gebhart/patrepeval huggingface dataset:
Identification of tumorigenic metabolites of benzo[j]fluoranthene formed in vivo in mouse skin. (1987)

The metabolism of benzo[j]fluoranthene (BjF) in vivo in mouse skin was investigated. trans-4,5-Dihydro-4,5-dihydroxybenzo[j]fluoranthene (BjF-4,5-diol) and trans-9,10-dihydro-9,10-dihydroxybenzo[j]fluoranthene (BjF-9,10-diol) have been identified as major metabolites. In addition, 4- and 10-hydroxybenzo[j]fluoranthene and benzo[j]fluoranthen-4,5-dione have been tentatively identified among the metabolites formed in vivo in mouse skin. The enantiomeric purity of the metabolic dihydrodiols of BjF as formed in vivo in mouse skin was determined. The major enantiomer of BjF-4,5-diol was present in 57-62% enantiomeric excess while that of BjF-9,10-diol was present in 66-71% enantiomeric excess. In each case the later-eluting enantiomer on chiral stationary-phase high performance liquid chromatography predominated. The tumor-initiating activity of trans-2,3-dihydro-2,3-dihydroxybenzo[j]fluoranthene (BjF-2,3-diol), BjF-4,5-diol, BjF-9,10-diol, and BjF was evaluated on the skin of female CD-1 mice. As a total initiation dose of 3 mumol/mouse BjF-4,5-diol resulted in a 100% incidence of tumor-bearing mice with 5.0 tumors/mouse. In comparison, BjF-9,10-diol elicited a 60% incidence of tumor-bearing mice with 1.7 tumors/mouse, while BjF-2,3-diol was inactive. At the same dose, BjF gave rise to a 90% incidence of tumor-bearing mice with 7.8 tumors/mouse. At a 1-mumol dose, BjF-4,5-diol induced a 78% incidence of tumor-bearing mice with 4.3 tumors/mouse while BjF gave rise to a 70% tumor incidence with 3.4 tumors/mouse while BjF gave rise to a 70% tumor incidence with 3.4 tumors/mouse. These studies indicate that while BjF-9,10-diol could contribute to the overall tumorigenic activity of BjF in mouse skin, BjF-4,5-diol is a more potent tumor initiator in the target tissue.
Privacy-Oriented Cryptography (Dagstuhl Seminar 12381) (2013)

This report documents the program of the Dagstuhl Seminar 12381 "Privacy-Oriented Cryptography", which took place at Schloss Dagstuhl in September 16-21, 2012. Being the first Dagstuhl seminar that explicitly aimed to combine cryptography and privacy research communities, it attracted a high number of participants, many of whom were new to Dagstuhl. In total, the seminar was attended by 39 international researchers, working in different areas of cryptography and privacy, from academia, industry, and governmental organizations. The seminar included many interactive talks on novel, so-far unpublished results, aiming at the design, analysis, and practical deployment of cryptographic mechanisms for protecting privacy of users and data. The seminar featured two panel discussions to address various approaches towards provable privacy and different challenges but also success stories for practical deployment of existing cryptographic privacy-oriented techniques.
Asymmetry in negative differential resistance driven by electron–electron interactions in two-site molecular devices (2001)

We demonstrate that Coulomb interactions within the Hartree–Fock approximation can induce a strong asymmetry in the negative differential resistance of a two-site resonant molecular device. This sharp cutoff at high voltage is generic and independent of the detailed single-particle electronic structure of the system. The intersite coupling between distinct molecular subunits controls a transition from staircase to resonant current–voltage characteristics. These studies clarify the relationship between weak screening and strong nonlinearity.
Flexor Hallucis Longus Tendon Transfer in Treatment of Achilles Tendinosis (2013)

