gebhart/patrepeval huggingface dataset:
Abstract 1777: REGN4018, a novel MUC16xCD3 bispecific T-cell engager for the treatment of ovarian cancer (2018)

Abstract Advanced ovarian cancer has a high rate of recurrence, thus there is a need for therapies that can produce durable responses and extend overall survival. Infiltrating CD3+ T cells are reported to correlate with improved clinical outcome in stage III/IV ovarian cancer. Bispecific antibodies that engage T cells via CD3 and a tumor antigen on ovarian tumor cells may be able to exploit these tumor-infiltrating T cells and have drawn interest as a novel strategy of antitumor immunotherapy. Mucin16 (MUC16) is a well described antigen highly expressed in ovarian cancer and several other tumors. We generated a human bispecific antibody (REGN4018) that binds MUC16 on tumor cells and CD3, bridging MUC16-expressing cells with CD3+ T cells. REGN4018 demonstrates MUC16-directed T cell activation and polyclonal T cell killing of MUC16-expressing tumor cells in vitro and in vivo. Binding and cytotoxicity are minimally affected by high concentrations of CA-125, the shed form of MUC16 that is used as a biomarker for ovarian cancer. Several murine tumor models were developed to determine the in vivo anti-tumor effects of REGN4018. As a xenogenic tumor model, human OVCAR-3 cells were grown as ascites in immunodeficient mice [NOD-SCID-IL2Rgamma deficient (NSG)] pre-implanted with human PBMC. Significant tumor inhibition by REGN4018 was observed at doses of ≥ 0.1 mg/kg. To enable investigation of clinical bispecific antibodies in tumor-bearing immune competent mice, mice were genetically engineered to humanize both CD3 and a part of MUC16 covering the antibody binding region. ImmunoPET imaging demonstrated localization of REGN4018 in both T cell-rich organs such as the spleen and lymph nodes as well as in MUC16-expressing tumors. REGN4018 inhibited growth of murine tumors transfected with human MUC16 in syngeneic tumor models at doses ≥ 0.05 mg/kg. The safety and tolerability of REGN4018 were evaluated in cynomolgous monkey studies. REGN4018 administration resulted in a minimal and transient increase in serum cytokines and C-reactive protein with no overt toxicity. Collectively, these data show the potent anti-tumor activity and tolerability of REGN4018 and provide strong support for the clinical testing of REGN4018 in patients with MUC16-expressing ovarian cancers. Citation Format: Alison Crawford, Lauric Haber, Kristin Vazzana, Lauren Canova, Priyanka Ram, Jennifer Principio, Arpita Pawashe, Curtis Colleton, Marcus Kelly, Sosina Makkonen, Carlos Hickey, Paurene Duramad, Stephen Godin, John Lin, Eric Smith, Gavin Thurston, Jessica R. Kirshner. REGN4018, a novel MUC16xCD3 bispecific T-cell engager for the treatment of ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1777.
Silicon hetero-interface photodetector (2002)

We propose and demonstrate a novel avalanche photodetector that uses separate InGaAs absorption and Si multiplication regions fabricated by wafer fusion. Directly integrating InGaAs and silicon layers in an avalanche photodetector combines the high long-wavelength absorption capabilities of InGaAs and the avalanche multiplication properties of Si. The large ratio of electron and hole ionization coefficients of silicon results in lower noise and a higher gain bandwidth product than achievable using III-V semiconductors in avalanche regions.
A system and design of extensible authentication protocols based on ECC and SKE mechanisms for mobile and wireless communications (2010)

We have introduced a system and method of extensible authentication protocols (EAPs) based on ECC and SKE with a permutation technique evolved. The permutation in our EAPs is a process of cubing a random number w.r. to a prime (= 2 mod 3). These EAPs are compatible with 3G and 4G networks and no certificates exchanged during the communication. Further, they play an important role to fulfill CAAA issues.
Packaging of Optical MEMS Devices (2003)

