gebhart/patrepeval huggingface dataset:
A Nanostructured SiAl0.2O Anode Material for Lithium Batteries (2010)

Silicon monoxide (SiO) is a promising candidate for anodes in lithium rechargeable batteries, because of its large capacity. The initial irreversible reaction and still dissatisfactory capacity retention during cycling, however, hinder its practical application. A nanostructured SiAl0.2O composite material has been developed via mechanochemical synthesis and investigated as an alternative anode. The SiAl0.2O is composed of quantitatively increased silicon nanocrystallites, each of which is less than 10 nm in size, embedded in an amorphous matrix; the compositional structure of the matrix is aluminosilica in which most of Si atoms are neighbored with two Al atoms over oxygen, as confirmed with X-ray diffraction (XRD), solid-state 29Si and 27Al nuclear magnetic resonance (NMR), and transmission electron microscopy (TEM). This electrode exhibits enhanced initial Coulombic efficiency of which the relative increase is >10%, compared to SiO, and also demonstrates improved cycling performance, offering a capacity of 800 mAh/g over 100 cycles. These improvements are attributed to the electrochemically inactive alumina component, which not only replaces part of the SiO2 phase that is regarded as an origin of initial irreversible reaction but also provides mechanically reinforcing properties, resulting in little pulverization of particles and less change in the impedance of the SiAl0.2O electrode during cycling.
A Video Gateway to Support Video Streaming to Mobile Clients (1997)

Abstract: This paper describes how video streaming from or to mobile participants of a video conference can be supported by a so called “Mobility Gateway“. The gateway interconnects a mobile client, through a wireless link, to a fixed network LAN or WAN multicast environment and performs intelligent operations on the video stream like transcoding, congestion control etc. in order to provide the mobile user with enhanced video services.
Action of Topical Thyroid Hormone Analogues on Glucocorticoid-Induced Skin Atrophy in Mice (2006)

Previously we demonstrated the stimulation of collagen synthesis in triiodothyroacetic acid (TRIAC)-topically treated human and mice. In the present study, we have evaluated the dose response effect of thyroid hormone (TH) analogues and tretinoin on glucocorticoid-induced skin atrophy in a haired mouse model. For this investigation, we treated haired mice twice daily for 7 days with various topically administered doses of TRIAC, triiodothyronine-sodium salt (T(3)-Na), diiodothyroacetic acid (DIAC), 3,5-diiodothyropropionic acid (DITPA), and tretinoin with 0.2 mM betamethasone17-valerate (BM), or with the vehicle as a control group. We also investigated a combination of commercial betamethasone dipropionate (BD) 0.05% cream and various doses of TRIAC on mouse skin. TRIAC was able to reverse the skin atrophy by 25% in a daily dose of 1 nmol/cm(2) in the presence of 0.2 mM BM (p < 0.05). Neither other TH analogues nor TRIAC in lower and higher concentrations had a significant inhibitory effect on dermal atrophy (p > 0.05). A combination of 0.2 mM BM and 10 nmol/cm(2) TRIAC was able to prevent dermal atrophy by 18%. The addition of TRIAC to 0.05% BD cream in a final concentration of 0.1% was able partially to reverse the dermal atrophy by 15% (p < 0.05). TRIAC alone in a concentration of 1,000 nmol/cm(2) stimulated dermal proliferation by 34% (p < 0.05). Other TH analogues alone had no stimulatory effect on dermal proliferation. Tretinoin 0.8 mM was able to inhibit dermal atrophy by 20% (p < 0.05) and had an effect on dermal thickness of 85% (p < 0.05). However, severe side effects with edema, erythema, and scaling were commonly observed in all tretinoin-treated mouse skin, which could partly explain the increase in dermal thickness. In contrast, no skin side effects were observed after treatment with TRIAC. This study indicates that TRIAC may have a therapeutic effect on BM-induced dermal atrophy in mouse skin and a direct stimulatory effect on dermal proliferation when given alone.
Structural basis for potent neutralization of SARS-CoV-2 and role of antibody affinity maturation (2020)

