gebhart/patrepeval huggingface dataset:
Two‐dimensional electrophoresis of liver proteins: Characterization of a drug‐induced hepatomegaly in rats (2000)

Two-dimensional electrophoresis (2-DE) of liver proteins was applied to further characterize an unusual drug-induced increase in hepatocellular rough endoplasmic reticulum (RER) in Sprague-Dawley rats given a substituted pyrimidine derivative. Absolute liver weights of drug-treated rats (9.9 +/- 0.4 g) increased above vehicle-treated controls (7.2 +/- 0.2 g) by 37%. Light microscopy revealed diffuse granular basophilia of the hepatocellular cytoplasm, uncharacteristic of hepatocytes and suggested cells rich in ribosomes, which was confirmed by electron microscopy. Immunostaining for cell proliferation, viz., 5-bromo-2'-deoxyuridine (BrdU) and proliferating cell nuclear antigen (PCNA), indicated marked hepatocellular proliferative activity. 2-DE of solubilized liver using an ISO-DALT gel system indicated significant (p<0.001) quantitative changes in at least 17 liver proteins (12 increased, 5 decreased) compared to controls. The protein with the largest increase was homologous to acute-phase reactant, contrapsin-like protein inhibitor-6. Other markedly upregulated proteins were methionine adenosyltransferase, a catalyst in methionine/ATP metabolism and mitochondrial HMG-CoA synthase, involved in cholesterol synthesis. The complementary strategies of 2-DE coupled either with database spot mapping or protein isolation and amino acid sequencing successfully identified a subset of proteins from xenobiotic-damaged rodent livers, the expression of which differed from controls. However, the current bioinformatics platform for rodent hepatic proteins and limited knowledge of specific protein functionality restricted application of this proteomics profile to further define a mechanistic basis for this unusual hepatotoxicity.
Decentralized Congestion Management for Multilateral Transactions Based on Optimal Resource Allocation (2007)

This paper proposes a decentralized model for DC load flow based congestion management for the forward markets via Optimal Resource Allocation (ORA). The available thermal capacities of possible congested transmission lines are considered as commonly shared resources for all bilateral and multilateral transactions in the market. In our model, each transaction maximizes its profit under the limits of transmission line capacities allocated by the ISO. The ISO searches the optimal allocation of line capacities to each transaction. Finally, the same market efficiency (social welfare) as centralized optimization can be reached. The ORA-based decentralized approach is more suitable for power market environment, since it always keeps the intermediate solution feasible during the iterations and does not require each transaction to submit their private and sensitive information. The mathematical model, computation procedure and relevant proof are presented. The computer test results from the IEEE 30 bus system illustrate the effectiveness of proposed approach.
428 Invariant Natural Killer T-cells Neutralization Is a Possible Target Therapy for Human Eosinophilic Esophagitis (2014)

Background: Neuro-immune interaction has evolved as an integral part in the pathophysiology of gut and crosstalk between nerves andmast cells is a typical example of such interactions. We have already reported that CGRP-immunoreactive intrinsic nerve fibers are specifically increased along with the development of food allergy in the colonic mucosa of our food allergy model mice. Furthermore, our previous studies have provided vivid evidences of mucosal mast cells (MMCs) juxtaposed with CGRP-positive enteric nerve fibers in the colonic mucosa of food allergy model mice. IgE-antigen stimulation has not only documented to cause degranulation in mast cells but also, recently, reported to cause activation of neurons in superior cervical ganglion. However, no study so far employed isolated enteric neurons and MMCs to elaborate this interaction which closely mimics to the pathophysiological state of the gut in the allergic condition. In the present study, we cultured both isolated enteric neurons and MMCs and examine their interaction. Material & methods: Enteric neurons were isolated from small intestine of BALB/c (4 to 6 weeks old) and examined by anti-β3tubulin antibody (anti-pan-neuronal marker antibody). Presence of high-affinity IgE receptors (FceRIs) on myentric neurons was examined in longitudinal muscle/myenteric plexus (LMMP) preparations by immunohistochemistry (IHC). Mucosal type bone marrow-derived mast cells (mBMMCs) were prepared from the femurs of BALB/c mice using four cytokines (SCF, IL-3, IL-9 and TGF-β1) and degranulation was performed by incubation with IgEantigen (IgE-DNP) to give mast cell juice (MCJ). Isolated enteric neurons were stimulated with either IgE-DNP or MCJ and analyzed by calcium imaging using fluo-8, a fluorescent calcium indicator. Finally, isolated enteric neurons were co-incubated with IgE-pretreated mBMMCs followed by stimulation with DNP. Only isolated enteric neurons were loaded with Fluo-8. Results: IHC studies revealed the presence of FceRI on the cell body of myentric neurons. Stimulation of isolated enteric neurons with IgE-DNP demonstrated an increase in intracellular calcium concentration ([Ca2+]i). Similarly, treatment of isolated enteric neurons with MCJ also led to an increase in [Ca2+]i. Furthermore, stimulation with DNP in an isolated enteric neuron/IgE-pretreated mBMMC co-culture condition produced an elevation of [Ca2+]i in isolated enteric neurons. Conclusion: We demonstrated here for the first time the activation of isolated enteric neurons by IgE-antigen, MCJ, and activated mBMMCs via calcium imaging. Therefore, we infer both direct and indirect involvement of crosstalk between enteric neurons and mucosal mast cells in allergic and inflammatory/ functional diseases of gut like food allergy or irritable bowel syndrome.
Supplementary Figure 5 from A687V EZH2 Is a Driver of Histone H3 Lysine 27 (H3K27) Hypertrimethylation (2023)

