immune parameters with each other and with specific physiologic traits. Such linkages limit freedom of movement for individual immune parameters, thereby imposing genetically regulated 'immunologic structures', the integrity of which was associated with immunocompetence. Hence, we provide an expanded genetic resource and structural perspective for understanding and monitoring immune variation in health and disease.

The Ontology for Biomedical Investigations

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.

A randomized controlled trial on the effects of goal-directed therapy on the inflammatory response open abdominal aortic aneurysm repair

Introduction

Goal-directed therapy (GDT) has been shown in numerous studies to decrease perioperative morbidity and mortality. The mechanism of benefit of GDT, however, has not been clearly elucidated. Targeted resuscitation of the vascular endothelium with GDT might alter the postoperative inflammatory response and be responsible for the decreased complications with this therapy.

Methods

This trial was registered at ClinicalTrials.gov as NCT01681251. Forty patients undergoing elective open repair of their abdominal aortic aneurysm, 18 years of age and older, were randomized to an interventional arm with GDT targeting stroke volume variation with an arterial pulse contour cardiac output monitor, or control, where fluid therapy was administered at the discretion of the attending anesthesiologist. We measured levels of several inflammatory cytokines (C-reactive protein, Pentraxin 3, suppressor of tumorgenicity--2, interleukin-1 receptor antagonist, and tumor necrosis factor receptor-III) preoperatively and at several postoperative time points to determine if there was a difference in inflammatory response. We also assessed each group for a composite of postoperative complications.

Results

Twenty patients were randomized to GDT and twenty were randomized to control. Length of stay was not different between groups. Intervention patients received less crystalloid and more colloid. At the end of the study, intervention patients had a higher cardiac index (3.4 ± 0.5 vs. 2.5 ± 0.7 l/minute per m², p < 0.01) and stroke volume index (50.1 ± 7.4 vs. 38.1 ± 9.8 ml/m², p < 0.01) than controls. There were significantly fewer complications in the intervention than control group (28 vs. 12, p = 0.02). The length of hospital and ICU stay did not differ between groups. There was no difference in the levels of inflammatory cytokines between groups.

Conclusions

Despite being associated with fewer complications and improved hemodynamics, there was no difference in the inflammatory response of patients treated with GDT. This suggests that the clinical benefit of GDT occurs in spite of a similar inflammatory burden. Further work needs to be performed to delineate the mechanism of benefit of GDT.

Trial registration

ClinicalTrials.gov Identifier: NCT01681251. Registered 18 May 2011.

Bim regulates alloimmune-mediated vascular injury through effects on T-cell activation and death

OBJECTIVE

Bim is a proapoptotic Bcl-2 protein known to downregulate immune responses and to also be required for antigen-induced T-cell activation. However, it is not known how the effect of Bim on these offsetting processes determines the outcome of allogeneic immune responses. We have defined the role of Bim in regulating alloantigen-driven T-cell responses in a model of vascular rejection.

APPROACH AND RESULTS

Bim was required for proliferation of CD4 and CD8 T cells, and for interleukin-2 production, in T cells stimulated with alloantigen in vitro. Moreover, a partial reduction in Bim expression was sufficient to attenuate T-cell activation, whereas a complete elimination of Bim was required to prevent CD4 T-cell death in response to cytokine withdrawl. When alloimmune-mediated vascular rejection was examined using an aortic interposition model, there was significantly less intimal thickening in Bim(+/-), but not Bim(-/-), graft recipients. T-cell proliferation in response to allograft arteries was significantly reduced in both Bim(+/-) and Bim(-/-) mice, but cell death was attenuated only in Bim(-/-) animals.

CONCLUSIONS

Bim controls both T-cell activation and death in response to alloantigen stimulation. These processes act cooperatively to determine the outcome of immune responses in allograft arteries.