Recently, optical MEMS devices have gained considerable attention in the telecommunications industry—particularly in the optical networking and switching arenas. Since optical MEMS are micro-systems which rely on high precision optics, electronics and mechanics working in close concert, these emerging devices pose some unique packaging challenges yet to be addressed by the general packaging industry. Optical MEMS packages often are required to provide both optical and electrical access, hermeticity, mechanical strength, dimensional stability, and long-term reliability. Hermetic optical access necessitates the use of metallized and anti-reflection coated windows, and ever-increasing electrical I/O count has prompted the use of higher density substrate/package technologies. Taking these requirements into consideration, we explore three ceramic packaging technologies, namely high-temperature co-fired ceramic (HTCC), low-temperature co-fired ceramic (LTCC), and thin-film ceramic technologies. In this paper, we describe some optical MEMS packages designed using these three technologies and discuss their substrate designs, package materials, ease of integration and assembly.
Evaluation of Gram-negative bacterial infection by a stable and conjugative bioluminescence plasmid in a mouse model (2014)

This is the first study to evaluate the conjugative and stable bioluminescence vehicle system of pSE-Lux1 in a wide range of Gram-negative bacteria, a system that can provide a useful reporter approach to trace systemic and gastrointestinal bacterial infections in a mouse model.
Focusing on Host–Vector–Pathogen Interactions for Vaccine Development (2006)

Anaplasma marginale and A. phagocytophylum are intracellular rickettsiae that cause bovine anaplasmosis and human granulocytic anaplasmosis, respectively. The ultimate vaccine for the control of anaplasmosis would be one that reduces infection and transmission of the pathogen by ticks. Effective vaccines for control of anaplasmosis are not available despite attempts using different approaches, such as attenuated strains, infected erythrocyte and tick cell-derived purified antigens, and recombinant pathogen and tick-derived proteins. Three lines of functional analyses were conducted by our laboratory to characterize host-tick-Anaplasma interactions to discover potential vaccine candidate antigens to control tick infestations and the infection and transmission of Anaplasma spp.: (1) characterization of A. marginale adhesins involved in infection and transmission of the pathogen, (2) global expression analysis of genes differentially expressed in HL-60 human promyelocytic cells in response to infection with A. phagocytophilum, and (3) identification and characterization of tick-protective antigens by expression library immunization (ELI) and analysis of expressed sequence tags (EST) in a mouse model of tick infestations and by RNA interference in ticks. These experiments have resulted in the characterization of the A. marginale MSP1a as an adhesin for bovine erythrocytes and tick cells, providing support for its use as candidate vaccine antigen for the control of bovine . Microarray analysis of genes differentially expressed in human cells infected with A. phagocytophilum identified key molecules involved in pathogen infection and multiplication. The screening for tick-protective antigens resulted in vaccine candidates reducing tick infestation, molting, and oviposition and affecting Anaplasma infection levels in ticks.
High Definition Single-Wire-Arc-Spray (2000)

Abstract Wire arc spray is a process for producing coatings and forming structures through the deposition of metal droplets. Wire arc spray has the advantage of low material coast and low power requirements when compared to other thermal spray technologies. This article elaborates on the assumptions made for using single consumable wire geometry, discusses experiments performed to test these assumptions, presents droplet generation results, and addresses required future work. Experiments revealed a critical relationship between wire polarity, wire position, and droplet beam dispersion. The article identifies a critical relationship between wire polarity, wire position, and spray pattern divergence in a single wire arc spray device.
High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer (2011)

These data demonstrate that high tumor-specific nuclear expression of RBM3 is an independent predictor of good prognosis in colorectal cancer.
Is Split Manufacturing Secure? (2013)

Split manufacturing of integrated circuits (IC) is being investigated as a way to simultaneously alleviate the cost of owning a trusted foundry and eliminate the security risks associated with outsourcing IC fabrication. In split manufacturing, a design house (with a low-end, in-house, trusted foundry) fabricates the Front End Of Line (FEOL) layers (transistors and lower metal layers) in advanced technology nodes at an untrusted high-end foundry. The Back End Of Line (BEOL) layers (higher metal layers) are then fabricated at the design house's trusted low-end foundry. Split manufacturing is considered secure (prevents reverse engineering and IC piracy) as it hides the BEOL connections from an attacker in the FEOL foundry. We show that an attacker in the FEOL foundry can exploit the heuristics used in typical floorplanning, placement, and routing tools to bypass the security afforded by straightforward split manufacturing. We developed an attack where an attacker in the FEOL foundry can connect 96% of the missing BEOL connections correctly. To overcome this security vulnerability in split manufacturing, we developed a fault analysis-based defense. This defense improves the security of split manufacturing by deceiving the FEOL attacker into making wrong connections.
<i>Alteromonas</i> As a Key Agent of Polycyclic Aromatic Hydrocarbon Biodegradation in Crude Oil-Contaminated Coastal Sediment (2012)

