gebhart/patrepeval huggingface dataset:
In vivo Treg expansion by TNFRSF25 stimulation inhibits allergic lung inflammation (97.11) (2010)

Abstract TNF receptor super family member 25 (TNFR25, DR3) is constitutively and highly expressed by CD4+FoxP3+ regulatory T cells (Treg). Here we have utilized a TNFR25 agonistic monoclonal antibody, 4C12, to study the effects of TNFR25 signaling on Treg in vivo. We have previously demonstrated that signaling through TNFR25, in the absence of TCR signals, induces rapid and selective expansion of natural Treg in vivo to 30-35% of all CD4+ T cells within 4 days. TNFR25-expanded Treg remained highly suppressive ex vivo. Here we demonstrate that although certain IL-2 antibody complexes expand Treg to a similar degree, only in vivo TNFR25-expanded Treg are protective against allergic lung inflammation, a model for asthma, by reversing the T-effector to T-regulatory ratio in the lung, suppressing IL-13 and Th2 cytokine production and blocking eosinophil exudation into bronchio-alveolar fluid. Unlike TNFR25 responses by T effector cells, which require TCR engagement, expansion of Treg by TNFR25 signaling is not dependent upon stimulation by exogenous antigens. Our studies define a novel mechanism for Treg control and important functions for TNFR25/TL1A in regulating auto aggression that balance its known role in enhancing auto immunity.
Fine-Grained Channel Access in Wireless LAN (2012)

With the increasing of physical-layer (PHY) data rate in modern wireless local area networks (WLANs) (e.g., 802.11n), the overhead of media access control (MAC) progressively degrades data throughput efficiency. This trend reflects a fundamental aspect of the current MAC protocol, which allocates the channel as a single resource at a time. This paper argues that, in a high data rate WLAN, the channel should be divided into separate subchannels whose width is commensurate with the PHY data rate and typical frame size. Multiple stations can then contend for and use subchannels simultaneously according to their traffic demands, thereby increasing overall efficiency. We introduce FICA, a fine-grained channel access method that embodies this approach to media access using two novel techniques. First, it proposes a new PHY architecture based on orthogonal frequency division multiplexing (OFDM) that retains orthogonality among subchannels while relying solely on the coordination mechanisms in existing WLAN, carrier sensing and broadcasting. Second, FICA employs a frequency-domain contention method that uses physical-layer Request to Send/Clear to Send (RTS/CTS) signaling and frequency domain backoff to efficiently coordinate subchannel access. We have implemented FICA, both MAC and PHY layers, using a software radio platform, and our experiments demonstrate the feasibility of the FICA design. Furthermore, our simulation results show FICA can improve the efficiency of WLANs from a few percent to 600% compared to existing 802.11.
Identification of sensitivity markers for BMS-536924, an inhibitor for insulin-like growth factor-1 receptor (2007)

3506 Background: Insulin-like growth factor-1 receptor (IGF-1R) signaling is an important regulator of mitogenesis, transformation to the oncogenic phenotype and anti-apoptotic effects in malignant cells. Over-expression of IGF-1R, seen in many tumors, may confer a growth advantage or drug resistance. A potent small-molecule inhibitor (BMS-536924) of IGF-1R tyrosine kinase showed anti-tumor activity in sarcoma, prostate, colon and pancreatic tumor models. One of the integral goals in the development of BMS-536924 as a cancer therapeutic is to identify molecular biomarkers predictive of response to the drug that ultimately will aid in selecting the patients who are most likely to benefit. Methods: The sensitivity (IC 50 ) to BMS-536924 was determined for a panel of 29 pediatric sarcoma and neuroblastoma cell lines. Both microarray and LC/MS based protein profiling were utilized to analyze the baseline gene or protein expression level. Drug treatment studies were performed using two rhabdomyosarcoma cell lines, Rh41 (sensitive to BMS-536924) and Rh36 (resistant to the drug) to identify markers that are modulated by BMS-536924. Results: (1). Sixteen out of the 29 cell lines were highly sensitive to BMS-536924; candidate markers that correlated with the sensitivity to BMS-536924 were identified by gene expression and protein profiling. (2). Histological correlation was also discovered, with specific subtypes of sarcoma having a low IC 50 to BMS-536924. (3). Pathway analysis noted that some major candidate markers are common key steps in the EGF-R pathway and the IGF1-R pathway. This observation of cross-talk between the two pathways led to the hypothesis of synergy with combined inhibition of both pathways. Combination studies of BMS-536924 and EGFR inhibitors were performed and synergism was observed. (4). Markers modulated by BMS-536924 in a sensitive cell line were identified. Conclusions: This work has identified candidate markers correlating to BMS-536924 sensitivity in vitro. The possible mechanism of synergistic activity of IGF1-R and EGFR inhibitors will be presented. No significant financial relationships to disclose.
Can fundamental gain limitations of nanostructure THz lasers be overcome? (2006)