Abstract SARS-CoV-2 is a betacoronavirus virus responsible for the COVID-19 pandemic. Here, we determined the X-ray crystal structure of a potent neutralizing monoclonal antibody, CV30, isolated from a patient infected with SARS-CoV-2, in complex with the receptor binding domain (RBD). The structure reveals CV30’s epitope overlaps with the human ACE2 receptor binding site thus providing the structural basis for its neutralization by preventing ACE2 binding.
Discovery of Potent Peptide-Mimetic Antagonists for the Human Thrombin Receptor, Protease-Activated Receptor-1 (PAR-1) (2003)

Protease-activated receptors (PARs) represent a unique family of seven-transmembrane G-protein-coupled receptors, which are enzymatically cleaved to expose a new extracellular N-terminus that acts as a tethered activating ligand. PAR-1 is cleaved and activated by the serine protease alpha-thrombin, is expressed in various tissues (e.g. platelets and vascular cells), and is involved in cellular responses associated with hemostasis, proliferation, and tissue injury. By using a de novo design approach, we have discovered a series of potent heterocycle-based peptide-miimetic antagonists of PAR-1, exemplified by advanced leads RWJ-56110 (22) and RWJ-58259 (32). These compounds are potent, selective PAR-1 antagonists, devoid of PAR-1 agonist and thrombin inhibitory activity: they bind to PAR-1, interfere with calcium mobilization and cellular functions associated with PAR-1, and do not affect PAR-2, PAR-3, or PAR-4. RWJ-56110 was determined to be a direct inhibitor of PAR-1 activation and internalization, without affecting PAR-1 N-terminal cleavage. At high concentrations of alpha-thrombin, RWJ-56110 fully blocked activation responses in human vascular cells, but not in human platelets; whereas, at high concentrations of TRAP-6, RWJ-56110 blocked activation responses in both cell types. This result is consistent with the presence of another thrombin receptor on human platelets, namely PAR-4. RWJ-56110 and RWJ-58259 clearly interrupt the binding of a tethered ligand to its receptor. RWJ-58259 demonstrated antirestenotic activity in a rat balloon angioplasty model and antithrombotic activity in a cynomolgus monkey arterial injury model. Such PAR-1 antagonists should not only serve as useful tools to delineate the physiological and pathophysiological roles of PAR-1, but also may have therapeutic potential for treating thrombosis and restenosis in humans.
BIOCOMPATIBLE SOLID PHASE MICROEXTRACTION (2006)

Today’s solid phase microextraction (SPME) is a well known technique that combines knowledge from different fields in an attractive, efficient, and economic way. The development of SPME has seen huge growth since its introduction as a new approach to sample preparation in the early 1990s. The applications of SPME are continuously expanding, and one of the most interesting current aspects consists of applying SPME for fast analysis of biological fluids, both in vitro and in vivo.&#13;\nIn spite of this great potential, development of new bio-applications is considerably hindered by the lack of suitable SPME products. The goal of this study is to find SPME coatings that can be utilized for in vivo and in vitro extractions, in direct contact with a biological matrix such as blood or tissue. This thesis presents several effective ways of preparing SPME coatings based on biocompatible polymers and silica-based extractive phases, focusing on their biocompatibility as a must. After fabrication, the proposed coatings are tested for biocompatibility and analytical utility.&#13;\nFinally, some practical applications of the new coatings are presented, such as fast drug analysis and determination of drug plasma protein binding. Six test drugs with different physico-chemical properties are chosen for the investigation: diazepam, verapamil, lorazepam, warfarin, nordiazepam, and loperamide. It is shown that the application of these new SPME fibers for biological sample analysis greatly reduces the time required for sample preparation and limits the exposure of the analytical personnel to potentially infectious biofluids.
Electric vehicles (1992)

The renewed interest in electric vehicles (EVs) in the wake of the California Air Resources Board mandate that 2% of the vehicles lighter than 3750 lb (1700 kg) sold by each manufacturer in that state in 1998 be zero-emission vehicles is examined. The reasons why replacing an internal combustion vehicle (ICV) with an electrically powered equivalent greatly reduces air pollution, not only where the EV is driven, but over the rest of the map as well are discussed. Three drawbacks that have kept EVs from taking over, despite the fact that they are quieter and more reliable as well as less polluting than their internal combustion counterparts, are discussed. They offer limited range on a simple charge, long recharge time, and higher cost than ICVs. The importance of an appropriate infrastructure is stressed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Sequence Analysis of Functional Regions of Homoserine Dehydrogenase Genes froml-Lysine andl-Threonine-producing Mutants ofBrevibacterium lactofermentum (1997)

