gebhart/patrepeval huggingface dataset:
Host Pathways Important for Coxiella burnetii Infection Revealed by Genome-Wide RNA Interference Screening (2013)

Q fever in humans is caused by the bacterium Coxiella burnetii. Infection with C. burnetii is marked by its unique ability to replicate within a large vacuolar compartment inside cells that resembles the harsh, acidic environment of a lysosome. Central to its pathogenesis is the delivery of bacterial effector proteins into the host cell cytosol by a Dot/Icm type IVB secretion system. These proteins can interact with and manipulate host factors, thereby leading to creation and maintenance of the vacuole that the bacteria grow within. Using high-throughput genome-wide screening in human cells, we identified host factors important for several facets of C. burnetii infection, including vacuole transport and membrane fusion events that promote vacuole expansion. In addition, we show that maturation of the C. burnetii vacuole is necessary for creating an environment permissive for the Dot/Icm delivery of bacterial effector proteins into the host cytosol.
University students, ladies, and tigers: defeasible reasoning and insufficient information (1992)

A simple problem in defeasible reasoning is analyzed using a number of methods from the literature. It is shown that any such method which arrives at a firm conclusion regarding this problem must necessarily import additional assumptions. The paper argues in favor of those methods which are candid in their assumptions, and which can support alternative decision making rules.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Catabolism of the Cholesterol Side Chain in <i>Mycobacterium tuberculosis</i> Is Controlled by a Redox-Sensitive Thiol Switch (2017)

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is a highly successful human pathogen and has infected approximately one-third of the world's population. Multiple drug resistant (MDR) and extensively drug resistant (XDR) TB strains and coinfection with HIV have increased the challenges of successfully treating this disease pandemic. The metabolism of host cholesterol by Mtb is an important factor for both its virulence and pathogenesis. In Mtb, the cholesterol side chain is degraded through multiple cycles of β-oxidation and FadA5 (Rv3546) catalyzes side chain thiolysis in the first two cycles. Moreover, FadA5 is important during the chronic stage of infection in a mouse model of Mtb infection. Here, we report the redox control of FadA5 catalytic activity that results from reversible disulfide bond formation between Cys59-Cys91 and Cys93-Cys377. Cys93 is the thiolytic nucleophile, and Cys377 is the general acid catalyst for cleavage of the β-keto-acyl-CoA substrate. The disulfide bond formed between the two catalytic residues Cys93 and Cys377 blocks catalysis. The formation of the disulfide bonds is accompanied by a large domain swap at the FadA5 dimer interface that serves to bring Cys93 and Cys377 in close proximity for disulfide bond formation. The catalytic activity of FadA5 has a midpoint potential of -220 mV, which is close to the Mtb mycothiol potential in the activated macrophage. The redox profile of FadA5 suggests that FadA5 is fully active when Mtb resides in the unactivated macrophage to maximize flux into cholesterol catabolism. Upon activation of the macrophage, the oxidative shift in the mycothiol potential will decrease the thiolytic activity by 50%. Thus, the FadA5 midpoint potential is poised to rapidly restrict cholesterol side chain degradation in response to oxidative stress from the host macrophage environment.
Fluorescence line narrowing applied to the study of proteins (1998)

Fluorescence line narrowing is a high resolution spectroscopic technique that uses low temperature and laser excitation to optically select specific subpopulations from the inhomogeneously broadened absorption band of the sample. When applied to the study of fluorescent groups in proteins one can obtain vibronically resolved spectra, which can be analyzed to give information on spectral line shapes, vibrational energies of both the ground and excited state molecule, and the inhomogeneous distribution function of the electronic transitions. These parameters reveal information about the chromophoric prosthetic group and the protein matrix and are functions of geometric strains and local electric fields imposed by the protein. Examples of the use of fluorescence line narrowing are discussed in investigations of heme proteins, photosynthetic systems and tryptophan-containing proteins.
C<sup>5</sup> (2008)