Flow cytometry bioinformatics

Flow cytometry bioinformatics is the application of bioinformatics to flow cytometry data, which involves storing, retrieving, organizing, and analyzing flow cytometry data using extensive computational resources and tools. Flow cytometry bioinformatics requires extensive use of and contributes to the development of techniques from computational statistics and machine learning. Flow cytometry and related methods allow the quantification of multiple independent biomarkers on large numbers of single cells. The rapid growth in the multidimensionality and throughput of flow cytometry data, particularly in the 2000s, has led to the creation of a variety of computational analysis methods, data standards, and public databases for the sharing of results. Computational methods exist to assist in the preprocessing of flow cytometry data, identifying cell populations within it, matching those cell populations across samples, and performing diagnosis and discovery using the results of previous steps. For preprocessing, this includes compensating for spectral overlap, transforming data onto scales conducive to visualization and analysis, assessing data for quality, and normalizing data across samples and experiments. For population identification, tools are available to aid traditional manual identification of populations in two-dimensional scatter plots (gating), to use dimensionality reduction to aid gating, and to find populations automatically in higher dimensional space in a variety of ways. It is also possible to characterize data in more comprehensive ways, such as the density-guided binary space partitioning technique known as probability binning, or by combinatorial gating. Finally, diagnosis using flow cytometry data can be aided by supervised learning techniques, and discovery of new cell types of biological importance by high-throughput statistical methods, as part of pipelines incorporating all of the aforementioned methods.

Open standards, data, and software are also key parts of flow cytometry bioinformatics. Data standards include the widely adopted Flow Cytometry Standard (FCS) defining how data from cytometers should be stored, but also several new standards under development by the International Society for Advancement of Cytometry (ISAC) to aid in storing more detailed information about experimental design and analytical steps. Open data is slowly growing with the opening of the CytoBank database in 2010 and FlowRepository in 2012, both of which allow users to freely distribute their data, and the latter of which has been recommended as the preferred repository for MIFlowCyt-compliant data by ISAC. Open software is most widely available in the form of a suite of Bioconductor packages, but is also available for web execution on the GenePattern platform.

FlowCAP: comparison of automated and manual gating of standardized lyoplate flow cytometry data (P3374)

Standardization of immunological assays, including flow cytometry, in terms of reagents, sample handling, instrument setup, and data analysis, is essential for successful cross-study and cross-center analysis in order to mitigate the effects of technical variability in assay results. The Human Immunology Project and the Federation of Clinical Immunology Societies (FOCIS) have partnered to develop five standardized, lyophilized, eight-color staining reagent panels (termed lyoplates) for this purpose. In collaboration with the FlowCAP consortium, standardized samples (Cytotrol control cells) were distributed to nine participating centers and analyzed by flow cytometry using the lyoplate reagents and SOP's to minimize experimental variability. Data from two of these panels (T-cell and B-cell) were entered into the FlowCAP-III challenge, where participants analyzed the data using automated gating methods for comparison against cell population statistics for major T and B-cell subsets as defined by a consensus manual gating scheme. This evaluation showed that several automated gating algorithms could successfully recapitulate centralized manual gating statistics for T-cell and B-cell subsets with little statistical bias, and with within-center and between-center variability as low or lower than centralized manual gating. These results demonstrate that automated gating algorithms are ready for use in performing reproducible analyses and comparisons of immunological data.

Critical assessment of automated flow cytometry data analysis techniques

In this analysis, the authors directly compared the performance of flow cytometry data processing algorithms to manual gating approaches. The results offer information of practical utility about the performance of the algorithms as applied to different data sets and challenges.

Traditional methods for flow cytometry (FCM) data processing rely on subjective manual gating. Recently, several groups have developed computational methods for identifying cell populations in multidimensional FCM data. The Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP) challenges were established to compare the performance of these methods on two tasks: (i) mammalian cell population identification, to determine whether automated algorithms can reproduce expert manual gating and (ii) sample classification, to determine whether analysis pipelines can identify characteristics that correlate with external variables (such as clinical outcome). This analysis presents the results of the first FlowCAP challenges. Several methods performed well as compared to manual gating or external variables using statistical performance measures, which suggests that automated methods have reached a sufficient level of maturity and accuracy for reliable use in FCM data analysis.

Computational analysis of high-dimensional flow cytometric data for diagnosis and discovery

Recent technological advancements have enabled the flow cytometric measurement of tens of parameters on millions of cells. Conventional manual data analysis and bioinformatics tools cannot provide a complete analysis of these datasets due to this complexity. In this chapter we will provide an overview of a general data analysis pipeline both for automatic identification of cell populations of known importance (e.g., diagnosis by identification of predefined cell population) and for exploratory analysis of cohorts of flow cytometry assays (e.g., discovery of new correlates of a malignancy). We provide three real-world examples of how unsupervised discovery has been used in basic and clinical research. We also discuss challenges for evaluation of the algorithms developed for (1) identification of cell populations using clustering, (2) identification of specific cell populations, and (3) supervised analysis for discriminating between patient subgroups.

