Failure Mode and Effects Analysis for Treatment Workflow of a Novel Ring Gantry Linac

PURPOSE/OBJECTIVE(S)

A new ring gantry Linac machine combined with a PET ring is available in the market. It has 3 separate centers, one for laser, one for CT imaging and a 3rd for the Linac. As a first-generation machine of its kind, the workflow heavily depends on user-input. As example, it uses two separate coordinate systems, IEC for lasers and CT localization offsets and DICOM for treatment planning. The planner must manually convert between the two systems. We hypothesize that the unique design of the machine that is heavily dependent on users' input increases the potential of failure of treatment. The present work investigates failure modes for treatment delivery using the methodology of failure modes and effects analysis (FMEA) and proposes solutions to mitigate some of the failure modes (FMs).

MATERIALS/METHODS

A group of two radiation oncologists, two radiation therapists and three medical physicists was assembled. The process map for treatment delivery on the X1 was created and FMs were identified. Members independently graded each FM on 3 parameters, likelihood of occurrence, detectability of FM and level of severity on patient treatment. A grading scale of 1-5 was used with five representing the worst outcome in each parameter. Each member also identified the origin of each FM to be human, machine or clinical process. Mitigation solutions were proposed.

RESULTS

The process map of treatment delivery on X1 consists of six major processes and 24 sub-processes. A total of 27 FMs were identified, with many 19/27 (70%) caused by human errors and 7/27 (27%) caused by machine. From all responses, we tallied a median of 11 FMs (40%) that have both S≥ 4 and O or D ≥ 4. To further focus our analysis, we looked at the highest PRN scores from each member and found 7 FMs that were common. 1 FM was in "initiation of Treatment" sub-process and 6 FMs in "Treatment delivery" sub-process. Proposed solutions to these FMs were concerned with software upgrades. Examples are, allow changes in fractionation, allow dose tracking, auto calculation of couch position for various sub processes, allow DICOM image transfer and many more. The current clinical workflow that we adopted for these FMs either puts the burden on the user to confirm/verify parameters or the use of third-party software. In addition to these high-scoring FMs, we adopted changes in clinical workflow to mitigate other FMs, most of them through third-party software.

CONCLUSION

This study confirmed that the unique design and user-dependent machine environment, human failures are high accounting for 70% of FMs in treatment delivery alone. Our current workflow of the machine depends on direct user input to calculate/confirm certain parameters or the use of third-party software, which also depends on the user for proper completion of the task. Suggested solutions also included proposed improvement to the machine's software and user interface.

Tissue-specific DNA methylation variability and its potential clinical value

Complex diseases have multifactorial etiologies making actionable diagnostic biomarkers difficult to identify. Diagnostic research must expand beyond single or a handful of genetic or epigenetic targets for complex disease and explore a broader system of biological pathways. With the objective to develop a diagnostic tool designed to analyze a comprehensive network of epigenetic profiles in complex diseases, we used publicly available DNA methylation data from over 2,400 samples representing 20 cell types and various diseases. This tool, rather than detecting differentially methylated regions at specific genes, measures the intra-individual methylation variability within gene promoters to identify global shifts away from healthy regulatory states. To assess this new approach, we explored three distinct questions: 1) Are profiles of epigenetic variability tissue-specific? 2) Do diseased tissues exhibit altered epigenetic variability compared to normal tissue? 3) Can epigenetic variability be detected in complex disease? Unsupervised clustering established that global epigenetic variability in promoter regions is tissue-specific and promoter regions that are the most epigenetically stable in a specific tissue are associated with genes known to be essential for its function. Furthermore, analysis of epigenetic variability in these most stable regions distinguishes between diseased and normal tissue in multiple complex diseases. Finally, we demonstrate the clinical utility of this new tool in the assessment of a multifactorial condition, male infertility. We show that epigenetic variability in purified sperm is correlated with live birth outcomes in couples undergoing intrauterine insemination (IUI), a common fertility procedure. Men with the least epigenetically variable promoters were almost twice as likely to father a child than men with the greatest number of epigenetically variable promoters. Interestingly, no such difference was identified in men undergoing in vitro fertilization (IVF), another common fertility procedure, suggesting this as a treatment to overcome higher levels of epigenetic variability when trying to conceive.

Multiple Subthreshold GPCR Signals Combined by the G-Proteins Gαq and Gαs Activate the Caenorhabditis elegans Egg-Laying Muscles

Individual neurons or muscle cells express many G-protein-coupled receptors (GPCRs) for neurotransmitters and neuropeptides, yet it remains unclear how cells integrate multiple GPCR signals that all must activate the same few G-proteins. We analyzed this issue in the Caenorhabditis elegans egg-laying system, where multiple GPCRs on muscle cells promote contraction and egg laying. We genetically manipulated individual GPCRs and G-proteins specifically in these muscle cells within intact animals and then measured egg laying and muscle calcium activity. Two serotonin GPCRs on the muscle cells, Gαq-coupled SER-1 and Gαs-coupled SER-7, together promote egg laying in response to serotonin. We found that signals produced by either SER-1/Gαq or SER-7/Gαs alone have little effect, but these two subthreshold signals combine to activate egg laying. We then transgenically expressed natural or designer GPCRs in the muscle cells and found that their subthreshold signals can also combine to induce muscle activity. However, artificially inducing strong signaling through just one of these GPCRs can be sufficient to induce egg laying. Knocking down Gαq and Gαs in the egg-laying muscle cells induced egg-laying defects that were stronger than those of a SER-1/SER-7 double knockout, indicating that additional endogenous GPCRs also activate the muscle cells. These results show that in the egg-laying muscles multiple GPCRs for serotonin and other signals each produce weak effects that individually do not result in strong behavioral outcomes. However, they combine to produce sufficient levels of Gαq and Gαs signaling to promote muscle activity and egg laying.SIGNIFICANCE STATEMENT How can neurons and other cells gather multiple independent pieces of information from the soup of chemical signals in their environment and compute an appropriate response? Most cells express >20 GPCRs that each receive one signal and transmit that information through three main types of G-proteins. We analyzed how this machinery generates responses by studying the egg-laying system of C. elegans, where serotonin and multiple other signals act through GPCRs on the egg-laying muscles to promote muscle activity and egg laying. We found that individual GPCRs within an intact animal each generate effects too weak to activate egg laying. However, combined signaling from multiple GPCR types reaches a threshold capable of activating the muscle cells.

