gebhart/patrepeval huggingface dataset:
Vaccinia Vectors as Candidate Vaccines: The Development of Modified Vaccinia Virus Ankara for Antigen Delivery (2003)

Vaccinia viruses engineered to express foreign genes are powerful vectors for production of recombinant proteins. Originating from highly efficacious vaccines securing world-wide eradication of smallpox, the most appealing use of vaccinia vectors is to serve as vaccine delivery system for heterologous antigens. Concerns about the safety of vaccinia virus have been addressed by the development of vectors based on attenuated viruses. One of them, modified vaccinia virus Ankara (MVA) can be considered as current vaccinia virus strain of choice for clinical investigation. Historical development and use of MVA as vaccine against smallpox allowed to establish an extraordinary safety profile. MVA can be used under conditions of biosafety level 1 because of its avirulence and its deficiency to productively grow in human cells. In recent years significant progress has been made with regard to the development of MVA vector technologies. Compared to replication competent vaccinia viruses, MVA provides similar levels of recombinant gene expression even in nonpermissive cells. In animal models, MVA vaccines have been found immunogenic and protective against various infectious agents including immunodeficiency viruses, influenza, parainfluenza, measles virus, flaviviruses, or plasmodium parasites. By now first data from clinical trials are becoming available. In this article we briefly review history of MVA and state-of-the art technologies with regard to generation of recombinant MVA vaccines, and describe the progress to develop MVA vector vaccines against important infectious diseases.
T1ρ Magnetic Resonance Imaging and Discography Pressure as Novel Biomarkers for Disc Degeneration and Low Back Pain (2011)

T1ρ and OP are quantitative measures of degeneration that are consistent across both control subjects and LBP patients. A significant and strong correlation exists between T1ρ values and in vivo OP measurements obtained by discography in LBP patients.
Gene Expression Profiling of Breast Cancers with Emphasis of β-Catenin Regulation (2004)

To gain molecular understanding of carcinogenesis of breast cancer, gene expression profiles were analyzed using cDNA microarray representing 4,600 cDNAs in 10 breast cancer samples and the adjacent noncancerous breast tissues from the same patients. The alterations in gene expression levels were confirmed by reversetranscription PCR in four randomly selected genes. Genes that were differently expressed in cancer and noncancerous tissues were identified. 106 (of which 55 were known) and 49 (of which 28 were known) genes were up- or down-regulated, respectively, in greater than 60% of the breast cancer samples. In cancer tissues, genes related to cell cycle, transcription, metabolism, cell structure/motility and signal transduction were mostly up-regulated. Furthermore, three cancer tissues showing immunohistochemically aberrant accumulation of beta-catenin in the nucleus and/or cytoplasm revealed down-regulation of Siah and Axin genes and up-regulation of Wnt and c-myc genes. These findings were highly consistent with Wnt signaling pathway associated with beta-catenin regulation previously suggested by others. Our studies, therefore, provide not only a molecular basis to understand biological processes of breast cancer but also useful resources to define the mechanism of beta-catenin expression in tumorigenesis of breast cancer.
The complete phosphotransferase system in Escherichia coli. (2001)

We here tabulate and describe all currently recognized proteins of the phosphoenolpyruvate:sugar phosphotransferase system (PTS) and their homologues encoded within the genomes of sequenced E. coli strains. There are five recognized Enzyme I homologues and six recognized HPr homologues. A nitrogen-metabolic PTS phosphoryl transfer chain encoded within the rpoN and ptsP operons and a tri-domain regulatory PTS protein encoded within the dha (dihydroxyacetone catabolic) operon, probably serve regulatory roles exclusively. In addition to several additional putative regulatory proteins, there are 21 (and possibly 22) recognized Enzyme II complexes. Of the 21 Enzyme II complexes, 7 belong to the fructose (Fru) family, 7 belong to the glucose (Glc) family, and 7 belong to the other PTS permease families. All of these proteins are briefly described, and phylogenetic data for the major families are presented.
Radiofluorinated Derivatives of 2-(Phosphonomethyl)pentanedioic Acid as Inhibitors of Prostate Specific Membrane Antigen (PSMA) for the Imaging of Prostate Cancer (2012)

