gebhart/patrepeval huggingface dataset:
Quantification of Factor H Mediated Self vs. Non-self Discrimination by Mathematical Modeling (2020)

The complement system is part of the innate immune system and plays an important role in the host defense against infectious pathogens. One of the main effects is the opsonization of foreign invaders and subsequent uptake by phagocytosis. Due to the continuous default basal level of active complement molecules, a tight regulation is required to protect the body's own cells (self cells) from opsonization and from complement damage. A major complement regulator is Factor H, which is recruited from the fluid phase and attaches to cell surfaces where it effectively controls complement activation. Besides self cells, pathogens also have the ability to bind Factor H; they can thus escape opsonization and phagocytosis causing severe infections. In order to advance our understanding of the opsonization process at a quantitative level, we developed a mathematical model for the dynamics of the complement system-termed <i>DynaCoSys model</i>-that is based on ordinary differential equations for cell surface-bound molecules and on partial differential equations for concentration profiles of the fluid phase molecules in the environment of cells. This hybrid differential equation approach allows to model the complement cascade focusing on the role of active C3b in the fluid phase and on the cell surface as well as on its inactivation on the cell surface. The <i>DynaCoSys model</i> enables us to quantitatively predict the conditions under which Factor H mediated complement evasion occurs. Furthermore, investigating the quantitative impact of model parameters by a sensitivity analysis, we identify the driving processes of complement activation and regulation in both the self and non-self regime. The two regimes are defined by a critical Factor H concentration on the cell surface and we use the model to investigate the differential impact of complement model parameters on this threshold value. The dynamic modeling on the surface of pathogens are further relevant to understand pathophysiological situations where Factor H mutants and defective Factor H binding to target surfaces results in pathophysiology such as renal and retinal disease. In the future, this DynaCoSys model will be extended to also enable evaluating treatment strategies of complement-related diseases.
Reasoning on the Air: An Implicit Semantic Communication Architecture (2022)

Semantic communication is a novel communication paradigm which draws inspiration from human communication focusing on the delivery of the meaning of a message to the intended users. It has attracted significant interest recently due to its potential to improve efficiency and reliability of communication, enhance users' quality-of-experience (QoE), and achieve smoother cross-protocol/domain communication. Most existing works in semantic communication focus on identifying and transmitting explicit semantic meaning, e.g., labels of objects, that can be directly identified from the source signal. This paper investigates implicit semantic communication in which the hidden information, e.g., implicit causality and reasoning mechanisms of users, that cannot be directly observed from the source signal needs to be transported and delivered to the intended users. We propose a novel implicit semantic communication (iSC) architecture for representing, communicating, and interpreting the implicit semantic meaning. In particular, we first propose a graph-inspired structure to represent implicit meaning of message based on three key components: entity, relation, and reasoning mechanism. We then propose a generative adversarial imitation learning-based reasoning mechanism learning (GAML) solution for the destination user to learn and imitate the reasoning process of the source user. We prove that, by applying GAML, the destination user can accurately imitate the reasoning process of the users to generate reasoning paths that follow the same probability distribution as the expert paths. Numerical results suggest that our proposed architecture can achieve accurate implicit meaning interpretation at the destination user.
Points to Patches: Enabling the Use of Self-Attention for 3D Shape Recognition (2022)

While the Transformer architecture has become ubiquitous in the machine learning field, its adaptation to 3D shape recognition is non-trivial. Due to its quadratic computational complexity, the self-attention operator quickly becomes inefficient as the set of input points grows larger. Furthermore, we find that the attention mechanism struggles to find useful connections between individual points on a global scale. In order to alleviate these problems, we propose a two-stage Point Transformer-in-Transformer (Point-TnT) approach which combines local and global attention mechanisms, enabling both individual points and patches of points to attend to each other effectively. Experiments on shape classification show that such an approach provides more useful features for downstream tasks than the baseline Transformer, while also being more computationally efficient. In addition, we also extend our method to feature matching for scene reconstruction, showing that it can be used in conjunction with existing scene reconstruction pipelines.
9-Fluorenylmethyl Chloroformate (2001)

