gebhart/patrepeval huggingface dataset:
Attenuation of the Langat tick-borne flavivirus by chimerization with mosquito-borne flavivirus dengue type 4 (1998)

Langat virus (LGT) strain TP21 is the most attenuated of the tick-borne flaviviruses for humans. Even though LGT has low-level neurovirulence for humans, it, and its more attenuated egg-passage derivative, strain E5, exhibit significant neurovirulence and neuroinvasiveness in normal mice, albeit less than that associated with tick-borne encephalitis virus (TBEV), the most virulent of the tick-borne flaviviruses. We sought to reduce or ablate these viral phenotypes of TP21 and E5 by using a strategy that had been used successfully in the past to reduce neurovirulence and abolish neuroinvasiveness of TBEV, namely substitution of structural protein genes of the tick-borne flavivirus for the corresponding genes of dengue type 4 virus (DEN4). In pursuit of these objectives different combinations of LGT genes were substituted into the DEN4 genome but only chimeras containing LGT structural proteins premembrane (preM) and envelope glycoprotein (E) were viable. The infectious LGT(preM-E)/DEN4 chimeras were restricted in replication in simian cell cultures but grew to moderately high titer in mosquito cell culture. Also, the chimeras were at least 5,000 times less neurovirulent than their parental LGT virus in suckling mice. Significantly, the chimeras lacked detectable evidence of neuroinvasiveness after i.p. inoculation of Swiss mice or the more permissive SCID mice with 10(5) or 10(7) plaque-forming units (PFU), respectively. Nonetheless, i.p. inoculation of Swiss mice with 10 or 10(3) PFU of either chimeric virus induced LGT neutralizing antibodies and resistance to fatal encephalitis caused by i.p. challenge with LGT TP21. The implications of these observations for development of a live attenuated TBEV vaccine are discussed.
Content-based, collaborative recommendation (1997)

By combining both collaborative and content-based filtering systems, Fab may eliminate many of the weaknesses found in each approach. ONLINE READERS ARE IN NEED OF TOOLS TO HELP THEM COPE with the mass of content available on the World-Wide Web. In traditional media, readers are provided assistance in making selections. This includes both implicit assistance in the form of editorial oversight and explicit assistance in the form of recommendation services such as movie reviews and restaurant guides. The electronic medium offers new opportunities to create recommendation services, ones that adapt over time to track their evolving interests. Fab is such a recommendation system for the Web, and has been operational in several versions since December 1994. The problem of recommending items from some fixed database has been studied extensively, and two main paradigms have emerged. In content-based recommendation one tries to recommend items similar to those a given user has liked in the past, whereas in collaborative recommendation one identifies users whose tastes are similar to those of the given user and recommends items they have liked. Our approach in Fab has been to combine these two methods. Here, we explain how a hybrid system can incorporate the advantages of both methods while inheriting the disadvantages of neither. In addition to what one might call the “generic advantages ” inherent in any hybrid system, the particular design of the Fab architecture brings two additional benefits. First, two scaling problems common to all Web services are addressed—an increas-
Diverse specificity and effector function among human antibodies to HIV-1 envelope glycoprotein epitopes exposed by CD4 binding (2012)

The HIV-1 envelope glycoprotein (Env) undergoes conformational transitions consequent to CD4 binding and coreceptor engagement during viral entry. The physical steps in this process are becoming defined, but less is known about their significance as targets of antibodies potentially protective against HIV-1 infection. Here we probe the functional significance of transitional epitope exposure by characterizing 41 human mAbs specific for epitopes exposed on trimeric Env after CD4 engagement. These mAbs recognize three epitope clusters: cluster A, the gp120 face occluded by gp41 in trimeric Env; cluster B, a region proximal to the coreceptor-binding site (CoRBS) and involving the V1/V2 domain; and cluster C, the coreceptor-binding site. The mAbs were evaluated functionally by antibody-dependent, cell-mediated cytotoxicity (ADCC) and for neutralization of Tiers 1 and 2 pseudoviruses. All three clusters included mAbs mediating ADCC. However, there was a strong potency bias for cluster A, which harbors at least three potent ADCC epitopes whose cognate mAbs have electropositive paratopes. Cluster A epitopes are functional ADCC targets during viral entry in an assay format using virion-sensitized target cells. In contrast, only cluster C contained epitopes that were recognized by neutralizing mAbs. There was significant diversity in breadth and potency that correlated with epitope fine specificity. In contrast, ADCC potency had no relationship with neutralization potency or breadth for any epitope cluster. Thus, Fc-mediated effector function and neutralization coselect with specificity in anti-Env antibody responses, but the nature of selection is distinct for these two antiviral activities.
Two different algorithms for seismic interference noise attenuation (2008)

