PCA-Plus: Enhanced principal component analysis with illustrative applications to batch effects and their quantitation

Background

Principal component analysis (PCA), a standard approach to analysis and visualization of large datasets, is commonly used in biomedical research for detecting similarities and differences among groups of samples. We initially used conventional PCA as a tool for critical quality control of batch and trend effects in multi-omic profiling data produced by The Cancer Genome Atlas (TCGA) project of the NCI. We found, however, that conventional PCA visualizations were often hard to interpret when inter-batch differences were moderate in comparison with intra-batch differences; it was also difficult to quantify batch effects objectively. We, therefore, sought enhancements to make the method more informative in those and analogous settings.

Results

We have developed algorithms and a toolbox of enhancements to conventional PCA that improve the detection, diagnosis, and quantitation of differences between or among groups, e.g., groups of molecularly profiled biological samples. The enhancements include (i) computed group centroids; (ii) sample-dispersion rays; (iii) differential coloring of centroids, rays, and sample data points; (iii) trend trajectories; and (iv) a novel separation index (DSC) for quantitation of differences among groups.

Conclusions

PCA-Plus has been our most useful single tool for analyzing, visualizing, and quantitating batch effects, trend effects, and class differences in molecular profiling data of many types: mRNA expression, microRNA expression, DNA methylation, and DNA copy number. An early version of PCA-Plus has been used as the central graphical visualization in our MBatch package for near-real-time surveillance of data for analysis working groups in more than 70 TCGA, PanCancer Atlas, PanCancer Analysis of Whole Genomes, and Genome Data Analysis Network projects of the NCI. The algorithms and software are generic, hence applicable more generally to other types of multivariate data as well. PCA-Plus is freely available in a down-loadable R package at our MBatch website.

RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data

SUMMARY

Reverse-Phase Protein Array (RPPA) is a robust high-throughput, cost-effective platform for quantitatively measuring proteins in biological specimens. However, converting raw RPPA data into normalized, analysis-ready data remains a challenging task. Here, we present the RPPA SPACE (RPPA Superposition Analysis and Concentration Evaluation) R package, a substantially improved successor to SuperCurve, to meet that challenge. SuperCurve has been used to normalize over 170 000 samples to date. RPPA SPACE allows exclusion of poor-quality samples from the normalization process to improve the quality of the remaining samples. It also features a novel quality-control metric, 'noise', that estimates the level of random errors present in each RPPA slide. The noise metric can help to determine the quality and reliability of the data. In addition, RPPA SPACE has simpler input requirements and is more flexible than SuperCurve, it is much faster with greatly improved error reporting.

AVAILABILITY AND IMPLEMENTATION

The standalone RPPA SPACE R package, tutorials and sample data are available via https://rppa.space/, CRAN (https://cran.r-project.org/web/packages/RPPASPACE/index.html) and GitHub (https://github.com/MD-Anderson-Bioinformatics/RPPASPACE).

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Digitization of Measurement-Based Care Pathways in Mental Health Through REDCap and Electronic Health Record Integration: Development and Usability Study

Background

The delivery of standardized self-report assessments is essential for measurement-based care in mental health. Paper-based methods of measurement-based care data collection may result in transcription errors, missing data, and other data quality issues when entered into patient electronic health records (EHRs).

Objective

This study aims to help address these issues by using a dedicated instance of REDCap (Research Electronic Data Capture; Vanderbilt University)—a free, widely used electronic data capture platform—that was established to enable the deployment of digitized self-assessments in clinical care pathways to inform clinical decision making.

Methods

REDCap was integrated with the primary clinical information system to facilitate the real-time transfer of discrete data and PDF reports from REDCap into the EHR. Both technical and administrative components were required for complete implementation. A technology acceptance survey was also administered to capture physicians’ and clinicians’ attitudes toward the new system.

