Artificial intelligence-assisted quantification and assessment of whole slide images for pediatric kidney disease diagnosis

MOTIVATION

Pediatric kidney disease is a widespread, progressive condition that severely impacts growth and development of children. Chronic kidney disease is often more insidious in children than in adults, usually requiring a renal biopsy for diagnosis. Biopsy evaluation requires copious examination by trained pathologists, which can be tedious and prone to human error. In this study, we propose an artificial intelligence (AI) method to assist pathologists in accurate segmentation and classification of pediatric kidney structures, named as AI-based Pediatric Kidney Diagnosis (APKD).

RESULTS

We collected 2935 pediatric patients diagnosed with kidney disease for the development of APKD. The dataset comprised 93 932 histological structures annotated manually by three skilled nephropathologists. APKD scored an average accuracy of 94% for each kidney structure category, including 99% in the glomerulus. We found strong correlation between the model and manual detection in detected glomeruli (Spearman correlation coefficient r = 0.98, P < .001; intraclass correlation coefficient ICC = 0.98, 95% CI = 0.96-0.98). Compared to manual detection, APKD was approximately 5.5 times faster in segmenting glomeruli. Finally, we show how the pathological features extracted by APKD can identify focal abnormalities of the glomerular capillary wall to aid in the early diagnosis of pediatric kidney disease.

AVAILABILITY AND IMPLEMENTATION

https://github.com/ChunyueFeng/Kidney-DataSet.

Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level

MOTIVATION

DNA fibre assay has a potential application in genomic medicine, cancer and stem cell research at the single-molecule level. A major challenge for the clinical and research implementation of DNA fibre assays is the slow speed in which manual analysis takes place as it limits the clinical actionability. While automatic detection of DNA fibres speeds up this process considerably, current publicly available software have limited features in terms of their user interface for manual correction of results, which in turn limit their accuracy and ability to account for atypical structures that may be important in diagnosis or investigative studies. We recognize that core improvements can be made to the GUI to allow for direct interaction with automatic results to preserve accuracy as well as enhance the versatility of automatic DNA fibre detection for use in variety of situations.

RESULTS

To address the unmet needs of diverse DNA fibre analysis investigations, we propose DNA Stranding, an open-source software that is able to perform accurate fibre length quantification (13.22% mean relative error) and fibre pattern recognition (R > 0.93) with up to six fibre patterns supported. With the graphical interface, we developed, user can conduct semi-automatic analyses which benefits from the advantages of both automatic and manual processes to improve workflow efficiency without compromising accuracy.

AVAILABILITY AND IMPLEMENTATION

The software package is available at https://github.com/lgole/DNAStranding.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Gathering Health Perspectives of the Justice Involved: A Multisite Needs Assessment Survey

The well-being of justice-involved individuals must be of high priority to achieve health equity, reduce health disparities, and improve community health. To better understand the health interests and needs of justice-involved individuals, a survey was administered inquiring about health information-seeking behavior and health topics of interest. The survey was administered using secure tablet computers and completed by 1,888 incarcerated participants in 35 jails in 17 states. Salient themes that emerged from this research include the relatively equal use of the internet and health care providers as resources for health information; the extensive interest in learning about multiple health care topics; and demographic variations in health information-seeking behaviors and health topics of interest. Tailoring correctional health education programs to coincide with the interests and needs of the justice-involved population may attract more participants and thus result in better self-care management skills and health outcomes upon reentering communities.

Detection of subtle white matter lesions in MRI through texture feature extraction and boundary delineation using an embedded clustering strategy

White matter lesions (WML) underlie multiple brain disorders, and automatic WML segmentation is crucial to evaluate the natural disease course and effectiveness of clinical interventions, including drug discovery. Although recent research has achieved tremendous progress in WML segmentation, accurate detection of subtle WML present early in the disease course remains particularly challenging. Here we propose an approach to automatic WML segmentation of mild WML loads using an intensity standardisation technique, gray level co-occurrence matrix (GLCM) embedded clustering technique, and random forest (RF) classifier to extract texture features and identify morphology specific to true WML. We precisely define their boundaries through a local outlier factor (LOF) algorithm that identifies edge pixels by local density deviation relative to its neighbors. The automated approach was validated on 32 human subjects, demonstrating strong agreement and correlation (excluding one outlier) with manual delineation by a neuroradiologist through Intra-Class Correlation (ICC = 0.881, 95% CI 0.769, 0.941) and Pearson correlation (r = 0.895, p-value < 0.001), respectively, and outperforming three leading algorithms (Trimmed Mean Outlier Detection, Lesion Prediction Algorithm, and SALEM-LS) in five of the six established key metrics defined in the MICCAI Grand Challenge. By facilitating more accurate segmentation of subtle WML, this approach may enable earlier diagnosis and intervention.

Comprehensive literature review on the radiographic findings, imaging modalities, and the role of radiology in the COVID-19 pandemic

Since the outbreak of the coronavirus disease 2019 (COVID-19) pandemic, over 103214008 cases have been reported, with more than 2231158 deaths as of January 31, 2021. Although the gold standard for diagnosis of this disease remains the reverse-transcription polymerase chain reaction of nasopharyngeal and oropharyngeal swabs, its false-negative rates have ignited the use of medical imaging as an important adjunct or alternative. Medical imaging assists in identifying the pathogenesis, the degree of pulmonary damage, and the characteristic features in each imaging modality. This literature review collates the characteristic radiographic findings of COVID-19 in various imaging modalities while keeping the preliminary focus on chest radiography, computed tomography (CT), and ultrasound scans. Given the higher sensitivity and greater proficiency in detecting characteristic findings during the early stages, CT scans are more reliable in diagnosis and serve as a practical method in following up the disease time course. As research rapidly expands, we have emphasized the CO-RADS classification system as a tool to aid in communicating the likelihood of COVID-19 suspicion among healthcare workers. Additionally, the utilization of other scoring systems such as MuLBSTA, Radiological Assessment of Lung Edema, and Brixia in this pandemic are reviewed as they integrate the radiographic findings into an objective scoring system to risk stratify the patients and predict the severity of disease. Furthermore, current progress in the utilization of artificial intelligence via radiomics is evaluated. Lastly, the lesson from the first wave and preparation for the second wave from the point of view of radiology are summarized.

