On Generalizations of the Nonwindowed Scattering Transform

In this paper, we generalize finite depth wavelet scattering transforms, which we formulate as L q ( ℝ n ) norms of a cascade of continuous wavelet transforms (or dyadic wavelet transforms) and contractive nonlinearities. We then provide norms for these operators, prove that these operators are well-defined, and are Lipschitz continuous to the action of C 2 diffeomorphisms in specific cases. Lastly, we extend our results to formulate an operator invariant to the action of rotations R ∈ SO ( n ) and an operator that is equivariant to the action of rotations of R ∈ SO ( n ) .

Classroom aerosol dispersion modeling: experimental assessment of a low-cost flow simulation tool

The purpose of this study was to assess the utility of a low-cost flow simulation tool for an indoor air modeling application by comparing its outputs with the results of a physical experiment, as well as those from a more advanced computational fluid dynamics (CFD) software package. Five aerosol dispersion tests were performed in two different classrooms by releasing a CO2 tracer gas from six student locations. Resultant steady-state concentrations were monitored at 13 locations around the periphery of the room. Subsequently, the experiments were modeled using both a low-cost tool (SolidWorks Flow Simulation) and a more sophisticated tool (STAR-CCM+). Models were evaluated based on their ability to predict the experimentally measured concentrations at the 13 monitoring locations by calculating four performance parameters commonly used in the evaluation of dispersion models: fractional mean bias (FB), normalized mean-square error (NMSE), fraction of predicted value within a factor of two (FAC2), and normalized absolute difference (NAD). The more sophisticated model performed better in 15 of the 20 possible cases (five tests at four parameters each), with parameters meeting acceptance criteria in 19 of 20 cases. However, the lower-cost tool was only slightly worse, with parameters meeting acceptance criteria in 18 of 20 cases, and it performed better than the other tool in 3 of 20 cases. Because it provides useful results at a fraction of the monetary and training cost and is already widely accessible to many institutions, such a tool may be worthwhile for many indoor aerosol dispersion applications, especially for students or researchers just beginning CFD modeling.

Inferring Metabolic States from Single Cell Transcriptomic Data via Geometric Deep Learning

The ability to measure gene expression at single-cell resolution has elevated our understanding of how biological features emerge from complex and interdependent networks at molecular, cellular, and tissue scales. As technologies have evolved that complement scRNAseq measurements with things like single-cell proteomic, epigenomic, and genomic information, it becomes increasingly apparent how much biology exists as a product of multimodal regulation. Biological processes such as transcription, translation, and post-translational or epigenetic modification impose both energetic and specific molecular demands on a cell and are therefore implicitly constrained by the metabolic state of the cell. While metabolomics is crucial for defining a holistic model of any biological process, the chemical heterogeneity of the metabolome makes it particularly difficult to measure, and technologies capable of doing this at single-cell resolution are far behind other multiomics modalities. To address these challenges, we present GEFMAP (Gene Expression-based Flux Mapping and Metabolic Pathway Prediction), a method based on geometric deep learning for predicting flux through reactions in a global metabolic network using transcriptomics data, which we ultimately apply to scRNAseq. GEFMAP leverages the natural graph structure of metabolic networks to learn both a biological objective for each cell and estimate a mass-balanced relative flux rate for each reaction in each cell using novel deep learning models.

Accurately modeling biased random walks on weighted networks using node2vec

MOTIVATION

Accurately representing biological networks in a low-dimensional space, also known as network embedding, is a critical step in network-based machine learning and is carried out widely using node2vec, an unsupervised method based on biased random walks. However, while many networks, including functional gene interaction networks, are dense, weighted graphs, node2vec is fundamentally limited in its ability to use edge weights during the biased random walk generation process, thus under-using all the information in the network.

RESULTS

Here, we present node2vec+, a natural extension of node2vec that accounts for edge weights when calculating walk biases and reduces to node2vec in the cases of unweighted graphs or unbiased walks. Using two synthetic datasets, we empirically show that node2vec+ is more robust to additive noise than node2vec in weighted graphs. Then, using genome-scale functional gene networks to solve a wide range of gene function and disease prediction tasks, we demonstrate the superior performance of node2vec+ over node2vec in the case of weighted graphs. Notably, due to the limited amount of training data in the gene classification tasks, graph neural networks such as GCN and GraphSAGE are outperformed by both node2vec and node2vec+.

AVAILABILITY AND IMPLEMENTATION

The data and code are available on GitHub at https://github.com/krishnanlab/node2vecplus_benchmarks. All additional data underlying this article are available on Zenodo at https://doi.org/10.5281/zenodo.7007164.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Spatiotemporal Graph Convolutional Networks for Earthquake Source Characterization

Accurate earthquake location and magnitude estimation play critical roles in seismology. Recent deep learning frameworks have produced encouraging results on various seismological tasks (e.g., earthquake detection, phase picking, seismic classification, and earthquake early warning). Many existing machine learning earthquake location methods utilize waveform information from a single station. However, multiple stations contain more complete information for earthquake source characterization. Inspired by recent successes in applying graph neural networks (GNNs) in graph-structured data, we develop a Spatiotemporal Graph Neural Network (STGNN) for estimating earthquake locations and magnitudes. Our graph neural network leverages geographical and waveform information from multiple stations to construct graphs automatically and dynamically by adaptive message passing based on graphs' edges. Using a recent graph neural network and a fully convolutional neural network as baselines, we apply STGNN to earthquakes recorded by the Southern California Seismic Network from 2000 to 2019 and earthquakes collected in Oklahoma from 2014 to 2015. STGNN yields more accurate earthquake locations than those obtained by the baseline models and performs comparably in terms of depth and magnitude prediction, though the ability to predict depth and magnitude remains weak for all tested models. Our work demonstrates the potential of using GNNs and multiple stations for better automatic estimation of earthquake epicenters.

