gebhart/patrepeval huggingface dataset:
Abstract LB-008: Intracellular delivery of SOCS3 suppresses hepatocelluar carcinoma progression (2018)

Abstract Background Practical methods to deliver proteins systemically in animals have been hampered by poor tissue penetration and inefficient cytoplasmic localization of internalized proteins. Therefore, we have developed novel cell-penetrating peptides (CPPs), named advanced macromolecule transduction domains (aMTDs), to deliver therapeutically active macromolecule including proteins systemically in vivo. The suppressor of cytokine signaling 3 (SOCS3) is negative feedback regulator of JAK/STAT signaling that plays a key role in inflammation, fibrosis and carcinogenesis in the liver. Furthermore, hypermethylation of CpG islands in the SOCS3 promoter is correlated with its transcriptional silencing in some cancers, including hepatocellular carcinoma (HCC). Objective The present study utilized aMTD sequences to develop improved cell-permeable (iCP-) SOCS3 as a protein-based biotherapeutics against HCC. Methods Cell permeable SOCS3 proteins, with and without a 12-amino acid aMTD sequence, were expressed at high yields in E. coli. The proteins also contained a solubilization domain (SD) to enhance the solubility of the recombinant proteins in physiological buffers. Results iCP-SOCS3 fused to aMTD/SD suppressed cancer cell phenotypes (e.g., 84% inhibition of proliferation, arrested cell cycle progression, 86% inhibition of migration/invasion), apoptotic loss of cell viability (40 ~ 80% in HCC cell lines: Hep3B2.1-7, HepG2, Huh7 and SK-Hep1) and changes in apoptosis biomarker expression (e.g., Bcl-2 and cleaved caspase-3). In contrast, iCP-SOCS3 did not affect proliferation and apoptosis of non-cancer cells (Chang). In addition, iCP-SOCS3 also significantly suppressed the tumor growth (70% inhibition in Hep3B2.1-7; 67% inhibition in HepG2, respectively) in human-mouse xenograft models. The anti-tumor activity of iCP-SOCS3 was accompanied by changes in the expression of biomarkers linked to SOCS3 signaling including cyclin E, p21, Bax and VEGF. Furthermore, iCP-SOCS3 suppressed tumor growth equivalently to Cisplatin®, a well-established cytotoxic agent, but without observed toxicity or adverse effects. These results suggest that iCP-SOCS3 inhibits the growth of HCC tumor cells and tumor xenografts. Conclusions These results provide further evidence that SOCS3 can function as a tumor suppressor and intracellular delivery of iCP-SOCS3 may provide a novel protein therapy against HCC. Citation Format: Seulmee Shin, Kuysook Lee, Yunseo Hwang, Youngsil Choi, Daewoong Jo. Intracellular delivery of SOCS3 suppresses hepatocelluar carcinoma progression [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 LB-008.
Evaluation of Takeoff Performance Monitoring Algorithm in Large Jet Transport Operations (2006)

The issue of monitoring aircraft performance during takeoffhas been repeatedly considered in the last 50 years. This has been in response to concern over the low safety margins associated with this phase of flight and the lack of adequate objective performance-related information available to the crew during the takeoff maneuver. Two major difficulties, however, have to date inhibited the successful introduction of an instrument providing such information on the flight deck, namely, the provision of a reliable quantification of actual performance during the takeoff maneuver and the provision of an adequate display. This paper focuses on the former issue and evaluates the accuracy of a predictive performance monitoring algorithm developed at Cranfield University. The major hurdles that are associated with takeoff performance monitoring are briefly discussed, and the results of flight-based tests using data from large jet-transport operations presented. These results, which confirm a robustness that warrants the application of the algorithm in real-time performance monitoring, are also compared with those of an earlier flight test program using a twin turboprop aircraft.
A human observer study for evaluation and optimization of reconstruction methods in breast tomosynthesis using clinical cases (2011)

In breast tomosynthesis (BT) a number of 2D projection images are acquired from different angles along a limited arc. The imaged breast volume is reconstructed from the projection images, providing 3D information. The purpose of the study was to investigate and optimize different reconstruction methods for BT in terms of image quality using human observers viewing clinical cases. Sixty-six cases with suspected masses and calcifications were collected from 55 patients.
A dual purpose universal influenza vaccine candidate confers protective immunity against anthrax (2016)

