gebhart/patrepeval huggingface dataset:
Redox-Active On-Surface Assembly of Metal–Organic Chains with Single-Site Pt(II) (2014)

The formation and stabilization of well-defined transition-metal single sites at surfaces may open new routes to achieve higher selectivity in heterogeneous catalysts. Organic ligand coordination to produce a well-defined oxidation state in weakly reducing metal sites at surfaces, desirable for selective catalysis, has not been achieved. Here, we address this using metallic platinum interacting with a dipyridyl tetrazine ligand on a single crystal gold surface. X-ray photoelectron spectroscopy measurements demonstrate the metal-ligand redox activity and are paired with molecular-resolution scanning probe microscopy to elucidate the structure of the metal-organic network. Comparison to the redox-inactive diphenyl tetrazine ligand as a control experiment illustrates that the redox activity and molecular-level ordering at the surface rely on two key elements of the metal complexes: (i) bidentate binding sites providing a suitable square-planar coordination geometry when paired around each Pt, and (ii) redox-active functional groups to enable charge transfer to a well-defined Pt(II) oxidation state. Ligand-mediated control over the oxidation state and structure of single-site metal centers that are in contact with a metal surface may enable advances in higher selectivity for next generation heterogeneous catalysts.
2-Formyl-3-Methoxymethylindole, 3-Ethoxymethyl-2-Formylindole and 2-Formyl-3-Methylindole (1986)

Abstract Base-catalysed hydrolysis of 2-formyl-3-methyl-1-phenyl-sulphonylindole results in the formation of 3-alkoxy-methyl-2-formylindoles. Cleavage of the 1-phenyl-sulphonyl group with sodium amalgam produces 2-hydroxymethyl-3-methylindole.
The GARP gene encodes a new member of the family of leucine-rich repeat-containing proteins. (1994)

We have characterized a new human gene, named GARP, localized in the 11q14 chromosomal region. GARP comprises two coding exons, is expressed as two major transcripts of 4.4 and 2.8 kilobases, respectively, and encodes a putative transmembrane protein of 662 amino acids, the extracellular portion of which is almost entirely made of leucine-rich repeats. The molecular weight of the protein immunoprecipitated from transfected cells is 80,000. The GARP protein has structural similarities with the human GP Ib alpha and GP V platelet proteins, and with the Chaoptin, Toll, and Connectin adhesion molecules of Drosophila.
Acute Pain Treatment (2008)

Acute Pain Treatment Pain is an unpleasant sensory and emotional experience usually arising from actual or potential tissue damage.Acute pain can be a difficult medical problem to diagnose and treat.It may be caused by many events or circumstances.Symptoms can last hours, days, or weeks and are commonly associated with tissue injury, inflammation, a surgical procedure, childbirth, or a brief disease process.Other types of pain may be classified as chronic (pain of long duration), neuropathic (pain resulting from damage to nerves), psychogenic (pain not due to visible signs of disease or injury), or cancer-related (effects of a malignant disease on the body).The January 2, 2008, issue of JAMA includes an article that identifies trends in the prescription of medicines to treat acute pain in US emergency departments.
Space and time savings through large data base compression and dynamic restructuring (1975)

The conventional general-purpose data management system tends to make inefficient use of storage space. By reducing the physical size of the data, substantial savings are available in the area of storage cost. Reduction ratios of 4:1 and more are realizable. This also reduces the amount of I/O time required to physically transfer data between secondary and primary memories. Since I/O time tends to be the pacing factor when processing large data bases, this could produce a 4:1 or greater reduction in response time. Data compression experience with four large data bases is described. In some applications, only a small fraction of the data transferred in an individual I/O operation is relevant to the query being processed. If usage patterns are measured and data records and fields are rearranged so that those which are commonly referenced together are also physically stored together, then additional savings are available. Once the data base has been partitioned into clusters of commonly accessed data, further efficiencies can be obtained by choosing data structures, compression strategies, and storage devices that are optimal for the recent usage pattern observed on that cluster.
Luminescence properties of CdSe quantum crystallites: Resonance between interior and surface localized states (1992)

