gebhart/patrepeval huggingface dataset:
Detecting security leaks in hybrid systems with information flow analysis (2019)

Information flow analysis is an effective way to check useful security properties, such as whether secret information can leak to adversaries. Despite being widely investigated in the realm of programming languages, information-flow-based security analysis has not been widely studied in the domain of cyber-physical systems (CPS). CPS provide interesting challenges to traditional type-based techniques, as they model mixed discrete-continuous behaviors and are usually expressed as a composition of state machines. In this paper, we propose a lightweight static analysis methodology that enables information security properties for CPS models. We introduce a set of security rules for hybrid automata that characterizes the property of non-interference. Based on those rules, we propose an algorithm that generates security constraints between each sub-component of hybrid automata, and then transforms these constraints into a directed dependency graph to search for non-interference violations. The proposed algorithm can be applied directly to parallel compositions of automata without resorting to model-flattening techniques. Our static checker works on hybrid systems modeled in Simulink/Stateflow format and decides whether or not the model satisfies non-interference given a user-provided security annotation for each variable. Moreover, our approach can also infer the security labels of variables, allowing a designer to verify the correctness of partial security annotations. We demonstrate the potential benefits of the proposed methodology on two case studies.
Cyclosporine therapy of rat heart allograft recipients and release of interleukins (IL 1, IL 2, IL 3): a role for IL 3 in graft tolerance? (1984)

LEW rat recipients of (LEW X BN)F1 strain heterotopic cardiac transplants treated with cyclosporine A (CsA) (15 mg/kg/day intramuscularly, 7 days) retain grafts indefinitely despite drug withdrawal. Donor-specific suppressor T cells that are active in passive transfer experiments have been harvested from long-term CsA-treated hosts. Although CsA is known to inhibit in vitro cytokine release, the in vivo effects of the CsA on the lymphokine cascade are not known. We investigated the action of the drug upon spontaneous and mitogen-induced interleukin 1 (IL 1), interleukin 2 (IL 2), and interleukin 3 (IL 3) release by spleen cells obtained from the following groups of rats: 1) normal, i.e., untreated and ungrafted; 2) grafted, acutely rejecting; 3) grafted, actively treated; and 4) under CsA-induced state of "tolerance." The results demonstrate that in vivo CsA therapy inhibits monocyte (IL 1 release) as well as lymphocyte function (IL 2 and IL 3 release) only during the inductive phase (the 7 days of treatment). During the "tolerant" phase, mitogen (Con A and LPS)-induced release of interleukins was quantitatively similar to that noted in normal animals. In contrast, a remarkable increase in the spontaneous production of IL 3 was observed in the "tolerant" group. Because cytokine release is not inhibited in the "tolerant" state, our data strongly support the concept that maintenance of the state of unresponsiveness is governed by the emergence of suppressor cells. The correlation of increased spontaneous production of IL 3 during this period leads us to postulate that this interleukin may be implicated in the activation or clonal expansion of suppressor cells, and hence may play a role in graft tolerance.
Mitochondrial nucleoid interacting proteins support mitochondrial protein synthesis (2012)

Mitochondrial ribosomes and translation factors co-purify with mitochondrial nucleoids of human cells, based on affinity protein purification of tagged mitochondrial DNA binding proteins. Among the most frequently identified proteins were ATAD3 and prohibitin, which have been identified previously as nucleoid components, using a variety of methods. Both proteins are demonstrated to be required for mitochondrial protein synthesis in human cultured cells, and the major binding partner of ATAD3 is the mitochondrial ribosome. Altered ATAD3 expression also perturbs mtDNA maintenance and replication. These findings suggest an intimate association between nucleoids and the machinery of protein synthesis in mitochondria. ATAD3 and prohibitin are tightly associated with the mitochondrial membranes and so we propose that they support nucleic acid complexes at the inner membrane of the mitochondrion.
Recovery of the simian immunodeficiency virus (SIV) and depression of colony formation in in vitro infected progenitor cell‐enriched rhesus bone marrow (BM) (1991)