This paper illustrates an automatic seismic interference noise attenuation algorithm and suggests studies to determine the propagation mechanism of seismic interference noise to help devise better algorithms. It also introduces another algorithm that relies on the assumption of a simple propagation mechanism to detect interfering source locations to attenuate such noise.
Structural insight into enhanced calcium indicator GCaMP3 and GCaMPJ to promote further improvement (2013)

Genetically encoded Ca(2+) indicators (GECI) are important for the measurement of Ca(2+) in vivo. GCaMP2, a widely-used GECI, has recently been iteratively improved. Among the improved variants, GCaMP3 exhibits significantly better fluorescent intensity. In this study, we developed a new GECI called GCaMPJ and determined the crystal structures of GCaMP3 and GCaMPJ. GCaMPJ has a 1.5-fold increase in fluorescence and 1.3-fold increase in calcium affinity over GCaMP3. Upon Ca(2+) binding, GCaMP3 exhibits both monomeric and dimeric forms. The structural superposition of these two forms reveals the role of Arg-376 in improving monomer performance. However, GCaMPJ seldom forms dimers under conditions similar to GCaMP3. St ructural and mutagenesis studies on Tyr-380 confirmed its importance in blocking the cpEGFP β-barrel holes. Our study proposes an efficient tool for mapping Ca(2+) signals in intact organs to facilitate the further improvement of GCaMP sensors.
Postcolonialism and Globalization (2020)

The position of Australia in a globalised postcolonial world is analysed, highlighting its ideological shift from England through the United States to Asia and the Pacific region. It is suggested that an Australian understanding of its violent settler past and its efforts to respect and treat all Aborigines and non-Aborigines equally would make it more suited to a better position in a postcolonial global order.
Epidermal growth factor receptor blockade with C225 modulates proliferation, apoptosis, and radiosensitivity in squamous cell carcinomas of the head and neck. (1999)

We examined effects of the anti-epidermal growth factor receptor monoclonal antibody C225 on proliferation, cell cycle phase distribution, apoptosis, and radiosensitivity in squamous cell carcinoma (SCC) cell lines derived from head and neck cancer patients. Exposure to C225 in culture inhibits SCC proliferation in a time-dependent manner, and the degree of growth inhibition, compared to controls, ranges from 20 to 75%. Flow cytometry analysis demonstrates that C225 treatment induces accumulation of cells in G1, which is accompanied by a 2-3-fold decrease in the percentage of cells in S phase. C225 exposure also induces apoptosis in SCC populations, as demonstrated by flow cytometry analysis using dual stainings of merocyanine 540 and Hoechst 33342. Western blot analysis indicates that C225 exposure induces accumulation of hypophosphorylated retinoblastoma protein and increases expression of p27KIP1. An increase in Bax expression and concurrent decrease in Bcl-2 expression are observed when SCC cells are exposed to C225. Examination of C225 effects on radiation response in SCCs demonstrates enhancement in radiosensitivity and amplification of radiation-induced apoptosis. These effects are observed in both single-dose and fractionated radiation experiments. C225 represents a promising growth-inhibitory agent that can influence cellular proliferation, apoptosis, and radiosensitivity in SCCs of the head and neck.
rRNA probe‐based cell fishing of bacteria (1999)