We use time-, wavelength-, temperature-, polarization-resolved luminescence to elucidate the nature of the absorbing and ‘‘band edge’’ luminescing states in 32 Å diameter wurtzite CdSe quantum crystallites. Time-resolved emission following picosecond size-selective resonant excitation of the lowest excited state shows two components—a temperature insensitive 100 ps component and a microsecond, temperature sensitive component. The emission spectrum, showing optic phonon vibrational structure, develops a ∼70 wave number red shift as the fast component decays. Photoselection shows the slow component to be reverse polarized at 10 K, indicating this component to be the result of a hole radiationless transition. The 100 ps emitting state is repopulated thermally as temperature increases from 10 to 50 K. All available data are interpreted by postulating strong resonant mixing between a standing wave molecular orbital delocalized inside the crystallite and intrinsic surface Se lone pair states. The apparent exciton transition is assigned to a ∼130 wave number wide band of eigenstates with the hole localized principally on the surface. The band contains strongly emitting ‘‘doorway’’ states and weakly emitting ‘‘background’’ states. The hole becomes mobile among these states as T increases to 50 K. It is suggested that such resonant mixing may be general in II–VI and III–V crystallites.
Biosynthesis of the Cyclotide Kalata B1 by Using Protein Splicing (2006)

The tides are turning: Kalata B1 (KB1) is the prototypical member of an exceptionally stable and resistant family of plant-derived miniproteins called cyclotides. The biosynthesis of KB1 and a small library of KB1-based cyclotides (variation occurs in five solvent-exposed loops) in E. coli has been performed by using recombinant-DNA expression techniques and protein splicing.
HIPS: A calibration-less hybrid indoor positioning system using heterogeneous sensors (2009)

Positioning is a crucial task in pervasive computing, aimed at estimating the user's positions to provide location-based services. In this paper, we study an interesting problem: when we wish to obtain hybrid positioning granularities in an office environment, how can we incorporate heterogeneous sensors to build an indoor positioning system with minimal human calibration effort? We propose a calibration-less solution by incorporating the ultrasound sensors with the radio-frequency sensors. In our solution, we use these two different types of sensors to satisfy the different granularities requirement; and meanwhile, we use the ultrasound sensors to help calibrate the radio-frequency sensors for positioning, so that we can minimize, or even eliminate the labeling effort for the radio-frequency positioning. Finally, we develop a system prototype with real-world sensor networks, and verify the feasibility and effectiveness of our proposed solution.
miRNA arm selection and isomiR distribution in gastric cancer (2012)

Arm selections and isomiR patterns are significantly varied in human cancers by using deep sequencing NGS data. Our results provided a novel research topic in miRNA regulation study. With advanced bioinformatics and molecular biology studies, more robust conclusions and insight into miRNA regulation can be achieved in the near future.
Changes in Titin Isoform Expression in Pacing-Induced Cardiac Failure Give Rise to Increased Passive Muscle Stiffness (2002)

Coexpression of titin isoforms with distinct mechanical properties allows modulation of passive stiffness via adjustment of the isoform expression ratio. The canine pacing-induced heart failure model uses this mechanism to increase myocardial stiffness. Thus, changes in titin isoform expression may play a role in diastolic dysfunction in heart failure.
Hemin Treatment Abrogates Monocrotaline-Induced Pulmonary Hypertension (2008)

Treatment of rats with monocrotaline (MCT), a pyrrolizidine alkaloid plant toxin, is known to cause pulmonary hypertension (PH), and it has been used as a useful experimental model of PH. Recent findings suggested that pulmonary inflammation may play a significant role in the pathogenesis of MCT-induced PH. We also demonstrated that, following MCT administration to rats, there was a significant and sustained increase in the pulmonary expression of heme oxygenase-1 (HO-1), which is known to be induced by various oxidative stresses, including inflammation and free heme, and is thought to be essential in the protection against oxidative tissue injuries. In this study, we administered hemin (ferriprotoporphyrin chloride, 30 micromol/kg b.w., subcutaneously), a potent inducer of HO-1, every 3 days to rats following subcutaneous administration of MCT (60 mg/kg) and examined its effect on MCT-induced PH and pulmonary inflammation. MCT administration caused pulmonary arterial wall thickening with marked elevation of right ventricular pressure, in association with prominent pulmonary inflammation as revealed by the increase in gene expression of tumor necrosis factor-alpha and the number of infiltrated neutrophils in the lung. In contrast, hemin treatment of MCT-administered animals, which led to a further increase in pulmonary HO-1 mRNA expression, significantly ameliorated MCT-induced PH as well as tissue inflammation. These findings suggest that hemin treatment ameliorates MCT-induced PH possibly mediated through induction of pulmonary HO-1 which leads to the attenuation of pulmonary inflammation.
Facile Fabrication of 3D-Ordered Macroporous Nanocrystalline Iron Oxide Films with Highly Efficient Visible Light Induced Photocatalytic Activity (2010)

