gebhart/patrepeval huggingface dataset:
Protein gradients on the nucleoid position the carbon-fixing organelles of cyanobacteria (2018)

Carboxysomes are protein-based bacterial organelles encapsulating key enzymes of the Calvin-Benson-Bassham cycle. Previous work has implicated a ParA-like protein (hereafter McdA) as important for spatially organizing carboxysomes along the longitudinal axis of the model cyanobacterium <i>Synechococcus elongatus</i> PCC 7942. Yet, how self-organization of McdA emerges and contributes to carboxysome positioning is unknown. Here, we identify a small protein, termed McdB that localizes to carboxysomes and drives emergent oscillatory patterning of McdA on the nucleoid. Our results demonstrate that McdB directly stimulates McdA ATPase activity and its release from DNA, driving carboxysome-dependent depletion of McdA locally on the nucleoid and promoting directed motion of carboxysomes towards increased concentrations of McdA. We propose that McdA and McdB are a previously unknown class of self-organizing proteins that utilize a Brownian-ratchet mechanism to position carboxysomes in cyanobacteria, rather than a cytoskeletal system. These results have broader implications for understanding spatial organization of protein mega-complexes and organelles in bacteria.
Scale Tests, In-situ Measurements and Simulation of Methane Gas Distribution at Heading Faces (1999)

Distributions of methane gas concentration at a heading face with an auxiliary fan were measured in both an actual coal mine and a scale model. As a result, general distribution pattern of methane gas concentration was elucidated and it was found that there exist several areas where gas concentrations tend to rise to dangerous levels. A CFD (Computational Fluid Dynamics) method was also developed and the results of the computation were compared with those obtained in these measurements. It was concluded that the CFD can be used for simulating the distributions of gas concentration that are affected by conditions in a heading.
<scp>UML</scp>‐Based Approach to Developing a <scp>CityGML</scp> Application Domain Extension (2013)

Abstract Recently a national 3D standard was established in the N etherlands as a CityGML Application Domain Extension (called IMGeo ). In line with the D utch practice of modeling geo‐information, the ADE is developed using a model driven approach. The classes are designed in UML and automatically mapped to GML schema. The current OGC CityGML specification does not provide rules or guidance on correctly modeling an ADE in UML . This article fills this gap by studying how CityGML can be extended for specific applications starting from the UML diagrams. Six alternatives for modeling ADEs in UML are introduced and compared. The optimal alternative is selected and applied to obtain the national 3D standard. The approach was extensively discussed with international experts, who were members of both SIG3D and other working groups. As a consequence the approach was adopted by the SIG3D , the Special Interest Group 3D which, among other things, work on the 3D standard CityGML in cooperation with OGC . Therefore the approach contains many issues that can be generalized and reused by future domain extensions of CityGML . To further support this, the article formulates a model‐driven framework to model CityGML ADEs . Open issues are described in the conclusions.
Targeting Immune Complex-Mediated Hypersensitivity with Recombinant Soluble Human FcγRIA (CD64A) (2008)

Binding of Ag-Ab immune complexes to cellular FcgammaR promotes cell activation, release of inflammatory mediators, and tissue destruction characteristic of autoimmune disease. To evaluate whether a soluble FcgammaR could block the proinflammatory effects of immune complexes, recombinant human (rh) versions of FcgammaRIA, FcgammaRIIA, and FcgammaRIIIA were prepared. Binding of rh-FcgammaRIA to IgG was of high affinity (KD=1.7x10(-10) M), whereas rh-FcgammaRIIA and rh-FcgammaRIIIA bound with low affinity (KD=0.6-1.9x10(-6) M). All rh-FcgammaR reduced immune complex precipitation, blocked complement-mediated lysis of Ab-sensitized RBC, and inhibited immune complex-mediated production of IL-6, IL-13, MCP-1, and TNF-alpha by cultured mast cells. Local or systemic delivery only of rh-FcgammaRIA, however, reduced edema and neutrophil infiltration in the cutaneous Arthus reaction in mice. 125I-labeled rh-FcgammaRIA was cleared from mouse blood with a rapid distribution phase followed by a slow elimination phase with a t1/2gamma of approximately 130 h. The highest percentage of injected radioactivity accumulated in blood approximately liver approximately carcass>kidney. s.c. dosing of rh-FcgammaRIA resulted in lower serum levels of inflammatory cytokines and prevented paw swelling and joint damage in a murine model of collagen Ab-induced arthritis. These data demonstrate that rh-FcgammaRIA is an effective inhibitor of type III hypersensitivity.
TOTAL ARTIFICIAL LUNG PERIOPERATIVE MANAGEMENT: A 7 DAY SURVIVAL STUDY IN SHEEP (1999)