What about lexical competition? Exploring the locus of lexical retrieval deficits in adults with developmental dyslexia

OBJECTIVE

Individuals with dyslexia do not only show deficits with reading but are also less accurate in naming pictures. This has mainly been linked to prevalent phonological deficits. However, deficits in lexical retrieval of picture names could also be due to increased lexical-semantic competition. The present study tested whether adults with dyslexia (AwDs) are more affected by a competitive lexical-semantic context than control participants.

METHOD

Twenty-seven AwD and 34 control participants completed the blocked-cyclic picture-naming paradigm and the Hayling sentence completion task.

RESULTS

In the blocked-cyclic naming task, AwDs showed a larger semantic interference effect than controls in terms of errors, especially producing competitor errors. In the Hayling sentence completion task, AwDs made more errors than controls when asked to complete sentences with semantically unrelated words, that is, in the competitive condition. They especially produced semantically related words or antonyms to target words.

CONCLUSIONS

We found that AwDs experience difficulties with resolving lexical competition that go beyond their phonological deficits. Future studies will need to establish the mechanisms behind the increased lexical competition that AwDs exhibit. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Practice patterns of pediatric total body irradiation techniques: A Children's Oncology Group survey

PURPOSE

The aim of this study was to examine current practice patterns in pediatric total body irradiation (TBI) techniques among xxx member institutions.

METHODS AND MATERIALS

Between Nov 2019 and Feb 2020 a questionnaire, containing 52 questions related to the technical aspects of TBI was sent to medical physicists at 152 xxx institutions. The questions were designed to obtain technical information on commonly used TBI treatment techniques. Another set of 9 questions related to the clinical management of patients undergoing TBI was sent to 152 xxx member radiation oncologists at the same institutions.

RESULTS

Twelve institutions were excluded because TBI was not performed in their institutions. A total of 88 physicists from 88 institutions (63% response rate) and 96 radiation oncologists from 96 institutions responded (69% response rate). The AP/PA technique was the most common (49 institutions - 56%); 44 institutions (50%) used the lateral technique and 14 institutions (16%) used volumetric modulated arc therapy (VMAT)/Tomotherapy. Mid-plane dose rates of 6-15 cGy/min were most commonly used. The most common specification for lung dose was the mid lung dose for both AP/PA (71%) and lateral (63%) techniques. All physician responders agreed with the need to refine current TBI techniques and 79% supported the investigation of new TBI techniques to further lower the lung dose.

CONCLUSION

There is no consistency in the practice patterns, methods for dose measurement and reporting of TBI doses among xxx institutions. The lack of a standardization precludes meaningful correlation between TBI doses and clinical outcomes including disease control and normal tissue toxicity. The xxx radiation oncology discipline is currently undertaking several steps to standardize the practice and dose reporting of pediatric TBI using detailed questionnaires and phantom-based credentialing for all xxx centers.

The neural G protein Gαo tagged with GFP at an internal loop is functional in C. elegans

Gα_o is the alpha subunit of the major heterotrimeric G protein in neurons and mediates signaling by every known neurotransmitter, yet the signaling mechanisms activated by Gα_o remain to be fully elucidated. Genetic analysis in Caenorhabditis elegans has shown that Gα_o signaling inhibits neuronal activity and neurotransmitter release, but studies of the molecular mechanisms underlying these effects have been limited by lack of tools to complement genetic studies with other experimental approaches. Here, we demonstrate that inserting the green fluorescent protein (GFP) into an internal loop of the Gα_o protein results in a tagged protein that is functional in vivo and that facilitates cell biological and biochemical studies of Gα_o. Transgenic expression of Gα_o-GFP rescues the defects caused by loss of endogenous Gα_o in assays of egg laying and locomotion behaviors. Defects in body morphology caused by loss of Gα_o are also rescued by Gα_o-GFP. The Gα_o-GFP protein is localized to the plasma membrane of neurons, mimicking localization of endogenous Gα_o. Using GFP as an epitope tag, Gα_o-GFP can be immunoprecipitated from C. elegans lysates to purify Gα_o protein complexes. The Gα_o-GFP transgene reported in this study enables studies involving in vivo localization and biochemical purification of Gα_o to compliment the already well-developed genetic analysis of Gα_o signaling.

Double triage to identify poorly annotated genes in maize: The missing link in community curation

The sophistication of gene prediction algorithms and the abundance of RNA-based evidence for the maize genome may suggest that manual curation of gene models is no longer necessary. However, quality metrics generated by the MAKER-P gene annotation pipeline identified 17,225 of 130,330 (13%) protein-coding transcripts in the B73 Reference Genome V4 gene set with models of low concordance to available biological evidence. Working with eight graduate students, we used the Apollo annotation editor to curate 86 transcript models flagged by quality metrics and a complimentary method using the Gramene gene tree visualizer. All of the triaged models had significant errors–including missing or extra exons, non-canonical splice sites, and incorrect UTRs. A correct transcript model existed for about 60% of genes (or transcripts) flagged by quality metrics; we attribute this to the convention of elevating the transcript with the longest coding sequence (CDS) to the canonical, or first, position. The remaining 40% of flagged genes resulted in novel annotations and represent a manual curation space of about 10% of the maize genome (~4,000 protein-coding genes). MAKER-P metrics have a specificity of 100%, and a sensitivity of 85%; the gene tree visualizer has a specificity of 100%. Together with the Apollo graphical editor, our double triage provides an infrastructure to support the community curation of eukaryotic genomes by scientists, students, and potentially even citizen scientists.

