gebhart/patrepeval huggingface dataset:
Trivalent Combination Vaccine Induces Broad Heterologous Immune Responses to Norovirus and Rotavirus in Mice (2013)

Rotavirus (RV) and norovirus (NoV) are the two major causes of viral gastroenteritis (GE) in children worldwide. We have developed an injectable vaccine design to prevent infection or GE induced with these enteric viruses. The trivalent combination vaccine consists of NoV capsid (VP1) derived virus-like particles (VLPs) of GI-3 and GII-4 representing the two major NoV genogroups and tubular RV recombinant VP6 (rVP6), the most conserved and abundant RV protein. Each component was produced in insect cells by a recombinant baculovirus expression system and combined in vitro. The vaccine components were administered intramuscularly to BALB/c mice either separately or in the trivalent combination. High levels of NoV and RV type specific serum IgGs with high avidity (>50%) as well as intestinal IgGs were detected in the immunized mice. Cross-reactive IgG antibodies were also elicited against heterologous NoV VLPs not used for immunization (GII-4 NO, GII-12 and GI-1 VLPs) and to different RVs from cell cultures. NoV-specific serum antibodies blocked binding of homologous and heterologous VLPs to the putative receptors, histo-blood group antigens, suggesting broad NoV neutralizing activity of the sera. Mucosal antibodies of mice immunized with the trivalent combination vaccine inhibited RV infection in vitro. In addition, cross-reactive T cell immune responses to NoV and RV-specific antigens were detected. All the responses were sustained for up to six months. No mutual inhibition of the components in the trivalent vaccine combination was observed. In conclusion, the NoV GI and GII VLPs combination induced broader cross-reactive and potentially neutralizing immune responses than either of the VLPs alone. Therefore, trivalent vaccine might induce protective immune responses to the vast majority of circulating NoV and RV genotypes.
New Elongase Gene And Production Of Delta-9-polyunsaturated Fatty Acids (Patent EP 1373519 A2) (2004)

The invention relates to a new elongase gene having the sequence SEQ ID NO: 1 or its derivatives, to a gene construct comprising this sequence or its derivatives and to its use. The inventive nucleic acid sequence encodes a polypeptide which elongates .alpha.-linolenic acid (C18:3 d9, 12, 15) by at least two carbon atoms whereas .gamma.-linolenic acid (C 18:3 d6, 9, 12) is not elongated. The invention additionally relates to vectors or organisms comprising an elongase gene having the sequence SEQ ID NO: 1 or its derivatives. The invention further relates to a process for the production of polyunsaturated fatty acids (=PUFAs) with an organism which comprises the elongase gene and which organism produces high amounts of oils and especially oils with a high content of unsaturated fatty acids. Additionally the invention relates to an oil and/or fatty acid composition with a higher content of polyunsaturated C20 or C22 fatty acids with at least two double bonds and/or to a triacylglycerol composition with a higher content of said polyunsaturated fatty acids.
Development of a signal measurement technique for application in multi‐analyte liposome immunomigration assays (1998)

The potential for development of a multi‐analyte liposome immunomigration solid‐phase competition (LIM‐SPC) assay based on multivariate calibration of spectral reflectance measurements was investigated. A simulation of a multi‐analyte LIM‐SPC assay was carried out using a mixture of three analyte‐tagged liposome preparations, each containing a different colored dye. The liposome preparations were combined according to a statistical experiment design and allowed to migrate up nitrocellulose test strips to a binding zone. After the liposomes were captured at this zone, the reflectance spectrum of the zone was measured. Partial least squares regression was used to develop multivariate calibrations. For the liposome‐encapsulated dyes, the coefficients of determination obtained for car‐boxyfluorescein, sulforhodamine B and isosulfan blue were 0.902, 0.990 and 0.977, respectively. It was concluded that the approach used was suitable for a multi‐analyte LIM‐SPC.
Managing Background Traffic in Cellular Networks (2019)

