gebhart/patrepeval huggingface dataset:
Delivery of a heterologous antigen by a registeredSalmonellavaccine (STM1) (2003)

STM1 is an aro A(-) attenuated mutant of Salmonella enterica serovar Typhimurium, and is a well-characterised vaccine strain available to the livestock industry for the prevention of salmonellosis in chickens. This strain has potential for heterologous antigen delivery, and here we show that the strain can be used to deliver a model antigen, ovalbumin, to immune cells in vitro and in vivo. Two plasmid constructs expressing the ovalbumin gene were utilised, one of which uses a prokaryotic promoter and the other the CMV promoter (DNA vaccine). In vitro, STM1 carrying ovalbumin-encoding plasmids was able to invade dendritic cells and stimulate a CD8(+) cell line specific for the dominant ovalbumin epitope, SIINFEKL. In vivo, spleen cells were responsive to SIINFEKL after vaccination of mice with ovalbumin-encoding plasmids in STM1, and finally, humoral responses, including IgA, were induced after vaccination.
Design of Many-Core Big Little μBrain for Energy-Efficient Embedded Neuromorphic Computing (2021)

As spiking-based deep learning inference applications are increasing in embedded systems, these systems tend to integrate neuromorphic accelerators such as $μ$Brain to improve energy efficiency. We propose a $μ$Brain-based scalable many-core neuromorphic hardware design to accelerate the computations of spiking deep convolutional neural networks (SDCNNs). To increase energy efficiency, cores are designed to be heterogeneous in terms of their neuron and synapse capacity (big cores have higher capacity than the little ones), and they are interconnected using a parallel segmented bus interconnect, which leads to lower latency and energy compared to a traditional mesh-based Network-on-Chip (NoC). We propose a system software framework called SentryOS to map SDCNN inference applications to the proposed design. SentryOS consists of a compiler and a run-time manager. The compiler compiles an SDCNN application into subnetworks by exploiting the internal architecture of big and little $μ$Brain cores. The run-time manager schedules these sub-networks onto cores and pipeline their execution to improve throughput. We evaluate the proposed big little many-core neuromorphic design and the system software framework with five commonlyused SDCNN inference applications and show that the proposed solution reduces energy (between 37% and 98%), reduces latency (between 9% and 25%), and increases application throughput (between 20% and 36%). We also show that SentryOS can be easily extended for other spiking neuromorphic accelerators.
Secondary Structure in the Core of Amyloid Fibrils Formed from Human β [subscript 2] m and Its Truncated Variant ΔN6 (2014)

Amyloid fibrils formed from initially soluble proteins with diverse sequences are associated with an array of human diseases. In the human disorder, dialysis-related amyloidosis (DRA), fibrils contain two major constituents, full-length human β[subscript 2]-microglobulin (hβ2m) and a truncation variant, ΔN6 which lacks the N-terminal six amino acids. These fibrils are assembled from initially natively folded proteins with an all antiparallel β-stranded structure. Here, backbone conformations of wild-type hβ[subscript 2]m and ΔN6 in their amyloid forms have been determined using a combination of dilute isotopic labeling strategies and multidimensional magic angle spinning (MAS) NMR techniques at high magnetic fields, providing valuable structural information at the atomic-level about the fibril architecture. The secondary structures of both fibril types, determined by the assignment of ~80% of the backbone resonances of these 100- and 94-residue proteins, respectively, reveal substantial backbone rearrangement compared with the location of β-strands in their native immunoglobulin folds. The identification of seven β-strands in hβ[subscript 2]m fibrils indicates that approximately 70 residues are in a β-strand conformation in the fibril core. By contrast, nine β-strands comprise the fibrils formed from ΔN6, indicating a more extensive core. The precise location and length of β-strands in the two fibril forms also differ. The results indicate fibrils of ΔN6 and hβ[subscript 2]m have an extensive core architecture involving the majority of residues in the polypeptide sequence. The common elements of the backbone structure of the two proteins likely facilitates their ability to copolymerize during amyloid fibril assembly.
Expression of nonmuscle myosin heavy and light chains in smooth muscle (1989)

