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Multispectral, multiplex immunofluorescence (mIF) microscopy has been used to great effect in research to identify cellular co-expression profiles and spatial relationships within tissue, providing a myriad of diagnostic advantages. As these technologies mature, it is essential that image data from mIF microscopes is reproducible and standardizable across devices. We sought to characterize and correct differences in illumination intensity and spectral sensitivity between three multispectral microscopes. We scanned eight melanoma tissue samples twice on each microscope and calculated their average tissue region flux intensities. We found a baseline average standard deviation of 29.9% across all microscopes, scans, and samples, which was reduced to 13.9% after applying sample-specific corrections accounting for differences in the tissue shown on each slide. We used a basic calibration model to correct sample- and microscope-specific effects on overall brightness and relative brightness as a function of the image layer. We tested the generalizability of the calibration procedure and found that applying corrections to independent validation subsets of the samples reduced the variation to 2.9 ± 0.03%. Variations in the unmixed marker expressions were reduced from 15.8% to 4.4% by correcting the raw images to a single reference microscope. Our findings show that mIF microscopes can be standardized for use in clinical pathology laboratories using a relatively simple correction model.

Summary Over the past decade, short-read sequence alignment has become a mature technology. Optimized algorithms, careful software engineering and high-speed hardware have contributed to greatly increased throughput and accuracy. With these improvements, many opportunities for performance optimization have emerged. In this review, we examine three general-purpose short-read alignment tools—BWA-MEM, Bowtie 2 and Arioc—with a focus on performance optimization. We analyze the performance-related behavior of the algorithms and heuristics each tool implements, with the goal of arriving at practical methods of improving processing speed and accuracy. We indicate where an aligner's default behavior may result in suboptimal performance, explore the effects of computational constraints such as end-to-end mapping and alignment scoring threshold, and discuss sources of imprecision in the computation of alignment scores and mapping quality. With this perspective, we describe an approach to tuning short-read aligner performance to meet specific data-analysis and throughput requirements while avoiding potential inaccuracies in subsequent analysis of alignment results. Finally, we illustrate how this approach avoids easily overlooked pitfalls and leads to verifiable improvements in alignment speed and accuracy. Contact richard.wilton@jhu.edu Supplementary information Appendices referenced in this article are available at Bioinformatics online.

BackgroundBisulfite sequencing is a powerful tool for profiling genomic methylation, an epigenetic modification critical in the understanding of cancer, psychiatric disorders, and many other conditions. Raw data generated by whole genome bisulfite sequencing (WGBS) requires several computational steps before it is ready for statistical analysis, and particular care is required to process data in a timely and memory-efficient manner. Alignment to a reference genome is one of the most computationally demanding steps in a WGBS workflow, taking several hours or even days with commonly used WGBS-specific alignment software. This naturally motivates the creation of computational workflows that can utilize GPU-based alignment software to greatly speed up the bottleneck step. In addition, WGBS produces raw data that is large and often unwieldy; a lack of memory-efficient representation of data by existing pipelines renders WGBS impractical or impossible to many researchers.ResultsWe present BiocMAP, a Bioconductor-friendly Methylation Analysis Pipeline consisting of two modules, to address the above concerns. The first module performs computationally-intensive read alignment using Arioc, a GPU-accelerated short-read aligner. The extraction module extracts and merges DNA methylation proportions - the fractions of methylated cytosines across all cells in a sample at a given genomic site. Since GPUs are not always available on the same computing environments where traditional CPU-based analyses are convenient, BiocMAP is split into two modules, with just the alignment module requiring an available GPU. Bioconductor-based output objects in R utilize an on-disk data representation to drastically reduce required main memory and make WGBS projects computationally feasible to more researchers.ConclusionsBiocMAP is implemented using Nextflow and available at http://research.libd.org/BiocMAP/. To enable reproducible analysis across a variety of typical computing environments, BiocMAP can be containerized with Docker or Singularity, and executed locally or with the SLURM or SGE scheduling engines. By providing Bioconductor objects, BiocMAP’s output can be integrated with powerful analytical open source software for analyzing methylation data.