The homoserine dehydrogenase (HD) genes from Brevibacterium lactofermentum lysine- and threonine-producing mutants were cloned, using the polymerase chain reaction, and sequenced. We found the amino acid substitutions, Val104Ile in the lysine-producing mutants in which HD may cause leaky mutation and Ser393Phe in the threonine-producing mutant with feedback-insensitive HD.
Membranoproliferative Glomerulonephritis Type II (Dense Deposit Disease) (2005)

Membranoproliferative glomerulonephritis type II (MPGN II) is a rare disease characterized by the deposition of abnormal electron-dense material within the glomerular basement membrane of the kidney and often within Bruch's membrane in the eye. The diagnosis is made in most patients between the ages of 5 and 15 yr, and within 10 yr, approximately half progress to end-stage renal disease, occasionally with the late comorbidity of visual impairment. The pathophysiologic basis of MPGN II is associated with the uncontrolled systemic activation of the alternative pathway (AP) of the complement cascade. In most patients, loss of complement regulation is caused by C3 nephritic factor, an autoantibody directed against the C3 convertase of the AP, but in some patients, mutations in the factor H gene have been identified. For the latter patients, plasma replacement therapy prevents renal failure, but for the majority of patients, there is no proven effective treatment. The disease recurs in virtually all renal allografts, and a high percentage of these ultimately fail. The development of molecular diagnostic tools and new therapies directed at controlling the AP of the complement cascade either locally in the kidney or at the systemic level may lead to effective treatments for MPGN II.
Synergistic Polymorphisms of β1- and α2C-Adrenergic Receptors and the Risk of Congestive Heart Failure (2002)

The alpha2CDel322-325 and beta1Arg389 receptors act synergistically to increase the risk of heart failure in blacks. Genotyping at these two loci may be a useful approach for identification of persons at risk for heart failure or its progression, who may be candidates for early preventive measures.
Selection against CpG dinucleotides in lentiviral genes: a possible role of methylation in regulation of viral expression (1990)

Extremely low frequencies of CpG dinucleotides are found in the genomes of the lentivirus subfamily of retroviruses, including the human, simian and feline immunodeficiency viruses (HIV1, HIV2, SIV, and FIV, respectively), equine infectious anemia virus (EIAV), and the ovine lentivirus, Visna. The occurrence of CpG dinucleotides is greater in the 2-3 (NCG) than in the 1-2 (CGN) codon-defined frame, as well as in the gag and env genes, compared to the more conserved pol gene. These differences suggest that CpG depletion in lentiviruses occurs as a result of selection against CpG rather than due to mutational bias, the latter is responsible for low CpG frequencies in vertebrate genomes. CpG levels in the onco-retrovirus subfamily are reduced to a lesser extent, principally due to mutational bias. The difference between the retrovirus subfamilies appears to reflect their evolutionary origin, that is, lentiviruses have no known endogenous counterparts whereas most oncoviruses have endogenous cellular counterparts with which they can undergo recombination. Furthermore, we suggest that the number of CpG dinucleotides in a lentiviral genome determines the maximum potential DNA methylation level of the provirus, which in turn affects viral transcription in host cells.
Genetic engineering of microorganisms (1993)

Principles of Genetic Engineering for Escherichia Coli Genetic Engineering of Gram Negative Bacteria Genetic Engineering of Gram Positive Bacteria Genetic Engineering of Yeast Genetic Engineering of Filamentous Fungi.
Chromosome sizes and phylogenetic relationships between serotypes of Actinobacillus pleuropneumoniae (1998)

