gebhart/patrepeval huggingface dataset:
Development of Cell-type specific anti-HIV gp120 aptamers for siRNA delivery (2011)

The global epidemic of infection by HIV has created an urgent need for new classes of antiretroviral agents. The potent ability of small interfering (si)RNAs to inhibit the expression of complementary RNA transcripts is being exploited as a new class of therapeutics for a variety of diseases including HIV. Many previous reports have shown that novel RNAi-based anti-HIV/AIDS therapeutic strategies have considerable promise; however, a key obstacle to the successful therapeutic application and clinical translation of siRNAs is efficient delivery. Particularly, considering the safety and efficacy of RNAi-based therapeutics, it is highly desirable to develop a targeted intracellular siRNA delivery approach to specific cell populations or tissues. The HIV-1 gp120 protein, a glycoprotein envelope on the surface of HIV-1, plays an important role in viral entry into CD4 cells. The interaction of gp120 and CD4 that triggers HIV-1 entry and initiates cell fusion has been validated as a clinically relevant anti-viral strategy for drug discovery. Herein, we firstly discuss the selection and identification of 2'-F modified anti-HIV gp120 RNA aptamers. Using a conventional nitrocellulose filter SELEX method, several new aptamers with nanomolar affinity were isolated from a 50 random nt RNA library. In order to successfully obtain bound species with higher affinity, the selection stringency is carefully controlled by adjusting the conditions. The selected aptamers can specifically bind and be rapidly internalized into cells expressing the HIV-1 envelope protein. Additionally, the aptamers alone can neutralize HIV-1 infectivity. Based upon the best aptamer A-1, we also create a novel dual inhibitory function anti-gp120 aptamer-siRNA chimera in which both the aptamer and the siRNA portions have potent anti-HIV activities. Further, we utilize the gp120 aptamer-siRNA chimeras for cell-type specific delivery of the siRNA into HIV-1 infected cells. This dual function chimera shows considerable potential for combining various nucleic acid therapeutic agents (aptamer and siRNA) in suppressing HIV-1 infection, making the aptamer-siRNA chimeras attractive therapeutic candidates for patients failing highly active antiretroviral therapy (HAART).
Evidence for persistent activation of cardiac slow channels in low-calcium solutions (1982)

Action potentials were recorded from frog ventricular strips superfused with calcium-free solutions. Very long action potentials (3-60 s) were induced by chelating residual calcium with 1-5 mM ethyleneglycol-bis(beta-aminoethylether)-N,N'-tetraacetic acid (EGTA). The kinetics of changes in action potential duration suggest that calcium influences action potential duration at an intracellular site. In low-calcium solutions isoproterenol was found to lengthen action potentials. The lengthening effect of isoproterenol became progressively greater as [Ca2+] was reduced by elevating [EGTA]. In the presence of 2 mM EGTA, 0.1 microM isoproterenol increased action potential duration from 4.3 +/- 0.4 to 43 +/- 14 s. Verapamil produced a greater than 90% reduction in the duration of very long action potentials (60 s) induced by EGTA, isoproterenol, or both. After rapid or prolonged depolarizations in low-calcium solutions the last 10-30 mV of repolarization took 10-15 s. We speculate that this slow phase of repolarization may be a manifestation of persistent slow channel activation. The data suggest that in low-calcium solutions slow channels can remain activated for many seconds.
Shear wave elastography in obstetrics: Quantification of cervix elasticity and uterine contraction (2011)

