gebhart/patrepeval huggingface dataset:
Expression profiling of the γ-subunit isoforms of AMP-activated protein kinase suggests a major role for γ3 in white skeletal muscle (2004)

Expression patterns of the three isoforms of the regulatory gamma-subunit of AMP-activated protein kinase (AMPK) were determined in various tissues from adult humans, mice, and rats, as well as in human primary muscle cells. Real-time PCR-based quantification of mRNA showed similar expression patterns in the three species and a good correlation with protein expression in mice and rats. The gamma3-isoform appeared highly specific to skeletal muscle, whereas gamma1 and gamma2 showed broad tissue distributions. Moreover, the proportion of white, type IIb fibers in the mouse and rat muscle samples, as indicated by real-time PCR quantification of Atp1b2 mRNA, showed a strong positive correlation with the expression of gamma3. In samples of white skeletal muscle, gamma3 clearly appeared to be the most abundant gamma-isoform. Differentiation of human primary muscle cells from myoblasts into multinucleated myotubes was accompanied by upregulation of gamma3 mRNA expression, whereas levels of gamma1 and gamma2 remained largely unchanged. However, even in these cultured myotubes, gamma2 was the most highly expressed isoform, indicating a considerable difference compared with adult skeletal muscle. Immunoblot analysis of mouse gastrocnemius and quadriceps muscle extracts precipitated with a gamma3-specific antibody showed that gamma3 was exclusively associated with the alpha2- and beta2-subunit isoforms. The observation that the AMPKgamma3 isoform is expressed primarily in white skeletal muscle, in which it is the predominant gamma-isoform, strongly suggests that gamma3 has a key role in this tissue.
Time-hopping code characterization for multi-user interference mitigation in ultra wide band impulse radio (2005)

We consider an ultra wide band impulse radio multiple access scheme based on time-hopping code under a realistic multipath channel model. As a novelty, we provide a closed-form expression for the variance of the multiuser interference at the output of the rake receiver of the user of interest. That enables us to characterize the optimal time-hopping codes minimizing the multiuser interference variance. Finally we observe through simulations that minimizing the multiuser interference variance translates into better performance by significantly decreasing the error probability.
Variable transmission output coupler and tuner for ring laser systems (1985)

Operation and characteristics of a novel variable transmission output coupler for ring laser systems are reported. It also provides tuning of the laser wavelength with negligible deviation of the output beam. The transmission coefficient can be changed continuously from 0 to ≳80%. The tuning capability is from the ultraviolet to the near infrared and depends only on the material of the prisms. No optical coatings are used, and all beams enter and exit the coupler at Brewster angle with minimal loss.
Backprop-MPDM: Faster Risk-Aware Policy Evaluation Through Efficient Gradient Optimization (2018)

In Multi-Policy Decision-Making (MPDM), many computationally-expensive forward simulations are performed in order to predict the performance of a set of candidate policies. In risk-aware formulations of MPDM, only the worst outcomes affect the decision making process, and efficiently finding these influential outcomes becomes the core challenge. Recently, stochastic gradient optimization algorithms, using a heuristic function, were shown to be significantly superior to random sampling. In this paper, we show that accurate gradients can be computed - even through a complex forward simulation - using approaches similar to those in deep networks. We show that our proposed approach finds influential outcomes more reliably, and is faster than earlier methods, allowing us to evaluate more policies while simultaneously eliminating the need to design an easily-differentiable heuristic function. We demonstrate significant performance improvements in simulation as well as on a real robot platform navigating a highly dynamic environment.
Chip design of wireless power transfer using frequency variation (2017)

Wireless power transfer (WPT) and rapid charging system is important issue for many applications, particularly on mobile and biomedical devices. To perform high efficiency, first the system tracks maximum power transfer by sweeping the resonant frequency. The transmitter can use the best resonant frequency for wireless power transfer, and the receiver device charges a battery as fast. This can correct the frequency drift in manufacture, to promote the transferring efficiency. A voltage detection circuit of the receiver device is detecting charging state of the battery. Transmitter device checks whether a high-frequency transmission circuit transmits a fully-charged signal. The transmitter device shuts down the power and enters standby mode as the battery is fully charged. By maximum power tracking approach, higher wireless transmission efficiency can be achieved. The prototyping chips of transmitter and receiver had been implemented using TSMC 0.25 μm HV process. Experiments shown the max. efficient of WPT can achieve about 60 ~ 70%.
Holographic focusing elements for far-IR radiation (1990)