&lt;p&gt;Supplementary Figure 5: H3K27me3 enrichment across genes modulated by EZH2 inhibition&lt;/p&gt;
Functions of OSBP/ORP Family Proteins and Their Relation to Dyslipidemia (2012)

The pathway of intracellular cholesterol synthesis, uptake and efflux is much affected by both the positive and the negative feedbacks from direct interaction between cholesterol and its oxygenated derivatives (oxysterols) as well as the regulatory factors such as the sterolregulatory-element-binding protein (SREBP)– cleavage-activating protein–Insig complex (Radhakrishnan, Ikeda et al. 2007), 3-hydroxy-3-methylglutaryl-CoA (HMG-CoA) reductase (Sever, Song et al. 2003) and liver X receptors (LXRs) (Chen, Chen et al. 2007). Since these regulatory factors are located in the compartments with comparatively low cholesterol density, they can react promptly on acute changes in local cholesterol or oxysterol density. While much is known about the interaction between these regulatory factors and cholesterol, only little has been studied about the mechanism to deliver the cholesterol or oxysterol to its appropriate compartments. Therefore, there arises a possibility that oxysterol-binding protein/oxysterol-binding protein-related protein (OSBP/ORP) family may regulate such processes by binding oxyterol and/or cholesterol and by functioning as a cholesterol sensor or cholesterol transporter. According to the study about the family members, it is now becoming clear that they affect the regulation such as the cholesterol or triglyceride level. For comprehensive information on OSBP/ORP family, please refer to several good reviews already published (Fairn and McMaster 2008; Ngo, Colbourne et al. 2010; Raychaudhuri and Prinz 2010; Vihervaara, Jansen et al. 2011). This review focuses more on the family’s association with dyslipidemia from a perspective of the individual features of the structure, the expression, the cellular localization, the molecular functions, and the epidemiologial study-based information of each member.
Transcription start site signal profiling improves transposable element RNA expression analysis at locus-level (2022)

The transcriptional activity of Transposable Elements (TEs) has been involved in numerous pathological processes, including neurodegenerative diseases such as amyotrophic lateral sclerosis and frontotemporal lobar degeneration. The TE expression analysis from short-read sequencing technologies is, however, challenging due to the multitude of similar sequences derived from singular TEs subfamilies and the exaptation of TEs within longer coding or non-coding RNAs. Specialised tools have been developed to quantify the expression of TEs that either relies on probabilistic re-distribution of multimapper count fractions or allow for discarding multimappers altogether. Until now, the benchmarking across those tools was largely limited to aggregated expression estimates over whole TEs subfamilies. Here, we compared the performance of recently published tools (SQuIRE, TElocal, SalmonTE) with simplistic quantification strategies (featureCounts in unique, fraction and random modes) at the individual loci level. Using simulated datasets, we examined the false discovery rate and the primary driver of those false positive hits in the optimal quantification strategy. Our findings suggest a high false discovery number that exceeds the total number of correctly recovered active loci for all the quantification strategies, including the best performing tool <i>TElocal</i>. As a remedy, filtering based on the minimum number of read counts or baseMean expression improves the F1 score and decreases the number of false positives. Finally, we demonstrate that additional profiling of Transcription Start Site mapping statistics (using a <i>k</i>-means clustering approach) significantly improves the performance of <i>TElocal</i> while reporting a reliable set of detected and differentially expressed TEs in human simulated RNA-seq data.
Real-Time Changes in Brain Activity during Sacral Neuromodulation for Overactive Bladder (2017)