Summary Preventive influenza vaccines must be reformulated annually because of antigen shift and drift of circulating influenza viral strains. However, seasonal vaccines do not always match the circulating strains, and there is the ever‐present threat that avian influenza viruses may adapt to humans. Hence, a universal influenza vaccine is needed to provide protective immunity against a broad range of influenza viruses. We designed an influenza antigen consisting of three tandem M2e repeats plus HA 2, in combination with a detoxified anthrax oedema toxin delivery system ( EF n plus PA ) to enhance immune responses. The EF n‐3×M2e‐ HA 2 plus PA vaccine formulation elicited robust, antigen‐specific, IgG responses; and was protective against heterologous influenza viral challenge when intranasally delivered to mice three times. Moreover, use of the detoxified anthrax toxin system as an adjuvant had the additional benefit of generating protective immunity against anthrax. Hence, this novel vaccine strategy could potentially address two major emerging public health and biodefence threats.
Interictal high‐frequency oscillations (HFOs) as predictors of high frequency and conventional seizure onset zones (2015)

We investigated the relationship between the interictal high-frequency oscillations (HFOs) and the seizure onset zones (SOZs) defined by the ictal HFOs or conventional frequency activity (CFA), and evaluated the usefulness of the interictal HFOs as spatial markers of the SOZs. We analysed seizures showing discrete HFOs at onset on intracranial EEGs acquired at ≥1000-Hz sampling rate in a training cohort of 10 patients with temporal and extratemporal epilepsy. We classified each ictal channel as: HFO+ (HFOs at onset with subsequent evolution), HFO- (HFOs at onset without evolution), CFA (1.6-70-Hz activity at onset with evolution), or non-ictal. We defined the SOZs as: hSOZ (HFO+ channels only), hfo+&-SOZ (HFO+ and HFO- channels), and cSOZ (CFA channels). Using automated methods, we detected the interictal HFOs and extracted five features: density, connectivity, peak frequency, log power, and amplitude. We created logistic regression models using these features, and tested their performance in a separate replication cohort of three patients. The models containing the five interictal HFO features reliably differentiated the channels located inside the SOZ from those outside in the training cohort (p<0.001), reaching the highest accuracy for the classification of hSOZ. Log power and connectivity had the highest odds ratios, both being higher for the channels inside the SOZ compared with those outside the SOZ. In the replication cohort of novel patients, the same models differentiated the HFO+ from HFO- channels, and predicted the extents of the hSOZ and hfo+&-SOZ (F1 measure >0.5) but not the cSOZ. Our study shows that the interictal HFOs are useful in defining the spatial extent of the SOZ, and predicting whether or not a given channel in a novel patient would be involved in the seizure. The findings support the existence of an abnormal network of tightly-linked ictal and interictal HFOs in patients with intractable epilepsy.
Thermally isolated deployable shield for spacecraft (1991)

A thermally isolated deployable shield for spacecraft is provided utilizing a plurality of lattice panels stowable generally against the craft and deployable to some fixed distance from the craft. The lattice panels are formed from replaceable shield panels affixed to lattice structures. The lattice panels generally encircle the craft providing 360 degree coverage therearound. Actuation means are provided from translating the shield radially outward from the craft and thermally isolating the shield from the craft. The lattice panels are relatively flexible, allowing the shield to deploy to variable diameters while retaining uniform curvature thereof. Restraining means are provided for holding the shield relatively tight in its stowed configuration. Close-out assemblies provide light sealing and protection of the annular spaces between the deployed shield and the crafts end structure.
Natural Expression of the Best-Match Search Godard Clock-Tone Algorithm for Blind Chromatic Dispersion Estimation in Digital Coherent Receivers (2012)

We reveal the natural expression of the "best-match search" Godard clock-tone algorithm for blind chromatic dispersion estimation. The complexity is reduced by more than 2 orders of magnitude compare to the conventional method.
Defining the Kv2.1–syntaxin molecular interaction identifies a first-in-class small molecule neuroprotectant (2019)