The annotation of hundreds of thousands of utterances for the training of statistical utterance classifiers requires a careful quality assurance procedure to make the data consistent and reliable. In this paper, we present five methods to analyze different aspects of annotated data to ensure their Completeness, Consistency, Correlation, Congruence and to avoid Confusion-collectively referred to as C <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">5</sup> .
Development of a Practical Synthesis of Stearoyl-CoA Desaturase (SCD1) Inhibitor MK-8245 (2011)

A practical kilogram scale chromatography-free synthesis of stearoyl-CoA desaturase 1 (SCD1) inhibitor MK-8245 is described. The key features of this sequence include an efficient addition–elimination reaction of a piperidine fragment with a 3-bromoisoxaline followed by an iodine-mediated oxidation to the corresponding isoxazole. The development of a safe and scalable tetrazole formation protocol is also presented.
Genomic mapping and sequence analysis of the fowl adenovirus serotype 10 hexon gene (1995)

The gene for the major capsid protein (hexon) of fowl adenovirus serotype 10 (FAV-10) has been identified by the use of the expression vector pGEX and rabbit polyclonal antisera raised against FAV-10. The nucleotide sequence of the entire hexon gene has been determined. Sequence analysis revealed an open reading frame of 2808 bp coding for a putative polypeptide 936 amino acids long with a molecular mass of 105.5 kDa. The translation initiation codon has a local sequence which conforms with the optimal translation start sequence of CC(A/G)CCATGG. The location of the hexon gene in the FAV genome was from 46.85 to 52.81 map units, which is to the left of the hexon gene in the genomes of both bovine and human adenovirus (52.4 to 60.5 map units.). A splice acceptor site was identified 12 bp upstream of the initiation codon by using mRNA and PCR. It had the sequence TAGG which conforms to the consensus sequence of (C/T)AGG. Comparison of the amino acid sequence of the FAV-10 hexon with those of the bovine, human and murine hexon gene products revealed highest levels of identity occurring in the regions corresponding to the pedestals which form the base region of the hexon, and the lowest levels of identity in the regions corresponding to the loops which are exposed to the external environment.
Changes to the length of the flexible linker region of the Rieske protein impair the interaction of ubiquinol with the cytochrome <i>bc</i><sub>1</sub> complex (2000)

Crystal structures of the cytochrome bc1 complex indicate that the catalytic domain of the Rieske iron-sulfur protein, which carries the [2Fe-2S] cluster, is connected to a transmembrane anchor by a flexible linker region. This flexible linker allows the catalytic domain to move between two positions, proximal to cytochrome b and cytochrome c1. Addition of an alanine residue to the flexible linker region of the Rieske protein lowers the ubiquinol-cytochrome c reductase activity of the mitochondrial membranes by one half and causes the apparent Km for ubiquinol to decrease from 9.3 to 2.6 microM. Addition of two alanine residues lowers the activity by 90% and the apparent Km decreases to 1.9 microM. Deletion of an alanine residue lowers the activity by approximately 40% and the apparent Km decreases to 5.0 microM. Addition or deletion of an alanine residue also causes a pronounced decrease in efficacy of inhibition of ubiquinol-cytochrome c reductase activity by stigmatellin, which binds analogous to reaction intermediates of ubiquinol oxidation. These results indicate that the length of the flexible linker region is critical for interaction of ubiquinol with the bc1 complex, consistent with electron transfer mechanisms in which ubiquinol must simultaneously interact with the iron-sulfur protein and cytochrome b.
Metal complexes of N-allylaniline. A palladium(II) complex with co-ordination number of greater than four (1977)

N-Allylaniline (aa) can act as a uni- or bi-dentate ligand in complexes of composition [PdCl2(aa)2] affording an orange-yellow (1) and a dark red isomer (2). The palladium in (1) is four-co-ordinate and planar, with the olefin group unbound in benzene and dimethyl sulphoxide (dmso) solution. The olefin groups in (2) are bound to the palladium, which, in solution (NN-dimethylformamide, dmso, or acetone), is at least five-co-ordinate. Both complexes lose methylacetylene and allene to form trans-[PdCl2(NPhH2)2] on standing in the solid state orinsolution. Isomer (1) requires elevated temperatures and long reaction times, but (2) decomposes readily at room temperature.
Catalytic Asymmetric Addition of β‐Ketoesters to Various Imines by Using Chiral Palladium Complexes (2005)

