gebhart/patrepeval huggingface dataset:
Persistent and Transient Replication of Full-Length Hepatitis C Virus Genomes in Cell Culture (2002)

The recently developed subgenomic hepatitis C virus (HCV) replicons were limited by the fact that the sequence encoding the structural proteins was missing. Therefore, important information about a possible influence of these proteins on replication and pathogenesis and about the mechanism of virus formation could not be obtained. Taking advantage of three cell culture-adaptive mutations that enhance RNA replication synergistically, we generated selectable full-length HCV genomes that amplify to high levels in the human hepatoma cell line Huh-7 and can be stably propagated for more than 6 months. The structural proteins are efficiently expressed, with the viral glycoproteins E1 and E2 forming heterodimers which are stable under nondenaturing conditions. No disulfide-linked glycoprotein aggregates were observed, suggesting that the envelope proteins fold productively. Electron microscopy studies indicate that cell lines harboring these full-length HCV RNAs contain lipid droplets. The majority of the core protein was found on the surfaces of these structures, whereas the glycoproteins appear to localize to the endoplasmic reticulum and cis-Golgi compartments. In agreement with this distribution, no endoglycosidase H-resistant forms of these proteins were detectable. In a search for the production of viral particles, we noticed that these cells release substantial amounts of nuclease-resistant HCV RNA-containing structures with a buoyant density of 1.04 to 1.1 g/ml in iodixanol gradients. The same observation was made in transient-replication assays using an authentic highly adapted full-length HCV genome that lacks heterologous sequences. However, the fact that comparable amounts of such RNA-containing structures were found in the supernatant of cells carrying subgenomic replicons demonstrates a nonspecific release independent of the presence of the structural proteins. These results suggest that Huh-7 cells lack host cell factors that are important for virus particle assembly and/or release.
Freeze-Drying of Aqueous Solutions of Deep Eutectic Solvents: A Suitable Approach to Deep Eutectic Suspensions of Self-Assembled Structures (2009)

This work describes how the preparation of deep eutectic solvents (DES) in its pure state can be accomplished through a simple approach based on the freeze-drying of aqueous solutions of the individual counterparts of DES. DES in its pure state obtained via freeze-drying are studied by (1)H NMR, which reveals the formation of halide ion-hydrogen-bond-donor supramolecular complexes (characteristic of DES), and by cryo-etch-SEM, which provides insight about the capability of aqueous solutions of DES to be segregated in DES and ice upon freezing. The paper also explores the suitability of the freeze-drying approach to incorporate organic self-assemblies (in particular, liposomes of ca. 200 nm) in DES with full preservation of their self-assembled structure. This is not a trivial issue given that amphiphilic molecules tend to be readily dissolved (hence, disassembled) in DES. The strategy proposed in this work is based on the freeze-drying of aqueous solutions containing the individual counterparts of DES and the preformed liposomes (also known as large unilamellar vesicles or LUV). The simplicity of the method should also make it suitable for the incorporation of different self-assembled structures (such other types of vesicles and micelles) in DES in its pure state.
Production of Liquid Hydrocarbons with CO2as Carbon Source based on Reverse Water‐Gas Shift and Fischer‐Tropsch Synthesis (2013)

Abstract The substitution of fossil fuels by renewable energy sources is needed to decrease greenhouse gas emissions, especially CO 2 . Wind and solar power are today considered as attractive alternatives for electric power generation, but are not suitable for providing base load. Thus, efficient storage of electrical energy is inevitable. Liquid hydrocarbons (HCs) exhibit an excellent volumetric energy density and offer various opportunities for storing electric energy. They can be produced by CO 2 and renewable H 2 (generated by water electrolysis) in a two step process. The first step is generation of syngas by reverse water‐gas shift (RWGS) at elevated temperatures; the second step comprises the production of liquid hydrocarbons by Fischer‐Tropsch (FT) synthesis. The experiments on RWGS with a commercial Ni‐catalyst show that a CO 2 conversion of around 80 % can be reached at 800 °C within a very short residence time of less than &lt; 0.1 s. The experiments on FTS with Fe as catalyst and syngas containing different amounts of CO 2 indicate that the influence of CO 2 on CO conversion and product selectivities (including net CO 2 production by water‐gas shift) is insignificant if the inlet partial pressures of H 2 and CO are kept constant. If CO is substituted by CO 2 , less HCs are formed, the water‐gas shift is repressed, and methane selectivity increases.
Occidiofungin's Chemical Stability and In Vitro Potency against Candida Species (2011)