A large variety of traffic - time-sensitive “foreground” traffic (e.g., web browsing) and time-insensitive “background” traffic (e.g., software updates) - compete for the scarce cellular bandwidth, especially on the downlink. While there is limited in-network support for traffic prioritization, existing endto-end, “low priority transport protocols” exhibit sub-optimal performance in cellular networks. We propose Sneaker, which yields to time-sensitive foreground traffic during periods of congestion and enables time-insensitive background traffic to efficiently utilize any spare capacity. Sneaker achieves the desired goal by randomly dropping packets coming into the base station, based on traffic type and network conditions. Our key contribution is the derivation of the optimal dropping rate and a practical dropping rate, which performs close to optimal. Further, Sneaker co-exists and performs well with existing cellular schedulers and transport protocols.
Reactive-ion etching of GaAs and InP using CCl2F2/Ar/O2 (1980)

We describe the reactive ion etching of GaAs, InP, and their derivative compounds using an etch gas composed of CCl2F2, O2, and argon. Etching was generally carried out at pressures between 1 and 10 μ, and power densities below 0.8 W/cm2. Clean etch profiles were obtained with etch rates as high as 0.25 μm/min. A strong dependence of etch rate on pressure was observed with a maximum at 5 μ total pressure. The etch profiles exhibited a ’’negative undercut’’ character which was also dependent upon the total pressure.
Single-chip CMUT-on-CMOS front-end system for real-time volumetric IVUS and ICE imaging (2014)

Intravascular ultrasound (IVUS) and intracardiac echography (ICE) catheters with real-time volumetric ultrasound imaging capability can provide unique benefits to many interventional procedures used in the diagnosis and treatment of coronary and structural heart diseases. Integration of capacitive micromachined ultrasonic transducer (CMUT) arrays with front-end electronics in single-chip configuration allows for implementation of such catheter probes with reduced interconnect complexity, miniaturization, and high mechanical flexibility. We implemented a single-chip forward-looking (FL) ultrasound imaging system by fabricating a 1.4-mm-diameter dual-ring CMUT array using CMUT-on-CMOS technology on a front-end IC implemented in 0.35-μm CMOS process. The dual-ring array has 56 transmit elements and 48 receive elements on two separate concentric annular rings. The IC incorporates a 25-V pulser for each transmitter and a low-noise capacitive transimpedance amplifier (TIA) for each receiver, along with digital control and smart power management. The final shape of the silicon chip is a 1.5-mm-diameter donut with a 430-μm center hole for a guide wire. The overall front-end system requires only 13 external connections and provides 4 parallel RF outputs while consuming an average power of 20 mW. We measured RF A-scans from the integrated single- chip array which show full functionality at 20.1 MHz with 43% fractional bandwidth. We also tested and demonstrated the image quality of the system on a wire phantom and an ex vivo chicken heart sample. The measured axial and lateral point resolutions are 92 μm and 251 μm, respectively. We successfully acquired volumetric imaging data from the ex vivo chicken heart at 60 frames per second without any signal averaging. These demonstrative results indicate that single-chip CMUT-on-CMOS systems have the potential to produce realtime volumetric images with image quality and speed suitable for catheter-based clinical applications.
Effect of charge-transfer acceptors on dynamic scattering in a nematic liquid crystal (1972)

The addition of charge-transfer acceptors to a nematic liquid crystal at concentrations &lt;0.1% has a profound effect on the voltage-transmission characteristics for dynamic scattering, reducing the threshold voltage by a factor of 2 for dc fields, but not appreciably altering the ac behavior. Charge-transfer bands in the visible may be introduced that depend on the concentration and nature of the acceptor molecule employed.
A NusG-like transcription anti-terminator is involved in the biosynthesis of the polyketide antibiotic TA of<i>Myxococcus xanthus</i> (1999)