DNA methylation (DNAm) is a key epigenetic regulator of gene expression across development. The developing prenatal brain is a highly dynamic tissue, but our understanding of key drivers of epigenetic variability across development is limited. We therefore assessed genomic methylation at over 39 million sites in the prenatal cortex using whole genome bisulfite sequencing and found loci and regions in which methylation levels are dynamic across development. We saw that DNAm at these loci was associated with nearby gene expression and enriched for enhancer chromatin states in prenatal brain tissue. Additionally, these loci were enriched for genes associated with psychiatric disorders and genes involved with neurogenesis. We also found autosomal differences in DNAm between the sexes during prenatal development, though these have less clear functional consequences. We lastly confirmed that the dynamic methylation at this critical period is specifically CpG methylation, with very low levels of CpH methylation. Our findings provide detailed insight into prenatal brain development as well as clues to the pathogenesis of psychiatric traits seen later in life.

Antipsychotic drugs are the current first-line of treatment for schizophrenia and other psychotic conditions. However, their molecular effects on the human brain are poorly studied, due to difficulty of tissue access and confounders associated with disease status. Here we examine differences in gene expression and DNA methylation associated with positive antipsychotic drug toxicology status in the human caudate nucleus. We find no genome-wide significant differences in DNA methylation, but abundant differences in gene expression. These gene expression differences are overall quite similar to gene expression differences between schizophrenia cases and controls. Interestingly, gene expression differences based on antipsychotic toxicology are different between brain regions, potentially due to affected cell type differences. We finally assess similarities with effects in a mouse model, which finds some overlapping effects but many differences as well. As a first look at the molecular effects of antipsychotics in the human brain, the lack of epigenetic effects is unexpected, possibly because long term treatment effects may be relatively stable for extended periods.

In large DNA sequence repositories, archival data storage is often coupled with computers that provide 40 or more CPU threads and multiple GPU (general-purpose graphics processing unit) devices. This presents an opportunity for DNA sequence alignment software to exploit high-concurrency hardware to generate short-read alignments at high speed. Arioc, a GPU-accelerated short-read aligner, can compute WGS (whole-genome sequencing) alignments ten times faster than comparable CPU-only alignment software. When two or more GPUs are available, Arioc's speed increases proportionately because the software executes concurrently on each available GPU device. We have adapted Arioc to recent multi-GPU hardware architectures that support high-bandwidth peer-to-peer memory accesses among multiple GPUs. By modifying Arioc's implementation to exploit this GPU memory architecture we obtained a further 1.8x-2.9x increase in overall alignment speeds. With this additional acceleration, Arioc computes two million short-read alignments per second in a four-GPU system; it can align the reads from a human WGS sequencer run–over 500 million 150nt paired-end reads–in less than 15 minutes. As WGS data accumulates exponentially and high-concurrency computational resources become widespread, Arioc addresses a growing need for timely computation in the short-read data analysis toolchain.

DNA methylation (DNAm) regulates gene expression and may represent gene-environment interactions. Using whole genome bisulfite sequencing, we surveyed DNAm in a large sample (n=344) of human brain tissues. We identify widespread genetic influence on local methylation levels throughout the genome, with 76% of SNPs and 38% of CpGs being part of methylation quantitative trait loci (meQTLs). These associations can further be clustered into regions that are differentially methylated by a given SNP, highlighting putative functional regions that explain much of the heritability associated with risk loci. Furthermore, some CpH sites associated with genetic variation. We have established a comprehensive, single base resolution view of association between genetic variation and genomic methylation, and implicate schizophrenia GWAS-associated variants as influencing the epigenetic plasticity of the brain.One-sentence summaryMost genetic variants associated with DNA methylation levels, and implicated schizophrenia GWAS variants in the human brain.

Publisher’s Note: This paper, originally published on 18 September 2018, was replaced with a corrected/revised version on 28 May 2020. If you downloaded the original PDF but are unable to access the revision, please contact SPIE Digital Library Customer Service for assistance.

Background: DNA methylation (DNAm) is a key epigenetic regulator of gene expression across development. The developing prenatal brain is a highly dynamic tissue, but our understanding of key drivers of epigenetic variability across development is limited. Results: We therefore assessed genomic methylation at over 39 million sites in the prenatal cortex using whole genome bisulfite sequencing and found loci and regions in which methylation levels are dynamic across development. We saw that DNAm at these loci was associated with nearby gene expression and enriched for enhancer chromatin states in prenatal brain tissue. Additionally, these loci were enriched for genes associated with psychiatric disorders and genes involved with neurogenesis. We also found autosomal differences in DNAm between the sexes during prenatal development, though these have less clear functional consequences. We lastly confirmed that the dynamic methylation at this critical period is specifically CpG methylation, with very low levels of CpH methylation. Conclusion: Our findings provide detailed insight into prenatal brain development as well as clues to the pathogenesis of psychiatric traits seen later in life.

