Deep Learning Approaches for Quantifying Ventilation Defects in Hyperpolarized Gas Magnetic Resonance Imaging of the Lung: A Review

This paper provides an in-depth overview of Deep Neural Networks and their application in the segmentation and analysis of lung Magnetic Resonance Imaging (MRI) scans, specifically focusing on hyperpolarized gas MRI and the quantification of lung ventilation defects. An in-depth understanding of Deep Neural Networks is presented, laying the groundwork for the exploration of their use in hyperpolarized gas MRI and the quantification of lung ventilation defects. Five distinct studies are examined, each leveraging unique deep learning architectures and data augmentation techniques to optimize model performance. These studies encompass a range of approaches, including the use of 3D Convolutional Neural Networks, cascaded U-Net models, Generative Adversarial Networks, and nnU-net for hyperpolarized gas MRI segmentation. The findings highlight the potential of deep learning methods in the segmentation and analysis of lung MRI scans, emphasizing the need for consensus on lung ventilation segmentation methods.

Glucose Infusion Induced Change in Intracellular pH and Its Relationship with Tumor Glycolysis in a C6 Rat Model of Glioblastoma

INTRODUCTION

The reliance on glycolytic metabolism is a hallmark of tumor metabolism. Excess acid and protons are produced, leading to an acidic tumor environment. Therefore, we explored the relationship between the tumor glycolytic metabolism and tissue pH by comparing ¹⁸F-fluorodeoxyglucose positron emission tomography (FDG-PET) and hyperpolarized [1-¹³C]pyruvate MR spectroscopy imaging (MRSI) to chemical exchange saturation transfer (CEST) MRI measurements of tumor pH.

METHODS

10⁶ C6 glioma cells were implanted in the brains of male Wistar rats (N = 11) using stereotactic surgery. A 60-min PET acquisition after a bolus of FDG was performed at 11-13 days post implantation, and standardized uptake value (SUV) was calculated. CEST measurements were acquired the following day before and during constant infusion of glucose solution. Tumor intracellular pH (pHi) was evaluated using amine and amide concentration-independent detection (AACID) CEST MRI. The change of pH_i (∆pH_i) was calculated as the difference between pH_i pre- and during glucose infusion. Rats were imaged immediately with hyperpolarized [1-¹³C]pyruvate MRSI. Regional maps of the ratio of Lac:Pyr were acquired. The correlations between SUV, Lac:Pyr ratio, and ∆pH_i were evaluated using Pearson's correlation.

RESULTS

A decrease of 0.14 in pH_i was found after glucose infusion in tumor region. Significant correlations between tumor glycolysis measurements of Lac:Pyr and ∆pH_i within the tumor (ρ = 0.83, P = 0.01) and peritumoral region (ρ = 0.76, P = 0.028) were observed. No significant correlations were found between tumor SUV and ∆pH_i within the tumor (ρ =  - 0.45, P = 0.17) and peritumor regions (ρ =  - 0.6, P = 0.051).

CONCLUSION

AACID detected the changes in pH_i induced by glucose infusion. Significant correlations between tumor glycolytic measurement of Lac:Pyr and tumoral and peritumoral pH_i and ∆pH_i suggest the intrinsic relationship between tumor glycolytic metabolism and the tumor pH environment as well as the peritumor pH environment.

Complementary early-phase magnetic particle imaging and late-phase positron emission tomography reporter imaging of mesenchymal stem cells in vivo

Stem cell-based therapies have demonstrated significant potential in clinical applications for many debilitating diseases. The ability to non-invasively and dynamically track the location and viability of stem cells post administration could provide important information on individual patient response and/or side effects. Multi-modal cell tracking provides complementary information that can offset the limitations of a single imaging modality to yield a more comprehensive picture of cell fate. In this study, mesenchymal stem cells (MSCs) were engineered to express human sodium iodide symporter (NIS), a clinically relevant positron emission tomography (PET) reporter gene, as well as labeled with superparamagnetic iron oxide nanoparticles (SPIOs) to allow for detection with magnetic particle imaging (MPI). MSCs were additionally engineered with a preclinical bioluminescence imaging (BLI) reporter gene for comparison of BLI cell viability data to both MPI and PET data over time. MSCs were implanted into the hind limbs of immunocompromised mice and imaging with MPI, BLI and PET was performed over a 30-day period. MPI showed sensitive detection that steadily declined over the 30-day period, while BLI showed initial decreases followed by later rapid increases in signal. The PET signal of MSCs was significantly higher than the background at later timepoints. Early-phase imaging (day 0-9 post MSC injections) showed correlation between MPI and BLI data (R² = 0.671), while PET and BLI showed strong correlation for late-phase (day 10-30 post MSC injections) imaging timepoints (R² = 0.9817). We report the first use of combined MPI and PET for cell tracking and show the complementary benefits of MPI for sensitive detection of MSCs early after implantation and PET for longer-term measurements of cell viability.