The antibiotic TA of Myxococcus xanthus is synthesized through a type I polyketide synthase mechanism. Previous studies have indicated that several genes essential for TA production are clustered within a 40-kb region and are transcriptionally co-regulated. In this study, we report the genetic analysis of the first gene in the TA gene cluster, identified as a NusG-like transcription anti-terminator. Functional analysis of this NusG-like anti-terminator gene by specific gene disruption confirms that it is essential for TA production but not for normal growth and development.
Antitumor Efficacy of Photodynamic Therapy Using Novel Nanoformulations of Hypocrellin Photosensitizer SL052 (2011)

Recent preclinical and clinical testing of hypocrellin-based photosensitizer SL052 for use in photodynamic therapy (PDT) of cancer has shown encouraging results. Further optimization of its formulation for delivery could considerably extend the therapeutic efficiency of this drug. A nanoformulation encapsulating SL052 into biodegradable polymer poly(lactic-co-glycolic acid) (PLGA) was developed using a single-emulsion solvent evaporation technique and characterized in terms of particle size and loading of the photosensitizing agent. This nanoformulation, SL052-PLGA-nanoparticles (NPs), was compared with recently created nanoformulation based on polyvinylpyrrolidone (SL052-PVP-NPs) and standard liposomal SL052 preparation in terms of efficacy when used for PDT treatment of squamous cell carcinomas SCCVII growing subcutaneously in syngeneic mice. The therapeutic effect of PDT using these three different SL052 formulations was tested for both 1 and 4 h intervals between drug injection and tumor light exposure. The longer time interval produced higher tumor cure rates with all SL052 preparations. With both drug-light intervals, PDT based on SL052-PLGA-NPs produced superior therapeutic benefit compared with the other two SL052 formulations.
Code division multiple access (CDMA) enhancement of wavelength division multiplexing (WDM) systems (2002)

Wavelength division multiplexing (WDM) is a mainstream technology for optical communications ranging from long haul applications to interconnections between and within high speed digital systems. WDM is, however, constrained (1) in density by the crosstalk associated with channel spacing and (2) by total number of channels which can be uniformly amplified by optical amplifiers. This number of effective WDM channels can be enhanced by overlaying code division multiple access (CDMA) on each WDM channel. The authors show by analysis and example that the number of effective WDM/CDMA hybrid channels exceeds the number of effective WDM channels, and with a reduced WDM crosstalk penalty.
Polyaniline nanofiber composites with amines: Novel materials for phosgene detection (2009)

Several orders of magnitude of change in resistance are observed upon chemical doping and dedoping of the conducting polymer polyaniline. This large conductivity range can be utilized to make sensitive chemical sensors. Polyaniline, in its nanofiber form, has even greater sensing capabilities due to the small fiber diameters, high surface area, and porous nanofiber network that enhances gas diffusion into the fibers. Polyaniline nanofibers have been synthesized using a rapid mixing method and dispersed in water allowing them to be easily modified with water soluble agents, making new composite materials. Polyaniline nanofiber composite materials can be used to enhance detection of analytes that unmodified polyaniline would not otherwise be able to detect. The detection mechanism involves the reaction of an additive with the analyte to generate a strong acid that is easily detected by polyaniline, resulting in orders of magnitude changes in resistance. The reaction of the additive alone with the analyte produces no electrical response, however. In this paper, an array of amine-polyaniline nanofiber composite materials is investigated for the detection of phosgene gas. The influence of environmental conditions such as humidity and temperature are examined and a detection mechanism is presented.
DeepNovoV2: Better de novo peptide sequencing with deep learning (2019)

Personalized cancer vaccines are envisioned as the next generation rational cancer immunotherapy. The key step in developing personalized therapeutic cancer vaccines is to identify tumor-specific neoantigens that are on the surface of tumor cells. A promising method for this is through de novo peptide sequencing from mass spectrometry data. In this paper we introduce DeepNovoV2, the state-of-the-art model for peptide sequencing. In DeepNovoV2, a spectrum is directly represented as a set of (m/z, intensity) pairs, therefore it does not suffer from the accuracy-speed/memory trade-off problem. The model combines an order invariant network structure (T-Net) and recurrent neural networks and provides a complete end-to-end training and prediction framework to sequence patterns of peptides. Our experiments on a wide variety of data from different species show that DeepNovoV2 outperforms previous state-of-the-art methods, achieving 13.01-23.95\% higher accuracy at the peptide level.
Explainable AI (xAI) for Anatomic Pathology (2020)