Results

The integration of REDCap with the EHR transitioned clinical workflows from paper-based methods of data collection to electronic data collection. This resulted in significant time savings, improved data quality, and valuable real-time information delivery. The digitization of self-report assessments at each appointment contributed to the clinic-wide implementation of the major depressive disorder integrated care pathway. This digital transformation facilitated a 4-fold increase in the physician adoption of this integrated care pathway workflow and a 3-fold increase in patient enrollment, resulting in an overall significant increase in major depressive disorder integrated care pathway capacity. Physicians’ and clinicians’ attitudes were overall positive, with almost all respondents agreeing that the system was useful to their work.

Conclusions

REDCap provided an intuitive patient interface for collecting self-report measures and accessing results in real time to inform clinical decisions and an extensible backend for system integration. The approach scaled effectively and expanded to high-impact clinics throughout the hospital, allowing for the broad deployment of complex workflows and standardized assessments, which led to the accumulation of harmonized data across clinics and care pathways. REDCap is a flexible tool that can be effectively leveraged to facilitate the automatic transfer of self-report data to the EHR; however, thoughtful governance is required to complement the technical implementation to ensure that data standardization, data quality, patient safety, and privacy are maintained.

The Influence of Legal Brothels on Illegal Sexual Service Purchasing Habits: The U.S. Context

In this study, we use a survey of sex workers' clients to examine the relationship between having paid for services in legal brothels in Nevada and paying for criminalized sexual services among male clients. Using ordinary least squares (OLS) and generalized ordered logistic regression models, the use of legal brothels is found to be negatively related to reported purchasing of criminalized sexual services, regardless of criminal history, income, and most other demographic factors. When tested by criminalized purchase context, purchases made using the Internet, from public, outdoor contacts (such as the street) and indoor, public contacts (like bars), were less likely to occur with brothel experience. This study addresses a critical gap in scholarship on sex workers' clients purchasing choices with consideration to both market choice and frequency of purchase when having been exposed to a legal replacement for an illegal transaction. Implications and areas of further study are discussed.

Qualitative socioecological factors of cervical cancer screening use among transgender men

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Attendance to cervical cancer screening is related to gender identity development.

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Provider attitudes are critical to improving cancer screening for transgender men.

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Healthcare public physical spaces can promote cancer screening for transgender men.

Lack of attendance to cervical cancer screening (CCS) services is the most attributable factor to the development of cervical cancer. Transgender men, individuals whose gender identity does match with their natal female sex, use CCS less often than the general female population. The underlying reasons for deficient CCS among transgender men relate mostly to their stigmatized identity, such as discrimination and unwelcoming healthcare environments. However, additional research is needed to expand our understanding of this complex issue. This exploratory qualitative research study aimed to identify the determinants of CCS from the perspective of transgender men. Twenty transgender men ages 21–65 were conveniently sampled to participate in a semi-structured interview in 2018. The data were analyzed using a deductive-inductive content analysis approach and the results were sorted into a socioecological framework (SEM). The participants were mostly non-Hispanic and white. The mean age was 33, and 55% of the sample had attended CCS in the last three years. Eight overarching factors were identified in the data. Each factor included descriptive sub-factors. At the institutional and interpersonal SEM levels, factors related to healthcare providers and healthcare organizations. At the individual level, factors related to past negative experiences, gender identity development, and socioeconomic status. To the investigators’ knowledge, this is the first study to report the relationship between gender identity development and CCS behaviors. Gender identity development refers to the transition or coming-out process and gender dysphoria. This suggests that attendance to CCS services change as a transgender person’s identity evolves.

SoS Notebook: an interactive multi-language data analysis environment

Motivation

Complex bioinformatic data analysis workflows involving multiple scripts in different languages can be difficult to consolidate, share and reproduce. An environment that streamlines the entire processes of data collection, analysis, visualization and reporting of such multi-language analyses is currently lacking.