Occidiofungin is a cyclic glyco-lipopeptide produced by Burkholderia contaminans. MICs against Candida species were between 0.5 and 2.0 μg/ml. Occidiofungin retains its in vitro potency in the presence of 5% and 50% human serum with a minimal lethal concentration (MLC) of 2 and 4 μg/ml, respectively. Time-kill and postantifungal effect (PAFE) experiments of occidiofungin against Candida albicans were performed. The results demonstrate that occidiofungin is fungicidal. Occidiofungin was also found to be a very stable molecule. It is resistant to extreme temperatures and pH and maintains its activity following exposure to gastric proteases.
The Prognostic Role of a Gene Signature from Tumorigenic Breast-Cancer Cells (2007)

The IGS is strongly associated with metastasis-free survival and overall survival for four different types of tumors. This genetic signature of tumorigenic breast-cancer cells was even more strongly associated with clinical outcomes when combined with the WR signature in breast cancer.
Motor Neuron Degeneration in Mice that Express a Human Cu,Zn Superoxide Dismutase Mutation (1994)

Mutations of human Cu,Zn superoxide dismutase (SOD) are found in about 20 percent of patients with familial amyotrophic lateral sclerosis (ALS). Expression of high levels of human SOD containing a substitution of glycine to alanine at position 93--a change that has little effect on enzyme activity--caused motor neuron disease in transgenic mice. The mice became paralyzed in one or more limbs as a result of motor neuron loss from the spinal cord and died by 5 to 6 months of age. The results show that dominant, gain-of-function mutations in SOD contribute to the pathogenesis of familial ALS.
Identification of T-Cell Epitopes (1993)

A novel method was developed to isolate immunogenic peptides (CD8+ T-cell epitopes) from class I complexes expressed at the cell surface of viable cells. Cells treated at pH 3.3 with citrate-phosphate buffer for periods as short as 15 s remained viable and became phenotypically class I deficient. Qualitative loss of class I determinants was verified both serologically and by the incapacity of acid-treated cells to be lysed by class I-restricted cytolytic T lymphocytes (CTLs) in contrast to non-acid-treated controls. Flow cytometric analysis of acid-treated cells suggests that class I heavy chains remain associated with the cell membrane, while the class I light chain (beta 2-microglobulin) is absent. Since the physical dissociation of beta 2-microglobulin from class I heavy chain is correlated with the release of previously class I-bound peptides, we examined acid-eluted cell-free supernatants for the presence of immunogenic peptides. Peptides were acid eluted from an influenza A strain-infected, HLA-A2+ cell line and were subsequently fractionated by reverse-phase high performance liquid chromatography (RP-HPLC). These fractionated peptides were examined for their capacity to sensitize an HLA-A2+ B cell line to lysis mediated by an influenza A matrix peptide- (Flu M1 57-68) specific, HLA-A2-restricted CTL line. A single peak of biologic activity was identified in HPLC fractions 47 and 48 derived from influenza-infected cells. These fractions contained a peptide of M(r) 968 with a sequence similar to the Flu M1 58-66 sequence GILGFVFTL. The application of this technique to other T-cell-based systems may aid in the definition of peptide epitopes relevant to viral, autoimmune, or neoplastic disorders.
Restricted expression of an early myeloid and monocytic cell surface antigen defined by monoclonal antibody M195. (1989)

