gebhart/patrepeval huggingface dataset:
Modified Western Blot Assay for Confirmation and Differentiation of Human T Cell Lymphotropic Virus Types I and II (1991)

Disease association studies of human T cell lymphotropic virus (HTLV) types I and II are hindered by the need for multiple assays to confirm and differentiate between the viruses. A modified Western blot assay has been developed using HTLV-I viral lysate and unique (MTA-4) and shared (p21E) HTLV recombinant proteins. By defining confirmation of infection as the presence of antibodies to p24 gag protein and to p21E, all 56 HTLV-I and 49 HTLV-II antisera were confirmed by this modified Western blot alone. Differentiation was determined by reactivity to MTA-4. All HTLV-I antisera reacted with MTA-4 and all HTLV-II antisera did not react with MTA-4. These findings indicate the utility of selected HTLV-I recombinant proteins in a single assay format to confirm and differentiate infections with HTLV-I and HTLV-II.
Abstract B022: Intratumoral CD40 activation and checkpoint blockade induces systemic anti-melanoma immunity that eradicates disseminated tumors (2016)

Abstract Although surgical resection is a reliable treatment for localized melanoma, treatment options for metastatic melanoma are limited. Melanoma Brain metastasis (MBM) is a major clinical problem in patients with advanced melanoma, and the incidence of brain metastasis is increasing every year. Thus, there is a significant unmet need for effective therapies for metastatic melanoma and MBM patients. Agonistic CD40 antibodies generate strong tumor specific CD8 T cell response and anti-tumor activity; however systemic anti-CD40 therapy has been associated with cytokine release syndrome and liver toxicity. We studied the anti-melanoma activity and mechanism of action of a non-replicating adenovirus encoding a CD40-targeting chimeric immunostimulatory protein (ISF35) by local intratumoral delivery approach to treat local and distant melanoma. Mice bearing established B16 melanomas on both right and left flanks or on right flank and in brain were treated intratumorally with ISF35 or rAd.empty to the right flank tumor and received anti-PD1 plus anti-CTLA-4 systemically. Anti-tumor effects of mono or combination therapies were determined by mice survival and tumor growth measurement. The mechanistic contribution of immune cells to this therapy was determined by using antibody blockades. Immune cell infiltrates in tumor and expression of activation markers on these cells were analyzed by flow cytometry. Intratumoral administration of ISF35 generates systemic anti-tumor immunity mediates by CD8 T cells and suppress both injected and distant uninjected wild-type B16.F10 melanomas. However, tumors did not completely regress after therapy. When combined with checkpoint inhibitors, ISF35 generates synergistic systemic anti-melanoma immunity that eradicates both injected and uninjected distant subcutaneous melanoma and uninjected brain melanoma with 40% of mice cured. The systemic anti-tumor activity of ISF35/anti-PD-1/anti-CTLA-4 was associated with greater production of melanoma-specific CD8 T cells with an activated phenotype. Immunotherapy based on intratumoral CD40 activation is potentiated by PD-1 and CTLA-4 blockade and this combination generates functional and long-lasting anti-tumor CD8 T cell immunity that systemically suppresses melanoma metastases. This approach will be a better option for treatment of patients with metastatic melanoma that does not respond to checkpoint blockage monotherapy. Citation Format: Manisha Singh, Christina Vianden, Adi Diab, Patrick Hwu, Willem W. Overwijk. Intratumoral CD40 activation and checkpoint blockade induces systemic anti-melanoma immunity that eradicates disseminated tumors [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr B022.
Investigations towards an efficacious and safe strangles vaccine: submucosal vaccination with a live attenuated Streptococcus equi (2000)

As part of a search for a safe and efficacious strangles vaccine, several different vaccines and different vaccination routes were tested in foals. The degree of protection was evaluated after an intranasal challenge with virulent Streptococcus equi by clinical, postmortem and bacteriological examinations. Inactivated vaccines containing either native purified M-protein (500 microg per dose) or whole S equi cells (10(10) cells per dose) administered at least twice intramuscularly at intervals of four weeks, did not protect against challenge. Different live attenuated S equi mutants administered at least twice at intervals of four weeks by the intranasal route were either safe but not protective or caused strangles. In contrast, a live attenuated deletion mutant administered intramuscularly, induced complete protection but also induced unacceptable local reactions at the site of vaccination. Submucosal vaccination in the inner side of the upper lip with the live attenuated mutant at > or =10(8) colony-forming units per dose, appeared to be safe and efficacious in foals as young as four months of age. The submucosal vaccinations caused small transient swellings that resolved completely within two weeks, and postmortem no vaccine remnants or other abnormalities were found at the site of vaccination.
Ultra-linear power amplifier characterization using dynamic range extension techniques (2002)