[28920-43-6] C15H11ClO2 (MW 258.71) InChI = 1S/C15H11ClO2/c16-15(17)18-9-14-12-7-3-1-5-10(12)11-6-2-4-8-13(11)14/h1-8,14H,9H2 InChIKey = IRXSLJNXXZKURP-UHFFFAOYSA-N (base-labile protecting group for primary and secondary amines;3 used in peptide synthesis;5 used for derivatization of amines and amino acids prior to HPLC analysis and fluorescence detection13) Alternate Names: 9-fluorenylmethoxycarbonyl chloride; FMOC-Cl. Physical Data: mp 62–64 °C. Solubility: sol organics (CH2Cl2, THF, dioxane); reacts with alcohols, amines, and water. Form Supplied in: white crystalline solid; widely available. Handling, Storage, and Precautions: FMOC-Cl is an acid chloride, and should be protected from moisture and heat. The reagent can evolve CO2 (pressure) upon prolonged storage; therefore bottles should be opened carefully. FMOC-Cl is harmful if swallowed, inhaled, or absorbed through skin, is corrosive, and is a strong lachrymator. Inhalation may be fatal. Use in a fume hood.
Supplementary Figure Legends from TMEM2 Is a SOX4-Regulated Gene That Mediates Metastatic Migration and Invasion in Breast Cancer (2023)

&lt;p&gt;This file contains supplementary figure legends only.&lt;/p&gt;
Correlation between baseline serum 1,5-anhydroglucitol levels and 2-hour post-challenge glucose levels during oral glucose tolerance tests (2010)

Since there is increasing evidence that postprandial hyperglycemia is a risk factor for the development of macrovascular complications, it is important to predict postprandial hyperglycemia in the early stages of glucose intolerance, and routine medical checkups provide a good opportunity to do so. The aim of this study was to evaluate the usability of 1,5-anhydroglucitol (1,5-AG) in routine medical checkups. The subjects were 77 Japanese men who participated in a routine medical checkup. First, we performed 75 g oral glucose tolerance tests (OGTTs), and examined the changes in glucose and 1,5-AG levels measured at 0, 30, 60, 90, 120, and 180 minutes (min). 1,5-AG levels did not significantly change until 90 min after the glucose load. Second, a linear regression analysis showed an inverse correlation between the 2-hour post-challenge glucose (2h-PG) and baseline 1,5-AG levels during the OGTT (P = 0.001, r(2) = 0.13), and the correlation was still significant after adjustment for age (2h-PG = 170 + 0.83 × (age in years) - 3.23 × (1,5-AG), P = 0.002, adjusted r(2) = 0.12). Finally, to investigate the test characteristics of 1,5-AG levels as a predictor of a 2h-PG level ≥200 mg/dL, we plotted a receiver operating characteristic (ROC) curve. The area under the ROC curve was 0.78, and the maximal sum of sensitivity and specificity (78% and 72%, respectively) was obtained at a 1,5-AG cutoff level of <14.2µg/mL. We conclude that 1,5-AG values may provide an ancillary predictor of 2h-PG of 75 g OGTTs in routine medical checkups.
Classification of Multi-Frequency Polarimetric SAR Images Based on Multi-Linear Subspace Learning of Tensor Objects (2015)

One key problem for the classification of multi-frequency polarimetric SAR images is to extract target features simultaneously in the aspects of frequency, polarization and spatial texture. This paper proposes a new classification method for multi-frequency polarimetric SAR data based on tensor representation and multi-linear subspace learning (MLS). Firstly, each cell of the SAR images is represented by a third-order tensor in the frequency, polarization and spatial domains, with each order of tensor corresponding to one domain. Then, two main MLS methods, i.e., multi-linear principal component analysis (MPCA) and multi-linear extension of linear discriminant analysis (MLDA), are used to learn the third-order tensors. MPCA is used to analyze the principal component of the tensors. MLDA is applied to improve the discrimination between different land covers. Finally, the lower dimension subtensor features extracted by the MPCA and MLDA algorithms are classified with a neural network (NN) classifier. The classification scheme is accessed using multi-band polarimetric SAR images (C-, L- and P-band) acquired by the Airborne Synthetic Aperture Radar (AIRSAR) sensor of the Jet Propulsion Laboratory (JPL) over the Flevoland area. Experimental results demonstrate that the proposed method has good classification performance in comparison with the classic multi-band Wishart classifier. The overall classification accuracy is close to 99%, even when the number of training samples is small.
Electrochemical Aromatization of Dihydroazines: Effect of Chalcogenophosphoryl (CGP) Substituents on Anodic Oxidation of 9-CGP-9,10-dihydroacridine (2021)

