gebhart/patrepeval huggingface dataset:
An improved reverse genetics system for influenza A virus generation and its implications for vaccine production (2005)

The generation of vaccines for highly pathogenic avian influenza viruses, including those of the H5N1 subtype, relies on reverse genetics, which allows the production of influenza viruses from cloned cDNA. In the future, reverse genetics will likely be the method of choice for the generation of conventional influenza vaccine strains because gene reassortment by more traditional methods is cumbersome. Established systems for the artificial generation of influenza A viruses require transfection of cells with the eight to 12 plasmids that provide the eight influenza viral RNAs as well as the polymerase and nucleoproteins of the virus. However, cell lines appropriate for human vaccine production (e.g., Vero cells) cannot be transfected with high efficiencies. To overcome these problems, we established a reverse genetics system in which the eight RNA polymerase I transcription cassettes for viral RNA synthesis are combined on one plasmid. Similarly, two cassettes encoding the hemagglutinin and neuraminidase segments and six cassettes encoding the remaining proteins were combined. We also combined three RNA polymerase II transcription cassettes for the expression of the polymerase subunits. By combining these cassettes, we reduced the number of plasmids required for virus generation significantly and produced influenza A virus in Vero cells with higher efficiency than with the traditional 12 plasmid system. This new system is thus suitable for influenza virus vaccine production and may be applicable to other reverse genetics systems that rely on the introduction of several plasmids into eukaryotic cells.
Fabrication and measurement of a Nb based superconducting single electron transistor (1994)

A new four-layer resist system was developed to fabricate small capacitance niobium tunnel junctions. Nb/AlOx/Al junctions were used to make a superconducting single electron transistor composed of two dc SQUIDs in series. The current-voltage characteristics were measured and two types of resonant tunneling of Cooper pairs were observed at different magnetic fields.
Preliminary demonstration of an allelic association of the IREB2 gene with Alzheimer's disease (2006)

The role of iron metabolism in Alzheimer's disease (AD) is well documented. Regulation of the proteins that maintain cellular iron metabolism is mediated by two cytoplasmic RNA-binding proteins, the Iron Regulatory Proteins (IRP1 and IRP2), that function through post-transcriptional interactions with RNA stem loop structures called iron-responsive elements. As the primary mediator of iron homeostasis in neuronal cells, IRP2 is a strong candidate for polymorphisms that could impact AD pathogenesis. Thus, we performed a pilot study to assess polymorphisms in the gene encoding IRP2 (IREB2) on clinically well-characterized, post-mortem samples (50 AD and 50 controls). DNA sequence analysis of the IREB2 gene region revealed 14 polymorphisms. Two (rs2656070 and rs13180) showed statistically significant skewing of allelic and genotypic distributions between AD patients and controls. In silico analyses revealed that rs2656070 lies within a probable promoter and disrupts the binding sites of at least two known transcription factors. Though silent and likely not functionally relevant, rs13180 is in complete LD with rs2656070 (D' > 0.999), creating an IREB2-haplotype that is significantly associated with AD. Confirmation of this association in a larger cohort of cases and controls would further support the role of iron regulation in the pathogenesis of this catastrophic and increasingly common neurodegenerative disorder.
Plasma and urinary soluble adhesion molecule expression is increased during first documented acute pyelonephritis (2002)

Plasma and urinary sE-selectin and sICAM-1 are significantly increased during acute pyelonephritis, though no correlation exists between the presence of high plasma or urine concentrations and DMSA scan changes, both during acute infection and six weeks post-infection.
A Hybrid Inductive-Ultrasonic Link for Wireless Power Transmission to Millimeter-Sized Biomedical Implants (2016)