Background: In patients with Achilles tendinosis, Achilles tendon debridement can be supplemented with flexor hallucis longus tendon transfer. Outcomes have not been studied prospectively in older, sedentary, and overweight patients. Methods: Fifty-eight consecutive limbs in fifty-six consecutive older, sedentary patients with insertional or midsubstance Achilles tendinosis were enrolled prospectively and underwent the procedure. Ten patients were lost to follow-up, leaving forty-eight limbs in forty-six patients available for evaluation after twenty-four months. Results: The forty-six patients who were included in the study had an average age of 54 ± 10 years with an average body mass index of 33.8 ± 6.8 kg/m2. Significant improvement was observed between baseline and twenty-four months in terms of the visual analog scale for overall pain intensity (6.7 ± 2.3 versus 0.8 ± 2.0; p < 0.001), the Short Form-36 physical score (34.3 ± 8.0 versus 49.0 ± 9.3; p < 0.001), the Ankle Osteoarthritis Scale pain (54.4 ± 19.2 versus 1.9 ± 2.7; p < 0.001) and dysfunction (62.6 ± 21.4 versus 11.0 ± 24.2; p < 0.001) subscale scores, and performance of a single-leg heel rise (1.9 ± 3.0 versus 7.3 ± 2.7 cm; p < 0.001). Significant improvement compared with baseline was observed at three or six months except in the single-leg heel rise. Improvements in terms of pain and function occurred over twenty-four months, with the most improvement occurring in the first twelve months. At twenty-four months, maximum gastrocnemius circumference was significantly less in the involved compared with the uninvolved leg (40.2 ± 5.1 versus 41.2 ± 4.8 cm; p < 0.001). The mean passive range of motion of the first metatarsophalangeal joint decreased from 85.1° ± 25.3° preoperatively to 68.1° ± 36.7° (a 20% change) at six months (p = 0.03). Most patients reported no hallux weakness (57%; twenty-six of forty-six patients) and no loss of balance due to hallux weakness (76%; thirty-five of forty-six patients). Postoperative peroneal tendinitis was observed in seven patients. Complications included deep-vein thrombosis (two patients), superficial infection or delayed wound-healing (six), scar pain (four), and early disruption of the reconstruction due to a fall (one). Conclusions: Surgical debridement of the Achilles tendon with flexor hallucis longus tendon transfer was associated with significant improvement in terms of Achilles tendon function, physical function, and pain intensity in a group of relatively inactive, older, overweight patients. When present, hallux weakness had minimal functional sequelae. Level of Evidence: Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.
Serum copeptin is associated with major complications of liver cirrhosis and spontaneous bacterial peritonitis (2023)

Serum copeptin is an independent risk factor for the presence of SBP and significantly increased in patients presented with major complications of liver cirrhosis, demonstrating its ability to reflect circulatory dysfunction and systemic inflammation.
DEAF1 Is a Pellino1-interacting Protein Required for Interferon Production by Sendai Virus and Double-stranded RNA* (2013)

Double-stranded (ds) RNA of viral origin, a ligand for Melanoma Differentiation-associated gene 5 (MDA5) and Toll-Like Receptor 3 (TLR3), induces the TANK-Binding Kinase 1 (TBK1)-dependent phosphorylation and activation of Interferon Regulatory Factor 3 (IRF3) and the E3 ubiquitin ligase Pellino1, which are required for interferon β (IFNβ) gene transcription. Here, we report that Pellino1 interacts with the transcription factor Deformed Epidermal Autoregulatory Factor 1 (DEAF1). The interaction is independent of the E3 ligase activity of Pellino1, but weakened by the phosphorylation of Pellino1. We show that DEAF1 binds to the IFNβ promoter and to IRF3 and IRF7, that it is required for the transcription of the IFNβ gene and IFNβ secretion in MEFs infected with Sendai virus or transfected with poly(I:C). DEAF1 is also needed for TLR3-dependent IFNβ production. Taken together, our results identify DEAF1 as a novel component of the signal transduction network by which dsRNA of viral origin stimulates IFNβ production.
Corrections to “Demonstration of Addressable Organic Resistive Memory Utilizing a PC-Interface Memory Cell Tester” [Jan 13 51-53] (2013)

In the above-named article [ibid., vol. 34, no. 1, pp. 51-53, Jan. 2013], the corresponding authors were not clearly specified. This correction is to indicate that Gun-Young Jung and Takhee Lee are the corresponding authors for the paper.
Analysis of triacetone triperoxide by gas chromatography/mass spectrometry and gas chromatography/tandem mass spectrometry by electron and chemical ionization (2006)

