gebhart/patrepeval huggingface dataset:
Flagellar proteins and type III‐exported virulence factors are the predominant proteins secreted into the culture media of Salmonella typhimurium (1999)

We analysed all major proteins secreted into culture media from Salmonella typhimurium. Proteins in culture supernatants were collected by trichloroacetic acid precipitation, separated in SDS-polyacrylamide gels and analysed by amino acid sequencing. Wild-type strain SJW1103 cells typically gave rise to nine bands in SDS gels: 89, 67, 58, 52, 50, 42, 40, 35 and (sometimes) 28 kDa. A search of the sequences in the available databases revealed that they were either flagellar proteins or virulence factors. Six of them were flagella specific: FlgK or HAP1 (58 kDa), FliC or flagellin (52 kDa), FliD or HAP2 (50 kDa), FlgE or hook protein (42 kDa), FlgL or HAP3 (35 kDa) and FlgD or hook-cap protein (28 kDa). The other four bands were specific for virulence factors: SipA (89 kDa), SipB (67 kDa), SipC (42 kDa) and InvJ (40 kDa). The 42 kDa band was a mixture of FlgE and SipC. We also analysed secreted proteins from more than 30 flagellar mutants, and they were categorized into four groups according to their band patterns: wild type, mot type, polyhook type and master gene type. Virulence factors were constantly secreted at a higher level in all flagellar mutants except a deltamot (motAB deletion) mutant, in which the amounts were greatly reduced. A new morphological pathway of flagellar biogenesis including protein secretion is presented.
Sample Size Calculation in Clinical Trials (2010)

In any clinical trial, the sample size has to be planned on a justifiable, rational basis. The purpose of sample size calculation is to determine the optimal number of participants (patients) to be included in the trial. Sample size calculation requires the collaboration of experienced biostatisticians and physician-researchers: expert medical knowledge is an essential part of it.
Picosecond radical kinetics. Rate constants for reaction of benzeneselenol with primary alkyl radicals and calibration of the 6-cyano-5-hexenyl radical cyclization (1992)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPicosecond radical kinetics. Rate constants for reaction of benzeneselenol with primary alkyl radicals and calibration of the 6-cyano-5-hexenyl radical cyclizationMartin Newcomb, Thomas R. Varick, Chau Ha, M. Beata Manek, and Xu YueCite this: J. Am. Chem. Soc. 1992, 114, 21, 8158–8163Publication Date (Print):October 1, 1992Publication History Published online1 May 2002Published inissue 1 October 1992https://pubs.acs.org/doi/10.1021/ja00047a026https://doi.org/10.1021/ja00047a026research-articleACS PublicationsRequest reuse permissionsArticle Views340Altmetric-Citations45LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Different modulatory effects of isoflurane and halothane on arrhythmogenesis elicited by dofetilide in rabbits. (2021)

We compared proarrhythmic effects of dofetilide under the isoflurane- and halothane- anesthesia using the acute atrioventricular block rabbit. In the isoflurane group (n=6), dofetilide at 10 and 100 µg/kg prolonged the monophasic action potential duration (MAP90) of the ventricle by 172±23 and 224±31 ms, and the numbers of R on T type premature ventricular contractions (PVCs) were 1.5±0.8 and 2.3±1.3 beats/min, respectively. Meanwhile, torsade de pointes (TdP) appeared in 2 out of 6 animals at the high dose, which terminated spontaneously. In the halothane group (n=6), dofetilide prolonged the MAP90 by 69±7 and 116±14 ms, and the numbers of R on T type PVCs were 6.4±4.9 and 0.4±0.2 beats/min at the low and high dose, respectively. Meanwhile, TdP appeared in 2 out of 6 animals at the low dose, which degenerated into ventricular fibrillation. The arrhythmia was not observed at the high dose in the survived 4 animals. Notably, the cycle length of TdP in the halothane group was significantly shorter than that in the isoflurane group (144±5 ms vs 234±8 ms). The responses of isoflurane and halothane to proarrhythmic actions of dofetilide may be associated with their different electrophysiological modification to trigger generation and ventricular conduction as indicated by R on T type PVCs and cycle length of TdP.
A Renaissance in Living Cationic Polymerization (2009)