Functional magnetic resonance imaging confirmed that sacral neuromodulation influences brain activity in women with overactive bladder who responded to therapy. These changes varied with stimulus intensity.
Photoacoustic imaging sounds the alarm on liver fibrosis (2016)

A handheld photoacoustic and ultrasound imaging system detects liver fibrosis in mice and has the potential to be translated for noninvasive imaging in patients.
The localization of phospholipase A2 in the secretory granule (1994)

A heat-resistant phospholipase A2 has been detected in the secretory granules of the mast cell [Chock, Rhee, Tang and Schmauder-Chock (1991) Eur. J. Biochem. 195, 707-713]. By using ultrastructural immunocytochemical techniques, we have now localized this enzyme to the matrix of the secretory granule. Like the cyclo-oxygenase [Schmauder-Chock and Chock (1989) J. Histochem. Cytochem. 37, 1319-1328], this enzyme also adheres tightly to the ribbon-like granule matrix components. The results from Western-blot analysis suggest that it has a molecular mass of about 14 kDa. The localization of the phospholipase A2, the presence of a phospholipid store with millimolar concentrations of calcium and the localization of the enzymes of the arachidonic acid cascade make the secretory granule a natural site for lipid-mediator synthesis. The packaging of phospholipase A2, together with its substrate and the components of the arachidonic acid cascade, in the secretory granule represents a physical arrangement by which the initiation of the cascade and the release of mediators can be directly linked to the stimulation of cell-surface receptors.
Stable Pushing: Mechanics, Controllability, and Planning (1996)

We would like to give robots the ability to position and orient parts in the plane by pushing, particularly when the parts are too large or heavy to be grasped and lifted. Unfortunately, the motion of a pushed object is generally unpredictable due to unknown support friction forces. With multiple pushing contact points, however, it is possible to find pushing directions that cause the object to remain fixed to the manipulator. These are called stable pushing directions. In this article we consider the problem of planning pushing paths using stable pushes. Pushing imposes a set of nonholonomic velocity constraints on the motion of the object, and we study the issues of local and global controllability during pushing with point contact or stable line contact. We describe a planner for finding stable pushing paths among obstacles, and the planner is demon strated on several manipulation tasks.
Photoelectron Spectra of Molecules. II. The Ionization Potentials of Azabenzenes and Azanaphthalenes (1969)

The ionization potentials of pyridine, pyrazine, pyrimidine, pyridazine, quinoline, isoquinoline, quinoxaline, quinazoline, cinnoline, and phthalazine have been derived from molecular photoelectron spectra. Simple first-order perturbation theory and the MINDO SCF MO method have been employed in assigning the experimental first ionization potentials to ionization from a π or nonbonding energy level.
Stem-like Cancer Cells Are Inducible by Increasing Genomic Instability in Cancer Cells (2009)

The existence of cancer stem cells (CSCs) or stem-like cancer cells (SLCCs) is regarded as the cause of tumor formation and recurrence. However, the origin of such cells remains controversial with two competing hypotheses: CSCs are either transformed from tissue adult stem cells or dedifferentiated from transformed progenitor cells. Compelling evidence has determined the chromosomal aneuploidy to be one of the hallmarks of cancer cells, indicating genome instability plays an important role in tumorigenesis, for which CSCs are believed to be the initiator. To gain direct evidence that genomic instability is involved in the induction of SLCCs, we utilized multiple approaches to enhance genomic instability and monitored the percentage of SLCC in cultured cancer cells. Using side population (SP) cells as a marker for SLCC in human nasopharyngeal carcinoma (NPC) and CD133 for human neuroblastoma cells, we found that DNA damage inducers, UV and mitomycin C were capable of increasing SP cells in NPC CNE-2 and neuroblastoma SKN-SH cells. Likewise, either overexpression of a key regulator of cell cycle, Mad2, or knock down of Aurora B, an important kinase in mitosis, or Cdh1, a key E3 ligase in cell cycle, resulted in a significant increase of SP cells in CNE-2. More interestingly, enrichment of SP cells was observed in recurrent tumor tissues as compared with the primary tumor in the same NPC patients. Our study thus suggested that, beside transformation of tissue stem cells leading to CSC generation, genomic instability could be another potential mechanism resulting in SLCC formation, especially at tumor recurrence stage.
Selective Deposition of Multiple Sensing Materials on Si Nanobelt Devices through Plasma-Enhanced Chemical Vapor Deposition and Device-Localized Joule Heating (2017)