Eine hoch enantioselektive Mannich-Reaktion von β-Ketoestern in Gegenwart katalytischer Mengen des Pd-Aqua-Komplexes 1 wurde entwickelt (siehe Schema; PG=Schutzgruppe). Unterschiedlichste Imine, abgeleitet von Glyoxylat sowie von einfachen aromatischen und α,β-ungesättigten Aldehyden, konnten in hohen Ausbeuten und mit ausgezeichneten Enantioselektivitäten in die Mannich-Addukte überführt werden. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2005/z462202_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Unsteady Rans Simulation of an Enclosed, Turbulent Reacting Methane Jet with the Premixed CMC Method (2015)

The premixed conditional moment closure (CMC) method has been shown to provide the capability to model turbulent, premixed methane flames with detailed chemistry and reasonable runtimes in a RANS environment [1]. Here the premixed CMC method is extended to Unsteady RANS. The new model is validated with the PIV and Raman turbulent, enclosed reacting methane jet data from DLR [2]. The experimental data has a rectangular test section at atmospheric pressure and 573 K with a single inlet jet. A jet velocity of 90 m/s is used with an adiabatic flame temperature of 2,064 K. Contours of major species, temperature and equivalence ratio along with their rms values are provided. The CMC model falls into the class of table lookup turbulent combustion models where the combustion model is solved offline over a range of conditions and stored in a table that is accessed by the CFD code. The scalar dissipation is used to account for the effects of the small scale mixing on the reaction rates. A presumed shape beta function PDF is used to account for the effects of large scale turbulence on the reactions. The unsteady RANS version of the open source CFD code OpenFOAM is used with the PISO algorithm solved with the finite volume method. Velocity, temperature and major species are compared to the experimental data. Once validated, this tool will be useful for designing lean premixed combustors for gas turbines. The results match the experimental data better than the steady RANS of [1] and are able to pick up the unsteadiness of the flame.
Cyanophage tRNAs may have a role in cross-infectivity of oceanic <i>Prochlorococcus</i> and <i>Synechococcus</i> hosts (2011)

Marine cyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic prokaryotes in oceanic environments, and are key contributors to global CO(2) fixation, chlorophyll biomass and primary production. Cyanophages, viruses infecting cyanobacteria, are a major force in the ecology of their hosts. These phages contribute greatly to cyanobacterial mortality, therefore acting as a powerful selective force upon their hosts. Phage reproduction is based on utilization of the host transcription and translation mechanisms; therefore, differences in the G+C genomic content between cyanophages and their hosts could be a limiting factor for the translation of cyanophage genes. On the basis of comprehensive genomic analyses conducted in this study, we suggest that cyanophages of the Myoviridae family, which can infect both Prochlorococcus and Synechococcus, overcome this limitation by carrying additional sets of tRNAs in their genomes accommodating AT-rich codons. Whereas the tRNA genes are less needed when infecting their Prochlorococcus hosts, which possess a similar G+C content to the cyanophage, the additional tRNAs may increase the overall translational efficiency of their genes when infecting a Synechococcus host (with high G+C content), therefore potentially enabling the infection of multiple hosts.
A Directional Loudspeaker Array for Surround Sound in Reverberant Rooms (2010)

We present a method to enhance the performance of the sound field reproduction approach to 2-D surround sound applicable for reverberant rooms, under the constraint that only a small number of loudspeakers is permissible. The method is based on the idea of using steerable directional loudspeakers to exploit the room reverberation. In home theater applications, exact sound field reproduction is currently handicapped by the unreasonably large numbers of loudspeakers required for operation over audible frequencies. However by exploiting reverberant wall reflections, mirror-sources may be used as additional loudspeakers to help perform the reproduction. Utilizing mirror-sources, the number of loudspeaker locations required throughout the room may be reduced. A large array of omnidirectional loudspeakers can then be replaced by a small number of compact configurable directional loudspeakers. Simulating in a reverberant room with each directional loudspeaker modeled as an array of monopoles, we show that the performance is comparable to a circular array with a much larger number of elements. We quantify the accuracy of the sound field reproduction and the robustness to calibration error, comparing the proposed scheme with the more standard circular array geometry.
EXAMINATION OF LANE CHANGE CRASHES AND POTENTIAL IVHS COUNTERMEASURES. FINAL REPORT (1993)