We argue that nanostructure based THz lasers of standard design have a principal limitations of gain value. These limitations rise from the obvious necessity to engineer both THz gap and population inversion simultaneously. Typical approach to the gap engineering inherited from midIR lasers utilizes intersubband transitions. However, contrary to midIR range, for THz lasing selective depopulation is problematic. The problem is that the selectivity of both depopulation mechanisms, LO phonon emission and electron - electron scattering, in THz region is substantially weaker than in midIR region. We suggest to use InAs/GaSb coupled quantum wells as a way to overcome this fundamental limitation. This is the only heterostructure where THz lasing can be based not on intersubband but on interband transitions. A proper design of this structure leads to a hybridization gap coming from anti-crossing of the GaSb valence band and InAs conduction band naturally appearing in the THz range. Two more advantages of this design are (i) a large value of the interband dipole matrix element and (ii) W-shaped spectrum leading to a singular density of states. These advantages lead to a gain much higher than for intersubband THz lasing.
Image-Based Automated Change Detection for Synthetic Aperture Sonar by Multistage Coregistration and Canonical Correlation Analysis (2015)

In this paper, an automated change detection technique is presented that compares new and historical seafloor images created with sidescan synthetic aperture sonar (SAS) for changes occurring over time. The method consists of a four-stage process: a coarse navigational alignment that relates and approximates pixel locations of reference and repeat-pass data sets; fine-scale coregistration using the scale-invariant feature transform (SIFT) algorithm to match features between overlapping data sets; local coregistration that improves phase coherence; and finally, change detection utilizing a canonical correlation analysis (CCA) algorithm to detect changes. The method was tested using data collected with a high-frequency SAS in a sandy shallow-water environment. Successful results of this multistage change detection method are presented here, and the robustness of the techniques that exploit phase and amplitude levels of the backscattered signals is discussed. It is shown that the coherent nature of the SAS data can be exploited and utilized in this environment over time scales ranging from hours through several days. Robustness of the coregistration methods and analysis of scene coherence over time is characterized by analysis of repeat pass as well as synthetically modified data sets.
Nitrogen deficiency and metal dopant induced sub-stoichiometry in titanium nitride thin films: a comparative study (2013)

Abstract Sub-stoichiometric (nitrogen-deficient) and Nb-substituted (Ti 1 – y Nb y N, 0 ≤ y ≤ 1) titanium nitride thin films were deposited by means of radio frequency magnetron sputtering on SiO 2 and Si (311) substrates and compared. Thickness of TiN x films varied in the range 116–230 nm, while the value was constant, at 500 nm, for Ti 1 – y Nb y N films. The sub-stoichiometric TiN x films deposited at room temperature are amorphous, independent of nitrogen partial pressure (in the range of 1.6 to 3.33 Pa). Annealing of the films at 600°C resulted in amorphous–crystalline transition only in the film deposited at 3.33 Pa, which crystallized into tetragonal ∊-Ti 2 N phase. The other films remained amorphous. The hardness and Young's modulus were highest for the film deposited at a nitrogen pressure of 3.33 Pa, viz., 5.9 GPa and 105 GPa respectively. In contrast, all as-deposited Nb substituted TiN (Ti 1 – y Nb y N) films crystallized into rock salt structure with (111) orientation up to y = 0.77. The hardness and Young's modulus for Ti 1 – y Nb y N films increased with increase in Nb concentration. The highest values of hardness and Young's modulus obtained were 29 GPa and 320 GPa respectively. This study shows that nitrogen deficient titanium nitrides are more difficult to crystallize and exhibit lower hardness than metal substituted nitrides.
Bidirectional Blockchain (2020)