Satellite cell activation and retention of muscle regenerative potential after long-term denervation

Irreversible denervation atrophy remains an unsolved clinical problem, and the role of skeletal muscle stem cell (MuSC, satellite cell) depletion in this process is unclear. We investigated the ability of MuSCs to regenerate muscle in the context of denervation. Three to 12 months following sciatic denervation in mice, MuSC number, size, EdU uptake, rate of division, and mitochondrial activity were increased. Following acute myotoxin injury, denervated muscles formed new muscle fibers in situ. MuSCs isolated via flow cytometry from denervated mouse muscle, or from atrophic denervated gluteus maximus muscles of humans with complete spinal cord injuries two decades prior, formed new muscle fibers and reoccupied the anatomic niche after transplantation into uninjured muscle. Our results show unequivocally that, even after prolonged denervation, MuSCs retain intrinsic regenerative potential similar to that of uninjured MuSCs. Treatment of denervation atrophy will require elucidating the non-MuSC environmental changes in muscle that prevent functional regeneration.

Constructing and optimizing 3D atlases from 2D data with application to the developing mouse brain

3D imaging data necessitate 3D reference atlases for accurate quantitative interpretation. Existing computational methods to generate 3D atlases from 2D-derived atlases result in extensive artifacts, while manual curation approaches are labor-intensive. We present a computational approach for 3D atlas construction that substantially reduces artifacts by identifying anatomical boundaries in the underlying imaging data and using these to guide 3D transformation. Anatomical boundaries also allow extension of atlases to complete edge regions. Applying these methods to the eight developmental stages in the Allen Developing Mouse Brain Atlas (ADMBA) led to more comprehensive and accurate atlases. We generated imaging data from 15 whole mouse brains to validate atlas performance and observed qualitative and quantitative improvement (37% greater alignment between atlas and anatomical boundaries). We provide the pipeline as the MagellanMapper software and the eight 3D reconstructed ADMBA atlases. These resources facilitate whole-organ quantitative analysis between samples and across development.

The research community needs precise, reliable 3D atlases of organs to pinpoint where biological structures and processes are located. For instance, these maps are essential to understand where specific genes are turned on or off, or the spatial organization of various groups of cells over time.

For centuries, atlases have been built by thinly ‘slicing up’ an organ, and then precisely representing each 2D layer. Yet this approach is imperfect: each layer may be accurate on its own, but inevitable mismatches appear between the slices when viewed in 3D or from another angle.

Advances in microscopy now allow entire organs to be imaged in 3D. Comparing these images with atlases could help to detect subtle differences that indicate or underlie disease. However, this is only possible if 3D maps are accurate and do not feature mismatches between layers. To create an atlas without such artifacts, one approach consists in starting from scratch and manually redrawing the maps in 3D, a labor-intensive method that discards a large body of well-established atlases.

Instead, Young et al. set out to create an automated method which could help to refine existing ‘layer-based’ atlases, releasing software that anyone can use to improve current maps. The package was created by harnessing eight atlases in the Allen Developing Mouse Brain Atlas, and then using the underlying anatomical images to resolve discrepancies between layers or fill out any missing areas. Known as MagellanMapper, the software was extensively tested to demonstrate the accuracy of the maps it creates, including comparison to whole-brain imaging data from 15 mouse brains. Armed with this new software, researchers can improve the accuracy of their atlases, helping them to understand the structure of organs at the level of the cell and giving them insight into a broad range of human disorders.

Whole-Brain Image Analysis and Anatomical Atlas 3D Generation Using MagellanMapper

MagellanMapper is a software suite designed for visual inspection and end-to-end automated processing of large-volume, 3D brain imaging datasets in a memory-efficient manner. The rapidly growing number of large-volume, high-resolution datasets necessitates visualization of raw data at both macro- and microscopic levels to assess the quality of data, as well as automated processing to quantify data in an unbiased manner for comparison across a large number of samples. To facilitate these analyses, MagellanMapper provides both a graphical user interface for manual inspection and a command-line interface for automated image processing. At the macroscopic level, the graphical interface allows researchers to view full volumetric images simultaneously in each dimension and to annotate anatomical label placements. At the microscopic level, researchers can inspect regions of interest at high resolution to build ground truth data of cellular locations such as nuclei positions. Using the command-line interface, researchers can automate cell detection across volumetric images, refine anatomical atlas labels to fit underlying histology, register these atlases to sample images, and perform statistical analyses by anatomical region. MagellanMapper leverages established open-source computer vision libraries and is itself open source and freely available for download and extension. © 2020 Wiley Periodicals LLC. Basic Protocol 1: MagellanMapper installation Alternate Protocol: Alternative methods for MagellanMapper installation Basic Protocol 2: Import image files into MagellanMapper Basic Protocol 3: Region of interest visualization and annotation Basic Protocol 4: Explore an atlas along all three dimensions and register to a sample brain Basic Protocol 5: Automated 3D anatomical atlas construction Basic Protocol 6: Whole-tissue cell detection and quantification by anatomical label Support Protocol: Import a tiled microscopy image in proprietary format into MagellanMapper.

Biopolymer Molecular Weight Can Modulate the Wound Healing Efficacy of Multivalent Sonic Hedgehog-Hyaluronic Acid Conjugates

There is a clinical need for new therapeutics to improve healing of chronic impaired wounds. Thus, we investigated how biopolymer conjugation could be used to improve the wound healing performance of a key growth factor for tissue regeneration: Sonic hedgehog (Shh). We generated two multivalent Shh conjugates (mvShh) using hyaluronic acid with two different MWs, which exhibited equivalent potency and proteolytic protection in vitro. Using db/db diabetic mice, we showed that mvShh made with smaller HyA MW resulted in more rapid and robust neovascularization compared to mvShh made with larger MW HyA. Further, smaller mvShh conjugates resulted in faster wound resolution compared to the unconjugated Shh. This study is the first to show how the wound healing efficacy of multivalent protein-polymer conjugates is sensitive to the polymer MW, and our findings suggest that this parameter could be used to enhance the efficacy of growth factor conjugates.