Motivation DNA sequencing archives have grown to enormous scales in recent years, and thousands of human genomes have already been sequenced. The size of these data sets has made searching the raw read data infeasible without high-performance data-query technology. Additionally, it is challenging to search a repository of short-read data using relational logic and to apply that logic across samples from multiple whole-genome sequencing samples. Results We have built a compact, efficiently-indexed database that contains the raw read data for over 250 human genomes, encompassing trillions of bases of DNA, and that allows users to search these data in real-time. The Terabase Search Engine enables retrieval from this database of all the reads for any genomic location in a matter of seconds. Users can search using a range of positions or a specific sequence that is aligned to the genome on the fly. Availability and implementation Public access to the Terabase Search Engine database is available at http://tse.idies.jhu.edu. Supplementary information Supplementary data are available at Bioinformatics online.

Motivation The alignment of bisulfite-treated DNA sequences (BS-seq reads) to a large genome involves a significant computational burden beyond that required to align non-bisulfite-treated reads. In the analysis of BS-seq data, this can present an important performance bottleneck that can be mitigated by appropriate algorithmic and software-engineering improvements. One strategy is to modify the read-alignment algorithms by integrating the logic related to BS-seq alignment, with the goal of making the software implementation amenable to optimizations that lead to higher speed and greater sensitivity than might otherwise be attainable. Results We evaluated this strategy using Arioc, a short-read aligner that uses GPU (general-purpose graphics processing unit) hardware to accelerate computationally-expensive programming logic. We integrated the BS-seq computational logic into both GPU and CPU code throughout the Arioc implementation. We then carried out a read-by-read comparison of Arioc's reported alignments with the alignments reported by well-known CPU-based BS-seq read aligners. With simulated reads, Arioc's accuracy is equal to or better than the other read aligners we evaluated. With human sequencing reads, Arioc's throughput is at least 10 times faster than existing BS-seq aligners across a wide range of sensitivity settings. Availability and implementation The Arioc software is available for download at https://github.com/RWilton/Arioc. It is released under a BSD open-source license. Supplementary information Supplementary data are available at Bioinformatics online.

Astronomy accelerates tumor imaging Immunohistochemical stains for individual markers revolutionized diagnostic pathology decades ago but cannot capture enough information to accurately predict response to immunotherapy. Newer multiplex immunofluorescent technologies provide the potential to visualize the expression patterns of many functionally relevant molecules but present numerous challenges in accurate image analysis and data handling, particularly over large tumor areas. Drawing from the field of astronomy, in which petabytes of imaging data are routinely analyzed across a wide spectral range, Berry et al. developed a platform for multispectral imaging of whole-tumor sections with high-fidelity single-cell resolution. The resultant AstroPath platform was used to develop a multiplex immunofluorescent assay highly predictive of responses and outcomes for melanoma patients receiving immunotherapy. Science , aba2609, this issue p. eaba2609

During the past decade, significant advancement has been made on InGaAsP/InP Geiger-mode APDs (GmAPDs) through improvements of material growth, device design and operating circuitry. With the increase in device performance and the growing maturity of device fabrication technology, high performance, large format InGaAsP/InP GmAPD arrays have been successfully designed and manufactured. These arrays have single photon sensitivity in the short wavelength infrared (SWIR) spectral band and can provide 3-D imagery. InGaAsP/InP GmAPD arrays provide an enabling technology for many active optical applications, such as 3-D light detection and ranging (LiDAR) and other photon-starved applications where single photon sensitivity in the SWIR band is critical. InGaAsP/InP-based Geigermode LiDAR has been extensively used on airborne platforms. By using optical wavelengths along with sub-ns laser pulse widths, 3-D Geiger-mode LiDAR techniques provide centimeter-scale range resolution over extremely long distances on the order of tens of kilometers. Through the use of high-performance single photon detectors, Geiger-mode LiDAR systems achieve an order of magnitude improvement in mapping rate over other competing LiDAR technologies. A more recent exciting application of InGaAsP/InP GmAPD-based LiDAR is to enable advanced driver assistance systems (ADAS) and vehicle autonomy on automotive platforms. The single-photon sensitivity of GmAPDs and greater eye-safety of diode lasers at wavelengths beyond 1400 nm provide disruptive automotive LiDAR performance that will be essential to future autonomous vehicle navigation. Single photon sensitivity and simple pixel circuit operation enable the reduction in overall system SWaP, while the scalability of these semiconductor devices enables dramatic reduction in LiDAR cost.