Abstract The effect of chalcogenophosphoryl fragments on the anodic oxidation of 9-chalcogenophosphoryl-9,10-dihydroacridines was studied in detail. The data of X-ray structural analyses, quantum chemical calculations, and cyclic voltammetry measurements obtained for these compounds provide an explanation of the observed features. The direct electrochemical phosphorylation of acridine was first carried out successfully.
Terpenoid and carbonyl emissions from Norway spruce in Finland during the growing season (2017)

Abstract. We present spring and summer volatile organic compound (VOC) emission rate measurements from Norway spruce (Picea abies L. Karst) growing in a boreal forest in southern Finland. The measurements were conducted using in situ gas chromatograph with 1 to 2 h time resolution to reveal quantitative and qualitative short-term and seasonal variability of the emissions. The measurements cover altogether 14 weeks in years 2011, 2014 and 2015. Monoterpene (MT) and sesquiterpene (SQT) emission rates were measured all the time, but isoprene only in 2014 and 2015 and acetone and C4–C10 aldehydes only in 2015. The emission rates of all the compounds were low in spring, but MT, acetone, and C4–C10 aldehyde emission rates increased as summer proceeded, reaching maximum emission rates in July. Late summer mean values (late July and August) were 29, 17, and 33 ng g(dw)−1 h−1 for MTs, acetone, and aldehydes respectively. SQT emission rates increased during the summer and highest emissions were measured in late summer (late summer mean value 84 ng g(dw)−1 h−1) concomitant with highest linalool emissions most likely due to stress effects. The between-tree variability of emission pattern was studied by measuring seven different trees during the same afternoon using adsorbent tubes. Especially the contributions of limonene, terpinolene, and camphene were found to vary between trees, whereas proportions of α-pinene (25 ± 5 %) and β-pinene (7 ± 3 %) were more stable. Our results show that it is important to measure emissions at canopy level due to irregular emission pattern, but reliable SQT emission data can be measured only from enclosures. SQT emissions contributed more than 90 % of the ozone reactivity most of the time, and about 70 % of the OH reactivity during late summer. The contribution of aldehydes to OH reactivity was comparable to that of MT during late summer, 10–30 % most of the time.
Molecular and biomorphometrical identification of ovine babesiosis in iran. (2010)

The causative organism of many cases of haemoprotozoal diseases, which recorded in previous studies, could be B. ovis or Theileria lestoquardi. The result confirmed that B. ovis was only species which causes babesiosis in the study areas. It seems that the biometrical polymorphisms could exist in B. ovis in Iran. This polymorphism could be a main problem in differentiation between B. ovis and B. motasi and it could be dissolved by specific PCR analysis.
A Learning-based Adaptive Routing Tree for Wireless Sensor Networks (2006)

One of the most common communication patterns in sensor networks is routing data to a base station, while the base station can be either static or mobile. Even in static cases, a static spanning tree may not survive for a long time due to failures of sensor nodes. In this paper, we present an adaptive spanning tree routing mechanism, using real-time reinforcement learning strategies. We demonstrate via simulation that without additional control packets for tree maintenance, adaptive spanning trees can maintain the best connectivity to the base station, in spite of node failures or mobility of the base station. And by using a general constraint-based routing specification, one can apply the same strategy to achieve load balancing and to control network congestion effectively in real time.
Lactoferrin Suppresses Loss of Corneal Epithelial Integrity in a Rabbit Short-Term Dry Eye Model (1998)

