gebhart/patrepeval huggingface dataset:
Characterization of Pattern Recognition Receptor Expression and Functionality in Liver Primary Cells and Derived Cell Lines (2018)

Different liver cell types are endowed with immunological properties, including cell-intrinsic innate immune functions that are important to initially control pathogen infections. However, a full landscape of expression and functionality of the innate immune signaling pathways in the major human liver cells is still missing. In order to comparatively characterize these pathways, we purified primary human hepatocytes, hepatic stellate cells, liver sinusoidal endothelial cells (LSEC), and Kupffer cells (KC) from human liver resections. We assessed mRNA and protein expression level of the major innate immune sensors, as well as checkpoint-inhibitor ligands in the purified cells, and found Toll-like receptors (TLR), RIG-I-like receptors, as well as several DNA cytosolic sensors to be expressed in the liver microenvironment. Amongst the cells tested, KC were shown to be most broadly active upon stimulation with PRR ligands emphasizing their predominant role in innate immune sensing the liver microenvironment. By KC immortalization, we generated a cell line that retained higher innate immune functionality as compared to THP1 cells, which are routinely used to study monocyte/macrophages functions. Our findings and the establishment of the KC line will help to understand immune mechanisms behind antiviral effects of TLR agonists or checkpoint inhibitors, which are in current preclinical or clinical development.
Variation in the Use of Active Surveillance for Low-Risk Prostate Cancer Across US Census Regions (2021)

Substantial geographic variation in healthcare practices exist. Active surveillance (AS) has emerged as a critical tool in the management of men with low-risk prostate cancer. Whether there have been regional differences in adoption is largely unknown. The SEER "Prostate with Watchful Waiting Database" was used to identify patients diagnosed with localized low-risk prostate cancer and managed with AS across US census regions between 2010 and 2016. Multivariable logistic regression models were used to determine the impact of region on undergoing AS and factors associated with AS use within each US census region. Between 2010 and 2016, the proportion of men managed with AS increased from 20.8% to 55.9% in the West, 11.5% to 50.0% in Northeast, 9.9% to 43.4% in the South and 15.1% to 56.2% in Midwest (<i>p</i> < 0.0001). On multivariable analysis, as compared to the West, men in all regions were less likely to undergo AS (<i>p</i> < 0.001). Black men in the West (OR 1.36, 95%CI 1.25-1.49) and Midwest (OR 1.62, 95%CI 1.35-1.95) were more likely to undergo AS, but less likely in Northeast (OR 0.80, 95%CI 0.69-0.92). Men with higher socioeconomic status (SES) were more likely to undergo AS in the West (OR 1.47, 95%CI 1.39-1.55), Northeast (OR 1.57, 95%CI 1.36-1.81), and South (OR 1.24, 95%CI 1.13-1.37) but not in the Midwest (OR 0.85, 95%CI 0.73-0.98). We found striking regional differences in the uptake of AS according to race and SES. Geography must be taken into consideration when assessing barriers to AS use.
Quantum dot superluminescent diodes at 1300 nm (2004)

A Superluminescent Light Emitting Diode (SLED) is an ideal optical broadband source for applications like Fiber Optic Gyroscopes and other fiber optic based sensors used in navigation systems. High optical output power and large optical bandwidth are key features for these devices. The short coherence length related to this large bandwidth allows the realization of sensors with improved sensitivity.
Semiconductor devices based on quantum dots (QD) are ideally suited as the active material for SLEDs since the size dispersion typical of self-assembled growth naturally produces a large inhomogeneous broadening. The large spacing between different energy levels can lead to improved thermal stability as well. In this paper we report, ridge-waveguide devices based on five stacks of self-assembled InAs/GaAs QDs. SLED devices with output powers up to 1.5 mW emitting around 1300 nm have been realized. Spectral analysis at 20°C shows a 121 nm FWHM. Temperature characteristics in the range 10-80°C are also reported.
Growth mode transition and photoluminescence properties of Si1−xGex/Si quantum well structures with high Ge composition (1995)