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTA Renaissance in Living Cationic PolymerizationSadahito Aoshima* and Shokyoku KanaokaView Author Information Department of Macromolecular Science, Graduate School of Science, Osaka University* To whom correspondence should be addressed. E-mail: [email protected]. Phone: +81-6-6850-5448. Fax: +81-6-6850-5448.Cite this: Chem. Rev. 2009, 109, 11, 5245–5287Publication Date (Web):October 5, 2009Publication History Received22 June 2009Published online5 October 2009Published inissue 11 November 2009https://doi.org/10.1021/cr900225gCopyright © 2009 American Chemical SocietyRIGHTS & PERMISSIONSACS AuthorChoiceArticle Views20340Altmetric-Citations532LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (2 MB) Get e-AlertsSUBJECTS:Cationic polymerization,Copolymers,Living polymerization,Polymers,Star polymers Get e-Alerts
Chronic black tea administration protects plasma proteins, plasma, liver and kidney lipids against oxidation. (2006)

These findings provide evidence that long term black tea supplementation is capable of protecting both plasma proteins and plasma lipids from oxidative injury, and demonstrate that chronic black tea administration protects both liver and kidney tissues - but not the jejunoileal mucosa - against oxidation.
FAM222B Is Not a Likely Novel Candidate Gene for Cerebral Cavernous Malformations (2016)

Cerebral cavernous malformations (CCMs) are prevalent slow-flow vascular lesions which harbour the risk to develop intracranial haemorrhages, focal neurological deficits, and epileptic seizures. Autosomal dominantly inherited CCMs were found to be associated with heterozygous inactivating mutations in 3 genes, CCM1 (KRIT1), CCM2 (MGC4607), and CCM3 (PDCD10) in 1999, 2003 and 2005, respectively. Despite the availability of high-throughput sequencing techniques, no further CCM gene has been published since. Here, we report on the identification of an autosomal dominantly inherited frameshift mutation in a gene of thus far unknown function, FAM222B (C17orf63), through exome sequencing of CCM patients mutation-negative for CCM1-3. A yeast 2-hybrid screen revealed interactions of FAM222B with the tubulin cytoskeleton and STAMBP which is known to be associated with microcephaly-capillary malformation syndrome. However, a phenotype similar to existing models was not found, neither in fam222bb/fam222ba double mutant zebrafish generated by transcription activator-like effector nucleases nor in an in vitro sprouting assay using human umbilical vein endothelial cells transfected with siRNA against FAM222B. These observations led to the assumption that aberrant FAM222B is not involved in the formation of CCMs.
Highly responsive ac scalar atomic magnetometer with long relaxation time (2013)

We propose an operating condition for an optically pumped scalar atomic magnetometer with a unique band-pass frequency response. Under this operating condition, the signal response of the magnetometer is increased threefold around a nonzero resonance frequency. The resonance frequency is equal to the detuning between the Larmor frequency and the frequency of the oscillating magnetic field used for excitation. The resonance is explained in terms of the characteristics of the first-order perturbation expansion of the Bloch equation for a modulated bias magnetic field. The scalar magnetometer provides an enhanced magnetic response around its resonance frequency even beyond the cutoff frequency, which is defined as the inverse of the phase relaxation time of the spin polarization.
PlayeRank: Multi-dimensional and role-aware rating of soccer player performance. (2018)

The problem of rating the performance of soccer players is attracting the interest of many companies, websites, and the scientific community, thanks to the availability of massive data capturing all the events generated during a game (e.g., tackles, passes, shots, etc.). Existing approaches fail to fully exploit the richness of the available data and lack of a proper validation. In this paper, we design and implement PlayeRank, a data-driven framework that offers a principled multi-dimensional and role-aware evaluation of the performance of soccer players. We validate the framework through an experimental analysis advised by soccer experts, based on a massive dataset of millions of events pertaining four seasons of the five prominent European leagues. Experiments show that PlayeRank is robust in agreeing with the experts' evaluation of players, significantly improving the state of the art. We also explore an application of PlayeRank --- i.e. searching players --- by introducing a special form of spatial query on the soccer field. This shows its flexibility and efficiency, which makes it worth to be used in the design of a scalable platform for soccer analytics.
Molecular genetic biomarkers in hematological malignancies (1996)

