gebhart/patrepeval huggingface dataset:
On the performance of MSK signal transmission over a multipath channel with small time dispersion (2002)

In this paper, the performance of MSK signal transmission over a mobile radio channel with small time dispersion is analyzed. In contrast to existing investigations, we made no restrictive assumptions about the impulse response of the channel or the sampling time and derive analytical expressions for the error floor and the optimum sampling instant. We found that the error probability depends not only on the delay spread, but also on the squared mean delays of echoes that are advanced or delayed with respect to the sampling point and on the power balance between them. Furthermore, we show that in the general case, the optimum sampling instant is not identical to the mean delay. Comparison of our results with Monte Carlo simulations show very good agreement.
Order effects: a randomised study of three major cancer-specific quality of life instruments (2005)

Presentation order is unlikely to alter the responses to these HRQoL instruments administered in cancer patients when any two of them are used together.
C. trachomatis-infection accelerates metabolism of phosphatidylcholine derived from low density lipoprotein but does not affect phosphatidylcholine secretion from hepatocytes (2004)

This study is the first to show that metabolism of LDL-derived PC is accelerated in C. trachomatis infection and to support the notion that LDL-delivered PC may potentially serve as a source of PC trafficked to Chlamydia. In addition, C. trachomatis-infection does not inhibit PC secretion from hepatocytes indicating that the pool of newly synthesized PC destined for lipoprotein secretion may differ from the pool of PC used for C. trachomatis membrane biosynthesis.
Design, synthesis and biological evaluation of substituted benzoate analogues of the selective nicotinic acetylcholine receptor antagonist, methyllycaconitine (1998)

The norditerpenoid alkaloid methyllycaconitine (MLA) acts as a competitive antagonist on the nicotinic acetylcholine receptor (nAChR) with a high preference for the neuronal α-bungarotoxin (αBgt)-sensitive nAChR over the muscle nAChR in mammals. MLA is thus a useful pharmacological tool. Furthermore, its efficient binding to insect nAChR indicates a high insecticidal potency.



Within the complex hexacyclic structure of MLA, we envisaged a potential simple pharmacophore. This led to the design and synthesis of acyclic and monocyclic analogues of MLA. The biological activity of these derivatives at both neuronal nicotinic and muscarinic AChR was evaluated. Some of these structurally simple compounds, despite displaying a modest affinity for the nAChR, showed good specificity.



We were able to show the importance of the 2-(methylsuccinimido)benzoate ester moiety and the E-ring of MLA. None of the analogues tested displayed any affinity for [3H]nicotine binding sites in brain membranes, indicating that α7-selectivity is already inherent in these simple structures. If higher affinities are to be obtained, however, there is a clear need for more structural information in the design of second generation simple analogues of MLA.
Controlled Synthesis of Single-Walled Carbon Nanotubes in an Aerosol Reactor (2011)

The growth mechanism and influence of synthesis parameters on the properties of single-walled carbon nanotubes (SWNTs) produced by ferrocene vapor decomposition in a carbon monoxide atmosphere have been investigated in detail by a combined study of Raman and UV−vis−NIR absorption spectroscopy and transmission electron microscopy (TEM). CO2 plays an essential role in selective etching of small diameter nanotubes and the purification of SWNTs. This etching effect is beneficial to narrow the diameter distribution and to control the average diameter of SWNTs. Increasing the synthesis temperature results in the formation of larger catalyst particles due to a higher agglomeration rate, thereby forming larger diameter nanotubes. Decreasing the CO flow rate, and thus lengthening the agglomeration time, also provides the possibility to enlarge the diameter of SWNTs. Therefore, by varying the growth parameters, the mean diameter of SWNTs can be effectively changed from 1.2 to 1.8 nm to satisfy the needs of various applications.
TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing (2021)

The development of the TMTpro-16plex series expanded the breadth of commercial isobaric tagging reagents by nearly 50% over classic TMT-11plex. In addition to the described 16plex reagents, the proline-based TMTpro molecule can accommodate two additional combinations of heavy carbon and nitrogen isotopes. Here, we introduce the final two labeling reagents, TMTpro-134C and TMTpro-135N, which permit the simultaneous global protein profiling of 18 samples with essentially no missing values. For example, six conditions with three biological replicates can now be perfectly accommodated. We showcase the 18plex reagent set by profiling the proteome and phosphoproteome of a pair of isogenic mammary epithelial cell lines under three conditions in triplicate. We compare the depth and quantitative performance of this data set with a TMTpro-16plex experiment in which two samples were omitted. Our analysis revealed similar numbers of quantified peptides and proteins, with high quantitative correlation. We interrogated further the TMTpro-18plex data set by highlighting changes in protein abundance profiles under different conditions in the isogenic cell lines. We conclude that TMTpro-18plex further expands the sample multiplexing landscape, allowing for complex and innovative experimental designs.
Effects of anti-factor VIII inhibitor antibodies on factor VIIa/tissue factor-catalysed activation and inactivation of factor VIII (2011)