Application of a 2D frequency encoding sectoral approach to hyperpolarized 129Xe MRI at low field

Inhaled hyperpolarized ¹²⁹Xe MRI is a non-invasive and radiation risk free lung imaging method, which can directly measure the business unit of the lung where gas exchange occurs: the alveoli and acinar ducts (lung function). Currently, three imaging approaches have been demonstrated to be useful for hyperpolarized ¹²⁹Xe MR in lungs: Fast Gradient Recalled Echo (FGRE), Radial Projection Reconstruction (PR), and spiral/cones. Typically, non-Cartesian acquisitions such as PR and spiral/cones require specific data post-processing, such as interpolating, regridding, and density-weighting procedures for image reconstruction, which often leads to smoothing effects and resolution degradation. On the other hand, Cartesian methods such as FGRE are not short-echo time (TE) methods; they suffer from imaging gradient-induced diffusion-weighting of the k-space center, and employ a significant number of radio-frequency (RF) pulses. Due to the non-renewable magnetization of the hyperpolarized media, the use of a large number of RF pulses (FGRE/PR) required for full k-space coverage is a significant limitation, especially for low field (<0.5 T) hyperpolarized gas MRI. We demonstrate an ultra-fast, purely frequency-encoded, Cartesian pulse sequence called Frequency-Encoding Sectoral (FES), which takes advantage of the long T₂* of hyperpolarized ¹²⁹Xe gas at low field strength (0.074 T). In contrast to PR/FGRE, it uses a much smaller number of RF pulses, and consequently maximizes image Signal-to-Noise Ratio (SNR) while shortening acquisition time. Additionally, FES does not suffer from non-uniform T₂* decay leading to image blurring; a common issue with interleaved spirals/cones. The Cartesian k-space coverage of the proposed FES method does not require specific k-space data post-processing, unlike PR/FGRE and spiral/cones methods. Proton scans were used to compare the FES sequence to both FGRE and Phase Encoding Sectoral, in terms of their SNR values and imaging efficiency estimates. Using FES, proton and hyperpolarized ¹²⁹Xe images were acquired from a custom hollow acrylic phantom (0.04L) and two normal rats (¹²⁹Xe only), utilizing both single-breath and multiple-breath schemes. For the ¹²⁹Xe phantom images, the apparent diffusion coefficient, T₁, and T₂* relaxation maps were acquired and generated. Blurring due to the T₂* decay and B₀ field variation were simulated to estimate dependence of the image resolution on the duration of the data acquisition windows (i.e. sector length), and temperature-induced resonance frequency shift from the low field magnet hardware.

TSPO PET detects acute neuroinflammation but not diffuse chronically activated MHCII microglia in the rat

Background

Accurate and sensitive imaging biomarkers are required to study the progression of white matter (WM) inflammation in neurodegenerative diseases. Radioligands targeting the translocator protein (TSPO) are considered sensitive indicators of neuroinflammation, but it is not clear how well the expression of TSPO coincides with major histocompatibility complex class II (MHCII) molecules in WM. This study aimed to test the ability of TSPO to detect activated WM microglia that are immunohistochemically positive for MHCII in rat models of prodromal Alzheimer’s disease and acute subcortical stroke.

Methods

Fischer 344 wild-type (n = 12) and TgAPP21 (n = 11) rats were imaged with [¹⁸F]FEPPA PET and MRI to investigate TSPO tracer uptake in the corpus callosum, a WM region known to have high levels of MHCII activated microglia in TgAPP21 rats. Wild-type rats subsequently received an endothelin-1 (ET1) subcortical stroke and were imaged at days 7 and 28 post-stroke before immunohistochemistry of TSPO, GFAP, iNOS, and the MHCII rat antigen, OX6.

Results

[¹⁸F]FEPPA PET was not significantly affected by genotype in WM and only detected increases near the ET1 infarct (P = 0.033, infarct/cerebellum uptake ratio: baseline = 0.94 ± 0.16; day 7 = 2.10 ± 0.78; day 28 = 1.77 ± 0.35). Immunohistochemistry confirmed that only the infarct (TSPO cells/mm²: day 7 = 555 ± 181; day 28 = 307 ± 153) and WM that is proximal to the infarct had TSPO expression (TSPO cells/mm²: day 7 = 113 ± 93; day 28 = 5 ± 7). TSPO and iNOS were not able to detect the chronic WM microglial activation that was detected with MHCII in the contralateral corpus callosum (day 28 OX6% area: saline = 0.62 ± 0.38; stroke = 4.30 ± 2.83; P = .029).

Conclusion

TSPO was only expressed in the stroke-induced insult and proximal tissue and therefore was unable to detect remote and non-insult-related chronically activated microglia overexpressing MHCII in WM. This suggests that research in neuroinflammation, particularly in the WM, would benefit from MHCII-sensitive radiotracers.

19 F MRI of the Lungs Using Inert Fluorinated Gases: Challenges and New Developments

Fluorine-19 (¹⁹ F) MRI using inhaled inert fluorinated gases is an emerging technique that can provide functional images of the lungs. Inert fluorinated gases are nontoxic, abundant, relatively inexpensive, and the technique can be performed on any MRI scanner with broadband multinuclear imaging capabilities. Pulmonary ¹⁹ F MRI has been performed in animals, healthy human volunteers, and in patients with lung disease. In this review, the technical requirements of ¹⁹ F MRI are discussed, along with various imaging approaches used to optimize the image quality. Lung imaging is typically performed in humans using a gas mixture containing 79% perfluoropropane (PFP) or sulphur hexafluoride (SF₆ ) and 21% oxygen. In lung diseases, such as asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis (CF), ventilation defects are apparent in regions that the inhaled gas cannot access. ¹⁹ F lung images are typically acquired in a single breath-hold, or in a time-resolved, multiple breath fashion. The former provides measurements of the ventilation defect percent (VDP), while the latter provides measurements of gas replacement (ie, fractional ventilation). Finally, preliminary comparisons with other functional lung imaging techniques are discussed, such as Fourier decomposition MRI and hyperpolarized gas MRI. Overall, functional ¹⁹ F lung MRI is expected to complement existing proton-based structural imaging techniques, and the combination of structural and functional lung MRI will provide useful outcome measures in the future management of pulmonary diseases in the clinic. Level of Evidence: 3 Technical Efficacy: Stage 1 J. Magn. Reson. Imaging 2019;49:343-354.

