gebhart/patrepeval huggingface dataset:
Fluorescence fluctuation analysis of BACE1-GFP fusion protein in cultured HEK293 cells (2016)

Beta-site APP cleaving enzyme 1 (BACE1) is a type I transmembrane aspartyl protease. In the amyloidogenic pathway, BACE1 provides &beta;-secretase activity that cleaves the amyloid precursor protein (APP) that leads to amyloid beta (A&beta;) peptides. The aggregation of these A&beta; will ultimately results in amyloid plaque formation, a hallmark of Alzheimer’s disease (AD). Amyloid aggregation leads to progressive memory impairment and neural loss. Recent detergent protein extraction studies suggest that the untreated BACE1 protein forms a dimer that has significantly higher catalytic activity than its monomeric counterpart. Here, we examine the dimerization hypothesis of BACE1 in cultured HEK293 cells using fluorescence correlation spectroscopy (FCS). Cells were transfected with a BACE1-EGFP fusion protein construct and imaged using confocal and DIC microscopy to monitor labeled BACE1 localization and distribution within the cell. Our one-photon fluorescence fluctuation autocorrelation of BACE1- EGFP on the plasma membrane of HEK cells is modeled using two diffusing species on the plasma membrane with estimated diffusion coefficients of 1.39 x 10<sup>-7</sup> cm<sup>2</sup>/sec and 2.8 x 10<sup>-8</sup> cm<sup>2</sup>/sec under resting conditions and STA-200 inhibition, respectively. Anomalous diffusion model also provided adequate description of the observed autocorrelation function of BACE1- EGFP on the plasma membrane with an estimate exponent (α) of 0.8 and 0.5 for resting and STA-200 treated cells, respectively. The corresponding hydrodynamic radius of this transmembrane fusion protein was estimated using the measured diffusion coefficients assuming both Stokes-Einstein and Saffman-Delbruck models. Our results suggest a complex diffusion pattern of BACE1-EGFP on the plasma membrane of HEK cells with the possibility for dimer formation, especially under STA-200 inhibition.
Objective and Subjective Investigation on a Novel Method for Digital Reverberator Parameters Estimation (2014)

Reverberation is a well known effect that has an important role in our listening experience. A great deal of research has been devoted in the last decades aiming to artificially reproduce the reverberation effect exploiting a hybrid reverberation structure. In this context, several automatic procedures have been presented in the literature in order to derive the reverberator structure considering the mixing time evaluation and the minimization functions definition for the late reverberation device. Taking into consideration these aspects, a deep analysis of hybrid digital reverberator audio quality is here proposed, introducing a new parameter for the definition of the mixing time and two new cost functions for the definition of the late reverberation parameters. More in detail, starting from the considerations derived from a previous accurate approach based on the mel frequency cepstral coefficients, the new cost functions are based on the evaluation of the perceptual linear predictive and power normalized cepstral coefficients. Several results are reported, in terms of objective measure, performance analysis and subjective measures, taking into consideration different real impulse responses and various input stimuli and making a comparison with the state of the art. In particular, the obtained results show that a good accuracy can be achieved also considering a low number of coefficients, therefore improving the computational performance.
THE RELATION BETWEEN CARDIAC OUTPUT AND BODY SIZE (1963)

A prerequisite in the study of abnormal body function is the ability to establish the limits of normal. In the case of parameters such as cardiac output that vary with the size of the subject, it has become an accepted practice to standardize values in relation to the body surface area. Thus the cardiac index describes the cardiac output per square metre of body surface area, and the stroke index describes the volume of blood per heart beat per square metre of body surface area. The validity of these expressions depends on the premise that there is a constant or straight line relation between body surface area on the one hand, and cardiac output and stroke volume on the other, over the whole range of body size to be studied, and that the relation can be described by a simple regression equation cutting the intercept at zero. Only where this is so is it meaningful to refer to "the normal" cardiac index or stroke index. Though this premise is backed by observations in the case of adult or adolescent subjects, it was until recently entirely unsupported in the case of children and is still unsupported by any data for infants. This report is an attempt to supply the necessary data.
“Spiritualizing the Political”: Christ and Christianity in Gandhi'sSatyagraha (1997)