We have compiled evidence that nonmuscle isoforms of both myosin heavy chain (NM MHC) and myosin regulatory light chain (NM LC20) are present in fully differentiated smooth muscles (SM). In swine carotid media sodium dodecyl sulfate-gel electrophoresis separated three MHC bands. The upper two bands were identified by immunoblotting as SM-specific isoforms. The lowest MHC band amounted to 14 +/- 2% of the total MHC and was electrophoretically and antigenically similar to platelet MHC. Two-dimensional gel electrophoresis of swine carotid media extracts resolved multiple LC20 species, including phosphorylated and "satellite" forms. Mass spectrometric analysis of tryptic peptides from blots of these gels demonstrated two LC20 isoforms. The measured peptide masses correspond with two published cDNA sequences proposed to represent SM and NM LC20 isoforms. These sequences readily explain the electrophoretic behavior of the isoforms. The minor isoform's abundance (16 +/- 3%, corresponding to NM MHC), antigenic properties, and pattern of expression in tissue culture all confirm that this is a NM LC20 isoform. The localization and functional significance of NM myosin in smooth muscle is unknown.
Structure−Activity Relationship of (1-Aryl-2-piperazinylethyl)piperazines:  Antagonists for the AGRP/Melanocortin Receptor Binding (2002)

Agouti-related protein (AGRP) is an endogenous antagonist of the melanocortin action.(1) In the hypothalamus, melanocortin peptide agonists act as satiety-inducing factors that mediate their action through the melanocortin-4 receptor (MC4R) whereas AGRP is an opposing orexigenic agent. Novel inhibitors of the AGRP/MC4 binding based on (piperazinylethyl)piperazines were prepared, and their structure-activity relationship was established.
Materials and inks for full color PLED-displays (2003)

This paper reports on the synthesis of polyspiro molecules that give red, green and blue electroluminescence. Based on the outstanding performance and stability of spiro-materials in small molecule devices (organic LEDs), the spiro-concept was adopted for polymers as well. This paper summarizes the progress in synthesis and performance that has been made for RGB polyspiros.
Engineering Diplomacy: How AI and Human Augmentation Could Remake the Art of Foreign Relations (2022)

Through collaborations among diplomats, scientists, and engineers, authors envision artificial intelligence (AI) paired with emerging human augmentation technologies significantly improving the bandwidth, speed, and optimality of diplomacy.
Randomly iterated search and statistical competency as powerful inversion tools for deformation source modeling: Application to volcano interferometric synthetic aperture radar data (2009)

Modern geodetic techniques provide valuable and near real‐time observations of volcanic activity. Characterizing the source of deformation based on these observations has become of major importance in related monitoring efforts. We investigate two random search approaches, simulated annealing (SA) and genetic algorithm (GA), and utilize them in an iterated manner. The iterated approach helps to prevent GA in general and SA in particular from getting trapped in local minima, and it also increases redundancy for exploring the search space. We apply a statistical competency test for estimating the confidence interval of the inversion source parameters, considering their internal interaction through the model, the effect of the model deficiency, and the observational error. Here, we present and test this new randomly iterated search and statistical competency (RISC) optimization method together with GA and SA for the modeling of data associated with volcanic deformations. Following synthetic and sensitivity tests, we apply the improved inversion techniques to two episodes of activity in the Campi Flegrei volcanic region in Italy, observed by the interferometric synthetic aperture radar technique. Inversion of these data allows derivation of deformation source parameters and their associated quality so that we can compare the two inversion methods. The RISC approach was found to be an efficient method in terms of computation time and search results and may be applied to other optimization problems in volcanic and tectonic environments.
ChemInform Abstract: The Synthesis of 5′‐O‐DMT‐Thymidine‐3′‐O‐(2‐thio‐1,3,2‐ oxaselenaphospholane) and Its Possible Application in Stereocontrolled Synthesis of Oligo(nucleoside phosphorothioate)s. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Polymer–Graphene Oxide Quadlayer Thin-Film Assemblies with Improved Gas Barrier (2015)