This report examines the potential for Intelligent Vehicle Highway System (IVHS) technology to improve the crash avoidance capability of drivers and vehicles for backing crashes. IVHS has the potential to greatly enhance highway traffic safety. This report attempts to determine the safety implications of IVHS by using analytical methods to model the backing crash type and potential IVHS crash avoidance countermeasures. The causal assessments show that approximately 87.0% of the cases occurred because drivers were unaware of (did not see or did not check for) the struck vehicle, object, or pedestrian. Of the causal factors which appear to be amenable to IVHS countermeasures in the near term, the main causal factor appeared to be that the backing vehicle's driver was unaware of an obstacle. This suggested that a vehicle-based IVHS countermeasure that warns drivers of obstacles in the backing path might be helpful. The suggested countermeasure was a rear-zone object detection system. It is estimated that the functional rear-zone object detection system would be approximately 70% effective in avoiding the parallel path, curved path, and pedestrian/pedalcyclist crash subtypes. In terms of all backing crash subtypes, the system would be approximately 28% effective.
Diastereoselective Synthesis of ψ[(<i>E</i>)-CHCMe]- and ψ[(<i>Z</i>)-CHCMe]-Type Dipeptide Isosteres by Organocopper-Mediated <i>anti</i>-S<sub>N</sub>2‘ Reaction (2002)

[reaction: see text] Acyclic psi[(E)-CH=CMe]- and psi[(Z)-CH=CMe]-type dipeptide isosteres were efficiently synthesized. In a key reaction, alpha-alkylation of gamma-mesyloxy-beta-methyl-alpha,beta-unsaturated esters with organocyanocuprates in diethyl ether or tetrahydrofuran preferentially afforded the psi[(E)-CH=CMe]- or psi[(Z)-CH=CMe]-isomer, respectively, via anti-S(N)2' mechanism.
Leflunomide prolongs pulmonary allograft and xenograft survival. (1996)

Allograft and xenograft control animals receiving vehicle yielded graft survival times of 6.0 +/- 0.0 and 5.4 +/- 0.6 days, respectively. Although xenograft recipients treated with cyclosporine (7.5 mg/kg/day orally) showed no significant graft prolongation, pulmonary allograft survival in recipients receiving cyclosporine alone was significantly prolonged to 28.2 +/- 0.7 days. Leflunomide-treated allograft (15 mg/kg/day orally) and xenograft (20 mg/kg/day orally) recipients displayed significant graft prolongation to 28.2 +/- 0.7 days and 15.8 +/- 3.3 days, respectively. Cyclosporine (7.5 mg/kg/day orally) enhanced the effect of leflunomide (20 mg/kg/day orally) in xenograft recipients with a mean graft survival time of 36.0 +/- 3.0 days achieved when both drugs were administered concomitantly. Cyclosporine significantly suppressed donor-specific immunoglobulin G antibody titers in both pulmonary allograft and xenograft recipients while not affecting immunoglobulin M levels. Leflunomide markedly suppressed both immunoglobulin G and immunoglobulin M donor-specific antibody titers in allograft and xenograft recipients. Except for mild leukopenia and anemia, both cyclosporine- and leflunomide-treated allograft recipients showed no evidence of toxic side effects after 14 days of therapy. However, leflunomide-treated xenograft recipients displayed significant weight loss, anemia, and leukopenia after 14 days of treatment with one death in each treatment group.
Antiphagocytic Function of an IgG Glycosyl Hydrolase from Streptococcus equi subsp. <i>equi</i> and Its Use as a Vaccine Component (2012)