Comparison of global and mode of action-based models for aquatic toxicity

The ability to estimate aquatic toxicity is a critical need for ecological risk assessment and chemical regulation. The consensus in the literature is that mode of action (MOA) based toxicity models yield the most toxicologically meaningful and, theoretically, the most accurate results. In this study, a two-step prediction methodology was developed to estimate acute aquatic toxicity from molecular structure. In the first step, one-against-the-rest linear discriminant analysis (LDA) models were used to predict the MOA. The LDA models were able to predict the MOA with 85.8-88.8% accuracy for broad and specific MOAs, respectively. In the second step, a multiple linear regression (MLR) model corresponding to the predicted MOA was used to predict the acute aquatic toxicity value. The MOA-based approach was found to yield similar external prediction accuracy (r(2) = 0.529-0.632) to a single global MLR model (r(2) = 0.551-0.562) fit to the entire training set. Overall, the global hierarchical clustering approach yielded a higher combination of accuracy and prediction coverage (r(2) = 0.572, coverage = 99.3%) than the other approaches. Utilizing multiple two-dimensional chemical descriptors in MLR models yielded comparable results to using only the octanol-water partition coefficient (log K(ow)).

Thyrocalcitonin: evidence for release in a spontaneous hypocalcemic disorder

Thyrocalcitonin content of thyroid gland extracts from normal postparturient cows was 3.9 times greater than in cows with postparturient paresis. The parafollicular cells in diseased cows were less numerous and appeared to have discharged their secretory products. An abrupt release of thyrocalcitonin near parturition may be related to the development of the hypocalcemia and hypophosphatemia in this disorder.

HOXA3 modulates injury-induced mobilization and recruitment of bone marrow-derived cells

The regulated recruitment and differentiation of multipotent bone marrow-derived cells (BMDCs) to sites of injury are critical for efficient wound healing. Previously we demonstrated that sustained expression of HOXA3 both accelerated wound healing and promoted angiogenesis in diabetic mice. In this study, we have used green fluorescent protein-positive bone marrow chimeras to investigate the effect of HOXA3 expression on recruitment of BMDCs to wounds. We hypothesized that the enhanced neovascularization induced by HOXA3 is due to enhanced mobilization, recruitment, and/or differentiation of BMDCs. Here we show that diabetic mice treated with HOXA3 displayed a significant increase in both mobilization and recruitment of endothelial progenitor cells compared with control mice. Importantly, we also found that HOXA3-treated mice had significantly fewer inflammatory cells recruited to the wound compared with control mice. Microarray analyses of HOXA3-treated wounds revealed that indeed HOXA3 locally increased expression of genes that selectively promote stem/progenitor cell mobilization and recruitment while also suppressing expression of numerous members of the proinflammatory nuclear factor κB pathway, including myeloid differentiation primary response gene 88 and toll-interacting protein. Thus HOXA3 accelerates wound repair by mobilizing endothelial progenitor cells and attenuating the excessive inflammatory response of chronic wounds.

Sustained expression of Hif-1alpha in the diabetic environment promotes angiogenesis and cutaneous wound repair

Impaired wound healing in diabetic patients is associated with deficiencies in the production of factors involved in cell proliferation and migration, such as vascular endothelial growth factor. However, it remains unclear how the transcriptional regulation of the genes encoding these factors is affected by the diabetic environment. Hypoxia-inducible factor-1alpha (Hif-1alpha), the regulatory subunit of the Hif-1 transcription factor, plays an important role in activating many of these genes. Therefore, we tested whether Hif-1alpha function is impaired in the diabetic wound environment and whether restoring Hif-1 function improves wound healing. Here, we show that Hif-1alpha protein levels are dramatically reduced in wounds of leptin receptor-deficient diabetic mice compared with nondiabetic littermates. Reduction in Hif-1alpha levels results in decreased DNA-binding activity and in decreased expression of several Hif-1 target genes, including vascular endothelial growth factor, heme oxygenase-1, and inducible nitric oxide synthase. Furthermore, we demonstrate that sustained expression of Hif-1alpha in leptin receptor-deficient diabetic wounds restores expression of these factors, enhances angiogenesis, and significantly accelerates wound healing. Taken together, these results suggest that Hif-1alpha function plays a significant role in wound healing and reduced levels of Hif-1alpha may contribute to impaired healing.

Effects of decreased insulin-like growth factor-1 stimulation on hypoxia inducible factor 1-alpha protein synthesis and function during cutaneous repair in diabetic mice

Insulin-like growth factor-1 (Igf-1), a critical mediator of tissue repair, is significantly decreased in diabetic wounds. Furthermore, decreased levels of hypoxia-inducible factor 1-alpha (Hif-1alpha) and its target genes are also associated with impaired wound healing in diabetic mice. The aim of our study was to examine whether the reduced levels of Igf-1 are responsible for the reduction in Hif-1alpha protein synthesis and activity in diabetic wounds. We provide evidence that Igf-1 regulates Hif-1alpha protein synthesis and activity during wound repair. In addition, Igf-1 stimulated phosphytidylinositol 3-kinase activity in diabetic fibroblasts, which, in turn, increased activation of the translational regulatory protein, p70 S6 kinase. Moreover, improved healing of diabetic wounds by addition of recombinant IGF-1 protein was associated with an increase in Hif-1alpha protein synthesis and function in vivo.