Ultrasound has recently been utilized for efficient wireless power transmission (WPT) to biomedical implants with millimeter (mm) dimensions and below. However, the power transmission efficiency (PTE) of ultrasonic links reduces significantly in mediums with different acoustic impedances. This brief presents a hybrid inductive-ultrasonic WPT link for powering mm-sized implants that utilizes two cascaded co-optimized inductive and ultrasonic links for WPT through bone/air and tissue, respectively. The ultrasonic link is first optimized based on the implant depth (d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">us</sub> ) and load (R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L</sub> ) to find the optimal geometries for ultrasonic transducers and operation frequency (f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> ). Then, the inductive link is optimized at f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> to drive the transmitter (Tx) transducer. A hybrid link was optimized and measured to transfer power to a receiver (Rx) transducer with the diameter of 1.1 mm, loaded by R <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">L</sub> of 2.5 kQ and located at d <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">us</sub> = 3 cm inside castor oil, as the tissue model. The Tx coil was placed in air and spaced from the Rx coil by 3 cm, resulting in a total powering distance (d) of 6 cm. At the optimal f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</sub> of 1.1 MHz, the hybrid link achieved a considerable measured PTE of 0.16%.
Single-molecule sequencing detection of N6-methyladenine in microbial reference materials (2019)

The DNA base modification N6-methyladenine (m<sup>6</sup>A) is involved in many pathways related to the survival of bacteria and their interactions with hosts. Nanopore sequencing offers a new, portable method to detect base modifications. Here, we show that a neural network can improve m<sup>6</sup>A detection at trained sequence contexts compared to previously published methods using deviations between measured and expected current values as each adenine travels through a pore. The model, implemented as the mCaller software package, can be extended to detect known or confirm suspected methyltransferase target motifs based on predictions of methylation at untrained contexts. We use PacBio, Oxford Nanopore, methylated DNA immunoprecipitation sequencing (MeDIP-seq), and whole-genome bisulfite sequencing data to generate and orthogonally validate methylomes for eight microbial reference species. These well-characterized microbial references can serve as controls in the development and evaluation of future methods for the identification of base modifications from single-molecule sequencing data.
Ipso- or Cine-Substitutions of 6-Haloimidazo[1,2-a]pyridine Derivatives with Different Azoles Depending on the Reaction Conditions (2003)

The reactivity of 6-haloimidazo[1,2-a]pyridine toward different azoles is reported. The process was shown to be highly dependent on the reaction conditions. Using copper(I) catalyst, the product of ipso substitution was obtained. In the absence of copper, with cesium carbonate in N,N-dimethylformamide, a cine substitution took place.
Metabolism of phenanthrene by the marine cyanobacterium Agmenellum quadruplicatum PR-6 (1992)

Under photoautotrophic growth conditions, the marine cyanobacterium Agmenellum quadruplicatum PR-6 metabolized phenanthrene to form trans-9,10-dihydroxy-9,10-dihydrophenanthrene (phenanthrene trans-9,10-dihydrodiol) and 1-methoxyphenanthrene as the major ethyl acetate-extractable metabolites. Small amounts of phenanthrols were also formed. The metabolites were purified by high-pressure liquid chromatography and identified from their UV, infrared, mass, and proton magnetic resonance spectral properties. A. quadruplicatum PR-6 formed phenanthrene trans-9,10-dihydrodiol with a 22% enantiomeric excess of the (-)-9S,10S-enantiomer. Incorporation experiments with 18O2 showed that one atom of oxygen from O2 was incorporated into the dihydrodiol. Toxicity studies, using an algal lawn bioassay, indicated that 9-phenanthrol and 9,10-phenanthrenequinone inhibit the growth of A. quadruplicatum PR-6.
Adult Olfactory Bulb Neural Precursor Cell Grafts Provide Temporary Protection From Motor Neuron Degeneration, Improve Motor Function, and Extend Survival in Amyotrophic Lateral Sclerosis Mice (2007)

Amyotrophic lateral sclerosis is a fatal disease caused by degeneration of motor neurons (MNs). We transplanted multipotent neural precursor cell (NPC)-neurospheres from mouse olfactory bulb (OB) into the spinal cord of transgenic mice that develop MN degeneration because of human mutant superoxide dismutase-1 (mSOD1). Adult NPCs were isolated from the OB core of transgenic mice expressing green fluorescent protein, human wild-type SOD1, or human mSOD1. mSOD1 mice received lumbar spinal cord transplants of OB-NPC neurospheres at preclinical stages of disease (70 days old). Control mSOD1 mice received dead cells or recombinant green fluorescent protein. OB-NPCs attenuated the loss of motor function and wasting. They delayed disease onset to approximately 117 days, compared with control onset at approximately 90 days. The lifespan of NPC recipient mice was extended (approximately 170 days) compared with the lifespan of controls (approximately 140 days). Transplanted OB-NPCs differentiated into large spinal neurons positive for choline acetyltransferase, interneurons, and glial cells. Loss of endogenous MNs was attenuated in mSOD1 mice with transplants. New neurons formed myelinated axons and synapses. NPC-derived neurons issued axons that grew into peripheral nerve. OB-NPCs also differentiated into oligodendrocytes and astrocytes that contacted neuronal processes. We conclude that transplantation of adult OB-NPCs is therapeutic for mouse amyotrophic lateral sclerosis.
Structure of influenza virus ribonucleoprotein complexes and their packaging into virions (2010)