The Manifold Scattering Transform for High-Dimensional Point Cloud Data

The manifold scattering transform is a deep feature extractor for data defined on a Riemannian manifold. It is one of the first examples of extending convolutional neural network-like operators to general manifolds. The initial work on this model focused primarily on its theoretical stability and invariance properties but did not provide methods for its numerical implementation except in the case of two-dimensional surfaces with predefined meshes. In this work, we present practical schemes, based on the theory of diffusion maps, for implementing the manifold scattering transform to datasets arising in naturalistic systems, such as single cell genetics, where the data is a high-dimensional point cloud modeled as lying on a low-dimensional manifold. We show that our methods are effective for signal classification and manifold classification tasks.

SCATTERING STATISTICS OF GENERALIZED SPATIAL POISSON POINT PROCESSES

We present a machine learning model for the analysis of randomly generated discrete signals, modeled as the points of an inhomogeneous, compound Poisson point process. Like the wavelet scattering transform introduced by Mallat, our construction is naturally invariant to translations and reflections, but it decouples the roles of scale and frequency, replacing wavelets with Gabor-type measurements. We show that, with suitable nonlinearities, our measurements distinguish Poisson point processes from common self-similar processes, and separate different types of Poisson point processes.

Wavelet invariants for statistically robust multi-reference alignment

We propose a nonlinear, wavelet-based signal representation that is translation invariant and robust to both additive noise and random dilations. Motivated by the multi-reference alignment problem and generalizations thereof, we analyze the statistical properties of this representation given a large number of independent corruptions of a target signal. We prove the nonlinear wavelet-based representation uniquely defines the power spectrum but allows for an unbiasing procedure that cannot be directly applied to the power spectrum. After unbiasing the representation to remove the effects of the additive noise and random dilations, we recover an approximation of the power spectrum by solving a convex optimization problem, and thus reduce to a phase retrieval problem. Extensive numerical experiments demonstrate the statistical robustness of this approximation procedure.

MagNet: A Neural Network for Directed Graphs

The prevalence of graph-based data has spurred the rapid development of graph neural networks (GNNs) and related machine learning algorithms. Yet, despite the many datasets naturally modeled as directed graphs, including citation, website, and traffic networks, the vast majority of this research focuses on undirected graphs. In this paper, we propose MagNet, a GNN for directed graphs based on a complex Hermitian matrix known as the magnetic Laplacian. This matrix encodes undirected geometric structure in the magnitude of its entries and directional information in their phase. A "charge" parameter attunes spectral information to variation among directed cycles. We apply our network to a variety of directed graph node classification and link prediction tasks showing that MagNet performs well on all tasks and that its performance exceeds all other methods on a majority of such tasks. The underlying principles of MagNet are such that it can be adapted to other GNN architectures.

CATMoS: Collaborative Acute Toxicity Modeling Suite

BACKGROUND

Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk management. However, it is cost- and time-prohibitive to evaluate all new and existing chemicals using traditional rodent acute toxicity tests. In silico models built using existing data facilitate rapid acute toxicity predictions without using animals.

OBJECTIVES

The U.S. Interagency Coordinating Committee on the Validation of Alternative Methods (ICCVAM) Acute Toxicity Workgroup organized an international collaboration to develop in silico models for predicting acute oral toxicity based on five different end points: Lethal Dose 50 (LD50 value, U.S. Environmental Protection Agency hazard (four) categories, Globally Harmonized System for Classification and Labeling hazard (five) categories, very toxic chemicals [LD50 (LD50≤50mg/kg)], and nontoxic chemicals (LD50>2,000mg/kg).

METHODS

An acute oral toxicity data inventory for 11,992 chemicals was compiled, split into training and evaluation sets, and made available to 35 participating international research groups that submitted a total of 139 predictive models. Predictions that fell within the applicability domains of the submitted models were evaluated using external validation sets. These were then combined into consensus models to leverage strengths of individual approaches.

RESULTS

The resulting consensus predictions, which leverage the collective strengths of each individual model, form the Collaborative Acute Toxicity Modeling Suite (CATMoS). CATMoS demonstrated high performance in terms of accuracy and robustness when compared with in vivo results.

DISCUSSION

CATMoS is being evaluated by regulatory agencies for its utility and applicability as a potential replacement for in vivo rat acute oral toxicity studies. CATMoS predictions for more than 800,000 chemicals have been made available via the National Toxicology Program's Integrated Chemical Environment tools and data sets (ice.ntp.niehs.nih.gov). The models are also implemented in a free, standalone, open-source tool, OPERA, which allows predictions of new and untested chemicals to be made. https://doi.org/10.1289/EHP8495.

A Hybrid Scattering Transform for Signals with Isolated Singularities

The scattering transform is a wavelet-based model of Convolutional Neural Networks originally introduced by S. Mallat. Mallat's analysis shows that this network has desirable stability and invariance guarantees and therefore helps explain the observation that the filters learned by early layers of a Convolutional Neural Network typically resemble wavelets. Our aim is to understand what sort of filters should be used in the later layers of the network. Towards this end, we propose a two-layer hybrid scattering transform. In our first layer, we convolve the input signal with a wavelet filter transform to promote sparsity, and, in the second layer, we convolve with a Gabor filter to leverage the sparsity created by the first layer. We show that these measurements characterize information about signals with isolated singularities. We also show that the Gabor measurements used in the second layer can be used to synthesize sparse signals such as those produced by the first layer.

Geometric Wavelet Scattering Networks on Compact Riemannian Manifolds

The Euclidean scattering transform was introduced nearly a decade ago to improve the mathematical understanding of convolutional neural networks. Inspired by recent interest in geometric deep learning, which aims to generalize convolutional neural networks to manifold and graph-structured domains, we define a geometric scattering transform on manifolds. Similar to the Euclidean scattering transform, the geometric scattering transform is based on a cascade of wavelet filters and pointwise nonlinearities. It is invariant to local isometries and stable to certain types of diffeomorphisms. Empirical results demonstrate its utility on several geometric learning tasks. Our results generalize the deformation stability and local translation invariance of Euclidean scattering, and demonstrate the importance of linking the used filter structures to the underlying geometry of the data.

European quality system for tissue banking

AIM

The aims of this project were to analyze the factors that influence quality and safety of tissues for transplantation and to develop the method to ensure standards of quality and safety in relation to tissue banking as demanded by European Directive 2004/23/EC and its technical annexes. It is organized in 4 Working Groups, the objectives of each one being focused in a specific area.