A facile approach of layer-by-layer depositing and hydrolysis of FeCl3 is developed to fabricate 3D-ordered Fe2O3 film. The 3D-ordered Fe2O3 film was characterized by SEM, XRD, and DRUV−vis. It has 3D-ordered interconnecting macropores (340 nm) with nanocrystalline hematite Fe2O3 walls (27.2 nm). The 3D-ordered macroporous nanocrystalline Fe2O3 film exhibits 2.4 times larger photocatalytic activity for the photodegradation of dye in the presence of H2O2 under visible irradiation than the nanocrystalline α-Fe2O3 film without macropores and very good photostability. The much higher photocatalytic activity of the 3D-ordered macroporous nanocrystalline Fe2O3 film than that of the reference Fe2O3 film is attributed to the unique nanostructure and architecture of the 3D-ordered Fe2O3 film, which result in the much greater light harvesting efficiency and efficient mass transport in the former than in the latter due to the existence of 3D-ordered interconnecting macropores. The effect of photonic stop band on the photocatalytic activity of the 3D-ordered Fe2O3 film was studied by angle-dependent solid-state photodegradation experiments with monochromatic irradiation. A slow photon enhancement of photocatalytic activity was achieved by adjusting the red edge of the photonic stop band of the 3D-ordered Fe2O3 film close to the electronic bandgap of Fe2O3. The photodegradation mechanism of crystal violet on the 3D-ordered Fe2O3 photocatalyst in the presence or absence of H2O2 was discussed.
Paradoxical actions of antioxidants in the oxidation of low density lipoprotein by peroxidases. (1995)

Oxidation of LDL by peroxidases has been suggested to be a model for in vivo oxidation. The mechanism might involve the generation of an intermediate radical such as a phenoxy radical. We show that, in contrast to the oxidation of LDL by copper, oxidation by peroxidase system (H2O2/horse radish peroxidase) showed less resistance. This suggested that either the antioxidants were consumed more rapidly or might have actually participated in the oxidation. Accordingly, addition of vitamin E increased the rate of oxidation of LDL. In contrast, probucol inhibited the oxidation even at low concentrations suggesting ineffective formation of probucol radical or the sterically hindered probucol radical was inefficient in catalyzing subsequent oxidation. The oxidation of LDL by horse radish peroxidase was also enhanced in the presence of diphenylphenylenediamine, an antioxidant that does not have a phenolic -OH group. Myeloperoxidase was able to oxidize LDL even in the absence of added tyrosine suggesting that it was able to utilize the LDL-associated vitamin E. Addition of free tyrosine inhibited the formation of conjugated dienes. We suggest that if peroxidases are involved in the initiation of LDL oxidation in vivo, higher concentrations of antioxidants may be indicated to inhibit propagation of oxidation.
Structural, functional and mutational analysis of the pfr gene encoding a ferritin from Helicobacter pylori (1998)

The function of the pfr gene encoding the ferritin from Helicobacter pylori was investigated using the Fur titration assay (FURTA) in Escherichia coli, and by characterization of a pfr-deficient mutant strain of H. pylori. Nucleotide sequence analysis revealed that the pfr region is conserved among strains (> 95% nucleotide identity). Two transcriptional start sites, at least one of them preceded by a sigma 70-dependent promoter, were identified. Provision of the H. pylori pfr gene on a multicopy plasmid resulted in reversal of the Fur-mediated repression of the fhuF gene in E. coli, thus enabling the use of the FURTA for cloning of the ferritin gene. Inactivation of the pfr gene, either by insertion of a resistance cassette or by deletion of the up- and downstream segments, abolished this function. Immunoblot analysis with a Pfr-specific antiserum detected the Pfr protein in H. pylori and in E. coli carrying the pfr gene on a plasmid. Pfr-deficient mutants of H. pylori were generated by marker-exchange mutagenesis. These were more susceptible than the parental strain to killing by various metal ions including irons, copper and manganese, whereas conditions of oxidative stress or iron deprivation were not discriminative. Analysis by element-specific electron microscopy revealed that growth of H. pylori in the presence of iron induces the formation of two kinds of cytoplasmic aggregates: large vacuole-like bodies and smaller granules containing iron in association with oxygen or phosphorus. Neither of these structures was detected in the pfr-deficient mutant strain. Furthermore, the ferritin accumulated under iron overload and the pfr-deficient mutant strains lacked expression of a 12 kDa protein which was negatively regulated by iron in the parental strain. The results indicate that the nonhaem-iron ferritin is involved in the formation of iron-containing subcellular structures and contributes to metal resistance of H. pylori. Further evidence for an interaction of ferritin with iron-dependent regulation mechanisms is provided.
The Effect of High-Dose Saquinavir on Viral Load and CD4+ T-Cell Counts in HIV-Infected Patients (1996)