Gandhi's intense study of Christ and Christianity, especially in South Africa, had a major impact on his satyagraha campaigns in both South Africa and India. Although satyagraha is often considered only in its political aspect, and although several studies of his religious beliefs have been done without reference to their political implications, Gandhi himself emphasized throughout his life that he sought to spiritualize the political, to establish a spiritual basis for all his social and political work. Gandhi was especially moved by the similar themes he found in the Sermon on the Mount and the Bhagavad Gita . Christ's ethic of Love, expressed especially in the admonitions to “resist not evil” and to “make this world the Kingdom of God,“ deepened Gandhi's inclusive Hindu faith and contributed to his theory of nonviolent direct action.
Magnetic Resonance-Guided High-Intensity Focused Ultrasound (MR-HIFU) in Treatment of Symptomatic Uterine Myomas (2014)

Magnetic Resonance-guided High-Intensity Focused Ultrasound (MR-HIFU) is a noninvasive technique for ablation therapy for uterine myomas, where focused ultrasound energy beam generates localized high temperature in the selected area and coagulates chosen tissue, leaving the skin and tissues in between unharmed. Magnetic resonance imaging enables accurate targeting for HIFU as well as temperature monitoring during treatment. MR guidance with 3D anatomical imaging provides reference data for treatment planning, while real-time temperature monitoring aids in controlling ablation process. This review provides basic information regarding methodology, clinical indications for this kind of treatment, expected outcome and patient management during MR-HIFU procedure. The aim of this work is to introduce a new, noninvasive treatment method for uterine leiomyomas and to present a comparison with other currently used methods.
Preignition and Autoignition Chemistry of the Xylene Isomers (2011)

The relative reactivity of the xylene isomers has been compared under preignition and autoignition conditions. Preignition experiments of each isomer with n-dodecane were conducted in a flow reactor facility at 600–850 K temperatures, 0.8 MPa pressure, and 0.23–0.30 equivalence ratios. Stable intermediates identified from xylene oxidation were tolualdehyde, toluene, and cresol, and the xylenes showed similar reactivity. Autoignition experiments of each isomer with n-decane were conducted in a single-cylinder research engine, and o-xylene was the more reactive isomer. Among several proposed JP-8 surrogates containing xylene, a six-component surrogate with m- or p-xylene was found to best approximate the autoignition conditions of average JP-8. The data can be used for the improvement of xylene chemical kinetic models, and the conclusions from this study will aid in the selection of the appropriate xylene isomer for JP-8 surrogate fuels.
Pseudospin relaxation in ferromagnetic clusters (1991)

A simple model Hamiltonian is proposed to explain the magnetic properties of size-selected cold iron clusters probed by Stern-Gerlach deflections in a molecular beam. Single-sided deflections are well reproduced by this model, which invokes the coupling of the spin system to the cluster framework via the magnetic anisotropy energy. The model does not assume thermal relaxation and the alignment of the magnetic moment with the field is reversible.
Granulosicoccaceae fam. nov., to include Granulosicoccus antarcticus gen. nov., sp. nov., a non-phototrophic, obligately aerobic chemoheterotroph in the order Chromatiales, isolated from Antarctic seawater. (2007)

A Gram-negative, motile by tuft flagella, obligately aerobic chemoorganoheterotrophic, sphere-form bacterium, designated IMCC3135(T), was isolated from the Antarctic surface seawater of King George Island, West Antarctica. The strain was mesophilic, neutrophilic, and requiring NaCl for growth, but neither halophilic nor halotolerant. The 16S rRNA gene sequence analysis indicated that the strain was most closely related to genera of the order Chromatiales in the class Gammaproteobacteria. The most closely related genera showed less than 90% 16S rRNA gene sequence similarity and included Thioalkalispira (89.9%), Thioalkalivibrio (88.0%-89.5%), Ectothiorhodospira (87.9%-89.3%), Chromatium (88.3%-88.9%), and Lamprocystis (87.7%-88.9%), which represent three different families of the order Chromatiales. Phylogenetic analyses showed that this Antarctic strain represented a distinct phylogenetic lineage in the order Chromatiales and could not be assigned to any of the defined families in the order. Phenotypic characteristics, including primarily non-phototrophic, non-alkaliphilic, non-halophilic, and obligately aerobic chemoheterotrophic properties, differentiated the strain from other related genera. The very low sequence similarities (<90%) and distant relationships between the strain and members of the order suggested that the strain merited classification as a novel genus within a novel family in the order Chromatiales. On the basis of these taxonomic traits, a novel genus and species is proposed, Granulosicoccus antarcticus gen. nov., sp. nov., in a new family Granulosicoccaceae fam. nov. Strain IMCC3135(T) (=KCCM 42676(T)=NBRC 102684(T)) is the type strain of Granulosicoccus antarcticus.
WEAKLY REGULAR FLOQUET HAMILTONIANS WITH PURE POINT SPECTRUM (2002)