Serotonin and neuropeptides are both released by the HSN command neuron to initiate Caenorhabditis elegans egg laying

Neurons typically release both a small-molecule neurotransmitter and one or more neuropeptides, but how these two types of signal from the same neuron might act together remains largely obscure. For example, serotonergic neurons in mammalian brain express the neuropeptide Substance P, but it is unclear how this co-released neuropeptide might modulate serotonin signaling. We studied this issue in C. elegans, in which all serotonergic neurons express the neuropeptide NLP-3. The serotonergic Hermaphrodite Specific Neurons (HSNs) are command motor neurons within the egg-laying circuit which have been shown to release serotonin to initiate egg-laying behavior. We found that egg-laying defects in animals lacking serotonin were far milder than in animals lacking HSNs, suggesting that HSNs must release other signal(s) in addition to serotonin to stimulate egg laying. While null mutants for nlp-3 had only mild egg-laying defects, animals lacking both serotonin and NLP-3 had severe defects, similar to those of animals lacking HSNs. Optogenetic activation of HSNs induced egg laying in wild-type animals, and in mutant animals lacking either serotonin or NLP-3, but failed to induce egg laying in animals lacking both. We recorded calcium activity in the egg-laying muscles of animals lacking either serotonin, NLP-3, or both. The single mutants, and to a greater extent the double mutant, showed muscle activity that was uncoordinated and unable to expel eggs. Specifically, the vm2 muscles cells, which are direct postsynaptic targets of the HSN, failed to contract simultaneously with other egg-laying muscle cells. Our results show that the HSN neurons use serotonin and the neuropeptide NLP-3 as partially redundant co-transmitters that together stimulate and coordinate activity of the target cells onto which they are released.

Activity of the brain results from neurons communicating with each other using chemical signals. A typical neuron releases two kinds of chemical signals: a small molecule neurotransmitter, such as serotonin, and one or more small proteins, called neuropeptides. For example, neurons in the human brain that release serotonin, a neurotransmitter thought to be involved in depression, also release the neuropeptide Substance P. Neuroscientists have typically studied the effects of neurotransmitters and neuropeptides separately, without considering how these two types of signals from the same neuron might be integrated. Here we analyzed how specific neurons in the model organism C. elegans use both serotonin and a neuropeptide together. The Hermaphrodite Specific Neurons (HSNs) activate a small group of neurons and muscles to generate egg-laying behavior. Killing the HSNs resulted in animals unable to lay eggs, but we found that eliminating either serotonin or the neuropeptide resulted in HSNs that still remained able to activate egg laying. However, eliminating both serotonin and the neuropeptide resulted in HSNs unable to activate coordinated contractions of the egg-laying muscles. Our results show that in a living animal, serotonin acts in concert with a co-released neuropeptide to carry out its functions.

Agreeing to disagree: deaf and hearing children's awareness of subject-verb number agreement

This study investigated deaf adolescents' implicit and explicit awareness of subject-verb number agreement. In Experiment 1, a self-paced reading task, the reading times of deaf and hearing children (matched for reading and chronological age, mean=8;3 and 13;10 years) increased when sentences contained disagreeing subject-verb number markers. However, deaf adolescents' slowing occurred later in the sentence than it did in both groups of hearing children. The same deaf adolescents were unable to detect and correct subject-verb agreement errors in Experiment 2, whereas both groups of hearing children performed well on this task. Thus, deaf adolescents demonstrated implicit awareness of agreement in the absence of explicit knowledge. Moreover, this nascent awareness was below that expected on the basis of their (substantially delayed) reading ability. Therefore, grammatical difficulties could be a significant impediment to deaf children's literacy. Future research should examine whether this is a result of late or incomplete learning of English, bilingualism, or another factor.

Cerebellar rTMS disrupts predictive language processing

The human cerebellum plays an important role in language, amongst other cognitive and motor functions [1], but a unifying theoretical framework about cerebellar language function is lacking. In an established model of motor control, the cerebellum is seen as a predictive machine, making short-term estimations about the outcome of motor commands. This allows for flexible control, on-line correction, and coordination of movements [2]. The homogeneous cytoarchitecture of the cerebellar cortex suggests that similar computations occur throughout the structure, operating on different input signals and with different output targets [3]. Several authors have therefore argued that this ‘motor’ model may extend to cerebellar nonmotor functions [3–5], and that the cerebellum may support prediction in language processing [6]. However, this hypothesis has never been directly tested. Here, we used the ‘Visual World’ paradigm [7], where on-line processing of spoken sentence content can be assessed by recording the latencies of listeners' eye movements towards objects mentioned. Repetitive transcranial magnetic stimulation (rTMS) was used to disrupt function in the right cerebellum, a region implicated in language [8]. After cerebellar rTMS, listeners showed delayed eye fixations to target objects predicted by sentence content, while there was no effect on eye fixations in sentences without predictable content. The prediction deficit was absent in two control groups. Our findings support the hypothesis that computational operations performed by the cerebellum may support prediction during both motor control and language processing.

The energetic difference between synthesis of correct and incorrect base pairs accounts for highly accurate DNA replication

To better understand the energetics of accurate DNA replication, we directly measured ΔG(o) for the incorporation of a nucleotide into elongating dsDNA in solution (ΔG(o)(incorporation)). Direct measurements of the energetic difference between synthesis of correct and incorrect base pairs found it to be much larger than previously believed (average ΔΔG(o)(incorporation) = 5.2 ± 1.34 kcal mol(-1)). Importantly, these direct measurements indicate that ΔΔG(o)(incorporation) alone can account for the energy required for highly accurate DNA replication. Evolutionarily, these results indicate that the earliest polymerases did not have to evolve sophisticated mechanisms to replicate nucleic acids; they may only have had to take advantage of the inherently more favorable ΔG(o) for polymerization of correct nucleotides. These results also provide a basis for understanding how polymerases replicate DNA (or RNA) with high fidelity.

Deaf and hearing children's plural noun spelling

The present study examines deaf and hearing children's spelling of plural nouns. Severe literacy impairments are well documented in the deaf, which are believed to be a consequence of phonological awareness limitations. Fifty deaf (mean chronological age 13;10 years, mean reading age 7;5 years) and 50 reading-age-matched hearing children produced spellings of regular, semiregular, and irregular plural nouns in Experiment 1 and nonword plurals in Experiment 2. Deaf children performed reading-age appropriately on rule-based (regular and semiregular) plurals but were significantly less accurate at spelling irregular plurals. Spelling of plural nonwords and spelling error analyses revealed clear evidence for use of morphology. Deaf children used morphological generalization to a greater degree than their reading-age-matched hearing counterparts. Also, hearing children combined use of phonology and morphology to guide spelling, whereas deaf children appeared to use morphology without phonological mediation. Therefore, use of morphology in spelling can be independent of phonology and is available to the deaf despite limited experience with spoken language. Indeed, deaf children appear to be learning about morphology from the orthography. Education on more complex morphological generalization and exceptions may be highly beneficial not only for the deaf but also for other populations with phonological awareness limitations.

