gebhart/patrepeval huggingface dataset:
The development of the BK-SE36 malaria vaccine candidate (2014)

Complex and widespread with about 90% of the global burden in sub-Saharan Africa, malaria remains a significant health problem. Malaria vaccines have the chance to make significant inroads, with RTS,S vaccine candidate as the most advanced candidate. However, the need for a highly efficacious, long-lasting vaccine is still unmet. Continued support for a repertoire of tools for Plasmodium falciparum is needed. A blood-stage vaccine is desirable to deal with morbidity and mortality secondary to P. falciparum infection, and thus would be a valuable strategy in the fight against malaria.

The P. falciparum serine repeat antigen-5 formulated with aluminum hydroxyl gel (BK-SE36) is a blood-stage malaria vaccine candidate. The processing of SERA5 is believed to mediate parasite egress from the infected red blood cell. Field studies show good correlations of anti-SERA antibodies to malaria protection against blood parasitemia, malaria symptoms and severe disease. A Phase 1a trial demonstrated its safety and immunogenicity in malaria naive Japanese adults. A Phase 1b trial was conducted in the malaria endemic area of Northern Uganda to assess the vaccine’s safety and immunogenicity. BK-SE36 had an acceptable safety and immunogenicity profile. Post-trial, Stage 2 subjects were age-matched to 50 control individuals to compare malaria episodes 130–365 days post-second vaccination. Log-rank test reveal significant differences in BK-SE36 vaccinees vs control group in time-to-first episodes with parasitemias ≥5,000/μL and those with ≥5,000/μL + fever (protective efficacy for the latter is 72%, P < 0.01). BK-SE36 vaccinees have fewer multiple malaria episodes with high parasitemia. We also observed that the antibody titers against SE36 were boosted after episodes of natural infection. Above results show that BK-SE36 could provide some protection against natural P. falciparum infection until 1 year post-second vaccination.
153. COMBINATION METHOTREXATE AND EPIDERMAL GROWTH FACTOR RECEPTOR INHIBITION AS A NOVEL MEDICATION-BASED CURE OF ECTOPIC PREGNANCIES (2010)

Ectopic pregnancies are serious gynaecological emergencies that can cause fatal haemorrhage. Most are treated surgically. Given the placenta is heavily reliant on Epidermal Growth Factor Receptor (EGFR) signaling, we set out to develop a medication-based treatment of ectopics using combination gefitinib (EGFR inhibitor) and methotrexate (folate antagonist). Both drugs are well tolerated and available in tablet form. We used in vitro and in vivo approaches to test the ability of gefitinib and methotrexate to regress placental tissue, and to explore molecular mechanisms. In vitro assays included immunohistochemistry (EGFR staining) western blot (EGFR phosphorylation), cell viability assays (Cell-Titre Blue, LDH cytotoxicity assay, xCELLigence system), apoptosis assays (PCR, FACS of M30 antibody) and The Bioplex Platform (phosphorylation of the EGFR pathway). JEG-3 xenografts were used to assess regression of placental tissue in vivo, where serum hCG was also measured (ELISA). EGFR was highly expressed in placentae from ectopic pregnancies. Combination treatment was supra-additive in inducing cell death of placental tissue in vitro, with >70% cell death by 48 hours (Syncytialised BeWos, JEG-3 and 1st trimester trophoblast). This supra-additive effect was demonstrated in both end point assays (cell viability) and regular monitoring using The xCELLigence system. Gefitinib potently blocks EGFR phosphorylation in placental tissues in vitro (Western blot). Both drugs may be converging to inhibit Akt phosphorylation (Bioplex analysis). Combination treatment increases apoptosis (FACS of M30 antibody). In vivo, Gefitinib or MTX as single agents induced significant decrease in xenograft tumour volume in a dose dependent manner (n ≤ 5 mice per treatment). However, combining these drugs was supra-additive in decreasing xenograph tumour volume and weight. Serum hCG in mice was lowest with combination treatment. Combination gefitinib and methotrexate potently regresses placental tissue. It may be a novel therapeutic approach to cure ectopic pregnancies, potentially replacing surgery with tablets.
Biological Characterizations of H5Nx Avian Influenza Viruses Embodying Different Neuraminidases (2017)