STANDARDS

The Guide of Recommendations for Tissue Banking is structured into 4 parts: (1) quality systems that apply to tissue banking and general quality system requirements, (2) regulatory framework in Europe, (3) standards available, and (4) recommendations of the fundamental quality and safety keypoints.

REGISTRY

This Working Group handled design of a multinational musculoskeletal tissue registry prototype.

TRAINING

This Working Group handled design and validation of a specialized training model structured into online and face-to-face courses. The model was improved with suggestions from students, and 100% certification was obtained.

AUDIT

The Guide for Auditing Tissue Establishments provides guidance for auditors, a self-assessment questionnaire, and an audit report form. The effectiveness and sustainability of the outputs were assessed. Both guides are useful for experienced tissue establishments and auditors and also for professionals that are starting in the field. The registry prototype proves it is possible to exchange tissues between establishments throughout Europe. The training model has been effective in educating staff and means having professionals with excellent expertise. Member states could adapt/adopt it. The guides should be updated periodically and perhaps a European organization should take responsibility for this and even create a body of auditors.

Cefuroxime, rifampicin and pulse lavage in decontamination of allograft bone

The risk of bacterial infection through allogenic bone transplantation is one of the major problems facing tissue banks. Different screening methods and decontamination procedures are being used to achieve a safe surgical result. The purpose of this study was to investigate the contamination rate in fresh frozen bone allografts after treating them with different decontamination methods. The allografts were contaminated by rubbing on the operating theatre floor for 60 min, after which they were rinsed either with sterile physiological saline, cefuroxime or rifampicin solution or they were washed with low-pressure pulse lavage of sterile physiological saline. Our findings show that low-pressure pulse lavage with sterile saline solution is very effective in removing bacteria from bone allograft, when compared with the antibiotic solutions tested.

Survival of 25 osteoarticular allografts followed more than 10 years

An evaluation of the long-term survival rate of 25 osteoarticular allografts was made. Clinical analysis was based on the Mankin scale and the Musculoskeletal Tumor Society (MSTS) Grading system. After a mean follow-up time of 15 years 76% of the osteoarticular allografts had good or excellent rating. The MSTS scale revealed a mean score of 89% for those 20 grafts still functioning according to their primary purpose. Allograft related complications occurred in 32% of the cases being most common among malignant cases. Due to the rather good long-term results, osteoarticular allografts can still be recommended for hemicondylar allograft reconstruction in benign lesions.

Pulse lavage washing in decontamination of allografts improves safety

We analyzed the bacterial contamination rate of 140 femoral head allografts after rinsing the allografts in different decontamination solutions. Bacterial screening methods and cleansing effect of antibiotics (cefuroxime and rifampicin) and pulse lavage were compared. Swabbing and taking small pieces of bone for culture were the screening methods used. Both methods proved to be quite unreliable. Approximately one-fourth of the results were false negative. Culturing small pieces of bone gave the most accurate and reliable results and, therefore, can be recommended as a bacterial screening method. The use of antibiotics in allograft decontamination is controversial. In prophylactic use antibiotics include risks of allergic reactions and resistant development and our results in the present study show that antibiotics do not improve the decontamination any better than low-pressure pulse lavage with sterile saline solution. Therefore, pulse lavage with sterile saline solution can be recommended for allograft decontamination. Our results demonstrate that it decreases bacterial bioburden as effectively as the antibiotics without persisting the disadvantages.

Management of clostridial gas gangrene and the role of hyperbaric oxygen

BACKGROUND AND AIMS

Clostridial gas gangrene is one of the most dreaded infections in surgery. The aim of this study was to investigate the efficacy of surgery, antibiotic treatment, surgical intensive care and especially the role of hyperbaric oxygen in the management of clostridial gas gangrene.

MATERIAL AND METHODS

53 patients, 42 of them submitted from other hospitals in Finland. After the diagnosis had been made the patients underwent surgical debridement, broad spectrum antibiotic therapy and a series of hyperbaric oxygen (HBO) treatments at 2.5 ATA pressure. The necrotic tissue was excised and incisions were made in the affected areas. Amputations were performed when necessary.

RESULTS

Twelve patients died (22.6%). Hyperbaric oxygen therapy decreased the systemic toxicity and prevented further extension of the infection thereby improving the overall outcome of the patients.

CONCLUSION

Hyperbaric oxygen therapy of gas gangrene seems to be life-, limb- and tissue saving. Early diagnosis remains essential. Patient survival can be improved if the disease is recognized early and appropriate therapy applied promptly. Surgical and antibiotic therapy as well as HBO treatment combined with surgical intensive care must be started as soon as possible.

Bone bank service in Finland. Experience of bacteriologic, serologic and clinical results of the Turku Bone Bank 1972-1995

560 bones were harvested by The Turku Bone Bank between 1972-1995. It was started with massive allografts for bone tumor surgery, but today most are femoral heads for hip revision surgery. The increase in harvested bones nearly trebled from 1984-1989 to 1990-1995. Only 1 positive hepatitis C test was found. There were no hepatitis B or HIV positive donors. The incidence of discarding after screening was 24%, with positive bacterial growth (8%, usually Staphylococcus epidermidis) as the commonest reason. 2 massive grafts with negative cultures when harvesting were positive after thawing and resulted in deep infection. 369 allografts were transplanted. The infection rate of massive allografts for bone tumor surgery was 5/63 in 1973-1995, and 2/52 in 1985-1995. The infection rate for hip revision surgery was 3.4%. The clinical functional results correspond to those reported in larger international series.