Ensuring the authenticity and integrity of data transferred over the Internet is still a daunting task. Although various mechanisms have been proposed to strengthen the key management infrastructure, they still rely on trusted third parties (TTPs) or require additional entities to monitor the system. This paper introduces Bidirectional Blockchain - a collection of protocols that ensure the authenticity of data sent from a collection of one or more servers to distributed clients (e.g., Internet of Things (IoT) devices) without relying on TTPs. Bidirectional Blockchain is based on the benefits of multi-party computation and blockchain to ensure the secrecy of keys used to sign the distributed data and the correctness and integrity of the received data, respectively. We implemented Bidirectional Blockchain on a Raspberry Pi, and our evaluation results confirm that Bidirectional Blockchain is lightweight and hence can be used to secure a variety of data transactions, including software updates, even on resource-constrained devices.
Use of E. coli for the Production of a Single Protein (2012)

E. coli has been widely used for recombinant protein production. Here, we introduce a novel expression method in E. coli, the Single Protein Production (SPP) system, in which E. coli is converted into a bioreactor producing only the target protein. In the SPP system, all E. coli cellular mRNAs are eliminated by the induction of MazF, an ACA-specific mRNA interferase, which results in complete cell growth arrest. However, the mRNA for a target protein was engineered to be devoid of ACA sequences, thus resistant to MazF cleavage. Therefore, the SPP system is unique and ideal for expression of toxic proteins and incorporation of toxic amino acid analogues. We have also demonstrated that the SPP system is a cost-effective protein production method for NMR structural studies because cell culture can be highly condensed without affecting protein yields.
Targeting and Treatment of Tumor Hypoxia by Newly Designed Prodrug Possessing High Permeability in Solid Tumors (2016)

Tumor hypoxia, which is associated with poor prognosis in cancer, is known to lead to resistance to radiotherapy and anticancer chemotherapy. Impaired drug penetration in hypoxic regions has been recognized as an essential barrier to drug development in solid tumors. Here, we propose novel hypoxia-activated prodrugs, which drastically improved the penetration property of commonly used anticancer drugs in the hypoxic region. In this design, conventional anticancer drugs were modified with 2-nitroimidazole derivatives. The most important point of this study was that the prodrug designed formed a 6-membered cyclic structure to allow liberation of the active drug in the hypoxic region. This design markedly increased the selectivity of the hypoxia-targeted prodrug, resulting in significant reduction of adverse effects in the normoxic region. In vitro studies confirmed the selective activation under hypoxic conditions. In vivo studies showed drastic reduction of adverse effects associated with conventional anticancer drugs and improvement of the survival rate of mice. Immunofluorescence analyses confirmed that the designed prodrug had a tendency to localize at the hypoxic region, in contrast to conventional anticancer drugs, which localize only at the normoxic region.
Image reconstructions from super-sampled data sets in PET imaging (2013)

Spatial resolution in positron emission tomography (PET) is still a limiting factor in many imaging applications. To improve the spatial resolution for an existing scanner with fixed crystal sizes, mechanical movements such as scanner wobbling and object shifting have been considered for PET systems. Multiple acquisitions from different positions provide both redundant and complementary information. The objective of this paper is to explore efficient and useful reconstruction framework to reconstruct super-resolution images from super-sampled low-resolution data. We first create a super-sampling data acquisition model based on the physical processes with tomographic, down-sampling and shifting matrices as its building blocks. Based on the model, we extend ML-EM and Landweber algorithms to reconstruct images from multiple data sets. We also derive a backprojection-filtration-type (BPF) method for the super-resolution reconstruction. Further, we explore variant methods for super-sampling reconstructions: the separate super-sampling resolution-modeling reconstruction and the reconstruction without down-sampling to further improve image quality at the cost of more computation. We used simulated reconstruction of a resolution phantom to evaluate the three types of algorithms with different super-samplings. Contrast recovery coefficient (CRC) versus background variability, as an image-quality metric, is calculated at each iteration. We observe that all three algorithms can significantly and consistently achieve increased CRCs and reduce background artifacts with super-sampled data sets at the same total counts. ML-EM achieves better image quality than Landweber, which in turn achieves better image quality than BPF. We also demonstrate that the reconstructions from super-sampled data sets using a fine system matrix yield improved image quality compared to the reconstructions using a coarse system matrix.
Poly(arylate‐phosphonate) copolymers with deoxybenzoin in the backbone: Synthesis, characterization, and thermal properties (2007)