The rapid growth of the wireless industry requires more efficient utilization of the available frequency spectrum. This has resulted in requirements for highly linear Multi-Channel Power Amplifiers (MCPAs) to support increases in voice and data traffic. To characterize the resulting ultra-linear MCPAs and to comply with intermodulation levels less than -80 dBc requires measurement systems with dynamic range performance beyond what is currently available. A new instrument, which extends the dynamic range of current distortion measurement systems by at least 25 dB, has been developed to meet this challenge.
One-step Split GFP Staining for Sensitive Protein Detection and Localization in Mammalian Cells (2010)

Although epitope tags are useful to detect intracellular proteins and follow their localization with antibodies, background and nonspecific staining often remain problematic. We describe a simple assay based on the split GFP complementation system. Proteins tagged with the 15-amino acid GFP 11 fragment are detected with a solution of the recombinant nonfluorescent complementary GFP 1-10 fragment to reconstitute a fluorescent GFP. In contrast to antibody-based staining methods, this one-step assay presents high specificity and very low background of fluorescence, thus conferring higher signal-to-noise ratios. We demonstrate that this new application of the split GFP tagging system facilitates detection of proteins displaying various subcellular localizations using flow cytometry and microscopy analysis.
Enhanced Staphylolytic Activity of the Staphylococcus aureus Bacteriophage vB_SauS-phiIPLA88 HydH5 Virion-Associated Peptidoglycan Hydrolase: Fusions, Deletions, and Synergy with LysH5 (2012)

Virion-associated peptidoglycan hydrolases have potential as antimicrobial agents due to their ability to lyse Gram-positive bacteria on contact. In this work, our aim was to improve the lytic activity of HydH5, a virion-associated peptidoglycan hydrolase from the Staphylococcus aureus bacteriophage vB_SauS-phiIPLA88. Full-length HydH5 and two truncated derivatives containing only the CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) domain exhibited high lytic activity against live S. aureus cells. In addition, three different fusion proteins were created between lysostaphin and HydH5, each of which showed higher staphylolytic activity than the parental enzyme or its deletion construct. Both parental and fusion proteins lysed S. aureus cells in zymograms and plate lysis and turbidity reduction assays. In plate lysis assays, HydH5 and its derivative fusions lysed bovine and human S. aureus strains, the methicillin-resistant S. aureus (MRSA) strain N315, and human Staphylococcus epidermidis strains. Several nonstaphylococcal bacteria were not affected. HydH5 and its derivative fusion proteins displayed antimicrobial synergy with the endolysin LysH5 in vitro, suggesting that the two enzymes have distinct cut sites and, thus, may be more efficient in combination for the elimination of staphylococcal infections.
Quantum Cascade Lasers: New Resonant Tunnelling Light Sources for the Mid-Infrared (1996)

Recent results on quantum cascade lasers are reviewed. In these quantum devices based on resonant tunnelling the wavelength can be selected over a broad range of the infrared spectrum using the same heterostructure material by tailoring the active layer thickness. High power room temperature operation at wavelengths of 5 and 8.5 pm has been achieved. These are the first semiconductor lasers to operate at 300 K and above in this wavelength region.
Static-Electric Field Induction by a Silicone Cushion for the Treatment of Hypertrophic and Keloid Scars (1998)