Connectionist models of neuropsychological disorders

Artificial neural networks ('connectionist models') embody aspects of real neuronal systems. But does studying the breakdown of performance in such models help us to understand cognitive impairments in humans following brain damage? Here we review recent attempts to capture different neuropsychological disorders using connectionist models with simulated lesions. We show how such lesion studies can be used to evaluate some of the standard assumptions made in neuropsychological research, concerning both double dissociations and associations between patterns of impairment. We also illustrate how lesioned models, like humans, can sometimes be more impaired on the easier of two tasks and demonstrate that connectionist models can incorporate forms of internal structure. Finally we discuss the utility of the models for understanding and predicting the effectiveness of different rehabilitation strategies. Future questions concern the role and possible development of internal structure within these models, whether the models can be generalized to larger-scale simulations, and whether they can accommodate higher-order linguistic disorders.

Model evaluation and case series data

We discuss aggregation of data from neuropsychological patients and the process of evaluating models using data from a series of patients. We argue that aggregation can be misleading but not aggregating can also result in information loss. The basis for combining data needs to be theoretically defined, and the particular method of aggregation depends on the theoretical question and characteristics of the data. We present examples, often drawn from our own research, to illustrate these points. We also argue that statistical models and formal methods of model selection are a useful way to test theoretical accounts using data from several patients in multiple-case studies or case series. Statistical models can often measure fit in a way that explicitly captures what a theory allows; the parameter values that result from model fitting often measure theoretically important dimensions and can lead to more constrained theories or new predictions; and model selection allows the strength of evidence for models to be quantified without forcing this into the artificial binary choice that characterizes hypothesis testing methods. Methods that aggregate and then formally model patient data, however, are not automatically preferred to other methods. Which method is preferred depends on the question to be addressed, characteristics of the data, and practical issues like availability of suitable patients, but case series, multiple-case studies, single-case studies, statistical models, and process models should be complementary methods when guided by theory development.

Regulation of influenza RNA polymerase activity and the switch between replication and transcription by the concentrations of the vRNA 5' end, the cap source, and the polymerase

The influenza RNA-dependent RNA polymerase (RdRp) both replicates the flu's RNA genome and transcribes its mRNA. Replication occurs de novo; however, initiation of transcription requires a 7-methylguanosine 5'-capped primer that is "snatched" from host mRNA via endonuclease and cap binding functions of the influenza polymerase. A key question is how the virus regulates the relative amounts of transcription and replication. We found that the concentration of a capped cellular mRNA, the concentration of the 5' end of the viral RNA, and the concentration of RdRp all regulate the relative amounts of replication versus transcription. The host mRNA, from which the RdRp snatches its capped primer, acts to upregulate transcription and repress replication. Elevated concentrations of the RdRp itself switch the influenza polymerase toward replication, likely through an oligomerization of the polymerase. The 5' end of the vRNA template both activates replication and inhibits transcription of the vRNA template, thereby indicating that RdRp contains an allosteric binding site for the 5' end of the vRNA template. These data provide insights into the regulation of RdRp throughout the viral life cycle and how it synthesizes the appropriate amounts of viral mRNA and replication products (vRNA and cRNA).

Breast cancer patients unknowingly dosing themselves with estrogen by using topical moisturizers

Abstract #4087

Background: Topically applied estrogens are more efficiently absorbed into the body than estrogens administered orally, due to the first pass effect by the liver. Estrogen receptor positive breast cancer patients need to avoid exogenously administered estrogen to minimize chance of recurrence. This is especially significant for women on aromatase inhibitor treatment,where topical estrogen may overcome the therapeutic effect. Also, non breast cancer patients using estrogen containing topical moisturizers may be unknowingly dosing themselves daily with estrogen, often for years, increasing their chances of developing breast cancer.
 Materials and Methods: Sixteen different topical moisturizers were purchased or donated from department stores or chain drugstores. None of the creams noted any estrogen content in their list of ingredients. Each of the sixteen commercial products was analyzed for estradiol, estriol and estrone utilizing High Performance Liquid Chromatography (HPLC). HPLC is commonly used in the pharmaceutical industry to provide component analysis. Detection was carried out through use of a Variable Wavelength Detector (VWD) and a Diode Array Detector.
 Results: Four samples contained greater than 0.40% estriol, one contained 0.17% estriol, and one contained 0.05% estrone, despite having no listing on the ingredient list.
 Discussion: Topical estrogens are considered effective in enhancing the “youthful look” of aging skin. Manufacturers are marketing incompletely labeled moisturizers containing estrogens. Consumers are unaware their moisturizer may be providing them with unwanted systemic estrogen exposure. The FDA cosmetics division is not presently testing for this potential risk for breast cancer patients. Other breast cancer advocacy groups and the FDA need to promptly repeat these procedures and also check for exotic "designer" estrogens.
 


Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 4087.

Atomic resolution structures of Escherichia coli and Bacillus anthracis malate synthase A: comparison with isoform G and implications for structure-based drug discovery

Enzymes of the glyoxylate shunt are important for the virulence of pathogenic organisms such as Mycobacterium tuberculosis and Candida albicans. Two isoforms have been identified for malate synthase, the second enzyme in the pathway. Isoform A, found in fungi and plants, comprises approximately 530 residues, whereas isoform G, found only in bacteria, is larger by approximately 200 residues. Crystal structures of malate synthase isoform G from Escherichia coli and Mycobacterium tuberculosis were previously determined at moderate resolution. Here we describe crystal structures of E. coli malate synthase A (MSA) in the apo form (1.04 A resolution) and in complex with acetyl-coenzyme A and a competitive inhibitor, possibly pyruvate or oxalate (1.40 A resolution). In addition, a crystal structure for Bacillus anthracis MSA at 1.70 A resolution is reported. The increase in size between isoforms A and G can be attributed primarily to an inserted alpha/beta domain that may have regulatory function. Upon binding of inhibitor or substrate, several active site loops in MSA undergo large conformational changes. However, in the substrate bound form, the active sites of isoforms A and G from E. coli are nearly identical. Considering that inhibitors bind with very similar affinities to both isoforms, MSA is as an excellent platform for high-resolution structural studies and drug discovery efforts.