FlowCAP: critical assessment of flow cytometry population identification methods (65.2)

Traditional methods for flow cytometry (FCM) data processing have relied on manual gating of cell events to define cell populations for statistical analysis. However, this approach has become increasingly problematic with the advances in instrumentation and reagents that allow for evaluation of larger numbers of cell properties. Recently several groups have developed computational methods for automatically identifying cell populations in multidimensional FCM data obviating the need for manual gating. In order to compare the performance of these methods, the Flow Cytometry: Critical Assessment of Population Identification Methods (FlowCAP) competition was established to make available a common set of FCM data together with manual gating results for comparative analysis. The first FlowCAP competition included 5 different data sets with data from 12-30 samples containing 5000-100,000 cell events stained with 3-10 fluorochrome markers. We received 36 analysis result submissions from 14 research groups. Both model fitting and density-based clustering methods were found to perform well in comparison with manual gating by domain experts as the gold standard, using statistical tests to measure and rank algorithm performance. In addition, combining results using a computational “ensemble” method was found to outperform all individual methods. These results suggest that, in the near future, automated computational methods may become an integral part of routine FCM data analysis.

A pipeline for automated analysis of flow cytometry data: preliminary results on lymphoma sub-type diagnosis

Flow cytometry (FCM) is widely used in health research and is a technique to measure cell properties such as phenotype, cytokine expression, etc., for up to millions of cells from a sample. FCM data analysis is a highly tedious, subjective and manually time-consuming (to the level of impracticality for some data) process that is based on intuition rather than standardized statistical inference. This study proposes a pipeline for automatic analysis of FCM data. The proposed pipeline identifies biomarkers that correlate with physiological/pathological conditions and classifies the samples to specific pathological/physiological entities. The pipeline utilizes a model-based clustering approach to identify cell populations that share similar biological functions. Support vector machine (SVM) and random forest (RF) classifiers were then used to classify the samples and identify biomarkers associated with disease status. The performance of the proposed data analysis pipeline has been evaluated on lymphoma patients. Preliminary results show more than 90% accuracy in differentiating between some sub-types of lymphoma. The proposed pipeline also finds biologically meaningful biomarkers that differ between lymphoma subtypes.

Long-term propagation of distinct hematopoietic differentiation programs in vivo

Heterogeneity in the differentiation behavior of hematopoietic stem cells is well documented but poorly understood. To investigate this question at a clonal level, we isolated a subpopulation of adult mouse bone marrow that is highly enriched for multilineage in vivo repopulating cells and transplanted these as single cells, or their short-term clonal progeny generated in vitro, into 352 recipients. Of the mice, 93 showed a donor-derived contribution to the circulating white blood cells for at least 4 months in one of four distinct patterns. Serial transplantation experiments indicated that two of the patterns were associated with extensive self-renewal of the original cell transplanted. However, within 4 days in vitro, the repopulation patterns subsequently obtained in vivo shifted in a clone-specific fashion to those with less myeloid contribution. Thus, primitive hematopoietic cells can maintain distinct repopulation properties upon serial transplantation in vivo, although these properties can also alter rapidly in vitro.

Review of solutions for 3D hydrodynamic modeling applied to aquaculture in South Pacific atoll lagoons

A workshop organized in French Polynesia in November 2004 allowed reviewing the current methods to model the three-dimensional hydrodynamic circulation in semi-enclosed atoll lagoons for aquaculture applications. Mollusk (e.g. pearl oyster, clam) aquaculture is a major source of income for South Pacific countries such as French Polynesia or Cook Islands. This aquaculture now requires a better understanding of circulation patterns to improve the spatial use of the lagoons, especially to define the best area to set larvae collectors. The pelagic larval duration of the relevant species (<20 days) and the size of the semi-closed lagoons (few hundreds of km2) drive the specifications of the model in terms of the spatial and temporal scale. It is considered that, in contrast with fish, mollusk larvae movements are limited and that their cycle occurs completely in the lagoon, without an oceanic stage. Atolls where aquaculture is productive are generally well-bounded, or semi-closed, without significant large and deep openings to the ocean. Nevertheless part of the lagoon circulation is driven by oceanic water inputs through the rim, ocean swells, tides and winds. Therefore, boundary conditions of the lagoon system are defined by the spatial structure of a very shallow rim (exposition and number of hoas), the deep ocean swell climate, tides and wind regimes. To obtain a realistic 3D numerical model of lagoon circulation with adequate forcing, it is thus necessary to connect in an interdisciplinary way a variety of methods (models, remote sensing and in situ data collection) to accurately represent the different components of the lagoon system and its specific boundary conditions. We review here the current methods and tools used to address these different components for a hypothetical atoll of the Tuamotu Archipelago (French Polynesia), representative of the semi-closed lagoons of the South Pacific Ocean. We hope this paper will serve as a guide for similar studies elsewhere and we provide guidelines in terms of costs for all the different stages involved.