Rhesus progenitor-enriched BM was exposed overnight to SIV and cultured in a limiting dilution assay where the potential for progenitor interaction with lymphocytes or macrophages was low. Virus was consistently isolated late in culture, detection being aided by coculture with CEM174 lymphoblasts. Although infected cells had reduced clonogenic activity, colonies were indistinguishable from those derived from uninfected BM with respect to proliferative potential, morphology, and longevity in culture. Primate immunodeficiency viruses, therefore, may infect immature BM populations, directly affecting hematopoietic activity.
Rapid Identification of Carbapenemase Types in Enterobacteriaceae and Pseudomonas spp. by Using a Biochemical Test (2012)

A biochemical test (Carba NP test II) was developed to identify carbapenemase production in Enterobacteriaceae and Pseudomonas spp. and to discriminate between the different types of carbapenemases (classes A, B, and D). It is based on the detection of the acidification resulting from imipenem hydrolysis, coupled with tazobactam and EDTA as inhibitors. This is an easy and reliable technique (100% sensitivity and specificity) for detection of not only carbapenemase activity but also carbapenemase types in Enterobacteriaceae and Pseudomonas aeruginosa.
ChemInform Abstract: Anionic Glucophospholipids (I) ‐ A New Family of Tubule‐Forming Amphiphiles. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
New Polyaminoisoprenyl Antibiotics Enhancers against Two Multidrug-Resistant Gram-Negative Bacteria from <i>Enterobacter</i> and <i>Salmonella</i> Species (2020)

A series consisting of new polyaminoisoprenyl derivatives were prepared in moderate to good chemical yields varying from 32 to 64% according to two synthetic pathways: (1) using a titanium-reductive amination reaction affording a 50/50 mixture of cis and trans isomers and (2) a direct nucleophilic substitution leading to a stereoselective synthesis of the compounds of interest. These compounds were then successfully evaluated for their <i>in vitro</i> antibiotic enhancer properties against resistant Gram-negative bacteria of four antibiotics belonging to four different families. The mechanism of action against <i>Enterobacter aerogenes</i> of one of the most efficient of these chemosensitizing agents was precisely evaluated by using fluorescent dyes to measure outer-membrane permeability and to determine membrane depolarization. The weak cytotoxicity encountered led us to perform an <i>in vivo</i> experiment dealing with the treatment of mice infected with <i>Salmonella typhimurium</i> and affording preliminary promising results in terms of tolerance and efficiency of the polyaminoisoprenyl derivative <b>5r</b>/doxycycline combination.
Four-channel spatial multiplexing over a millimeter-wave line-of-sight link (2009)

A scalable system architecture is proposed and demonstrated for spatial multiplexing over millimeter-wave line-of-sight communication links. This architecture provides increased data capacity without increasing the channel bandwidth. The modulation format is simple (BPSK or QPSK); this facilitates high-rate operation. The spatially multiplexed channels are separated at the receiver using broadband adaptive analog I/Q vector signal processing, a technique which should readily scale to data rates exceeding 10 Gb/s per channel. A control loop continuously tunes the channel separation electronics to correct for changes with time in either the propagation environment or the system components. Design and characterization of a four channel 60 GHz hardware prototype is presented.
Additive manufacturing of open porous functional structures: roadmap from manufacturing to the application (2022)

Additive Manufacturing has proven to be a valuable complement to conventional means of manufacturing. As it is a data-driven process, its flexible customization of part shapes and manufacturing parameters plays a crucial role for this development. This study investigates the novel possibilities enabled by laser-based powder bed fusion for the development of functionality driven design. As an example, open porosities are manufactured, structures known to be advantageous to flow and heat transfer applications. Samples are investigated by laboratory tests and 3D imaging to gain knowledge about application-related properties. The results contribute to correlating manufacturing parameters to resulting properties and thus to design future applications.
A full GPU implementation of a numerical method for simulating capsule suspensions (2014)

