Ari D. Brooks

Inadequate T follicular cell help impairs B cell immunity during HIV infection

The majority of HIV-infected individuals fail to produce protective antibodies and have diminished responses to new immunizations. We report here that even though there is an expansion of follicular helper T (TFH) cells in HIV-infected individuals, the cells are unable to provide adequate B cell help. We found a higher frequency of programmed cell death ligand 1 (PD-L1)+ germinal center B cells from lymph nodes of HIV-infected individuals suggesting a potential role for PD-1–PD-L1 interaction in regulating TFH cell function. In fact, we show that engagement of PD-1 on TFH cells leads to a reduction in cell proliferation, activation, inducible T-cell co-stimulator (ICOS) expression and interleukin-21 (IL-21) cytokine secretion. Blocking PD-1 signaling enhances HIV-specific immunoglobulin production in vitro. We further show that at least part of this defect involves IL-21, as addition of this cytokine rescues antibody responses and plasma cell generation in vitro. Our results suggest that deregulation of TFH cell–mediated B cell help diminishes B cell responses during HIV infection and may be related to PD-1 triggering on TFH cells. These results demonstrate a role for TFH cell impairment in HIV pathogenesis and suggest that enhancing their function could have a major impact on the outcome and control of HIV infection, preventing future infections and improving immune responses to vaccinations.

Nonthermal Dielectric-Barrier Discharge Plasma-Induced Inactivation Involves Oxidative DNA Damage and Membrane Lipid Peroxidation in Escherichia coli

ABSTRACT Oxidative stress leads to membrane lipid peroxidation, which yields products causing variable degrees of detrimental oxidative modifications in cells. Reactive oxygen species (ROS) are the key regulators in this process and induce lipid peroxidation in Escherichia coli. Application of nonthermal (cold) plasma is increasingly used for inactivation of surface contaminants. Recently, we reported a successful application of nonthermal plasma, using a floating-electrode dielectric-barrier discharge (FE-DBD) technique for rapid inactivation of bacterial contaminants in normal atmospheric air (S. G. Joshi et al., Am. J. Infect. Control 38:293-301, 2010). In the present report, we demonstrate that FE-DBD plasma-mediated inactivation involves membrane lipid peroxidation in E. coli. Dose-dependent ROS, such as singlet oxygen and hydrogen peroxide-like species generated during plasma-induced oxidative stress, were responsible for membrane lipid peroxidation, and ROS scavengers, such as α-tocopherol (vitamin E), were able to significantly inhibit the extent of lipid peroxidation and oxidative DNA damage. These findings indicate that this is a major mechanism involved in FE-DBD plasma-mediated inactivation of bacteria.

Control of methicillin-resistant Staphylococcus aureus in planktonic form and biofilms: A biocidal efficacy study of nonthermal dielectric-barrier discharge plasma

BACKGROUND Bacterial contamination of surfaces with methicillin-resistant Staphylococcus aureus (MRSA) is a serious problem in the hospital environment and is responsible for significant nosocomial infections. The pathogenic contaminants form biofilms, which are difficult to treat with routine biocides. Thus, a continuous search for novel disinfection methods is essential for effective infection control measures. This demonstration of a novel technique for the control of virulent pathogens in planktonic form as well as in established biofilms may provide a progressive alternative to standard methodology. METHODS We evaluated a novel technique of normal atmospheric nonthermal plasma known as floating-electrode dielectric-barrier discharge (FE-DBD) plasma against a control of planktonic and biofilm forms of Escherichia coli, S aureus, multidrug-resistant methicillin-resistant S aureus (MRSA) -95 (clinical isolate), -USA300, and -USA400, using widely accepted techniques such as colony count assay, LIVE/DEAD BacLight Bacterial Viability assay, and XTT (2,3-Bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide) assay. RESULTS Exposure of free living planktonic forms of E coli, S aureus, and MRSA were rapidly inactivated by DBD plasma. Approximately 10(7) bacterial cells were completely (100%) killed, whereas 10(8) and 10(9) were reduced by approximately 90% to 95% and 40% to 45%, respectively, in less than 60 seconds (7.8 J/cm(2)) and completely disinfected in < or =120 seconds. In established biofilms, the susceptibility of MRSA USA400 was comparable with USA300 but less susceptible than MRSA95 (clinical isolate), S aureus, and E coli (P < .05) to FE-DBD plasma, and plasma was able to kill MRSA more than 60% within 15 seconds (1.95 J/cm(2)). The killing responses were plasma exposure-time dependent, and cell density dependent. The plasma was able disinfect surfaces in a less than 120 seconds. CONCLUSION Application of DBD plasma can be a valuable decontamination technique for the removal of planktonic and biofilm-embedded bacteria such as MRSA -USA 300, -USA 400, methicillin-sensitive S aureus (MSSA), and E coli, the more common hospital contaminants. Of interest, E coli was more resistant than S aureus phenotypes.