Supersonic Shear Imaging (SSI) is a real-time and quantitative imaging technique that has been proved efficient for tissue elasticity investigation. Very little is known about the physiology of cervix and uterus and SSI could be an efficient tool for a deeper understanding of uterine mechanisms. This could considerably help prevention of premature birth, which consequences on neonate morbidity and pathologies are tremendous. The purpose of this paper is to investigate in vivo the elasticity of the cervix and uterus during pregnancy using SSI with three objectives: the quantification of cervix elasticity, the follow up of uterine elasticity during contraction, and the investigation of uterine anisotropy. In this study, remote palpation using radiation force and ultrafast imaging sequences were adapted on the Aixplorer for the investigation of uterine contraction, as well as for uterine anisotropy estimation. Cervix elasticity was quantified in 20 gravid women using a 7 MHz endocavitary probe. Uterus elasticity was quantified externally on 5 patients, through the abdomen, using an 8 MHz linear probe. Changes of elasticity were tracked in real time during uterus contraction. Shear wave tractography (imaging of fiber orientation) was performed with the same probe by assessing shear wave speed variations with respect to probe angle. This allowed the investigation of uterine anisotropy at different depths. Elasticity values during contraction were correlated to uterine pressure data, which is the gold standard for contraction monitoring. Finally, uterine fiber orientation was observed at different depths.
“Undiagnosing” multiple sclerosis (2012)

The misdiagnosis of MS is common and has significant consequences for patient care and health care system costs. Caring for a patient with a misdiagnosis of MS is challenging, and at times honest disclosure of a misdiagnosis represents an important ethical concern for neurologists. More data are needed on this patient population to improve diagnostic acumen and the care of these patients.
Functional Characterization of BAX 855, a PEGylated Recombinant FVIII (2011)

Abstract Abstract 4359 Baxter and Nektar have developed BAX 855, a longer-acting PEGylated form of Baxter’s recombinant FVIII (ADVATE process) using stable PEG technology from Nektar. BAX 855 was functionally characterized in vitro and its features were compared with those of the unmodified parent rFVIII. The overall hemostatic potency of BAX 855 was assessed using a thrombin generation assay. Human FVIII-deficient plasma containing less than 1% of FVIII was supplemented with different concentrations of BAX 855 and unmodified rFVIII and coagulation was triggered by adding a small amount of recombinant human tissue factor complexed with phospholipid (PL) micelles to the plasma. Similar to unmodified rFVIII, BAX 855 corrected the impaired thrombin generation of the FVIII deficient plasma in a concentration-dependent manner. The role of FVIII within the tenase complex was determined by measuring the kinetics of FXa generation with a FIXa-cofactor activity assay, using either untreated or thrombin activated BAX 855. Comparison of the kinetic parameters and the maximum FXa generated revealed similar characteristics between BAX 855 and unmodified rFVIII. A similar approach revealed that BAX 855 fully retained its ability to be activated and inactivated by thrombin. The susceptibility of BAX 855 to activated protein C (APC) inactivation was also similar for BAX 855 and unmodified rFVIII. The binding affinities for VWF were similar for unmodified rFVIII (KD 0.6 nM) and BAX 855 (KD 0.8 nM) and the binding capacity of BAX 855 was also only slightly reduced. In contrast, the binding capacity of BAX 855 to the low-density lipoprotein-receptor-related protein (LRP) clearance receptor was 55% less than that of the unmodified rFVIII. In summary, the functional properties of BAX 855 were fully retained, indicating that PEGylation did not have an impact on the functional properties of rFVIII. Disclosures: Schrenk: Baxter Innovations GmbH: Employment. Varadi:Baxter Innovations GmbH: Employment. Gritsch:Baxter Innovations GmbH: Employment. Rottensteiner:Baxter Innovations GmbH: Employment. Ehrlich:Baxter Innovations GmbH: Employment. Scheiflinger:Baxter Innovations GmbH: Employment. Turecek:Baxter Innovations GmbH: Employment.
Channel estimation in UWB channels using compressed sensing (2014)

We consider sub-Nyquist sampling and Compressed Sensing (CS) for channel estimation in Ultra Wideband (UWB) communication systems, by exploiting the sparse nature of the channel impulse response. Receiver hardware schemes are presented that directly sample the analog channel output at rates far below Nyquist and allow access to a predefined subset of channel Fourier coefficients. CS methods are then applied to these coefficients in order to estimate the unknown channel. Simulations on Channel Model (CM) 1 of the IEEE 802.15.4a standard show that estimation is possible from low rate samples with little performance degradation paving the way to sub-Nyquist UWB channel sounding.
Probabilistic Atlases to Enforce Topological Constraints (2020)