Localizing the deficit in a case of jargonaphasia

We report the case of a neologistic jargonaphasic and ask whether her target-related and abstruse neologisms are the result of a single deficit, which affects some items more severely than others, or two deficits: one to lexical access and the other to phonological encoding. We analyse both correct/incorrect performance and errors and apply both traditional and formal methods (maximum-likelihood estimation and model selection). All evidence points to a single deficit at the level of phonological encoding. Further characteristics are used to constrain the locus still further. V.S. does not show the type of length effect expected of a memory component, nor the pattern of errors associated with an articulatory deficit. We conclude that her neologistic errors can result from a single deficit at a level of phonological encoding that immediately follows lexical access where segments are represented in terms of their features. We do not conclude, however, that this is the only possible locus that will produce phonological errors in aphasia, or, indeed, jargonaphasia.

High-throughput purification and quality assurance of Arabidopsis thaliana proteins for eukaryotic structural genomics

The Center for Eukaryotic Structural Genomics (CESG) has established procedures for the purification of Arabidopsis proteins in a high-throughput mode. Recombinant proteins were fused with (His)(6)-MBP tags at their N-terminus and expressed in Escherichia coli. Using an automated AKTApurifier system, fusion proteins were initially purified by immobilized metal affinity chromatography (IMAC). After cleavage of (His)(6)-MBP tags by TEV protease, (His)(6)-MBP tags were separated from target proteins by a subtractive 2nd IMAC. As a part of quality assurance, all purified proteins were subjected to MALDI-TOF and ESI mass spectrometry to confirm target identity and integrity, and determine incorporation of seleno-methionine (SeMet) and (15)N and (13)C isotopes. The protocols have been used successfully to provide high quality proteins that are suitable for structural studies by X-ray crystallography and NMR.

Orthographic structure and deaf spelling errors: syllables, letter frequency, and speech

Syllable structure influences hearing students' reading and spelling (e.g., Badecker, 1996; Caramazza & Miceli, 1990; Prinzmetal, Treiman, & Rho, 1986; Rapp, 1992; Treiman & Zukowski, 1988). This may seem unsurprising since hearers closely associate written and spoken words. We analysed a corpus of spelling errors made by deaf students. They would have learned English orthography with an attenuated experience of speech. We found that the majority of their errors were phonologically implausible but orthographically legal. A tendency to replace uncommon letter sequences with common sequences could not account for this pattern, nor could residual influence from speech. Since syllabically defined constraints are required to keep sequences orthographically legal, the deaf data are marked by an influence of syllable structure. Two main conclusions follow: (1) Our results contribute to evidence that abstract constraints, not derived from peripheral speech or hearing mechanisms, govern the organization of linguistic knowledge; and (2) statistical redundancy could not explain the deaf results. It does not offer a general alternative to suprasegmental structure.

Syllabic organization and deafness: orthographic structure or letter frequency in reading?

For hearing people, structure given to orthographic information may be influenced by phonological structures that develop with experience of spoken language. In this study we examine whether profoundly deaf individuals structure orthographic representation differently. We ask "Would deaf students who are advanced readers show effects of syllable structure despite their altered experience of spoken language, or would they, because of reduced influence from speech, organize their orthographic knowledge according to groupings defined by letter frequency?" We used a task introduced by Prinzmetal (Prinzmetal, Treiman, & Rho, 1986) in which participants were asked to judge the colour of letters in briefly presented words. As with hearing participants, the number of errors made by deaf participants was influenced by syllable structure (Prinzmetal et al., 1986; Rapp, 1992). This effect could not be accounted for by letter frequency. Furthermore, there was no correlation between the strength of syllable effects and residual speech or hearing. Our results support the view that the syllable is a unit of linguistic organization that is abstract enough to apply to both spoken and written language.

Quantitative analysis of disturbed cell maturation in dysplastic lesions of the respiratory tract epithelium

Autoradiographic patterns of [3H]thymidine incorporation, nuclear/cytoplasmic ratios (N/C), and the percentage of dark epithelial cells were analyzed in a group of epithelial lesions induced by 7,12-dimethylbenz[a]anthracene (DMBA) in rat tracheal transplants. It was found that similar lesions of different age exhibit the same labeling indices (LIs), therefore the lesions of different age were subsequently pooled in the following groups and studied by high resolution light microscopic autoradiography: squamous metaplasia without or with only mild atypia, squamous metaplasia with moderate atypia, squamous metaplasia with severe atypia, carcinoma in situ, and microinvasive carcinoma. Normal tracheal and esophageal epithelia were also analyzed. Whereas the normal tracheal basal layer exhibited an LI smaller than 1%, a clear difference between the carcinomas (in situ and invasive) on one hand (LI approximately 32%) and all the remaining epithelia on the other hand (LI approximately 18%) was detected. The LIs of the suprabasal cells exhibited a statistically significant difference between the squamous epithelia without atypia (LI approximately 2%) and the group comprising all the atypical lesions (LI approximately 9%). Gradients of increasing N/C (nucleus-cytoplasm ratios) values could be observed as the lesions increased in severity, especially in the middle and surface layers (e.g., in the surface layer regular metaplasia N/C = 0.08, squamous metaplasia with moderate atypia N/C = 0.26, and carcinoma in situ N/C = 0.50). Dark cells were absent in the normal esophageal epithelium, were present in moderate numbers in the basal layer of regular squamous metaplasia (18%), and increased markedly in the atypical epithelial lesions (approximately 50% in the atypical squamous metaplasias and 70% in carcinoma in situ). In the suprabasal layer dark cells increased from 3% in squamous metaplasia with moderate atypia to 28% in metaplasia with severe atypia and 56% in carcinoma in situ. The results confirm in a quantitative fashion that disturbances of cell maturation and cell proliferation are key features of dysplastic lesions induced by chemical carcinogens, and suggest the use of objective parameters for evaluation and classification of preneoplastic alterations.