The authors present a method for designing and recording computer-generated holographic optical elements (HOES) for far-infrared radiation. The design method is based on minimising the mean-squared difference of the propagation vectors between the actual output wavefronts and the desired output wavefronts. This minimisation yields an analytic solution for the optimal grating vector. The design method is illustrated by recording a reflective off-axis focusing element with a laser scanner and lithographic techniques. The element is then tested, and the results indicate that diffraction-limited performance for a relatively large range of incidence angles can be obtained.
Clutter suppression using elevationinterferometry fused with space-time adaptive processing (2001)

Radar space-time adaptive processing (STAP) techniques characteristically offer adaptivity in Doppler and azimuth. This research extends STAP concepts by incorporating elevation adaptivity using a two channel vertical interferometer. Using multi-stage processing and measured airborne radar data, clutter suppression improvement of 15 dB is achieved.
Epitope-based vaccine against influenza (2007)

The currently available vaccines against influenza are viral strain specific and, hence, their efficacy is limited when the circulating strain is not the one included in them. We review herewith some of the more recently developed influenza vaccines and further describe our own data on the design of epitope-based broad-spectrum vaccine for human use. This vaccine is comprised of recombinant flagella that act as a carrier and adjuvant, expressing conserved epitopes of influenza proteins. These epitopes are common to the vast majority of influenza virus strains regardless of their antigenic drifts and shifts. The vaccine, activating both the humoral and cellular arms of the immune response, induces long-lasting protection against many strains of the influenza virus. Consequently, it is expected to protect against future strains as well.
On the Linkage among Strong Stratospheric Mass Circulation, Stratospheric Sudden Warming, and Cold Weather Events (2018)

Abstract It is well established that sudden stratospheric warming (SSW) events tend to be accompanied by continental-scale, surface cold-air outbreaks (CAOs) in midlatitudes in boreal winter. However, SSW events occur at most one to two times per winter, whereas CAOs occur three to seven times over each of the North American and Eurasian continents. Using the ERA-Interim dataset for 37 winters (November–March) from 1979 to 2016, we reveal that SSW events correspond to a large-amplitude or long-lasting subset of pulse-like, anomalously strong, stratospheric mass circulation events. The anomalously strong, stratospheric mass circulation events (referred to as PULSE events) occur more than nine times in an average winter. The “displacement” versus “split” types of SSWs tend to correspond to the “wavenumber 1” versus “wavenumber 2” types of PULSEs, though the relationship between split-type SSWs and wavenumber-2-type PULSEs is weaker. Like SSW events, PULSEs also have a close relationship with CAOs. The robust relationship with CAOs still holds for the PULSE events not accompanied by SSW events. Using PULSE events, we determine that more than 70% of CAOs in the 37 winters occur in the week before and after a PULSE event, with a false alarm rate of CAO occurrence of about 25.7%. SSW events, however, are associated with only about 5.7% of CAOs, with a false alarm rate of 21.7%. Therefore, the linkage between individual continental-scale CAOs and PULSE events represents a more generalized relationship between the stratospheric circulation anomalies and surface weather. PULSE signals should also be considered as a potentially useful stratospheric indicator of the occurrence of individual CAO events.
Abstract 10306: Identification and Characterization of Orally Bioavailable Small Molecule Protease Proprotein Convertase Subtilisin-like Kexin Type 9 Inhibitors <i>(Best of Basic Science Abstract)</i> (2015)