Probabilistic atlases (PAs) have long been used in standard segmentation approaches and, more recently, in conjunction with Convolutional Neural Networks (CNNs). However, their use has been restricted to relatively standardized structures such as the brain or heart which have limited or predictable range of deformations. Here we propose an encoding-decoding CNN architecture that can exploit rough atlases that encode only the topology of the target structures that can appear in any pose and have arbitrarily complex shapes to improve the segmentation results. It relies on the output of the encoder to compute both the pose parameters used to deform the atlas and the segmentation mask itself, which makes it effective and end-to-end trainable.
Sub-wavelength nano-electrode structures to improve the performance of terahertz photomixers (2016)

By utilizing the sub-wavelength metallic structures in the active region of the photomixer, the confinement and concentration of electric field from optical pump lasers on a photoconductive substrate can be efficiently achieved as these sub-wavelength metallic structures are exhibiting the nano-antenna effect over a high index photoconductive substrate. Designing the sub-wavelength metallic structures, branch-like nano-electrodes structures, a new strategy to improve carrier capture was developed in which more carrier collection points occupy across the area of the pumping laser source. These branch-like nano-electrode structures were found to improve THz emission intensity of a photomixer by approximately one order of magnitude and optical-to-THz conversion efficiency by 10 times higher than that of photomixer with one row of nano-electrodes separated by the same 100nm gap. The enhancement is attributed to a more efficient collection of generated carriers due to a more intense electric field under the branch-like nano-electrodes structures. This is coupled with increased effective areas where strong tip-to-tip THz field enhancements were observed. The more efficient THz photomixer will greatly benefit the development of continuous wave THz imaging and spectroscopy system.
Radar image processing with clusters of computers (2002)

Some radar image processing algorithms such as shape-from-shading are particularly compute-intensive and time consuming. If, in addition, a data set to be processed is large, then it may make sense to perform the processing of images on multiple workstations or parallel processing systems. We have implemented shape-from-shading, stereo matching, resampling, gridding and visualization of terrain models in such a manner that they execute either on parallel machines or on clusters of workstations. We were motivated by the large image data set from NASA's Magellan mission to planet Venus, but received additional inspiration from the European Union's Center for Earth Observation program (CEO) and Austria's MISSION initiative for distributed processing of remote sensing images on remote workstations, using publicly accessible algorithms. We have developed a multi-processor approach that we denote as CDIP for Concurrent and Distributed Image Processing. The speedup for image processing tasks increases nearly linearly with the number of processors, be they on a parallel machine or arranged in a cluster of distributed workstations. Our approach adds benefits for users of complex image processing algorithms: the efforts for code porting and code maintenance are reduced and the necessity for specialized parallel processing hardware is eliminated.
Polyvalent Interactions in Unnatural Recognition Processes (2004)

The synthesis of two cluster compounds, one containing six secondary dialkylammonium ion centers and the other possessing six benzo-m-phenylene[25]crown-8 (BMP25C8) macrocycles, both appended to hexakis(thiophenyl)benzene cores, is described. The binding of these clusters with complementary mono- and divalent ligands is investigated with NMR spectroscopy to probe polyvalency in these unnatural recognition systems. The ability of the two different families of clusters to bind complementary monovalent ligands is compared with that of the monovalent receptor pair, namely the dibenzylammonium ion and BMP25C8. This comparison is made possible by determining an average association constant (K(AVE)) for the binding of each recognition site on the cluster with the corresponding monovalent ligand. We have found that the clustering of recognition sites together in one molecule is detrimental to their individual abilities to bind monovalent ligands. In the case of the polyvalent interaction between the hexakisBMP25C8 cluster and divalent dialkylammonium ions, an association constant, K(POLY), was calculated from the value of K(AVE) determined for the complexation of the individual component recognition sites. This polyvalent interaction is significantly stronger than that associated with the averaged monovalent interactions.
Node Clustering (2008)

This chapter contains sections titled: Introduction Node Clustering Algorithms Node Clustering Algorithms for Wireless Sensor Networks Summary and Future Directions References
Response of bacterial soil communities to a small diesel-spill at the Argentine station Carlini on King George Island (Antarctica) (2012)