Results

We developed Script of Scripts (SoS) Notebook, a web-based notebook environment that allows the use of multiple scripting language in a single notebook, with data flowing freely within and across languages. SoS Notebook enables researchers to perform sophisticated bioinformatic analysis using the most suitable tools for different parts of the workflow, without the limitations of a particular language or complications of cross-language communications.

Availability and implementation

SoS Notebook is hosted at http://vatlab.github.io/SoS/ and is distributed under a BSD license.

Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps

Clustered heat maps are the most frequently used graphics for visualization and interpretation of genome-scale molecular profiling data in biology.  Construction of a heat map generally requires the assistance of a biostatistician or bioinformatics analyst capable of working in R or a similar programming language to transform the study data, perform hierarchical clustering, and generate the heat map.  Our web-based Interactive Heat Map Builder can be used by investigators with no bioinformatics experience to generate high-caliber, publication quality maps.  Preparation of the data and construction of a heat map is rarely a simple linear process.  Our tool allows a user to move back and forth iteratively through the various stages of map generation to try different options and approaches.  Finally, the heat map the builder creates is available in several forms, including an interactive Next-Generation Clustered Heat Map that can be explored dynamically to investigate the results more fully.

Interactive Clustered Heat Map Builder: An easy web-based tool for creating sophisticated clustered heat maps

Clustered heat maps are the most frequently used graphics for visualization and interpretation of genome-scale molecular profiling data in biology.  Construction of a heat map generally requires the assistance of a biostatistician or bioinformatics analyst capable of working in R or a similar programming language to transform the study data, perform hierarchical clustering, and generate the heat map.  Our web-based Interactive Heat Map Builder can be used by investigators with no bioinformatics experience to generate high-caliber, publication quality maps.  Preparation of the data and construction of a heat map is rarely a simple linear process.  Our tool allows a user to move back and forth iteratively through the various stages of map generation to try different options and approaches.  Finally, the heat map the builder creates is available in several forms, including an interactive Next-Generation Clustered Heat Map that can be explored dynamically to investigate the results more fully.

Differential Sensitivity Analysis for Resistant Malignancies (DISARM) Identifies Common Candidate Therapies across Platinum-Resistant Cancers

PURPOSE

Despite a growing arsenal of approved drugs, therapeutic resistance remains a formidable and, often, insurmountable challenge in cancer treatment. The mechanisms underlying therapeutic resistance remain largely unresolved and, thus, examples of effective combinatorial or sequential strategies to combat resistance are rare. Here, we present Differential Sensitivity Analysis for Resistant Malignancies (DISARM), a novel, integrated drug screen analysis tool designed to address this dilemma.

EXPERIMENTAL DESIGN

DISARM, a software package and web-based application, analyzes drug response data to prioritize candidate therapies for models with resistance to a reference drug and to assess whether response to a reference drug can be utilized to predict future response to other agents. Using cisplatin as our reference drug, we applied DISARM to models from nine cancers commonly treated with first-line platinum chemotherapy including recalcitrant malignancies such as small cell lung cancer (SCLC) and pancreatic adenocarcinoma (PAAD).

RESULTS

In cisplatin-resistant models, DISARM identified novel candidates including multiple inhibitors of PI3K, MEK, and BCL-2, among other classes, across unrelated malignancies. Additionally, DISARM facilitated the selection of predictive biomarkers of response and identification of unique molecular subtypes, such as contrasting ASCL1-low/cMYC-high SCLC targetable by AURKA inhibitors and ASCL1-high/cMYC-low SCLC targetable by BCL-2 inhibitors. Utilizing these predictions, we assessed several of DISARM's top candidates, including inhibitors of AURKA, BCL-2, and HSP90, to confirm their activity in cisplatin-resistant SCLC models.

CONCLUSIONS

DISARM represents the first validated tool to analyze large-scale in vitro drug response data to statistically optimize candidate drug and biomarker selection aimed at overcoming candidate drug resistance.