Although boundary element (BE) based methods are highly accurate for simulating capsule suspensions in Stokes flows, computational time has been a major issue, even when only a few capsules are simulated. We propose a full graphics processing unit (GPU) implementation of a numerical method coupling the BE method of fluid mechanics with the finite element method of membrane mechanics. In single GPU computing, the performance achieves 0.12 TFlop/s when computing one capsule (2562 nodes and 5120 elements) and 0.29 TFlop/s for two capsules. The performance increases with the number of capsules, achieving a maximum of 0.59 TFlop/s. We also implement a multi-GPU method with the data communication overlapping the computation. A weak scaling test shows perfect scalability for any number of computational nodes per GPU, indicating that the communication time is completely hidden. For a practical use of the present results, we estimate the computational time required for 10000 time steps. When we simulate one capsule and two capsules on one GPU, only 2.0 and 9.1 minutes are required to complete the simulation, respectively, and a simulation with 256 capsules on 16 GPUs takes 3.8 days.
Rational design of supramolecular hemin/G-quadruplex–dopamine aptamer nucleoapzyme systems with superior catalytic performance (2016)

The rational design of a set of hemin/G-quadruplex (hGQ)-dopamine binding aptamer (DBA) conjugates, acting as nucleoapzymes, is described. The nucleoapzyme constructs consist of a hGQ DNAzyme as a catalytic unit and DBA as a substrate binding unit that are brought into spatial proximity by a duplex scaffold composed of complementary oligonucleotide strands. When the hGQ unit is linked to the duplex scaffold <i>via</i> a single-strand DNA tether of variable length, the resulting nucleoapzymes reveal a moderate catalytic enhancement toward the H<sub>2</sub>O<sub>2</sub>-mediated oxidation of dopamine to aminochrome as compared to the process stimulated by the separated hGQ and DBA units (5-7 fold enhancement). This limited enhancement is attributed to inappropriate spatial positioning of the hGQ in respect to the dopamine binding site, and/or to the flexibility of the tether that links the hGQ catalytic site to the double-stranded scaffold. To solve this, rigidification of the hGQ/DBA conjugates by triplex oligonucleotide structures that anchor the hGQ to a duplex domain associated with the DBA units was achieved. By the sequential, programmed, triplex-controlled rigidification of the hGQ/DBA structure, a nucleoapzyme with superior catalytic activity toward the oxidation of dopamine to aminochrome is identified (30-fold catalytic enhancement). Molecular dynamics simulations reveal that in the resulting highly active rigidified nucleoapzyme structure, the hGQ catalytic site is positioned in spatial proximity to the opening of the DBA substrate binding site, thus rationalizing and supporting the enhanced catalytic functions of the system. Finally, the most active nucleoapzyme system was subjected to fuel- and anti-fuel strands that separate and re-assemble the nucleoapzyme structure, allowing "ON" and "OFF" switching of the nucleoapzyme catalytic functions.
New Formamide Catalyst for Ketone Reductions with Trichlorosilane (2006)

Various arylketones 2 could be reduced with trichlorosilane in the presence of a catalytic amount of formamide 1. The enantiomerically enriched alcohols 3 were generated in good yields (61-94%) and excellent enantiomeric ratios (from 96:4 to >99:1). Other reducable groups were preserved. No decrease in yield and selectivity was observed after five recovering/reusing cycles. Starting from lactone 5, which is produced by the reported method followed by cyclization, several biologically active compounds can be synthesized.
Circulating cytokines associated with clinical response to systemic therapy in metastatic renal cell carcinoma (2021)

For patients receiving VEGF-TKI or ICI therapy, distinct plasma cytokines were associated with clinical benefit. Our findings support additional investigation into plasma cytokines as biomarkers in metastatic RCC.
Optical manipulation and defect creation in a liquid crystal on a photoresponsive surface (2017)