Following the 2007 oil spill in South Korean tidal flats, we sought to identify microbial players influencing the environmental fate of released polycyclic aromatic hydrocarbons (PAHs). Two years of monitoring showed that PAH concentrations in sediments declined substantially. Enrichment cultures were established using seawater and modified minimal media containing naphthalene as sole carbon source. The enriched microbial community was characterized by 16S rRNA-based DGGE profiling; sequencing selected bands indicated Alteromonas (among others) were active. Alteromonas sp. SN2 was isolated and was able to degrade naphthalene, phenanthrene, anthracene, and pyrene in laboratory-incubated microcosm assays. PCR-based analysis of DNA extracted from the sediments revealed naphthalene dioxygenase (NDO) genes of only two bacterial groups: Alteromonas and Cycloclasticus, having gentisate and catechol metabolic pathways, respectively. However, reverse transcriptase PCR-based analysis of field-fixed mRNA revealed in situ expression of only the Alteromonas-associated NDO genes; in laboratory microcosms these NDO genes were markedly induced by naphthalene addition. Analysis by GC/MS showed that naphthalene in tidal-flat samples was metabolized predominantly via the gentisate pathway; this signature metabolite was detected (0.04 μM) in contaminated field sediment. A quantitative PCR-based two-year data set monitoring Alteromonas-specific 16S rRNA genes and NDO transcripts in sea-tidal flat field samples showed that the abundance of bacteria related to strain SN2 during the winter season was 20-fold higher than in the summer season. Based on the above data, we conclude that strain SN2 and its relatives are site natives--key players in PAH degradation and adapted to winter conditions in these contaminated sea-tidal-flat sediments.
Estimating Spatially Varying Defocus Blur From A Single Image (2013)

Estimating the amount of blur in a given image is important for computer vision applications. More specifically, the spatially varying defocus point-spread-functions (PSFs) over an image reveal geometric information of the scene, and their estimate can also be used to recover an all-in-focus image. A PSF for a defocus blur can be specified by a single parameter indicating its scale. Most existing algorithms can only select an optimal blur from a finite set of candidate PSFs for each pixel. Some of those methods require a coded aperture filter inserted in the camera. In this paper, we present an algorithm estimating a defocus scale map from a single image, which is applicable to conventional cameras. This method is capable of measuring the probability of local defocus scale in the continuous domain. It also takes smoothness and color edge information into consideration to generate a coherent blur map indicating the amount of blur at each pixel. Simulated and real data experiments illustrate excellent performance and its successful applications in foreground/background segmentation.
Electrical detection of current generated spin in topological insulator surface states: Role of interface resistance (2019)

Current generated spin polarization in topological insulator (TI) surface states due to spin-momentum locking has been detected recently using ferromagnet/tunnel barrier contacts, where the projection of the TI spin onto the magnetization of the ferromagnet is measured as a voltage. However, opposing signs of the spin voltage have been reported, which had been tentatively attributed to the coexistence of trivial two-dimensional electron gas states on the TI surface which may exhibit opposite current-induced polarization than that of the TI Dirac surface states. Models based on electrochemical potential have been presented to determine the sign of the spin voltage expected for the TI surface states. However, these models neglect critical experimental parameters which also affect the sign measured. Here we present a Mott two-spin current resistor model which takes into account these parameters such as spin-dependent interface resistances, and show that such inclusion can lead to a crossing of the voltage potential profiles for the spin-up and spin-down electrons within the channel, which can lead to measured spin voltages of either sign. These findings offer a resolution of the ongoing controversy regarding opposite signs of spin signal reported in the literature, and highlight the importance of including realistic experimental parameters in the model.
A New Strategy for the Prevention of Clostridium difficile Infection (2013)