Abstract The explosive triacetone triperoxide (TATP) has been analyzed by gas chromatography/mass spectrometry (GC/MS) and sub‐nanogram detection limits are reported by ammonia positive ion chemical ionization (PICI), electron ionization (EI) and methane negative ion chemical ionization (NICI). Analysis by methane PICI and ammonia NICI gave detection limits in the low nanogram range. Analyses were carried out on (linear) quadrupole and ion trap instruments. Analysis of TATP by PICI using ammonia reagent gas is the preferred analytical method, producing low limits of detection as well as an abundant (greater than 60% of base peak) diagnostic adduct ion at m/z 240 corresponding to [TATP + NH 4 ] + . Isolation of the [TATP + NH 4 ] + ion with subsequent collision‐induced dissociation (CID) produces extremely low abundance product ions at m/z values greater than 60, and the m/z 223 ion corresponding to [TATP + H] + was not observed. Density functional theory (DFT) calculations at the B88LYP/DVZP level indicate that dissociation of the complex to form NH and TATP occurs at energies lower than peroxide bond dissociation, while protonation of TATP leads to cleavage of the ring structure. These results provide a method for pico‐gram detection levels of TATP using commercial instrumentation commonly available in forensic laboratories. As a point of comparison, a detection limit of 15 ng was obtained by flame ionization detection. Copyright © 2006 John Wiley &amp; Sons, Ltd.
Structural Basis for Catalytic Activation of Thiocyanate Hydrolase Involving Metal-Ligated Cysteine Modification (2009)

Thiocyanate hydrolase (SCNase) is a member of a family of nitrile hydratase proteins, each of which contains a unique noncorrin cobalt center with two post-translationally modified cysteine ligands, cysteine-sulfenic acid or -sulfenate (Cys-SO(H)), and cysteine-sulfininate (Cys-SO(2)(-)), respectively. We have found that a partially matured recombinant SCNase was activated during storage. The crystal structures of SCNase before and after storage demonstrated that Cys-SO(2)(-) modification of gammaCys131 proceeded to completion prior to storage, while Cys-SO(H) modification of gammaCys133 occurred during storage. SCNase activity was suppressed when gammaCys133 was further oxidized to Cys-SO(2)(-). The correlation between the catalytic activity and the extent of the gammaCys133 modification indicates that the cysteine sulfenic acid modification of gammaCys133 is of primary importance in determining the activity of SCNase.
Methyloceanibacter caenitepidi gen. nov., sp. nov., a facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent (2013)

A moderately thermophilic, methanol-oxidizing bacterium (strain Gela4(T)) was isolated from methane-utilizing mixed-culture originating from marine sediment near a hydrothermal vent. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain Gela4(T) was closely related to members of the genus 'Methyloligella' (94.7% similarity) within the class Alphaproteobacteria. Strain Gela4(T) was a Gram-staining-negative and aerobic organism. Cells were rod-shaped and non-motile. The temperature range for growth of strain Gela4(T) was 19-43 °C (optimal growth at 35 °C). Strain Gela4(T) tolerated up to 9% NaCl with an optimum at 1%. The organism was a facultative methylotroph that could utilize methanol, methylamine, trimethylamine and a variety of multi-carbon compounds. The major cellular fatty acid and major respiratory quinone were C18 : 1ω7c and ubiquinone-10, respectively. The predominant phospholipids were phosphatidylcholine, phosphatidylglycerol and phosphatidylethanolamine. The DNA G+C content was 63.9 mol%. On the basis of the morphological, physiological, biochemical and genetic information, a novel genus and species, Methyloceanibacter caenitepidi is proposed, with Gela4(T) ( = NBRC 109540(T) = DSM 27242(T)) as the type strain.
Abstract 4743: Exosomes in motion: Visualizing cancer metastasis via the Synaptotagmin C2B domain (2012)

Abstract Exosomes play pivotal roles in intercellular communication and cancer progression. Recent findings have shown exosomes to incite proangiogenesis and prepare lymph nodes as remote niches for accumulation and migration of melanoma cells. Exosomes present a highly curved morphology with a size range of ∼30-100 nm that is distinct from other lipid vesicles. Furthermore, exosomes have the potential as a general metastasis biomarker since their increased secretion in the peripheral blood has been correlated with cancer metastasis. Since aqueous suspensions of exosomes cannot be seen by conventional optical methods, we hypothesized that a molecular probe that binds to exosomes could be a novel tool for detecting these vesicles. We aim to develop a minimally-invasive diagnostic tool to detect and measure secreted exosomes as biomarkers of cancer metastasis that may help clinicians and patients decide on an appropriate therapeutic action. Taking a cue from nature and using solid phase ‘Click’ chemistry as a technique for peptide modification, we created a fluorophore-tagged cyclic peptide based on the membrane penetrating C2B domain of Synaptotagmin I. We investigated the peptide-lipid interactions using synthetic liposomes as preliminary models of exosomes through a combination of spectroscopic techniques. We found that the peptide probe was selective for highly curved liposomes (d &amp;lt;100 nm) and does not bind to low curvature liposomes (d &amp;gt;100 nm). We tested blood plasma samples from rat models to find out if our preliminary findings would translate to the detection of exosomes. Our results showed that blood plasma treated with the peptide probe showed fluorescence intensity that was remarkably higher than the untreated peptide, which indicated binding to exosomes. Furthermore, we used a real time nanoparticle tracking analysis system to visualize the exosomes in a dynamic and physiologically-relevant medium. The peptide-treated exosomes were detected as fast-moving, fluorescent particles even in the complex matrix of blood plasma. This technique provided us with a platform to study the size distribution and concentration of exosomes in blood plasma. We have created a peptide probe that selectively binds to exosomes from an animal model. The investigation of the exosome binding property of this probe on clinically relevant samples is ongoing. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4743. doi:1538-7445.AM2012-4743
Supplementary Figure S5 from Targeting DNA Damage Repair Functions of Two Histone Deacetylases, HDAC8 and SIRT6, Sensitizes Acute Myeloid Leukemia to NAMPT Inhibition (2023)