Light-induced modulations of the refractive index and pattern formation are desirable to generate complex photonic structures via exposure to light. Here we show that local modulations of the effective refractive index and reconfigurable defects can be locally induced in a hybridized thin birefringent film of a nematic liquid crystal (LC) on a photoresponsive (generating photoinduced electric fields) iron doped lithium niobate surface via exposure to a focused laser beam. Samples were studied with a tailored imaging approach, which provided the ability to investigate these optically excited, field-induced responses on a microscopic level. Upon exposure with a focused laser beam, the fluent LC was expanded on the substrate's surface and localized field-induced defects were optically created. Both umbilic (central) and line defects were observed. The formation of field-induced umbilic defects was modeled in numerical simulations. In addition, line defects were experimentally studied. It was seen that line defects interconnected the centers of two central defects (field-induced defects, which were present at the upper and lower surfaces of the LC layer). In addition, line disclinations separating reverse tilt domains (caused by the inhomogeneous distribution of the photogenerated fields) were seen. These line disclinations were pinned to the central defects. By exposure with two adjacent focused laser beams two umbilic defects were created side by side and interconnected with a line defect (the line defects pinned to each umbilic defect were joined in a single defect line). An alternative technique is presented to field-induce promising photonic motives (microlenses, resonators, line defects) in a liquid crystalline, hybridized birefringent film on a microscopic scale by using a low-power laser (opposed to the high power necessary to induce optical Kerr responses in a neat LC).
Numbers needed to detect a significant change in myocardial strain and left ventricular twist measured by complementary spatial modulation of magnetization (CSPAMM) (2012)

We have calculated the inter-study reproducibility of myocardial strain and twist measured by CSPAMM and calculated the number of subjects required to detect a significant change in these parameters.
New insights into the morphology and phylogeny of<i>Heterosigma akashiwo</i>(Raphidophyceae), with the description of<i>Heterosigma minor sp. nov</i>. (2016)

:Heterosigma akashiwo is one of the smallest raphidophytes and is known for its ability to form dense, fish-killing blooms. In many parts of the world, H. akashiwo is a permanent resident of the algal community, and blooms have caused extensive financial losses for the aquaculture industry. Different aspects of its biology have been the focus of numerous investigations over the last two decades but, perhaps because of its small size and fragile nature, few morphological studies have been carried out. We conducted phylogenetic and morphological studies of 24 strains of Heterosigma from the coastal waters of Europe, North America, Australia and New Zealand. Complete 18S, ITS region and the D1–D2 region of 28S rDNA were sequenced and compared with all available raphidophyte sequences, revealing a novel species of Heterosigma, Heterosigma minor sp. nov. All strains of H. akashiwo were genetically very similar across the rDNA region (> 99.8% similarity) and morphologically very similar in light microscopy and scanning electron microscopy. Heterosigma minor shared only 98.2% similarity with H. akashiwo, and there were several morphological differences: it was smaller, rounder and had fewer mucocysts than H. akashiwo. The secondary structure of ITS2 was reconstructed, revealing three compensatory base changes between the two species, further indicating that H. minor is a sister to H. akashiwo. The phylogeny of Raphidophyceae was reconstructed to include all currently described raphidophytes.
Evaluation of the effects of L-carnitine on medaka (Oryzias latipes) fatty liver (2017)

Lifestyle-related diseases have become a major issue in recent years. The increasing incidence of fatty liver underlines the urgency with which the issues of non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) need to be addressed. L-carnitine is a compound known to transport fatty acids into the mitochondria to enhance β-oxidation-mediated metabolism of fats. In this study, the effects of L-carnitine administration on fatty liver of medaka (Oryzias latipes) were analysed, to check for disease improvement and metabolic changes. Additionally, the effects of the concomitant administration of L-carnitine and eicosapentaenoic acid (20:5n-3) (EPA) were investigated. Findings indicated reduced lipid deposition, increase in metabolites associated with β-oxidation, and significant reduction in fatty acid levels in the liver, implying improvement in fatty liver condition. Concomitant administration of L-carnitine and EPA resulted in further benefits, via changes in fatty acid composition in the medaka fatty liver model.
Proliferation and Cdk4 expression in microsatellite unstable colon cancers with <i>TGFBR2</i> mutations (2005)