Structure-function relationships of alkyl-lysophospholipid analogs in selective antitumor activity

This investigation was initiated in order to delineate the structure-function relationship of the anticancer alkyl-lysophospholipids and assess their degree of selective cytotoxicity toward neoplastic cells. A series of glycerol phosphocholine analogs with varying substitutions in the sn-1 and sn-2 position were tested for their inhibitory activity as measured by thymidine incorporation, clonogenic assays and effects on protein kinase C activity against a series of human leukemic cell lines and healthy bone marrow progenitor cells. The IC50 was determined for each of the compounds in each cell line and healthy bone marrow cells following a 4-h incubation. The data indicated that a 16-18 carbon chain at the sn-1 coupled with a short substitution at sn-2 had the broadest antitumor activity and was the least toxic to normal bone marrow cells. The results provide a number of useful leads toward the design and development of potentially more active phospholipid compounds.

Use of the polymerase chain reaction to detect hypermethylation in the calcitonin gene. A new, sensitive approach to monitor tumor cells in acute myelogenous leukemia

Based on the recent observations that, in a majority of patients with acute leukemia, the 5' end of the calcitonin gene was hypermethylated and abnormal DNA fragments were observed following HpaII restriction digestion, we have developed a PCR-based method to sensitively detect this abnormal methylation of the calcitonin gene in AML. Applying the concept of competitive PCR, a semi-quantitative correlation was obtained between the amount of hypermethylation and the amount of leukemic cells present. These results suggest that this method will be useful to monitor the amount of tumor cells in bone marrow from patients with AML.

Autologous bone marrow transplantation in acute leukemia with marrow purged with alkyl-lysophospholipid

Alkyl-lysophospholipids are anticancer agents that are selectively toxic to leukemic cells and relatively sparing of normal bone marrow cells. Thus, they would be likely candidates for purging remission marrows before autologous bone marrow transplant. One of the more promising agents is edelfosine, which could be safely used for purging without prolonging marrow recovery. Assays for marrow progenitor cells were performed before and after purging and cryopreservation in 64 patients. There was no significant reduction in colony formation after purging when compared with unpurged cryopreserved marrow, but there was a significant reduction after cryopreservation. Twenty-four patients with acute leukemia in second (16 patients) or third remission (3 patients), early relapse (3 patients), or in first remission with successfully treated extramedullary relapse (2 patients) received marrow-ablative chemotherapy and total body irradiation followed by infusion of marrow purged for 4 hours with 50 to 100 micrograms/mL of edelfosine. There were 9 lymphoblastic and 15 myelogenous leukemia patients. The median time to granulocyte recovery to 500/microL was 26 and 33 days for the 50 and 75 microgram/mL doses, respectively. The patient whose marrow was purged at the dose of 100 micrograms/mL failed to engraft. The median time to platelet recovery to 25,000/microL was 45 and 37 days for the 50 and 75 micrograms/mL doses, respectively. Twenty-nine percent of the patients remain disease free from 131 to 1,291 days, with a median of 356 days. These results have established that purging with 75 micrograms/mL of edelfosine is a safe dose and is recommended for a phase II trial.

Comparison of selective cytotoxicity of alkyl lysophospholipids

Alkyl lysophospholipids have been shown to be cytooxic to a number of neoplastic tissues. One, ET-18-OCH3, has been used to selectively purge leukemic cells from mixtures with normal marrow progenitor cells, in vitro and in vivo. We have measured the 50% inhibitory (IC50) effect of a series of ether lipids (EL) on leukemic cells (HL60, K562, Daudi, KG-1, KG-1a) and normal marrow progenitor cells. Cells were incubated with varying concentrations of EL for 4 hr and assayed for viability, [3H]thymidine incorporation and clonogenicity in semi-solid media. The effect on protein kinase C (PKC) activity was assayed for each compound. Compounds tested included three glycerophosphocholine analogs--ET-18-OCH3, ET-16-NHCOCH3, and BM 41.440. In addition, a lipoidal amine, CP 46665, an ethyleneglycolphospholipid, AEPL, and four single chain alkylphosphocholine analogs, HePC2, HePC3, HePC4 and HePC6 were also tested. During the period of incubation, the cells remained viable (greater than 70%) as judged by trypan blue dye exclusion. The glycerophosphocholines were the most active and showed the highest therapeutic index. The lipoidal amine was active, but toxic to normal marrow progenitor cells. The ethyleneglycolphospholipid was active against HL60, but not against the other cell lines. The single chain alkylphosphocholine analogs were less active. All of the compounds inhibited PKC activity; however, the glycerophosphocholines were the most inhibitory.

Purging of acute myeloid leukemic cells by ether lipids and hyperthermia

Ether lipids (EL) and hyperthermia have been shown to possess a relatively selective cytotoxicity to leukemic cells. In this study, the combined effects of EL (ET-18-OCH3, ET-16-NHCOCH3, or BM 41.440) and hyperthermia on the growth of hematopoietic progenitors, myeloid leukemic cell lines, and leukemic cells obtained from patients with acute myeloid leukemia (AML) were examined to determine if this combination resulted in a greater selective killing of leukemic cells than that achieved by either EL or heat alone. When the cells were treated simultaneously with EL (50 micrograms/mL) and hyperthermia (42 degrees C) for one hour, the killing of leukemic cell line cells was enhanced considerably. Among the three EL, however, the combination of ET-18-OCH3 and heat seemed to be the most cytotoxic to leukemic cell line cells with no effect on the growth of hematopoietic progenitors. An increase in the duration of treatment with ET-18-OCH3 to four hours with heat added during the last hour resulted in a further reduction of leukemic cell line cells while sparing 50% of hematopoietic progenitors after cryopreservation. The combined treatment with ET-18-OCH3 and heat also inhibited the growth of leukemic progenitors obtained from AML patients by 97% to 100%. These data indicate that the combined treatment with EL and hyperthermia might offer an efficient means to eliminate myeloid leukemic cells in vitro.