&lt;p&gt;Combinations of AR-42 and KPT-9274 have no overlapping toxicities in vivo.&lt;/p&gt;
The relationship between lymphocyte transformation and immune response. (1969)

A comparison was made between the number of cells forming or carrying antibody and those stimulated to transform in vitro by antigen, by using blood lymphocytes from rabbits immunized against sheep erythrocytes. In blood samples collected 7–77 days after a single immunization, the number of transformed cells was always markedly higher than that of cells forming plaques or rosettes. It is suggested that unsensitized cells are induced to transform by a stimulus transferred from other reacting cells.
Supplementary Table 9 from Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq (2023)

Supplementary Table 9 from Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq
646. Isolation and Evaluation of Novel Anti-AAV2 and AAV3B Antibody Clones from a Human Donor (2015)

Neutralizing antibodies against AAV, whether generated via natural exposure or viral vector, have been shown to significantly reduce the efficiency of gene transfer, particularly following intravenous administration. One proposed approach to overcoming this obstacle is the engineering of an AAV capsid that is able to evade neutralization by these antibodies. The epitopes of a handful of antibodies have been mapped to their respective AAV capsids via cryo-EM or X-ray crystallography, but these antibodies are most often mouse monoclonals and their relevance to human vector immunology is unknown. In addition, these antibodies likely represent only a small fraction of the humoral response to AAV, as no comprehensive panel against a single serotype has been studied; rather, one or two quality capsid:Fab structures have been obtained for a given serotype. Given recent advancements in B cell cloning technologies, it is now possible to develop a panel of human monoclonals against AAV for the evaluation of neutralizing capacity and epitope mapping to identify the immunodominant regions of the AAV capsid. To obtain these monoclonals, we screened 30 human donors for NAbs against AAV2 and AAV3B and selected the donors with a titer of 1:320 against AAV3 and a titer of 1:40 against AAV3B. We obtained bulk switched memory B cells via magnetic bead sorting and seeded single sorted cells on irradiated 3T3-msCD40L cells in the presence of IL-2 and IL-21 and cultured cells for 2 weeks to promote expansion and antibody secretion. Culture supernatants were screened for AAV2 and AAV3B reactivity via ELISA; of positive clones obtained, 39% were specific for AAV2, 41% were specific for AAV3B, and the remaining 20% were reactive towards both AAV2 and AAV3B. In order to obtain heavy and light chain sequences for expression and characterization of these antibodies, we have performed nested PCR based on conserved regions in the immunoglobulin gene for some anti-AAV monoclonals and are currently completing PCR on the remaining clones. Of the sequences obtained thus far, the majority display a substantial amount of somatic hypermutation relevant to corresponding germline sequences; the percentage of base pair substitutions resulting in a missense mutation within the complementarity-determining regions was approximately 80%, with the frequency of mutation averaging 0.26 per residue. Mutations preferentially occurred in CDRs over framework regions, again suggesting that these antibodies have undergone maturation in response to exposure to AAV antigen. Subsequent analysis of the neutralizing capacity of these antibodies as well as the mapping of their epitopes will provide critical information for evaluating the feasibility of designing AAV variants capable of evading neutralization by anti-AAV antibodies.
Distal hereditary motor neuronopathy of the Jerash type is caused by a novel SIGMAR1 c.500A>T missense mutation (2019)