The influenza A virus genome consists of eight segmented, single-stranded, negative-sense RNAs. Each viral RNA (vRNA) segment forms a ribonucleoprotein (RNP) complex together with NPs and a polymerase complex, which is a fundamental unit for transcription and replication of the viral genome. Although the exact structure of the intact RNP remains poorly understood, recent electron microscopic studies have revealed certain structural characteristics of the RNP. This review focuses on the findings of these various electron microscopic analyses of RNPs extracted from virions and RNPs inside virions. Based on the morphological and structural observations, we present the architecture of RNPs within a virion and discuss the genome packaging mechanism by which the vRNA segments are incorporated into virions.
A New Etching Solution System,  H 3 PO 4 ‐  H 2 O 2 ‐  H 2 O  , for GaAs and Its Kinetics (1978)

A new solution system consisting of , , and was found useful for etching wafers. This solution system can be divided into four regions a–d, according to etching characteristics. The boundaries between the regions are given by a mole ratio of to of about 2.3 and a mole fraction of of about 0.9 at room temperature. Rate‐limiting processes are: a, adsorption of (, ); b, diffusion of (, ); c, dissolution of oxidized products (, ); and d, adsorption of (,). Solutions in region a have a reproducible etching rate of 0.01–0.1 μm/min, which is useful for MESFET processing. Crystallographic etching is also available with solutions in region c.
Hemangioblast development and regulation (1998)

Hematopoietic and endothelial cell lineages are the first to mature from mesoderm in the developing embryo. However, little is known about the molecular and (or) cellular events leading to hematopoietic commitment. The recent applications of technology utilizing gene targeted mice and the employment of many available in vitro systems have facilitated our understanding of hematopoietic establishment in the developing embryo. It is becoming clear that embryonic hematopoiesis occurs both in the extra-embryonic yolk sac and within the embryo proper in the mouse. The existence of the long pursued hemangioblast, a common progenitor of hematopoietic and endothelial cells, is now formally demonstrated. Based on this new information, many studies are being conducted to understand hematopoietic commitment events from mesoderm. In this review, we will first discuss the establishment of the hematopoietic system with special emphasis on the most primitive hematopoietic committed cells, the hemangioblast. We will then discuss mesoderm-inducing factors and their possible role in hematopoietic lineage commitment.Key words: hematopoietic commitment, hemangioblast, in vitro embryonic stem cell differentiation.
A morphable model for the synthesis of 3D faces (1999)

In this paper, a new technique for modeling textured 3D faces is introduced.3D faces can either be generated automatically from one or more photographs, or modeled directly through an intuitive user interface.Users are assisted in two key problems of computer aided face modeling.First, new face images or new 3D face models can be registered automatically by computing dense one-to-one correspondence to an internal face model.Second, the approach regulates the naturalness of modeled faces avoiding faces with an "unlikely" appearance.Starting from an example set of 3D face models, we derive a morphable face model by transforming the shape and texture of the examples into a vector space representation.New faces and expressions can be modeled by forming linear combinations of the prototypes.Shape and texture constraints derived from the statistics of our example faces are used to guide manual modeling or automated matching algorithms.We show 3D face reconstructions from single images and their applications for photo-realistic image manipulations.We also demonstrate face manipulations according to complex parameters such as gender, fullness of a face or its distinctiveness.
A new in vivo method to study P-glycoprotein transport in tumors and the blood-brain barrier. (1999)