An anti-CD4 (CDR3-loop) monoclonal antibody inhibits human immunodeficiency virus type 1 envelope glycoprotein-induced apoptosis

Inhibition of human immunodeficiency virus type 1 (HIV-1)-inducing programmed cell death (PCD) by anti-CD4 monoclonal antibodies (mAbs) was investigated using DNA intercalant YOPRO-1 assay. We found that 13B8.2, an mAb that binds the CDR3-like loop in domain 1 (D1) of CD4, protected infected CEM cell cultures against HIV-1-induced PCD. Protection was not observed using another anti-CD4 mAb (BL4) that binds D1-D2, suggesting that the mechanism involved in cell protection against HIV-1-induced PCD requires engagement of precise CD4 epitopes. Because 13B8.2 is known to inhibit syncytia formation and virus transcription, this mAb could inhibit HIV-1-induced PCD by (1) inhibiting virus gene expression, (2) preventing viral envelope-CD4 interaction, and/or (3) interfering with apoptotic signals. Our data indicated that the absence of enhanced PCD in infected cell cultures treated with 13B8.2 mAb probably was the result of inhibition of HIV-1 replication and virus spread. Moreover, 13B8.2 mAb was found to inhibit PCD mediated by membrane-expressed HIV-1 envelope glycoproteins. Finally, we found that 13B8.2 mAb displayed no protective interference with apoptotic signal induced by Fas, dexamethasone, and serum withdrawal.

Anti-GM-CSF monoclonal antibody therapy for refractory acute leukemia

Several phase I trials and pilot studies using Monoclonal Antibody (MoAb) have been performed in B-cell neoplasms, but this approach has not until now been extensively tested in myeloid leukemias. Recently, we evaluated the use of anti-Granulocyte-Macrophage Colony-Stimulating Factor MoAb (Anti-GM-CSF MoAb) in acute myeloid leukemia (AML). Eight patients fulfilled inclusion criteria and received a single course of Anti-GM-CSF MoAb infusion during 5 to 15 days. Anti-GM-CSF MoAb was well tolerated and was detectable in pharmacokinetics studies. Using Human Anti-Rat Antibodies (HARA), we also observed an immunological response to the MoAb. Despite sufficient levels detected in the serum and biological activity of Anti-GM-CSF MoAb in vivo, no anti-leukemic effect was noted, except for one patient who had a decrease of 50% in the marrow blast cell mass. These observations indicate that leukemic proliferation in vivo involves a complex network spanning many mechanisms, and inhibition of leukemia is not effective if only one of these key targets is attacked. The development of these new approaches may be more effective in the future.

Hyperbaric oxygen in the treatment of Fournier's gangrene

OBJECTIVE

To investigate the efficacy of operation, antibiotic treatment, hyperbaric oxygen, and surgical intensive care in the management of Fournier's gangrene.

DESIGN

Retrospective study.

SETTING

University hospital, Finland.

SUBJECTS

33 patients, most of them referred from other hospitals.

INTERVENTION

Debridement, broad spectrum antibiotics, and hyperbaric oxygen (HBO) treatment at 2.5 atmospheres absolute pressure. Excision of necrotic tissue and incisions in the affected areas. Urinary and faecal diversions when necessary.

MAIN OUTCOME MEASURES

Morbidity and mortality.

RESULTS

Only three patients died (9%). Hyperbaric oxygen reduced systemic toxicity, prevented extension of the necrotising infection, and increased demarcation, thereby improving the overall outcome.

CONCLUSION

To reduce mortality and morbidity, effective treatment of Fournier's gangrene should be started promptly. Debridement and antibiotics combined with surgical intensive care must be started as soon as possible. Hyperbaric oxygen is both life and tissue saving. It is an important adjunct that prevents extension of necrosis and reduces systemic toxicity.

In vitro selection of HIV-1 resistant to an anti-CD4 monoclonal antibody that inhibits virus transcription

Phase I studies using monoclonal antibodies (mAbs) that bind to the Ig-CDR3-like loop in domain 1 of CD4 (e.g., 13B8-2 mAb) have already been documented for HIV-1-infected patients. In vitro, such mAbs do not inhibit virus to cell fusion but are able to inhibit virus envelope-mediated syncytia formation. Moreover, these mAbs inhibit Tat-induced activation of HIV-1 promoter and HIV-1 transcription in infected CD4+ cells. Here, we report the selection of escaped mutant virus or viruses derived from HIV-1Lai capable of replicating in vitro in the presence of concentrations of 13B8-2 mAb, that usually inhibit HIV-1Lai particle production. The escaped mutant virus or viruses, termed HIV-1Lai13EM, kept the major enzymatic restriction sites found in HIV-1Lai and remained sensitive to anti-CD4 mAb-, soluble CD4-, and recombinant gp120-mediated inhibition of syncytia formation. Possible genetic changes affecting the tat gene or the 5' long terminal repeat (LTR) were investigated. Partial sequence analysis of HIV-1Lai13EM and a control HIV-1Lai grown for 85 days in CEM cells, demonstrated that the first tat exon of these two viruses encoded identical proteins. Although a point mutation G>A was frequently encountered (6 of 13 sequences) in the LTRs of HIV-1Lai13EM at position -188 within the negative regulatory element (NRE), this mutation did not confer the escape mutant phenotype. Our study indicates that the mutant phenotype probably requires genetic changes in a region or regions outside the LTRs.

Inhibition of human immunodeficiency virus type 1 production in infected peripheral blood mononuclear cells by human leukocyte antigen class I-specific antibodies: evidence for a novel antiviral mechanism

A well-characterized mechanism by which anti-HLA class I monoclonal antibodies (MAb) inhibit human immunodeficiency virus type 1 (HIV-1) propagation in in vitro cell cultures is the neutralization of the virus through interactions with HLA molecules associated with the virion envelope. Yet, the possibility that another mechanism of inhibition might affect a postbinding stage of the virus life cycle has been strongly suggested by our previous investigations. To demonstrate that the interaction of MAb B1-1G6 with the light chain of cell surface-expressed HLA class I molecules inhibits a postbinding step of the HIV-1 life cycle, peripheral blood mononuclear cells (PBMCs) were exposed to viruses grown in HLA class I-negative, CD4-positive cells (these viruses, which did not carry HLA class I molecules, cannot be neutralized by anti-HLA MAb during the first round of infection), and PCR was used at various times postexposure to search for the different forms of HIV-1 DNA and RNA in virus-exposed PBMCs cultured in either the presence or [correction of] absence of MAb B1-1G6. Although viral DNA was found in MAb B1-1G6-treated cells, spliced HIV-1 mRNA could not be detected in those cells. In contrast, HIV-1 gene expression was found in HIV-1-infected PBMCs treated with B9-12-1, another HLA class I-specific MAb which prevents infection of cells by cell-free viruses but which fails to inhibit cell-to-cell transmission of HIV-1. These results highlight a second antiviral mechanism by which anti-HLA MAb inhibit in vitro HIV-1 propagation.