The H5 subtype virus of Highly Pathogenic Avian Influenza Virus has caused huge economic losses to the poultry industry and is a threat to human health. Until 2010, H5N1 subtype virus was the major genotype in China. Since 2011, reassortant H5N2, H5N6, and H5N8 viruses were identified in domestic poultry in China. The clade 2.3.4.4 H5N6 and H5N8 AIV has now spread to most of China. Clade 2.3.4.4 H5N6 virus has caused 17 human deaths. However, the prevalence, pathogenicity, and transmissibility of the distinct NA reassortment with H5 subtypes viruses (H5Nx) is unknown. We constructed five clade 2.3.4.4 reassortant H5Nx viruses that shared the same HA and six internal gene segments. The NA gene segment was replaced with N1, N2, N6, ΔN6 (with an 11 amino acid deletion at the 58th to 68th of NA stalk region), and N8 strains, respectively. The reassortant viruses with distinct NAs of clade 2.3.4.4 H5 subtype had different degrees of fitness. All reassortant H5Nx viruses formed plaques on MDCK cell monolayers, but the ΔH5N6 grew more efficiently in mammalian and avian cells. The reassortant H5Nx viruses were more virulent in mice as compared to the H5N2 virus. The H5N6 and H5N8 reassortant viruses exhibited enhanced pathogenicity and transmissibility in chickens as compared to the H5N1 reassortant virus. We suggest that comprehensive surveillance work should be undertaken to monitor the H5Nx viruses.
Stimulated Brillouin Scattering (SBS) Suppression and Long Delivery Fibers at the Multikilowatt Level with Chirped Seed Lasers (2017)

Abstract : In a high-power fiber amplifier, a frequency-chirped seed interrupts the coherent interaction between the laser and Stokes waves, raising the threshold for stimulated Brillouin scattering (SBS). Moving the external mirror of a vertical cavity surface-emitting diode laser 0.2 m in 10 s can yield a frequency chirp of 5 1017 Hz/s at a nearly constant output power. Opto-electronic feedback loops can linearize the chirp and stabilize the output power. The simple and deterministic variation of phase with time preserves temporal coherence, in the sense that it is straightforward to coherently combine multiple amplifiers despite a large path-length mismatch. The seed bandwidth, as seen by the counterpropagating SBS, also increases linearly with fiber length, resulting in a nearly length-independent SBS threshold. Experimental results at the 1.6-kW level with a 19-m delivery fiber are presented. A numerical simulation is also presented.
Smart Signage: An Interactive Signage System with Multiple Displays (2013)

Digital signs (e.g. electronic billboards), as the replacement of traditional static signs (e.g. paper posters), have gained increasing popularity, especially for out-of-home advertising. The pervasiveness of the smartphones makes it possible to implement new interactive signage systems for advertising purpose. A new drag gable cyber-physical broadcast/multicast media system, Smart Signage, is proposed in our previous work. It allows multiples users simultaneously obtaining the displayed content with an intuitive ``dragging" hand gesture. With the increasing number of deployed digital signs, it is possible that there are multiple signs in one location. In this paper, a new approach is proposed using the existing Smart Signage infrastructure to allow smartphones to interact with multiple digital signs in one location. This approach differentiates signs by the orientations of the signage displays, which are measured by smartphone-embedded orientation sensors. A user can interact with the intended sign by simply pointing his/her smartphone at the target signage display. With this new approach, Smart Signage successfully extends from one-to-many interaction to many-to-many interaction.
Dynamic partitioning for enterprise applications (2011)

Today's enterprise applications face a severe change in how they process data. They evolved from simple data entry applications to complex systems where the focus is to make the right decision based on latest transactional data instead of pre-processed outdated business intelligence data from secondary systems. This paradigm shift results in more analytical queries executed on the transactional database system. In addition we see a change in how the persistence layer is seen and that more and more effort is spent on developing database engines that are designed to address special needs and requirements, e.g. for Web 2.0 applications. In this paper we discuss that it is crucial for enterprise applications to share application semantics with the database to increase performance. Furthermore we show how this principle can be applied to dynamically partition application data. In contrast to static partitioning we propose to adapt the life-cycle semantics of the application and move data from active to different passive partitions, by leveraging the merge process of our database prototype. The goal is to reduce the amount of data that is touched during query execution to increase the performance of the main workload by the same factor. We present how our HYRISE prototype is implemented and how it can be extended to fully support this use case.
Derivation and large-scale expansion of multipotent astroglial neural progenitors from adult human brain (2006)