Abstract Deoxybenzoin‐based copolymers containing various relative ratios of arylate and phosphonate units in the backbone were synthesized by solution polycondensation. These copolymers were characterized by gel permeation chromatography, Fourier Transform infrared spectrometry, and proton, carbon, and phosphorous nuclear magnetic resonance spectroscopy ( 1 H, 13 C, and 31 P NMR). Pyrolysis combustion flow calorimetry (PCFC) performed on these copolymers revealed their very low heat release capacity, making them attractive for applications in which halogen‐free, low flammability materials are desired. Integration of phosphonate units into the polymer backbone is advantageous for achieving high molecular weight polymers with solution processbility while retaining the low flammability inherent to deoxybenzoin‐based polymers. Char yields greater than 50% and heat release capacities of 40–60 J/g K, were observed for these copolymers by PCFC. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 4573–4580, 2007
Transient optical neural stimulation in vivo (2007)

The traditional method of stimulating neural activity has been based on electrical methods and remains the gold standard to date despite inherent limitations. We have developed a new paradigm - transient optical neural stimulation (TONS) to in vivo neural activation based on pulsed infrared light, which provides a contact-free, spatially selective, artifact-free method without incurring tissue damage that may have significant advantages over electrical stimulation in a variety of diagnostic and therapeutic applications. Results demonstrate that low-level laser energy can be used to consistently and reproducibly stimulate action potentials in discrete populations of peripheral nerves with resulting compound nerve and muscle potentials in frogs and rats in vivo with no appreciable tissue damage using radiant exposures well below damage threshold. This phenomenon is wavelength dependent and stimulation threshold follows the inverse of soft tissue absorption. Thus stimulation threshold is a function of the penetration depth of light in tissue. We have developed in conjunction with our industrial partner, an optical stimulator that can be used to stimulate nerves for research purposes. This unit has been shown to successfully stimulate peripheral nerves in vivo in an animal model. Preliminary investigation of the physical mechanism underlying this phenomenon, indicate that TONS is most likely a photo-thermal effect from transient tissue temperature changes resulting in direct or indirect activation of transmembrane ion channels causing propagation of the action potential.
Experimental Demonstration of Gain Guided Lasing in an Index Anti-Guiding Large Mode Area Fiber (2007)

Recent observations of apparently single mode gain-guided lasing in Nd3+ fibers with 100 µm diameter index anti-guided cores demonstrate the potential of gain guiding for single mode fiber lasers with very large mode areas.
Room temperature terahertz quantum cascade laser source based on intracavity difference-frequency generation (2008)

We report on our progress in the development of a terahertz quantum cascade laser source based on intracavity terahertz difference-frequency mixing in a dual-wavelength mid-infrared quantum cascade laser with the active region engineered to possess giant second-order nonlinear susceptibility. In this letter, we demonstrate devices that operate in mid-infrared at λ1=8.9μm and λ2=10.5μm and produce terahertz output at λ≈60μm via difference-frequency generation with 7μW output power at 80K, 1μW output at 250K, and still approximately 300nW output at 300K.
Magnetic and metallurgical properties of directionally solidified eutectic Bi/MnBi composites: The effects of annealing (1979)

Eutectic Bi/MnBi (97.8 a/o Bi) samples have been plane-front directionally solidified. The resultant microstructures consist of elongated, aligned particles of MnBi dispersed in a Bi-matrix. Magnetization as a function of temperature (4.2 to 300 K) and applied field (up to 220 kG) has been used to evaluate solidification parameters and magnetic properties. At room temperature, in addition to the diamagnetic contribution of Bi, one finds a superposition of the ferromagnetic, low temperature (LTP) MnBi phase and paramagnetic phases. At cryogenic temperatures, one of the room temperature paramagnetic phases is ferromagnetic with an intrinsic coercivity of 120 kOe while the other remains paramagnetic for low fields and orders ferromagnetically at high fields in a complicated way. Annealing of as-grown samples was found to produce significant changes in magnetic properties. The origins of the paramagnetic phases and their relation to the mechanisms which control the coercive field of the hard magnetic LTP MnBi phase are discussed.
Unmanned Aircraft System (UAS) Traffic Management (UTM): Enabling Civilian Low-Altitude Airspace and Unmanned Aerial System Operations (2016)