Society Of Critical Care Medicine 29Th Educational And Scientific Symposium; Orlando, Florida, Usa; February 11-15, 2000: Oral Presentations
Neutral to alkaline rosin sizing using polyethyleneimine-epichlorohydrin (PEI-epi) as a mordant (2000)

L'appret alcalin a base de colophane de resine a recemment suscite un grand interet parmi les chercheurs. Toutefois, une application commerciale employant la resine comme agent de collage alcalin n'etait pas disponible. La presente etude a employe le polyethyleneimine-epichlorohydrine (PEI-epi) comme mordant alcalin pour le collage a la resine. Nous avons trouve que le mordant pouvait effectivement accroitre l'efficacite du collage dans des conditions neutres a alcalines, sans exiger d'alun. Le degre de collage obtenu a l'aide de cette methode utilisant la resine/le mordant de polymere dans des conditions alcalines etait comparable a celui d'une methode alun-resine dans des conditions acides. Nous croyons que des liaisons chimiques entre les fibres, le PEI-epi, et les molecules de resine se sont formees pendant le developpement du collage. Nous avons aussi observe que le papier colle avec du PEI-epi/resine montrait un certain degre de reversion du collage. Il faudra proceder a une recherche plus poussee pour determiner les facteurs qui contribuent a la reversion du collage.
ChemInform Abstract: Regioselective Functionalization of Bis(trimethylsilyl)methylimines with Electrophiles. (1995)

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.
Hydration of aromatic alkynes catalyzed by a self-assembled hexameric organic capsule (2016)

The combination of a Brønsted acid catalyst and a supramolecular organic capsule formed by the self-assembly of six resorcin[4]arene units efficiently promotes the mild hydration of aromatic alkynes to their corresponding ketones.
<title>Investigation of focused Gaussian beam diffraction in narrow capillaries</title> (1994)

Theoretical investigations into the processes of focused Gaussian beam diffraction in blood capillaries with a diameter about erythrocyte size have been carried out. A correlation function of dynamic speckles formed in this case has been analyzed.
Studies on the δ‐form complex in the syndiotactic polystyrene–organic molecule system. II. Structural investigation of the δ‐form with <i>p</i>‐ and <i>m</i>‐xylene isomers (2003)

Abstract Syndiotactic polystyrene (sPS) membranes containing different mole fractions of p ‐xylene were prepared by a solution‐casting procedure. Complex formation between sPS and xylene was studied by thermogravimetric analysis and Fourier transform infrared spectroscopy. The stability and desorption behavior of the sPS–guest solvent and phase transitions were studied by differential scanning calorimetry. The formation of the δ‐form complex in the presence of different mole fractions of xylene isomers was analyzed and confirmed. The mole fraction of p ‐xylene in the dried membrane was found to be higher than that of the corresponding mole fraction in the isomer solvent solution used for casting. This was attributed to the preferential complexing ability of p ‐xylene with sPS. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 89: 2882–2887, 2003
Nonreversible loss of platelet aggregability induced by calcium deprivation (1978)

Platelets lose their ability to aggregate when deprived of divalent cations. This usually was studied by incubating human citrated platelet-rich plasma with EDTA or EGTA and then adding enough CaCl2 to combine with the chelating agent. Incubation for 5-7 min at 37 degrees C caused irreversible loss of the platelets' ability to adhere to glass and to aggregate with ADP, epinephrine, A23187, vasopressin, or serotonin or upon rewarming after chilling and markedly reduced aggregation with collagen or thrombin. Control samples incubated with saline, CaEDTA, or CaEGTA were not inhibited. Untreated platelets washed and incubated in solutions treated with resins that remove divalent cations lost their ability to aggregate in 30 min. More than about 0.26 mM Mg2+ partially protected the platelets. Unlike aggregation, ADP-induced shape change, clot retraction caused by thrombin or ADP plus reptilase, and thrombin-induced 14C-serotonin release were not inhibited after incubation. Aggregability was not restored by prolonged incubation with CaCl2, adding normal plasma, or washing the platelets. Its loss was temperature and pH dependent, occurring in 2 min at 43 degrees C but not in 7 min at 30 degrees C, and at pH 7.8 but much less at pH 7.2. The defect was not associated with an increase in platelet cyclic AMP, a decrease in metabolic ATP, or the presence of free ADP.
Oxidized low-density lipoprotein antibodies in myocardial infarction patients without classical risk factors (2013)