Hemangiomas and homeobox gene expression

Hemangiomas are the most common benign tumor of childhood. Clinical management is limited primarily to observation. Non-surgical treatment modalities have had mixed results and with morbid side effects. Improved understanding of angiogenesis over the last two decades is helping to delineate differences between various vascular tumors. This molecular understanding will be central in helping to properly diagnose and potentially treat these childhood tumors. While a number of downstream effector cytokines have been shown to have altered expression in hemangiomas, a cause for the primary dysregulation within hemangiomas has not yet been clarified. Upstream modulators of angiogenesis are now being defined. Homeobox (Hox) genes are master transcription factors, which have a centrol role during organogenesis, and more recently have been documented to be involved in postnatal tissue remodeling and tumor angiogenesis. We document increased expression of Hox D3 in proliferating hemangiomas and propose a potential role for Hox A3, B3, A5 and D10.

Inappropriate Antibiotic Use in Soft Tissue Infections

HYPOTHESIS

Many soft tissue infections treated with surgical drainage resolve even when treated with antibiotics not active against the organism isolated from the infection.

DESIGN

Retrospective.

SETTING

Integrated Soft Tissue Infection Services clinic.

PATIENTS

All patients treated from July 19, 2000, to August 1, 2001, who underwent surgical drainage of a soft tissue infection and had microbiological culture results.

MAIN OUTCOME MEASURES

Documented resolution of the infection with drainage of the abscess and antibiotic therapy alone was deemed a cure. An infection resulting in death or other surgical therapy was deemed a failure. Therapy was appropriate when the organism was sensitive to prescribed antibiotics and was inappropriate when the organism was insensitive.

RESULTS

The study included 376 patients with 450 infections. Staphylococcus aureus as the primary organism was isolated from 441 of the cultures. Methicillin sodium-sensitive S aureus and methicillin-resistant S aureus were found in 157 and 284 of these isolates, respectively. Appropriate antibiotics were prescribed in 153 infections with methicillin-sensitive S aureus and in 25 with methicillin-resistant S aureus. Of 441 episodes, 408 were clinically evaluated for cure. Three patients failed treatment, 2 in the appropriately treated group (resulting in death and amputation) and 1 patient with osteomyelitis in the inappropriately treated group. The cure rate for infections treated appropriately or inappropriately was the same.

CONCLUSIONS

Treatment of soft tissue infections after surgical drainage, even with inappropriate antibiotics, has a high cure rate. Further studies to evaluate the efficacy of treating these infections without antibiotics are needed.

Telavancin versus standard therapy for treatment of complicated skin and skin structure infections caused by gram-positive bacteria: FAST 2 study

Telavancin is a bactericidal lipoglycopeptide with a multifunctional mechanism of action. We conducted a randomized, double blind, active-control phase II trial. Patients > or = 18 years of age with complicated skin and skin structure infections caused by suspected or confirmed gram-positive organisms were randomized to receive either telavancin at 10 mg/kg intravenously every 24 h (q24h) or standard therapy (antistaphylococcal penicillin at 2 g q6h or vancomycin at 1 g q12h). A total of 195 patients were randomized and received at least one dose of study medication. Clinical success rates were similar in all analysis populations at test of cure. In microbiologically evaluable patients with Staphylococcus aureus at baseline (n = 91), 96% of the telavancin group and 90% of the standard-therapy group were cured. Among patients with methicillin-resistant S. aureus (MRSA) at baseline (n = 45), clinical cure rates were also 96% for telavancin and 90% for standard therapy. Microbiologic eradication in patients with S. aureus infection was better with telavancin compared to standard therapy (92% versus 78%, P = 0.07) and significantly better in patients with MRSA (92% versus 68%; P = 0.04). Therapy was discontinued for an adverse event (AE) in 6% and 3% of the patients receiving telavancin and standard therapy, respectively. Except for two cases of rash in the telavancin group, these AEs were similar in type and severity in the two groups. The overall incidences and severities of AEs and laboratory abnormalities were similar between the two groups. These data support the ongoing studies assessing the efficacy and safety of telavancin in the treatment of serious gram-positive infections, particularly involving MRSA.

Naturally transformable Acinetobacter sp. strain ADP1 belongs to the newly described species Acinetobacter baylyi

Genotypic and phenotypic analyses were carried out to clarify the taxonomic position of the naturally transformable Acinetobacter sp. strain ADP1. Transfer tDNA-PCR fingerprinting, 16S rRNA gene sequence analysis, and selective restriction fragment amplification (amplified fragment length polymorphism analysis) indicate that strain ADP1 and a second transformable strain, designated 93A2, are members of the newly described species Acinetobacter baylyi. Transformation assays demonstrate that the A. baylyi type strain B2(T) and two other originally identified members of the species (C5 and A7) also have the ability to undergo natural transformation at high frequencies, confirming that these five strains belong to a separate species of the genus Acinetobacter, characterized by the high transformability of its strains that have been cultured thus far.

OPPORTUNITIES FOR GENETIC INVESTIGATION AFFORDED BYACINETOBACTER BAYLYI, A NUTRITIONALLY VERSATILE BACTERIAL SPECIES THAT IS HIGHLY COMPETENT FOR NATURAL TRANSFORMATION

The genetic and physiological properties of Acinetobacter baylyi strain ADP1 make it an inviting subject for investigation of the properties underlying its nutritional versatility. The organism possesses a relatively small genome in which genes for most catabolic functions are clustered in several genetic islands that, unlike pathogenicity islands, give little evidence of horizontal transfer. Coupling mutagenic polymerase chain reaction to natural transformation provides insight into how structure influences function in transporters, transcriptional regulators, and enzymes. With appropriate selection, mutants in which such molecules have acquired novel function may be obtained. The extraordinary competence of A. baylyi for natural transformation and the ease with which it expresses heterologous genes make it a promising platform for construction of novel metabolic systems. Steps toward this goal should take into account the complexity of existing pathways in which transmembrane trafficking plays a significant role.