Factor (F)VIIa/tissue factor (TF) rapidly activates FVIII activity by proteolysis at Arg372 and Arg740, and subsequently inactivates FVIIIa activity by proteolysis at Arg336, although this activation is weaker than that by thrombin. The effects of anti-FVIII inhibitor antibodies on these reactions remain unknown, however. In this study, 13 of anti-FVIII inhibitor antibodies recognising the A2 or C2 domain were prepared. None of them, irrespective of epitope specificity, significantly affected FVIIa/TF-catalysed FVIII activation in one-stage clotting assays. Anti-A2 and anti-C2 type 2 antibodies had little effect on the inactivation phase. Anti-C2 type 1 antibodies, however, modulated inactivation by 40-60% of that seen with control IgG, suggesting that the activity of FVIIIa generated by FVIIa/TF persisted in the presence of this specific type of inhibitor. SDS-PAGE analysis demonstrated that all antibodies had little effect on FVIIa/TF-catalyzed proteolysis at Arg372 and Arg740. Anti-C2 type 1, however, significantly delayed cleavage at Arg336 in dose- dependent manners. Neither anti-A2 nor anti-C2 type 2 affected this reaction, and the findings were consistent with the results of the functional assays. In addition, anti-C2 monoclonal antibodies with type 1 and 2 demonstrated similar patterns of reaction as the anti-C2 polyclonal antibodies in FVIIa/TF-mediated FVIII mechanisms. We demonstrated that FVIIa/TF activated FVIII even in the presence of anti-FVIII antibodies, but inactivation patterns appeared to depend on inhibitor type. It could be important to determine the characteristic of these inhibitor antibodies for prediction of their effects on FVIIa-related FVIII reactions, and the results could have significant therapeutic implications.
Human Cytomegalovirus-Induced Degradation of CYTIP Modulates Dendritic Cell Adhesion and Migration (2017)

As potent antigen-presenting cells, dendritic cells (DCs) are essential for the initiation of effective antiviral immune responses. Viruses and especially herpesviruses, which are able to establish lifelong persistence, exploit several immune evasion mechanisms targeting DC biology. Our group has previously shown that the α-herpesvirus herpes simplex virus type 1 inhibits mature DC (mDC) migration by inducing adhesion <i>via</i> degrading the cellular protein CYTIP (cytohesin-1 interacting protein), an important negative regulator of β2-integrin activity. In the present study, we extended our analysis to the β-herpesvirus human cytomegalovirus (HCMV), to investigate whether other <i>herpesviridae</i> also induce such modulations. Indeed, HCMV impairs mDC transwell migration capability following a CCL19-chemokine gradient, despite equivalent expression levels of the cognate chemokine receptor CCR7 at the corresponding time points post-infection. Remarkably, HCMV infection potently induced β2-integrin activity on mDCs. Furthermore, directly HCMV-infected mDCs, exhibiting viral gene expression, strongly adhere to fibronectin and ICAM-1, in contrast to mDCs lacking infection or viral gene expression. Interestingly, HCMV-positive mDCs display a proteasome-dependent degradation of CYTIP. Contrasting the migration toward CCL19, elevated expression levels of the chemokine receptor CXCR4 in HCMV-infected mDCs were associated with functional CXCL12-chemotaxis under the herein used conditions. In summary, our results show that HCMV shapes mDC adhesion to compromise migration toward CCL19, but retaining CXCL12 responsiveness. Thus, we hypothesize that a preferred migration pattern toward the bone marrow, but not to secondary lymphoid organs, could ultimately cause a failure in the induction of potent antiviral immune responses.
Hybrid DOT and MRI system (2003)

Recently, there has been a great deal of interest in further improving the in-vivo characterization of tumors by interrogating tissues with multiple simultaneous image based measurement techniques that provide complementary information about the functional state of the tissue under investigation. Besides offering the possibility of complementary information, multi-modality techniques could also be used to improve the measurements done by either modality as well as providing cross validation measurements. Magnetic resonance imaging (MRI) and near-infrared diffuse optical tomography (DOT) are two techniques that, when combined, provide complementary structural and functional information. MRI can be used to obtain detailed structural and metabolic information regarding tumors. On the other hand, DOT can be used to determine local quantitative information regarding tumor composition and metabolism. Thus, a combined system consisting of MRI and DOT has the potential to enhance understanding of the complex biological processes in tumors. In this work, we describe the design of the hybrid DOT-MRI system.
The 16S-like, 5.8S and 23S-like rRNAs of the two varieties ofCryptococcus neoformans: sequence, secondary structure, phylogenetic analysis and restriction fragment polymorphisms (1994)