The cytoplasmic tail of CD4 is required for inhibition of human immunodeficiency virus type 1 replication by antibodies that bind to the immunoglobulin CDR3-like region in domain 1 of CD4

Monoclonal antibodies (MAb) directed against the immunoglobulin complementary determining region 3 (CDR3)-like region of the CD4 molecule inhibit human immunodeficiency virus type 1 (HIV-1) transcription. We report here data showing that the cytoplasmic tail of CD4 is required for such inhibition to be achieved. To this aim, we studied the effect of MAb 13B8-2 treatment on (i) HIV-1 production in A2.01 cells, which express different forms of the CD4 gene, (ii) Tat-induced HIV-1 promoter activation, and (iii) mitogen-activated protein kinase (MAPK) activation, which is induced in CD4-positive cells by HIV-1 cross-linking of CD4. Inhibition of HIV production by 13B8-2 MAb treatment was consistently observed in cells expressing wild-type CD4 and cells expressing a hybrid CD4-CD8 molecule (amino acids 1 to 177 of CD4 fused to the hinge, transmembrane, and cytoplasmic domains of CD8). However, no delay in HIV-1 production was observed in cells expressing a truncated CD4 which lacks the cytoplasmic domain (CD4.401). Chloramphenicol acetyltransferase assays demonstrated that Tat-dependent activation of the HIV-1 long terminal repeat promoter was inhibited by MAb 13B8-2 in A2.01/CD4 and A2.01/CD4-CD8 but not in A2.01/CD4.401 cells. Finally, we found that MAb 13B8-2 treatment inhibited the activation of MAPK induced in A2.01/CD4 and A2.01/CD4-CD8 following cross-linking of CD4 by HIV-1.

Functional epitope analysis of the human CD4 molecule: antibodies that inhibit human immunodeficiency virus type 1 gene expression bind to the immunoglobulin CDR3-like region of CD4

We recently demonstrated that monoclonal antibody (MAb) 13B8-2, specific for the immunoglobulin (Ig) complementary determining region 3 (CDR3)-like region of the CD4 molecule, inhibits viral transcription in human immunodeficiency virus (HIV)-infected CEM cells and HIV type 1 (HIV-1) promoter activity. Here, we have studied the capacity of several MAb specific for the D1 domain of CD4, including anti-CDR2-like (Leu-3a and ST4) and anti-CDR3-like (13B8-2 and ST40) MAb, and for the D2 domain of CD4 (BL4) to inhibit both provirus transcription in HIV-1LAI-infected CEM cells and transcription of the chloramphenicol acetyltransferase (CAT) gene under control of the HIV-1 long terminal repeat in transiently transfected CEM cells. We found that HIV-1 promoter activity and provirus transcription are inhibited only by MAb that bind to the CDR3-like region in domain 1 of CD4. Moreover, we demonstrated that the Fab fragment of an anti-CDR3-like region-specific anti-CD4 MAb is a powerful inhibitor of HIV-1 promoter activity. These results have implications for understanding the role of the CDR3-like region in CD4 T-cell signaling, which controls provirus transcription.

Human pancreatic lipase. Importance of the hinge region between the two domains, as revealed by monoclonal antibodies

Several monoclonal antibodies (mAbs) were prepared against human pancreatic lipase (HPL). Two enzyme-linked immunosorbent assay (ELISA) procedures were set up for screening hybridomas producing specific antibodies. Four mAbs (81-23, 146-40, 315-25, and 320-24) of the IgG1 isotype were found to react with HPL in both simple sandwich and double sandwich ELISAs, while mAb 248-31, of the IgG2b isotype, reacted only with HPL in a double sandwich ELISA. The results of Western blot analysis carried out with native and SDS-denatured HPLs indicated that mAb 248-31 recognized only native HPL, while all the other mAbs recognized both forms of HPL. Since mAb 248-31 did not recognize SDS-denatured HPL, it was not possible to localize its epitope. To carry out epitope mapping along the primary sequence of HPL, four fragments (14, 26, 30, and 36 kDa) resulting from a limited chymotryptic cleavage of HPL were characterized by Western blotting as well as N-terminal amino acid sequence analysis. Of the above five anti-HPL mAbs, four (81-23, 248-31, 315-25, and 320-24) were found to inhibit the lipolytic activity of HPL (in both the presence and absence of bile salts and colipase), while mAb 146-40 had no inhibitory effects. The epitope recognized by mAb 146-40 was found to be located in the N-terminal domain (Lys1-Phe335). Combined immunoinactivation and epitope mapping studies showed that three inhibitory mAbs (81-23, 315-25, and 320-24) recognize overlapping epitopes from the hinge region between the N- and C-terminal domains of HPL, belonging to the 26-kDa fragment. In the presence of lipids, a significant decrease has been observed in the bending angle between the N- and C-terminal domains of the HPL tertiary structure (van Tilbeurgh, H., Egloff, M. P., Martinez, C., Rugani, N., Verger, R. and Cambillau, C. (1993) Nature 362, 814-820). From the present immunochemical data, we further propose that locking the hinge movement with mAbs may induce lipase immunoinactivation.

Involvement of human leukocyte antigen class I molecules in human immunodeficiency virus infection of CD4-positive cells

We have studied the putative roles of human immunodeficiency virus (HIV)-associated and cell surface-expressed major histocompatibility complex class I (MHC-I) molecules in the course of the HIV life cycle by the combined use of MHC-I molecule-positive and MHC-I molecule-negative virus particles and MHC-I molecule-positive and MHC-I molecule-negative CD4+ human cells. We found (i) that several anti-MHC-I monoclonal antibodies neutralize cell infection by direct interaction with HIV-associated MHC-I antigens, (ii) that these HIV-associated MHC-I antigens are however dispensable for cell infection, and (iii) that the cell surface-expressed MHC-I molecules are unnecessary for productive infection of CD4+ human cells. These results clarify further the functions of MHC-I molecules during the HIV life cycle.