Human tear fluid contains lactoferrin at the highest concentration. In patients with dry eye such as Sjogren's syndrome, the concentration of lactoferrin in the tears is approximately half the normal value. The present study utilizes a short-term rabbit dry eye model to evaluate if lactoferrin containing eye drops can reverse any of the damage produced by blockage of blinking with an ocular speculum. Damage was evaluated based on the extent of methylene blue staining in histological sections. After 3 h of desiccation, the amount of extractable dye recovered following sacrifice increased by more than 4-fold in the vehicle-treated eyes. However, in those rabbits treated with 1% lactoferrin, dye recovery was only 40% of the value in the vehicle-treated eyes. Between 1-3 h and over a concentration range from 0.01 to 1% lactoferrin, the decreases in staining were both time and concentration dependent. Alternatively, if 1% lactoferrin was applied during the desiccation period, there was partial restoration of corneal epithelial integrity. These results suggest that lactoferrin may be of therapeutic value in decreasing the loss of corneal epithelial integrity in dry eye.
An investigation into the scattering and radiation characteristic of RF-absorbers (2003)

The attenuation and radiation characteristics of a pyramidal absorber are studied, both analytically and experimentally, including bulk-parameter data for commercially available, measured samples. Absorber attenuation is modeled as a plane wave incident on a layered medium with a varying complex permittivity. Attenuation experiments performed in a TEM cell confirm the validity of this approach. The antenna behavior of the pyramidal absorber is also considered, treating it as a monopole antenna. The input impedance and radiation are both modeled and measured. It is shown that the absorber can radiate significantly, which can affect its usefulness, depending on the intended application. Special consideration has been given to the low-frequency performance (<100 MHz) of absorbers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Gb/s Visible Light Communication With Low-Cost Receiver Based on Single-Color LED (2020)

The exhausted radio frequency spectrum in mobile networks calls for light-based wireless solutions. However, visible light communication builds on dedicated receiver sub-systems. As an alternative to traditional photodetectors, we exploit low-cost commercial light emitting diodes (LED) that enjoy abundance in consumer electronics. In particular, surface-mounted LEDs with emission in the yellow spectrum are employed as photodetectors in a line-of-sight optical wireless communication link that is sourced by a green laser diode as a pencil beam emitter. Together with their corresponding transimpedance amplifiers, the LED-based receivers show an opto-electrical 3-dB bandwidth of up to 260 MHz, which enables data rates of 3.1 Gb/s using orthogonally frequency division multiplexed signal transmission over in-door distances. We further show that costly digital signal processing functions can be omitted through a fully analogue design of the optical link. Passive frequency response equalization in combination with simple duobinary signaling allows for 1.25 Gb/s transmission over the same link distance. Moreover, we prove that there is neither a rate nor a quality-of-experience penalty when collapsing an Ethernet connection over the optical wireless link in order to transfer large amounts of data or to stream high-definition video. The high-speed properties of commercial LEDs, together with their established role as a transmitter, promise to open new application possibilities in low-cost, short-reach segments.
Impact of Upscaling on 3-D Modelling of SAGD in a Meander Belt (2011)

Abstract This work aims at assessing the impact of heterogeneities on heavy oil recovery through SAGD process by using numerical models of a reservoir analogue of meander belt. These models are obtained with different scales of upscaling of the geological model. Meander belts consist of point bar deposits, characterized by a 3D complex internal architecture, with different scales of heterogeneities, which distribution is associated with the depositional processes. Based on a 3D outcrop description of a meander belt analogue to the Canadian heavy-oil fields, the approach includes four steps: 1/ the construction of a reference static reservoir model based on a very fine description of the outcrops in terms of architecture and geological heterogeneities, 2/ upscaling of the grid at different scales using different methods in order to evaluate their impact on the heterogeneity distribution in the reservoir, 3/ reservoir SAGD simulations using horizontal well doublet (steam injector and producer) across the meander belt, to assess the impact of upscaling of heterogeneities effect and on heavy oil production. The impact of heterogeneities on simulation results are evaluated for several upscaling stages. Results show that heterogeneity distribution has an impact on fluid flow at different stages of production. On the fine gridded model, small scale heterogeneities impact the steam chamber development and fluid flow in the wellbore vicinity at the beginning of the steam injection, whereas large scale heterogeneities strongly influence oil recovery during the whole recovery process and lower the efficiency of the reservoir drainage. On coarser grids, the effect of small scale heterogeneities can be smoothed, depending on the upscaling stage. The geomechanical effect is not taken into account in this work, the goal being to assess the impact of heterogeneities on oil recovery. The performance of SAGD is clearly linked to the steam chamber development, which depends on the degree of heterogeneities present in the reservoir. The simulation workflow and the sensitivity study based on different upscaling methods contribute to better restore the heterogeneity distribution in the reservoir. The negative impact of these heterogeneities during the oil recovery must thus be quantified in order to monitor the thermal production at crucial periods of production.
Synthesis and Reactivity of Heterodinuclear Fe−Ni Complexes with a Bridging Alkoxysilyl Ligand. Crystal Structure of [(OC)3Fe{μ-Si(OMe)2(OMe)}(μ-dppm)NiMe] (2001)