We study the Floquet Hamiltonian -i∂ t + H + V(ωt), acting in L 2 ([0,T],ℋ, dt), as depending on the parameter ω = 2π/T. We assume that the spectrum of H in ℋ is discrete, [Formula: see text], but possibly degenerate, and that t ↦ V(t) ∈ ℬ(ℋ) is a 2π-periodic function with values in the space of Hermitian operators on ℋ. Let J &gt; 0 and set [Formula: see text]. Suppose that for some σ &gt; 0 it holds true that ∑ h m &gt; h n M m M n (h m - h n ) -σ &lt; ∞ where M m is the multiplicity of h m . We show that in that case there exist a suitable norm to measure the regularity of V, denoted ∊ V , and positive constants, ∊ ⋆ and δ ⋆ , with the property: if ∊ V &lt; ∊ ⋆ then there exists a measurable subset Ω ∞ ⊂ Ω 0 such that its Lebesgue measure fulfills |Ω ∞ | ≥ |Ω 0 | - δ ⋆ ∊ V and the Floquet Hamiltonian has a pure point spectrum for all ω∈Ω ∞ .
SCN Confirmed for First Time in Lyon County (2008)

Research and extension personnel in Iowa have tracked soybean cyst nematode (SCN) infestations by county since initial discovery of the nematode in Winnebago County in 1978.SCN was discovered for the first time in many different Iowa counties in the 1980s and 1990s. But by 2000, there were only nine Iowa counties in which SCN had not yet been found. The nematode was discovered in a few new Iowa counties from 2000 to 2006, but, it had still not yet been found, or at least officially confirmed, in three Iowa counties – Allamakee, Ida, and Lyon Counties – by the end of 2007.
Changes in the concentration of selected metals in sediments of the River Chotla in northwest Poland in its section affected by various anthropogenic factors (2015)

Abstract The purpose of the paper was to assess the changes in the concentration of selected metals in the bottom sediment and interstitial water of the River Chotla in northwest Poland. The research was conducted on the river section flowing through Zaspy Małe and a salmonid fish breeding farm. Samples of water and bottom sediment were taken in four control and measurement points, located above and below the village and on a backwater above the trouteries and below the fish breeding ponds. The pH and the concentration of the metals potassium, iron, calcium, manganese and zinc were determined in the water and sediment samples. The lowest concentrations of the metals were found in the samples collected above and below Zaspy Małe, while the highest concentrations of metals in the water and sediment were found in the samples taken in the backwater, above the fish breeding ponds. Exceptions were calcium and potassium, with the highest concentrations of metals in the water being found in the samples taken below the fish breeding ponds. The content of metals in sediments of the analysed section of the River Chotla was mainly determined by the content of organic matter, which varied as it is dependent on water accumulation processes and the operation of nearby fishery facilities. The slightly alkaline pH facilitated long-lasting accumulation of metals in sediments.
Impact of geography on organ allocation: Beyond the distance to the transplantation center (2015)

GIS represents a new method to evaluate the access to liver transplantation within one region and can be used to identify the presence of disparities and reasons for their existence in order to alleviate them.
Biocompatible tailored zirconia mesoporous nanoparticles with high surface area for theranostic applications (2015)