Determination of the specificities of monoclonal antibodies recognizing members of the CEA family using a panel of transfectants

Carcinoembryonic antigen (CEA), one of the most clinically important tumor markers, is mainly used in the post-surgical surveillance of patients with colorectal carcinomas. CEA belongs to a large protein family, which includes cross-reacting antigens, e.g., non-specific cross-reacting antigens (NCAs) and biliary glycoprotein (BGP) as well as pregnancy-specific glycoproteins (PSGs). The genes encoding these proteins can be subdivided into the CEA and PSG subgroups. The members of the subgroups share antigenic determinants and show high similarity in amino-acid sequences. Their derived secondary structures show them to belong to the immunoglobulin superfamily. Due to the close relationship of the members of the CEA subgroup, it is very difficult to distinguish between the individual members with MAbs. Here we have used flow cytometric analysis of transfectants expressing individual members of the CEA subgroup as an alternative approach to determine the specificities of 13 MAbs. This allows us to examine the specificities of these antibodies for members of the CEA family, even of those which have not yet been characterized at the protein level. In addition, binding of the MAbs to NCAs expressed by polymorphonuclear cells (PMN) was tested by Western-blot analysis, immunoprecipitation and flow cytometry. Four antibodies bound exclusively to NCA-50/90 and one MAb (80H3) only to NCA-95. MAb 4/3/17 recognizes CEA and BGP on the surface of transfectants and NCA-160 from granulocytes. We assume that NCA-160 is a product of the BGP gene. On granulocytes, which do not express CEA, MAb 4/3/17 is specific for NCA-160 (BGP). Mutual inhibition of the MAbs binding to NCA-50/90 revealed 3 different epitope groups.

Purification of human gastric lipase by immunoaffinity and quantification of this enzyme in the duodenal contents using a new ELISA procedure

Human gastric lipase (HGL) is the first lipolytic enzyme involved in the digestion of dietary lipids along the gastrointestinal tract. We describe an improved procedure for isolating the enzyme using immunoaffinity chromatography in combination with ion-exchange chromatography. The purified enzyme, showing a single band on SDS-PAGE, expressed a specific activity of 1000 U/mg using tributyrin as the substrate. We also describe a specific enzyme-linked immunosorbent assay (ELISA) procedure for measuring duodenal HGL levels. The ELISA was performed using an anti-HGL polyclonal antibody (pAb) as the captor antibody and a biotinylated monoclonal antibody (mAb) as the detector antibody. With the double sandwich ELISA technique, HGL in the range of 1-60 ng/ml was measured in less than 5 h. Identical HGL concentrations were obtained using the above ELISA procedure when compared to those based on the enzymatic activity using the potentiometric method (correlation coefficient: r = 0.95). No significant interference from other duodenal components was observed, as proved by the quantitative HGL determinations performed on intestinal samples.

Expression of CD5 and CD72 on T and B cell subsets in rheumatoid arthritis and Sjögren's syndrome

A minority of B cells express the CD5 marker, which is found on virtually all T cells, and CD72 has been defined as the CD5 ligand on the B cell membrane. The mean fluorescence intensity (MFI) of the CD5 molecules was shown to be higher on CD4+CD29+ than CD4+CD45RA+ in peripheral blood (PB) and synovial fluid (SF) of rheumatoid arthritis (RA) patients (P < 0.0001 and < 0.001), and PB of Sjögren's syndrome (SS) patients and normal controls (P < 0.02 and < 0.03). This MFI declined once the CD4 expressed HLA-DR in PB of SS patients (P < 0.004) and normal controls (P < 0.02) or CD25 in PB of RA (P < 0.004) and SS patients (P < 0.0004). There was a correlation between the CD5 MFI on CD4+CD45RA+ and CD4+CD29+ in RA (P < 0.001) as well as SS (P < 0.0007) PB. The CD72 MFI was impressively higher on CD5+ than CD5- B cells in PB and SF of RA patients (P < 0.0001 and P < 0.005) and PB of SS patients (P < 0.005) and normal controls (P < 0.005). Our data suggest that, in association with CD4CD29, CD5 is involved in CD5+B/CD5+ B cell interactions in non-organ-specific autoimmune diseases.

[Post infection antiidiotype vaccination against HIV: results of a phase Ia pilot study]

The mAb IOT4A against the HIV-gp 120 binding site on CD4 was shown to elicit the production of specific anti-idiotypes in rabbits neutralising HIV-1 in vitro. This study was designed in order to determine the safety and efficacy of the mAb IOT4A for the immunization of HIV+ volunteers. 10 patients in stages WR2-WR4B of HIV-disease were given six s.c. injections of the mAb IOT4A as an alum precipitate (each 3 patients receiving 0.6 or 1.2 mg, 4 patients receiving 2.4 mg). 6 patients subsequently received a booster immunization with the same dose of the mAb IOT4A. The immunization schedule was accompanied by monitoring clinical, immunologic and virologic parameters. No systemic toxic or allergic effects of the idiotype vaccine were observed. 8/10 vaccinees displayed a delayed-type hypersensitivity at the location of antibody administration beyond the third injection. The relative and absolute CD4 count showed a sustained increase in 8/10 patients at the end of the booster immunization and an additional raise after booster immunization in 6/6 patients. 624 antigen levels became negative in 2/2 patients during vaccination. In 4/10 patients in increase in HIV/gp 120 antigen binding titres was observed. HIV neutralisation titer remained stable throughout the observation period, and no progression in HIV disease was observed in all patients included in this study. The administration of the mAb IOT4A as a vaccine in HIV-infected volunteers was well tolerated. The mAb ITO4A induced the production of specific anti-idiotypes, that might have been of clinical benefit.(ABSTRACT TRUNCATED AT 250 WORDS)

Epitope mapping and immunoinactivation of human gastric lipase using five monoclonal antibodies

Five monoclonal antibodies (mAb) directed against human gastric lipase (HGL) have been produced by hybridization of myeloma cells with spleen cells of BALB/c immunized mice. All these mAb belong to the IgG1 class with a kappa light chain. The effects of these mAb on the enzymic activity of HGL were studied and used to define three classes of antibodies, depending upon their immunoinactivation properties. As determined by ELISA and immunoinactivation studies, four overlapping epitopes were found to be part of the functional sites of the enzyme. The mAb appear to be suitable probes for studying the lipid binding and catalytic domains of HGL. The results of the ELISA additivity test were used to describe tentatively the epitopes of HGL in terms of a schematic spatial map.