Correlation between growth mode transition and photoluminescence (PL) properties of Si1−xGex/Si quantum wells (QWs) with high Ge composition grown by gas-source molecular beam epitaxy is investigated. With increasing Ge composition in the QWs, significant deviation from the theoretical calculation is observed for x≳0.4 in the emission energy and the activation energy obtained from the temperature dependence of integrated PL intensity. Transmission electron microscopy reveals emergence of islands for x≳0.4, implying strong correlation with the anomalous PL properties. Observed PL properties are shown to be well explained by the breakdown of two-dimensional growth. An attempt to grow luminescent QWs with flat interfaces is also presented.
Tachykinins and Calcitonin Gene-Related Peptide (1995)

The study of airway sensory innervation has been a major topic in respiratory physiology because of the importance of afferent neural input for regulating lung function and activating reflex bronchoconstriction and cough. In this context, capsaicin, the natural pungent ingredient of red peppers, has been extensively used by respiratory physiologists as a chemical probe to activate reflexes arising from the airways.
Classification of conformation for sugar amino acid systems using chiroptical spectroscopy (2006)

A number of structurally related sugar amino acid systems have been examined by chiroptical methods to aid interpretation of their conformational preference. The use of circular dichroism, in addition to NMR and solution IR, has enabled classification of the conformations adopted by sugar amino acid systems as hydrogen-bonded regular, non-hydrogen-bonded regular, and non-hydrogen-bonded irregular. A set of tetrameric SAAs are examined and the effect of change in primary structure related to conformation.
Ceramic Laser Materials (2005)

Transparent ceramic materials have several major advantages over single crystals in laser applications, not the least of which is the ability to make large aperture parts in a robust manufacturing process. After more than a decade of working on making transparent YAG:Nd, Japanese workers have recently succeeded in demonstrating samples that performed as laser gain media as well as their single crystal counterparts. Since then several laser materials have been made and evaluated. For these reasons, developing ceramic laser materials is the most exciting and futuristic materials topic in today's major solid-state laser conferences. We have established a good working relationship with Konoshima Ltd., the Japanese producer of the best ceramic laser materials, and have procured and evaluated slabs designed by us for use in our high-powered SSHCL. Our measurements indicate that these materials will work in the SSHCL, and we have nearly completed retrofitting the SSHCL with four of the largest transparent ceramic YAG:Nd slabs in existence. We have also begun our own effort to make this material and have produced samples with various degrees of transparency/translucency. We are in the process of carrying out an extensive design-of-experiments to establish the significant process variables for making transparent YAG. Finally because transparent ceramics afford much greater flexibility in the design of lasers, we have been exploring the potential for much larger apertures, new materials, for example for the Mercury laser, other designs for SSHL, such as, edge pumping designs, slabs with built in ASE suppression, etc. This work has just beginning.
Capillary Electrophoresis-Electrospray Ionization Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for Direct Analysis of Cellular Proteins (1995)

The combination of capillary electrophoresis (CE) with electrospray ionization (ESI) mass spectrometry has proven to be broadly applicable to a wide range of biologically important compounds. When combined with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry, the combined method, in addition to high-resolution separations, affords high-resolution precision mass measurements for analytes separated from complex mixtures. Direct chemical analysis of single cells has received considerable attention in recent years; the single cell approach provides a major step toward answering important questions in the field of cellular biochemistry. In this work we present preliminary results which demonstrate the feasibility of using the CE-ESI-FTICR combination as a high-performance detection scheme for the analysis of cellular proteins acquired directly from small populations (i.e., 5-10) of intact living cells. The human erythrocyte was chosen as a model system owing to its availability, relatively homogeneous composition, and thorough documentation of contents by previous researchers. In this work we demonstrate the on-line acquisition of high-resolution mass spectra (average resolution > or = 45,000 fwhm) of both the alpha and the beta chains of hemoglobin acquired from the injection of 10 human erythrocytes (corresponding to 4.5 fmol of hemoglobin). Given the extremely small volume of the human erythrocyte (typically 87 fl/cell), the techniques implemented here should also be adaptable to the study of larger mammalian cell systems.
Collagen Stability:  Insights from NMR Spectroscopic and Hybrid Density Functional Computational Investigations of the Effect of Electronegative Substituents on Prolyl Ring Conformations (2002)