Most hematopoietic malignancies are widely disseminated even in their “early” stages and often do not have a well-defined localized phase. This makes them less amenable to conventional early screening methods such as imaging and observation. Furthermore, the staging systems for lymphomas are not particularly useful prognostically, with the possible exception of Hodgkin's disease. However, as currently compared with solid tumors, the extensively detailed understanding of the acquired (somatic) genetic lesions in leukemias and lymphomas provide useful molecular biomarkers for early detection. Moreover, well described high risk groups have been identified. These include individuals who are immunosuppressed, for example, iatrogenically following organ transplantation or those with AIDS. Also at high risk are patients treated with certain chemotherapeutic agents who are at risk for the development of acute non-lymphoblastic leukemia. Accordingly, these clinical settings might prove to be good models for evaluating molecular cancer risk markers and the possible introduction of chemoprevention. Here, we outline the biological basis for the application of biomarkers for the early detection of hematological neoplasia. These concepts may provide the stage for the creation of chemoprevention studies in leukemia and lymphoma. J. Cell. Biochem. 25S:165–171. © 1997 Wiley-Liss, Inc.
Verbal noun as ‘equivalent’ of finite verb in Welsh (1991)

AbstractIn the Brythonic languages—in Welsh more commonly than in Cornish and Breton—a construction is encountered in which the verbal noun (a more satisfactory term than ‘infinitive’) performs the function of a finite verb. It that role it does not act eliptically, or ana-phorically, for it can begin a work (an essay, article, letter—not frequently a novel) and there is no possibility of discerning what would fill the alleged ellipsis. Some writers avoid the construction, others favor it, a state of affairs reminiscent of the Latin ‘historical infinitive’.In the Goidelic group of Celtic (Irish, Gaelic, Manx) the same construction also occurs, but more sparsely by far.A similar, but not identical, formation is found in Russian, the so- called ‘actor-infinitive construction,’ but there is usually nothing to express the actor in Celtic occurrences of verbal noun instead of finite verb.Other languages have shown nominal expressions in place of verbal ones, including Homeric Greek, scholastic Latin, certain types (and periods) of Sanskrit, etc. In some of these there is a certain artificiality present. In Welsh, whether scholarly or colloquial, that is not the case. There seems to be something similar in certain non-Indo-European languages too. It is, however, difficult to say whether there was transmission in one direction or another, although a few scholars have indulged in such speculation.
Surviving sensor network software faults (2009)

We describe Neutron, a version of the TinyOS operating system that efficiently recovers from memory safety bugs. Where existing schemes reboot an entire node on an error, Neutron's compiler and runtime extensions divide programs into recovery units and reboot only the faulting unit. The TinyOS kernel itself is a recovery unit: a kernel safety violation appears to applications as the processor being unavailable for 10-20 milliseconds.
Automated detection of myocardial ischaemia by epicardial miniature ultrasound transducers — a novel tool for patient monitoring during cardiac surgery☆ (2010)

The ultrasonic system detected regional ischaemia during LAD occlusion. An automated analysis algorithm demonstrated excellent ability to detect ischaemia. This technology can develop into a useful tool to detect ischaemia in cardiac surgery.
Computing Hulls And Centerpoints In Positive Definite Space (2009)