A mouse monoclonal IgG2a antibody, M195, with reactivity restricted to early myeloid cells, acute non-lymphoid leukemia cells (ANLL), and monocytic cells is described. The antibody was derived from a mouse immunized with live human leukemic myeloblasts. Specificity of binding of mAb M195 was determined by protein-A red blood cell rosetting assays, immunoabsorption, radioimmunoassays with iodine-125 labeled M195 IgG and F(Ab)'2, and complement cytotoxicity with live human cells and cell lines representing a broad range of lineages and tissues. Antigen expression was restricted to myeloid and monocytic leukemia cell lines and a fraction of mature adherent monocytes. Mature myeloid cells, T and B cells, erythrocytes, and platelets were negative. The antigen was not expressed on adult human tissues in immunoperoxidase and immunofluorescence assays. Blocking antigen was not found in the serum of patients with ANLL. Ten thousand sites per cell were expressed on myeloid or monocytic leukemia cell lines and 5000 sites per cell on mature monocytes. M195 IgG bound to its antigen target with an avidity of 3 x 10(9) liters/mol and induced rapid modulation of the antigen. M195 IgG was able to effectively kill cells with rabbit or guinea pig complement, but not human complement. The antibody did not mediate antibody dependent cellular cytotoxicity. The molecular nature of the target antigen remains unknown but it appears to be carried on the CD33 protein p67. Because of its restricted distribution on myelomonocytic cells, mAb M195 may be useful in studying myeloid differentiation, in the clinical diagnosis of ANLL, in purging of bone marrow of ANLL, and/or in monoclonal antibody therapy in vivo.
Imaging of Superoxide Generation in the Dopaminergic Area of the Brain in Parkinson’s Disease, Using Mito-TEMPO (2013)

We report a new methodology for direct visualization of superoxide production in the dopaminergic area of the brain in Parkinson's disease, based on the redox cycle of mito-TEMPO, a blood-brain barrier-, cell-, and mitochondria-penetrating nitroxide derivative with superoxide scavenging properties and T1 magnetic resonance imaging (MRI) contrast. The experiments were conducted on healthy and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated mice. In healthy mice, the nitroxide-enhanced MRI signal was weak and short-lived (half-life ∼ 40 s; duration ∼ 80 s). The profile of the histograms indicated a high reducing activity of normal brain tissues against mito-TEMPO. In MPTP-treated mice, the nitroxide-enhanced MRI signal was strong and long-lived (half-life > 20 min; duration > 20 min), especially in the dopaminergic area of the brain. The histograms indicated a high oxidative activity in dopaminergic tissues of MPTP-treated mice. The results show directly, on intact mammals, that superoxide is a major inducer and/or mediator of neurodegenerative damage in Parkinson's disease. The high oxidative status of brain tissue in Parkinson's disease was also confirmed on isolated tissue specimens, using total reducing capacity assay and ROS/RNS assay.
The PDZ Ligand Domain of the Human Papillomavirus Type 16 E6 Protein Is Required for E6's Induction of Epithelial Hyperplasia In Vivo (2003)

Human papillomaviruses (HPVs) are the causative agent of warts. Infections with high-risk HPVs are associated with anogenital and head and neck cancers. One of the viral genes responsible for HPV's oncogenic activity is E6. Mice expressing the HPV-16 E6 protein in their epidermis (K14E6(WT)) develop epithelial hyperplasia and squamous carcinomas. Numerous cellular proteins interact with E6, some of which can be grouped based on common amino acid motifs in their E6-binding domains. One such group, the PDZ partners, including hDLG, hSCRIBBLE, MUPP1, and MAGI, bind to the carboxy-terminal four amino acids of E6 through their PDZ domains. E6's interaction with the PDZ partners leads to their degradation. Additionally, E6's binding to PDZ proteins has been correlated with its ability to transform baby rat kidney cells in tissue culture and to confer tumorigenicity onto cells in xenograft experiments. To address whether the ability of E6 to bind PDZ domain partners is necessary for E6 to confer epithelial hyperproliferation in vivo, we generated transgenic mice that express in stratified squamous epithelia a mutant of E6 lacking the last six amino acids at its carboxyl terminus, E6(Delta 146-151), from the human keratin 14 (K14) promoter. The K14E6(Delta 146-151) mice exhibit a radiation response similar to that of the K14E6(WT) mice, demonstrating that this protein, as predicted, retains an ability to inactivate p53. However, the K14E6(Delta 146-151) mice fail to display epithelial hyperplasia. These results indicate that an interaction of E6 with PDZ partners is necessary for its induction of epithelial hyperplasia.
Phase 3 Trial of Ibrutinib plus Rituximab in Waldenström’s Macroglobulinemia (2018)