First AMI patients without classical risk factors had lower levels of OLAB compared with healthy controls. It is likely that the immunological reaction due to oxidized LDL participates as a preventive factor in the physiopathology of atherosclerosis.
Testis and scrotum: cytology of testicular and scrotal masses and male infertility (2010)

Enlargement of the male external genitalia implies any one of various events within and around the scrotum, while the testes themselves may or may not be enlarged. The condition occurs in all age groups, is usually associated with pain, as with haematocele after surgical procedures, testicular torsion and similar events and may be accompanied by other local or general symptoms. A number of causes may lead to either unilateral or bilateral scrotal enlargement. Any testicular enlargement, oedema or pain requires a thorough diagnostic work-up to exclude the possibility of carcinoma of the testis.
Osteoclast-mediated osteolysis in bone metastasis from renal cell carcinoma (1988)

Osteolytic characteristics of bone metastasis from renal cell carcinoma were morphologically and biochemically investigated. First, undecalcified ground sections of bone metastases were made from four patients with renal cell carcinoma. Second, renal cell carcinoma cell line (RCC-K1) was established from one of the four patients, and its effect on bone resorption in vitro was examined. Marked proliferation and activation of osteoclasts around the tumor cells was histologically demonstrated. Conditioned medium from the RCC-K1 cells contained potent bone-resorbing activity in vitro. The activity was reduced to basal level by calcitonin, but was not blocked by indomethacin. The activity was lost after dialysis (MW cutoff 3500), while it was retained after 2 weeks of storage. Levels of prostaglandin E2 and 1,25-dihydroxyvitamin D of the RCC-K1-conditioned medium were insufficient to cause bone resorption in vitro. The conditioned medium did not stimulate cAMP accumulation in rat osteoblastic cells. These results suggest that renal cell carcinoma causes bone destruction through the stimulation of osteoclasts by locally secreting an unknown humoral factor or factors.
Stroboscopic Backaction Evasion in a Dense Alkali-Metal Vapor (2011)

We explore experimentally quantum nondemolition measurements of atomic spin in a hot potassium vapor in the presence of spin-exchange relaxation. We demonstrate a new technique for backaction evasion by stroboscopic modulation of the probe light. With this technique we study spin noise as a function of polarization for atoms with spin greater than 1/2 and obtain good agreement with a simple theoretical model. We point that, in a system with fast spin exchange, where the spin-relaxation rate is changing with time, it is possible to improve the long-term sensitivity of atomic magnetometry by using quantum nondemolition measurements.
Diphosphetes—substituent stabilized ring systems (2000)

The mechanism of the formation of σ2P, σ4P-1,2-diphosphetes from phosphaacetylene and phosphinocarbene has been explored by quantum chemical methods. A stepwise mechanism has been established, and no transition state for a concerted pathway could be obtained. The electron distribution of the ring can be understood in terms of a MO model, where the two substituents at phosphorus act as a pseudo π center. Amino substituents on the σ4 phosphorus and silyl group on the neighbouring carbon change the stability order of the possible isomers, stabilizing the 1,2-diphosphete ring. Substitution at the σ2P—by increasing its valence—destabilizes the diphosphete ring, which remains stable only as a result of the amino and silyl substituents.
Landslide risk analysis by means of remote sensing techniques: results from the ESA/SLAM project (2004)