In this paper, we present algorithms for computing approximate hulls and centerpoints for collections of matrices in positive definite space. There are many applications where the data under consideration, rather than being points in a Euclidean space, are positive definite (p.d.) matrices. These applications include diffusion tensor imaging in the brain, elasticity analysis in mechanical engineering, and the theory of kernel maps in machine learning. Our work centers around the notion of a horoball: the limit of a ball fixed at one point whose radius goes to infinity. Horoballs possess many (though not all) of the properties of halfspaces; in particular, they lack a strong separation theorem where two horoballs can completely partition the space. In spite of this, we show that we can compute an approximate "horoball hull" that strictly contains the actual convex hull. This approximate hull also preserves geodesic extents, which is a result of independent value: an immediate corollary is that we can approximately solve problems like the diameter and width in positive definite space. We also use horoballs to show existence of and compute approximate robust centerpoints in positive definite space, via the horoball-equivalent of the notion of depth.
Normal Forms for Some Classes of Sequential Spiking Neural P Systems (2013)

Spiking neural P systems (SN P systems, for short) are a class of distributed parallel computing devices inspired from the way neurons communicate by means of spikes, where each neuron can have several spiking rules and forgetting rules and neurons work in parallel in the sense that each neuron that can fire should fire at each computation step. In this work, we consider SN P systems with the restrictions: 1) systems are simple (resp. almost simple) in the sense that each neuron has only one rule (resp. except for one neuron); 2) at each step the neuron(s) with the maximum number of spikes among the neurons that can spike will fire. These restrictions correspond to that the systems are simple or almost simple and a global view of the whole network makes the systems sequential. The computation power of simple SN P systems and almost simple SN P systems working in the sequential mode induced by maximum spike number is investigated. Specifically, we prove that such systems are Turing universal as both number generating and accepting devices. The results improve the corresponding ones in Theor. Comput. Sci., 410 (2009), 2982-2991.
New Photoremovable Protecting Groups for Carboxylic Acids with High Photolytic Efficiencies at Near‐UV Irradiation. Application to the Photocontrolled Release of L‐Glutamate (2006)

We report here the syntheses and the photolytic properties of 3-(4,5-dimethoxy-2-nitrophenyl)-2-butyl (DMNPB) esters as new photoremovable groups for carboxylic acids, and their use for the caging of L-glutamate. A high-yielding synthesis of the DMNPB esters led to a 4:1 threo/erythro diastereomeric mixture, which could be separated by HPLC. While these esters were stable in neutral buffer, photolysis at 364 nm induced a > or =95 % release of the carboxylic acid, with a 0.26 quantum yield for L-glutamate formation. L-Glutamate release was also possible by two-photon photolysis with an action cross section of 0.17 GM at 720 nm. Laser photolysis at 350 nm generated a transient species at around 410 nm, attributed to a quinonoid aci-nitro intermediate that decayed in the submillisecond time range (t(1/2)=0.53 ms) for the faster gamma-L-glutamyl threo-esters. Given the absorbance of these esters (lambda(max)=350 nm; epsilon=4500), the threo DMNPB esters represent new caging groups that can be efficiently photolyzed at near-UV wavelengths. An efficient and rapid photolytic release of L-glutamate has been demonstrated on hippocampal neurons in primary culture.
Preparation of Superconducting Ba2YCu3O7-y/Ag Composite Films by the Dipping-Pyrolysis Process Using Metal Naphthenates at 750°C (1991)

Superconducting Ba 2 YCu 3 O 7- y /Ag composite films were prepared on yttria-stabilized zirconia substrates by the dipping-pyrolysis process. Metal naphthenates were used as starting materials. Homogeneous Ba-Y-Cu-Ag solutions with (Ag/BYCO) molar ratios of 0-1.0 were spin-coated onto the substrates and pyrolyzed at 500°C. Subsequently, these prefired films were heat-treated at 750°C under a low-oxygen partial pressure (=2×10 -4 atm) followed by higher- p (O 2 ) annealing. High superconducting transition temperatures, T c,onset ( s )'s and T c,zero$( r )' s , o f 88 K -90 K w e r e o b t a i n e d f o r t h e c o m p o s i t e f i l m s w i t h ( A g / B Y C O ) m o l a r r a t i o s o f 0.1-0.5.
Scaling of pneumatic digital logic circuits (2015)