19F-perfluorocarbon-labeled human peripheral blood mononuclear cells can be detected in vivo using clinical MRI parameters in a therapeutic cell setting

A ¹⁹Fluorine (¹⁹F) perfluorocarbon cell labeling agent, when employed with an appropriate cellular MRI protocol, allows for in vivo cell tracking. ¹⁹F cellular MRI can be used to non-invasively assess the location and persistence of cell-based cancer vaccines and other cell-based therapies. This study was designed to determine the feasibility of labeling and tracking peripheral blood mononuclear cells (PBMC), a heterogeneous cell population. Under GMP-compliant conditions human PBMC were labeled with a ¹⁹F-based MRI cell-labeling agent in a manner safe for autologous re-injection. Greater than 99% of PBMC labeled with the ¹⁹F cell-labeling agent without affecting functionality or affecting viability. The ¹⁹F-labeled PBMC were detected in vivo in a mouse model at the injection site and in a draining lymph node. A clinical cellular MR protocol was optimized for the detection of PBMC injected both at the surface of a porcine shank and at a depth of 1.2 cm, equivalent to depth of a human lymph node, using a dual ¹H/¹⁹F dual switchable surface radio frequency coil. This study demonstrates it is feasible to label and track ¹⁹F-labeled PBMC using clinical MRI protocols. Thus, ¹⁹F cellular MRI represents a non-invasive imaging technique suitable to assess the effectiveness of cell-based cancer vaccines.

Fractional ventilation mapping using inert fluorinated gas MRI in rat models of inflammation and fibrosis

The purpose of this study was to extend established methods for fractional ventilation mapping using (19) F MRI of inert fluorinated gases to rat models of pulmonary inflammation and fibrosis. In this study, five rats were instilled with lipopolysaccharide (LPS) in the lungs two days prior to imaging, six rats were instilled with bleomycin in the lungs two weeks prior to imaging and an additional four rats were used as controls. (19) F MR lung imaging was performed at 3 T with rats continuously breathing a mixture of sulfur hexafluoride and O2 . Fractional ventilation maps were obtained using a wash-out approach, by switching the breathing mixture to pure O2 , and acquiring images following each successive wash-out breath. The mean fractional ventilation (r) was 0.29 ± 0.05 for control rats, 0.23 ± 0.10 for LPS-instilled rats and 0.19 ± 0.03 for bleomycin-instilled rats. Bleomycin-instilled rats had a significantly decreased mean r value compared with controls (P = 0.010). Although LPS-instilled rats had a slightly reduced mean r value, this trend was not statistically significant (P = 0.556). Fractional ventilation gradients were calculated in the anterior/posterior (A/P) direction, and the mean A/P gradient was -0.005 ± 0.008 cm(-1) for control rats, 0.013 ± 0.005 cm(-1) for LPS-instilled rats and 0.009 ± 0.018 cm(-1) for bleomycin-instilled rats. Fractional ventilation gradients were significantly different for control rats compared with LPS-instilled rats only (P = 0.016). The ventilation gradients calculated from control rats showed the expected gravitational relationship, while ventilation gradients calculated from LPS- and bleomycin-instilled rats showed the opposite trend. Histology confirmed that LPS-instilled rats had a significantly elevated alveolar wall thickness, while bleomycin-instilled rats showed signs of substantial fibrosis. Overall, (19)F MRI may be able to detect the effects of pulmonary inflammation and fibrosis using a simple and inexpensive imaging approach that can potentially be translated to humans.

Fluorine-19 MRI Contrast Agents for Cell Tracking and Lung Imaging

Fluorine-19 (¹⁹F)-based contrast agents for magnetic resonance imaging stand to revolutionize imaging-based research and clinical trials in several fields of medical intervention. First, their use in characterizing in vivo cell behavior may help bring cellular therapy closer to clinical acceptance. Second, their use in lung imaging provides novel noninvasive interrogation of the ventilated airspaces without the need for complicated, hard-to-distribute hardware. This article reviews the current state of ¹⁹F-based cell tracking and lung imaging using magnetic resonance imaging and describes the link between the methods across these fields and how they may mutually benefit from solutions to mutual problems encountered when imaging ¹⁹F-containing compounds, as well as hardware and software advancements.

Inert fluorinated gas MRI: a new pulmonary imaging modality

Fluorine-19 ((19)F) MRI of the lungs using inhaled inert fluorinated gases can potentially provide high quality images of the lungs that are similar in quality to those from hyperpolarized (HP) noble gas MRI. Inert fluorinated gases have the advantages of being nontoxic, abundant, and inexpensive compared with HP gases. Due to the high gyromagnetic ratio of (19)F, there is sufficient thermally polarized signal for imaging, and averaging within a single breath-hold is possible due to short longitudinal relaxation times. Therefore, the gases do not need to be hyperpolarized prior to their use in MRI. This eliminates the need for an expensive polarizer and expensive isotopes. Inert fluorinated gas MRI of the lungs has been previously demonstrated in animals, and more recently in healthy volunteers and patients with lung diseases. The ongoing improvements in image quality demonstrate the potential of (19)F MRI for visualizing the distribution of ventilation in human lungs and detecting functional biomarkers. In this brief review, the development of inert fluorinated gas MRI, current progress, and future prospects are discussed. The current state of HP noble gas MRI is also briefly discussed in order to provide context to the development of this new imaging modality. Overall, this may be a viable clinical imaging modality that can provide useful information for the diagnosis and management of chronic respiratory diseases.