For prostate cancer, prostate specific membrane antigen (PSMA) has been identified as a diagnostic and therapeutic target. Fluorinated derivatives of 2-(phosphonomethyl)pentanedioic acid were designed and synthesized to explore whether this fluorine-substituent is tolerated in the pentanedioic acid moiety that is common to almost all PSMA targeting small molecule inhibitors. The binding affinities of the racemic and individual stereoisomers of 2-fluoro-4-(phosphonomethyl)pentanedioic acid were determined and showed that the introduction of fluorine was well tolerated. The radiosynthesis of the analogous 2-[(18)F]fluoro-4-(phosphonomethyl)pentanedioic acid was developed and evaluated in vivo with the PSMA positive LNCaP human prostate cancer cell. The biological results demonstrated specific binding of the tracer to PSMA positive tumors in mice. These results warrant the further evaluation of this class of compounds as radiolabeled tracers for the detection and staging of prostate cancer.
High level protein expression in plants through the use of a novel autonomously replicating geminivirus shuttle vector (2009)

We constructed a novel autonomously replicating gene expression shuttle vector, with the aim of developing a system for transiently expressing proteins at levels useful for commercial production of vaccines and other proteins in plants. The vector, pRIC, is based on the mild strain of the geminivirus Bean yellow dwarf virus (BeYDV-m) and is replicationally released into plant cells from a recombinant Agrobacterium tumefaciens Ti plasmid. pRIC differs from most other geminivirus-based vectors in that the BeYDV replication-associated elements were included in cis rather than from a co-transfected plasmid, while the BeYDV capsid protein (CP) and movement protein (MP) genes were replaced by an antigen encoding transgene expression cassette derived from the non-replicating A. tumefaciens vector, pTRAc. We tested vector efficacy in Nicotiana benthamiana by comparing transient cytoplasmic expression between pRIC and pTRAc constructs encoding either enhanced green fluorescent protein (EGFP) or the subunit vaccine antigens, human papillomavirus subtype 16 (HPV-16) major CP L1 and human immunodeficiency virus subtype C p24 antigen. The pRIC constructs were amplified in planta by up to two orders of magnitude by replication, while 50% more HPV-16 L1 and three- to seven-fold more EGFP and HIV-1 p24 were expressed from pRIC than from pTRAc. Vector replication was shown to be correlated with increased protein expression. We anticipate that this new high-yielding plant expression vector will contribute towards the development of a viable plant production platform for vaccine candidates and other pharmaceuticals.
SWR Mice Are Highly Susceptible to Pulmonary Infection with Mycobacterium tuberculosis (2003)

Inbred mice differ in their abilities to control the growth of Mycobacterium tuberculosis in the lung and can as a result be regarded as either resistant or susceptible strains. In this study we report that the SWR mouse is both highly susceptible and in addition appears incapable of establishing a characteristic state of chronic disease after low-dose aerosol infection. In comparison to C57BL/6 mice, SWR mice were unable to contain the bacterial load in the lungs, resulting in progressive fatal disease. Histologic analysis of the lung tissue revealed evidence of a florid inflammatory cell response in the SWR mice leading to degeneration and necrosis and consolidation of a large percentage of the lung surface area. Digestion of infected lungs and analysis by flow cytometry demonstrated an initially similar but eventually higher number of lymphocytes accumulating in the SWR mice. Additionally, in contrast to the C57BL/6 mice, SWR mice had a significantly lower percentage of CD4 T cells in the lungs showing evidence of proliferation and positive intracellular staining for gamma interferon during the first two months of infection, and a lower percentage of both CD4 and CD8T cells exhibiting differentiation to an effector/memory phenotype during the first month of infection. We propose that further investigation of the SWR mouse may provide a new animal model for immunocompetent individuals apparently unable to effectively control the growth of M. tuberculosis in the lung.
The Rhizobium meliloti exoZl exoB fragment of megaplasmid 2: ExoB functions as a UDP‐glucose 4‐epimerase and ExoZ shows homology to NodX of Rhizobium leguminosarum biovar viciae strain TOM (1991)