Saquinavir is a potent antiviral agent that has a favorable toxicity profile at high doses. Higher doses produce a greater and more durable suppression of viral load and elevation in CD4+ T-cell counts and may delay the development of resistance mutations. Therapy with high-dose saquinavir alone or in combination with other antiretroviral agents should be investigated further.
Negative Ion Electrospray Mass Spectrometry of Polyphenols, Catecholamines and their Oxidation Products (1996)

Polyphenols, catecholamines and their oxidation products have a variety of physiological effects and are key components of insect cuticle and other biological structures. Three dihydroxybenzene isomers were easily differentiated using negative ion electrospray mass spectrometry (ESMS) or tandem mass spectrometry (MS/MS). Ions at m/z 107-109 were diagnostic for more complex polyphenols and catecholamines with a dihydroxybenzene moiety. The product ion spectra of other compounds including 3,4-dihydroxyphenylacetic acid, 3,4-dihydroxyphenylalanine (DOPA) and N-acetyldopamine (NADA) had product ions at m/z 121-123 corresponding to methylene homologues of dioxygenated benzene. Oxidation of DOPA using tyrosinase, Ag2O or NaIO4 could be followed using ESMS and several proposed intermediates proceeding from DOPA through a quinone methide intermediate, 5,6-dihydroxyindole and dihydroxyindole quinone were confirmed using negative ion ESMS/MS. Spectra of the NaIO4 oxidation products of 1,2,3-trihydroxybenzene (pyrogallol) were consistent with tetrahydroxybenzene, two non-cyclic tetraoxygenated derivatives and a bicyclic polymerization product, purpurogallin. ESMS can be used to analyse complex polyphenolic conjugates commonly encountered in biological specimens.
Intracellular Distribution and Nuclear Activity of Antisense Oligonucleotides After Unassisted Uptake in Myoblasts and Differentiated Myotubes In Vitro (2017)

Clinical efficacy of antisense oligonucleotides (AONs) for the treatment of neuromuscular disorders depends on efficient cellular uptake and proper intracellular routing to the target. Selection of AONs with highest in vitro efficiencies is usually based on chemical or physical methods for forced cellular delivery. Since these methods largely bypass existing natural mechanisms for membrane passage and intracellular trafficking, spontaneous uptake and distribution of AONs in cells are still poorly understood. Here, we report on the unassisted uptake of naked AONs, so-called gymnosis, in muscle cells in culture. We found that gymnosis works similarly well for proliferating myoblasts as for terminally differentiated myotubes. Cell biological analyses combined with microscopy imaging showed that a phosphorothioate backbone promotes efficient gymnosis, that uptake is clathrin mediated and mainly results in endosomal-lysosomal accumulation. Nuclear localization occurred at a low level, but the gymnotically delivered AONs effectively modulated the expression of their nuclear RNA targets. Chloroquine treatment after gymnotic delivery helped increase nuclear AON levels. In sum, we demonstrate that gymnosis is feasible in proliferating and non-proliferating muscle cells and we confirm the relevance of AON chemistry for uptake and intracellular trafficking with this method, which provides a useful means for bio-activity screening of AONs in vitro.
Mechanism of the Synergistic Inactivation of Escherichia coli by UV-C Light at Mild Temperatures (2013)