This paper describes a novel method, using device-localized Joule heating (JH) in a plasma enhanced atomic layer deposition (PEALD) system, for the selective deposition of platinum (Pt) and zinc oxide (ZnO) in the n<sup>-</sup> regions of n<sup>+</sup>/n<sup>-</sup>/n<sup>+</sup> polysilicon nanobelts (SNBs). COMSOL simulations were adopted to estimate device temperature distribution. However, during ALD process, the resistance of SNB device decreased gradually and reached to minima after 20 min JH. As a result, thermal decomposition of precursors occurred during PEALD process. Selective deposition in the n<sup>-</sup> region was dominated by CVD instead of ALD. Selective deposition of Pt and ZnO films has been achieved and characterized using atomic force microscopy, scanning electron microscopy, and transmission electron microscopy.
Erythropoietin‐Stimulated Proliferation of Human Red Cell Precursors in Vitro (1974)

S ummary . A liquid culture system is described that supports human erythropoiesis in vitro. Replication and maturation of red cell precursors in bone marrow from normal subjects and from patients with various disturbances of haemopoiesis were sustained in culture for periods up to 2 weeks. Added erythropoietin stimulated erythroid precursor DNA synthesis and cell replication. The erythropoietin effect was inhibited by a rabbit antibody to human erythropoietin. The culture system provides a means to study directly normal and abnormal human erythropoiesis in vitro.
One-pot and Solventless Synthesis of Ionic Liquids under Ultrasonic Irradiation (2007)

A novel method is described for the one-pot synthesis of various ionic liquids in a competitive time. By using ultrasonic irradiation, different families of nitrogen-bearing ionic liquids can be obtained in a solvent-free or in aqueous medium, which gives a greener touch to the overall process.
Transient diffusion of low-concentration B in Si due to 29Si implantation damage (1990)

The effects of implantation damage on B diffusion are analyzed through the use of 29Si implants. Implant doses of 29Si ranging from 1×1012/cm2 to 1×1014/cm2 were used to create controlled amounts of damage. Temperatures ranging from 800 to 1000 °C were used to anneal the implant damage. For all anneal temperatures, the peak B concentration was well below the intrinsic electron concentration. Even for 29Si doses as low as 1×1012/cm2 significantly enhanced B diffusion was observed. The largest enhancement in B diffusion was observed for the highest 29Si implant dose and lowest anneal temperature. The kinetics of damage annealing determine the transient enhancement in the B profile. These results have important implications for the formation of shallow junctions using ion implantation.
Antitumor activity of IMO-2055, an agonist of TLR9, in combination with erlotinib and bevacizumab in non-small cell lung cancer xenografts in mice (2008)

2078 IMO-2055 is an agonist of TLR9. It has shown potent Th1-type innate and adaptive immune responses, and antitumor activity in preclinical tumor models. In the present study, we have evaluated IMO-2055 alone and in combination with erlotinib, an inhibitor of EGFR tyrosine kinase, and bevacizumab, a monoclonal antibody against VEGF, in H358 human non-small cell lung cancer (NSCLC) xenograft model. Peritumoral injections of IMO-2055 three times a week for 7 weeks resulted in 53.6% growth inhibition on week 7 compared with PBS control group. Intra-gastric administration of erlotinib once a week or intra-peritoneal administration of bevacizumab two times a week for 7 weeks resulted in 47.6% and 46.4% tumor growth inhibition, respectively. Moreover, treatment with the combination of IMO-2055 and erlotinib or bevacizumab showed 63.0% and 76.1% tumor growth inhibition, respectively. Treatment of mice with triple combination of IMO-2055, erlotinib and bevacizumab lead to 88.8% tumor growth inhibition. Median survival (days for tumor nodules to reach 1.5 gram) of mice in IMO-2055, erlotinib, or bevacizumab treated groups was prolonged about 25, 7, or 22 days, respectively, compared with PBS control group. The combination of IMO-2055 and erlotinib or bevacizumab prolonged survival of tumor bearing mice by 36 and 40 days, respectively. The treatment with combination of all three agents resulted in complete regression of tumors in 43% of the mice, and extended median survival longer than 121 days. These results demonstrate that IMO-2055 exerts potent antitumor activity and enhances antitumor effects of erlotinib and bevacizumab in mice bearing H358 NSCLC. A clinical trial to evaluate IMO-2055 in combination with erlotinib and bevacizumab is planned.
An Overview of NASA Hypersonic Experimental Diagnostic and Instrumentation Technologies for Ground and Flight Testing (2009)