EndoSe from Streptococcus equi subsp. equi is an enzyme hydrolyzing glycosyl groups on IgG, analogous to EndoS from Streptococcus pyogenes. We here show that the activity of EndoSe leads to an antiphagocytic function and may thus be a contributory factor to immune evasion of S. equi. Despite the damaging effect that EndoSe has on IgG, antibodies against EndoSe can neutralize its function. Antibodies against EndoSe restored the opsonic activity of specific opsonizing antibodies. Mice infected with either S. equi subsp. equi or subsp. zooepidemicus or S. pyogenes could be protected by vaccination with EndoSe. It is speculated that EndoSe could be a suitable vaccine candidate against streptococcal infections.
Histaminergic activation of the hypothalamic-pituitary-adrenal axis (1994)

Centrally administered histamine (HA) stimulates the secretion of adenohypophysial POMC-derived peptides, which subsequently cause release of corticosterone. The effect of HA on POMC-derived peptide release is indirect, and it is possible that hypothalamic neurons containing corticotropin-releasing hormone (CRH), arginine vasopressin (AVP), or oxytocin (OT) are involved in the mediation of this response. We studied the effect of HA on: 1) expression of CRH, AVP, and OT messenger RNA (mRNA) at the hypothalamic level; 2) expression of c-fos and POMC mRNA at the pituitary level; and 3) peripheral plasma levels of AVP, OT, ACTH, beta-endorphin (beta-END), and corticosterone. HA (270 nmol) infused intracerebroventricularly increased the expression of CRH, AVP, and OT mRNA in the paraventricular nucleus as well as that of OT mRNA in the supraoptic nucleus of the hypothalamus. At the pituitary level the expression of mRNA for c-fos and POMC increased in the anterior but not in the intermediate lobe in response to HA. Plasma levels of AVP, OT, ACTH, beta-END, and corticosterone all increased in response to central HA administration. Circulating levels of AVP and OT peaked after 5 min, ACTH and beta-END after 15 min, whereas corticosterone levels were highest after 30 min. In concert with our earlier discoveries, the present data support the hypothesis that HA-induced secretion of ACTH and beta-END is mediated via central activation of hypothalamic neuroendocrine neurons containing CRH, AVP, and/or OT.
Search for greener Li-ion batteries: an alternative offered by organic electroactive materials (2011)

The threats of climate change and the issues of secure energy supply are among the fundamental challenges of the 21<sup>st</sup>century that push humanity to adopt a sustainable development and to favour the use of renewable sources of energy. In addition to their historical use, LIBs seem on the road to power the next "Zero Emission" vehicles or could be used to assist the integration of renewable energy sources both on- and off-the-grid. Consequently, production of LIBs is expected to keep on growing. However LIBs are nearly exclusively based on inorganic compounds, non-renewable and energy-greedy materials. Thus in parallel with regular research on inorganic-based LIBs, we have recently proposed to probe an alternative pathway by searching for redox-active organic materials, easier to discard while possibly derived from biomass resources. As solid-state electrochemistry of organics is not that well documented, our current approach consists in a global survey of selected organic structures in order to grasp relevant parameters that affect the redox potential, the stability upon cycling and so on. In this report, we extend our current database of redox-active organic structures by evaluating vs. Li bulky pyrazine-based structures and dilithium polyporate as a supplementary specimen of <i>p</i>-benzoquinone derivatives.
The Challenge of Multimedia Mail. (1989)

Abstract Multimedia messages will contain various types of information, such as text and voice components, images and graphics, structured data and animations. The paper explains why this application will only develop after provision of adequate document standards, multi mediawork stations and high speed networks. After these prerequisites are solved, we demonstrate that not only multimedia mail, but all sorts of multimedia communications will develop, with requirements that the current narrow band ISDN will not be in a position to fulfill.
CCDC 1943047: Experimental Crystal Structure Determination (2019)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
ChemInform Abstract: Binuclear Platinum Diphosphite Complexes: X‐Ray Crystal Structures of K<sub>4</sub>[Pt<sub>2</sub>(pop)<sub>4</sub>Cl]·3 H<sub>2</sub>O and K<sub>4</sub>[Pt<sub>2</sub>(pop)<sub>4</sub>Br<sub>2</sub>]·2 H<sub>2</sub>O (II) (pop: P<sub>2</sub>O<sub>5</sub>H<sub>2</sub><sup>2‐</sup> ). (1986)

Abstract Both title complexes (prepared by literature procedures) are tetragonal.