HOXA3 induces cell migration in endothelial and epithelial cells promoting angiogenesis and wound repair

Wound repair requires both the recruitment and coordination of numerous cell types including inflammatory cells, fibroblasts, endothelial and epithelial cells. Each cell type has a distinct set of cell behavior such as formation of granulation tissue and basement membrane, migration, proliferation and redifferentiation. These processes are dependent on cell-cell and cell-ECM signaling, intracellular signal transduction cascades, and ultimately, changes in gene transcription. We have investigated the role of the transcription factor HOXA3 in wound repair and angiogenesis. Here we show that HOXA3 increases endothelial cell migration, induces angiogenesis in vivo, and leads to increased expression of the matrix metalloproteinase-14 (MMP-14) and urokinase-type plasminogen activator receptor (uPAR) genes in endothelial cells in culture and in vivo in response to injury. We find that HOXA3 gene expression is upregulated during wound healing in angiogenic endothelial cells and keratinocytes, and that HOXA3 is not induced in genetically diabetic mice that have impaired angiogenesis and wound repair. We demonstrate that gene transfer of HOXA3 into diabetic mouse wounds leads to dramatic improvements in both angiogenesis and wound closure. In addition, we show that HOXA3 promotes migration of endothelial cells and keratinocytes in a uPAR-dependent manner. Together these findings illustrate how the morphoregulatory protein, HOXA3 can facilitate tissue remodeling via coordinated changes in both epithelial and endothelial cell gene expression and behavior in adult tissues during wound repair.

Photochemically Knocking Out Glutamate Receptors in Vivo

AMPA (alpha-amino-3-hydroxy-5-methyl-4-isooxazole) receptors, a major subtype of ionotropic glutamate receptors (iGluRs), mediate the majority of the fast communication between neurons, and the activity-dependent trafficking of AMPA receptors at synapses plays a role in mammalian learning and memory. Here we describe the design, synthesis, and evaluation of a photoreactive AMPA receptor antagonist that provides a means of "knocking out" AMPA receptors present on the surface of cells. The antagonist, 6-azido-7-nitro-1,4-dihydroquinoxaline-2,3-dione (ANQX), was designed by introducing a photoreactive azido group onto a quinoxalinedione inhibitor scaffold. Computational docking of ANQX to the AMPA receptor ligand-binding core predicted efficient binding to AMPA receptors. Glutamate-evoked currents were reversibly blocked at micromolar ANQX concentrations prior to photolysis and irreversibly blocked following photolysis. ANQX provides a means of directly evaluating the trafficking of native AMPA receptors with unparalleled spatiotemporal resolution.

An Epidemic of Methicillin-Resistant Staphylococcus aureus Soft Tissue Infections Among Medically Underserved Patients

HYPOTHESIS

A high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in soft tissue infections presents a treatment challenge.

DESIGN

Retrospective analysis.

SETTING

The San Francisco General Hospital Integrated Soft Tissue Infection (ISIS) Clinic.

PATIENTS

Patients treated at the ISIS Clinic from July 1, 2000, to June 30, 2003.

MAIN OUTCOME MEASURES

Information on patient demographics, surgical procedures, microbiologic studies, and antibiotic treatments was obtained for all patients treated in the ISIS Clinic. Microbial data and antibiotic susceptibility pattern of S aureus, treatment outcome, and antibiotic prescribed were analyzed for all evaluable patients.

RESULTS

The ISIS Clinic treated 6156 unique patients for 12,012 episodes of infection. In this cohort, 5164 (84%) were either homeless or had no health insurance. More than half of the patients (58%) were injection drug users, but most had only 1 prior visit to the clinic (62%). Patients underwent a surgical procedure 7707 times (64%). Of the 837 positive cultures obtained, S aureus was recovered 695 times (83%), and 525 (63%) of the cultures contained MRSA. Therefore, a full 76% of all S aureus isolated was MRSA. In a subset analysis of 622 cultures collected prospectively from consecutive patients, 282 (45%) grew organisms, of which 256 (91%) were S aureus. MRSA represented 59% of all S aureus isolated. Homelessness and injection drug use were risk factors for infection by S aureus and MRSA. In another subgroup of patients with soft tissue infections that required admission to the hospital, MRSA was recovered from the cultures in 149 patients. In these patients with MRSA, 44 (30%) only received a beta-lactam antibiotic, inactive against MRSA, and had full resolution of their infection.

CONCLUSIONS

The prevalence of MRSA soft tissue infections in the medically underserved ISIS Clinic cohort is extremely high. The transmission of the MRSA seems to be in the community. Antibiotic therapy directed at MRSA may not be needed in a large number of patients with these soft tissue infections. Studies to identify the source and cause of this MRSA outbreak are urgently needed. Clinical trials to examine the need for antibiotic therapy in soft tissue infections should be conducted.

HoxD3 expression and collagen synthesis in diabetic fibroblasts

Diabetic wound healing is characterized by deficiencies in both growth factor and collagen production. We have observed that expression of homeobox D3 (HoxD3), a collagen-inducing transcription factor, and expression of collagen are reduced in an established animal model of diabetic wound repair, the leptin-deficient diabetic (db/db) mouse. We sought to evaluate whether the diminished expression of collagen and HoxD3 would be maintained once fibroblasts were removed from the diabetic wound environment. Fibroblasts were isolated from both wild-type and diabetic animals and expression of HoxD3 and collagen assessed. We found that when removed from the diabetic wound environment, HoxD3 and type I collagen expression are increased in diabetic fibroblasts when compared to wild-type fibroblasts. The increase in type I collagen is not related to increased production or activation of transforming growth factor-beta1. However, when the diabetic fibroblasts are cultured in a 3D collagen matrix, expression of type I collagen and HoxD3 is markedly reduced and reflects the pattern of gene expression observed in the in vivo diabetic wound environment. Thus, although diabetic fibroblasts can regain the capacity to express high levels of collagen and HoxD3 once removed from the diabetic wound environment, culturing cells in the presence of a 3D collagen matrix is sufficient to revert these fibroblasts to their previous nonsynthetic state.