The alignment of bisulfite-treated DNA sequences (BS-seq reads) to a large genome involves a significant computational burden beyond that required to align non-bisulfite-treated reads. In the analysis of BS-seq data, this can present an important performance bottleneck that can potentially be addressed by appropriate software-engineering and algorithmic improvements. One strategy is to integrate this additional programming logic into the read-alignment implementation in a way that the software becomes amenable to optimizations that lead to both higher speed and greater sensitivity than can be achieved without this integration.We have evaluated this approach using Arioc, a short-read aligner that uses GPU (general-purpose graphics processing unit) hardware to accelerate computationally-expensive programming logic. We integrated the BS-seq computational logic into both GPU and CPU code throughout the Arioc implementation. We then carried out a read-by-read comparison of Arioc's reported alignments with the alignments reported by the most widely used BS-seq read aligners. With simulated reads, Arioc's accuracy is equal to or better than the other read aligners we evaluated. With human sequencing reads, Arioc's throughput is at least 10 times faster than existing BS-seq aligners across a wide range of sensitivity settings.The Arioc software is available at https://github.com/RWilton/Arioc. It is released under a BSD open-source license.

Preface: What this book is about Part 1: The Characteristics of Scientific Explanation and its Application to Psychology Chapter 1: The defining characteristic of science 1.1 Test your understanding of Chapter 1 Chapter 2: The structure of scientific explanation: The Standard View 2.1 The Standard View 2.2 Observation statements 2.3 Statements that assert laws 2.4 Testing laws 2.5 Theoretical statements 2.6 Testing theories 2.7 More on testing theories 2.8 Criteria used in deciding between theories 2.9 Test your understanding of Chapter 2 Chapter 3: The structure of scientific explanation: The Alternative View 3.1 The structure of scientific explanation 3.2 General conclusion 3.3 Must we conclude that no observation statement is incorrigible? 3.4 Conclusion 3.5 Implications for what one is free to believe about the world 3.6 Criteria used to decide between theories 3.7 Test your understanding of Chapter 3 Chapter 4: Some historical examples of responses to a contradiction between a theory and some apparent fact 4.1 Summary: the state of affairs at any one historical time 4.2 Test your understanding of Chapter 4 Chapter 5: The criteria used for choosing between competing theories 5.1 Axiomatic beliefs 5.2 Can selection according to one's axiomatic beliefs be justified? 5.3 Power, scope, simplicity 5.4 Historical evidence favouring simple theories 5.5 Can a criterion of simplicity be justified? 5.6 Truth 5.7 Prediction 5.8 Explanatory content 5.9 Summary 5.10 Test your understanding of Chapter 5 Summary of Part 1: The characteristics of scientific explanation Part 2. Understanding Behaviour Chapter 6: Typical approaches in psychology: Internal mechanisms 6.1 The psychologist's goal 6.2 Internal operations with no reference to embodiment 6.3 Granularity of explanation 6.4 Coarse-grained analysis 6.5 Fine-grained analysis 6.6 Connectionism 6.7 Some additional important points 6.8 Direct inspection of individual units 6.9 Test your understanding of Chapter 6 Chapter 7: Typical approaches in psychology: Skinner's functional analysis 7.1 Objections 7.2 Test your understanding of Chapter 7 Chapter 8: Common-sense psychology and its implications 8.1 Common-sense explanations of human behaviour 8.2 Intentional states and causal explanations 8.3 Consequences of the two accounts differing in kind 8.4 The relevance of Tolman's theory 8.5 The two cases of sneezing, again 8.6 Verbal utterances 8.7 Some more examples 8.8 Some possible objections 8.9 Summary 8.10 Why do we like intentional accounts? 8.11 Test your understanding of Chapter 8 Chapter 9: Free will and determinism 9.1 Do laws of nature imply causality? 9.2 Laws of human behaviour: Causality or free will? 9.3 Test your understanding of Chapter 9 Chapter 10: The possible impact on social institutions (the legal system) if we relinquish our present disposition to believe in free will 10.1 Criteria for imposing punishment on offenders 10.2 Moral culpability 10.3 Deterrence 10.4 The possible impact of psychology upon the legal system 10.5 Comment on possible change in public attitude 10.6 Overall conclusion 10.7 Test your understanding of Chapter 10 Chapter 11: The problem of consciousness 11.1 Consciousness 11.2 The characteristics of sensations 11.3 Direct apprehension 11.4 Not subject to error 11.5 The relationship between sensations and physical events 11.6 Test your understanding of Chapter 11 Summary of Part 2: Understanding behaviour Part 3: What Psychology Tells Us About The Practice of Science Chapter 12: The use of imagery in scientific thought 12.1 Characteristics of mental problem solving 12.2 Are human disposed to use imagery in solving problems? 12.3 Examples of our disposition to use imagery 12.4 Conclusions so far 12.5 The history of scientific thought 12.6 Test your understanding of Chapter 12 Chapter 13: Why are cultures that practise science better at controlling the material world than non-scientific cultures? 13.1 (a) Structure of scientific theories (b) The development of the written word (c) The systematic testing of ideas (d) Different a priori assumptions about the world (e) Acceptance of fundamental change 13.2 Conclusion 3.3 Test your understanding of Chapter 13 Summary of Part 3: Psychological constraints on scientific explanations References