A 2.6 kb ClaI-BamHI DNA fragment of megaplasmid 2 of Rhizobium meliloti 2011 was found to carry genes involved in exopolysaccharide synthesis and infection of alfalfa nodules. The analysis of the nucleotide sequence of this DNA fragment revealed the existence of two open reading frames (ORFs) running in opposite directions. Plasmid integration mutagenesis showed that these ORFs are organized as two monocistronic transcription units. One of the ORFs represents a new exo gene designated exoZ, which is involved in, but not essential for, the production of acidic exopolysaccharide. However, exoZ is not necessary for nodule formation with alfalfa. The ExoZ protein was found to show homology (23.3%) to the NodX protein of the R. leguminosarum biovar viciae strain TOM, known to be essential for nodulating the primitive Afghanistan pea. The second identified ORF corresponds to the exoB locus. The deduced amino acid sequence of the ExoB protein is homologous (39.6%) to that of the Escherichia coli GalE protein. In R. meliloti, exoB codes for a UDP-glucose 4-epimerase. A deficiency in the activity of this enzyme fully accounts for all the multiple carbohydrate defects that have been observed in exoB mutants.
Identification of a Cytopathogenic Agent Infectious for Puppies as a Canine Herpesvirus. (1965)

An agent (strain F-205V) isolated in dog kidney cell cultures from puppies that died of a fatal hemorrhagic disease has been identified as a cytopathogenic virus. Properties of the virus indicate that it is a canine herpesvirus.
Chemopreventive Effects of Cuminum cyminum in Chemically Induced Forestomach and Uterine Cervix Tumors in Murine Model Systems (2003)

Lately, a strong correlation has been established between diet and cancer. For ages, cumin has been a part of the diet. It is a popular spice regularly used as a flavoring agent in a number of ethnic cousins. In the present study, cancer chemopreventive potentials of different doses of a cumin seed-mixed diet were evaluated against benzo(a)pyrene [B(a)P]-induced forestomach tumorigenesis and 3-methylcholanthrene (MCA)-induced uterine cervix tumorigenesis. Results showed a significant inhibition of stomach tumor burden (tumors per mouse) by cumin. Tumor burden was 7.33 +/- 2.10 in the B(a)P-treated control group, whereas it reduced to 3.10 +/- 0.57 (P < 0.001) by a 2.5% dose and 3.11 +/- 0.60 (P <0.001) by a 5% dose of cumin seeds. Cervical carcinoma incidence, compared with the MCA-treated control group (66.67%), reduced to 27.27% (P < 0.05) by a diet of 5% cumin seeds and to 12.50% (P < 0.05) by a diet of 7.5% cumin seeds. The effect of 2.5 and 5% cumin seed-mixed diets was also examined on carcinogen/xenobiotic metabolizing phase I and phase II enzymes, antioxidant enzymes, glutathione content, lactate dehydrogenase (LDH), and lipid peroxidation in the liver of Swiss albino mice. Levels of cytochrome P-450 (cyt P-450) and cytochrome b5 (cyt b(5)) were significantly augmented (P < 0.05) by the 2.5% dose of cumin seed diet. The levels of cyt P-450 reductase and cyt b(5) reductase were increased (significance level being from P < 0.05 to P < 0.01) by both doses of cumin. Among the phase II enzymes, glutathione S-transferase specific activity increased (P < 0.005) by the 5% dose, whereas that of DT-diaphorase increased significantly (P < 0.05) by both doses used (2.5 and 5%). In the antioxidant system, significant elevation of the specific activities of superoxide dismutase (P < 0.01) and catalase (P < 0.05) was observed with the 5% dose of cumin. The activities of glutathione peroxidase and glutathione reductase remained unaltered by both doses of cumin. The level of reduced glutathione measured as nonprotein sulfhydryl content was elevated (significance level being from P < 0.05 to P < 0.01) by both doses of cumin. Lipid peroxidation measured as formation of MDA production showed significant inhibition (P < 0.05 to P < 0.01) by both doses of cumin. LDH activity remained unaltered by both doses of cumin. The results strongly suggest the cancer chemopreventive potentials of cumin seed and could be attributed to its ability to modulate carcinogen metabolism.
Expression of Rod-Derived Cone Viability Factor: Dual Role of CRX in Regulating Promoter Activity and Cell-Type Specificity (2010)

The regulation of the Nucleoredoxin-like genes involves a CRX responsive element that can act as both as a positive regulator of promoter activity and as a modulator of cell-type specificity.
The Synuclein Family (1998)