The isolation and expansion of human neural cell types has become increasingly relevant in restorative neurobiology. Although embryonic and fetal tissue are frequently envisaged as providing sufficiently primordial cells for such applications, the developmental plasticity of endogenous adult neural cells remains largely unclear. To examine the developmental potential of adult human brain cells, we applied conditions favoring the growth of neural stem cells to multiple cortical regions, resulting in the identification and selection of a population of adult human neural progenitors (AHNPs). These nestin(+) progenitors may be derived from multiple forebrain regions, are maintainable in adherent conditions, co-express multiple glial and immature markers, and are highly expandable, allowing a single progenitor to theoretically form sufficient cells for approximately 4x10(7) adult brains. AHNPs longitudinally maintain the ability to generate both glial and neuronal cell types in vivo and in vitro, and are amenable to genetic modification and transplantation. These findings suggest an unprecedented degree of inducible plasticity is retained by cells of the adult central nervous system.
A normalized rate-distortion model for H.263-compatible codecs and its application to quantizer selection (2002)

This paper proposes a new normalized parametric rate-distortion model which can be efficiently applied to H.263-compatible video codecs and other codecs of similar type. The model is very efficient in terms of computational complexity and amount of required memory since it approximates all 31 rate-distortion relations (one for each quantization parameter QP) with only one curve by normalizing the energy of signals and the quantization distortion with functions of QP. We show how the model parameters can be obtained from experimental data. We also propose a quantizer selection scheme which uses the model to estimate the number of bits required for encoding 8/spl times/8 residual blocks. Experiments show that the model provides very good approximations of the rate and the distortion characteristics for all QPs, and that the proposed quantizer selection scheme works better than the scheme used in the MPEG-4 Video Verification Model Version 5.1.
A Proteomics Approach to Investigate miR-153-3p and miR-205-5p Targets in Neuroblastoma Cells (2015)

MicroRNAs are key regulators associated with numerous diseases. In HEK293 cells, miR-153-3p and miR-205-5p down-regulate alpha-synuclein (SNCA) and Leucine-rich repeat kinase 2 (LRRK2), two key proteins involved in Parkinson's disease (PD). We have used two-dimensional gel electrophoresis (2D-PAGE) coupled to mass spectrometry (MS) to identify a spectrum of miR-153-3p and miR-205-5p targets in neuronal SH-SY5Y cells. We overexpressed and inhibited both microRNAs in SH-SY5Y cells and through comparative proteomics profiling we quantified ~240 protein spots from each analysis. Combined, thirty-three protein spots were identified showing significant (p-value < 0.05) changes in abundance. Modulation of miR-153-3p resulted in seven up-regulated proteins and eight down-regulated proteins. miR-205 modulation resulted in twelve up-regulated proteins and six down-regulated proteins. Several of the proteins are associated with neuronal processes, including peroxiredoxin-2 and -4, cofilin-1, prefoldin 2, alpha-enolase, human nucleoside diphosphate kinase B (Nm23) and 14-3-3 protein epsilon. Many of the differentially expressed proteins are involved in diverse pathways including metabolism, neurotrophin signaling, actin cytoskeletal regulation, HIF-1 signaling and the proteasome indicating that miR-153-3p and miR-205-5p are involved in the regulation of a wide variety of biological processes in neuroblastoma cells.
Graphite based Schottky diodes formed on Si, GaAs, and 4H-SiC substrates (2009)

We demonstrate the formation of semimetal graphite/semiconductor Schottky barriers where the semiconductor is either silicon (Si), gallium arsenide (GaAs), or 4H-silicon carbide (4H-SiC). Near room temperature, the forward-bias diode characteristics are well described by thermionic emission, and the extracted barrier heights, which are confirmed by capacitance voltage measurements, roughly follow the Schottky–Mott relation. Since the outermost layer of the graphite electrode is a single graphene sheet, we expect that graphene/semiconductor barriers will manifest similar behavior.
Engineering of a Line-Scanning Confocal Microscope Toward Imaging Epithelial Tissues (2008)