HoxD3 accelerates wound healing in diabetic mice

Poorly healing diabetic wounds are characterized by diminished collagen production and impaired angiogenesis. HoxD3, a homeobox transcription factor that promotes angiogenesis and collagen synthesis, is up-regulated during normal wound repair whereas its expression is diminished in poorly healing wounds of the genetically diabetic (db/db) mouse. To determine whether restoring expression of HoxD3 would accelerate diabetic wound healing, we devised a novel method of gene transfer, which incorporates HoxD3 plasmid DNA into a methylcellulose film that is placed on wounds created on db/db mice. The HoxD3 transgene was expressed in endothelial cells, fibroblasts, and keratinocytes of the wounds for up to 10 days. More importantly, a single application of HoxD3 to db/db mice resulted in a statistically significant acceleration of wound closure compared to control-treated wounds. Furthermore, we also observed that the HoxD3-mediated improvement in diabetic wound repair was accompanied by increases in mRNA expression of the HoxD3 target genes, Col1A1 and beta 3-integrin leading to enhanced angiogenesis and collagen deposition in the wounds. Although HoxD3-treated wounds also show improved re-epithelialization as compared to control db/db wounds, this effect was not due to direct stimulation of keratinocyte migration by HoxD3. Finally, we show that despite the dramatic increase in collagen synthesis and deposition in HoxD3-treated wounds, these wounds showed normal remodeling and we found no evidence of abnormal wound healing. These results indicate that HoxD3 may provide a means to directly improve collagen deposition, angiogenesis and closure in poorly healing diabetic wounds.

Genes for chlorogenate and hydroxycinnamate catabolism (hca) are linked to functionally related genes in the dca-pca-qui-pob-hca chromosomal cluster of Acinetobacter sp. strain ADP1

Hydroxycinnamates are ubiquitous in the environment because of their contributions to the structure and defense mechanisms of plants. Additional plant products, many of which are formed in response to stress, support the growth of Acinetobacter sp. strain ADP1 through pathways encoded by genes in the dca-pca-qui-pob chromosomal cluster. In an appropriate genetic background, it was possible to select for an Acinetobacter strain that had lost the ability to grow with caffeate, a commonly occurring hydroxycinnamate. The newly identified mutation was shown to be a deletion in a gene designated hcaC and encoding a ligase required for conversion of commonly occurring hydroxycinnamates (caffeate, ferulate, coumarate, and 3,4-dihydroxyphenylpropionate) to thioesters. Linkage analysis showed that hcaC is linked to pobA. Downstream from hcaC and transcribed in the direction opposite the direction of pobA transcription are open reading frames designated hcaDEFG. Functions of these genes were inferred from sequence comparisons and from the properties of knockout mutants. HcaD corresponded to an acyl coenzyme A (acyl-CoA) dehydrogenase required for conversion of 3,4-dihydroxyphenylpropionyl-CoA to caffeoyl-CoA. HcaE appears to encode a member of a family of outer membrane proteins known as porins. Knockout mutations in hcaF confer no discernible phenotype. Knockout mutations in hcaG indicate that this gene encodes a membrane-associated esterase that hydrolyzes chlorogenate to quinate, which is metabolized in the periplasm, and caffeate, which is metabolized by intracellular enzymes. The chromosomal location of hcaG, between hcaC (required for growth with caffeate) and quiA (required for growth with quinate), provided the essential clue that led to the genetic test of HcaG as the esterase that produces caffeate and quinate from chlorogenate. Thus, in this study, organization within what is now established as the dca-pca-qui-pob-hca chromosomal cluster provided essential information about the function of genes in the environment.

Care of injection drug users with soft tissue infections in San Francisco, California

CONTEXT

Illicit injection drug use results in serious soft tissue infections that are the number one nonpsychiatric reason for admission to San Francisco General Hospital (SFGH), San Francisco, Calif.

OBJECTIVE

To establish a specialized clinic to provide accessible, high-quality, and cost-effective medical care to patients with soft tissue infections. DESIGN, SETTING, INTERVENTION, AND OUTCOME MEASURES: The Integrated Soft Tissue Infection Services (ISIS) Clinic was established to provide coordinated surgical intervention, substance abuse counseling, and social services for patients with soft tissue infections treated in a public hospital. Demographic information, treatment outcome, and hospital utilization data were analyzed.

RESULTS

In the clinic's first year of operation, there were 3365 patient visits and 2255 surgical procedures. A large number of patients reported recent injection of illicit drugs (61%), were homeless (30%), and either had hepatitis C, hepatitis B, or human immunodeficiency virus infection (62%). Patients using heroin were enrolled in either a detoxification or maintenance program (42%). Few patients were designated as treatment failures (2%) or were lost to follow-up (14%). The ISIS Clinic dramatically reduced emergency department visits (-33.9%), surgical service admissions (-47.3%), inpatient acute care bed days (-33.7%), and operating room procedures (-71%), saving approximately $8 765 200 in the first year of operation.

CONCLUSIONS

This clinical intervention was notably cost-effective while preserving a high quality of medical services. Owing to limited data, we can only assume that other communities are similarly confronted with this public health problem. The ISIS Clinic could serve as a model intervention and thus have significant impact on the treatment of this prevalent but often overlooked challenge.

Functions of the mismatch repair gene mutS from Acinetobacter sp. strain ADP1

The genus Acinetobacter encompasses a heterogeneous group of bacteria that are ubiquitous in the natural environment due in part to their ability to adapt genetically to novel challenges. Acinetobacter sp. strain ADP1 (also known as strain BD413) is naturally transformable and takes up DNA from any source. Donor DNA can be integrated into the chromosome by recombination provided it possesses sufficient levels of nucleotide sequence identity to the recipient's DNA. In other bacteria, the requirement for sequence identity during recombination is partly due to the actions of the mismatch repair system, a key component of which, MutS, recognizes mismatched bases in heteroduplex DNA and, along with MutL, blocks strand exchange. We have cloned mutS from strain ADP1 and examined its roles in preventing recombination between divergent DNA and in the repair of spontaneous replication errors. Inactivation of mutS resulted in 3- to 17-fold increases in transformation efficiencies with donor sequences that were 8 to 20% divergent relative to the strain ADP1. Strains lacking MutS exhibited increased spontaneous mutation frequencies, and reversion assays demonstrated that MutS preferentially recognized transition mismatches while having little effect on the repair of transversion mismatches. Inactivation of mutS also abolished the marker-specific variations in transforming efficiency seen in mutS(+) recipients where transition and frameshift alleles transformed at eightfold lower frequencies than transversions or large deletions. Comparison of the MutS homologs from five individual Acinetobacter strains with those of other gram-negative bacteria revealed that a number of unique indels are conserved among the Acinetobacter amino acid sequences.