A Galaxy Implementation of Next-Generation Clustered Heatmaps for Interactive Exploration of Molecular Profiling Data

Clustered heatmaps are the most frequently used graphics for visualization of molecular profiling data in biology. However, they are generally rendered as static, or only modestly interactive, images. We have now used recent advances in web technologies to produce interactive "next-generation" clustered heatmaps (NG-CHM) that enable extreme zooming and navigation without loss of resolution. NG-CHMs also provide link-outs to additional information sources and include other features that facilitate deep exploration of the biology behind the image. Here, we describe an implementation of the NG-CHM system in the Galaxy bioinformatics platform. We illustrate the algorithm and available computational tool using RNA-seq data from The Cancer Genome Atlas program's Kidney Clear Cell Carcinoma project. Cancer Res; 77(21); e23-26. ©2017 AACR.

International cross-cultural validation study of the Canadian haemophilia outcomes: kids' life assessment tool

Health-related quality of life (HRQoL) assessment is recognized as an important outcome in the evaluation of different therapeutic regimens for persons with haemophilia. The Canadian Haemophilia Outcomes-Kids' Life Assessment Tool (CHO-KLAT) is a disease-specific measure of HRQoL for 4 to 18-year-old boys with haemophilia. The purpose of this study was to extend this disease-specific, child-centric, outcome measure for use in international clinical trials. We adapted the North American English CHO-KLAT version for use in five countries: France, Germany, the Netherlands, Spain and the United Kingdom (UK). The process included four stages: (i) translation; (ii) cognitive debriefing; (iii) validity assessment relative to the PedsQL (generic) and the Haemo-QoL (disease-specific) and (iv) assessment of inter and intra-rater reliability. Cognitive debriefing was performed in 57 boys (mean age 11.4 years), validation was performed in 144 boys (mean age 11.0 years) and reliability was assessed for a subgroup of 64 boys (mean age 12.0 years). Parents also participated. The mean scores reported by the boys were high: CHO-KLAT 77.0 (SD = 11.2); PedsQL 83.8 (SD = 11.9) and Haemo-QoL 79.6 (SD = 11.5). Correlations between the CHO-KLAT and PedsQL ranged from 0.63 in Germany to 0.39 in the Netherlands and Spain. Test-retest reliability (concordance) for child self-report was 0.67. Child-parent concordance was slightly lower at 0.57. The CHO-KLAT has been fully culturally adapted and validated for use in five different languages and cultures (in England, the Netherlands, France, Germany and Spain) where treatment is readily available either on demand or as prophylaxis.

Communication and consent: discussion and organ donation decisions for self and family

BACKGROUND

Organ transplantation is a significant medical advancement. However, number of individuals registering as donors and next-of-kin's refusal to grant consent are notable limitations on the availability of organs for transplantation. Therefore, investigation into factors that influence willingness to donate and consent decisions is warranted. We examined the relationship between attitudes and family communication in relation to consent decisions for self and family member organ donation (OD). Data were collected from students at an Australian university and individuals from the wider community (N = 267).

METHOD

Participants completed an on-line survey composed of questions relating to demographic information, questionnaires from previous research, and several single items relating to family communication and consent created specifically for the study. The main outcome measure was participants' willingness to consent to OD for themselves or for a family member.

RESULTS

Attitudes and prior discussion of OD were predictive of registration and willingness to consent. Positive attitudes were also related to previous conversations regarding OD. A more open level of communication within families was associated with an increased tendency to discuss OD, but was not directly related to consent decisions.

CONCLUSION

Findings reiterate the importance of promoting positive attitudes within the community and specific, informed discussion within families. The positive influence these factors exert on next-of-kin decisions may be vital to maximize donation rates in opt-in systems (such as Australia).