We have developed a new, cultivation-independent, fast and flexible method for the rRNA-targeted probe-based enrichment of bacteria. The target cells were labelled by in situ hybridization with biotinylated polyribonucleotide probes. These probes were generated by in vitro transcription of amplified rDNA of a variable region in domain III of the 23S rRNA molecules. The probes were about 300 nucleotides in length and were labelled by incorporation of biotin-UTP during the transcription. Probes were hybridized with bacterial cells and incubated with paramagnetic streptavidin-coated particles. The labelled target cells can be separated in a column filled with steel wool inserted into the field of a permanent magnet. Unlabelled, non-target cells pass through the column, whereas labelled cells are retained. They were eluted from the column after removal of the magnetic field. Up to now, the method has been tested with mixtures of different pure cultures. For the first time, transcript probes have been used for the labelling of the target cells and for their specific separation. The enrichment of the target cells can be monitored by a streptavidin-fluorescein staining of the biotinylated target cells and/or by a subsequent in situ hybridization with fluorescently labelled oligonucleotide probes. Enrichment rates of up to 90-fold, depending on the original abundance of the cells of interest, could be determined. To demonstrate that the sorted cells were amenable to molecular analysis, we amplified and sequenced a part of the tuf gene of enriched Acinetobacter calcoaceticus cells.
The use of a guide catheter extension system as an aid during transradial percutaneous coronary intervention of coronary artery bypass grafts (2011)

The use of guide catheter extension systems facilitated transradial graft intervention via several mechanisms including aid to graft cannulation, increasing backup support, and as an adjunctive aspiration device.
Fusarium-Induced Osteochondrosis (Tibial Dyschondroplasia) in Chickens (1982)

Broiler chickens were started and maintained on rations containing 2%, 5%, and 10% grain contaminated with Fusarium roseum. There was mortality of 75% and 100%, respectively, in chicks fed 5% and 10% levels, and osteochondrosis was present in chicks which died at 12 to 17 days of age. Chicks on 2% or 3% F. roseum-contaminated grain survived the experimental period and osteochondrosis was well-developed in the proximal tibias of 85 or 99% of these chicks. The number of chondroclasts was reduced markedly in the affected bones. Defective chondroclasis may play a role in the pathogenesis of osteochondrosis associated with F. roseum.
High-Throughput Lens-Free Blood Analysis on a Chip (2010)

We present a detailed investigation of the performance of lens-free holographic microscopy toward high-throughput on-chip blood analysis. Using a spatially incoherent source that is emanating from a large aperture, automated counting of red blood cells with minimal sample preparation steps at densities reaching up to approximately 0.4 x 10(6) cells/muL is presented. Using the same lens-free holographic microscopy platform, we also characterize the volume of the red blood cells at the single-cell level through recovery of the optical phase information of each cell. We further demonstrate the measurement of the hemoglobin concentration of whole blood samples as well as automated counting of white blood cells, also yielding spatial resolution at the subcellular level sufficient to differentiate granulocytes, monocytes, and lymphocytes from each other. These results uncover the prospects of lens-free holographic on-chip imaging to provide a useful tool for global health problems, especially by facilitating whole blood analysis in resource-poor environments.
Controlled Assembly of Hydrogenase-CdTe Nanocrystal Hybrids for Solar Hydrogen Production (2010)

We present a study of the self-assembly, charge-transfer kinetics, and catalytic properties of hybrid complexes of CdTe nanocrystals (nc-CdTe) and Clostridium acetobutylicum [FeFe]-hydrogenase I (H(2)ase). Molecular assembly of nc-CdTe and H(2)ase was mediated by electrostatic interactions and resulted in stable, enzymatically active complexes. The assembly kinetics was monitored by nc-CdTe photoluminescence (PL) spectroscopy and exhibited first-order Langmuir adsorption behavior. PL was also used to monitor the transfer of photogenerated electrons from nc-CdTe to H(2)ase. The extent to which the intramolecular electron transfer (ET) contributed to the relaxation of photoexcited nc-CdTe relative to the intrinsic radiative and nonradiative (heat dissipation and surface trapping) recombination pathways was shown by steady-state PL spectroscopy to be a function of the nc-CdTe/H(2)ase molar ratio. When the H(2)ase concentration was lower than the nc-CdTe concentration during assembly, the resulting contribution of ET to PL bleaching was enhanced, which resulted in maximal rates of H(2) photoproduction. Photoproduction of H(2) was also a function of the nc-CdTe PL quantum efficiency (PLQE), with higher-PLQE nanocrystals producing higher levels of H(2), suggesting that photogenerated electrons are transferred to H(2)ase directly from core nanocrystal states rather than from surface-trap states. The duration of H(2) photoproduction was limited by the stability of nc-CdTe under the reactions conditions. A first approach to optimization with ascorbic acid present as a sacrificial donor resulted in photon-to-H(2) efficiencies of 9% under monochromatic light and 1.8% under AM 1.5 white light. In summary, nc-CdTe and H(2)ase spontaneously assemble into complexes that upon illumination transfer photogenerated electrons from core nc-CdTe states to H(2)ase, with low H(2)ase coverages promoting optimal orientations for intramolecular ET and solar H(2) production.
Active terahertz metamaterials (2010)