The initial coverage and impact of the pneumococcal and influenza vaccination program for at-risk indigenous adults in Far North Queensland

OBJECTIVES

To describe the initial coverage and impact of a pneumococcal and influenza vaccination program for at-risk Indigenous adults in Far North Queensland that formally commenced in 1996.

DESIGN

Ascertainment of vaccine coverages, and prospective laboratory surveillance of invasive pneumococcal disease occurring in Indigenous adults in the region.

MAIN OUTCOME MEASURES

Coverages of the first doses of both vaccines administered since 1995, and the incidence of invasive pneumococcal disease in Indigenous adults in the region between 1993-2000.

RESULTS

Most (96% and 73%) of the Indigenous adults > or = 50 years of age received influenza and pneumococcal vaccines, respectively, for the first time between 1995-2000. Assuming that either 33% or 50% of Indigenous adults 15-49 years of age in Far North Queensland were eligible for vaccination, then either 109% or 72% of this population received influenza vaccine, and either 75% or 50% received pneumococcal vaccine, respectively, for the first time between 1995-2000. The incidence of vaccine-preventable invasive pneumococcal disease fell from 111 (95% confidence interval [CI] 77-154) cases per 100,000 per year in 1993/94 to 28 (95% CI 13-53) cases per 100,000 per year in 1999-2000 (p<0.05).

CONCLUSION

Although there was a significant decline in the incidence of invasive pneumococcal disease, the vaccine coverages after five years of the program were suboptimal. Because of the difficulties in targeting the 15-49 years age group and because of unrecognised risk factors, we suggest that a universal Indigenous adult pneumococcal and influenza vaccination program should be considered.

Prediction of the acute toxicity (96-h LC50) of organic compounds to the fathead minnow (Pimephales promelas) using a group contribution method

A group contribution method has been developed to correlate the acute toxicity (96-h LC50) to the fathead minnow (Pimephales promelas) for 397 organic chemicals. Multilinear regression and computational neural networks (CNNs) were used for model building. The models were able to achieve a fairly good correlation of the data (r2 > 0.9). The linear model, which included four specific interaction terms, provided a rapid means of predicting the toxicity of a compound. The CNN model was able to yield virtually the same predictions with or without the four interaction terms that were included in the multilinear model.

Hox D3 expression in normal and impaired wound healing

BACKGROUND

We have previously shown that Hox D3 and Hox B3 can promote angiogenesis. As angiogenesis is essential for wound healing, we examined expression of these genes in the vasculature following wounding in normal and genetically diabetic adult mice with impaired healing.

METHODS

In situ hybridization was performed on tissues taken 0, 1, 4, 7, and 14 days following administration of linear wounds in wild-type and genetically diabetic mice. Expression of Hox D3 and Hox B3, angiogenesis, and synthesis of type I collagen were assessed in the wound.

RESULTS

Hox B3 was expressed in endothelial cells (ECs) of both medium and small vessels in unwounded tissue, whereas little Hox D3 was detected in resting ECs. Hox D3 expression was significantly upregulated by 1 day after wounding in ECs of vessels immediately adjacent to the wound site, and expression was maintained for at least 7 days. In the diabetic mice, expression of Hox B3 was similar to that of wild-type mice. In contrast, expression of Hox D3 in ECs was significantly lower and delayed during wound repair in diabetic mice. In cultured microvascular ECs, Hox D3 selectively induced high levels of collagen I mRNA expression. Hox D3-deficient wounds of diabetic animals also displayed a reduction in expression and deposition of type I collagen.

CONCLUSIONS

These results suggest that reduced angiogenesis and type I collagen in diabetic mice with impaired wound healing may be related to deficient Hox D3 expression, and restoring Hox D3 expression may enhance angiogenesis and wound repair.

Expression of heat shock proteins in a linear rodent wound

Heat shock proteins (hsps) are ubiquitous and known to be expressed in all organisms. These stress proteins are likely to be induced in the wound environment and may play a critical role in the overall process of wound repair. Linear incisions were made in Sprague-Dawley rats. Serial skin biopsies were taken, the dermis and epidermis were separated and a protein lysate made. The expression of hsp 72, 47, and 32 were analyzed by Western blotting and immunohistochemistry. There were distinct patterns of expression of hsp 72, 47, and 32 in the wound. In unwounded dermis, there was no constitutive expression of any of the heat shock proteins studied. In the epidermis, there was constitutive expression of hsp 32 and 72, but not hsp 47. With wounding, all hsps exhibited increased expression both in the dermis and epidermis. These patterns of protein expression are suggestive of the individual heat shock proteins' molecular function, such as hsp 72's role as an indicator of cellular stress and injury, hsp 47's role in collagen synthesis, and hsp 32's role as an antioxidant.

Mercury-reactive lymphocytes in peripheral blood are not a marker for dental amalgam associated disease

OBJECTIVES

The popular press and publications associated with alternative medicine increasingly report that chronic ill health, particularly myalgic encephalitis like conditions, are associated with mercury amalgam fillings. There are no scientifically proven definitive tests to support these claims. One of the more scientific tests in vogue is to assess the level of blood-borne mercury-reactive lymphocytes and to conclude that patients with high levels have developed a hypersensitivity reaction to mercury. The objective of this study was to determine the diagnostic value of this test.