Interaction of normal and expanded CAG repeat sizes influences age at onset of Huntington disease

Huntington disease (HD) is a neurodegenerative disorder caused by the abnormal expansion of CAG repeats in the HD gene on chromosome 4p16.3. Past studies have shown that the size of expanded CAG repeat is inversely associated with age at onset (AO) of HD. It is not known whether the normal Huntington allele size influences the relation between the expanded repeat and AO of HD. Data collected from two independent cohorts were used to test the hypothesis that the unexpanded CAG repeat interacts with the expanded CAG repeat to influence AO of HD. In the New England Huntington Disease Center Without Walls (NEHD) cohort of 221 HD affected persons and in the HD-MAPS cohort of 533 HD affected persons, we found evidence supporting an interaction between the expanded and unexpanded CAG repeat sizes which influences AO of HD (P = 0.08 and 0.07, respectively). The association was statistically significant when both cohorts were combined (P = 0.012). The estimated heritability of the AO residual was 0.56 after adjustment for normal and expanded repeats and their interaction. An analysis of tertiles of repeats sizes revealed that the effect of the normal allele is seen among persons with large HD repeat sizes (47-83). These findings suggest that an increase in the size of the normal repeat may mitigate the expression of the disease among HD affected persons with large expanded CAG repeats.

Broad-host-range shuttle vectors for screening of regulated promoter activity in viridans group streptococci: isolation of a pH-regulated promoter

Viridans group streptococci are major constituents of the normal human oral flora and are also identified as the predominant pathogenic bacteria in native valve infective endocarditis. Little information is available regarding the regulation of gene expression in viridans group streptococci, either in response to changes in the oral environment or during development of endocarditis. We therefore constructed a set of broad-host-range vectors for the isolation of promoters from viridans group streptococci that are activated by specific environmental stimuli in vitro or in vivo. A genomic library of Streptococcus gordonii strain CH1 was constructed in one of the new vectors, and this library was introduced into a homologous bacterium by using an optimized electroporation protocol for viridans group streptococci. Because viridans group streptococci entering the bloodstream from the oral cavity encounter an increase in pH, we selected promoters upregulated by this specific stimulus. One of the selected promoter sequences showed homology to the promoter region of the hydA gene from Clostridium acetobutylicum, the expression of which is known to be regulated by the environmental pH. The isolation of this pH-regulated promoter shows that S. gordonii can sense an increase in the environmental pH, which serves as a signal for bacterial gene activation. Furthermore, this demonstrates the usefulness of these new selection vectors in research on adaptive gene expression of viridans group streptococci and possibly also of other gram-positive bacteria.

A worldwide assessment of the frequency of suicide, suicide attempts, or psychiatric hospitalization after predictive testing for Huntington disease

Prior to the implementation of predictive-testing programs for Huntington disease (HD), significant concern was raised concerning the likelihood of catastrophic events (CEs), particularly in those persons receiving an increased-risk result. We have investigated the frequency of CEs-that is, suicide, suicide attempt, and psychiatric hospitalization-after an HD predictive-testing result, through questionnaires sent to predictive-testing centers worldwide. A total of 44 persons (0.97%) in a cohort of 4,527 test participants had a CE: 5 successful suicides, 21 suicide attempts, and 18 hospitalizations for psychiatric reasons. All persons committing suicide had signs of HD, whereas 11 (52.4%) of 21 persons attempting suicide and 8 (44.4%) of 18 who had a psychiatric hospitalization were symptomatic. A total of 11 (84.6%) of 13 asymptomatic persons who experienced a CE during the first year after HD predictive testing received an increased-risk result. Factors associated with an increased risk of a CE included (a) a psychiatric history </=5 years prior to testing and (b) unemployed status. The frequency of CEs did not differ between those persons receiving results of predictive testing through linkage analysis in whom there was only changes in direction of risk and those persons receiving definitive results after analysis for the mutation underlying HD. These findings provide insights into the frequency, associated factors, and timing of CEs in a worldwide cohort of persons receiving predictive-testing results and, as such, highlight persons for whom ongoing support may be beneficial.