Experimental studies on the role of alkyl lysophospholipids in autologous bone marrow transplantation

The selective cytocidal effect of alkyl lysophospholipids against neoplastic cells while sparing normal cells make these ideal candidates for purging leukemic cells from bone marrows obtained during remission. To test the feasibility of such an approach, a murine model and an in vitro human cell model were developed. In the murine system a mixture of normal bone marrow cells and WEHI IIIB myelomonocytic leukemic cells was incubated with varying doses of 1-O-octadecyl-2-O-methyl-rac-glycero-3-phosphocholine (ET-Me) for 24 hr before being injected into tail veins of lethally irradiated Balb/c mice. At doses of 20 and 100 micrograms/ml, long-term survivors were noted. The additional steps of freezing and thawing following incubation resulted in significantly longer survival with doses of 10 to 50 micrograms/ml, but were toxic to marrow stem cells at 100 micrograms/ml. In the in vitro model, normal marrow progenitor cells and leukemic cells (the promyelocytic cell line HL60) were exposed to varying concentrations of ET-Me for 1 and 4 hr alone or mixed, and clonogenicity was assayed by colony formation in semisolid medium during 7-14 days' incubation. At doses up to 100 micrograms/ml exposed for 4 hr normal progenitor cells were spared and HL60 colonies eliminated. Other phospholipids analogues were less effective in eliminating leukemic cells, but spared normal progenitor cells. A survey of fresh leukemic cells found varying degrees of sensitivity to ET-Me, indicating the need for testing a variety of compounds. These studies clearly indicated the potential usefulness of alkyl lysophospholipid compounds in selectively purging leukemic cells from remission marrows for autologous bone marrow transplantation.

Elimination of leukemic cells by the combined use of ether lipids in vitro

Two ether lipids, CP-46,665-1 (4-aminomethyl-1-[2,3-(di-n-decyloxy)-n- propyl]-4-phenylpiperidine) and ET-18-OCH3 (racemic 1-O-octadecyl-2-O-methylglycero-3-phosphocholine) have been shown to possess antileukemic activity in vitro. To explore the possible use of these compounds for purging remission bone marrow cells of leukemic cells, we examined the cytotoxic effect of these compounds on normal hematopoietic progenitor cells and leukemic cell line cells (HL-60, K-562, KG-1a, KG-1, and Daudi) by using the clonogenic assay. When cells were treated with CP-46,665-1 or ET-18-OCH3 (50 micrograms/ml for 1 h), these compounds did not inhibit the growth of normal progenitors, whereas the growth of the clonogenic leukemic cells was inhibited with differences in their sensitivities to the cytotoxic effect of CP-46,665-1 and ET-18-OCH3. Incubation of leukemic cells (HL-60 and Daudi cells) with both CP-46,665-1 (50 micrograms/ml) and ET-18-OCH3 (50 micrograms/ml) for 1 h resulted in a greater reduction of clonogenic leukemic cells than treated with each compound alone. Approximately a 3 log killing of clonogenic HL-60 cells and a 5 log killing of Daudi cells was achieved; however, the combined treatment of normal bone marrow cells with CP-46,665-1 and ET-18-OCH3 did not alter the growth of normal progenitors. This combined treatment also selectively eliminated the leukemic cells (HL-60 and Daudi cells) from a mixture (1000:1) of normal bone marrow cells and leukemic cells. It is conceivable that the pronounced difference in sensitivity to this combined treatment can be exploited for the elimination of residual leukemic cells in autologous remission marrow grafts.

Purging leukemic cells from simulated human remission marrow with alkyl-lysophospholipid

Alkyl-lysophospholipids (ALP) are analogues of 2-lysophosphatidylcholine that have been reported to have selective antitumor activity. These compounds could potentially be useful in purging bone marrow of leukemic cells in autologous marrow transplantation in acute leukemia. To determine the efficacy of pharmacological purging by ALP, we have designed a human assay system to mimic the conditions expected in the clinical setting of autotransplantation using remission marrow. A simulated remission marrow (SRM) was prepared by mixing normal marrow cells and HL60 cells in a ratio of 1,000:1. The effect of cryopreservation on ALP-treated normal, HL60, and SRM cells was examined. In separate experiments, ALP significantly reduced the number of clonogenic HL60 cells with no effect on normal marrow progenitors. The effect of ALP was more apparent after cryopreservation. Incubation of HL60 cells with 50 micrograms/mL ALP for four hours followed by cryopreservation resulted approximately in a 3 log reduction of clonogenic HL60 cells. ALP also selectively purged the small number of leukemic cells from SRM. In SRM, the data suggested that ALP had indirect cytotoxic activity on leukemic cells by enhancing the cytotoxic activity of monocytes in addition to its direct effect. We found no evidence that clonogenic HL60 cells decreased because of induction of differentiation by ALP. These data indicated that treatment of marrow cells with ALP offers an efficient means to eliminate leukemic cells from the graft.

Effect of alkyl-lysophospholipids on phosphatidylcholine biosynthesis in leukemic cell lines

Alkyl-lysophospholipids are ether analogues of lysophospholipids that have tumoricidal activity mediated through activation of macrophages or by direct effect on tumor cells by disturbance of phospholipid metabolism. The effect of racemic 1-octadecyl-2-methyl-sn-glycero-3 phosphocholine on phosphatidylcholine synthesis was investigated in sensitive (HL-60) and resistant (K-562) human leukemic cell lines. Radiolabeled lysophosphatidyl-choline, choline, and methionine incorporation into phosphatidylcholine was measured in intact cells exposed for 24 h to varying concentrations of the compound. In HL-60 cells, marked inhibition of phosphatidylcholine synthesis was demonstrated using lysophosphatidylcholine or choline as precursors, but no effect was observed on methionine incorporation. No effects were observed in K-562 cells. These investigations suggest that alkyl-lysophospholipids inhibit phosphatidylcholine synthesis via the acyltransferase reaction and from choline, but not from methionine.

Proper identification of anisakine worms

Luminal, gastric, intestinal and mesenteric forms of anisakiasis are known and can be encountered where raw or undercooked marine fish or squid are eaten. Although the anisakine nematodes which cause infection in humans are usually identified after surgical removal, laboratory personnel should be aware of their similarities to other nematodes. Cases have been reported of detection of larval nematodes in the throats or mouths of patients who have vomited or coughed. When such specimens are submitted to the clinical laboratory, problems in identification can be minimized by proper fixation and clearing. Systems for study involving clearing in phenol-ethanol and dissection to observe presence or absence of a ventricular appendix or intestinal cecum to distinguish Anisakis-, Phocanema- and Contracaecum-type larvae are described. Distinguishing characteristics are illustrated. The recovery of a Phocanema-type larva from a California woman is reported; the presence of the larvae in fish sold for human consumption in San Diego is exemplified.