In this paper we present an overview of research in our group in terahertz (THz) metamaterials and their applications. We have developed a series of planar metamaterials operating at THz frequencies, all of which exhibit a strong resonant response. By incorporating natural materials, e.g., semiconductors, as the substrates or as critical regions of metamaterial elements, we are able to effectively control the metamaterial resonance by the application of external stimuli, e.g., photoexcitation and electrical bias. Such actively controllable metamaterials provide novel functionalities for solid-state device applications with unprecedented performance, such as THz spectroscopy, imaging, and many others.
Development of Radiation Image Sensor using Heterojunction (2009)

In this study, the basic research verifying possibility of applications as radiology image sensor in Digital Radiography was performed, the radiology image sensor was fabricated using double layer technique tio decrease dark current. High efficiency material in substitution for a-Se have been studied as a direct method of imaging detector in Digital Radiography to decrease dark current by using Hetero junction already used as solar cell, semiconductor. Particle-In-Binder method is used to fabricate radiology image sensor because it has a lot of advantages such as fabrication convenient, high yield, suitability for large area sensor. But high leakage current is one of main problem in PIB method. To make up for the weak points, double layer technique is used, and it is considered that high efficient digital radiation sensor can be fabricated with easy and convenient process. In this study, electrical properties such as leakage current, sensitivity is measured to evaluate double layer radiation sensor material.
RNase H cleavage for processing of in vitro transcribed RNA for NMR studies and RNA ligation. (1996)

Large quantities of RNA for study by NMR and X-ray crystallography can be produced by transcription reactions in vitro using T7 bacteriophage RNA polymerase. A limitation on producing RNA with this polymerase has been the strong dependence of the yield of the transcription reaction on the sequence at the 5' end of the RNA produced. We report a procedure for obtaining large quantities of enzymatically synthesized RNA from T7 RNA polymerase that has no dependence on the 5' end sequence of the target RNA. Ribonuclease H has been shown previously (Inoue H, Hayase Y, Iwai S, Ohtsuka E, 1987, FEBS Lett 215:327-330) to cleave RNA site specifically using 2'-O-methyl RNA/DNA chimeras to direct the cleavage site. We show that 2'-O-methyl RNA nucleotides on the 5'-side of the DNA nucleotides in the chimera are not essential for site-specific cleavage. This allowed us to design the method such that the same 2'-O-methyl chimera may be used to process any RNA sequence. We have adapted this reaction to the cleavage of NMR-scale quantities of RNA at high yield. RNA is synthesized using T7 RNA polymerase with a 15-nt high-yielding leader sequence at the 5' end, and then this sequence is cleaved off with the RNase H cleavage reaction. The cleaved RNA has 3'-hydroxyl and 5'-phosphate ends, so that the products can be used directly as substrates for ligation by T4 DNA ligase. We show that the cleavage reaction occurs efficiently in solution and on a solid streptavidin/agarose matrix. We report an example in which we are able to improve transcription yield by more than five-fold using this technique in the synthesis of a 15N isotopically labeled hairpin found in the Crithidia fasciculata spliced leader RNA. We are able to obtain a 0.5-mM NMR sample from this inherently poorly transcribing sequence, while minimizing the amount of isotopically labeled rNTPs used to produce it. The NMR spectroscopic results are consistent with the predicted RNA secondary structure.
The Dynamic Range of Neonatal Heart Rate Variability (1994)