The synuclein gene family recently came into the spotlight, when one of its members, alpha-synuclein, was found to be mutated in several families with autosomal dominant Parkinson's disease (PD). A peptide of the alpha-synuclein protein had been characterized previously as a major component of amyloid plaques in brains of patients with Alzheimer's disease (AD). The mechanism by which this presynaptic protein is involved in the two most common neurodegenerative disorders, AD and PD, remains unclear. Remarkably, another member of this gene family, gamma-synuclein, has been shown to be overexpressed in breast carcinomas and may also be overexpressed in ovarian cancer. The possible involvement of the synuclein proteins in the etiology of common human diseases has raised exciting questions and is the subject of intense investigation. Details of the properties of any member of the synuclein family may provide useful information for understanding the characteristics and function of other family members. The present review offers a synopsis of the current state of knowledge of all synuclein family members in different species.
TROSY-type Triple-Resonance Experiments for Sequential NMR Assignments of Large Proteins (1999)

Transverse relaxation-optimized spectroscopy (TROSY) was implemented in the four triple resonance experiments [15N,1H]-TROSY-HN(CO)CA, [15N,1H]-TROSY-HN(CA)CO, [15N,1H]-TROSY-HNCACB, and [15N,1H]-TROSY-HN(CO)CACB. Combined with [15N,1H]-TROSY-HNCA and [15N,1H]-TROSY-HNCO (Salzmann, M.; Pervushin, K.; Wider, G.; Senn, H. Wüthrich, K. Proc. Natl. Acad. Sci. U.S.A. 1998, 13585−13590) these experiments represent a suite of TROSY-type triple resonance experiments that enables sequential backbone assignment of proteins. When used with the 23 kDa 2H/13C/15N-labeled protein gyrase 23B, a comparison with the corresponding conventional NMR experiments showed, on average over the entire amino acid sequence, a 3-fold sensitivity gain for each of the four experiments. The use of the TROSY principle in triple resonance experiments thus promises to enable resonance assignments for significantly larger proteins than what is achievable today with the corresponding conventional NMR experiments.
Structural Changes and Melting Behavior of γ-Irradiated Polyethylene (1981)

The structural changes and melting behavior of high density polyethylene irradiated at room temperature were studied by X-ray diffraction and differential scanning calorimetry up to about 4000 Mrad. The melting point and the heat of fusion were depressed by irradiation. A monotonic lattice expansion and an increase in overall specific volume with increasing dose, which lead to a decrease in the specific volume of the amorphous region, were also observed. These changes are thought to be caused by the formation of crosslinks near the surfaces of crystallites and in the amorphous region. The melting point depression can be explained by the effects of lattice distortion and crosslinks outside the crystallites introduced by irradiation. Above 1000 Mrad, a phase transformation into the hexagonal form was observed below the melting point.
Identification of a subset of patients with acute myeloid leukemia characterized by long-termin vitroproliferation and altered cell cycle regulation of the leukemic cells (2014)

We identified a subset of AML patients characterized by long-term in vitro cell proliferation and altered expression of cell cycle regulators that may be potential candidates for treatment of AML.
Epidermal Growth Factor Receptor, c-erbB-2 Proto-Oncogene and Estrogen Receptor Expression in Human Papillomavirus Lesions of the Uterine Cervix (1994)

The expression of epidermal growth factor receptor (EGF-R), c-erbB-2 proto-oncogene, and estrogen receptor (ER) was studied immunohistochemically in a series of 97 human papillomavirus (HPV) lesions of the uterine cervix, with special emphasis on their association with the HPV type, grade of intraepithelial neoplasia (CIN), and the natural history of the disease. EGF-R expression was found in 95 of 97 (98%) specimens, mainly in basal and parabasal cells. Diffuse nuclear and cytoplasmic staining was detected in 36 of 97 (37%) samples, of which 29 were HPV positive. This staining pattern was most prominent in HPV 18-positive and in CIN lesions. Weak or moderate c-erbB-2 expression was found in 26 of 97 (27%) specimens. Estrogen receptor expression was observed in 28 of 77 (36%) samples, epithelial staining was seen in 11 of 77 (14%), and stromal staining occurred in 24 of 77 (31%) specimens. No clear-cut associations were established between the EGF-R, c-erbB-2, or ER expression and HPV type, nor in CIN or the clinical course of HPV infections. This failure for EGF-R, c-erbB-2, and ER to be associated with the specific HPV types, grade of CIN, or the clinical course of cervical HPV lesions suggests that the assessment of these factors is of limited value in explaining the development of HPV-associated CIN and in predicting the prognosis of this disease.
A new class of single-phase multilevel inverters (2010)