Representation of cloned genomic sequences in two sequencing vectors: correlation of DNA sequence and subclone distribution

Representation of subcloned Caenorhabditis elegans and human DNA sequences in both M13 and pUC sequencing vectors was determined in the context of large scale genomic sequencing. In many cases, regions of subclone under-representation correlated with the occurrence of repeat sequences, and in some cases the under-representation was orientation specific. Factors which affected subclone representation included the nature and complexity of the repeat sequence, as well as the length of the repeat region. In some but not all cases, notable differences between the M13 and pUC subclone distributions existed. However, in all regions lacking one type of subclone (either M13 or pUC), an alternate subclone was identified in at least one orientation. This suggests that complementary use of M13 and pUC subclones would provide the most comprehensive subclone coverage of a given genomic sequence.

The construction and analysis of M13 libraries prepared from YAC DNA

Yeast artificial chromosomes (YACs) provide a powerful way to isolate and map large regions of genomic DNA and their use in genome analysis is now extensive. We modified a series of procedures to produce high quality shotgun libraries from small amounts of YAC DNA. Clones from several different libraries have been sequenced and analyzed for distribution, sequence integrity and degree of contamination from yeast DNA. We describe these procedures and analyses and show that sequencing at about 1-fold coverage, followed by database comparison (survey sequencing) offers a relatively quick method to determine the nature of previously uncharacterized cosmid or YAC clones.

Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII

The complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII reveals that it contains 269 predicted or known genes (300 base pairs or larger). Fifty-nine of these genes (22 percent) were previously identified. Of the 210 novel genes, 65 are predicted to encode proteins that are similar to other proteins of known or predicted function. Sixteen genes appear to be relatively recently duplicated. On average, there is one gene approximately every 2 kilobases. Although the coding density and base composition across the chromosome are not uniform, no regular pattern of variation is apparent.

Toxicity of alkyldihydrofurans to metabolically active organs in the mouse

Alkylfurans inflict toxicity in several mammalian species to lung, liver and kidney. Organ specificity of the alkylfurans is a sensitive function of the nature of the alkyl group. To determine if this toxicity requires an aromatic ring in the compound, we synthesized 4-methyl-2,3-dihydrofuran, 4-ethyl-2,3-dihydrofuran and 4-pentyl-2,3-dihydrofuran and determined their toxicity to lung, liver and kidney in mice. Lung damage was evaluated by light microscopy and the incorporation of [14C]thymidine into lung DNA. The results indicated that 4-methyl-2,3-dihydrofuran and 4-ethyl-2,3-dihydrofuran were toxic to the lung whereas 4-pentyl-2,3-dihydrofuran did not produce lung toxicity. Histological examination of liver sections revealed that 4-ethyl-2,3-dihydrofuran induced vacuolar degeneration of hepatocytes. Kidney toxicity was evaluated by light microscopy and determining plasma urea levels. Both 4-ethyl-2,3-dihydrofuran and 4-pentyl-2,3-dihydrofuran exhibited kidney toxicity, while equimolar doses of 4-methyl-2,3-dihydrofuran did not damage the kidney. A quantitative comparison of the nephrotoxicity of 4-pentyl-2,3-dihydrofuran with the corresponding aromatic compound 3-pentylfuran was made. We also sought to determine if renal injury resulting from these 2 agents is related to their oxidative metabolism. Uptake of organic ions by kidney slices and plasma urea nitrogen levels were used to assess renal function. 3-Pentylfuran caused greater renal injury than an equimolar dose of 4-pentyl-2,3-dihydrofuran. Phenobarbital pretreatment protected mice against 3-pentylfuran-induced nephrotoxicity. Cotreatment with piperonyl butoxide did not affect renal injury resulting from 3-pentylfuran. N-octylimidazole significantly reduced 3-pentylfuran-induced nephrotoxicity as well as that caused by 4-pentyl-2,3-dihydrofuran. These results point to metabolic activation as a basis for the nephrotoxicity induced by both compounds.