In October 2009, a diesel pipe connecting two storage tanks at Carlini station (Antarctica) cracked, leaking fuel and contaminating the surrounding soil which, at that time, was covered by a thick snow layer. Three months later, the snow began to melt and the diesel moved with runoff water from the fuel tanks through the residential and laboratory area, towards the Potter Cove. Five months after the spill, soil samples were taken at 10 sites close to, as well as further away, from the spill site. Marine sediment samples were also taken from Potter Cove basin, with the aim to monitor the bacterial communities in relation to the presence of hydrocarbons. One year later, in January 2011, sampling was repeated at approximately the same sites and additional sites that could not be sampled before due to the snow cover. At this time, neither smell nor visual appearance of diesel residues were noticeable on the surface or at 30 cm-depth soil, and measured total petroleum hydrocarbons decreased in the most affected sites, except in front of the pool containing the tanks where the spill originated. At this site, an underground leaking pipe had caused a more recent small event of acute contamination that is being used as a proxy to better understand the effect of the main spill on bacterial communities at Carlini station area. The impact of the spill on soils and sediments was monitored by total carbon and nitrogen content, C/N ratio, presence of hydrocarbons and differences in bacterial community structure. DGGE based on the 16S rRNA gene was used to identify the main changes in community composition over the 14-months period. Most samples showed a quite high diversity few months after the spill, as well as one year later, and only marginal changes in the taxonomic structure were observed during the study period. However, the bacterial community composition in the samples taken near the cracked underground pipe, which experienced a larger input of diesel and less time between impact and sampling, showed clear changes. The DGGE gels exhibited a reduction in diversity and an enrichment of specific bacterial groups. Clone libraries revealed enrichment in Actinobacteria and one Betaproteobacterium closely related to Polaromonas napthalenivorans, indicating an actively growing hydrocarbon-degrading community. After one more year (January 2012), there was no visual presence or smell of hydrocarbons at this site, the same that had been observed after the main spill. Our results show that in Potter peninsula the bacterial communities undergo a fast shift to lower diversity and higher dominance when a sudden spill occurs on a soil with certain history of exposure to hydrocarbons. The unusually fast disappearance of the spilled diesel in such a cold habitat is favoured by the kind of diesel used (containing mostly light aliphatic hydrocarbons), the sandy texture of soil, snowmelt runoff, summer rains and a well adapted microbiota, with a promising oil-bioremediation potential
Antagonistic interactions between odorants alter human odor perception (2023)

The olfactory system uses hundreds of odorant receptors (ORs), the largest group of the G-protein-coupled receptor (GPCR) superfamily, to detect a vast array of odorants. Each OR is activated by specific odorous ligands, and like other GPCRs, antagonism can block activation of ORs. Recent studies suggest that odorant antagonisms in mixtures influence olfactory neuron activities, but it is unclear how this affects perception of odor mixtures. In this study, we identified a set of human ORs activated by methanethiol and hydrogen sulfide, two potent volatile sulfur malodors, through large-scale heterologous expression. Screening odorants that block OR activation in heterologous cells identified a set of antagonists, including β-ionone. Sensory evaluation in humans revealed that β-ionone reduced the odor intensity and unpleasantness of methanethiol. Additionally, suppression was not observed when methanethiol and β-ionone were introduced simultaneously to different nostrils. Our study supports the hypothesis that odor sensation is altered through antagonistic interactions at the OR level.
Mild Method for the Conversion of Amides to Thioamides (2003)

Aqueous ammonium sulfide was found to be an ideal substitute for hydrogen sulfide for the thiolysis of activated amides. High yields of the corresponding thioamides were obtained for a broad range of substrates, using two different procedures that are both operationally simple and inexpensive, as well as amenable to large-scale preparation. Preliminary results indicate that aqueous ammonium sulfide may also replace hydrogen sulfide in the synthesis of thionoesters from amides.
Integrated Module and Gene-Specific Regulatory Inference Implicates Upstream Signaling Networks (2013)