A novel intubation technique for minimally invasive longitudinal studies of rat lungs using hyperpolarized 3He magnetic resonance imaging

Hyperpolarized noble gas (HNG) magnetic resonance imaging (MRI) has been shown to be useful for studying rodent models of lung disease. Image quality can be substantially degraded by signal loss from molecular oxygen entering the airway, requiring invasive surgery to ensure a good seal between the endotracheal (ET) tube and trachea. A modified Foley catheter having an inflatable cuff near the tip provides a novel approach for ensuring image quality for HNG MRI, thereby enabling longitudinal studies and reducing animal numbers. A Foley catheter was modified for rodent intubation and to minimize dead space. Three pairs of age-matched male Sprague Dawley rats 400 (30) g were used. Two pairs were intubated using the Foley and the third with an intravenous catheter. Leak rates were measured from pressure versus time curves within each animal. The pairs were euthanized immediately or six days postrecovery to assess the effects of the procedure on animal health, as reflected by histological examination. The Foley catheter resulted in minimal leak rates (−0.20 (0.03) versus −0.16 (0.05) cmH2O/s), and were shown to be well below upper-limit leak rates of −0.5 and −0.7 cmH2O/s. Tracheal samples from rats in a separate Foley group (not mechanically ventilated) showed superficial damage six days postextubation (grade = 0). 3He imaging performed using the Foley showed good image quality. Though some technical issues remain to be solved, a modified Foley catheter used as an ET tube offers the potential to enable longitudinal studies in rodents and reduce animal numbers.

Male infertility, genetic analysis of the DAZ genes on the human Y chromosome and genetic analysis of DNA repair

Many genes that are required for fertility have been identified in model organisms (). Mutations in these genes cause infertility due to defects in development of the germ cell lineage, but the organism is otherwise healthy. Although human reproduction is undoubtedly as complex as that of other organisms, very few fertility loci have been mapped (). This is in spite of the prevalence of human infertility, the lack of effective treatments to remedy germ cell defects, and the cost to couples and society of assisted reproductive techniques. Fifteen percent of couples are infertile and half of all cases can be traced to the male partner. Aside from defects in sperm production, most infertile men are otherwise healthy. This review is divided into two distinct parts to discuss work that: (i) led to the identification of several genes on the Y chromosome that likely function in sperm production; and (ii) implicates DNA repair in male infertility via increased frequency of mutations in DNA from men with meiotic arrest.

Transposon stability and a role for conjugational transfer in adaptive mutability

Lac(+) revertants of Escherichia coli that occur after prolonged nonlethal selection display a high frequency of transposon loss when the transposon Tn10 and the reverting lacI33 allele are linked on an F'128 episome. As many as 20% of the Lac(+) revertants are sensitive to tetracycline, about half because of transposon loss, nearly all by precise excision, and the remainder because of amplification of both the transposon and the linked lac allele. Lethality of the amplified products in the presence of tetracycline is a peculiarity of the tetA gene at high gene dosage. The selective conditions on lactose medium result in 10% transposon-free revertants, whether or not a requirement for conjugal DNA transfer is imposed. In addition, a similar fraction, about 5% of Lac(-) unreverted colonies that are products of transfer between cells experiencing nonlethal selection are also tetracycline-sensitive, and all are attributable to loss of the Tn10 transposon. These results suggest the possibility that the high frequency of transposon loss is a consequence of conjugal transfer, making this loss a marker for that transfer. We suggest that conjugal DNA transfer may be a prominent feature in the mutability process that occurs during nonlethal selection and that the subset of bacteria displaying hypermutability are those that experience such transfer.

Some features of the mutability of bacteria during nonlethal selection

We describe the mutability of the Trp(-) chromosomal +1 frameshift mutation trpE7999 during nonlethal selection, finding that the appearance of Trp(+) revertants behaves similarly to that of episomal Lac(+) revertants. In addition, we show that a feature of the Lac(+) and Trp(+) mutability is the accumulation of Trp(+) and Lac(+) revertants with additional unselected mutations, most of which are not due to heritable mutators. The cells undergoing nonlethal selection apparently experience an epigenetic change resulting in a subset of bacteria with elevated mutability that often remain hypermutable for the duration of selection. The epigenetic change provoked by nonlethal selection appears to be mediated by a unique function provided by the F'128 episome.

Cloning and characterization of hOGG1, a human homolog of the OGG1 gene of Saccharomyces cerevisiae

The OGG1 gene of Saccharomyces cerevisiae encodes a DNA glycosylase activity that is a functional analog of the Fpg protein from Escherichia coli and excises 7,8-dihydro-8-oxoguanine (8-oxoG) from damaged DNA. The repair of this ubiquitous kind of oxidative damage is essential to prevent mutations both in bacteria and in yeast. A human cDNA clone carrying an ORF displaying homology to the yeast protein was identified. The predicted protein has 345 amino acids and a molecular mass of 39 kDa. This protein shares a 38% sequence identity with the yeast Ogg1 protein, adding this novel human gene product to the growing family of enzymes that the repair of oxidatively damaged bases and are related to the E. coli endonuclease III. Northern blot analysis indicates that this gene, localized to chromosome 3p25, is ubiquitously expressed in human tissues. The cloned coding sequence was expressed in an E. coli strain that carried a disrupted fpg gene, the bacterial functional analog of OGG1. Cell-free extracts from these cultures displayed a specific lyase activity on duplex DNA that carried an 8-oxoG/C base pair. The products of the reaction are consistent with an enzymatic activity like the one displayed by the yeast Ogg1. Analysis of the substrate specificity reveals a very strong preference for DNA fragments harboring 8-oxoG/C base pairs. The pattern of specificity correlates well with the one found for the yeast enzyme. Moreover, when the human coding sequence was expressed in a yeast strain mutant in OGG1 it was able to complement the spontaneous mutator phenotype. These results make this novel gene (hOGG1) a strong candidate for the human homolog of the yeast OGG1 and suggest an important role of its product in the protection of the genome from the mutagenic effects of the oxidatively damaged purines.