Abstract 5132: Interactively exploring patterns in TCGA data: a web-based compendium of ‘next-generation’ clustered heat maps

Each of the 5 TCGA marker paper published in Nature to date has included at least one clustered heat map (CHM). We introduced CHMs in the early 1990’s for pharmacogenomic analysis (1) and later for integrated visualization of genomic, transcriptomic, proteomic, pharmacological, and functional data (1). As the ubiquitous first-order way of visualizing omic data, CHMs have appeared in many thousands of publications (3–9), including those from TCGA. We have elsewhere summarized their limitations (10).

One such limitation is that CHMs are generally static images. We therefore initiated the next-generation CHM (NG-CHM) project, using an image-tiling technology similar to that in Google Maps for navigation and extreme drill-down without loss of resolution. Once the CHM has been zoomed sufficiently, labels (e.g., gene, protein, or drug names) appear on the image's axes. Clicking on a label produces a menu of link-outs (e.g., to GeneCards, Google, PubMed). For gene vs. gene maps, each pixel can represent a color-coded Pearson correlation coefficient. Clicking on the pixel pulls up the corresponding data scattergram, bootstrap statistics, literature references, or pathway relationships. Strong usability features include floating windows, flexible search tools, cluster selection tools, customizable re-coloring of the CHM, and high-quality PDF's suitable for publication. NG-CHMs are a major resource for exploratory analysis and visualization in multiple projects of TCGA and other large-scale molecular profiling programs. Explore interactive versions for TCGA breast, colorectal, lung squamous, and glioblastoma data at http://bioinformatics.mdanderson.org/main/TCGA/NGCHM.

Supported in part by NCI Grant No. U24CA143883, by a gift from the Mary K. Chapman Foundation, and by a grant from the Michael and Susan Dell Foundation honoring Lorraine Dell.

Citation Format: John N. Weinstein, David W. Kane, Rehan Akbani, Deepti Dodda, Lam Nguyen, Michael C. Ryan, Chris Wakefield, Bradley M. Broom. Interactively exploring patterns in TCGA data: a web-based compendium of ‘next-generation’ clustered heat maps. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5132. doi:10.1158/1538-7445.AM2013-5132

Automating and simplifying the SOFA score in critically ill patients with cancer

The aim was to demonstrate the performance of a modified version of the Sequential Organ Failure Assessment (SOFA) score to predict mortality in medical and surgical patients with cancer. We performed an electronic retrospective review of databases. We included adult patients with cancer admitted into a 53-bed ICU over 28 months. We electronically calculated a modified SOFA (mSOFA) score at admission. A majority of the patients were admitted into the surgical ICU. Of 328 nonsurvivors, 85.1 per cent were medical patients and only 14.9 per cent surgical patients. The mean admission mSOFA scores for medical and surgical patients were 4.7 +/- 3.2 and 1.7 +/- 1.9, respectively. The overall area under the curve (AUC) of the mSOFA score was 0.84. The AUCs for medical and surgical patients were 0.72 and 0.78, respectively. Our results demonstrate that electronic assessment of mSOFA score has potential in resource allocation decisions as well as in critical care outreach programs.

Factors associated with anemia in patients with cancer admitted to an intensive care unit

PURPOSE

The study aimed to evaluate the relative impact of clinical and demographic factors associated with the prevalence and incidence of anemia (hemoglobin [Hb] <12 g/dL) in critically ill patients with cancer.

MATERIALS AND METHODS

We performed an electronic chart review for demographic and clinical data of adult patients with cancer with or without anemia admitted to the intensive care unit (ICU). Prevalence of anemia was determined at admission, and incidence determined if anemia developed during ICU stay. Anemia was classified as mild, moderate, or severe. The additive impact of clinical and demographic factors was evaluated by using a hierarchical linear regression model.