The scaling of integrated circuits to smaller dimensions is critical for achieving increased system complexity and speed. Digital logic circuits composed of pneumatic microfluidic components have to this point been limited to a circuit density of 2-4 gates cm(-2), constraining the complexity of the digital systems that can be achieved. We explored the use of precision machining techniques to reduce the size of pneumatic valves and resistors, and to achieve more accurate and efficient placement of ports and vias. In this way, we attained an order of magnitude increase in circuit density, reaching as high as 36 gates cm(-2). A 12-bit binary counter circuit composed of 96 gates was realized in an area of 360 mm(2). The reduction in size also brought an order of magnitude increase in speed. The frequency of a 13-stage ring oscillator increased from 2.6 Hz to 22.1 Hz, and the maximum clock frequency of a binary counter increased from 1/3 Hz to 6 Hz.
Supplementary Table S3 from A Combinatorial CRISPR–Cas9 Screen Identifies Ifenprodil as an Adjunct to Sorafenib for Liver Cancer Treatment (2023)

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Simple flow through reaction cells for in situ transmission and fluorescence x-ray-absorption spectroscopy of heterogeneous catalysts (2006)

We report on the design of both transmission and fluorescence x-ray-absorption spectroscopy cells suitable for in situ characterization of heterogeneous catalysts. The heart of both cells is a quartz tube used to house the catalyst sample. Both cells allow in situ x-ray-absorption fine-structure (XAFS) data to be recorded from −196 to 825 °C using a wide range of gas flows at atmospheric pressure. Excellent temperature control is demonstrated with both designs. XAFS data can be recorded over a wide x-ray energy range (2.1–29 keV). These designs are simple, robust, relatively low cost, and, moreover, are reliable and easy to operate. All of the critical components of the transmission reactor can be purchased commercially, with little machining required. The design of the fluorescence reactor requires access to a skilled glass blower.
ChemInform Abstract: SYNTHESIS OF DIALKYL PHOSPHOROSELENOCYANATIDATES AND THEIR REARRANGEMENT TO DIALKYL PHOSPHORISOSELENOCYANATIDATES (1979)

Abstract Aus den Verbindungen (I) erhält man direkt oder über die Silylverbindungen (V) die Selenverbindungen (III), die ohne Isolierung zu den Verbindungen (VI) umgelagert werden.
Mechanistic basis for the allosteric activation of mitochondrial glutaminase C, a key driver of glutamine metabolism in cancer cells (2022)

The dependence of cancer cells on glutamine metabolism, the most abundant amino acid in plasma, has been observed in many highly aggressive and deadly cancers including pancreatic cancer, triple‐negative breast cancer, and glioblastoma. The mitochondrial enzyme glutaminase C (GAC) catalyzes the hydrolysis of glutamine to glutamate, the first step in glutamine metabolism, highlighting GAC as a potentially important therapeutic target. GAC acquires maximal catalytic activity upon binding to anionic activators like inorganic phosphate. To delineate the mechanism of GAC activation, we used the tryptophan substitution of tyrosine 466 in the catalytic site of the enzyme as a fluorescence reporter for glutamine binding in the presence and absence of phosphate. We show that in the absence of phosphate, glutamine binding to the GAC (Y466W) tetramer exhibits positive cooperativity. A high‐resolution X‐ray structure of tetrameric GAC (Y466W) bound to glutamine suggests that cooperativity in substrate binding is coupled to tyrosine 249, located at the edge of the catalytic site (i.e. designated the ‘lid’), adopting two distinct conformations. In one dimer within the GAC tetramer, the lids are open and glutamine binds weakly, whereas, in the adjoining dimer, the lids are closed over the substrates resulting in higher affinity interactions. When crystallized in the presence of glutamine and phosphate, all four subunits of the GAC (Y466W) tetramer have bound glutamine with closed lids. Glutamine now binds with high affinity to each subunit, which then undergo simultaneous catalysis. These findings show how the regulated transitioning of GAC between different conformational states ensures maximal catalytic activity is reached in cancer cells only when an allosteric activator is available.
ChemInform Abstract: Quinoidal Tetrazines: Formation of a Fascinating Compound Class. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.