The new heterobimetallic complex (1) was obtained in 95% yield by reaction of [NiCl2(PPh3)2] in THF with K[Fe{Si(OMe)3}(CO)3(dppm-P)] at −78 °C. The analogous bromo and iodo complexes were also obtained; the latter is, however, less stable and could not be isolated pure. They display the first examples of a bridging alkoxysilyl ligand between Fe and Ni, and the μ2-η2-SiO bridge is also present in the methyl complex (4) and its phenyl analogue 5. The presence of the four-membered rings was confirmed by a crystal structure determination of 4. Treatment of 1 with excess (allyl)MgCl led to the expected bimetallic allyl complex (6). The rapid η3-allyl → η1-allyl → η3-allyl rearrangement is potentially assisted through stabilization of the coordinatively unsaturated Ni center by a SiO→Ni interaction. The bimetallic benzyl derivative 7 was also isolated. Purging a THF or benzene solution of 4 at room temperature with CO yielded after a few seconds the acyl complex (8), which readily decarbonylates. Its reaction with norbornadiene leads to the insertion product, which is thought to exist as an isomeric mixture with terminal or chelating acyl group (11 ⇌ 11‘). When complex 4 was reacted with tBuNC, rapid insertion occurred and further coordination of a terminal tBuNC ligand to Ni led to the iminoacyl complex (12). Complex 1 proved to be a more efficient catalyst (TON = 4100) for the dehydrogenative coupling of Ph3SnH than its mononuclear counterpart [NiCl2(PPh3)2] (TON = 1050). The maximum turnover frequency (TOF) was ca. 9800 h-1.
Enzymatic activation of oleuropein: A protein crosslinker used as a chemical defense in the privet tree (1999)

Leaves of the privet tree, Ligustrum obtusifolium, contain a large amount of oleuropein, a phenolic secoiridoid glycoside, which is stably kept in a compartment separate from activating enzymes. When the leaf tissue is destroyed by herbivores, enzymes localized in organelles start to activate oleuropein into a very strong protein denaturant that has protein-crosslinking and lysine-decreasing activities. These activities are stronger than ever reported from plant systems and have adverse effects against herbivores by decreasing the nutritive value of dietary protein completely. We report here that strong oleuropein-specific beta-glucosidase in organelles activates oleuropein by converting the secoiridoid glucoside moiety of oleuropein into a glutaraldehyde-like structure, which is also an alpha,beta-unsaturated aldehyde. Oleuropein activated by beta-glucosidase had very strong protein-denaturing, protein-crosslinking, and lysine-alkylating activities that are very similar to, but stronger than, those of glutaraldehyde. Aucubin, another iridoid glycoside, had similar activities after beta-glucosidase treatment. We also detected polyphenol oxidase activity in organelles that activate the dihydroxyphenolic moiety to have protein-crosslinking activities. These data suggest that the privet tree has developed an effective defense mechanism with oleuropein, a unique multivalent alkylator ideal as a protein-crosslinker. Our results that iridoid glycosides are precursors of alkylators may elucidate the chemical bases that underlie various bioactivities and ecological roles of iridoid glycosides.
Figure S1 from Fibroblast-Derived IL33 Facilitates Breast Cancer Metastasis by Modifying the Immune Microenvironment and Driving Type 2 Immunity (2023)

&lt;p&gt;Figure S1 complements Figure 1 in showing the specific upregulation of IL-33 in metastases-associated fibroblasts&lt;/p&gt;