The nucleotide sequences of the 16S-like, 5.8S and 23S-like rDNAs from the two varieties of Cryptococcus neoformans, C. neoformans var. neoformans and C. neoformans var. gattii, were determined. The rRNA locus has the typical eukaryote organization of 16S-5.8S-23S with the 16S-like and 5.8S rRNA genes separated by a 124-nucleotide spacer and the 5.8S and 23S-like rRNA genes separated by a 187-nucleotide spacer in each strain. The C. neoformans var. neoformans and C. neoformans var. gattii 16S-like, 5.8S and 23S-like rRNAs are, respectively 1802, 158, and 3358 nucleotides in length and share > 99% nucleotide sequence identity, a finding which strongly supports the present taxonomic classification of two varieties within a species. Comparative structure analysis was used to construct secondary-structure models for the deduced 16S-like and 5.8S-23S-like rRNA sequences, which are similar to those of other fungal rRNAs. The C. neoformans 16S-like and 23S-like rRNA sequences were aligned with other eukaryote sequences based on secondary and higher-order structures predicted by comparative structure analysis for phylogenetic analysis. There was good correspondence between the 16S-like and 23S-like derived phylogenetic trees. The closest known fungal relative is Trichosporon beigelii. Southern blot analysis revealed one C. neoformans strain with two types of DNA repeats coding for rRNA which differed in size by about 1000 bp. Restriction fragment length polymorphisms in the rDNA locus provide useful markers for the study of epidemiology and pathogenesis of C. neoformans infections.
Diazotization of S-Sulfonyl-cysteines (2019)

We report the preparation of enantiomerically enriched β-thio-α-hydroxy and α-chloro carboxylic acid and ester building blocks by diazotization of <i>S</i>-sulfonyl-cysteines. The thiosulfonate protecting group demonstrated resistance to oxidation and attenuation of sulfur's nucleophilicity by the anomeric effect. The key transformation was optimized by a 2<sup>2</sup> factorial design of experiment, highlighting the unique reactivity of cysteine derivatives in comparison with aliphatic amino acids.
Retardation of CO2 due to Capillary Pressure Hysteresis: a New CO2 Trapping Mechanism (2010)

Abstract Trapping of CO2 improves containment security of geologically stored CO2. To be able to asses the potential of a storage site using reservoir simulators, it is necessary to include all of the possible trapping mechanisms in the numerical algorithms. Currently, four trapping mechanisms are identified in the CO2 sequestration literature: structural, residual, dissolution, and mineralization. Although capillary pressure hysteresis has been accounted for in the historical development of simulators, it has not been recognized as a process for hindering movement of the injected CO2. Capillary pressure hysteresis reduces the buoyancy driven plume movement significantly compared to relative permeability hysteresis; but it is the latter that has been emphasized in the published literature. In this paper, we focus on a quantitative measure for the contribution of hysteresis in reducing plume transport. Rocks with large pore body to throat size ratio are the best candidates for this mechanism to be operative. In the present work, a self-consistent relative-permeability capillary-pressure hysteresis model is incorporated within a simulator. With this model, it is possible to compare and contrast hysteresis induced retardation to other mechanisms of trapping. The self-consistent parametrization of all of the transport properties is used to quantify sensitivity compactly. The sensitivity of the CO2 plume shape and the amount of CO2 trapped, to the strength of the capillary pressure hysteresis, is also described. Simulated results show that CO2 plume shape with and without capillary pressure hysteresis are significantly different. As expected, capillary pressure hysteresis retards the buoyant transport of the CO2 plume. Although a portion of the CO2 is connected, and therefore not residual, the plume remains immobile for all practical purposes. Also, due to decreased driving potential, gravity tonguing below the caprock is reduced in comparison to the case without capillary pressure hysteresis, thus suggesting enhanced storage efficiency. However, the total dissolution of CO2 in saline water is reduced because of the reduced diffusive transport of CO2 within the brine. Thus, one mechanism of containment is offset by the other. Inclusion of accurate hysteresis models is important for qualifying storage sites constrained by spatial domain limits. It is anticipated that site acceptability criteria would change as a result of this study, thus impacting risk evaluation.
Manchester Coding based Re-modulation Scheme for Optical Access Network (2006)

We proposed a novel re-modulation scheme using Manchester coded downstream and NRZ upstream for passive optical networks (PON). We experimentally analyzed the transmission performance for upstream and downstream signals over 20-km transmission distance.
Simultaneous ultrafiltration and affinity sorptive separation of proteins in a hollow fiber membrane module (1990)