A joint hazard and time scaling model to compare survival curves

To provide a more general method for comparing survival experience, we propose a model that independently scales both hazard and time dimensions. To test the curve shape similarity of two time-dependent hazards, h1(t) and h2(t), we apply the proposed hazard relationship, h12(tKt)/ h1(t) = Kh, to h1. This relationship doubly scales h1 by the constant hazard and time scale factors, Kh and Kt, producing a transformed hazard, h12, with the same underlying curve shape as h1. We optimize the match of h12 to h2 by adjusting Kh and Kt. The corresponding survival relationship S12(tKt) = [S1(t)]KtKh transforms S1 into a new curve S12 of the same underlying shape that can be matched to the original S2. We apply this model to the curves for regional and local breast cancer contained in the National Cancer Institute's End Results Registry (1950-1973). Scaling the original regional curves, h1 and S1 with Kt = 1.769 and Kh = 0.263 produces transformed curves h12 and S12 that display congruence with the respective local curves, h2 and S2. This similarity of curve shapes suggests the application of the more complete curve shapes for regional disease as templates to predict the long-term survival pattern for local disease. By extension, this similarity raises the possibility of scaling early data for clinical trial curves according to templates of registry or previous trial curves, projecting long-term outcomes and reducing costs. The proposed model includes as special cases the widely used proportional hazards (Kt = 1) and accelerated life (KtKh = 1) models.

Adaptive mutation in Escherichia coli: a role for conjugation

When subjected to selective conditions that impose starvation, a bacterial population can accumulate mutations, called adaptive, that allow colony formation. Here, the reversion of a lac allele under selective conditions, in a model system using Escherichia coli with the lac mutation on an F' plasmid, was shown to require the conjugational capacity of the plasmid. Reversion associated with transfer was shown, and when the same lac allele was chromosomal, reversion to Lac+ was 25 to 50 times less frequent. Postplating reversion was 25 times less when mating was inhibited by the presence of detergent. Mutability associated with conjugation provides new ways of thinking about the origin of adaptive mutations.

Some features of base pair mismatch repair and its role in the formation of genetic recombinants

For the formation of recombinants involving closely linked markers, two distinct processes play a role. The recombinational interaction between homologous DNA molecules results in the presence of heteroduplex DNA joining the parental components of the recombinant. The presence of markers distinguishing the parents in the region of heteroduplex DNA can result in base pair mismatches. The post recombination repair of such mismatches can contribute to the separation of closely linked markers. The processes responsible for such repair also play roles in mutation avoidance. The specificities, functions and contribution to the formation of recombinants for closely linked markers of the processes in Escherichia coli are described.

Patch length of localized repair events: role of DNA polymerase I in mutY-dependent mismatch repair

In vivo experiments with heteroduplex lambda genomes show that the MutY mismatch repair system of Escherichia coli defines an average repair tract that is shorter than 27 nucleotides and longer than 9 nucleotides and extends 3' from the corrected adenine. The phenotype of a mutant defective in DNA polymerase I shows that this enzyme plays a significant, though not an essential, role in the in vivo repair of apurinic sites generated by this system. Evidence is presented that in the absence of polymerase I the repair tracts are modestly longer than in the polA+ extending in the 5' direction from the corrected adenine, suggesting a role for another DNA polymerase.

Effect on herd health and productivity of controlling tsetse and trypanosomosis by applying deltamethrin to cattle

A large cattle ranch was established in 1954 in a heavily tsetse infested part of north-east Tanzania. Trypanosomosis was controlled for 30 years by prophylactic drugs but in 1988 drug resistance seemed to be developing as cases of trypanosomosis were being confirmed 4 or 5 weeks after treatment with isometamidium chloride (Samorin). Herd health had deteriorated and productivity was uneconomically low. In order to control the tsetse population the 8,000 cattle, grazing over 250 km2, were regularly dipped in the synthetic pyrethroid deltamethrin (Decatix Cattle Dip and Spray formulation). Within a year the tsetse population, as monitored by traps, had decreased by more than 90%. Disease mortality decreased by 66% and a range of productivity measures such as calving percentages and weaning weights were raised to levels above those prevailing before the decline in herd health.

Break-join recombination in phage lambda

In phage lambda, when DNA replication is blocked, recombination mediated by the Red pathway occurs only near the double-chain break site, cos, that defines the termini of the virion chromosome. The recombinants initiated by cos contain newly synthesized DNA near cos, in amount corresponding to a few percent of the length of lambda. A restriction enzyme cut delivered to one parent far from cos results in elevated recombination near the restriction site. Recombinants induced by this cut have a similarly small amount of DNA synthesis in these replication-blocked crosses. When restriction cuts are introduced in the presence of normal amounts of all of the DNA replication enzymes, many of the resulting recombinants still enjoy, at most, a small amount of DNA synthesis associated with the exchange event. Thus, these experiments fail to support the previously considered possibility that Red-mediated recombination in lambda proceeds largely through a break-copy pathway.