The genome size of Actinobacillus pleuropneumoniae was determined by pulsed field gel electrophoresis of AscI and ApaI digested chromosomal DNA. The genome size of the type strain 4074T (serotype 1) was determined to be 2404±40 kb. The chromosome sizes for the reference strains of the other serotypes range between 2.3 and 2.4 Mb. The restriction pattern profiles of AscI, ApaI and NheI digested chromosomes showed a high degree of polymorphism among the different serotype reference strains and allowed their discrimination. The analysis of the macrorestriction pattern polymorphism revealed phylogenetic relationships between the different serotype reference strains which reflect to some extent groups of serotypes known to cross-react serologically. In addition, different pulsed fields gel electrophoresis patterns also revealed heterogeneity in the chromosomal structure among different field strains of serotypes 1, 5a, and 5b, while strains of serotype 9 originating from most distant geographical places showed homogeneous ApaI patterns in pulsed field gel electrophoresis.
Genetic Alterations in the Tyrosine Kinase Transcriptome of Human Cancer Cell Lines (2007)

Protein tyrosine kinases (PTKs) play a critical role in the manifestation of cancer cell properties, and respective signaling mechanisms have been studied extensively on immortalized tumor cells. To characterize and analyze commonly used cancer cell lines with regard to variations in the primary structure of all expressed PTKs, we conducted a cDNA-based sequence analysis of the entire tyrosine kinase transcriptome of 254 established tumor cell lines. The profiles of cell line intrinsic PTK transcript alterations and the evaluation of 155 identified polymorphisms and 234 somatic mutations are made available in a database designated "Tykiva" (tyrosine kinome variant). Tissue distribution analysis and/or the localization within defined protein domains indicate functional relevance of several genetic alterations. The cysteine replacement of the highly conserved Y367 residue in fibroblast growth factor receptor 4 or the Q26X nonsense mutation in the tumor-suppressor kinase CSK are examples, and may contribute to cell line-specific signaling characteristics and tumor progression. Moreover, known variants, such as epidermal growth factor receptor G719S, that were shown to mediate anticancer drug sensitivity could be detected in other than the previously reported tumor types. Our data therefore provide extensive system information for the design and interpretation of cell line-based cancer research, and may stimulate further investigations into broader clinical applications of current cancer therapeutics.
Serum microRNA characterization identifies miR-885-5p as a potential marker for detecting liver pathologies (2010)

Circulating miRNAs (microRNAs) are emerging as promising biomarkers for several pathological conditions, and the aim of this study was to investigate the feasibility of using serum miRNAs as biomarkers for liver pathologies. Real-time qPCR (quantitative PCR)-based TaqMan MicroRNA arrays were first employed to profile miRNAs in serum pools from patients with HCC (hepatocellular carcinoma) or LC (liver cirrhosis) and from healthy controls. Five miRNAs (i.e. miR-885-5p, miR-574-3p, miR-224, miR-215 and miR-146a) that were up-regulated in the HCC and LC serum pools were selected and further quantified using real-time qPCR in patients with HCC, LC, CHB (chronic hepatitis B) or GC (gastric cancer) and in normal controls. The present study revealed that more than 110 miRNA species in the serum samples and wide distribution ranges of serum miRNAs were observed. The levels of miR-885-5p were significantly higher in sera from patients with HCC, LC and CHB than in healthy controls or GC patients. miR-885-5p yielded an AUC [the area under the ROC (receiver operating characteristic) curve] of 0.904 [95% CI (confidence interval), 0.837-0.951, P<0.0001) with 90.53% sensitivity and 79.17% specificity in discriminating liver pathologies from healthy controls, using a cut off value of 1.06 (normalized). No correlations between increased miR-885-5p and liver function parameters [AFP (α-fetoprotein), ALT (alanine aminotransferase), AST (aspartate aminotransferase) and GGT (γ-glutamyl transpeptidase)] were observed in patients with liver pathologies. In summary, miR-885-5p is significantly elevated in the sera of patients with liver pathologies, and our data suggest that serum miRNAs could serve as novel complementary biomarkers for the detection and assessment of liver pathologies.
Mechanistic and prognostic significance of aberrant methylation in the molecular pathogenesis of human hepatocellular carcinoma (2007)

Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide, accounting for an estimated 600,000 deaths annually. Aberrant methylation, consisting of DNA hypomethylation and/or promoter gene CpG hypermethylation, is implicated in the development of a variety of solid tumors, including HCC. We analyzed the global levels of DNA methylation as well as the methylation status of 105 putative tumor suppressor genes and found that the extent of genome-wide hypomethylation and CpG hypermethylation correlates with biological features and clinical outcome of HCC patients. We identified activation of Ras and downstream Ras effectors (ERK, AKT, and RAL) due to epigenetic silencing of inhibitors of the Ras pathway in all HCC. Further, selective inactivation of SPRY1 and -2, DAB2, and SOCS4 and -5 genes and inhibitors of angiogenesis (BNIP3, BNIP3L, IGFBP3, and EGLN2) was associated with poor prognosis. Importantly, several epigenetically silenced putative tumor suppressor genes found in HCC were also inactivated in the nontumorous liver. Our results assign both therapeutic and chemopreventive significance to methylation patterns in human HCC and open the possibility of using molecular targets, including those identified in this study, to effectively inhibit HCC development and progression.
Dasatinib attenuated bleomycin-induced pulmonary fibrosis in mice (2015)

Anti-fibrotic effect of dasatinib, a platelet-derived growth factor receptor (PDGFR) and Src-kinase inhibitor, was tested on pulmonary fibrosis (PF). Adult mice were divided into four groups: mice dissected 21 d after the bleomycin (BLM) instillation (0.08 mg/kg in 200 µl) (I) and their controls (II), and mice treated with dasatinib (8 mg/kg in 100 µl, gavage) for one week 14 d after BLM instillation and dissected 21 d after instillation (III) and their controls (IV). The fibrosis score and the levels of fibrotic markers were analyzed in lungs. BLM treatment-induced cell proliferation and increased the levels of collagen-1, alpha smooth muscle actin, phospho (p)-PDGFR-alpha, p-Src, p-extracellular signal-regulated kinases1/2 and p-cytoplasmic-Abelson-kinase (c-Abl) in lungs, and down-regulated PTEN expression. Dasatinib reversed these alterations in the fibrotic lung. Dasatinib limited myofibroblast activation and collagen-1 accumulation by the inhibition of PDGFR-alpha, and Src and c-Abl activations. In conclusion, dasatinib may be a novel tyrosine and Src-kinase inhibitor for PF regression in mice.
Development and validation of a chiral capillary electrophoresis method for melagatran and ximelagatran drug substances (2002)

This work presents the development and validation of an enantioselective capillary electrophoresis (CE) method for two new drug substances, the novel direct thrombin inhibitor melagatran and its oral prodrug ximelagatran. CE with a derivatised cyclodextrin as the chiral discriminant was examined as a viable alternative after failing to achieve sufficient selectivity and sensitivity using chiral liquid chromatography (LC). A robust and sensitive chiral method was developed which utilised a low pH phosphate buffer with heptakis(2,6-Di-O-methyl)-β-cyclodextrin to achieve chiral recognition for both drugs with additional organic modifier to fine tune selectivity. Quantitation at the 0.05% (w/w) level was achieved by employing sample stacking effects possible with a 200 mM phosphate buffer in combination with a narrow 50 μm ID capillary. A full validation was subsequently carried out according to the ICH guidelines, including selectivity, linearity, detection and quantitation limits, accuracy, precision, stability of analytical solutions, and robustness. Linearity, precision, and accuracy data were shown to be adequate over the entire range including at the 0.05% (w/w) quantitation limit. Several electrolyte parameters in addition to buffer depletion and cyclodextrin batch variations were amongst the parameters verified for method robustness.
Intracerebroventricular Administration of Drugs (2009)

Intracerebroventricular drug administration is a method that bypasses the blood-brain barrier and other mechanisms that limit drug distribution into the brain, allowing high drug concentrations to enter the central compartment. Instillation of drugs directly into the ventricles of the brain must be done carefully and with full consideration of factors affecting the efficacy and safety of this route of administration. These factors include the osmolarity, pH, volume, and presence of preservatives and diluents of the drug solution being administered. Very few studies have formally investigated intraventricular therapies, and dosing recommendations may vary widely depending on the agent and the patient. Many antimicrobials have been given intraventricularly, although very few prospective studies have evaluated this strategy. There are wide variations among the reports regarding dosage regimens and the pharmacokinetics of the antimicrobials used. Guidance on appropriate formulations and their use is lacking. Clinicians should be aware of their patients' ongoing disease processes and neurologic status, as well as pertinent physiochemical properties of drugs when formulating them for intracerebroventricular administration; a high index of suspicion should be maintained when monitoring patients for adverse drug events after instillation.