Collagen-like peptides of the type (Pro-Pro-Gly)(10) fold into stable triple helices. An electron-withdrawing substituent at the H(gamma)(3) ring position of the second proline residue stabilizes these triple helices. The aim of this study was to reveal the structural and energetic origins of this effect. The approach was to obtain experimental NMR data on model systems and to use these results to validate computational chemical analyses of these systems. The most striking effects of an electron-withdrawing substituent are on the ring pucker of the substituted proline (Pro(i)) and on the trans/cis ratio of the Xaa(i-1)-Pro(i) peptide bond. NMR experiments demonstrated that N-acetylproline methyl ester (AcProOMe) exists in both the C(gamma)-endo and C(gamma)-exo conformations (with the endo conformation slightly preferred), N-acetyl-4(R)-fluoroproline methyl ester (Ac-4R-FlpOMe) exists almost exclusively in the C(gamma)-exo conformation, and N-acetyl-4(S)-fluoroproline methyl ester (Ac-4S-FlpOMe) exists almost exclusively in the C(gamma)-endo conformation. In dioxane, the K(trans/cis) values for AcProOMe, Ac-4R-FlpOMe, and Ac-4S-FlpOMe are 3.0, 4.0, and 1.2, respectively. Density functional theory (DFT) calculations with the (hybrid) B3LYP method were in good agreement with the experimental data. Computational analysis with the natural bond orbital (NBO) paradigm shows that the pucker preference of the substituted prolyl ring is due to the gauche effect. The backbone torsional angles, phi and psi, were shown to correlate with ring pucker, which in turn correlates with the known phi and psi angles in collagen-like peptides. The difference in K(trans/cis) between AcProOMe and Ac-4R-FlpOMe is due to an n-->pi interaction associated with the Bürg-Dunitz trajectory. The decrease in K(trans/cis) for Ac-4S-FlpOMe can be explained by destabilization of the trans isomer because of unfavorable electronic and steric interactions. Analysis of the results herein along with the structures of collagen-like peptides has led to a theory that links collagen stability to the interplay between the pyrrolidine ring pucker, phi and psi torsional angles, and peptide bond trans/cis ratio of substituted proline residues.
Multi-Domain Spoken Language Understanding with Approximate Inference (2011)

This paper presents a semi-latent topic model for semantic domain detection in spoken language understanding systems. We use labeled utterance information to capture latent topics, which directly correspond to semantic domains. Additionally, we introduce an ’informative prior’ for Bayesian inference that can simultaneously segment utterances of known domains into classes and divide them from out-of-domain utterances. We show that our model generalizes well on the task of classifying spoken language utterances and compare its results to those of an unsupervised topic model, which does not use labeled information.
Intra-system load balancing between adjacent GSM cells (2004)

The target of this paper is to quantify some of the benefits of different intra-layer load balancing methods in GSM system. The performance of two different load balancing algorithms are studied in irregular network scenario. The benefits of 1) changing the power budget handover threshold between adjacent cells depending on the load differences of the neighboring intra-system/layer cells, and 2) prioritising the handover candidates based on the load differences within some predefined tuning/prioritisation margins are investigated by dynamic simulations for real-time (speech) traffic. The obtained results show that the overall capacity of the network can be significantly improved (up to 30-14%) by utilising intra-system load balancing algorithms, in irregular simulation scenario. The traffic in the cells with high load is distributed over the neighbor cells, allowing to increase the traffic supported by the whole system maintaining the same (or almost the same) quality for the connections.
Direct Asymmetric Intermolecular Aldol Reactions Catalyzed by Amino Acids and Small Peptides (2006)