Our results support a mechanism whereby the antigermination effect of CamSA is responsible for preventing CDI signs. This approach represents a new paradigm in CDI treatment. Instead of further compromising the microbiota of CDI patients with strong antibiotics, antigermination therapy could serve as a microbiota surrogate to curtail C. difficile colonization of antibiotic-treated patients.
Effect of PDGF, IL-1alpha, and BMP2/4 on corneal fibroblast chemotaxis: expression of the platelet-derived growth factor system in the cornea. (1999)

The PDGF growth factor receptor system is expressed in the human cornea. PDGF, BMP2, BMP4, and IL-1alpha may modulate keratocyte chemotaxis and proliferation during homeostasis and wound healing.
Molecular Imaging Agents Specific for the Annulus Fibrosus of the Intervertebral Disk (2010)

Low back pain is a prevalent medical condition that is difficult to diagnose and treat. Current imaging methods are unable to correlate pain reliably with spinal structures, and surgical removal of painful damaged or degenerating disks is technically challenging. A contrast agent specific for the intervertebral disk could assist in the detection, diagnosis, and surgical treatment of low back pain. The styryl pyridinium (FM) fluorophores were characterized and structure-activity relationships between chemical structure and in vivo uptake were established. Two novel FM fluorophores with improved optical properties for imaging the intervertebral disks were synthesized and evaluated in mice, rats, and pigs. After a single systemic injection, eight of eight FM fluorophores provided high-contrast imaging of the trigeminal ganglia, whereas six of eight provided high-contrast imaging of the dorsal root ganglia. Unexpectedly, three of eight FM fluorophores provided high-contrast imaging of annulus fibrosus tissue of the intervertebral disks, confirmed histologically. We present the first known contrast agent specific for the intervertebral disks and identify the chemical structural motif that mediates uptake. FM fluorophores could be used for image-guided surgery to assist in the removal of intervertebral disk and lay the foundation for derivatives for magnetic resonance imaging and positron emission tomography.
Amphiphilic Modulation of Glycosylated Antitumor Ether Lipids Results in a Potent Triamino Scaffold against Epithelial Cancer Cell Lines and BT474 Cancer Stem Cells (2017)

The problems of resistance to apoptosis-inducing drugs, recurrence, and metastases that have bedeviled cancer treatment have been attributed to the presence of cancer stem cells (CSCs) in tumors, and there is currently no clinically indicated drug for their eradication. We previously reported that glycosylated antitumor ether lipids (GAELs) display potent activity against CSCs. Here, we show that by carefully modulating the amphiphilic nature of a monoamine-based GAEL, we can generate a potent triamino scaffold that is active against a panel of hard-to-kill epithelial cancer cell lines (including triple-negative breast) and BT474 CSCs. The most active compound of this set, which acts via a nonmembranolytic, nonapoptotic caspase-independent mechanism, is more effective than cisplatin and doxorubicin against these cell lines and more potent than salinomycin against BT474 CSCs. Understanding the combination of factors crucial for the enhanced cytotoxicity of GAELs opens new avenues to develop potent compounds against drug-resistant cancer cells and CSCs.
Design and Synthesis of Nonionic Copolypeptide Hydrogels with Reversible Thermoresponsive and Tunable Physical Properties (2015)

Polypeptide-based formulations that undergo liquid to hydrogel transitions upon change in temperature have become desirable targets since they can be mixed with cells or injected into tissues as liquids, and subsequently transform into rigid scaffolds or depots. Such materials have been challenging to prepare using synthetic polypeptides, especially when reversible gelation and tunable physical properties are desired. Here, we designed and prepared new nonionic diblock copolypeptide hydrogels (DCH) containing hydrophilic poly(γ-[2-(2-methoxyethoxy)ethyl]-rac-glutamate) and hydrophobic poly(l-leucine) segments, named DCHEO, and also further incorporated copolypeptide domains into DCHEO to yield unprecedented thermoresponsive DCH, named DCHT. Although previous attempts to prepare nonionic hydrogels composed solely of synthetic polypeptides have been unsuccessful, our designs yielded materials with highly reversible thermal transitions and tunable properties. Nonionic, thermoresponsive DCHT were found to support the viability of suspended mesenchymal stem cells in vitro and were able to dissolve and provide prolonged release of both hydrophilic and hydrophobic molecules. The versatility of these materials was further demonstrated by the independent molecular tuning of DCHT liquid viscosity at room temperature and DCHT hydrogel stiffness at elevated temperature, as well as the DCHT liquid to hydrogel transition temperature itself.
Dye-based non-volatile holographic data storage media (2007)