Silicone gel and silicone occlusive sheeting are widely used at present for the treatment of hypertrophic and keloid scars, without any scientific explanation as to their mode of action. In a recent paper the possibility was raised that static electricity generated by friction-activated silicone sheeting could be the reason for this effect, and that it can, with time, cause involution of hypertrophic and keloid scars. The objective of this study was to test this hypothesis and to observe whether a continuous and also an increased negatively charged static-electric field will shorten the treatment period. A device to implement these requirements gradually evolved over a 5-year period. A number of prototypes were tested until the final product was attained. Some of the patients in this study were treated initially with a silicone sponge inserted in the cushion. Later this version was changed to the final design described herein. A silicone cushion was developed with the purpose of increasing a negative static-electric charge to accelerate the regression process. The cushion is custom-made using a silicone occlusive sheeting envelope of 0.75-mm thickness, which does not deteriorate with use, and is partially filled with high viscosity silicone oil. Its edges are sealed, and its size is designed to extend a little beyond the scarred area. Static electricity readings, generated by activating the cushion by pumping action with the fingers, stretching or deforming the cushion, are invariably much higher when compared with those obtained with silicone occlusive sheeting and silicone gel sheeting. The interaction between the negatively charged ions of the cushion and the ionic charges of the tissue fluids may be the critical factor in achieving hypertrophic and keloid scars involution. Of the 30 patients enrolled in the study, 3 patients dropped out. Treatment with the silicone cushions yielded 63.3 percent cessation of itching and burning followed by pallor and flattening of the scar, some markedly so, over a few weeks to 6-month period. An additional 26.6 percent had their scars resolved in up to 12 months of treatment. Good contact of the cushion over the scar has been shown to be important in this clinical trial, and much creativity is needed for making elastic strap bindings that ensure this contact. The clinical trials extended over a 12-month period. Ten patients (33.3 percent) who had recalcitrant scars with little response to the use of the silicone cushion were given intralesional corticosteroid injections, in addition to the continued use of the cushion, resulting in a fairly rapid resolution of these scars over a period of months to a year.
IN VIVO TARGETING OF TIRC7, A NOVEL MEMBRANE PROTEIN, BY SPECIFIC ANTIBODY SIGNIFICANTLY PREVENTS SKIN ALLOGRAFT REJECTION (1999)

883 TIRC7, is described to exhibits a central role in T cell activation in vitro and in vivo. Modulation of TIRC7 mediated signals with specific anti-TIRC7 antibodies in vitro efficiently prevents human T cell proliferation and IL-2 secretion. Moreover, anti-TIRC7 antibodies specifically inhibit type 1 subset specific IFN-γ expression but spare the type 2 cytokine IL-4. Crosslinking of TIRC7 by using an anti-TIRC7 antibody in vivo was shown to significantly prevent acute organ rejection after kidney transplantation in Lewis rats (Utku et al., Immunity 9, 1998). To examine whether TIRC7 specific antibodies are able to prolong allograft survival in a different transplantation model skin transplantats were performed between DA (donor) and Lewis (recipient) rats. Lewis recipients underwent an induction therapy with a with a cross-reacting human anti-TIRC7 antibody prior, immediately and at days 1, 2, 4 and 6 after allotransplantation. Control groups recieved either an unrelated antibody or remained untreated. Anti-TIRC7 antibody treated rats (n=7) demonstrated a significantly prolonged survival (p>0,001) (37-41 days), whereas control antibody treated rats (n=7) as well as untreated rats (n=7) uniformly rejected their grafts after 11-14 days skin transplantation. The results of this study demonstrates that TIRC7 delivers essential and distinct signals during T cell activation and play an important role as a novel target molecule to modulate undesired T cell activation upon organtransplantation.
Prohibitin Overexpression in Adipocytes Induces Mitochondrial Biogenesis, Leads to Obesity Development, and Affects Glucose Homeostasis in a Sex-Specific Manner (2014)

Adipocytes are the primary cells in the body that store excess energy as triglycerides. To perform this specialized function, adipocytes rely on their mitochondria; however, the role of adipocyte mitochondria in the regulation of adipose tissue homeostasis and its impact on metabolic regulation is not understood. We developed a transgenic mouse model, Mito-Ob, overexpressing prohibitin (PHB) in adipocytes. Mito-Ob mice developed obesity due to upregulation of mitochondrial biogenesis in adipocytes. Of note, Mito-Ob female mice developed more visceral fat than male mice. However, female mice exhibited no change in glucose homeostasis and had normal insulin and high adiponectin levels, whereas male mice had impaired glucose homeostasis, compromised brown adipose tissue structure, and high insulin and low adiponectin levels. Mechanistically, we found that PHB overexpression enhances the cross talk between the mitochondria and the nucleus and facilitates mitochondrial biogenesis. The data suggest a critical role of PHB and adipocyte mitochondria in adipose tissue homeostasis and reveal sex differences in the effect of PHB-induced adipocyte mitochondrial remodeling on whole-body metabolism. Targeting adipocyte mitochondria may provide new therapeutic opportunities for the treatment of obesity, a major risk factor for type 2 diabetes.
The Neurofibromatosis Type 1 (NF1) Gene: Identification and Partial Characterization of a Putative Tumor Suppressor Gene (1992)