Recovery from severe neonatal illness is accompanied by large and rapid increases in heart rate variability, but not by large changes in heart rate. This increase can be effectively assessed in the time domain, in the frequency domain, and by using a neural network.
A class of codes for asymmetric channels and a problem from the additive theory of numbers (1973)

A method of constructing codes capable of correcting an arbitrary number of asymmetrical errors is given. The method is related to a problem in the additive theory of numbers.
Characteristics of Sustained Blood-Brain Barrier Opening and Tissue Injury in a Model for Focal Trauma in the Rat (2001)

Minor stab wounding of rodent brain by needle or razor blade is a standard model for immunohistochemical investigations of secondary neuronal degeneration and scarring. Opening of the blood-brain barrier (BBB) to plasma molecules and inflammatory cells is integral to the secondary injury process. To facilitate quantitative study of these BBB phenomena, we tested the utility of a stereotaxic wire knife as a minimally invasive way for modeling of focal trauma and bleeding in brain parenchyma and substantial, reproducible BBB damage. Adult rats were anesthetized, and through a skull burr hole, the 0.3-mm dia guide cannula housing a laterally extendable tungsten wire (0.13 mm dia) was inserted into the right striatum. A layering of horizontal disk-like cuts (3 mm dia) was made, producing a cylindrical lesion of approximately 18 mm3 volume, approximately 2.7% of the cerebral hemisphere. Transfer constants (Ki) for blood to brain permeation of [3H]sucrose measured from 30 min to 2 weeks postlesion showed sustained BBB leakiness; for example, mean Ki +/- SEM (nL.g(-1) x s(-1)) for a standard, matrix-dissected forebrain sample enclosing the lesion were 7.2 +/- 1.2 (day 1 postlesion), 8.1 +/-1.4 (day 3), 5.4 +/- 0.8 (day 14) compared with values for contralateral nonlesioned forebrain ranging from 1.3 +/- 0.05 to 1.6 +/- 0.3 (n = 3-4 samples per time point). Analysis of the simultaneous transport of [14C]sucrose (MW = 342 Da) and [3H]inulin (MW approximately 5,000) showed significantly larger upward increments in Ki for sucrose than inulin, indicating a pore-like opening mechanism. Significant edema was measured 3 days postlesion. A reactive glial response was indicated by an increase in S100beta by 6 h and a glial scar forming around the lesion by 7 days. Secondary brain injury was indicated by a 10% loss of hemisphere mass, measured at 2 months. The wire knife enabled tailoring of interstitial trauma with a minimum of extraneous injury and supported reproducible measurements of sustained BBB injury using relatively few animals.
Recombinant protein-based polymers for advanced drug delivery (2012)

Advances in recombinant techniques have led to the development of genetically engineered polymers with exquisite control over monomer sequence and polymer length. The ability to study how precise structures correlate with function has provided opportunities for the utility of these polymers in drug delivery. Chemically derived and developed methods of synthesis have yielded many useful polymers for drug delivery to-date, including those currently used in patients. However they have drawbacks, including limitations involved in statistical characterization of conventional polymer synthetic techniques. Encoding at the genetic level and production of such recombinant polymers in organisms allow for precise order and accuracy of amino acid residues and production of monodisperse polymers with specific function and physicochemical properties. Research into elastin-like, silk-like, and silk-elastinlike protein polymers for example has led to the development of delivery systems based on natural motifs of structural proteins to take advantage of their physicochemical properties. Additionally, protein based polymers on other natural motifs and de novo designs are starting to produce promising constructs for drug and gene delivery applications where precise control over structure promises correlation with function and guides the development of new and improved constructs. Clinical applications based on recombinant polymers for delivery of bioactive agents have not been realized at this point. However lessons learned from fundamental research with these polymers can be used to guide design of safe and effective systems for use in the clinic. This tutorial review summarizes progress made in the design and utility of recombinant polymers in drug and gene delivery and discusses challenges and future directions of such polymers for this purpose.