Holographic data storage materials are presented that are based on a thermoplastic host doped with narrow-band absorption dyes. The dyes are photosensitive and undergo non-reversible photobleaching reactions upon exposure. Samples were produced using different dyes and various concentrations in a polymer host with a focus on sensitivity and capacity of the media. A challenging obstacle for a successful dye-doped system is the inherent remaining photosensitivity of the material after the writing process. This paper will introduce the concept of a highly sensitive yet non-volatile dye-based data storage system. The chromophore is subjected to a post-treatment step at a second wavelength which removes the photosensitivity. The stored data can therefore be secured against degradation during read-out at the writing wavelength.
Recognizing Commercials in Real-Time using Three Visual Descriptors and a Decision-Tree (2006)

We present a new approach for classifying mpeg-2 video sequences as `commercial' or `non-commercial' by analyzing specific color, texture and motion features of consecutive frames in real-time. This is part of the well-known video-genre-classification problem, where popular TV-broadcast genres like cartoon, commercial, music, news and sports are studied. Such applications have also been discussed in the context of MPEG-7. In our method the extracted features from three visual descriptors are logically combined using a decision tree to produce a reliable recognition. The results demonstrate a high identification rate based on a large collection of 200 representative video sequences (40 `commercials' and 4*40 `non-commercials') gathered from free digital TV-broadcasting in Germany
Purification and Characterization of Heparan Sulfate 6-Sulfotransferase from the Culture Medium of Chinese Hamster Ovary Cells (1995)

Heparan sulfate 6-sulfotransferase, which catalyzes the transfer of sulfate from 3'-phosphoadenylyl sulfate to position 6 of N-sulfoglucosamine in heparan sulfate, was purified 10,700-fold to apparent homogeneity with a 40% yield from the serum-free culture medium of Chinese hamster ovary cells. The isolation procedure included affinity chromatography of the first heparin-Sepharose CL-6B column (stepwise elution), 3',5'-ADP-agarose, and the second heparin-Sepharose CL-6B column (gradient elution). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the purified enzyme showed two protein bands with molecular masses of 52 and 45 kDa. Both proteins appeared to be glycoproteins, because their molecular masses decreased after N-glycanase digestion. When completely desulfated and N-resulfated heparin was used as acceptor, the purified enzyme transferred sulfate to position 6 of N-sulfoglucosamine residue but did not transfer sulfate to the amino group of glucosamine residue or to position 2 of the iduronic acid residue. Heparan sulfate was also sulfated by the purified enzyme at position 6 of N-sulfoglucosamine residue. Chondroitin and chondroitin sulfate did not serve as acceptors. The optimal pH for enzyme activity was around 6.3. The enzyme activity was inhibited by dithiothreitol and was stimulated strongly by protamine. The Km value for adenosine 3'-phosphate 5'-phosphosulfate was 0.44 microM.
BBM-928, a new antitumor antibiotic complex I. Production, isolation, characterization and antitumor activity. (1980)

A complex of the antitumor antibiotic BBM-928 was produced by an actinomycete strain No. G455-101. Four components, BBM-928 A, B, C and D, were isolated in crystalline form and characterized. They were shown to be cyclic depsipeptide antibiotics containing a quinoline nucleus as the chromophore. BBM-928 A is a monoacetyl derivative of BBM-928 B and a diacetyl derivative of BBM-928 C. BBM-928 components exhibit antimicrobial activity against Gram-positive and acid-fast bacteria. BBM-928 A is highly active in mice against various experimental tumors including leukemia P388, leukemia L1210, melanoma B16, LEWIS lung carcinoma and sarcoma 180. BBM-928 B is less active than BBM-928 A, and BBM-928 C has no antitumor activity.