A confocal reflectance line-scanning microscope provides optical sectioning of 1.4 µm and shows promise to image nuclear and cellular detail in human tissues. Line-scanning may be a simpler alternative to point-scanning for imaging epithelial tissues.
Tunnel Junction based Rectenna—A Key to Ultrahigh Efficiency Solar∕Thermal Energy Conversion (2010)

This paper presents a quantum approachto increasing the efficiency of solar/thermal energyconversionby converting waste heat to electrical energy using rectenna. The approach of using a rectenna (a combination of high frequency antennae and tunnel diodes) would improve efficiency of all systems. This paper presents the current state of the art in the field of rectenna based conversion with a focus on its critical component‐a nanoscale MIM diode.
<title>Advances in optical-scanning holography</title> (1994)

Holographic information pertaining to an object can be generated using an active optical heterodyne scanning technique. In this technique, the holographic information manifests itself as an electrical signal which can be sent to an electron-beam-addressed spatial light modulator for coherent image reconstruction. Real-time holographic imaging of 2-D objects has recently been demonstrated. The use of alternate waveforms in the scanning beam can process the holographic content of the object in real time. In this communication, we propose a holographic edge extraction technique which utilizes alternate waveforms in the optical scanning holographic recording stage. We have developed a 1-D computer model of the optical heterodyne scanning holographic system using Fourier analysis which we use to simulate holographic edge extraction.
A speech codec for cellular radio at a gross bit rate of 11.4 kb/s (1991)

A speech codec, called TRPE-HLTP (transformed binary regular pulse excitation, high-resolution long-term prediction) has been developed. It has been submitted as a candidate for the half-rate codec in the GSM (Group Special Mobile) system and its gross bit rate is 11.4 kb/s. The speech coding algorithm is of the type often called analysis-by-synthesis linear prediction. Its key elements are LSF (line spectral frequency)-coded spectral parameters, a high resolution closed-loop adaptive codebook, and a speech-trained low-complexity transformed binary regular pulse innovation generator, resulting in a net bit rate of 6.9 kb/s. The channel coding scheme consists of forward error correction with convolutional encoding, interleaving, and error detection.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Dye-sensitized solar cells constructed using titanium oxide nanoparticles and green dyes as photosensitizers (2023)

Recently, researchers have taken a particular interest in dye-sensitized solar cells (DSSCs) based on titanium dioxide (TiO2) nanoparticles (NPs) due to their exceptional physico-chemical characteristics and excellent photoconversion efficiency. This research is dedicated to fabricating dye-sensitized solar cells (DSSCs) using TiO2NPs and green natural dyes. The average particle size appeared about 151.6 nm of the synthesized TiO2NPs, measured by dynamic light scattering technique. The nanostructured TiO2 was characterized optically with a UV–visible and X-ray fluorescence spectrophotometer, and structurally by using X-ray diffraction (XRD). Analysis of the particle size and morphology of TiO2NPs has been confirmed by Transmission Electron Microscopy (TEM), and the Energy-dispersive spectroscopy (EDS) analysis indicated the elemental composition. The TiO2NPs thin film of paste was spread on the transparent conducting glass as the substrate with copper metal attached to the surface using the doctor-blade method. Green dyes extracted from Lawsonia inermis (Henna) and spinach were used as sensitizers, iodine as electrolytes, and TiO2NPs as photoelectrode to fabricate dye sensitized solar cells (DSSCs). The DSSCs were evaluated with a fill factor of 0.09 and 0.37, which were obtained with an efficiency of 0.24 %, and 2.19 % for spinach and henna dyes, respectively.
ralGDS Family Members Interact with the Effector Loop of <i>ras</i> p21 (1994)