The neuronal cell death-promoting loss of cytoplasmic K<sup>+</sup> following injury is mediated by an increase in Kv2.1 potassium channels in the plasma membrane. This phenomenon relies on Kv2.1 binding to syntaxin 1A via 9 amino acids within the channel intrinsically disordered C terminus. Preventing this interaction with a cell and blood-brain barrier-permeant peptide is neuroprotective in an in vivo stroke model. Here a rational approach was applied to define the key molecular interactions between syntaxin and Kv2.1, some of which are shared with mammalian uncoordinated-18 (munc18). Armed with this information, we found a small molecule Kv2.1-syntaxin-binding inhibitor (cpd5) that improves cortical neuron survival by suppressing SNARE-dependent enhancement of Kv2.1-mediated currents following excitotoxic injury. We validated that cpd5 selectively displaces Kv2.1-syntaxin-binding peptides from syntaxin and, at higher concentrations, munc18, but without affecting either synaptic or neuronal intrinsic properties in brain tissue slices at neuroprotective concentrations. Collectively, our findings provide insight into the role of syntaxin in neuronal cell death and validate an important target for neuroprotection.
Development of Ionomer-membrane Water Processor (IWP) technology for water recovery from urine (2014)

The 44th International Conference on Environmental Systems was held in Tuscon, Arizona, USA on 13 July 2014 through 17 July 2014.
Configuration for an Optically Differential Reconfigurable Gate Array (2003)

An Optically Differential Reconfigurable Gate Array (ODRGA) has been proposed to enable dynamic reconfiguration of an arbitrary location on its gate array. The dynamic reconfiguration of an arbitrary location can be realized by calculating the difference between previous configuration data stored on a VLSI chip and subsequent optically-supplied configuration data. This paper presents an optical reconfiguration system for ODRGA VLSI chips using a liquid crystal television spatial light modulator and shows the experimental results of dynamic reconfiguration of an arbitrary location on an ODRGA VLSI chip.
Effect of lectin on nodulation by wild-type Bradyrhizobium japonicum and a nodulation-defective mutant (1986)

The nodulation characteristics of wild-type Bradyrhizobium japonicum USDA 110 and mutant strain HS111 were examined. Mutant strain HS111 exhibits a delayed-nodulation phenotype, a result of its inability to initiate successful nodulation promptly following inoculation of the soybean root. Previously, we showed that the defect in initiation of infection leading to subsequent nodulation which is found in HS111 can be phenotypically reversed by pretreatment with soybean root exudate or soybean seed lectin. This effect is not seen after pretreatment with root exudates and lectins obtained from other plant species. Treatment of strain HS111 with as little as 10 soybean seed lectin molecules per bacterium (3.3 X 10 (-12) M) resulted in enhancement of nodule formation. Pretreatment of wild-type B. japonicum USDA 110 with soybean root exudate or seed lectin increased nodule numbers twofold on 6-week-old plants. Wild-type strain USDA 110 cells inoculated at 10(4) cells per seedling exhibited a delay in initiation of infection leading to subsequent nodulation. Wild-type cells pretreated in soybean root exudates or seed lectin did not exhibit a delay in nodulation at this cell concentration. Mutant strain HS111 pretreated in seed lectin for 0 or 1 h, followed by washing with the hapten D-galactose to remove the lectin, exhibited a delay in initiation of nodulation. Phenotypic reversal of the delayed-nodulation phenotype exhibited by strain HS111 was seen if incubation was continued for an additional 71 h in plant nutrient solution following 1 h of lectin pretreatment. Reversal of the delayed-nodulation phenotype of HS111 through lectin pretreatment was prevented by chloramphenicol or rifampin.(ABSTRACT TRUNCATED AT 250 WORDS)
Real-time Raman spectroscopy for in vivo, online gastric cancer diagnosis during clinical endoscopic examination (2012)