Drug resistance is a major cause of chemotherapy failure in cancer treatment. One reason is the overexpression of the drug efflux pump P-glycoprotein (P-gp), involved in multidrug resistance (MDR). In vivo pharmacokinetic analysis of P-gp transport might identify the capacity of modulation by P-gp substrate modulators, such as cyclosporin A. Therefore, P-gp function was measured in vivo with positron emission tomography (PET) and [11C]verapamil as radiolabeled P-gp substrate. Studies were performed in rats bearing tumors bilaterally, a P-gp-negative small cell lung carcinoma (GLC4) and its P-gp-overexpressing subline (GLC4/P-gp). For validation, in vitro and biodistribution studies with [11C]daunorubicin and [11C]verapamil were performed. [11C]Daunorubicin and [11C]verapamil accumulation were higher in GLC4 than in GLC4/P-gp cells. These levels were increased after modulation with cyclosporin A in GLC4/P-gp. Biodistribution studies showed 159% and 185% higher levels of [11C]daunorubicin and [11C]verapamil, respectively, in GLC4 than in GLC4/P-gp tumors. After cyclosporin A, [11C]daunorubicin and [11C]verapamil content in the GLC4/P-gp tumor was raised to the level of GLC4 tumors. PET measurements demonstrated a lower [11C]verapamil content in GLC4/P-gp tumors compared with GLC4 tumors. Pretreatment with cyclosporin A increased [11C]verapamil levels in GLC4/P-gp tumors (184%) and in brains (1280%). This pharmacokinetic effect was clearly visualized with PET. These results show the feasibility of in vivo P-gp function measurement under basal conditions and after modulation in solid tumors and in the brain. Therefore, PET and radiolabeled P-gp substrates may be useful as a clinical tool to select patients who might benefit from the addition of a P-gp modulator to MDR drugs.
Apoptotic rate: A new indicator for the quantification of the incidence of apoptosis in cell cultures (2002)

This study reveals the superiority of the proposed method over the widely used Nicoletti method and current annexin-V binding methods. The AI did not reflect the true incidence of lymphocyte apoptosis, neither in response to lectins or phorbol esters, nor to serum deprivation. AR was more sensitive than AI, detecting apoptosis at lower concentrations of cell death inducers in all the subsets studied.
Functional evidence for a nasopharyngeal carcinoma tumor suppressor gene that maps at chromosome 3p21.3 (1998)

Nasopharyngeal carcinoma is a malignancy that is prevalent among populations from Southeast Asia. Epidemiological studies indicate that genetic predisposition, Epstein-Barr virus, and environmental conditions may play a role in determining incidence. Molecular studies have implicated a tumor suppressor gene(s) on the short arm of chromosome 3. In this study we provide functional evidence, via monochromosome transfer, for a tumor suppressor gene(s) activity in chromosome 3p21.3.
Physical characterisation and over-expression of theBacillus caldotenaxsuperoxide dismutase gene (1992)

The gene (sod) encoding Bacillus caldotenax (BC) Mn-superoxide dismutase (MnSOD) has been cloned in Escherichia coli and its entire nucleotide sequence determined. Within the coding region of the gene there were 21 nucleotide differences to the previously sequenced sod of Bacillus stearothermophilus (BS). The predicted amino acid sequence of BCMnSOD had two amino acid dissimilarities to the BSMnSOD, containing Asp and Val at positions 13 and 188, respectively, compared to Glu and Ile at the respective equivalent positions of BSMnSOD. Recombinant BCMnSOD was shown to be functionally active in E. coli, both in vitro and in vivo, and was produced at levels representing over 40% of the cells' soluble protein by coupling sod transcription to the E. coli trp promoter. The sequenced region of DNA was also found to encompass part of a second open-reading frame, of unknown function, previously noted 3′ to the B. stearothermophilus gene.
The Abdominal Trauma Index—A Critical Reassessment and Validation (1990)

The Abdominal Trauma Index (ATI) was devised to quantify the risk of complications following abdominal trauma. With scores greater than 25, the risk of postoperative complications became exponential. The purpose of the present study was to determine if: 1) the organ risk factors previously assigned were more statistically valid; and 2) the addition of physiologic variables would enhance the prediction of postinjury intra-abdominal sepsis. Fifteen abdominal organ systems and 17 physiologic variables in 300 consecutive patients were analyzed to determine ability to predict intraabdominal sepsis. There were no significant differences in predictive ability between the old and new organ risk factors. The addition of physiologic factors did not enhance the prediction of intra-abdominal sepsis. This clinical study demonstrates that: 1) the risk of intra-abdominal sepsis increases with increasing ATI score; 2) the previous (1979-initial) organ risk grading concept is statistically valid; 3) six of the 15 organ systems warrant a change in their relative rank order (1989-revision); 4) the addition of demographic, physiologic, and immunologic variables did not significantly improve the prediction of intra-abdominal sepsis.
The intergroup rhabdomyosarcoma study-II (1993)