More recently polymer flooding recovery processes are becoming increasingly attractive due to the improvements in polymer manufacturing, hydration and implementation successes worldwide. This is especially true in the application of polymer for enhancing heavy oil recovery. It has been suggested that the elastic nature of the polymer is equally important to the viscous properties. In the present study, a specialized rheometer was used to determine the viscoelastic properties of both hydrolyzed polyacrylamides (HPAM) and hydrophobically associating polyacrylamides (HAP) used in heavy enhanced oil recovery (EOR) processes. The rheometer has the capability to measure rheological properties in porous capillary plugs providing a more representative picture of non-Newtonian fluid flow in reservoirs. The rheological parameters were determined as influenced by polymer type, concentration, molecular weight, hydrophobicity, salinity and temperature. Increases in elastic tendencies were observed as a function of the first four; however, salinity and temperature were found to have a slightly negative effect. A medium density, hydrophobic polymer showed an earlier onset of elastic contribution at in-depth reservoir shear rates as determined by its Weissenberg number. For heavy oil reservoirs utilizing higher polymer concentrations, the viscoelastic properties of a polymer system should be evaluated in the screening process. Recent studies suggest that viscoelastic polymers can reduce the residual oil saturation below that to waterflood with two different plausible mechanisms at play, depending whether the media is water- or oil-wet. However, in both theories, polymer elasticity is believed to be the dominant force that contributes to the additional reduction in oil saturation. Aside from measuring the elasticity directly, other parameters that quantify a polymer's elastic potential are its relaxation time and Weissenberg number; therefore, the change in these parameters with respect to dynamic shear rate or flow velocity can be further useful for screening purposes.

Objective. To evaluate the accuracy of immunization records transcribed into a computer-based immunization tracking system and to assess factors that contribute to inaccurate or incomplete immunization record keeping. Design. Computer-stored immunization records were analyzed for 2098 children up to 2 years of age at the time of their most recent well-child visit to the UCLA Children's Health Center over a 12-month period. For children whose immunizations were not up to date, the computer-stored records were analyzed for sources of inaccuracy by comparison with the handwritten records from which the computer-stored data were transcribed. Results. An underimmunization rate of 22.5% (472 of 2098) was observed based on analysis of the computer-stored records. Comparison of the computer-stored and handwritten records revealed an overall transcription error rate of at least 10.2%. In addition, 38.4% of these apparently underimmunized children had received unrecorded immunizations from providers outside UCLA. When transcription errors were corrected and other available sources of immunization data were taken into account, the estimated rate of underimmunization decreased from 22.5% to 10.9%. Conclusion. Unavoidable inaccuracies can diminish the utility of the data recorded in an immunization tracking system. Some inaccuracies are related to the process of transcription, but failures to record and communicate immunization data consistently also contribute to the inaccuracy of computer-stored immunization records.