We would like to point out an error of omission of a citation and present an accurate definition of eutectic in reference [29] in our paper (DOI: 10.1002/chem.200501639; submitted: December 29, 2005, published online: April 25, 2005). We were remiss not to state that the concept relating eutectics of amino acids to nonlinear effects in asymmetric catalysis had previously been presented at the Erdtman Lecture at KTH Stockholm by Prof. D. G. Blackmond on November 29, 2005. This work is now published (see M. Klussmann, H. Iwamura, S. P. Matthew, D. H. Wells, U. Pandya, A. Armstrong, D. G. Blackmond, Nature 2006, 441, 621; submitted November 21, 2005). We fully agree that the Blackmond group was the first to introduce this concept. Our discussion implied that we measured the eutectics of valine and alanine in this work, which we did not. We would like to clarify the definition of a eutectic with respect to these scalemic amino acid systems. We stated that the eutectic point is the point at which all three phases, (R)-amino acid, (S)-amino acid and DMSO can exist simultaneously. We are grateful to Prof. Donna Blackmond for providing us with the correct definition of a eutectic in the context of these amino acid systems: In an isothermal, three-component system at equilibrium consisting of (R)-amino acid, (S)-amino acid, and solvent, containing two distinct solid phases and one solution phase, the eutectic composition is dictated by the phase rule and is described as a point on the phase diagram where three separate phases intersect. The phase rule also dictates that the solution composition at the eutectic is fixed in this case and hence this composition is identical for any given (R)- and (S)-enantiomeric composition employed. The ee [%] for the (S)-alanine-catalyzed reaction in water given in Table 3, entry 17, should read 0 % ee and not 67 % ee. Editorial Note: D. G. Blackmond and co-workers transmitted their experimental observations prior to A. Cordova et al. The data in the paper by Cordova and co-workers describing nonlinear effects at higher alanine and valine concentrations were obtained during the week December 1–6, 2005. In addition, the experimental data presented in Figure 2 in the paper by Cordova and co-workers (showing striking asymmetric amplification in an asymmetric aldol reaction using scalemic serine as catalyst) were acquired on December 5, 2005. The Nature paper by Blackmond and co-workers referenced above represents, to our knowledge, the first measurement of eutectic points of free amino acids that form racemic compounds and the first comprehensive interpretation of nonlinear effects in asymmetric catalysis using acyclic amino acids as catalysts.
Effects of bisacodyl on ascending colon emptying and overall colonic transit in healthy volunteers (2009)

Oral 5 mg bisacodyl accelerates ascending colon in the unprepared colon in healthy adults; this action may contribute to the drug's efficacy in constipation.
Magnetic field dependence of the resistivity and susceptibility of the above-100-K Bi-Sr-Ca-Cu superconductor (1988)

The magnetic field dependence of the resistivity and susceptibility of multiphase Bi-Sr-Ca-Cu-O compounds exhibiting transport and diamagnetic anomalies at \ensuremath{\simeq}115 and \ensuremath{\simeq}75 K are reported. The field dependence of the latter yields values of ${H}_{c1}$ and $d\frac{{H}_{c2}}{\mathrm{dT}}(T={T}_{c})$ very similar to those found for the $\mathrm{Y}(R){\mathrm{Ba}}_{2}{\mathrm{Cu}}_{3}{\mathrm{O}}_{7\ensuremath{-}x}$ family of Cu perovskitelike superconductors. The field dependence of the above-100-K region strongly suggests that bulk superconductivity, as opposed to filamentary or fluctuation behavior, dominates at these temperatures.
Tying It All Together: Epigenetics, Genetics, Cell Cycle, and Cancer (1997)

The methylation state of DNA can be transferred from generation to generation of cells, qualifying this gene-regulatory event as epigenetic. In his Perspective, Baylin discusses the new link between DNA replication and DNA methylation, demonstrated in this week's issue, and speculates that this linkage is disrupted in tumor cells. On page [1996][1], Chuang et al . suggest that replication and methylation are linked through the binding of DNA-methyltransferase to proliferating cell nuclear antigen (PCNA).