Layer-by-layer assembly was used to create quadlayers (QLs) of chitosan (CH), poly(acrylic acid) (PAA), CH, and graphene oxide (GO). Electron microscopy confirmed GO coverage over the film and a highly ordered nanobrick wall structure. By varying pH deviation between CH and PAA, a thick and interdiffused polymer matrix was created because of the altered chain conformation. A 5 CH (pH 5.5)/PAA (pH 3)/CH (pH 5.5)/GO QL assembly (48 nm) exhibits very low oxygen permeability (3.9 × 10(-20) cm(3) cm cm(-2) Pa(-1) s(-1)) that matches SiOx barrier coatings. In an effort to maintain barrier performance under high humidity, GO was thermally reduced to increase hydrophobicity of the film. This reduction step increased H2/CO2 selectivity of a 5 QL film from 5 to 215, exceeding Robeson's upper bound limit. This unique water-based multilayer nanocoating is very promising for a variety of gas purification and packaging applications.
Self-organized nanostructure formation during femtosecond-laser inscription of fiber Bragg gratings (2017)

Periodic planar nanostructures are found in Type II-IR Bragg gratings produced in SMF-28 fiber by side-illuminating it with infrared femtosecond-laser pulses through a phase mask. The planar nanostructures are aligned perpendicular to the laser polarization, as demonstrated using scanning electron microscopy analysis of cleaved fiber samples. Dark field optical microscopy is employed for real-time monitoring of structural changes occurring inside the fiber during the inscription process.
Pilot Designs for Consistent Frequency Offset Estimation in OFDM Systems (2006)

This paper presents pilot designs for consistent frequency offset estimation of OFDM systems in frequency-selective fading channels. We describe two design approaches, namely consistency in the probabilistic sense and absolute consistency. Existing preambles and pilot designs in the literature do not guarantee the absolute consistency. We derive general criteria for both approaches, present sufficient conditions on the pilot structures, and derive simple pilot designs satisfying these conditions. Absolute consistency should not be compromised in emergency-related or other critical communication scenarios and our proposed consistent pilot designs address this need.
Pulmonary emboli followed total hip arthroplasty (1979)

We compared twenty-five total hip-arthroplasty patients with twenty-five patients who underwent other operations on the lower extremity, with regard to evidence of pulmonary embolism as determined preoperatively and postoperatively from lung perfusion scans, ventilation scans, and pulmonary angiography. Blood gases and serum enzymes also were studied. The over-all incidence of pulmonary embolism was 6 per cent, despite the absence of clinical evidence of that complication. Abnormalities in scans and blood studies were common preoperatively, so that the diagnosis often depended on the detection of additional abnormalities postoperatively.
Pathologic Outcomes in Men with Low-risk Prostate Cancer Who Are Potential Candidates for Contemporary, Active Surveillance Protocols (2015)

The purpose of this study was to determine whether contemporary active surveillance (AS) protocols could sufficiently discriminate significant from indolent tumors in men with low-risk prostate cancer. We retrospectively analyzed 312 patients with low-risk prostate cancer treated with radical prostatectomy. After exclusion of patients with fewer than 10 cores taken at biopsy and those who received neo-adjuvant treatment, 205 subjects satisfied the final inclusion criteria. Five widely accepted AS protocols were employed in this study. A total of 82.0% of the patients met the inclusion criteria of at least one protocol, and 18% did not meet any criteria of published AS protocols. A significant proportion of patients had non-organ-confined disease (8.6% to 10.6%) or a Gleason score of 7 or greater (18.6% to 23.9%) between the different AS criteria. Among patients who did not meet any AS criteria, 32.4% of patients had a pathologically insignificant cancer. Our results indicated a significant adverse pathology in patients who met the contemporary AS protocols. On the other hand, some patients in whom expectant management would be appropriate did not meet any criteria of published AS protocols. None of the clinical or histological criteria reported to date is able to sufficiently discriminate aggressive tumors from indolent ones.
Cohort Modeling Based App Category Usage Prediction (2020)