The economic life of a typical heavy oil reservoir under primary or secondary recovery schemes can be short lived or near their limit, with recovery factors in the range of 5–15%. Waterflooding alone has been successfully practiced in the Lloydminster area of the Western Canada for decades. Heavy oils located in thick reservoirs have benefited from the application of thermal, gravity drainage processes; however, thin, unconsolidated heavy oil reservoirs are unsuitable due to lack of drainage height. These reservoirs may benefit from immiscible CO2 or CO2-WAG processes. This paper examines the effect of oil viscosity, permeability and injection rate on the performance of heavy oil waterflooding, immiscible CO2 flooding and immiscible CO2 water-alternating-gas (WAG) processes. A series of 11 sand packfloods were conducted using 440 and 1,500 mPa·s heavy oils and sand packs with absolute permeabilities of 12 and 40 μm2. Water injection volumes for the waterfloods were 1.5 pore volumes (PVs) at rates of 0.112, 1.124, and 5.62 cc/min. For the CO2 flooding process, 4.5 PVs of gas were injected at a rate of 1 cc/min. For the WAG process, the water:CO2 slug ratios were varied from 1:1, 1:2 and 2:1. A 99.9% purity CO2 gas stream was used for all gas floods. All experiments were performed at a controlled temperature of 25°C and 345 kPa. Among the 11 sand packfloods conducted, the waterfloods consistently yielded the highest recovery factor for both heavy oils and sand packs, with 48-52% OOIP recovered and most of this recovery occurring during 0.112 cc/min. During CO2 flooding of the 440 mPa·s oil, 48.5% OOIP was produced from the 40 μm2 sand pack. From the same fluid-sand system, a 1:1 slug ratio, CO2-WAG process produced 42% OOIP. For the 1,500 mPa·s heavy oil, 1:2 and 2:1 slug ratios of CO2-WAG both produced ~25% OOIP from the 40 μm2 sand pack and a 1:1 slug ratio produced 35% OOIP from the 12 μm2 sand pack. All WAG injection schemes were compared on a 2.5 PV injected basis. These results suggest that the role of displaced fluid viscosity plays the most prominent role in the recovery of heavy oil.

The production flow rate in classical VAPEX is far too low for the process to be considered commercially viable. This is largely because the classical process utilizes forces of buoyancy to distribute the solvent and gravity to drain the diluted oil to the producer. This paper presents a new well pattern that may enhance the oil flow rate two to ten times over the classical approach. In the new well pattern, additional horizontal injectors, perpendicular to the injector and the producer in classical VAPEX, are placed in the top-most region of the reservoir. The enhanced oil rate mechanism for this new well pattern involves two features. First, the injection pressure of the top injectors is set slightly higher than the bottom injector pressure. This facilitates a downward driving force to assist gravity drainage of diluted oil to the producer. Second, the supplementary injectors generate an additional diluted oil profile perpendicular to the diluted oil profile of the classical VAPEX process. Therefore, in the new well pattern, the heavy oil is solvent contacted and diluted in both ik and jk planes, whereas in classical VAPEX, the heavy oil is diluted in only one. A series of numerical simulations were conducted to evaluate this process. In order to obtain reliable evaluation results, the numerical dispersion was eliminated through extrapolating the simulation results at different grid sizes to an infinitesimal grid size (Δy→0). The simulation results suggest that the oil flow rate can be enhanced two to ten times greater than with classical VAPEX, depending on the well spacing of the top injectors. For example, for a well spacing of the top horizontal injectors of 120 m, the oil flow rate from the original producers will be 5.5 times higher than in the VAPEX scenario. The paper also discusses the effects of the design factors and formation/fluid uncertainties on the performance of this process. Finally, thinner reservoirs and reservoirs with a gas cap are discussed.