Abstract Approximately 15% of human colon cancers have microsatellite instability (MSI) and carry frameshift mutations in a polyadenine tract ( BAT‐RII ) in the type II transforming growth factor β (TGF‐β) receptor ( TGFBR2 ), a required component of the TGF‐β receptor. The BAT‐RII mutations in MSI colon cancers make the tumors resistant to the effects of TGF‐β. In cultured epithelial cells, TGF‐β can inhibit cell proliferation and induce apoptosis, and in vitro it can regulate the expression of a variety of cyclins, cyclin‐dependent kinases (cdks) and cdk inhibitors. These effects are context‐ and tissue type‐dependent, raising questions about which of these in vitro effects of TGF‐β signaling inactivation contribute to the formation of primary colon cancer. Thus, this study sought to determine the pathogenetically relevant effects of TGFBR2 inactivation in primary MSI colon cancers with mutant BAT‐RII . Colon cancers with mutant BAT‐RII were found to have increased proliferation compared to cancers with wild‐type BAT‐RII . Assessment of cdk4, cyclin D1 and p27 kip1 expression revealed that only cdk4 expression was increased in the cancers with mutant BAT‐RII . In order to determine if TGFBR2 inactivation was the cause of these changes, TGFBR2 was reconstituted in an MSI colon cancer cell line, resulting in decreased proliferation and decreased cdk4 expression and kinase activity. These results suggest that TGFBR2 mutations in primary colon cancers may be responsible for the increased proliferation and cdk4 expression in these tumors and provide evidence that deregulation of cdk4 is a pathogenic in vivo consequence of TGFBR2 inactivation in primary colon cancer. © 2005 Wiley‐Liss, Inc.
InAs hole inversion and bandgap interface state density of 2 × 1011 cm−2 eV−1 at HfO2/InAs interfaces (2013)

High-k/InAs interfaces have been manufactured using InAs surface oxygen termination and low temperature atomic layer deposition of HfO2. Capacitance–voltage (C–V) curves revert to essentially classical shape revealing mobile carrier response in accumulation and depletion, hole inversion is observed, and predicted minority carrier response frequency in the hundred kHz range is experimentally confirmed; reference samples using conventional techniques show a trap dominated capacitance response. C–V curves have been fitted using advanced models including nonparabolicity and Fermi-Dirac distribution. For an equivalent oxide thickness of 1.3 nm, an interface state density Dit = 2.2 × 1011 cm−2 eV−1 has been obtained throughout the InAs bandgap.
Pharmacokinetics and pharmacodynamics of ch14.18/CHO in relapsed/refractory high-risk neuroblastoma patients treated by long-term infusion in combination with IL-2 (2016)

Ch14.18 manufactured in Chinese hamster ovary (CHO) cells is currently being evaluated in clinical trials. Short-term infusion (STI) (8-20 h/day; 4-5 days) of 100 mg/m2 ch14.18/CHO (dinutiximab β) per cycle in combination with cytokines is standard treatment of neuroblastoma (NB) patients. As pain is a limiting factor, we investigated a novel delivery method by continuous long-term infusion (LTI) of 100 mg/m2 over 10 days. 53 NB patients were treated with 5-6 cycles of 6 × 106 IU/m2 subcutaneous interleukin-2 (d 1-5, 8-12), LTI of 100 mg/m2 ch14.18/CHO (d 8-18) and 160 mg/m2 oral 13-cis-retinoic acid (d 22-35). Human anti-chimeric antibody (HACA), antibody-dependent cell-mediated cytotoxicity and complement-dependent cytotoxicity were determined. With LTI, we observed a maximum concentration of ch14.18/CHO (Cmax) of 12.56 ± 0.68 µg/ml and a terminal half-life time (t1/2 β) of 32.7 ± 16.2 d. The clearance values for LTI and STI of 0.54 ± 0.13 and 0.41 ± 0.29 L/d m2 and area under the serum concentration-time curve (AUC) values of 189.6 ± 41.4 and 284.8 ± 156.8 µg×d/ml, respectively, were not significantly different. Importantly, we detected ch14.18/CHO trough concentration of ≥ 1 µg/ml at time points preceding subsequent antibody infusions after cycle 1, allowing a persistent activation of antibody effector mechanisms over the entire treatment period of 6 months. HACA responses were observed in 10/53 (19%) patients, similar to STI (21%), indicating LTI had no effect on the immunogenicity of ch14.18/CHO. In conclusion, LTI of ch14.18/CHO induced effector mechanisms over the entire treatment period, and may therefore emerge as the preferred delivery method of anti-GD2 immunotherapy to NB patients.