Synapsis-mediated fusion of free DNA ends forms inverted dimer plasmids in yeast

When yeast (Saccharomyces cerevisiae) is transformed with linearized plasmid DNA and the ends of the plasmid do not share homology with the yeast genome, circular inverted (head-to-head) dimer plasmids are the principal product of repair. By measurements of the DNA concentration dependence of transformation with a linearized plasmid, and by transformation with mixtures of genetically marked plasmids, we show that two plasmid molecules are required to form an inverted dimer plasmid. Several observations suggest that homologous pairing accounts for the head-to-head joining of the two plasmid molecules. First, an enhanced frequency of homologous recombination is detected when genetically marked plasmids undergo end-to-end fusion. Second, when a plasmid is linearized within an inverted repeat, such that its ends could undergo head-to-tail homologous pairing, it is repaired by intramolecular head-to-tail joining. Last, in the joining of homologous linearized plasmids of different length, a shorter molecule can acquire a longer plasmid end by homologous recombination. The formation of inverted dimer plasmids may be related to some forms of chromosomal rearrangement. These might include the fusion of broken sister chromatids in the bridge-breakage-fusion cycle and the head-to-head duplication of genomic DNA at the sites of gene amplifications.

Effects of DNA heterologies on bacteriophage lambda packaging

We have examined the impact of DNA heterologies on the packaging of lambda DNA in vitro. Heterology-containing DNA molecules were constructed by denaturing and reannealing a mixture of DNA from cI+ phage and DNA front phage carrying small insertion or deletion mutations in the cI gene. We found that molecules with heterologies of up to 19 base pairs (bp) can be packaged as viable heterozygous phage with approximately the same efficiency as molecules with a base pair mismatch. In contrast, with a heterology of 26-bp heterozygous plaque formers are rare. In principle, the absence of cI heterozygotes among packaged phage may be due either to a failure to encapsulate the DNA or a failure to inject the packaged DNA on infection. Southern blot analysis of DNA isolated from packaged phage indicates that DNA harboring a 26-bp heterology is almost completely absent in packaged phage. Thus, an upper limit has been established for the size of heterology that can be accommodated by the packaging apparatus The size of the connector portal could be the basis for this limit.

Effects of DNA heterologies on bacteriophage lambda recombination

Previous studies of bacteriophage lambda recombination have provided indirect evidence that substantial sequence nonhomologies, such as insertions and deletions, may be included in regions of heteroduplex DNA. However, the direct products of heterology-containing heteroduplex DNA--heterozygous progeny phage--have not been observed. We have constructed a series of small insertion and deletion mutations in the cI gene to examine the possibility that small heterologies might be accommodated in heterozygous progeny phage. Genetic crosses were carried out between lambda cI- Oam29 and lambda cI+ Pam80 under replication-restricted conditions. Recombinant O+P+ progeny were selected on mutL hosts and tested for cI heterozygosity. Heterozygous recombinants were readily observed with crosses involving insertions of 4 to 19 base pairs (bp) in the cI gene. Thus, nonhomologies of at least 19 bp can be accommodated in regions of heteroduplex DNA during lambda recombination. In contrast, when a cI insertion or deletion mutation of 26 bp was present, few of the selected recombinants were heterozygous for cI. Results using a substitution mutation, involving a 26-bp deletion with a 22-bp insertion, suggest that the low recovery of cI heterozygotes containing heterologies of 26 bp or more is due to a failure to encapsulate DNA containing heterologies of 26 bp or more into viable phage particles.

Some features of base pair mismatch and heterology repair in Escherichia coli

We have used artificially constructed heteroallelic heteroduplex molecules of bacteriophage lambda DNA to transfect Escherichia coli, and E. coli mutants deficient in various functions involved in the adenine methylation-directed mismatch repair system, MutL, MutS, MutH, and UvrD (MutU). Analysis of the allele content of single infective centers shows that this repair system often acts on several mismatches, separated by as many as 2000 bp, on one of the strands of a heteroduplex molecule. When the methyl-directed mismatch repair system is disabled by mutH or uvrD mutations, localized mismatch repair becomes prominent. This prominent localized repair that can result in separation of very closely linked markers requires the functions MutL and MutS, is independent of adenine methylation, and appears to reflect another mechanism of mismatch repair. Heterology-containing heteroduplex molecules with a deletion in one strand often escape processing. However, when the heterology includes the stem and loop structure of a transposon, Tn10, the transposon is lost.

Fine structure recombinational analysis of cloned genes using yeast transformation

We describe a general method for analyzing the genetic fine structure of plasmid-borne genes in yeast. Previously we had reported that a linearized plasmid is efficiently rescued by recombination with a homologous restriction fragment when these are co-introduced by DNA-mediated transformation of yeast. Here, we show that a mutation can be localized to a small DNA interval when members of a deletion series of wild-type restriction fragments are used in the rescue of a linearized mutant plasmid. The resolution of this method is to at least 30 base pairs and is limited by the loss of a wild-type marker with proximity to a free DNA end. As a means for establishing the nonidentity of two mutations, we determined the resolution of two-point crosses with a mutant linearized plasmid and a mutant homologous restriction fragment. Recombination between mutations separated by as little as 100 base pairs was detected. Moreover, the results indicate that exchange within a marked interval results primarily from one of two single crossovers that repair the linearized plasmid. These approaches to mapping the genetic fine structure of plasmids should join existing methods in a robust approach to the mutational analysis of gene structure in yeast.