The NF1 gene has been isolated and partially characterized. The discovery that NF1 functions as a ras GTPase activator protein has led to new opportunities for understanding the pathology of this disease. The approximately 11 kilobase (kb) NF1 consensus cDNA sequence contains an open reading frame encoding a peptide of 2818 amino acids. DNA blot and polymerase chain reaction analysis indicate that the NF1 gene consists of over 50 exons spanning 300 kb of chromosome 17.
Towards functional optical imaging in layered tissues using modulated imaging (2006)

We present forward modeling and measurement of spatially modulated illumination in layered turbid tissue systems to provide quantitative, depth-resolved functional information in tissues including cortex, retina and skin.
Electrothermally bonded carbon nanotube interfaces (2008)

Applications that exploit the exceptional transport properties of carbon nanotubes (CNTs) at practical length scales almost invariably require good contact of the CNTs with the contacting surface. For example, vertically aligned and dense arrays of carbon nanotubes have been demonstrated to be good thermal interface materials. However, interfacial resistance to thermal and electrical transport between CNTs and bulk substrates is found to adversely affect device performance in such applications. In this work, we present a method to attach CNTs to contacting surfaces with low-temperature electrostatic bonding, and the effects of bonding conditions are studied in terms of the resulting interface morphology, mechanical bond strength, and thermal conductance. We show that the bonding process results in thermal resistance reductions of as much as 64% compared to unbonded CNT joints. Optimization of such bonded interfaces can lead to utilization of CNT interfaces closer to their full potential.
XNMP &#8212; An XML Based Network Management Protocol over VoIP (2005)

A commonly used network protocol that administrators rely on for managing IP networks is simple network management protocol (SNMP). SNMP enables network administrators to remotely monitor and manage their data network in ad hoc manner. One suggestion to resolve this is to apply eXtensible Markup Language (XML) related technologies with SNMP to network management. This paper describes how taking advantage of an XML-based network management protocol (XNMP) can greatly simplify the overhead needed to design data structures and algorithms in VoIP setting. It further illustrates that with its straightforwardness, XML also fashions easier data manipulation. Finally, this paper analyzes the performance of XNMP and potential benefit in the real world.
Cascade One‐Pot Synthesis of Orange‐Red‐Fluorescent Polycyclic Cinnolino[2,3‐<i>f</i>]phenanthridin‐9‐ium Salts by Palladium(II)‐Catalyzed C−H Bond Activation of 2‐Azobiaryl Compounds and Alkenes (2019)

Quaternary ammonium salts were synthesized in moderate to good yields through double oxidative C-H bond activation on azobenzenes. The mechanism of the highly regioselective reaction of 2-azobiaryls with alkenes to give orange-red-fluorescent cinnolino[2,3-f]phenanthridin-9-ium salts and 15H-cinnolino[2,3-f]phenanthridin-9-ium-10-ide is proposed to involve ortho C-H olefination of the 2-azobiaryl compound with the alkene, intramolecular aza-Michael addition, concerted metalation-deprotonation (CMD), reductive elimination, and oxidation.
Signal detection for MIMO-OFDM wireless communications (2002)

In this paper, orthogonal frequency division multiplexing (OFDM) for MIMO channels (MIMO-OFDM) is considered for wideband transmission to mitigate intersymbol interference and enhance system capacity. The MIMO-OFDM system uses two independent space-time codes for two sets of two transmit antennas. At the receiver, the independent space-time codes are decoded using pre-whitening followed by maximum-likelihood (ML) decoding or ML decoding based on successive interference cancellation. Computer simulation shows that for 4-input and 4-output systems transmitting data at 4 Mbits/sec over a 1.25 MHz channel, the required SNRs for a 10% and 1% WER are 10.5 dB and 13.8 dB, respectively, when each codeword contains 500 information bits and the channel's Doppler frequency is 40 Hz.
Nuclear fuel assembly. [LMFBR] (1976)