Effect of hyperbaric oxygen and surgery on experimental multimicrobial gas gangrene

An experimental multimicrobial gas gangrene rat model was developed and the therapeutic effect of surgery was compared to the combined effect of surgery and hyperbaric oxygen (HBO). The infection was caused by an intramuscular injection of a mixture of bacteria including Clostridium perfringens, Bacteroides fragilis, Escherichia coli and Streptococcus faecalis. The mortality, morbidity and wound healing were assessed during a follow-up of 2 weeks. The mortality of the control rats was 60%, with rats treated with surgery alone 35% and the combined treatment group 20% (NS). In the combined treatment group, 84.4% of the survivors healed completely; the corresponding figure in the surgery group was 15.4% (p < 0.001). In experimental multimicrobial gas gangrene the addition of HBO to surgery reduces morbidity and improves wound healing but does not reduce mortality statistically significantly.

Treatment of central nervous system B lymphoproliferative syndrome by local infusion of a B cell-specific monoclonal antibody

A 9-month-old infant developed Epstein-Barr virus-induced lymphoproliferative syndrome with mediastinal and central nervous system localizations, associated with mediastinal tuberculosis, 5 months after heart transplantation. As a combination of anti-B cell antibodies (CD21- and CD24-specific) and recombinant interferon alpha 2b, given intravenously, was not effective on the central nervous system disease, the anti-CD21 antibody was infused intrathecally via an Ommaya reservoir. High local concentrations of monoclonal antibodies were achieved, with no adverse effects. A dramatic clinical response was obtained, with clearance of abnormal cells from the cerebrospinal fluid and a clear reduction in the abnormalities on the brain images. The patient is well 7 months later. This observation indicates that treatment of B lymphoproliferative syndrome with central nervous system localization is feasible using a nontoxic, local B cell-specific approach.

Raising polyclonal antibodies using nitrocellulose-bound antigen

Highly specific antibodies directed against minor proteins, present in small amounts in biological fluids, or against nonsoluble cytoplasmic or membraneous proteins, are often difficult to obtain. The main reasons for this are the small amounts of protein available after the various classical purification processes and the low purity of the proteins.

Effect of hyperbaric oxygen and surgery on experimental gas gangrene

An experimental model of clostridial gas gangrene was developed in rats and the therapeutic value of surgical debridement alone versus a combination of surgery and hyperbaric oxygen (HBO) was assessed. The infection was produced by an intramuscular injection of Clostridium perfringens microorganisms. The mortality of untreated rats was 100%. The mortality of the rats treated only with surgery was 37.5% compared to 12.5% when HBO was added to the treatment protocol (p < 0.01). In the group treated with HBO and surgery 82.5% of the animals healed completely and were able to walk normally, whereas the corresponding figure in the rats treated with surgery alone was 12.5% (p < 0.001). In the present experimental setting HBO treatment was an important therapeutic adjunct to surgery reducing both mortality and morbidity.

Prevention of acute GVHD by in vivo use of anti-interleukin-2 receptor monoclonal antibody (33B3.1): a feasibility trial in 15 patients

Results of allogeneic bone marrow transplantation (BMT) are still impaired due mainly to acute graft-versus-host disease (GVHD). Successful T cell depletion may abolish GVHD but causes increased rates of rejection and relapse. In vivo blocking of the CD25 receptor on T cells induces efficient and selective immunosuppression. We present results of a pilot trial studying the use of a CD25 MoAb (33B3.1) to prevent acute GVHD after allogeneic BMT. Fifteen patients were included in the study; 14 had a fully HLA matched sibling donor. In association with short methotrexate and cyclosporin A post-graft immunosuppression, the patients received 10 mg of 33B3.1 monoclonal antibody daily according to three successive schedules to study toxicity on marrow graft. No major adverse clinical experiences occurred. Engraftment was not delayed; after 4 months, full chimerism was documented in 14/15 studied patients. No human anti-rat antibody was detected during treatment period. No GVHD occurred during the period of antibody administration. Two patients relapsed; seven are alive and well with a median follow-up of 650 days. This study justifies a prospective controlled study to determine the real impact of 33B3.1 on GVHD prophylaxis.

Effect of anti-LFA1 (CD11a) monoclonal antibodies in acute rejection in human kidney transplantation

A murine IgG1 monoclonal antibody, 25-3 (Immunotech, France), directed against the alpha chain (CD11a) of the human LFA1 molecule was used in the treatment of 7 histologically documented first acute rejection in first kidney transplantations under cyclosporine. Four patients (group I) received 20 mg/day for 2 days and 10 mg/day for 8 days of 25-3 MoAb. One developed Quincke's edema after the first injection of 25-3 and was immediately withdrawn from the study. In 2 patients, whose serum creatinine continued to increase, 25-3 MoAb was replaced by steroids, followed by ALG after 3 and 4 days of treatment, respectively. In the last case, rejection was reversed by 25-3 MoAb alone. As the clinical response of rejection to 25-3 was poor, another group of 3 patients (group II) was treated with 25-3 at a dose of 40 mg/day for 2 days, 20 mg/day for 2 days, and 10 mg/day for 6 days, but 25-3 was still unsuccessful in reversing acute rejection, and rescue treatment was initiated between days 5 and 8 in all cases. MoAb tolerance was excellent in 3 patients. With the exception of the one case of Quincke's edema, only minor side effects were noted in the last 3 recipients. 25-3 MoAb serum trough levels peaked between 1.5-3.5 micrograms/ml at day 3 in group I and between 2-9 micrograms/L at day 2 in group II. Surprisingly, only one patient, in group I, exhibited a borderline IgG immune response against 25-3. These findings suggest that the 25-3 anti-CD11a MoAb is ineffective in controlling the course of acute rejection in kidney transplantation. However as already reported for another anti-LFA1 or with an anti-CD4 MoAb in mouse, 25-3 would be the first example in humans of a MoAb that does not elicit a strong immune response against its own determinants. This property might have important applications if 25-3 can prevent rejection in a prophylactic protocol or block the immune response against other MoAbs.