METHODS

This study represents an open comparison of mercury-reactive lymphocyte levels in healthy control individuals with those in patients complaining of symptoms associated with adverse effects of dental metal amalgam fillings. The healthy control group consisted of 51 male and female individuals, aged between 12 and 82 years, with and without dental amalgam fillings. The patient group consisted of 70 male and female individuals, aged between 12 and 87 years, and with the exception of one patient, with three or more mercury amalgam fillings of more than 1 year's duration. In vitro lymphocyte responses to mercury, and to nickel, as an example of a metal commonly associated with hypersensitivity reactions, and to more conventional protein antigens were determined.

RESULTS

In the blood of patients and controls, there were similar levels of specifically reactive lymphocytes to all of the in vitro stimulating agents, but there were significantly higher numbers of sub-normal and non-responders within the patient group.

CONCLUSIONS

The incidence and quantity of mercury-reactive lymphocytes in the blood are not pathogenic markers of illness associated with dental metal amalgams, but may rather reflect exposure to mercury. The clinical relevance of the decreased in vitro lymphocyte responses in the patient group needs further investigation.

West Nile virus infection in birds and mosquitoes, New York State, 2000

West Nile (WN) virus was found throughout New York State in 2000, with the epicenter in New York City and surrounding counties. We tested 3,403 dead birds and 9,954 mosquito pools for WN virus during the transmission season. Sixty-three avian species, representing 30 families and 14 orders, tested positive for WN virus. The highest proportion of dead birds that tested positive for WN virus was in American Crows in the epicenter (67% positive, n=907). Eight mosquito species, representing four genera, were positive for WN virus. The minimum infection rate per 1,000 mosquitoes (MIR) was highest for Culex pipiens in the epicenter: 3.53 for the entire season and 7.49 for the peak week of August 13. Staten Island had the highest MIR (11.42 for Cx. pipiens), which was associated with the highest proportion of dead American Crows that tested positive for WN virus (92%, n=48) and the highest number of human cases (n=10).

Neutralizing vascular endothelial growth factor activity inhibits thyroid cancer growth in vivo

BACKGROUND

Without angiogenesis, tumor growth is limited to a few millimeters, the limit of diffusion. Vascular endothelial growth factor (VEGF) is an endothelial-specific mitogen and a major regulator of angiogenesis.

METHODS

To investigate the relationship between VEGF and thyroid tumor angiogenesis, we xenografted human dermal matrix inoculated with FTC-133 cells into nude mice or directly injected FTC-133 cells subcutaneously. To block the function of VEGF, the neutralizing anti-VEGF monoclonal antibody A.4.6.1 (mAb A.4.6.1) was injected intraperitoneally twice weekly. As control, an antibody of the same isotype (Ab 5B6) or phosphate buffer saline solution (PBS) was used. To evaluate the dermal matrix as a model for angiogenesis studies, recombinant human VEGF was inoculated into the dermal matrix pocket and xenografted into mice.

RESULTS

In the dermal matrix angiogenesis model, the number of blood vessels paralleled the concentration of recombinant human VEGF and was highest at 100 ng/mL. Mice that were treated with the mAb A4.6.1 developed fewer blood vessels (mean, 6.6 per HPF) than control mice (18 per HPF in Ab 5B6 and 22 per HPF in PBS; P <.01). Tumors from mice that were treated with mAb A.4.6.1 were much smaller (mean +/- SD, 0.09 +/- 0.02 gm) at 5 weeks, compared with the tumors treated with Ab 5B6 (5.38 +/- 1.15 gm) or PBS (4.0 +/- 0.72 gm; P <.001).

CONCLUSIONS

VEGF is produced by the follicular thyroid cancer cell line and stimulates angiogenesis and growth of thyroid cancer. This stimulation can be blocked by mAb A.4.6.1.

Cranial nerve VII region of the traumatized facial skeleton: optimizing fracture repair with the endoscope

OBJECTIVE

Cranial nerve VII (CN VII) is anatomically positioned adjacent to the condylar neck of the mandible and arch of the midface. Fracture treatment of this region of the facial skeleton remains controversial because of difficult surgical access. Conservative management rarely achieves anatomic fracture repair and can result in irreversible structural deformity and dysfunction. Traditional operative methods require access through very visible facial incisions and risk injury to the facial nerve. We report endoscopic methods of facial fracture repair in the region of CN VII that achieve excellent fracture reduction and stabilization, with minimal risk of facial nerve injury by using hidden incisions.

METHODS

A consecutive series of 65 endoscopically assisted facial fracture repairs were analyzed. Endoscopic repairs of the condylar neck (n = 40) of the mandible were performed through an intraoral incision. Endoscopic arch repairs (n = 25) of the midface were performed through a preauricular incision. Outcomes were evaluated by postoperative fracture reduction on radiographs, occlusion, interincisal jaw opening, and facial nerve function.

RESULTS

Thirty-seven of 40 condylar neck mandible fractures went on to anatomic bone union, whereas 3 of 40 had either incomplete fracture reduction or re-fracture through the plate. There was one temporary palsy of CN VII that completely resolved spontaneously. Jaw opening exceeded 40 mm by the 8th postoperative week. Computed tomographic images demonstrated anatomic arch repair in all 25 endoscopically repaired cases. Six of seven endoscopically repaired Le Fort III facial fractures went on to restoration of their premorbid occlusion. One of seven had an excellent restoration of the occlusal interface but a cant to the occlusal plane. Two of seven had improved but incomplete restoration of the malar prominence and enopthalmos ipsilateral to the side of endoscopic arch repair. Eight of 25 endoscopic arch repairs developed temporary paralysis of the frontal branch of CN VII that recovered completely by the 10th postoperative week.

CONCLUSION

We have developed novel endoscopically assisted techniques to facilitate repair of facial fractures in the region of CN VII. These techniques have been successfully applied to accurately restore the facial skeleton to its preinjury anatomic position in the region of CN VII with minimal risk of facial paralysis by using limited and well-hidden incisions.