Optical spectroscopic techniques including reflectance, fluorescence and Raman spectroscopy have shown promising potential for in vivo precancer and cancer diagnostics in a variety of organs. However, data-analysis has mostly been limited to post-processing and off-line algorithm development. In this work, we develop a fully automated on-line Raman spectral diagnostics framework integrated with a multimodal image-guided Raman technique for real-time in vivo cancer detection at endoscopy. A total of 2748 in vivo gastric tissue spectra (2465 normal and 283 cancer) were acquired from 305 patients recruited to construct a spectral database for diagnostic algorithms development. The novel diagnostic scheme developed implements on-line preprocessing, outlier detection based on principal component analysis statistics (i.e., Hotelling's T2 and Q-residuals) for tissue Raman spectra verification as well as for organ specific probabilistic diagnostics using different diagnostic algorithms. Free-running optical diagnosis and processing time of < 0.5 s can be achieved, which is critical to realizing real-time in vivo tissue diagnostics during clinical endoscopic examination. The optimized partial least squares-discriminant analysis (PLS-DA) models based on the randomly resampled training database (80% for learning and 20% for testing) provide the diagnostic accuracy of 85.6% [95% confidence interval (CI): 82.9% to 88.2%] [sensitivity of 80.5% (95% CI: 71.4% to 89.6%) and specificity of 86.2% (95% CI: 83.6% to 88.7%)] for the detection of gastric cancer. The PLS-DA algorithms are further applied prospectively on 10 gastric patients at gastroscopy, achieving the predictive accuracy of 80.0% (60/75) [sensitivity of 90.0% (27/30) and specificity of 73.3% (33/45)] for in vivo diagnosis of gastric cancer. The receiver operating characteristics curves further confirmed the efficacy of Raman endoscopy together with PLS-DA algorithms for in vivo prospective diagnosis of gastric cancer. This work successfully moves biomedical Raman spectroscopic technique into real-time, on-line clinical cancer diagnosis, especially in routine endoscopic diagnostic applications.
Detection of H5 Avian Influenza Viruses by Antigen-Capture Enzyme-Linked Immunosorbent Assay Using H5-Specific Monoclonal Antibody (2007)

The unprecedented spread of highly pathogenic avian influenza virus subtype H5N1 in Asia and Europe is threatening animals and public health systems. Effective diagnosis and control management are needed to control the disease. To this end, we developed a panel of monoclonal antibodies (MAbs) against the H5N1 avian influenza virus (AIV) and implemented an antigen-capture enzyme-linked immunosorbent assay (AC-ELISA) to detect the H5 viral antigen. Mice immunized with denatured hemagglutinin (HA) from A/goose/Guangdong/97 (H5N1) expressed in bacteria or immunized with concentrated H5N2 virus yielded a panel of hybridomas secreting MAbs specific for influenza virus HA. The reactivity of each MAb with several subtypes of influenza virus revealed that hybridomas 3D4 and 8B6 specifically recognized H5 HA. Therefore, purified antibodies from hybridomas 3D4 and 8B6, which secrete immunoglobulin G (IgG) and IgM, respectively, were used as the capture antibodies and pooled hyperimmune guinea pig serum IgG served as the detector antibody. The specificity of the optimized AC-ELISA was evaluated by using AIV subtypes H5 H3, H4, H7, H9, and H10. Specimens containing AIV subtype H5 subtype yielded a specific and strong signal above the background, whereas specimens containing all other subtypes yielded background signals. The detection limits of the AC-ELISA were 62.5 ng of bacterium-expressed H5N1 HA1 protein and 124, 62, and 31 50% tissue culture infective doses of influenza virus subtypes H5N1/PR8, H5N2, and H5N3, respectively. Reconstituted clinical samples consisting of H5 AIVs mixed with pharyngeal-tracheal mucus from healthy chickens also yielded positive signals in the AC-ELISA, and the results were confirmed by reverse transcription-PCR. The tracheal swab samples from H9N2-infected chickens did not give positive signals. Taken together, the newly developed MAb-based AC-ELISA offers an attractive alternative to other diagnostic approaches for the specific detection of H5 AIV.
Sub-volt switching of nanoscale voltage-controlled perpendicular magnetic tunnel junctions (2022)

Abstract Magnetic random-access memory (MRAM) based on voltage-controlled magnetic anisotropy in magnetic tunnel junctions (MTJs) is a promising candidate for high-performance computing applications, due to its lower power consumption, higher bit density, and the ability to reduce the access transistor size when compared to conventional current-controlled spin-transfer torque MRAM. The key to realizing these advantages is to have a low MTJ switching voltage. Here, we report a perpendicular MTJ structure with a high voltage-controlled magnetic anisotropy coefficient ~130 fJ/Vm and high tunnel magnetoresistance exceeding 150%. Owing to the high voltage-controlled magnetic anisotropy coefficient, we demonstrate sub-nanosecond precessional switching of nanoscale MTJs with diameters of 50 and 70 nm, using a voltage lower than 1 V. We also show scaling of this switching mechanism down to 30 nm MTJs, with voltages close to 2 V. The results pave the path for the future development and application of voltage-controlled MRAMs and spintronic devices in emerging computing systems.
Kinetic Analysis of tRNA-Directed Transcription Antitermination of the <i>Bacillus subtilis glyQS</i> Gene In Vitro (2004)