Abstract A protein separation scheme combining affinity or ion exchange sorption with hollow fiber cross‐flow filtration is described. Sorptive gel particles were loaded into the shell side of a hollow fiber membrane module. In the adsorption step, crude protein mixtures were passed through the lumen and permeating proteins passed through the membrane to bind on the gel particles in the shell. During elution, a buffer of adequate ionic strength to desorb the bound proteins was passed through the lumen and permeated through the shell. The eluant was then collected at the outlet to the shell of the hollow fiber module. The concept is illustrated by two examples: the purification of butyrylcholinesterase (EC 3.1.1.7) from raw horse serum using the affinity gel procainamide–Sepharose as the packing and the separation of carboxylesterase (EC 3.1.1.1) from beef liver homogenate using DEAE–Sephadex as the packing. The technique has the advantage of high volumetric throughputs typical of hollow fiber membrane modules as well as the high capacity characteristic of chromatographic packings. In addition, cross‐flow filtration of particulates, agglomerates, and debris in passing protein from lumen to shell side can help eliminate the need for extensive pretreatment.
Role of a "soundguide" and "antisoundguide" in stimulated Brillouin scattering in a single-mode waveguide (1988)

An analysis is made of steady-state stimulated Brillouin scattering (STBS) in planar and cylindrical single-mode waveguides taking into account sound diffraction and refraction in a given transverse sound velocity profile ("soundguide" and "antisoundguide"). For a strong soundguide the STBS line has the same width and Lorentzian profile, the intensity being slightly attenuated compared with STBS of plane waves in an unbounded medium. For a strong antisoundguide the sound is "expelled," the attenuation length becomes of the order of the sound diffraction length, so that the STBS line is substantially broadened, attenuated, and becomes asymmetric.
Acute kidney injury: from clinical to molecular diagnosis (2016)

The RIFLE classification was introduced in 2004 to describe the presence of acute kidney injury (AKI) and to define its clinical stage, based upon the serum creatinine level and urine output. The same criteria, although slightly modified, are used in the other scoring systems AKIN and KDIGO. Mortality and morbidity remain high in AKI, suggesting that current diagnostic methods are suboptimal, poorly accurate, and often timely inadequate in detecting the presence of early kidney injury. Conversely, a growing body of evidence indicates that new AKI biomarkers can be used to both rule out AKI and to assess high-risk conditions or the presence of subclinical forms. Neutrophil gelatinase-associated lipocalin or cell cycle arrest biomarkers seem to be sensitive and specific enough to be used in conjunction with existing markers of AKI for better classifying renal injury as well as dysfunction. Improvements in diagnosis, risk identification, stratification, prognosis, and therapeutic monitoring may improve prevention and protection from organ damage and help to identify patients at risk, allowing individualized therapy. In this view, we may say that AKI diagnosis has finally moved from clinical to molecular level with potential benefits for the patients because similar progress has been shown in other disciplines.
Enzymes Used in Baking (2019)

In baking, the use of enzymes is well established to help improve the bread making process and the quality of the final product. These enzymes execute actions on a molecular level, resulting in macroscopic effects on, amongst others, waterbinding, gas bubble stability, crumb structure, color, loaf volume, and shelf life. This chapter gives a comprehensive overview of the various steps in the bread making process, and the impact of enzymes thereon, based on the baker's and consumer's needs. An outlook on the use of enzymes in fine baking and trends related to health and convenience is also given.
Percolated microstructures for multi-modal transport enhancement in porous active materials (2023)

A method of forming a composite material for use in multi-modal transport includes providing three-dimensional graphene having hollow channels, enabling a polymer to wick into the hollow channels of the three-dimensional graphene, curing the polymer to form a cured three-dimensional graphene, adding an active material to the cured three-dimensional graphene to form a composite material, and removing the polymer from within the hollow channels. A composite material formed according to the method is also provided.
Adsorption of single 1,8-octanedithiol molecules on Cu(100) (2016)

Single 1,8-octanedithiol (ODT) molecules adsorbed onto the Cu(100) surface have been characterized by using scanning tunneling microscopy (STM) and studied by semi-empirical calculations. STM images have revealed two types of chiral molecules on the surface upon adsorption and both types of molecules showed two bright spots at the extremities of a small rod due to the enhanced electronic density contrast of the chemisorbed sulfur atoms. In sub-monolayer regime deposition, ODT molecules exhibit preferential adsorption directions and the relaxation mechanism is driven by the chemisorption of the two sulfur atoms in a hollow site of the surface. By means of calculations several conformations of the molecule according to the energetically favorable alkane body stretching constraint have been studied. The comparison between relaxed conformations and between calculated and experimental STM images, followed by an analysis of different orientations, has allowed determining unambiguously the most favorable position of the ODT molecule on Cu(100).