Among patients with Waldenström's macroglobulinemia, the use of ibrutinib-rituximab resulted in significantly higher rates of progression-free survival than the use of placebo-rituximab, both among those who had received no previous treatment and among those with disease recurrence. Atrial fibrillation and hypertension were more common with ibrutinib-rituximab, whereas infusion reactions and IgM flare were more common with placebo-rituximab. (Funded by Pharmacyclics and Janssen Research and Development; ClinicalTrials.gov number, NCT02165397 .).
Bevacizumab Plus Interferon Alfa Compared With Interferon Alfa Monotherapy in Patients With Metastatic Renal Cell Carcinoma: CALGB 90206 (2008)

Bevacizumab plus IFN produces a superior PFS and ORR in untreated patients with metastatic RCC as compared with IFN monotherapy. Toxicity is greater in the combination therapy arm.
JAMAICA (2014)

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Influence of pH and thermal treatment on the intramolecular mobility of pepsin (1976)

In connection with a hypothesis of segmental flexibility of pepsin and its derivative aminopepsin (containing 3-aminotyrosine residues), a dynamic behaviour of pepsin and dansylated aminopepsin in aqueous solutions at pH 1.0--8.3 in investigated. It is shown that a dynamic structure of pepsin at pH 2.5--6.0 is almost invariant and very close to a structure studied in detail at pH 5.5. The lowering of a solution pH value from 2.5 to 1.0 is accompanied by labilization of pepsin and dansylated aminopepsin structures. Denaturation phenomena after thermal treatment of dansylated aminopepsin are also studied. An incubation of the latter in 0.1 M acetate buffer at pH 5.5 and temperature 50--80 degrees C with a subsequent cooling leads to irreversible conformational changes. The character of these changes is essentially dependent upon the incubation conditions.
Disulfide bond mapping and structural characterization of spruce budworm antifreeze protein (1998)

The 9-kDa, Thr-, Ser-, and Cys-rich thermal hysteresis protein from spruce budworm (sbwTHP) is 10-30 times more effective than fish antifreeze proteins (AFPs) at depressing solution freezing points via ice-crystal growth inhibition. Since this insect protein is only available in microgram quantities from its natural source, recombinant sbwTHP was produced from inclusion bodies in Escherichia coli by a refolding protocol. Incompletely folded forms were removed during ion-exchange and reverse-phase chromatography, resulting in fully active sbwTHP that was indistinguishable in its properties from native sbwTHP. The antifreeze was completely inactivated by reduction, showed no reaction with sulfhydryl reagents, and was not inhibited by EDTA. All eight cysteine residues appear to be involved in disulfide bond formation. Tryptic cleavage and peptide analysis is consistent with linkages between the first and second cysteine residues, the third and fourth, fifth and eighth, and the sixth and seventh. NMR analysis confirmed that the fully folded form of sbwTHP was well structured and had a single conformation. Both NMR and CD spectra indicate the presence of extensive beta structure (70-80%) with little or no alpha helix. The protein maintains antifreeze activity over a broad range of pH values, and its conformation is independent of both temperature (over the range 0 degrees C to 20 degrees C), and the presence of 50% trifluoroethanol.
The leaky-wave antenna with ferroelectric substrate (2003)

The leaky-wave antenna is investigated using the 3D FDTD method. The structure analyzed is a ferroelectric dielectric waveguide on the ground plate. The top of the ferroelectric material is covered with a conducting sheet with slots. It is shown that this antenna may have further advantages of smaller thickness, simpler beam-steering control and lower cost.
A human identification technique using images of the iris and wavelet transform (1998)

A new approach for recognizing the iris of the human eye is presented. Zero-crossings of the wavelet transform at various resolution levels are calculated over concentric circles on the iris, and the resulting one-dimensional (1-D) signals are compared with model features using different dissimilarity functions.
Genetic alterations in seborrheic keratoses (2017)