Binding of uncharged tRNA to the nascent transcript promotes readthrough of a leader region transcription termination signal in genes regulated by the T box transcription antitermination mechanism. Each gene in the T box family responds independently to its cognate tRNA, with specificity determined by base pairing of the tRNA to the leader at the anticodon and acceptor ends of the tRNA. tRNA binding stabilizes an antiterminator element in the transcript that sequesters sequences that participate in formation of the terminator helix. tRNA(Gly)-dependent antitermination of the Bacillus subtilis glyQS leader was previously demonstrated in a purified in vitro assay system. This assay system was used to investigate the kinetics of transcription through the glyQS leader and the effect of tRNA and transcription elongation factors NusA and NusG on transcriptional pausing and antitermination. Several pause sites, including a major site in the loop of stem III of the leader, were identified, and the effect of modulation of pausing on antitermination efficiency was analyzed. We found that addition of tRNA(Gly) can promote antitermination as long as the tRNA is added before the majority of the transcription complexes reach the termination site, and variations in pausing affect the requirements for timing of tRNA addition.
Low-power partial-parallel Chien search architecture with polynomial degree reduction (2016)

The Chien search for the error locator polynomial root computation in BCH and Reed-Solomon decoding accounts for a significant part of the overall decoder power consumption, especially r long codes over finite fields of high order. For serial Chien search, the power consumption is substantially lowered by a polynomial degree reduction (PDR) scheme. Every time a root is found, it is factored out of the error locator polynomial. Only the hardware units associated with the reduced-degree polynomial coefficients are active. However, this PDR scheme can not be directly extended to partial-parallel Chien search, which is needed in any systems to achieve high throughput. By analyzing the formulas of the evaluation values over finite field elements and available intermediate results of the Chien search, this paper proposes a partial-parallel Chien search architecture that reduces the error locator polynomial degree on the fly whenever a root is found without using long division. For a 122-error-correcting BCH code over GF(215), an 8-parallel Chien search using the proposed architecture achieves 32% power reduction over existing partial-parallel architectures for a typical case.
Selective Hydrogenation of Carbon Dioxide to Methanol on Cu–ZnO/SiO2 Catalysts Prepared by Alkoxide Method (1992)

Abstract Hydrogenation of CO2 to methanol was carried out on Cu–ZnO/SiO2 catalysts at 493 K and 3 MPa with a flow rate of 100 cm3 min−1 (H2/CO2 = 2). Higher selectivity ( &gt; 90%) was observed on the catalysts prepared by the alkoxide method than on a conventional catalyst prepared by the impregnation method. The selectivity was higher on the catalysts pretreated with H2 at a higher temperature, except at 873 K. The activity of the catalyst pretreated at 873 K was extremely low, probably because of alloy formation. The results of XRD, XPS, and EXAFS demonstrate that the active species for methanol formation is a large metallic Cu particle covered with a partially oxidized layer interacting with highly dispersed ZnO.
Image-Guided Radiation Therapy (2012)

The disclosed systems and methods for Image-Guided Radiation Therapy (IGRT), utilises an iterative approach which adjusts a treatment plan based on inter- or intra-fraction images to improve the accuracy of the radiation delivered during the overall treatment. The prescribed dose of radiotherapeutic radiation is mapped onto the patient's anatomy using an image acquired of the region, which is to be the target for radiotherapeutic radiation. Following beam-angle-optimisation, fluence optimisation and segmentation, the efficiency of delivery of each segment is determined using an objective function, and the segments ranked according to their efficiency. The plan proceeds with the choice of the most efficient segment (or segments) to be delivered first. When this radiation has been delivered, having been tracked to establish its distribution, this delivered distribution can be subtracted from the original prescribed dose and the process repeated so that the delivered radiation gradually converges on the original prescribed dose.