Changes in lung ultrastructure following heterologous and homologous serum albumin infusion in the treatment of hemorrhagic shock

The object of this study was to compare the ultrastructure pulmonary effects of the infusion of homologous and heterologous serum albumin solution in the treatment of hemorrhagic shock in baboons. Adult baboons subjected to hemorrhagic shock were resuscitated with either baboon serum albumin, human serum albumin, or Ringer's lactate solution. The lungs were fixed in vivo with potassium pyroantimony, a solution which produces electron dense interstitial precipitation of sodium. The lungs from animals resuscitated with baboon serum albumin showed evidence of interstitial edema, including dispersion of collagen fibers, interstitial smudging and increased interstital sodium concentrations. Similar changes were seen following human serum albumin infusions. Lung tissue from animals treated with Ringer's lactate solution showed minimal changes from normal. These results suggest that interstitial pulmonary edema develops after either homologous or heterologous serum albumin infusion in the treatment of hemorrhagic shock in baboons.

Problem hydromorphic soils in north-east Thailand. 3. Saline-acid conditions, reclamation, improvement and management

Saline-acid conditions have developed in patches in the irrigated areas on the low terrace in north-east Thailand. There are also traditionally uncultivated, virtually barren, saline-acid strips adjoining higher terrace remnants, in spite of the excess of monsoon rainfall over evapotranspiration. Calculations show that the salts in the shallow groundwater of the low terrace may have originated from rainfall, but that salts in the main rivers are mainly derived from salt beds. The local surface salinity, mainly of NaCl, is caused by continual evapotranspiration during the dry season and locally impeded leaching. The latter is due to a combination of a shallow water-table, slow vertical permeability and in some cases the slight elevation above the normal level of monsoon flooding. The high salt concentrations in and on the soil surface bring originally exchangeable aluminium into solution, which lowers the pH. In extreme cases even some ferric iron is dissolved at the soil surface. Reclamation, improvement and management practices on these soils should include leaching, for example under two rice crops per year; judicious liming, to eliminate most of the exchangeable aluminium but not to exceed the small buffer capacity of these soils; and emphasis on paddy rice, both in the monsoon season, and, irrigated, in the dry season. If, however, dry-season dryland crops are to be grown, physical problems of different kinds may necessitate further land improvement and management practices. These include, principally, lowering and keeping down the water-table, for example by control of irrigation water losses from canals and ditches; ploughing or disking in chopped crop residues with added nitrogen; and locally, chiselling the upper part of a dense subsurface horizon. (Abstract retrieved from CAB Abstracts by CABI’s permission)

Problem hydromorphic soils in north-east Thailand. 2. Physical and chemical aspects, mineralogy and genesis

The Roi Et soil, which occurs on the extensive seasonally wet low terrace, is a silt loam with low clay contents in the surface horizon; the clay content increases with depth. The soil is seasonally water-saturated and seasonally dry, has considerable porosity, but has a dense ploughpan at a depth of about 0.2 m and a dense substratum below 1.4 m. The soil is strongly acid with a low base saturation and a very low cation exchange capacity. The silt and sand are 98% quartz. Disordered kaolinite is the main clay mineral. About a fifth of the clay fraction is soil chlorite - a strongly Al-interlayered vermiculite in the upper horizons but partially Al-interlayered in the substratum. The interlayers contain a small amount of ferrous iron. The quartz contents in the clay fractions range from one tenth in most of the profile to about three tenths in the surface horizon, with a corresponding decrease in kaolinite. The kaolinite in the upper horizons shows signs of dissolution. These data are in accordance with hypothetical clay eluviation-illuviation and long-continued Fe redistribution and ferrolysis, the ferrolysis involving clay alteration and dissolution under conditions of alternating reduction and oxidation of Fe. (Abstract retrieved from CAB Abstracts by CABI’s permission)

Problem hydromorphic soils in north-east Thailand. 1. Environment and soil morphology

The Roi Et soil, a Gleyic Acrisol (FAO, 1974) is one of the main soils on the extensive seasonally wet, low terrace in north-east Thailand. The soil looks poor and produces traditionally low yields of one paddy rice crop/year. With fertilizers and dry-season irrigation, problems of water-logging, surface salinity and acidity caused poor germination and low yields of both rice and dry-season dryland crops. X-ray stereo radiographs, and macro- and micromorphological data indicate that the processes that have taken place in this soil include perforation and homogenization by roots and soil fauna; iron mobilization and redistribution; clay translocation; alteration of clay and formation of secondary silica; and surface slaking alternated with ploughing. The clay translocated appears to be fossil clay. Two stages of iron mobilization under (seasonally) wet conditions are indicated, the later one, with clay alteration, continuing at present. The soil has considerable macroporosity, due to worms and termites, mainly in the subsoil. The ploughpan and the deep subsoil have low porosity. (Abstract retrieved from CAB Abstracts by CABI’s permission)