Evaluating the Effect of Force Feedback in Cell Injection

Conventional methods of manipulating individual biological cells have been prevalent in the field of molecular biology. These methods do not have the ability to provide force feedback to an operator. Poor control of cell injection force is one of the primary reasons for low success rates in cell injection and transgenesis in particular. Therefore, there exists a need to incorporate force feedback into a cell injection system. We have developed a force feedback interface, which has the capability of measuring forces in the range of and provide a haptic display of the cell injection forces in real time. Using this force feedback interface, we performed several human factors studies to evaluate the effect of force feedback on cell injection outcomes. We tested our system with 40 human subjects and our experimental results indicate that the subjects were able to feel the cell injection force and confirmed our research hypothesis that the use of combined vision and force feedback leads to a higher success rate in cell injection task compared to using vision feedback alone.

The use of domain-specific concepts in biomedical text summarization

Text summarization is a method for data reduction. The use of text summarization enables users to reduce the amount of text that must be read while still assimilating the core information. The data reduction offered by text summarization is particularly useful in the biomedical domain, where physicians must continuously find clinical trial study information to incorporate into their patient treatment efforts. Such efforts are often hampered by the high-volume of publications. This paper presents two independent methods (BioChain and FreqDist) for identifying salient sentences in biomedical texts using concepts derived from domain-specific resources. Our semantic-based method (BioChain) is effective at identifying thematic sentences, while our frequency-distribution method (FreqDist) removes information redundancy. The two methods are then combined to form a hybrid method (ChainFreq). An evaluation of each method is performed using the ROUGE system to compare system-generated summaries against a set of manually-generated summaries. The BioChain and FreqDist methods outperform some common summarization systems, while the ChainFreq method improves upon the base approaches. Our work shows that the best performance is achieved when the two methods are combined. The paper also presents a brief physicians evaluation of three randomly-selected papers from an evaluation corpus to show that the authors abstract does not always reflect the entire contents of the full-text.

Approaches to text mining for clinical medical records

Clinical medical records contain a wealth of information, largely in free-text form. Means to extract structured information from free-text records is an important research endeavor. In this paper, we describe a MEDical Information Extraction (MedIE) system that extracts and mines a variety of patient information with breast complaints from free-text clinical records. MedIE is a part of medical text mining project being conducted in Drexel University. Three approaches are proposed to solve different IE tasks and very good performance (precision and recall) was achieved. A graph-based approach which uses the parsing result of link-grammar parser was invented for relation extraction; high accuracy was achieved. A simple but efficient ontology-based approach was adopted to extract medical terms of interest. Finally, an NLP-based feature extraction method coupled with an ID3-based decision tree was used to perform text classification.

A biplanar fluoroscopic approach for the measurement, modeling, and simulation of needle and soft-tissue interaction.