*† ‡ § ¶ †‡ ¶ Advances to the state of the art in experimental capabilities are required to support almost every aspect of the Hypersonics Project. These capabilities will be used to generate experimental data with quantified uncertainties for the creation and validation of advanced prediction models, as well as evaluate and provide understanding of the operation and performance of advanced concepts in laboratories, ground facilities, and flight. Current effort at NASA is to, a) Develop advanced instrumentation and testing methods for testing hypersonic vehicles and components of vehicles on the ground and in flight, so that performance can be more accurately evaluated and better understood, b) The development of robust diagnostic tools capable of measuring transient phenomena as well as withstanding a hypersonic flight environment during ascent, entry and landing. I. Introduction
Cover Picture: Chemically Programmed Supramolecular Assembly of Hemoprotein and Streptavidin with Alternating Alignment (Angew. Chem. Int. Ed. 16/2012) (2012)

An alternating protein assembly of myoglobin dimer (green) and streptavidin (gray) was made by using a synthesized cofactor dyad, which has a flexible linker between a heme moiety (red) and a bis(biotin) unit (blue). The specific interactions between the three components resulted in formation of a supramolecular submicrometer-sized fibrous assembly, which was characterized by AFM, as reported by T. Hayashi, T. R. Ward, and co-workers in their Communication on page 3818 ff. Gas-Phase Reactions Using a combination of gas-phase ion–molecule reactions and theoretical studies G. N. Khairallah, R. A. J. O'Hair et al. show in their Communication on page 3812 ff. that bisligated AuI complexes are unable to oxidatively add iodobenzene, but the clusters activate the CI bond.1 Biomimetic Catalysis In their Communication on page 3822 ff., Y. Huang, X. Duan, et al. report stable hemin–graphene conjugates with excellent catalytic activity that approaches that of natural enzymes.1 Nanoreactors V. Salgueiriño, M A. Correa-Duarte, and co-workers show in their Communication on page 3877 ff. that hydrazine reduces nickel ions in the presence of dendritic Pt nanoparticles inside a porous silica capsule.1
ChemInform Abstract: Recent Developments in Nucleophilic Radical Addition to Imines. The Key Role of Transition Metals and the New Porta Radical‐Type Version of the Mannich and Strecker Reactions (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
InSight Communications Degradation During Peak Heating Phase of Atmospheric Entry (2021)

This paper discusses the analysis of the UHF (401 MHz) plasma-induced communications blackout (and brownout) experienced by the Mars InSight spacecraft during its entry, descent, and landing (EDL) phase into the Martian atmosphere on 26 November 2018. The UHF relay links from InSight to the Mars Reconnaissance Orbiter and to the Mars Cube One A and Mars Cube One B CubeSats suffered a period of about 52 s of degradation, consisting of a combination of brownout (signal fades) and blackout (complete loss of signal). The observed signal fades and outages on these proximity links spanned the interval from about 48 to 100 s after entry started at the atmospheric interface. In addition, the degradation of the weaker signal received at the Green Bank, West Virginia 100 m radio telescope is also discussed, which occurred from about 40 to 120 s after atmospheric entry. The observations were in agreement with existing models of signal degradation given the entry trajectory of the vehicle. This paper discusses model estimates and measurements of signal degradation during the peak heating phase of the InSight EDL, as well as the results of high-fidelity analysis performed using computational fluid dynamics tools.
Finding the positive feedback loops underlying multi-stationarity (2015)

We have developed and implemented an automated procedure to find relevant positive feedback loops in reaction networks. The results of the procedure are useful for interpretation and summary of the network's dynamics.