Using a yeast two-hybrid system, we identified a novel protein which interacts with ras p21. This protein shares 69% amino acid homology with ral guanine nucleotide dissociation stimulator (ralGDS), a GDP/GTP exchange protein for ral p24. We designated this protein RGL, for ralGDS-like. Using the yeast two-hybrid system, we found that an effector loop mutant of ras p21 was defective in interacting with the ras p21-interacting domain of RGL, suggesting that this domain binds to ras p21 through the effector loop of ras p21. Since ralGDS contained a region highly homologous with the ras p21-interacting domain of RGL, we examined whether ralGDS could interact with ras p21. In the yeast two-hybrid system, ralGDS failed to interact with an effector loop mutant of ras p21. In insect cells, ralGDS made a complex with v-ras p21 but not with a dominant negative mutant of ras p21. ralGDS interacted with the GTP-bound form of ras p21 but not with the GDP-bound form in vitro. ralGDS inhibited both the GTPase-activating activity of the neurofibromatosis gene product (NF1) for ras p21 and the interaction of Raf with ras p21 in vitro. These results demonstrate that ralGDS specifically interacts with the active form of ras p21 and that ralGDS can compete with NF1 and Raf for binding to the effector loop of ras p21. Therefore, ralGDS family members may be effector proteins of ras p21 or may inhibit interactions between ras p21 and its effectors.
Alda-1 attenuates hyperoxia-induced mitochondrial dysfunction in lung vascular endothelial cells (2019)

Acute lung injury (ALI) is a major cause of morbidity and mortality worldwide, especially in aged populations. Mitochondrial damage is one of the key features of ALI. Hyperoxia-induced lung injury model in mice has been widely used for ALI study because it features many ALI phenotypes including, but not limited to, mitochondrial and vascular endothelial cell damage. Recently, accumulating evidence has shown that mitochondrial aldehyde dehydrogenase 2 (ALDH2) has a protective effect against oxidative stress mediated cell damage in epithelial cells. However, it is not known whether ALDH2 protects against oxidative stress in vascular endothelial cells. In this current study, we attempted to find the capacity of Alda-1 [(N-(1,3benzodioxol-5-ylmethyl)-2,6- dichloro-benzamide), an ALDH2 activator] to protect against oxidative stress in human microvascular endothelial cells (HMVEC). HMVEC pretreated with Alda-1 prior to hyperoxic exposure vs non-treated controls showed i) lower 4-hydroxynonenal (4-HNE) levels, ii) significantly decreased expressions of Bax and Cytochrome C, iii) partially restored activity and expression of ALDH2 and iv) significantly improved mitochondrial membrane potential. These results suggest that ALDH2 protein in lung vascular endothelial cells is a promising therapeutic target for the treatment of ALI and that Alda-1 is a potential treatment option.
Design and synthesis of a 3′- <i>O</i> -allyl photocleavable fluorescent nucleotide as a reversible terminator for DNA sequencing by synthesis (2005)

DNA sequencing by synthesis (SBS) offers an approach for potential high-throughput sequencing applications. In this method, the ability of an incoming nucleotide to act as a reversible terminator for a DNA polymerase reaction is an important requirement to unambiguously determine the identity of the incorporated nucleotide before the next nucleotide is added. A free 3'-OH group on the terminal nucleotide of the primer is necessary for the DNA polymerase to incorporate an incoming nucleotide. Therefore, if the 3'-OH group of an incoming nucleotide is capped by a chemical moiety, it will cause the polymerase reaction to terminate after the nucleotide is incorporated into the DNA strand. If the capping group is subsequently removed to generate a free 3'-OH, the polymerase reaction will reinitialize. We report here the design and synthesis of a 3'-modified photocleavable fluorescent nucleotide, 3'-O-allyl-dUTP-PC-Bodipy-FL-510 (PC-Bodipy, photocleavable 4,4-difluoro-4-bora-3alpha,4alpha-diaza-s-indacene), as a reversible terminator for SBS. This nucleotide analogue contains an allyl moiety capping the 3'-OH group and a fluorophore Bodipy-FL-510 linked to the 5 position of the uracil through a photocleavable 2-nitrobenzyl linker. Here, we have shown that this nucleotide is a good substrate for a DNA polymerase. After the nucleotide was successfully incorporated into a growing DNA strand and the fluorophore was photocleaved, the allyl group was removed by using a Pd-catalyzed reaction to reinitiate the polymerase reaction, thereby establishing the feasibility of using such nucleotide analogues as reversible terminators for SBS.