 [1]: http://www.sciencemag.org/cgi/content/short/277/5334/1996
Block Merging for Quadtree-Based Partitioning in HEVC (2012)

The joint development of the upcoming High Efficiency Video Coding (HEVC) standard by ITU-T Video Coding Experts Group and ISO/IEC Moving Picture Experts Group marks a new step in video compression capability. In technical terms, HEVC is a hybrid video-coding approach using quadtree-based block partitioning together with motion-compensated prediction. Even though a high degree of adaptability is achieved by quadtree-based block partitioning, this approach has certain intrinsic drawbacks, which may result in redundant sets of motion parameters being transmitted. Previous work has shown that those redundancies can effectively be removed by merging the leafs of a particular quadtree structure. Following this concept, a block merging algorithm for HEVC is now proposed. This algorithm generates a single motion parameter set for a whole region of contiguous motion-compensated blocks. In this paper, we describe the various components of the proposed block merging algorithm and, using experimental evidence, demonstrate their benefits in terms of coding efficiency.
A Polymeric Composite Material (rGO/PANI) for Acid Blue 129 Adsorption (2020)

Over the years, polyaniline (PANI) has received enormous attention due to its unique properties. Herein, it was chosen to develop a new polymeric composite material: reduced graphene oxide/polyaniline (rGO/PANI). The composite was prepared by a simple and cost-effective fabrication method of formation by mixing and sonication in various conditions. The obtained materials were characterized and identified using various techniques such as scanning electron microscopy (SEM), Raman and ATR-FTIR spectroscopy, and X-ray diffraction (XRD). The objective of the paper was to confirm its applicability for the removal of contaminants from water. Water could be contaminated by various types of pollutants, e.g., inorganics, heavy metals, and many other industrial compounds, including dyes. We confirmed that the Acid Blue 129 dyes can be substantially removed through adsorption on prepared rGO/PANI. The adsorption kinetic data were modeled using the pseudo-first-order and pseudo-second-order models and the adsorption isotherm model was identified.
The influence of aberrations in third harmonic generation microscopy (2010)

We present an analysis of the effects of aberrations in third harmonic generation (THG) microscopy by considering different specimen geometries. Numerical simulations show the general trend that signal intensity and resolution are reduced as aberrations increase in amplitude. It is also shown that there are certain combinations of specimen structure and focusing position for which the presence of aberrations results in an increase in the image intensity. This occurs, for example, when there are several interfaces near the focal volume. The axial spreading of the excitation focal volume increases the characteristic coherence length for THG signal build-up, resulting in a significant contribution to the image brightness from axial planes near the focal plane. These results have important consequences for the interpretation of THG microscope images and for image based aberration correction in adaptive optics THG microscopy.
Up to 10.7-Gb/s High-PDG RSOA-Based Colorless Transmitter for WDM Networks (2013)

The operation of a network-embedded colorless self-tuning transmitter for WDM networks is experimentally demonstrated from 2.5- up to 10.7-Gb/s data rates. Colorless operation is achieved by self-seeding an ultra-fast reflective semiconductor optical amplifier (RSOA) with the feedback signal reflected at the WDM multiplexer filter. In particular, the transmitter exploits a 2-Faraday rotators configuration to ensure polarization insensitive operation and allowing for the exploitation of high gain RSOAs, which can be designed to operate on a single polarization. The impact on the transmission of the fiber chromatic dispersion at different bit-rates and with different channel bandwidths of the WDM multiplexer filter is experimentally investigated up to 10.7 Gb/s. The tolerance to positive and negative dispersive loads is also assessed.