Role of pH in production of hydrogen from carbohydrates by colonic bacterial flora. Studies in vivo and in vitro

Hydrogen produced by colonic bacteria and excreted in breath is a useful index of carbohydrate malabsorption. Since colonic contents are often acidic in individuals with carbohydrate malabsorption and in normal newborns, we determined the effect of colonic acidification on H2 production. Acidification of colonic contents by dietary means significantly reduced excess breath H2 excretion from 55.4 +/- 11.1 (SEM) to 12.2 +/- 3.1 ml/4 h (P less than 0.05) after administration of 0.3 g/kg of the nonabsorbable sugar lactulose to five normal adult subjects. Similarly, the breath H2 response to lactose was reduced or eliminated in two proven lactose malabsorbers after acidification. The correlation between pH and H2 production from carbohydrate was further investigated in adults and neonates, using an in vitro fecal incubation system. Glucose disappearance and H2 production were pH dependent and highly correlated (r = 0.94) in the pH range 5.5-7.6. Maximal production of H2 from glucose by fecal incubates occurred at pH 7.0-7.45. Inhibition of H2 production from carbohydrate occurred at acid pH. H2 per hour from glucose at pH 6.2 and 5.5 averaged 60.2% and 24.2%, respectively, of that produced at neutral pH. Rapid reversal of pH-induced inhibition by neutralization indicated a metabolic, rather than a bactericidal process. The observations indicate that the breath H2 response to malabsorbed carbohydrate is affected by colonic pH. It appears that the efficiency of bacterial carbohydrate metabolism in the colon is pH dependent.

Classification of cultured mammalian cells by shape analysis and pattern recognition

We have developed a method for classifying cultured cells on the basis of shape characteristics. High-resolution optical information on three-dimensional shape was obtained by anodic oxide interferometry. Each interference order formed in a cell was considered as a closed figure; measurement of 37 mathematical descriptors was carried out for each figure. The individual cells were classified according to the values of their descriptors. We used standard principles of pattern recognition, such as hierarchical cluster analysis and nearest neighbor analysis, as a basis for ordering the cells into groups. Alternatively, linear discriminant functions could be used, but they provided only a slight improvement in correct classification of the cells. We anticipate that the method will be appropriate for classification of cultured cell lines and for determination of the magnitude and direction of cell shape changes implicated in various biological processes.

Electron microscopic studies of bacteriophage M13 DNA replication

Intracellular forms of M13 phage DNA isolated after infection of Escherichia coli with wild-type phage have been studied by electron microscopy and ultracentrifugation. The data indicate the involvement of rolling-circle intermediates in single-stranded DNA synthesis. In addition to single-stranded circular DNA, we observed covalently closed and nicked replicative-form (RF) DNAs, dimer RF DNAs, concatenated RF DNAs, RF DNAs with single-stranded tails (theta, rolling circles), and, occasionally, RF DNAs with theta structures. The tails in theta molecules are always single stranded and are never longer than the DNA from mature phage; the proportion of theta to other RF molecules does not change significantly with time after infection. The origin of single-stranded DNA synthesis has been mapped by electron microscopy at a unique location on RF DNA by use of partial denaturation mapping and restriction endonuclease digestion. This location is between gene IV and gene II, and synthesis proceeds in a counterclockwise direction on the conventional genetic map.

Asymphylodora atherinopsidis (Trematoda: Monorchiidae) from the California grunion, Leuresthes tenuis, including a redescription

Asymphylodora (Asymphylodoroides) atherinopsidis from the California grunion, Leuresthes tenuis, a new host record, and jacksmelt, Atherinopsis californiensis, the type host, is redescribed and illustrated using more symmetrical as well as larger and smaller specimens than the holotype. The geographic distribution is extended from the type locality of Stinson Beach, Marin Co., California to Estero Beach, 10 km south of Ensenada, Baja California Norte, Mexico. Two tubular externat seminal vesicles opening independently into the internal seminal vesicle are reported apparently for the first time in a trematode. The genital pore is at the left posterolateral margin of the acetabulum which is midway between the lateral margins. Worms may grow to a length of 5.6 mm but eggs were present in one specimen 1.3 mm long.

The use of alpha-galactosidase and invertase in hollow fiber reactors

Invertase and alpha-galactosidase have been immobilized in hollow fiber cartridges with no detectable enzyme leakage and used for the hydrolysis of sucrose and raffinose, respectively. For both hollow fiber immobilized enzymes nearly complete substrate conversion is possible. Enzyme stabilities in polysulfonate hollow fibers which have been preconditioned with bovine albumin approach the stabilities of the free enzymes.

DNA replication in Chinese hamster ovary cells made permeable to nucleotides by tween-80 treatment

We have developed a method for permeabilizing CHO cells to nucleotides under conditions which allow most cells to remain viable. Permeabilized cells can carry out ATP-dependent, semiconservative synthesis of DNA. The data are consistent with the continuation of DNA synthesis in those cells in S phase at the time of treatment, possibly limited to completion of replicon synthesis without new initiations.

Hydrogen production in the rat following ingestion of raffinose, stachyose and oligosaccharide-free bean residue

Raffinose and stachyose were compared to cooked California Small White beans (CSW) containing 4% alpha-oligosaccharides (stachyose and raffinose) and to oligosaccharide-free CSW solids (residue from hexane and 70% ethanol extraction of CSW) as sources of hydrogen when ingested by rats maintained in life support systems. If the oligosaccharide content were the only hydrogen source in CSW, it would have had to be 25 times as potent as CSW, but raffinose was only five times and stachyose seven times as potent as CSW. Oligosaccharide-free residue was 0.4 to 0.5 as active as CSW. Hydrogen producing potencies of stachyose and raffinose were enhanced by feeding in combinations with residue. The increases in hydrogen production from the combinations were more than additive. Thus, CSW contains at least one 70% alcohol-insoluble substance which, in addition to the oligosaccharides, is essential to bring about quantitatively the physiological response to whole beans observed in rats.