UV light only penetrates liquid food surfaces to a very short depth, thereby limiting its industrial application in food pasteurization. One promising alternative is the combination of UV light with mild heat (UV-H), which has been demonstrated to produce a synergistic bactericidal effect. The aim of this article is to elucidate the mechanism of synergistic cellular inactivation resulting from the simultaneous application of UV light and heat. The lethality of UV-H treatments remained constant below ∼45°C, while lethality increased exponentially as the temperature increased. The percentage of synergism reached a maximum (40.3%) at 55°C. Neither the flow regimen nor changes in the dose delivered by UV lamps contributed to the observed synergism. UV-H inactivation curves of the parental Escherichia coli strain obtained in a caffeic acid selective recovery medium followed a similar profile to those obtained with uvrA mutant cells in a nonselective medium. Thermal fluidification of membranes and synergistic lethal effects started around 40 to 45°C. Chemical membrane fluidification with benzyl alcohol decreased the UV resistance of the parental strain but not that of the uvrA mutant. These results suggest that the synergistic lethal effect of UV-H treatments is due to the inhibition of DNA excision repair resulting from the membrane fluidification caused by simultaneous heating.
Downregulation of CXCR-2 but not CXCR-1 expression by human keratinocytes by UVB (2000)

Interleukin-8 (IL-8) belongs to the CXC chemokine family. IL-8 exerts its biological activities by binding to specific cell surface receptors, CXCR-1 and CXCR-2. Both receptors bind IL-8 with high affinity but they have different affinities for MGSA/Groalpha and NAP-2. It has been shown that the expression of epidermal CXCR-2 is increased in psoriasis, suggesting that activation of KC mediated by CXCR-2 contributes to the characteristic epidermal changes observed in psoriasis. In order to examine the mechanism(s) by which UVB therapy is effective for several dermatoses including psoriasis, we sought to examine if UVB would modulate the expression of CXCR-1 and CXCR-2 in human keratinocytes (KC). Constitutive expression of CXCR-1 and CXCR-2 mRNA was detected by RT-PCR in normal cultured human KC. After 100 or 300 J/m(2) irradiation, a decrease in CXCR-2 mRNA was detectable from 12 h after irradiation; this downregulation was observed until 48 h after irradiation. In contrast, the CXCR-1 mRNA level was unchanged. Immunohistochemical studies and flow cytometry analysis confirmed the suppressive effect of UVB on the expression of CXCR-2 protein in cultured human keratinocytes. Immunohistochemical studies on two minimal erythema doses (2MED)-exposed and 2MED-unexposed skin from healthy volunteers revealed that CXCR-2 staining occurred over the whole layer of the epidermis but at 24 h after 2MED irradiation, the positive staining of CXCR-2 was decreased. A faint CXCR-1 staining was observed in the lower part of the epidermis both in unexposed and exposed skins. Our results indicate that UVB-induced growth inhibition of KC in hyperproliferative skin disorders may, in part, be related to downregulation of CXCR-2.
Molecular Profiling of Premalignant Lesions in Lung Squamous Cell Carcinomas Identifies Mechanisms Involved in Stepwise Carcinogenesis (2014)

Lung squamous cell carcinoma (SCC) is thought to arise from premalignant lesions in the airway epithelium; therefore, studying these lesions is critical for understanding lung carcinogenesis. Previous microarray and sequencing studies designed to discover early biomarkers and therapeutic targets for lung SCC had limited success identifying key driver events in lung carcinogenesis, mostly due to the cellular heterogeneity of patient samples examined and the interindividual variability associated with difficult to obtain airway premalignant lesions and appropriate normal control samples within the same patient. We performed RNA sequencing on laser-microdissected representative cell populations along the SCC pathologic continuum of patient-matched normal basal cells, premalignant lesions, and tumor cells. We discovered transcriptomic changes and identified genomic pathways altered with initiation and progression of SCC within individual patients. We used immunofluorescent staining to confirm gene expression changes in premalignant lesions and tumor cells, including increased expression of SLC2A1, CEACAM5, and PTBP3 at the protein level and increased activation of MYC via nuclear translocation. Cytoband enrichment analysis revealed coordinated loss and gain of expression in chromosome 3p and 3q regions, respectively, during carcinogenesis. This is the first gene expression profiling study of airway premalignant lesions with patient-matched SCC tumor samples. Our results provide much needed information about the biology of premalignant lesions and the molecular changes that occur during stepwise carcinogenesis of SCC, and it highlights a novel approach for identifying some of the earliest molecular changes associated with initiation and progression of lung carcinogenesis within individual patients.