Smartphones utilize context signals, such as time and location, to predict users' app usage tailored to individual users. To be effective, such personalization relies on access to sufficient information about each user's behavioral habits. For new users, the behavior information may be sparse or non-existent. To handle these cases, app category usage prediction approaches can employ signals from users who are similar along one or more dimensions, i.e., those in the same cohort. In this paper, we describe a characterization and evaluation of the use of such cohort modeling to enhance app category usage prediction. We experiment with pre-defined cohorts from three taxonomies - demographics, psychographics, and behavioral patterns - independently and in combination. We also evaluate various approaches to assign users into the corresponding cohorts. We show, through extensive experiments with large-scale mobile app usage logs from a mobile advertising company, that leveraging cohort behavior can yield significant prediction performance gains than when using the personalized signals at the individual prediction level. In addition, compared to the personalized model, the cohort-based approach can significantly alleviate the cold-start problem, achieving strong predictive performance even with limited amount of user interactions.
Response to Comment on “PP2A inhibition sensitizes cancer stem cells to ABL tyrosine kinase inhibitors in BCR-ABL + human leukemia” (2019)

LB100 sensitizes resistant chronic phase CML stem and progenitor cells to TKIs and spares healthy bone marrow cells.
It Is Not About the Bike, It Is About the Pedaling (2011)

Forced exercise has resulted in neuroprotective effects and improved motor function in animal studies. These promising results have not yet been translated fully to humans with Parkinson's disease (PD), as traditional exercise interventions have not yielded global improvements in function. A novel forced exercise intervention is described that has resulted in improved motor function and central nervous system function in PD patients.
The Linear and Nonlinear Ultrasound Field of Convex Arrays Operating in a Diverging Wave Mode (2018)

High frame rate (ultrafast) ultrasound imaging has received a lot of attention recently. Ultrafast imaging facilitated innovations such as shear wave elastography, super-resolution imaging, and ultrafast contrast-enhanced Doppler imaging. It requires the use of large apertures to send plane or diverging waves to insonify the whole imaged area in one transmit event. Combining diverging wave imaging (DWI) with tissue harmonic imaging (THI) may offer improvements in image quality comparable to those obtained in conventional focused imaging. No studies have reported simulations of the nonlinear acoustic fields produced by diagnostic arrays in diverging wave mode. The aim of this study is to model convex arrays operating in diverging wave mode with the KZK equation. We considered 2 specific problems: (a) increased bubble destruction during ultrafast contrast imaging due to the nature of the diverging field; and (b) whether the second harmonic generated in DWI is adequate for THI. In linear simulations, we showed that using convex arrays for ultrafast contrast imaging produced pressures that are greater in the nearfield and lower in the farfield than those of focused beams, and may induce more nearfield bubble destruction. In nonlinear simulations, the second harmonic produced by ultrafast THI was found to be 2-13 dB lower than that of focused beams when operated at the same maximum MI. This moderate difference of the second harmonic between DWI and focused ultrasound suggests it may be feasible to combine DWI and THI.
Single-chip multiple-frequency RF microresonators based on aluminum nitride contour-mode and FBAR technologies (2006)

This work reports experimental results on a new class of multiple-frequency contour-mode bulk acoustic wave aluminum nitride resonators that were co-fabricated on the same silicon chip with suspended thin film bulk acoustic resonators (FBAR). The novel contour-mode technology combined with FBAR resonators permit the fabrication of integrated single-chip RF platforms that can cover IF and RF frequencies of particular interest to the handset market. High Q ranging from 2,000 to 4,000 were demonstrated for rectangular and ring shaped contour-mode resonators in air at frequencies as high as 473 MHz. FBAR resonators with Q of 2,000 at 1.75 GHz were fabricated on the same substrate. To further prove the contour-mode technology, ladder filters at 93 and 236 MHz were demonstrated with insertion losses of 4 and 8 dB, respectively, 3 dB bandwidth of 0.3 % and high out-of-band rejection (larger than 26 dB). In addition a low phase noise (less than - 110 dBc/Hz at 10 kHz offset) oscillator was realized using a 224 MHz ring resonator in a standard pierce design.
End-to-end performance analysis of a paris in-orbit demostrator ocean altimeter (2011)