Intervention with drugs to reduce low density lipoprotein-cholesterol (LDL-C) has proven to decrease mortality and morbidity. Here, we report the development of small molecules that lower LDL-C by targeting the LDL-receptor (LDLR) degradation pathway, which is modulated by the protease proprotein convertase subtilisin-like kexin type 9 (PCSK9). PCSK9 is synthesized as a 72-kDa zymogen that undergoes autocatalytic processing between the prodomain and catalytic domain, an important step that is absolutely required for secretion of PCSK9 and its function. Secreted PCSK9 binds to the LDLR and enhances its degradation. We have identified inhibitors of the autocatalytic processing by virtual docking of millions of commercial compounds into the atomic structure of the PCSK9 active site. Top scoring compounds that showed the best fit in the active site were selected for screening. These compounds were tested for their ability to inhibit the autocatalytic processing/secretion of PCSK9. The most potent compounds exhibited a concentration-dependent inhibition of the PCSK9 processing/secretion with IC50’s in the nanomolar range. These compounds were tested for selectivity against other PCSK’s. The data demonstrated that these compounds were selective in that they inhibit PCSK9 processing/secretion without affecting the secretion of other related PCSK’s. Furthermore, these compounds exhibited a 5- to 10-fold LDLR upregulation at 1.6 μM in two recombinant cell-based assays as well as exhibited an increase in the fluorescently labeled DiI-LDL uptake in situ in the nanomolar range. In animal studies, intraperitoneal (IP) injection of these compounds administered alone resulted in more than 20% reduction in LDL-C in mice fed a high fat/high cholesterol diet and over 40% reduction in LDL-C if administered in combination with atorvastatin. In vivo pharmacokinetic (PK) and pharmacodynamic (PD) evaluation of these compounds demonstrated that they are orally efficacious, with one compound exhibiting 43% oral bioavailability. Thus, identifying small molecule, orally active PCSK9 modulators represents a significant advance and opportunityfor drug development.
Optical Free-Form Couplers for High-density Integrated Photonics (OFFCHIP): A Universal Optical Interface (2020)

Coupling of light between different photonic devices, for example on-chip waveguides, fibers, and free-space optical elements, is an essential function enabling integrated optical systems. Efficient optical coupling demands matching the optical mode profiles and effective indices between two devices, and often changing propagation direction of the light. To date, such coupling is pre-dominantly accomplished via direct butt coupling of two devices, or meticulously optimized diffraction gratings. In this article, we present a new coupling scheme based on microfabricated free-form optical reflectors. The free-form reflector simultaneously achieves the functions of light beam re-directing and shaping (for mode matching), and can be versatilely adapted for coupling between photonic chips, fibers, and free-space surface-incident devices. We show that this technology uniquely fulfills all key performance requirements for optical interfaces with exceptionally low coupling loss (0.2-0.3 dB per coupler), large bandwidth (over half an octave), high density (large 2-D coupler arrays), polarization diversity, and superior alignment tolerance commensurate with passive alignment techniques. Preliminary experimental validation demonstrates waveguide-to-fiber coupling with a low insertion loss (IL) of 0.9 dB. We foresee that the technology will become a promising solution to the chip-level photonic interconnection and packaging challenges plaguing integrated photonics.
Synthesis and two-dimensional electrophoretic analysis of mixed populations of circular and linear RNAs (1997)

Spontaneous cleavage of the less abundant form of tobacco ringspot virus satellite RNA is readily reversible. Capitalizing on earlier observations by Feldstein and Bruening that small 'mini-monomer' RNAs derived from this molecule and containing little more than covalently attached ribozyme and substrate cleavage products are able to efficiently circularize, we have constructed a series of self-circularizing RNAs of precisely known size. Mixtures of linear and circular RNAs synthesized in vitro and containing 225-1132 nt could be completely resolved using a novel two-dimensional denaturing polyacrylamide gel electrophoresis system. Similar analyses of a complex mixture of coconut cadang-cadang viroid RNAs revealed the presence of relatively large amounts of a previously undescribed 'fast-slow' heterodimeric RNA species in infected palms. Only a single DNA template is required to prepare each pair of circular and linear RNA markers.
Immunohistochemical Markers Distinguishing Cholangiocellular Carcinoma (CCC) from Pancreatic Ductal Adenocarcinoma (PDAC) Discovered by Proteomic Analysis of Microdissected Cells (2015)