When computing alignments of DNA sequences to a large genome, a key element in achieving high processing throughput is to prioritize locations in the genome where high-scoring mappings might be expected. We formulated this task as a series of list-processing operations that can be efficiently performed on graphics processing unit (GPU) hardware.We followed this approach in implementing a read aligner called Arioc that uses GPU-based parallel sort and reduction techniques to identify high-priority locations where potential alignments may be found. We then carried out a read-by-read comparison of Arioc’s reported alignments with the alignments found by several leading read aligners. With simulated reads, Arioc has comparable or better accuracy than the other read aligners we tested. With human sequencing reads, Arioc demonstrates significantly greater throughput than the other aligners we evaluated across a wide range of sensitivity settings. The Arioc software is available at https://github.com/RWilton/Arioc. It is released under a BSD open-source license.

• To examine the relationship between insurance coverage and the diagnostic content of residents' experience in a hospital-based pediatric teaching clinic, we analyzed outpatient problem lists for 6543 patients seen in our clinic over a 15-month period. Problem-list contents were categorized using diagnostic clusters. The frequency distribution of clustered problems was compared for patients with four types of insurance coverage: indemnity insurance, health maintenance organization, Medicaid, and no insurance. The four insurance categories differed in the overall distribution of problems, but the differences could not be attributed to a disparity in the frequency of any single diagnosis or diagnostic cluster. We conclude that there was no important effect of insurance coverage on the diagnostic content of residents' experience in a teaching clinic. (AJDC. 1993;147:284-289)

Wie bereits erwahnt, ist es am klugsten, zum Schreiben aller Programme fur die PC-Familie eine hohere Programmiersprache (wie BASIC, Pascal oder C) zu verwenden. Wenn es sich als notig erweisen sollte, setzen Sie einzelne DOS- oder BIOS-Routinen ein. Gelegentlich mussen Sie wohl auch Assembler-Routinen schreiben, um spezialisierte Aufgaben zu erfullen, die weder Ihre Programmiersprache noch Systemroutinen zu bieten haben.

Ein Geheimnis des erfolgreichen Programmierens eines Modells der PC-Familie liegt in der effizienten Nutzung der eingebauten Software: den ROM BIOS-Routinen. Diese liegen zwischen der Hardware-Ebene und der Ebene der hoheren Programmiersprachen (inklusive des Betriebssystems). Die ROM BIOS-Routinen arbeiten direkt mit der Hardware des Computers und den Peripheriegeraten zusammen und fuhren einige der grundlegendsten Aufgaben wie z.B. das Lesen und Schreiben einzelner Daten-Bytes vom bzw. auf den Bildschirm oder von bzw. auf Diskette aus. DOS-Routinen und Routinen hoherer Programmiersprachen sind oft aus diesen Grundfunktionen aufgebaut, gehen aber entsprechend der jeweiligen Aufgabenstellung daruber hinaus. Auch Sie konnen die Leistung Ihrer Programme steigern, indem Sie auf diese Routinen zuruckgreifen. Sie erhalten damit einen gut sortierten “Werkzeugkasten”, mit dem Sie Ihre Computer so verwenden konnen, wie sich das die Entwickler des IBM PC vorgestellt hatten.

Obwohl die Tastaturroutinen des ROM BIOS nicht so zahlreich und auch nicht so kompliziert sind wie die Bildschirm- (Kapitel 9) oder Disketten-/Festplatten-Routinen (Kapitel 10), sind sie doch wichtig genug, um ihnen ein eigenes Kapitel zu widmen. Die restlichen ROM BIOS-Routinen sind in Kapitel 12 zusammengefast.

Die folgenden drei Kapitel behandeln die DOS-Funktionen, auf die man uber den Interrupt 21H zugreift. DOS-Version 1 hatte 42 Interrupt 21H-Funktionen. Diese Vielzahl von Funktionen hatte ihre Ursache in der 8-Bit-Mikrocomputerwelt, die vom Betriebssystem CP/M beherrscht wurde, dessen Routinen vielen der DOS-Funktionen ahnelten.

In diesem Kapitel werden die Disketten- und Festplattenroutinen, die das ROM-BIOS bereitstellt, ausfuhrlich beschrieben. Um den logischen Aufbau einer Diskette/Festplatte zu verstehen, lesen Sie bitte in Kapitel 5, insbesondere auf den Seiten 104 bis 120, nach. Informationen uber Disketten- und Festplattenroutinen auf hoherer Ebene (DOS) finden Sie in den Kapiteln 15 bis 18.