Seborrheic keratoses are common benign epidermal lesions that are associated with increased age and sun-exposure. Those lesions despite harboring multiple somatic alterations in contrast to malignant tumors appear to be genetically stable. In order to investigate and characterize the presence of recurrent mutations, we performed exome sequencing on DNA from one seborrheic keratosis lesion and corresponding blood cells from the same patients with follow up investigation of alterations identified by exome sequencing in 24 additional lesions from as many patients. In addition we investigated alterations in all lesions at specific genes loci that included FGFR3, PIK3CA, HRAS, BRAF, CDKN2A and TERT and DHPH3 promoters. The exome sequencing data indicated three mutations per Mb of the targeted sequence. The mutational pattern depicted typical UV signature with majority of alterations being C>T and CC>TT base changes at dipyrimidinic sites. The FGFR3 mutations were the most frequent, detected in 12 of 25 (48%) lesions, followed by the PIK3CA (32%), TERT promoter (24%) and DPH3 promoter mutations (24%). TERT promoter mutations associated with increased age and were present mainly in the lesions excised from head and neck. Three lesions also carried alterations in CDKN2A. FGFR3, TERT and DPH3 expression did not correlate with mutations in the respective genes and promoters; however, increased FGFR3 transcript levels were associated with increased FOXN1 levels, a suggested positive feedback loop that stalls malignant progression. Thus, in this study we report overall mutation rate through exome sequencing and show the most frequent mutations seborrheic keratosis.
Diagnosing the root-causes of failures from cluster log files (2010)

System event logs are often the primary source of information for diagnosing (and predicting) the causes of failures for cluster systems. Due to interactions among the system hardware and software components, the system event logs for large cluster systems are comprised of streams of interleaved events, and only a small fraction of the events over a small time span are relevant to the diagnosis of a given failure. Furthermore, the process of troubleshooting the causes of failures is largely manual and ad-hoc. In this paper, we present a systematic methodology for reconstructing event order and establishing correlations among events which indicate the root-causes of a given failure from very large syslogs. We developed a diagnostics tool, FDiag, to extract the log entries as structured message templates and uses statistical correlation analysis to establish probable cause and effect relationships for the fault being analyzed. We applied FDiag to analyze failures due to breakdowns in interactions between the Lustre file system and its clients on the Ranger supercomputer at the Texas Advanced Computing Center (TACC). The results are positive. FDiag is able to identify the dates and the time periods that contain the significant events which eventually led to the occurrence of compute node soft lockups.
New role of a medical documentation system (1992)

Architecture of a new medical documentation system (MDS) is proposed. First, we studied the traditional MDS in terms of organizational structure, main functions, means (resources) and personnel. Special emphasis is given to the information retrieval (IR) system which is the kernel of a MDS. Then, some achievements of information technology is summarized, and concept of a mixed IR system which is the kernel of the new system is presented. New architecture is then presented. Units which compose the entire system are: host documentation centre, local documentation centres, and documentation units. Eventually, objective and features of every part are discussed.
Colonization of the tonsils and nasopharynx of calves by a rifampicin-resistant Pasteurella haemolytica and its inhibition by vaccination. (1995)

A rifampicin-resistant Pasteurella haemolytica serotype 1 with 2 added plasmids was used as a colonization-challenge strain in calves to test the resistance to colonization elicited by vaccination. Nine calves were vaccinated with a tissue culture-derived P haemolytica serotype-1 vaccine which, in a prior study, had elicited a serotype-specific inhibition of nasal and tonsillar colonization by the homologous serotype under field conditions. The vaccinates and 9 nonvaccinated control calves were exposed by tonsillar instillation with the challenge strain. The P haemolytica were enumerated in nasal secretion and tonsil wash specimens collected biweekly for 3 weeks. Rifampicin-supplemented agar medium inhibited growth of other bacterial species in the specimens and, thus, increased the sensitivity of detection of the challenge P haemolytica by 100-fold. The challenge strain retained its plasmids during the period of colonization. Inhibition of colonization was evidenced by lower frequency of isolations and fewer isolations of the challenge strain from nasal secretion and tonsil wash specimens of the vaccinates than from those of the nonvaccinates.