A methodology for modeling the needle and soft-tissue interaction during needle insertion is presented. The approach consists of the measurement of needle and tissue motion using a dual C-arm fluoroscopy system. Our dual C-arm fluoroscopy setup allows real time 3-D extraction of the displacement of implanted fiducials in the soft tissue during needle insertion to obtain the necessary parameters for accurate modeling of needle and soft-tissue interactions. The needle and implanted markers in the tissue are tracked during the insertion and withdrawal of the needle at speeds of 1.016 mm/s, 12.7 mm/s and 25.4 mm/s. Both image and force data are utilized to determine important parameters such as the approximate cutting force, puncture force, the local effective modulus (LEM) during puncture, and the relaxation of tissue. We have also validated the LEM computed from our finite element model with arbitrary needle puncture tasks. Based on these measurements, we developed a model for needle insertion and withdrawal that can be used to generate a 1-DOF force versus position profile that can be experienced by a user operating a haptic device. This profile was implemented on a 7-DOf haptic device designed in our laboratory.

Reality-based needle insertion simulation for haptic feedback in prostate brachytherapy

There is a strong need to improve the tools clinicians use for training in procedures such as prostate brachytherapy where the success rate is directly related to the clinicians level of experience. Accurate haptic feedback is needed for developing improved surgical simulators and trainers for such procedures. In prostate brachytherapy, accurate needle placement of radioactive seeds in the prostate is crucial to the success of the surgery and to the quality of life of the patient. Therefore, a trainer or simulator for this and other types of needle insertion tasks require an accurate reality-based quantification and model of the needle and soft tissue interaction. To achieve this, we utilize the X-ray images produced by a dual C-arm fluoroscope setup during a needle insertion task to obtain parameters needed for accurate modeling of soft tissue and needle interactions. The needle and implanted markers in the tissue are tracked during the insertion and withdrawal of the needle at speeds of 1.016 mm/sec, 12.7 mm/sec and 25.4 mm/sec. Both image and force data are utilized to determine important parameters such as the local effective modulus during puncture and the approximate cutting force for soft tissue samples. A finite element model was built using the data to model needle puncture of tissue

Force feedback interface for cell injection

Manual pronuclei injection and intracytoplasmic sperm injection (ICSI) requires long training and has low success rates primarily due to poor control over the injection force. Consequently, there is a need for quantification of forces during biological cell injection and for an automated cell injection system, which can provide force feedback to the operator improving the success rate of the injection task. We have developed a force feedback interface, which has the capability of measuring forces in the range of /spl mu/N-mN and provide a haptic display of the cell injection forces. The force sensor has been integrated with the biomanipulation system to detect forces in real time. Experiments were performed on two different varieties of egg cells to demonstrate the success in measuring forces in the range in /spl mu/N-mN. Our experimental results indicate the cell puncturing forces were consistent and the operator was able to feel the celt injection forces.

Inflammatory Cytokines Drive CD4+ T-Cell Cycling and Impaired Responsiveness to Interleukin 7: Implications for Immune Failure in HIV Disease

BACKGROUND Systemic inflammation has been linked to a failure to normalize CD4(+) T-cell numbers in treated human immunodeficiency virus (HIV) infection. Although inflammatory cytokines such as interleukin 6 (IL-6) are predictors of disease progression in treated HIV infection, it is not clear how or whether inflammatory mediators contribute to immune restoration failure. METHODS We examined the in vitro effects of IL-6 and interleukin 1β (IL-1β) on peripheral blood T-cell cycling and CD127 surface expression. RESULTS The proinflammatory cytokine IL-1β induces cell cycling and turnover of memory CD4(+) T cells, and IL-6 can induce low-level cycling of naive T cells. Both IL-1β and IL-6 can decrease T-cell surface expression and RNA levels of CD127, the interleukin 7 receptor α chain (IL-7Rα). Preexposure of healthy peripheral blood mononuclear cells (PBMCs) to IL-6 or IL-1β attenuates IL-7-induced Stat5 phosphorylation and induction of the prosurvival factor Bcl-2 and the gut homing integrin α4β7. We found elevated expression of IL-1β in the lymphoid tissues of patients with HIV infection that did not normalize with antiretroviral therapy. CONCLUSIONS Induction of CD4(+) T-cell turnover and diminished T-cell responsiveness to IL-7 by IL-1β and IL-6 exposure may contribute to the lack of CD4(+) T-cell reconstitution in treated HIV-infected subjects.