Pathologists are adopting whole slide images (WSIs) for diagnosis, thanks to recent FDA approval of WSI systems as class II medical devices. In response to new market forces and recent technology advances outside of pathology, a new field of computational pathology has emerged that applies artificial intelligence (AI) and machine learning algorithms to WSIs. Computational pathology has great potential for augmenting pathologists' accuracy and efficiency, but there are important concerns regarding trust of AI due to the opaque, black-box nature of most AI algorithms. In addition, there is a lack of consensus on how pathologists should incorporate computational pathology systems into their workflow. To address these concerns, building computational pathology systems with explainable AI (xAI) mechanisms is a powerful and transparent alternative to black-box AI models. xAI can reveal underlying causes for its decisions; this is intended to promote safety and reliability of AI for critical tasks such as pathology diagnosis. This article outlines xAI enabled applications in anatomic pathology workflow that improves efficiency and accuracy of the practice. In addition, we describe HistoMapr-Breast, an initial xAI enabled software application for breast core biopsies. HistoMapr-Breast automatically previews breast core WSIs and recognizes the regions of interest to rapidly present the key diagnostic areas in an interactive and explainable manner. We anticipate xAI will ultimately serve pathologists as an interactive computational guide for computer-assisted primary diagnosis.
On secondary transforms for prediction residual (2012)

In this paper, we present a transform scheme that utilizes a secondary transform after the conventional DCT for intra as well as inter prediction residues. Our approach is applicable to any block-based video codec that employs transforms along the horizontal and vertical direction separably. The secondary transform is applied to the lower K (K=4 or 8) frequency coefficients of the output of conventional DCT at block with dimensions 8 and higher. The proposed transform scheme has low complexity as it is applied only to the top-left portion of DCT output, especially in the context of large blocks such as 32×32 where an alternate transform of size 32×32 other than DCT would be expensive to be implemented in hardware. The proposed technique works in single-pass, and the choice of whether to use the secondary transform is solely based on the prediction direction for intra residue, and transform unit location in the prediction unit for the inter residue. The scheme requires no additional signaling information or R-D search. Our simulation results show that the proposed transform scheme provides significant BD-Rate improvement over the conventional DCT-based coding scheme for video sequences in the ongoing HEVC standardization.
Prevalence and Clinical Features of Inflammatory Bowel Diseases Associated With Monogenic Variants, Identified by Whole-Exome Sequencing in 1000 Children at a Single Center (2020)

In whole-exome sequencing analyses of more than 1000 children with IBD at a single center, we found that 3% had rare variants in genes previously associated with pediatric IBD. These were associated with different IBD phenotypes, and 1% of the patients had variants that could be potentially corrected with allogeneic hematopoietic stem cell transplantation. Monogenic IBD is rare, but should be considered in analysis of all patients with pediatric onset of IBD.
Development of Foil Journal Bearings for High Load Capacity and High Speed Whirl Stability (1982)

This paper describes the development of two types of air-lubricated foil journal bearings, designed for separate purposes; stability and load capacity. The first was a three-pad configuration, with each pad forming a wedge whose convergence increases with operating speed (of 120,000 rpm max.). The net result is a highly stable bearing at high operating speed. The second was a single pad journal bearing (43.7 mm diameter × 34.9 mm long) that produced a load capacity of 352 KPa (51 psi) at an operating speed of 68,000 rpm.
Stimuli-responsive hydrogels based on acrylic acid and acrylamide (2015)