Combining all Groups and treatments in IRS-II, the major improvement in S rate at 5 years between studies was in nonmetastatic patients (71% for IRS-II versus 63% for IRS-I, P = 0.01).
Toward a Universal Influenza Virus Vaccine: Prospects and Challenges (2013)

Current influenza virus vaccines are annually reformulated to elicit protection by generating an immune response toward the virus strains that are predicted to circulate in the upcoming influenza season. These vaccines provide limited protection in cases of antigenic mismatch, when the vaccine and the circulating viral strains differ. The emergence of unexpected pandemic viruses presents an additional challenge to vaccine production. To increase influenza virus preparedness, much work has been dedicated to the development of a universal vaccine. Focusing on regions of viral proteins that are highly conserved across virus subtypes, vaccine strategies involving the matrix 2 protein, stalk domain of the hemagglutinin, and multivalent approaches have provided broad-based protection in animal models and show much promise. This review summarizes the most encouraging advances in the field with a focus on novel vaccine designs that have yielded promising preclinical and clinical data.
Adenovirus 5 early region 1A host range mutants hr3, hr4, and hr5 contain point mutations which generate single amino acid substitutions (1985)

The early region 1A (E1A) gene of adenovirus 5 encodes two proteins, 289AA and 243AA, which are translated from mRNAs of 13S and 12S, respectively. These two E1A proteins are identical except for an internal stretch of 46 amino acids unique to the larger protein. The 289AA protein activates transcription from promoters of other early adenoviral genes. The adenovirus type 5 host range mutants hr3, hr4, and hr5 are unable to activate transcription of these early viral genes. We show here that hr3, hr4, and hr5 each contain a distinct missense mutation in the E1A gene. We first localized the mutations in a series of constructed wild-type-hr hybrid E1A genes by using a biological assay which can discriminate between functional and nonfunctional E1A proteins. We then identified the mutations by DNA sequencing. In hr3 lysine replaced methionine at position 176, and in hr4 phenylalanine replaced leucine at position 173; both substitutions occurred in the region unique to the 289AA protein. In hr5, due to the splicing patterns of the two mRNAs, asparagine replaced serine as the last amino acid in the unique region of the 289AA protein at position 185, while aspartic acid replaced glycine at position 139 in the 243AA protein, which is the last amino acid common to both proteins before the unique region. These results substantiate the role of the 289AA protein in transcriptional activation and underscore the importance of the unique region as the basis of the functional difference between the two E1A proteins. Implications as to how these mutations affect the structure and function of the E1A proteins in transcriptional activation and transformation are discussed.
Possible Involvement of Toluene-2,3-Dioxygenase in Defluorination of 3-Fluoro-Substituted Benzenes by Toluene-Degrading Pseudomonas sp. Strain T-12 (1989)

Pseudomonas sp. strain T-12 cells in which the toluene-degradative pathway enzymes have been induced can transform many 3-fluoro-substituted benzenes to the corresponding 2,3-catechols with simultaneous elimination of the fluorine substituent as inorganic fluoride. Substrates for this transformation included 3-fluorotoluene, 3-fluorotrifluorotoluene, 3-fluorohalobenzenes, 3-fluoroanisole, and 3-fluorobenzonitrile. While 3-fluorotoluene and 3-fluoroanisole produced only defluorinated catechols, other substrates generated catechol products with and without the fluorine substituent. The steric size of the C-1 substituent affected the ratio of defluorinated to fluorinated catechols formed from a substrate. A mechanism for the defluorination reaction involving toluene-2,3-dioxygenase is proposed.
Protective effect of yogurt extract on dental enamel demineralization in vitro (2008)

The results demonstrated that CPPs contained in yogurt have an inhibitory effect on demineralization and promote the remineralization of dental enamel.
Suicide Risk and Treatments for Patients With Bipolar Disorder (2003)

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