The PARIS in orbit demonstrator is a novel altimeter concept recently proposed by the European Space Agency with has the objective of observing ocean mesoscale features with an expected sea surface height estimation accuracy of about 20 cm and unprecedented simultaneous spatial-temporal sampling of the ocean. This altimeter is based on the well known PARIS (also defined as GNSS-R) technique, which performs altimetry by exploiting the properties of GNSS signals scattered off the ocean surface. The PARIS IoD is novel because it is based on the so called "interferometric" concept, which, by cross-correlating direct and reflected navigations signals, allows exploiting at the maximum possible the spectral characteristics of GPS and Galileo signals and thus maximizing the height accuracy of such altimeter. This paper will present an analysis of the expected altimetry performance of such instrument by analyzing the major error contributors.
Tunable protein synthesis by transcript isoforms in human cells (2015)

Eukaryotic genes generate multiple mRNA transcript isoforms though alternative transcription, splicing, and polyadenylation. However, the relationship between human transcript diversity and protein production is complex as each isoform can be translated differently. We fractionated a polysome profile and reconstructed transcript isoforms from each fraction, which we term Transcript Isoforms in Polysomes sequencing (TrIP-seq). Analysis of these data revealed regulatory features that control ribosome occupancy and translational output of each transcript isoform. We extracted a panel of 5′ and 3′ untranslated regions that control protein production from an unrelated gene in cells over a 100-fold range. Select 5′ untranslated regions exert robust translational control between cell lines, while 3′ untranslated regions can confer cell-type-specific expression. These results expose the large dynamic range of transcript-isoform-specific translational control, identify isoform-specific sequences that control protein output in human cells, and demonstrate that transcript isoform diversity must be considered when relating RNA and protein levels.
Calibrated Reliable Regression using Maximum Mean Discrepancy (2020)

Accurate quantification of uncertainty is crucial for real-world applications of machine learning. However, modern deep neural networks still produce unreliable predictive uncertainty, often yielding over-confident predictions. In this paper, we are concerned with getting well-calibrated predictions in regression tasks. We propose the calibrated regression method using the maximum mean discrepancy by minimizing the kernel embedding measure. Theoretically, the calibration error of our method asymptotically converges to zero when the sample size is large enough. Experiments on non-trivial real datasets show that our method can produce well-calibrated and sharp prediction intervals, which outperforms the related state-of-the-art methods.
Coarray synthesis with circular and elliptical boundary arrays (1992)

An elliptical boundary aperture is a collection of points lying on an ellipse from which energy is transmitted and/or received. An important special case is the circular boundary aperture. When these apertures are used with beamforming to produce a narrowband image of a far-field source, the corresponding point spread function (PSF) is characterized by high sidelobes. The concept of the coarray of an imaging system is used here to develop techniques which synthesize the effect of a more desirable PSF with an elliptical boundary aperture. Techniques are given for use in active imaging of spatially coherent sources, as well as passive imaging of spatially incoherent sources. Discrete arrays and continuous apertures are considered separately. The approach shows that the PSF synthesis problem can be solved in many more ways than previously recognized, and this fact is exploited to develop procedures which have a least-squares optimality property.
A Dual Palladium and Copper Hydride Catalyzed Approach for Alkyl–Aryl Cross‐Coupling of Aryl Halides and Olefins (2017)

Abstract We report an efficient means of sp 2 –sp 3 cross coupling for a variety of terminal monosubstituted olefins with aryl electrophiles using Pd and CuH catalysis. In addition to its applicability to a range of aryl bromide substrates, this process was also suitable for electron‐deficient aryl chlorides, furnishing higher yields than the corresponding aryl bromides in these cases. The optimized protocol does not require the use of a glovebox and employs air‐stable Cu and Pd complexes as precatalysts. A reaction on 10 mmol scale further highlighted the practical utility of this protocol. Employing a similar protocol, a series of cyclic alkenes were also examined. Cyclopentene was shown to undergo efficient coupling under these conditions. Lastly, deuterium‐labeling studies indicate that deuterium scrambling does not take place in this sp 2 ‐sp 3 cross coupling, implying that β‐hydride elimination is not a significant process in this transformation.