Neural stem cells (NSCs) play vital roles in brain homeostasis and exhibit a broad repertoire of potentially therapeutic actions following neurovascular injury. One such injury is stroke, a worldwide leading cause of death and disability. Clinically, extensive injury from ischemic stroke results from ischemia-reperfusion (IR), which is accompanied by inflammation, blood-brain barrier (BBB) damage, neural cell death, and extensive tissue loss. Tissue plasminogen activator (tPA) is still the only US Food and Drug Administration-approved clot-lysing agent. Whereas the thrombolytic role of tPA within the vasculature is beneficial, the effects of tPA (in a non-thrombolytic role) within the brain parenchyma have been reported as harmful. Thus, new therapies are needed to reduce the deleterious side effects of tPA and quickly facilitate vascular repair following stroke. The Stroke Treatment Academic Industry Roundtable (STAIR) recommends that stroke therapies "focus on drugs/devices/treatments with multiple mechanisms of action and that target multiple pathways". Thus, based on multifactorial ischemic cascades in various stroke stages, effective stroke therapies need to focus on targeting and ameliorating early IR injury as well as facilitating angiogenesis, neurogenesis, and neurorestorative mechanisms following stroke. This review will discuss the preclinical perspectives of NSC transplantation as a promising treatment for neurovascular injury and will emphasize both the subacute and chronic phase of ischemic stroke.
Koi: a location-privacy platform for smartphone apps (2012)

Abstract — With mobile phones becoming first-class citizens in the online world, the rich location data they bring to the table is set to revolutionize all aspects of online life including content delivery, recommendation systems, and advertising. However, user-tracking is a concern with such location-based services, not only because location data can be linked uniquely to individuals, but because the low-level nature of current location APIs and the resulting dependence on the cloud to synthesize useful representations virtually guarantees such tracking. In this paper, we propose privacy-preserving locationbased matching as a fundamental platform primitive and as an alternative to exposing low-level, latitude-longitude (lat-long) coordinates to applications. Applications set rich location-based triggers and have these be fired based on location updates either from the local device or from a remote device (e.g., a friend’s phone). Our Koi platform, comprising a privacy-preserving matching service in the cloud and a phone-based agent, realizes this primitive across multiple phone and browser platforms. By masking low-level lat-long information from applications, Koi not only avoids leaking privacy-sensitive information, it also eases the task of programmers by providing a higher-level abstraction that is easier for applications to build upon. Koi’s privacy-preserving protocol prevents the cloud service from tracking users. We verify the non-tracking properties of Koi using a theorem prover, illustrate how privacy guarantees can easily be added to a wide range of location-based applications, and show that our public deployment is performant, being able to perform 12K matches per second on a single core. 1
Fluorescent labeling and tracking of nanoclay (2012)

We report a methodology developed to detect and track stable fluorescent-labeled nanoclay, in polymer-clay nanocomposite films, and in a contact solvent after migration testing. Fluorescein-5-maleimide (fluorescein) or tetramethylrhodamine-5-maleimide (rhodamine) was covalently bonded to organically modified montmorillonite (o-MMT). Fluorescein- and rhodamine-labeled nanoclay showed good thermal stability up to 220 °C and the rhodamine-labeled nanoclay remained stable at 250 °C. Confocal laser scanning microscopy was used to confirm the tagging and to detect the fluorescent-labeled nanoclays in various systems.
Performance of a Partial Burst Retransmission Mechanism in OBS Networks (2006)

We investigate the effects on performance of using a partial retransmission mechanism in Optical Burst Switched (OBS) networks. In our scheme, the lost segments of a burst are retransmitted in the OBS layer. We also propose an optical resource reservation using the partial retransmission mechanism. Our scheme attempts to improve the burst contention resolution and optical channel utilization. Simulation results indicate that the link utilization of the OBS network is improved markedly at the expense of signaling and ingress buffers.