A genetic analysis of primary products of bacteriophage lambda recombination

Primary products of bacteriophage lambda recombination that display heterozygosity as a consequence of the presence of regions of heteroduplex DNA are rare in standard lambda crosses. Phage manifesting heterozygosity at a given allele are evident when recombinants, emerging from a cross, are selected for an exchange in a neighboring interval. We show that the abundance of such heterozygotes can be increased 10- to 20-fold by selection on an E. coli indicator that is defective in methyl-directed mismatch repair (mutL). Thus, the activity of the methyl-directed mismatch repair system is, at least in part, responsible for the low frequency of detectably heterozygous phage emerging from a standard cross. In a mutL indicator, many primary products of recombination are replicated without the intervention of mismatch repair.--The products of a six-factor phage cross have been plated on a mutL indicator allowing visual detection of those phage products heterozygous for one of the allelic pairs, cI. By genetic analysis, we show that the heteroduplex regions of these primary products of recombination are on the average about 4 kb in length and can include as much as half of the lambda genome.

On mutation fixation resulting from nitrosoguanidine-induced DNA damage in Escherichia coli K12 ada-

Brief treatment with nitrosoguanidine of E. coli defective in the removal of the pre-mutagenic lesion, gives rise to cells that segregate mutant clones. No depletion in the number of such cells occurs for at least 4 generations of growth in liquid medium. It is concluded that pre-mutagenic lesions persist and result in copying errors by an otherwise normal replication machinery.

Transformation of yeast with linearized plasmid DNA. Formation of inverted dimers and recombinant plasmid products

The molecular products of DNA double strand break repair were investigated after transformation of yeast (Saccharomyces cerevisiae) with linearized plasmid DNA. DNA of an autonomous yeast plasmid cleaved to generate free ends lacking homology with the yeast genome, when used in transformation along with sonicated non-homologous carrier DNA, gave rise to transformants with high frequency. Most of these transformants were found to harbor a head-to-head (inverted) dimer of the linearized plasmid. This outcome of transformation contrasts with that observed when the carrier DNA is not present. Transformants occur at a much reduced frequency and harbor either the parent plasmid or a plasmid with deletion at the site of the cleavage. When the linearized plasmid is introduced along with sonicated carrier DNA and a homologous DNA restriction fragment that spans the site of plasmid cleavage, homologous recombination restores the plasmid to its original circular form. Inverted dimer plasmids are not detected. This relationship between homologous recombination and a novel DNA transaction that yields rearrangement could be important to the cell, as the latter could lead to a loss of gene function and lethality.

Representation of activity knowledge for project management

Representation of activity knowledge is important to any application which must reason about activities such as new product management, factory scheduling, robot control, vehicle control, software engineering, and air traffic control. This paper provides an integration of the underlying theories needed for modeling activities. Using the domain of large computer design projects as an example, the semantics of activity modeling is described. While the past research in knowledge representation has discovered most of the underlying concepts, our attempt is toward their integration. This includes the epistemological concepts for erecting the required knowledge structure; the concepts of activity, state, goal, and manifestation for the adequate description of the plan and the progress; and the concepts of time and causality to infer the progression among the activities. We also address the issues which arise due to the integration of aggregation, time, and causality among activities and states.

A growth rate distribution model for the age dependence of human cancer incidence: a proposed role for promotion in cancer of the lung and breast

A biological model is proposed to account for the steep rise of human cancer incidence with age. The model casts in mathematical terms the assumptions that each clone destined to give rise to a detectable tumor displays a characteristic net growth rate and that the assembly of such clones displays a distribution of growth rates. Incidence is introduced as the rate of appearance of clones whose size permits detection. While the cancer formation process may involve a series of stages, we assume that the overall kinetics of tumor detection reflect one stage of development whose duration spans the major portion of the latent period between initial cell alteration and final detection. We further assume that the net growth rates of tumor-forming clones increase in the presence of promotors and resume their original growth rates when the promoting substance is removed. Assuming that cigarette smoke has promoting activity, we show how the model could account for the abrupt impact of cessation of smoking on subsequent lung cancer incidence. If we assume that clones destined to be detected as breast cancers experience promotional activity during the period of a woman's fertility, the model predicts that as a consequence of the slowing down of the clones a discontinuous decline in incidence would follow menopause. Since women experience menopause over a range of ages, we show how aggregating the contributions from these menopausal ages results in an overall age dependence of incidence with no discontinuities and with the observed change in the incidence rate for breast cancer near the age range of menopause.

Evidence for inclusion of regions of nonhomology in heteroduplex products of bacteriophage lambda recombination

Total intracellular DNA was isolated from replication-restricted bacteriophage lambda crosses in which the infecting parents were heteroallelic for wild-type and deletion mutant alleles. This DNA was examined for the presence of heteroduplex DNA molecules that contained wild-type sequences in one strand and deletion-mutant sequences in the other. Molecules hybrid for a 689-nucleotide deletion in the immunity region of lambda were detected at significant levels only in crosses in which both the red recombination system of lambda and the rec recombination system of Escherichia coli were active. Molecules hybrid for a 1300-nucleotide deletion in the central portion of the lambda genome were detected at significant levels in DNA isolated from both red+ and red- crosses in which recA function was present.

Acute acalculous cholecystitis

Sixty-eight patients with acute acalculous cholecystitis were reviewed. The results of history and physical examinations were usually nondiagnostic. IDA cholescintigraphy (93 per cent accuracy rate) was the only reliable diagnostic modality. The results of oral cholecystography, intravenous cholangiography and ultrasonography were considerably less reliable. One-half of the patients had gangrenous cholecystitis. Cholecystectomy was the preferred operation with an over-all mortality of 9 per cent. IDA cholescintigraphy is an important new modality for the diagnosis of acute acalculous cholecystitis which, in the past, has often been difficult to diagnose.