RESULTS

A total of 4705 patients were included in the study. The prevalence and incidence of anemia were 68.0% and 46.6%, respectively. In prevalent cases, we found that the clinical covariates modified sequential organ failure assessment score, admission to the medical ICU, prior chemotherapy, diagnosis of hematologic cancer, and length of hospital stay before ICU admission explained 18.7% of the variance in the model, whereas the demographic covariates (age, sex, and race) explained only an additional 0.6%. The pattern was similar for incidence cases.

CONCLUSIONS

Clinical factors are more influential than demographic factors in the observed rates of prevalence and incidence of anemia in the ICU; thus, protocols are needed to identify subgroups of patients with cancer who could benefit from novel management strategies.

Anti-D (WinRho SD) treatment of children with chronic autoimmune thrombocytopenic purpura stimulates transient cytokine/chemokine production

Intravenous anti-D is often used in the treatment of autoimmune thrombocytopenic purpura (AITP), but little is known about its mechanisms of action. To investigate anti-D's potential in vivo mechanism(s) of action, a small group (N = 7) of children with chronic AITP was studied. The children initially received either 25 or 50 microg/kg of WinRho-SD in a four-cycle cross-over trial, and peripheral blood samples from the first and third cycles were assessed for cytokine levels at pre-treatment, 3 hr, 1 day, and 8 days post-treatment. Results showed that platelet counts significantly increased in all the children by day 8 post-treatment. Analysis of serum by ELISA showed that there was a significant but transient rise in both pro- and anti-inflammatory cytokine/chemokine levels (e.g., IL1RA, IL6, GM-CSF, MCP-1 alpha, TNF-alpha and MCP-1) by 3 hr post-treatment in both cycles which returned to baseline levels by 8 days post-treatment. These results suggest that anti-D administration may initially activate the RES in the form of cytokine/chemokine secretion, which is subsequently followed by an increase in platelet counts. It is possible that the induced cytokine/chemokine storm may have an effect on several physiological processes such as those mediating either adverse effects or potentially RES phagocytic activity.

The cardiovascular, endocrine and renal response of tetraplegic and paraplegic subjects to dietary sodium restriction

1. The effects of change from a high to low sodium diet upon renal sodium and water excretion and hormone responses were studied in patients with dissociated sympathetic control (DS, tetraplegic) and controls with sympathetic control largely intact (IS, paraplegic). 2. Total and fractional urinary sodium excretion fell in response to sodium restriction in both groups, but the fall in fractional sodium excretion was greater in the DS group compared with the IS group (DS, 1.34 +/- 0.12 to 0.42 +/- 0.05%; IS, 0.96 +/- 0.08 to 0.52 +/- 0.06%). 3. Supine mean arterial pressure fell during the low salt period in the DS group (80.2 +/- 2.7 to 74.4 +/- 2.3 mmHg) but was unaffected by salt restriction in the IS group (101 +/- 2.3 to 98.8 +/- 2.7 mmHg). In the DS group, creatinine clearance remained constant throughout the low salt period (103.7 +/- 7.9 to 98.3 +/- 9.7 ml min-1), but fell during salt restriction in the IS group (101.4 +/- 8.5 to 83.2 +/- 5 ml min-1). 4. Plasma renin activity was lower during salt loading in DS subjects but increased more rapidly and to higher levels in response to salt restriction (DS, 1021 +/- 142 to 4439 +/- 355; IS, 1765 +/- 269 to 3683 +/- 465 pg angiotensin I ml-1 h-1). Plasma atrial natriuretic peptide concentration was higher in the DS group during salt loading and salt restriction (DS, 37.6 +/- 5.6 to 22 +/- 3.8; IS, 20.2 +/- 2.3 to 11 +/- 1.6 pg ml-1).(ABSTRACT TRUNCATED AT 250 WORDS)

An electron microscopy method for studying full cross-sections of the human renal glomerulus

Images

Phaeochromocytoma in pregnancy. Caesarean section under epidural analgesia

Two cases are reported in which Caesarean section was successfully performed under epidural analgesia in patients whose pregnancy was complicated by a phaeochromcytoma. Pre-operative phenoxybenzamine therapy together with careful peri-operative monitoring produced cardiovascular stability and led in both cases to the delivery of a healthy infant.