In conclusion, the homozygous <i>SIGMAR1</i> c.500A>T mutation causes dHMN of the Jerash type, possibly due to a significant drop of protein levels. This finding is in agreement with other <i>SIGMAR1</i> mutations that have been associated with autosomal recessive dHMN with pyramidal signs; thus, our findings further support that <i>SIGMAR1</i> be added to the dHMN genes diagnostic panel.
Ondansetron treatment in patients with Tourette??s syndrome (1999)

Ondansetron, a selective 5-HT3 antagonist, may lower mesolimbic dopaminergic hyperactivity. The present open-label pilot study evaluated the effect of ondansetron in Tourette's syndrome. Six Tourette's syndrome men aged 14-48 years resistant to haloperidol participated in the study. Assessments included the Yale Global Tic Severity Scale (YGTSS), Yale-Brown Obsessive-Compulsive Scale (Y-BOCS), and Tourette's syndrome-Clinical Global Impression (TS-CGI) scale. The maximal ondansetron dosage (8-16 mg per day) was given for 3 weeks. Ondansetron treatment was associated with a significant decrease in the severity of tics. Two patients showed a definite response (score improvement of 40% or more), and two showed a probable response (> 25%). Two patients did not improve. Side-effects were transient and included abdominal pain (n = 5) and constipation (n = 2). Ondansetron may possess anti-tic effects in some Tourette's syndrome patients.
Non-radiative complete surface acoustic wave bandgap for finite-depth holey phononic crystal in lithium niobate (2012)

We demonstrate the existence of non-radiative complete surface acoustic wave (SAW) bandgaps for two-dimensional piezoelectric phononic crystals of holes. Holes of finite depth in a semi-infinite LiNbO3 substrate are specifically considered. SAW bandgaps are determined from the band structure calculated with a three-dimensional finite element method taking into account material anisotropy and piezoelectricity. The effect of hole geometry on the bandgaps has been investigated. It is further found that the complete band gap does not close for moderately conical holes.
An electrostatic slow positron beam apparatus for positron scattering experiments (2010)

An electrostatic slow positron beam system has been developed for positron scattering studies. The apparatus uses a remoderator in reflection geometry in conjunction with an electrostatic hemispherical energy analyzer for the brightness enhancement. It is possible to determine absolute total scattering cross section values under magnetic field-free conditions down to a few mG. Measurement of the energy distribution of the positrons that are reemitted from the remoderator and total cross sections for positron-He scattering are presented.
Leti-UTSOI2.1: A Compact Model for UTBB-FDSOI Technologies—Part I: Interface Potentials Analytical Model (2015)

A detailed presentation of the latest version of the Leti-UTSOI compact model is provided. Leti-UTSOI2 is the first available model able to describe the behavior of low-doped ultrathin body and buried oxide fully depleted silicon-on-insulator transistors in all bias configurations, including strong forward back bias. In this part, a full analytical calculation of interface potentials, valid for all regimes of independent double-gate device operation, is detailed. This analytical computation, which is the heart of Leti-UTSOI2, provides explicit expressions for all quantities required to build dc and ac core models.
Chemical and ecotoxicological characterization of the “Erika” petroleum: Bio-tests applied to petroleum water-accommodated fractions and natural contaminated samples (2004)

Oil spills are an important source of PAHs in marine and coastal areas and comprise a short- and long-term threat for aquatic organisms. Some PAHs are known to be toxic, in particular mutagenic and/or carcinogenic, and their toxicological effects must be evaluated. Here, the impact of the “Erika” oil spill, which occurred at the end of 1999, was studied by combining chemical (PAH analyses) and toxicological approaches (biological effect assessment). “Erika” elutriates have been found to be more toxic than the elutriate obtained with a crude oil, Bal 250, inducing deleterious effects in Mytilus galloprovincialis and Crassostrea gigas embryos and in Isochrysis galbana algae. The embryotoxicity test in mussel is more sensitive than growth test in I. galbana. Naphthalenic compounds make up more than 95% of total PAHs quantified in elutriates. “Erika” elutriates are enriched with naphthalene, methyl-naphthalene, anthracene and higher-molecular-weight compounds. On the contrary, Bal 250 elutriate is characterized by the highest dibenzothiophene, methyl-dibenzothiophene and dimethyl-dibenzothiophene levels. Weathering does not highly affect the toxicity of the “Erika” oil. This study also confirms the potential impact of the “Erika” fuel on the biological quality of sea water and sediments from Traict du Croisic on the Atlantic coast of France.