Formation of inverted dimer plasmids after transformation of yeast with linearized plasmid DNA

The formation of an inverted dimer plasmid on transformation with linear molecules is formally analogous to the fusion of the daughters of a broken chromosome at their broken ends. In the latter case, this leads to the formation of a dicentric chromosome, which could break at anaphase. Hence the process is cyclic. Similarly, when our linear molecules are modified by the addition of a cloned yeast centromere, dicentric inverted dimers are not obtained. Instead, we obtain monocentric plasmids with partial duplication and deletion that apparently derive from a process of fusion, bridge-breakage, and fusion. This is not surprising, since it is known that dicentric plasmids undergo breakage in yeast (Mann and Davis 1983). However, any apparent similarity of this process to that which occurs with a broken chromosome in maize must be tempered by the special nature of the transformation process. Most significantly, inverted dimers are rare when sonicated carrier DNA is not present during the transformation. This requirement is not understood, but it is a condition that may not be met in a yeast cell harboring a broken chromosome. It is possible that carrier DNA induces a repair process that results in fusion. On the other hand, a property of the transformation process that results in an inhibition of fusion may be overcome by the presence of carrier DNA. Most inverted dimers are apparently formed from an interaction between two input linear molecules. We cannot rule out the possibility that a minor fraction derive from a single molecule. Thus, the fusion of two input molecules is a much more efficient process than a replicative process that could occur with single linear molecule. For a similar fusion process to occur with a broken yeast chromosome, replication would be required. We do not know if a broken yeast chromosome can replicate. Evidence consistent with the presence of a breakage-fusion-bridge process in yeast has been obtained through the formation of dicentric chromosomes via meiotic recombination (Haber et al. 1984). Spores from these meioses sometimes give rise to a clone that is mixed for markers of the chromosome that could have been dicentric. A process of fusion-bridge-breakage could account for the formation of some of these mixed clones. However, the dicentric chromosomes apparently often survive meiotic disjunction and break in the spore's first mitotic anaphase or possibly in a later generation. Thus, the interpretation of the origin of these mixed clones is uncertain. Some aspects of the fusion process are especially intriguing.(ABSTRACT TRUNCATED AT 400 WORDS)

Detection of non-homology-containing heteroduplex molecules

Heteroduplex DNA molecules which contain both the wild-type and mutant sequences of a deletion nonhomology possess a characteristic electrophoretic mobility in agarose and can be readily separated from both the wild-type and deletion-containing parental homoduplex fragments. Because of the partial single stranded character of these deletion-containing heteroduplex molecules, they are selectively bound to nitrocellulose filters, and once bound, can be selectively detected by hybridization with radioactively labeled single-stranded DNA which is homologous to the sequences absent in the deletion mutation.

A screening procedure for the efficient recognition of Escherichia coli K-12 mutants

A method is described for the rapid screening of large numbers of E. coli colonies for detection of auxotrophs and mutants defective in sugar or succinate metabolism. The procedure permits recognition of forward mutations in a large number of functions and is applicable to the isolation of temperature-sensitive mutants in essential and nonessential genes.

Effects of nonhomology on bacteriophage lambda recombination

When crosses are performed under conditions severely restricting DNA synthesis, the presence of DNA sequence nonhomologies in the lac region of lambda plac5 limits the parental material contribution to and the yield of phage recombinant in a region bracketed by the nonhomologies. These observations are consistent with the expectation of a role for branch migration in the formation of heteroduplex structures under these conditions. Under conditions permissive for DNA replication, bracketing a region with nonhomologies has an only modest effect on the yield of recombinants within that interval. In addition, recombinants within such a bracketed interval manifest an excess of coincident exchange events in an adjacent region. These observations suggest the possibility that, under conditions permissive for DNA replication, regions of nonhomology can be included in heteroduplex structures.

The role of technetium-99m iminodiacetic acid (IDA) cholescintigraphy in acute acalculous cholecystitis

Technetium-99m iminodiacetic acid (IDA) cholescintigraphy was performed in 15 patients with acute acalculous cholecystitis. Fourteen of the 15 patients with acute disease had positive findings, indicating the presence of cystic duct or common duct obstruction. One case in which the gallbladder was visualized failed to respond to sincalide stimulation; this was classified as a suggestive finding of disease. The diagnostic accuracy of 99mTc-IDA cholescintigraphy was far superior to the other imaging studies used (8 sonograms, 1 intravenous cholangiogram, 3 oral cholecystograms, 1 percutaneous transhepatic cholangiogram). The 99mTc-IDA study is recommended as the imaging procedure of choice for examining patients with suspected acute acalculous cholecystitis.

Workmen's compensation hearing loss claims

This presentation deals with the evaluation of occupational hearing loss claims, the tests used over the years to determine the hearing status of the claimants, and the various methods used to convert the results of the audiometric tests in terms of percentage of hearing impairment. A significant modification of the 1961 American Medical Association formula has recently been adopted by the Board of Directors of both the American Academy of Otolaryngology and the American Council of Otolaryngology. The modified formula has been published: "Guide for the Evaluation of Hearing Handicap," JAMA, 241, (19): May 11, 1979. The reasons for this modification and its application in the evaluation of occupational hearing loss claims are discussed. Otolaryngologists are urged to become acquainted with the modified AAO formula and to apply it in the evaluation of hearing loss claims.