Just a year ago we laid out the UTM challenges and NASA's proposed solutions. During the past year NASA's goal continues to be to conduct research, development and testing to identify airspace operations requirements to enable large-scale visual and beyond visual line-of-sight UAS operations in the low-altitude airspace. Significant progress has been made, and NASA is continuing to move forward.
Abstract A110: Mutant MHC class II epitopes drive therapeutic immune responses to cancer (2016)

Abstract Mutations are regarded as ideal targets for cancer immunotherapy. As neoepitopes with strict lack of expression in any healthy tissue, they are expected to be safe and could bypass the central tolerance mechanisms. Recent advances in nucleic acid sequencing technologies have revolutionized the field of genomics, allowing the readily targeting of mutated neoantigens for personalized cancer vaccination. We demonstrated in three independent murine tumor models that a considerable fraction of non-synonymous cancer mutations is immunogenic and that unexpectedly the immunogenic mutanome is pre-dominantly recognized by CD4+ T cells. RNA vaccination with such MHC class II restricted immunogenic mutations leads to infiltration of CD4+ and CD8+ T cells into the tumor, reduces intratumoral regulatory T cells and ultimately confers strong anti-tumor activity. Encouraged by these findings we set up a process comprising mutation detection by exome sequencing, selection of vaccine targets by solely bioinformatical prioritization of mutated epitopes predicted to be abundantly expressed and presented on MHC class II molecules. Synthetic mRNA vaccines encoding multiple of these prioritized mutated epitopes induce potent tumor control and complete rejection of established aggressively growing tumors in mice. Moreover, we demonstrate that CD4+ T cell neoepitope vaccination primes CTL responses against an independent immunodominant antigen in tumor bearing mice indicating orchestration of antigen spread. Our findings reveal that cancer mutation based MHC class II restricted epitopes are attractive vaccination targets and provide the preclinical proof of concept for an integrated process from tumor sample to a cancer vaccine customized to the unique repertoire of each patient`s tumor. Citation Format: Mathias Vormehr, Sebastian Kreiter, Niels van de Roemer, Mustafa Diken, Martin Löwer, Fulvia Vascotto, Jan Diekmann, Sebastian Boegel, Barbara Schroers, Arbel D. Tadmor, Özlem Türeci, Ugur Sahin. Mutant MHC class II epitopes drive therapeutic immune responses to cancer. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr A110.
Effects of Administration of Estradiol and Progesterone on Ovarian Stimulation Response, and In Vitro Developmental Competence of Oocytes in CIDR-Treated Calves (2014)

The present study was conducted to investigate the effects of administering estradiol (estradiol-17β, 2.5 mg) plus progesterone (P4, 50 mg) as a part of a controlled internal drug release (CIDR)-based superovulation protocol on ovarian follicles development, and oocyte recovery as well as on in vitro development in prepubertal calves after follicle stimulating hormone (FSH) stimulation. Calves in the treatment group exhibited significantly decreased (P < 0.05) numbers of both small and large antral follicles compared to the control group A and B (<3 mm in diameter [small], 3.4 versus 12.8, 11.6; > 7 mm in diameter [large], 0 versus 7.6, 7.2). The treated animals also exhibited an increased (P < 0.05) proportion of usable oocytes from the total oocytes recovered compared with those of the control group A and B (77% versus 50.2%, 47.8%). Moreover, the rate of cleavage and the percentage of blastocysts displayed an increased trend in the treatment group compared to controls A and B (59.2% versus 50.5%, 50.8%; 15% versus 12.4%, 11.6%, respectively). In conclusion, the application of estradiol-17β plus P4 at CIDR insertion prior to FSH stimulation affected ovarian follicles development and exerted a beneficial effect on the in vitro development of calf oocytes.