In the framework of the SLAM (Service for Landslides Monitoring) project funded by the European Space Agency, the Permanent Scatterers (PS) processing and the analysis of high resolution images (e.g. SPOT5 and aerial-photos) have been performed at a basin scale, on the whole territory of the Arno River basin (Central Italy). About 350 SAR images have been interferometrically processed by means of the PS technique, detecting about 650,000 PS. The processing of SPOT5 images and aerial-photos, still in progress, have been performed for the extraction of features related to the landslide presence, useful for the geomorphological analysis and, as a consequence in order to give a spatial meaning to the punctual information provided by the PS. This procedure has been coupled with a intense geological interpretation phase characterized by the analysis of traditional in situ monitoring data, ancillary data and the performing of field surveys. The final results will impact on the current instruments used by the Arno Basin Authority for the landslide risk management (e.g. Hydrogeological Management Plan - Piano per l'Assetto Idrogeologico - PAI).
Deployment optimization of IoT devices through attack graph analysis (2019)

The Internet of things (IoT) has become an integral part of our life at both work and home. However, these IoT devices are prone to vulnerability exploits due to their low cost, low resources, the diversity of vendors, and proprietary firmware. Moreover, short range communication protocols (e.g., Bluetooth or ZigBee) open additional opportunities for the lateral movement of an attacker within an organization. Thus, the type and location of IoT devices may significantly change the level of network security of the organizational network. In this paper, we quantify the level of network security based on an augmented attack graph analysis that accounts for the physical location of IoT devices and their communication capabilities. We use the depth-first branch and bound (DFBnB) heuristic search algorithm to solve two optimization problems: Full Deployment with Minimal Risk (FDMR) and Maximal Utility without Risk Deterioration (MURD). An admissible heuristic is proposed to accelerate the search. The proposed method is evaluated using a real network with simulated deployment of IoT devices. The results demonstrate (1) the contribution of the augmented attack graphs to quantifying the impact of IoT devices deployed within the organization on security, and (2) the effectiveness of the optimized IoT deployment.
Immune Complex in the Renal Glomerulus during Normal Pregnancy. A Study in the Guinea Pig and the Mouse (1974)

Abstract Normal pregnant guinea pigs and mice accumulate immune complex in their renal glomeruli. Evidence of immune complex included specific immunofluorescence finding of IgG deposition and typical electron dense deposits on the endothelial and mesangial sides of the glomerular basement membrane. In the guinea pig, C3 was found in the glomeruli; and half of the glomeruli exhibited histopathologic changes although obvious functional disturbance was not evidenced. In the mouse, IgG deposition was not accompanied by C3 or significant histologic changes; and the phenomenon was observed in seven of nine inbred strains of mice studied. Immune complex of pregnancy was found a) to increase with successive pregnancy; b) to appear in the second half of pregnancy; c) not to decrease following pregnancy; and d) to be present in pregnancy of syngeneic mating. Deposition of immune complex, on the other hand, was not found in pseudopregnant mice. The possible nature and significance of the immune complex found in normal pregnancy are discussed.
Surface Characterization of a Biochip Prototype for Cell-Based Biosensor Applications (1999)

Time-of flight secondary ion mass spectrometry (ToF-SIMS) has been employed to characterize and evaluate the surface of a novel biochip prototype, consisting of an array of gold microelectrodes on which the laminin-derived oligopeptide CDPGYIGSR-NH2 was immobilized. The microelectrodes were isolated from each other via a thin film of amorphous Teflon (Teflon AF). Prior to studying biochip surfaces, characterization of gold surfaces (supported on oxidized silicon wafers) incorporating the oligopeptide was carried out, to serve as reference standards. With positive-mode ToF-SIMS, the whole peptide could be observed, and in addition, ions that were characteristic of the constituent amino acids of the oligopeptide could also be observed. The microfabrication process for biochip realization comprised several steps which included the use of compounds that could potentially contaminate the resultant surface. Therefore, it was important to investigate the chemical composition of these surfaces with the highest level of sensitivity. With ToF-SIMS imaging it was possible to detect oligopeptide-related ions only on the microelectrodes and nowhere else. Assessment of the spectral data from user-defined regions within the imaged areas revealed that the microelectrode and Teflon surfaces were devoid of any process-related contamination. In some cases, ToF-SIMS revealed some defects on the biochip surface, which would otherwise not be readily detectable, thereby offering some insight into areas that might require further optimization in the fabrication process.
Role of<i>mgrA</i>and<i>sarA</i>in Methicillin‐Resistant<i>Staphylococcus aureus</i>Autolysis and Resistance to Cell Wall–Active Antibiotics (2008)