Hydrogels are three-dimensional polymeric networks that can absorb and retain large quantities of water in relation to their physical size. By incorporating stimuli-responsive units into the gel structure, hydrogels can be actuated by external stimuli such as light[1], temperature[2] and pH[3], among others. In this study pH responsive hydrogels were developed using copolymers of acrylic acid (AA) and acrylamide (Am) in different molar ratios (30:70, 50:50 and 70:30, respectively). In order to turn this pH response into a photo-response, a reversible photo-acid generator, namely spiropyran acrylate (SP-A), was copolymerised in the polymer backbone.
An Enzyme-Linked Immunosorbent Assay (ELISA) for <i>in Vitro</i> Pollen Growth Based on Binding of a Monoclonal Antibody to the Pollen Tube Surface (1987)

An indirect method of quantifying in vitro pollen growth has been developed. This is based on the finding that a monoclonal antibody (PCBC3), which has a primary specificity for alpha-l-arabinofuranosyl residues, binds to the surface of in vitro grown pollen tubes of the ornamental tobacco, Nicotiana alata. This binding was quantified using an enzyme linked immunosorbent assay (ELISA). The method was used to determine the effects of 2-deoxy-d-glucose and nonanoic acid on in vitro pollen growth.
A Survey on Graph Processing Accelerators: Challenges and Opportunities (2019)

Graph is a well known data structure to represent the associated relationships in a variety of applications, e.g., data science and machine learning. Despite a wealth of existing efforts on developing graph processing systems for improving the performance and/or energy efficiency on traditional architectures, dedicated hardware solutions, also referred to as graph processing accelerators, are essential and emerging to provide the benefits significantly beyond those pure software solutions can offer. In this paper, we conduct a systematical survey regarding the design and implementation of graph processing accelerator. Specifically, we review the relevant techniques in three core components toward a graph processing accelerator: preprocessing, parallel graph computation and runtime scheduling. We also examine the benchmarks and results in existing studies for evaluating a graph processing accelerator. Interestingly, we find that there is not an absolute winner for all three aspects in graph acceleration due to the diverse characteristics of graph processing and complexity of hardware configurations. We finially present to discuss several challenges in details, and to further explore the opportunities for the future research.
Ruthenium(II) Sensitizers with Heteroleptic Tridentate Chelates for Dye‐Sensitized Solar Cells (2011)

Ziemlich sensibel: In neuartigen RuII-Sensibilisatoren wird das Metallzentrum von zwei dreizähnigen Liganden koordiniert: einem Tricarboxyterpyridin und einem dianionischen Bis(pyrazolyl)pyridin mit erweitertem π-konjugiertem Auxochrom (siehe Struktur; Ru magenta, N blau, O rot, F grün, S gelb, C grau). Diese Thiocyanat-freien RuII-Sensibilisatoren ergeben Farbstoffsolarzellen mit Konversionseffizienzen bis η=10.7 %. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Including Spatial Information in Nonlinear Inversion MR Elastography Using Soft Prior Regularization (2013)

Tissue displacements required for mechanical property reconstruction in magnetic resonance elastography (MRE) are acquired in a magnetic resonance imaging (MRI) scanner, therefore, anatomical information is available from other imaging sequences. Despite its availability, few attempts to incorporate prior spatial information in the MRE reconstruction process have been reported. This paper implements and evaluates soft prior regularization (SPR), through which homogeneity in predefined spatial regions is enforced by a penalty term in a nonlinear inversion strategy. Phantom experiments and simulations show that when predefined regions are spatially accurate, recovered property values are stable for SPR weighting factors spanning several orders of magnitude, whereas inaccurate segmentation results in bias in the reconstructed properties that can be mitigated through proper choice of regularization weighting. The method was evaluated in vivo by estimating viscoelastic mechanical properties of frontal lobe gray and white matter for five repeated scans of a healthy volunteer. Segmentations of each tissue type were generated using automated software, and statistically significant differences between frontal lobe gray and white matter were found for both the storage modulus and loss modulus . Provided homogeneous property assumptions are reasonable, SPR produces accurate quantitative property estimates for tissue structures which are finer than the resolution currently achievable with fully distributed MRE.