Reinnervation of the gastrocnemius muscle by the contralateral S1 nerve root

Functional regeneration after transposition of a ventral nerve root was established in the adult cat. Reconstruction of the ventral root, using microsurgical methods, directed the right S1 ventral nerve root to innervate the left gastrocnemius muscle. Stimulus-induced unit responses were recorded from the left gastrocnemius muscle 5 to 8 months after the root cross, demonstrating the reestablishment of neuromuscular connections. The innervation of the left gastrocnemius muscle by neurons in the right ventral horn of the spinal cord was verified by injecting horseradish peroxidase into the muscle. Horseradish peroxidase reaction product was located in alpha and gamma motor neurons in the right S1 segment of the spinal cord. Computer-assisted determination of the soma area of the labeled neurons was compared with a normal S1 innervation of the gastrocnemius muscle. Analysis of the percentage of cells of a given soma area demonstrated an overall decrease in soma area in the operated animals. Because ventral root reconstruction can result in innervation of a foreign muscle, studies such as this may encourage repair or reconstruction of nerve roots to gain some functional recovery after spinal cord or nerve root injuries.

Scanning electron microscopic observations of normal and regenerating nerve roots in the cat

The surface morphology of normal and regenerated nerve roots was studied using correlated scanning and transmission electron microscopic methods. Nerve roots of the cauda equina were either cut and rejoined or crossed from a segment above to a segment below. Good regeneration was observed in both experimental procedures. The regenerated nerve root sheath had alterations in surface structure created by extensive growth of collagen. Despite this collagen formation, regenerated axons crossed the anastomotic site with relative ease. Surface features of the regenerated axons were similar in appearance to those of the normal axon. Schwann cells were easily recognized, as were the collagen fibers of the endoneurium, although the endoneurium was more prominent and occupied more of the interaxonal space. Macrophages were identified as round structures with a laminated surface or as a honeycomb structure. Internal features of the regenerating axons were more difficult to identify, but mitochondria and a fibrous network were observed. These studies have demonstrated the application of scanning electron microscopic methods to visualize surface structures and cells in regenerated nerve roots.

The topographical organization and laminar origin of some cortico-amygdaloid connections

Injections of horseradish peroxidase were made into the basolateral nuclei of the amygdaloid complex in cats. It was shown that the periamygdaloid cortex immediately below the rhinal sulcus and extending medially to the amygdaloid fissure projects to the lateral nucleus. The rest of the periamygdaloid cortex medial to the amygdaloid fissure and including the cortical nucleus of the amygdala projects primarily to the basomedial nucleus. These cortico-amygdaloid projections originate in the deeper one-third of the cortex. No projections from the neocortex could be demonstrated.

Observations of HRP labeling following injection through a chronically implanted cannula--a method to avoid diffusion of HRP into injured fibers

One of the limitations of the horseradish peroxidase (HRP) tracer method is the diffusion of HRP into injured axons resulting in unintended labeling of neurons not terminating in the injection area. To overcome this limitation, an experiment was designed to inject the HRP through an implanted cannula after degeneration and healing had taken place. It was shown that implantation of a cannula into the internal capsule significantly decreased the number of labeled axons in the injection site, thus limiting the unintended labeling of neurons from that injection. When injections followed implantation of the cannula by 24 h or more, fibers damaged by the cannula had healed or degenerated sufficiently that intraaxonal diffusion of HRP into those injured fibers did not occur. A significant difference between control (without the cannula) and experimental (with the cannula) injections was observed. Extensive axonal and neuronal labeling following the control injections was seen at the injection site and caudate nucleus, and in the thalamus and parietal cortex, respectively. Experimental injections resulted in sparse axonal and neuronal labeling evident mostly with the larger injections of HRP.