Cholangiocellular carcinoma (CCC) and pancreatic ductal adenocarcinoma (PDAC) are two highly aggressive cancer types that arise from epithelial cells of the pancreatobiliary system. Owing to their histological and morphological similarity, differential diagnosis between CCC and metastasis of PDAC located in the liver frequently proves an unsolvable issue for pathologists. The detection of biomarkers with high specificity and sensitivity for the differentiation of these tumor types would therefore be a valuable tool. Here, we address this problem by comparing microdissected CCC and PDAC tumor cells from nine and eleven cancer patients, respectively, in a label-free proteomics approach. The novel biomarker candidates were subsequently verified by immunohistochemical staining of 73 CCC, 78 primary, and 18 metastatic PDAC tissue sections. In the proteome analysis, we found 180 proteins with a significantly differential expression between CCC and PDAC cells (p value < 0.05, absolute fold change > 2). Nine candidate proteins were chosen for an immunohistochemical verification out of which three showed very promising results. These were the annexins ANXA1, ANXA10, and ANXA13. For the correct classification of PDAC, ANXA1 showed a sensitivity of 84% and a specificity of 85% and ANXA10 a sensitivity of 90% at a specificity of 66%. ANXA13 was higher abundant in CCC. It presented a sensitivity of 84% at a specificity of 55%. In metastatic PDAC tissue ANXA1 and ANXA10 showed similar staining behavior as in the primary PDAC tumors (13/18 and 17/18 positive, respectively). ANXA13, however, presented positive staining in eight out of eighteen secondary PDAC tumors and was therefore not suitable for the differentiation of these from CCC. We conclude that ANXA1 and ANXA10 are promising biomarker candidates with high diagnostic values for the differential diagnosis of intrahepatic CCC and metastatic liver tumors deriving from PDAC.
Separation of EPA and DHA in fish oil by lipase‐catalyzed esterification with glycerol (2003)

Abstract The objective of this study was to investigate the use of lipases as catalysts for separating EPA and DHA in fish oil by kinetic resolution based on their FA selectivity. Esterification of FFA from various types of fish oils with glycerol by immobilized Rhizomucor miehei lipase under water‐deficient, solvent‐free conditions resulted in a highly efficient separation of EPA and DHA. Reactions were conducted at 40°C with a 10% dosage of the lipase preparation under vacuum to remove the coproduced water, thus rapidly shifting the reaction toward the products. The bulk of the FA, together with EPA, were converted into acylglycerols, whereas DHA remained in the residual FFA. As an example, when FFA from tuna oil comprising 5% EPA and 25% DHA were esterified with glycerol, 90% conversion into acylglycerols was obtained after 48 h. The residual FFA contained 78% DHA and only 3% EPA, in 79% DHA recovery. EPA recovery in the acylglycerol fraction was 91%. The type of fish oil and extent of conversion were highly important parameters in controlling the degree of concentration.
Induction of autophagy by drug-resistant esophageal cancer cells promotes their survival and recovery following treatment with chemotherapeutics. (2011)

We investigated the cell-death mechanisms induced in esophageal cancer cells in response to the chemotherapeutic drugs, 5-fluorouracil (5-FU) and cisplatin. Chemosensitive cell lines exhibited apoptosis whereas chemoresistant populations exhibited autophagy and a morphology resembling type II programmed cell death (PCD). Cell populations that respond with autophagy are more resistant and will recover following withdrawal of the chemotherapeutic agents. Specific inhibition of early autophagy induction with siRNA targeted to Beclin 1 and ATG7 significantly enhanced the effect of 5-FU and reduced the recovery of drug-treated cells. Pharmacological inhibitors of autophagy were evaluated for their ability to improve chemotherapeutic effect. The PtdIns 3-kinase inhibitor 3-methyladenine did not enhance the cytotoxicity of 5-FU. Disruption of lysosomal activity with bafilomycin A 1 or chloroquine caused extensive vesicular accumulation but did not improve chemotherapeutic effect. These observations suggest that an autophagic response to chemotherapy is a survival mechanism that promotes chemoresistance and recovery and that selective inhibition of autophagy regulators has the potential to improve chemotherapeutic regimes. Currently available indirect inhibitors of autophagy are, however, ineffective at modulating chemosensitivity in these esophageal cancer cell lines.
Direct Generation of Immortalized Erythroid Progenitor Cell Lines from Peripheral Blood Mononuclear Cells (2021)