Nanocarriers as theranostic agents are under the spotlight in modern nanomedicine, and mesoporous nanomaterials represent a class of devices of major interest. Zirconia is biocompatible, inert with good mechanical and thermal properties for in vivo biomedical applications. Although a few examples of zirconia nanoparticles have been described, a major limitation was the low surface area, which is fundamental for payload transport. Here, a simple and highly efficient method is described for the synthesis of spherical mesoporous zirconia nanoparticles (MZNs) with a high surface area through a neutral surfactant-assisted sol-gel method. The combination of alkali halides and vacuum extraction allowed stabilization of the shape and size of MZNs and to avoid porous network failure, respectively. In comparison to published synthesis procedures, a high surface area has been obtained. Biological experiments demonstrated that MZNs were biocompatible, cell permeable and degradable providing a proof of concept for theranostic applications. A comparison with the properties of mesoporous silica nanoparticles has also been performed.
Experimental air embolism: measurement of microbubbles using the Coulter counter. (1973)

Microbubbles in the range 20-250 μm were produced with fine hypodermic needles (0·001, 0·002 and 0·003 inch internal diameter) and were measured using a conventional Coulter Counter. Various bubble sizes could be obtained by varying combinations of needle size, gas pressure, liquid surfactant content and liquid flow rate. Bubbles produced and measured in this way were found to have a very narrow size distribution (80% of the bubbles falling within ± 2 μm of the mean radius) and could be generated at relatively constant frequencies. Over the entire bubble size range, the Coulter Counter method correlated well with two other bubble measuring methods: terminal rise velocity and volume flow rate of gas divided by bubble frequency. It is suggested that this method will enable the introduction of a known number of accurately sized microbubbles into the circulation for the purpose of studying experimental gas embolism.
The effect of mechanical ventilation systems on the chemistry in the supply air (2003)

Chemicals in indoor air, either emitted from a source or from a reaction, have been suggested to cause ill health in buildings. However, no clear correlations between exposure and health effects have been made. In this thesis we studied the reaction between monoterpenes, a group of biogenic unsaturated C10 hydrocarbons, and ozone. Ozonolysis of monoterpenes was used as model reactions for unsaturated compounds in ambient air. Also the products formed from these reactions have been suggested as important participants in the occurrence of discomfort and ill health in buildings. To enable a reliable and sensitive measurement of ppb-ppt levels of monoterpenes and the formed products in the presence of ozone an evaluation of available scrubber materials was made. Potassium iodide was shown to remove ambient levels of ozone and have a recovery of >95% for all monoterpenes and formed products included in the investigation. Experimental conditions showed to have a large impact on the initial steps of the ozonolysis, and also on the composition of the formed products. We showed that water plays an important and complex role both in the initial stage of ozonolysis of ∆3-carene and in the formation and composition of products from the ozonolysis of ∆-pinene. The use of experimental design facilitated the evaluation of the investigated reactions. We showed that the formation of OH radicals could be studied using multiple linear regression models and that the presence or absence of OH radicals had a profound impact on the formation of many of the formed products. We also made an observation of the lack of formed OH radicals in the ozonolysis of limonene and discussed probable causes of this observation. Despite the short reaction times and the ambient levels of ozone and monoterpenes used in our experiments we showed that a number of oxidation products were formed, and that the reaction rate is significantly increased in a ventilation system. This formation is underestimated by theoretical calculations and leads to high amounts of known irritants in the indoor air. We showed that theoretical calculations underestimate the formation of these oxidation products 3-13 times, depending on ventilation system and monoterpene.
Ruptur am wehenfreien Uterus: Zwei Fallvorstellungen (2011)

Ziel: Bei abdominalen Schmerzen in der Schwangerschaft, muss auch am wehenfreien Uterus, an die seltene für Mutter und Kind lebensbedrohliche Situation der Uterusruptur gedacht werden. Ziel war es, dies anhand zweier Fallbeispiele zu verdeutlichen.
The effect of inosine on the spectroscopic properties and crystal structure of a NIR-emitting DNA-stabilized silver nanocluster (2022)