These results suggest that down-regulation of mgrA/sarA in combination with use of cell wall-active antibiotics may represent a novel approach to treat MRSA infections.
Emission Peculiarities of TR^3+-doped KPb_2Cl_5 Laser Crystals under Selective Direct, Upconversion and Excitonic/host Excitation of Impurity Centers (2005)

We considered the emission properties of TR3+-doped KPb2Cl5 crystals under different ways of impurity ion excitation: direct excitation of TR 4fn-configuration levels via ground state absorption, upconversion processes, and UV excitonic or crystalline-matrix excitation. It was shown that under UV selective direct excitation of TR ions the population of low energy levels goes via cascade schemes. Under upconversion IR continuous-wave or pulsed excitation the population of upper energy levels goes via ESA or nonradiative energy transfer, accordingly. Pumping into UV exciton band leads to fast energy transfer from exciton to low-energy excited TR levels.
Horizontal Well Fracture Initiation and Extension from Cemented Cased Wells (2013)

Abstract This paper discusses two critical aspects of fracturing in cemented cased horizontal wells; the role of cement bond strength in fracture initiation, and the influence of spacing between perforation clusters on fracture width. It shows that opening of inclined and transverse fractures requires shear sliding between the formation and cemented casing. Strong cement bond or external casing attachments near the perforated interval hinder this shear sliding and hamper free opening of the fracture. If the initiated fracture is longitudinal, its opening causes tensile failure of the bond between casing and cement. This enhances the link between fracture and perforations and assists successful execution of the job. Close spacing between perforation clusters also results in fractures that are narrower than predicted by theories of fracture mechanics. Furthermore fracture width tapers quickly as it extend beyond the wellbore. Together these two mechanisms can explain why these types of fractures are known to occasionally encounter operational problems that include inability to inject at the planned rate during the early stage of each fracture and sudden screen-outs even with very low proppant concentration. The paper offers perforation recommendations for enhancing borehole/fracture connection, as well as guidelines for successful execution of the treatment.
Ultraviolet-ozone jet cleaning process of organic surface contamination layers (1999)

To understand the ultraviolet (UV)-ozone jet cleaning process of organic surface contamination layers, adventitious hydrocarbon layers on Si, self-assembled octadecyltrichlorosilane monolayers on Si, and self-assembled C60H–(CH2)12–SH monolayers on Au were cleaned with pure ozone jet and UV irradiation. Cleaned surfaces were analyzed with in situ x-ray photoelectron spectroscopy measurements. Ozone molecules could react with the unsaturated C–C bonds in self-assembled C60H–(CH2)12–SH monolayers on Au surfaces at room temperature. However, the saturated C–C bonds in OTS hydrocarbon molecules adsorbed on Au surfaces reacted not with ozone molecules but with oxygen radicals generated by the dissociation of ozone molecules under UV irradiation. For adventitious carbon contamination on Si surfaces, only a fraction could be cleaned by ozone at room temperature but it could be almost cleaned with UV-ozone jet.
Fullerene radicals, electrochemistry and electron spin resonance: Part A: Anomalous rotational dependence of the ESR signals of single crystals of [C[sub 70]][I][(C[sub 6]H[sub 5])[sub 4]P][sub 2] Part B: Electrochemical and ESR characterization of mono-anionic radicals of four minor isomers of C[sub 84]: [84]C[sub 1], [84]C[sub s](V), [84]D[sub 2d](I) and [84]D[sub 2](III) (1998)

In part A, the angular dependence of ESR spectra of single crystals of [C70][I][(C6H5)4P]2 is presented showing evidence for an anomalous behavior qualitatively explained in terms of a weak inter-radicals interaction. In part B, preliminary results on the electrochemical and ESR characterization of four recently isolated C84 minor isomers are presented.
X-ray Damage in Protein−Metal Hybrid Structures: A Photoemission Electron Microscopy Study (2010)

Bacterial surface layer protein sheets (S layer) coated with an ultrathin cobalt or silver film were studied by means of laterally resolved near-edge X-ray absorption fine structure spectroscopy performed by photoemission electron microscopy. Comparison with results obtained on pristine S layers allowed us to characterize both chemical interaction and X-ray damage in these protein-metal hybrid systems. In particular, we found that besides direct damage upon exposure to X-ray radiation the biomolecules experience additional contribution of the deposited metals, by low-energy electron generation in the metal particles.