Reliable human erythroid progenitor cell (EPC) lines that can differentiate to the later stages of erythropoiesis are important cellular models for studying molecular mechanisms of human erythropoiesis in normal and pathological conditions. Two immortalized erythroid progenitor cells (iEPCs), HUDEP-2 and BEL-A, generated from CD34<sup>+</sup> hematopoietic progenitors by the doxycycline (dox) inducible expression of human papillomavirus E6 and E7 (HEE) genes, are currently being used extensively to study transcriptional regulation of human erythropoiesis and identify novel therapeutic targets for red cell diseases. However, the generation of iEPCs from patients with red cell diseases is challenging as obtaining a sufficient number of CD34<sup>+</sup> cells require bone marrow aspiration or their mobilization to peripheral blood using drugs. This study established a protocol for culturing early-stage EPCs from peripheral blood (PB) and their immortalization by expressing HEE genes. We generated two iEPCs, PBiEPC-1 and PBiEPC-2, from the peripheral blood mononuclear cells (PBMNCs) of two healthy donors. These cell lines showed stable doubling times with the properties of erythroid progenitors. PBiEPC-1 showed robust terminal differentiation with high enucleation efficiency, and it could be successfully gene manipulated by gene knockdown and knockout strategies with high efficiencies without affecting its differentiation. This protocol is suitable for generating a bank of iEPCs from patients with rare red cell genetic disorders for studying disease mechanisms and drug discovery.
The value of Doppler information for multiple access and power control in LEO satellite systems (2002)

A key feature of LEO satellite systems is the fast changing geometry between the satellite and the ground based mobile terminals. This feature manifests itself in the significant and smooth "S" shaped variation of the Doppler time curve of the forward channel (from satellite to mobile terminal) frequency. We provide an overview of the processing of this Doppler information and its value to communication functions such as multiple access and power control at the terminal. The Doppler curve has a simple and accurate analytic approximation for circular orbit LEO satellites. Also, the Doppler curve parameters can be estimated at the mobile terminals from two Doppler and Doppler-rate measurements. In Doppler based multiple access (DBMA), traffic on the inbound channel (from mobile terminal to satellite) can be controlled by specifying a region of eligibility (ROE) in terms of the Doppler curve parameters. Only terminals located in the ROE are permitted to transmit. For one scheme of power control, termed Doppler based transmit power control (DBTPowC), terminals estimate their distance from the satellite using the Doppler-time curve and modify their transmitted power to compensate for the path loss differential to the satellite. In the second scheme, termed Doppler based transmit permission control (DBTPermC), the earth-station permits only those terminals to transmit whose distance from the satellite is within a specified range.
Flat-plate /vapor-chamber/ heat pipes (1975)

This paper discusses the design, fabrication and testing of heat pipes constructed in the form of flat-plate panels. The test panels were constructed of copper with methyl alcohol as the working fluid. Capillary grooves etched on the internal surfaces provided evaporation and condensation heat-transfer coefficients on the order of 1600 Btu/hr-sq ft-deg F. Two panels were launched on board a sounding rocket; the payload reached an altitude of 140 miles, and zero gravity was achieved for almost six minutes. The panel with working fluid inside demonstrated a heat input flux of 2.5 watts/sq cm, with only a 3 to 5 C temperature difference throughout the entire panel.
Coagulation dynamics of a blood sample by multiple scattering analysis (2011)

We report a new technique to measure coagulation dynamics on whole-blood samples. The method relies on the analysis of the speckle figure resulting from a whole-blood sample mixed with coagulation reagent and introduced in a thin chamber illuminated with a coherent light. A dynamic study of the speckle reveals a typical behavior due to coagulation. We compare our measured coagulation times to a reference method obtained in a medical laboratory.