The effect of replacing guanosines with inosines in the two stabilizing strands (5'-CACCTAGCGA-3') of the NIR emissive DNA-Ag<sub>16</sub>NC was investigated. The spectroscopic behavior of the inosine mutants is position-dependent: when the guanosine in position 7 was exchanged, the nanosecond fluorescence decay time shortened, while having the inosine in position 9 made the decay time longer. Thanks to structural information gained from single crystal X-ray diffraction measurements, it was possible to propose a mechanistic origin for the observed changes.
Larval rearing environment affects several post-copulatory traits in Drosophila melanogaster (2007)

In Drosophila melanogaster, accessory gland proteins (Acps) that a male transfers during mating affect his reproductive success by altering the female's behaviour and physiology. To test the role of male condition in the expression of Acps, we manipulated the pre-adult environment and examined adult males for relative transcript abundance of nine Acps, and for post-copulatory traits that Acps influence. Larval culture density had no effect on any measured trait. Larval nutrient availability impacted the number of sperm transferred and stored, the male's ability to induce refractoriness in his mate, but relative transcript abundance of only a single Acp (Acp36DE). Reduced male body size due to low yeast levels affected sperm competition. Our data indicate that some female-mediated post-copulatory traits (induced refractoriness and sperm transfer and storage) might be influenced by the male's developmental environment, but relative expression of most Acps and some traits they influence (P1') are not.
Suppl.Mat., Suppl. Table, Suppl. Figs Legends from Phenformin-Induced Mitochondrial Dysfunction Sensitizes Hepatocellular Carcinoma for Dual Inhibition of mTOR (2023)

&lt;p&gt;Supplementary data and supplementary table and figures Legends&lt;/p&gt;
Monitoring the kinetics of glycoprotein synthesis and secretion in the filamentous fungus Trichoderma reesei: cellobiohydrolase I (CBHI) as a model protein (2000)

The authors have developed methodology to study the kinetics of protein synthesis and secretion in filamentous fungi. Production of cellobiohydrolase I (CBHI) by Trichoderma reesei was studied by metabolic labelling of the proteins in vivo with [35S]methionine or [14C]mannose, and subsequent analysis of the labelled proteins using two-dimensional gel electrophoresis. Analysis of the different pl forms of the nascent proteins allowed monitoring of the maturation of CBHI during the transport along the biosynthetic pathway. The maturation of the pi pattern of CBHI as well as secretion into culture medium was prevented by treatment with the reducing agent DTT. The pl forms of CBHI detectable in the presence of DTT corresponded to the early endoplasmic reticulum forms of the protein. Removal of N-glycans by enzymic treatment (endoglycosidase H or peptide-N-glycosidase F), or chemical removal of both N- and O-glycans, changed the pl pattern of CBHI, showing that glycan structures are involved in formation of the different pl forms of the protein. By quantifying the labelled proteins during a time course, parameters describing protein synthesis and secretion were deduced. The mean synthesis time for CBHI under the conditions used was 4 min and the minimum secretion time was 11 min. The methodology developed in this study provides tools to reveal the rate-limiting factors in protein production and to obtain information on the intracellular events involved in the secretion process.
gp130, The Cytokine Common Signal-Transducer of Interleukin-6 Cytokine Family, Is Downregulated in T Cells In Vivo by Interleukin-6 (1998)

gp130 is a common signal-transducing receptor component for the interleukin-6 (IL-6) family of cytokines. To investigate the expression of gp130 in T-cell subsets and its regulation, anti-murine gp130 monoclonal antibody (MoAb) was used for flow cytometric analysis. In normal mice, gp130 was differentially expressed in thymocyte and splenic T-cell subpopulations defined by CD4/CD8 expression. In aged MRL/lpr mice, although gp130 expression was detectable in splenic CD4+ or CD8+ T cells, gp130 expression was significantly downregulated. Because serum levels of IL-6 and soluble IL-6 receptor (sIL-6R) are elevated in these mice, we examined the possibility that the downregulation of gp130 expression on splenic T cells might be produced in response to continuous activation of gp130 by high levels of serum IL-6. In transgenic mice overexpressing IL-6, gp130 expression in the splenic T cells was significantly decreased. After stimulation with IL-6 in vitro, the level of gp130 on CD4+ or CD8+ splenic T cells from normal mice was significantly decreased. These results suggest that the expression of gp130 in splenic T cells could be downregulated by the IL-6 stimulation under physiological or pathological circumstances.