In diesem Kapitel werden alle ROM BIOS-Routinen behandelt, die entweder nicht wichtig oder nicht komplex genug sind, um ein eigenes Kapitel zu fullen. Das sind die Routinen fur die serielle RS-232-Kommunikation, Systemroutinen, ROM BIOS-Abfangroutinen und die Druckerroutinen. Einige weitere, ausgefallene Routinen sind am Ende des Kapitels kurz aufgefuhrt.

In diesem Kapitel werden die mit der Version 2.0 eingefuhrten Interrupt 21H-Funktionen behandelt. Diese Funktionen bieten ein breites Spektrum von Betriebssystemroutinen innerhalb eines leistungsfahigeren und flexibleren Rahmens als die in Kapitel 16 beschriebenen 42 ursprunglichen.

Uhren und Zeitgeber werden als Herzschlag eines Computers bezeichnet. Die wesentlichen Computerfunktionen — Rechenoperationen und Datentransfer — werden durch die von elektronischen Uhren erzeugten Zeitimpulse gesteuert. PC und PS/2 beherbergen mehrere Uhren und Zeitgeber, uber die Sie Bescheid wissen sollten: Der Systemzeitgeber erzeugt ein “Uhrticken” und andere zeitgebende Impulse nach genau bestimmten Intervallen. Der Tongenerator erzeugt uber einen Lautsprecher Tone in einem weiten Frequenzbereich und von unterschiedlichster Dauer. Die Echtzeituhr bzw. der Echtzeitkalender sind standig uber Datum und Uhrzeit informiert und konnen auch als “Wecker” dienen (nur in PC/AT und PS/2).

Dieses Kapitel fast die DOS-Funktionen zusammen und ist als schnelle Nachschlagequelle gedacht. Genauere Erlauterungen uber die Arbeitsweise jeder Funktion finden Sie in den Kapiteln 15, 16 und 17. Wenn Sie diese drei Kapitel uber DOS durchgearbeitet haben, sollten Ihnen die Tabellen eigentlich die meisten der zum Programmieren notwendigen Informationen liefern.

In diesem Kapitel geht es um die IBM PC- und PS/2-Tastaturen. Im ersten Teil dieses Kapitels wird erklart, wie die Tastatur mit dem Computer auf Hard- und Software-Ebene zusammenarbeitet. Im zweiten Teil beschreiben wir, wie das ROM BIOS Tastaturinformationen behandelt und Programmen zuganglich macht.

Die meisten Computersysteme konnen Information permanent speichern, entweder auf Lochstreifen, auf Magnetplatten oder -bandern oder auf Laserplatten. Doch das am weitaus haufigsten verwendete Medium in der PC- und PS/2-Familie sind Disketten (floppy disks) und Festplatten (hard disks). Disketten und Festplatten gibt es in den verschiedensten Grosen und Variationen, sie arbeiten aber im Grunde alle nach dem gleichen Prinzip: die Information befindet sich magnetisch verschlusselt auf ihrer Oberflache. Das Muster der Verschlusselung wird durch das Laufwerk und die zugehorige Steuerungssoftware bestimmt.

In diesem Kapitel fanden Sie alle ROM BIOS-Routinen systematisch aufgelistet, die in den Kapiteln 8 bis 12 beschrieben sind.

Aus der Sicht des Programmierers bestehen alle PC-Modelle aus folgenden Grundelementen: Prozessor, Speicherbausteinen und mehreren intelligenten oder programmierbaren Chips fur diverse Aufgaben. Die wichtigsten Bauteile, die der Computer zum Arbeiten benotigt, sind auf der System- oder Hauptplatine untergebracht. Andere, ebenfalls wichtige Teile befinden sich auf Erweiterungskarten, sogenannten Add-on-Boards. Diese konnen in entsprechende Erweiterungsplatze der Hauptplatine eingesteckt werden.

Damit ein Computer funktioniert, benotigt er Software. Wenn die Software permanent im Computer verfugbar ist, ist es noch einfacher, einen Computer in Gang zu setzen. Das genau ist die Bedeutung der ROM-Programme. ROM bedeutet Read-Only Memory (Nur-Lese-Speicher) — die Informationen sind fest in den ROM-Chips des Computers eingebrannt; sie konnen nicht geandert oder geloscht werden und nicht verlorengehen.