Multilevel power converters make it possible to use mature but voltage-limited power semiconductors in high voltage, high power industry and utility applications. Different from high frequency approach, the concept of direct output synthesizing provides efficient power conversion with the advantages of better harmonic cancellation and compact ac filtering. Conventional multilevel inverters, including diode-clamped, flying capacitor, and cascaded H-bridge, are well defined but become clumsy for higher levels. This paper proposes a new single-phase full-bridge multilevel topology, which requires less split-rail dc sources and significantly reduced semiconductor switch devices. An n-capacitor switching problem is proposed and analyzed, which leads to the new class of generalized multilevel structure featured with asymmetrical dc sources and maximized output levels. Cascading basic five-level cells provides another structure to build higher-level inverters with separate dc sources. The proposed multilevel inverters can be potential for solar photovoltaics and energy storage applications.
Frequency-Resolved Measurements of Signal, Noise, and Signal-Signal Beat Interference in Self-Coherent Direct-Detection Receivers (2018)

We demonstrate a novel measurement technique that uniquely identifies the power spectral densities of signal, signal-signal-beat interference, and noise in direct-detection receivers.
Ultracompact Electroabsorption Modulators Based on Tunable Epsilon-Near-Zero-Slot Waveguides (2012)

We present a promising application of epsilon-near-zero (ENZ) materials in optical modulators. When a thin ENZ film is sandwiched in a single-mode waveguide, an ENZ-slot waveguide is formed, where the absorption can be greatly enhanced. We propose electroabsorption modulators based on tunable ENZ materials and slot waveguides. Transparent conducting oxides (TCOs) may be employed as the active slot, which can be tuned between ENZ (high absorption) and epsilon-far-from-zero (low absorption) by accumulation carriers. Numerical simulation shows that over 3-dB modulation depth can be achieved in a 250-nm-long TCO-slot waveguide. The modulators have the advantages of nanoscale footprints, small insertion loss, potentially ultrahigh speed, and easy fabrication.
Angiogenesis — Biomedical technology (1992)

All of these studies show that angiogenesis research can benefit from new biomedical technology tools currently being developed, as well as contribute by providing new technologies that can be used in other areas of medicine. It is hoped that the chapters in this book in this area will provide the reader with an up-to-date appreciation of some of the exciting research that is currently being pursued.
A Decade of Rituximab: Improving Survival Outcomes in Non-Hodgkin's Lymphoma (2008)

The anti-CD20 monoclonal antibody rituximab, first approved for clinical use in 1997, has changed the standard of care for many patients with non-Hodgkin's lymphoma (NHL). Recent data from large randomized clinical trials confirm that the addition of rituximab to standard chemotherapy regimens (chemoimmunotherapy) improves both response rates and survival outcomes in patients with follicular NHL and diffuse large B cell lymphoma (DLBCL), the two most common subtypes of NHL. Population-based analyses have found substantial improvements in NHL survival over the past decade; studies indicate that rituximab has favorably altered the long-term prognosis of follicular NHL and DLBCL patients. This review discusses the clinical development of rituximab-based therapies for patients with low-grade or follicular NHL and newly diagnosed DLBCL, highlighting recent key randomized trials with a focus on survival outcomes.
Real-time high-fidelity facial performance capture (2015)

We present the first real-time high-fidelity facial capture method. The core idea is to enhance a global real-time face tracker, which provides a low-resolution face mesh, with local regressors that add in medium-scale details, such as expression wrinkles. Our main observation is that although wrinkles appear in different scales and at different locations on the face, they are locally very self-similar and their visual appearance is a direct consequence of their local shape. We therefore train local regressors from high-resolution capture data in order to predict the local geometry from local appearance at runtime. We propose an automatic way to detect and align the local patches required to train the regressors and run them efficiently in real-time. Our formulation is particularly designed to enhance the low-resolution global tracker with exactly the missing expression frequencies, avoiding superimposing spatial frequencies in the result. Our system is generic and can be applied to any real-time tracker that uses a global prior, e.g. blend-shapes. Once trained, our online capture approach can be applied to any new user without additional training, resulting in high-fidelity facial performance reconstruction with person-specific wrinkle details from a monocular video camera in real-time.