Anti-LFA1 monoclonal antibody (25.3) for treatment of steroid-resistant grade III-IV acute graft-versus-host disease

The in vivo efficacy of 25.3 monoclonal antibody (mAb) directed against human LFA1 molecule was assessed in ten patients with steroid-resistant grade III-IV acute graft-versus-host disease (AGVHD). These patients received non-T-cell-depleted allogeneic bone marrow transplantation for aplastic anemia in two cases and hematologic malignancies in eight cases. Five grafts were fully matched, three were one antigen-mismatched, and two were two antigen-mismatched. Despite GVHD prophylaxis with cyclosporin A and short-term methotrexate, AGVHD occurred after a median of 24 days and clearly progressed under prednisone (median 2 mg/kg), given for a median of 12 days. 25.3 mAb was given at a dosage of 0.1 mg/kg in a 4-h perfusion for five daily doses without any clinical or biological side effects. Thirty percent of the patients experienced a reduction in the overall grading with two complete responses. Partial response in at least one involved organ (mostly skin) occurred in 80% of the patients. However, seven out of the eight responding patients experienced a new episode of AGVHD. This observation, which confirms that inhibiting a functional molecule is as efficient as a cytolytic therapy, offers an alternative strategy to antithymocyte globulin (ATG) and cytotoxic mAb in controlling steroid-resistant GVHD.

The soluble receptor of interleukin 2 is not a serum marker of the autoimmune activity in type I diabetes mellitus

In order to determine if soluble interleukin 2 receptor (IL2R) was useful as a marker in screening for early Type 1 diabetes and in monitoring immunological treatment, we assayed serum IL2R levels in 67 controls, 43 patients with newly diagnosed diabetes and 28 first degree relatives of diabetic patients (5 subjects were islet cell antibody positive). In 23 diabetes, specimens were analysed at 3 and 6 months after diagnosis whether or not cyclosporin A was administered. Seven patients were in a clinical trial using anti IL2R monoclonal antibody and cyclosporin A. Since IL2R level in the normal population is elevated in the first 5 years of life then decreases until adulthood (age:IL2R correlation between 0 and 15 years: r = -0.42, P less than 0.05), subjects were carefully matched in age. In recent onset diabetes, this negative correlation disappeared and IL2R levels tended to decrease particularly in younger subjects. In Type 1 prediabetic subjects presenting persistent islet-cell antibody serum IL2R was not elevated. During immunological treatment of recent onset diabetes, serum IL2R remained stable and was not modified by cyclosporin A. As expected IL2R became undetectable during treatment with anti IL2R MC Ab. But it rebounded when treatment was stopped with no effect on remission. We concluded that IL2R levels in Type 1 diabetic patients is not useful in screening autoimmune activity or in evaluating the effectiveness of immunosuppressors.

Functional studies of soluble low-affinity interleukin-2 receptors in rheumatoid synovial fluid

Since abnormal regulation of interleukin-2 (IL-2) has been demonstrated in rheumatoid arthritis (RA), the functional role of low-affinity soluble IL-2 receptors (sIL-2R) purified from RA synovial fluids (SF) was studied. Picomolar levels of sIL-2R were detected in RA SF using an enzyme-linked immunosorbent assay. Levels were higher in serum and SF from RA patients than in controls (P less than 0.001) and higher in RA SF than in paired RA serum (P less than 0.01). Soluble IL-2R from RA SF had estimated molecular weights of 40-50 kd and 80-100 kd by gel filtration analysis. The 80-100-kd peak is likely to be a dimer of the 40-50-kd peak, since a single 45-kd peak was found after elution from sodium dodecyl sulfate-polyacrylamide gels. Since inhibitory activity for lymphocyte proliferation was found in the 80-100-kd range, the sIL-2R were purified with an anti-CD25 affinity column and further analyzed. The purified fractions did not interfere with the proliferation of mitogen-stimulated lymphocytes or with the binding of radiolabeled IL-2 to CTLL-2 cells, although direct binding of IL-2 was demonstrated. The affinity of sIL-2R from RA SF for binding IL-2 was in the range of 25 nM, which is similar to the affinity of sIL-2R purified from a human T cell clone, indicating that both sIL-2R are low-affinity receptors for IL-2. We conclude that the concentration and binding affinity of low-affinity sIL-2R purified from RA SF render them unable to interfere with IL-2-related activities.

Randomized controlled trial of a monoclonal antibody against the interleukin-2 receptor (33B3.1) as compared with rabbit antithymocyte globulin for prophylaxis against rejection of renal allografts

Interleukin-2 is a major growth factor for activated T lymphocytes, and antibodies reacting with the Tac-chain component of the interleukin-2 receptor can prevent allograft rejection in animals. Because Tac chains are expressed only on a small fraction of activated lymphocytes, monoclonal antibodies against the interleukin-2 receptor may offer a more specific means of immunosuppression than polyclonal antilymphocyte globulin in prophylaxis against graft rejection. Therefore, we compared the immunosuppressive effect of 33B3.1, a rat monoclonal antibody against the human Tac chain, with the effect of a rabbit polyclonal antithymocyte globulin in a randomized study of 100 recipients of first renal transplants. Injections of 33B3.1 (10 mg per day) were tolerated well, whereas major side effects in 15 of 47 patients (32 percent) receiving antithymocyte globulin required discontinuation of treatment before day 14. The incidence of rejection episodes was not statistically different in the two groups at days 14, 30, 60, and 90 after transplantation. Patient and graft survival was also equal in the two groups at one year (96 and 85 percent, respectively, in both groups), and graft function was similar. The total number of infectious episodes within the first three months was lower in the 33B3.1 group than in the antithymocyte group (47 vs. 72). The drop in peripheral-blood lymphocyte concentrations was significantly larger in the patients treated with antithymocyte globulin. The level of circulating Tac-chain-bearing lymphocytes remained below 1 percent during 33B3.1 treatment, as compared with 4 to 5 percent during antithymocyte-globulin treatment (P not significant). We conclude that 33B3.1 is as effective as antithymocyte globulin in the prevention of renal-transplant rejection, and its use results in fewer infections and side effects.