Regulatory networks that control gene expression are important in diverse biological contexts including stress response and development. Each gene's regulatory program is determined by module-level regulation (e.g. co-regulation via the same signaling system), as well as gene-specific determinants that can fine-tune expression. We present a novel approach, Modular regulatory network learning with per gene information (MERLIN), that infers regulatory programs for individual genes while probabilistically constraining these programs to reveal module-level organization of regulatory networks. Using edge-, regulator- and module-based comparisons of simulated networks of known ground truth, we find MERLIN reconstructs regulatory programs of individual genes as well or better than existing approaches of network reconstruction, while additionally identifying modular organization of the regulatory networks. We use MERLIN to dissect global transcriptional behavior in two biological contexts: yeast stress response and human embryonic stem cell differentiation. Regulatory modules inferred by MERLIN capture co-regulatory relationships between signaling proteins and downstream transcription factors thereby revealing the upstream signaling systems controlling transcriptional responses. The inferred networks are enriched for regulators with genetic or physical interactions, supporting the inference, and identify modules of functionally related genes bound by the same transcriptional regulators. Our method combines the strengths of per-gene and per-module methods to reveal new insights into transcriptional regulation in stress and development.
Nonlinearity-Tolerant Four-Dimensional 2A8PSK Family for 5–7 Bits/Symbol Spectral Efficiency (2017)

We describe in detail the recently proposed four-dimensional modulation format family based on 2-ary amplitude 8-ary phase-shift keying (2A8PSK), supporting spectral efficiencies of 5, 6, and 7 bits/symbol. These formats nicely fill the spectral efficiency gap between the dual-polarization (DP) quadrature PSK (QPSK) and DP 16-ary quadrature-amplitude modulation (16QAM), with excellent linear and nonlinear performance. Since these modulation formats just use different parity bit expressions in the same constellation, similar digital signal processing can be seamlessly used for different spectral efficiency. A series of nonlinear transmission simulation results shows that this modulation format family outperforms the conventional modulation formats at the corresponding spectral efficiency. We also investigate the adaptive equalizer for these modulation formats.
Optically Driven Ultrawideband Phased Array With an Optical Interleaving Feed Network (2014)

A novel optically driven ultrawideband phased array is presented. In the array, two coherent optical signals mixing at photodiodes produce RF signals that are tunable over an ultra-wide bandwidth. An optical interleaving feed network is used to drive the array, which is capable of mitigating phase drift due to acoustic vibration and maintaining phase fidelity. In addition, excess noises in the system are analyzed and found to be responsible for spurious beams. The excess noise can be suppressed by optimizing polarization states of optical signals in polarization-maintaining (PM) fibers. Accordingly, the sensitivity can be significantly increased. In the end, the concept is proven by demonstrating experimental results from a 1 × 2 array consisting of two wideband Vivaldi antennas.
Revisiting topology optimization with buckling constraints (2018)

We review some features of topology optimization with a lower bound on the critical load factor, as computed by linearized buckling analysis. The change of the optimized design, the competition between stiffness and stability requirements and the activation of several buckling modes, depending on the value of such lower bound, are studied. We also discuss some specific issues which are of particular interest for this problem, as the use of non-conforming finite elements for the analysis, the use of inconsistent sensitivities in the optimization and the replacement of the single eigenvalue constraints with an aggregated measure. We discuss the influence of these practices on the optimization result, giving some recommendations.
Beyond 110 GHz InP-HEMT Based Mixer Module Using Flip-Chip Assembly for Precise Spectrum Analysis (2015)

A wide-bandwidth fundamental mixer operating at a frequency above 110GHz for precise spectrum analysis was developed using the InP HEMT technology. A single-ended resistive mixer was adopted for the mixer circuit. An IF amplifier and LO buffer amplifier were also developed and integrated into the mixer chip. As for packaging into a metal block module, a flip-chip bonding technique was introduced. Compared to face-up mounting with wire connections, flip-chip bonding exhibited good frequency flatness in signal loss. The mixer module with a built-in IF amplifier achieved a conversion gain of 5dB at an RF frequency of 135GHz and a 3-dB bandwidth of 35GHz. The mixer module with an LO buffer amplifier operated well even at an LO power of -20dBm.