gebhart/patrepeval huggingface dataset:
Synthesis, In Vitro, and Computational Studies of PTP1B Phosphatase Inhibitors Based on Oxovanadium(IV) and Dioxovanadium(V) Complexes (2022)

One of the main goals of recent bioinorganic chemistry studies has been to design and synthesize novel substances to treat human diseases. The promising compounds are metal-based and metal ion binding components such as vanadium-based compounds. The potential anticancer action of vanadium-based compounds is one of area of investigation in this field. In this study, we present five oxovanadium(IV) and dioxovanadium(V) complexes as potential PTP1B inhibitors with anticancer activity against the MCF-7 breast cancer cell line, the triple negative MDA-MB-231 breast cancer cell line, and the human keratinocyte HaCaT cell line. We observed that all tested compounds were effective inhibitors of PTP1B, which correlates with anticancer activity. [VO(dipic)(dmbipy)]·2 H<sub>2</sub>O (Compound <b>4</b>) and [VOO(dipic)](2-phepyH)·H<sub>2</sub>O (Compound <b>5</b>) possessed the greatest inhibitory effect, with IC<sub>50</sub> 185.4 ± 9.8 and 167.2 ± 8.0 nM, respectively. To obtain a better understanding of the relationship between the structure of the examined compounds and their activity, we performed a computer simulation of their binding inside the active site of PTP1B. We observed a stronger binding of complexes containing dipicolinic acid with PTP1B. Based on our simulations, we suggested that the studied complexes exert their activity by stabilizing the WPD-loop in an open position and limiting access to the P-loop.
Abnormalities of chromosome 1p/q are highly associated with chromosome 13/13q deletions and are an adverse prognostic factor for the outcome of high‐dose chemotherapy in patients with multiple myeloma (2007)

The prognostic value of chromosomal abnormalities was studied in untreated multiple myeloma patients who were registered into a prospective randomised multicentre phase 3 study for intensified treatment (HOVON24). A total of 453 patients aged less than 66 years with stage II and III A/B disease were registered in the clinical study. Cytogenetic analysis was introduced as a standard diagnostic assay in 1998. It was performed at diagnosis in 160 patients and was successful in 137/160 patients (86%). An abnormal karyotype was observed in 53/137 (39%) of the patients. Abnormalities of chromosome 1p and 1q were found in 19 (36% of patients with an abnormal karyotype) and 21 patients (40%). There was a strong association between chromosome 1p and/or 1q abnormalities and deletion of chromosome 13 or 13q (n = 27, P < 0.001). Patients with karyotypic abnormalities had a significantly shorter overall survival (OS) than patients with normal karyotypes. Complex abnormalities, hypodiploidy, chromosome 1p abnormalities, chromosome 1q abnormalities, and chromosome 13 abnormalities were associated with inferior OS on univariate analysis, as well as after adjustment for other prognostic factors. In conclusion, chromosome 13 abnormalities and chromosome 1p and/or 1q abnormalities were highly associated, and are risk factors for poor outcome after intensive therapy in multiple myeloma.
Simulating and Measuring Structural Intensity Fields in Plates Induced by Spatially and Temporally Random Excitation (2005)

The structure-borne power in bending waves is well understood, and has been studied by many investigators in ideal beam and plate structures. All studies to date, however, have considered only the structural intensity induced by deterministic, localized drives. Since many structures of practical interest are excited by spatially random pressure fields, such as diffuse and turbulent boundary layer pressure fluctuations, techniques for measuring and predicting the structural intensity patterns in flat plates excited by such fields are presented here. The structural intensity at various frequencies in a simply supported, baffled, flat plate driven by a diffuse pressure field is simulated using analytical techniques and measured by post-processing data from a scanning laser Doppler vibrometer and reference accelerometer using finite differencing techniques. The measured and simulated fields are similar, and show intensity patterns different from those caused by deterministic point drives. Specifically, no clear source regions are apparent in the randomly driven intensity fields, although the energy flow patterns do clearly converge toward a point damper attached to the plate.
Comparative Study on Cardiotoxic Effect of Tinuvin 770: A Light Stabilizer of Medical Plastics in Rat Model (2003)

Tinuvin 770 [bis(2,2,6,6-tetramethyl-4-piperidinyl) sebacate], is a UV light stabilizer plastic additive used worldwide. It is a component of many plastic materials used in medical and food industries. Earlier studies demonstrated its in vitro L-type Ca2+ channel and nicotinic acetylcholine receptor blocking properties. Our previous experiments have proved the toxic effects of Tinuvin 770 on isolated rat cardiomyocytes. The present study investigates the cardiotoxic effects of Tinuvin 770 in vivo. Wistar rats were intraperitoneally injected with increasing doses of Tinuvin 770 (1, 10, 100 microg, and 1 mg) 15 times during a 5-week period. Myocardial samples were analyzed by light, electron, and fluorescent microscopy. The lead-acetate method was used to detect intracellular Ca2+, and glyoxylic acid technique to assess alteration in adrenergic innervation. Focal myocytolysis and hypercontraction necrosis could be observed in rats treated with higher doses of Tinuvin 770. In these groups, intracellular Ca2+ accumulation and increased catecholamine release were detected. Tinuvin 770 not only displays L-type Ca2+ channel blocking properties, but can also lead to catecholamine release, similar to effects of the first generation of L-type Ca2+ channel blockers. Morphological results correspond to catecholamine-induced myocardial damage. Current literature, as well as our study, indicates that more detailed toxicological analysis of Tinuvin 770 should be required, and current regulations in medical and food industries should adopt the new results.
Permutation-symmetric critical phases in disordered non-Abelian anyonic chains (2009)

Topological phases supporting non-Abelian anyonic excitations have been proposed as candidates for topological quantum computation. In this paper, we study disordered non-Abelian anyonic chains based on the quantum groups $\text{SU}{(2)}_{k}$, a hierarchy that includes the $\ensuremath{\nu}=5/2$ fractional quantum Hall state and the proposed $\ensuremath{\nu}=12/5$ Fibonacci state, among others. We find that for odd $k$ these anyonic chains realize infinite-randomness critical phases in the same universality class as the ${S}_{k}$ permutation symmetric multicritical points of Damle and Huse [Phys. Rev. Lett. 89, 277203 (2002)]. Indeed, we show that the pertinent subspace of these anyonic chains actually sits inside the ${\mathbb{Z}}_{k}\ensuremath{\subset}{S}_{k}$ symmetric sector of the Damle-Huse model, and this ${\mathbb{Z}}_{k}$ symmetry stabilizes the phase.
Handbook of Antennas in Wireless Communications (2001)

From the Publisher:
The move toward worldwide wireless communications continues at a remarkable pace, and the antenna element of the technology is crucial to its success. With contributions from more than 30 international experts, the Handbook of Antennas in Wireless Communications brings together all of the latest research and results to provide engineering professionals and students with a one-stop reference on the theory, technologies, and applications for indoor, hand-held, mobile, and satellite systems.Beginning with an introduction to wireless communications systems, it offers an in-depth treatment of propagation prediction and fading channels. It then explores antenna technology with discussion of antenna design methods and the various antennas in current use or development for base stations, hand held devices, satellite communications, and shaping beams. The discussions then move to smart antennas and phased array technology, including details on array theory and beamforming techniques. Space diversity, direction-of-arrival estimation, source tracking, and blind source separation methods are addressed, as are the implementation of smart antennas and the results of field trials of systems using smart antennas implemented. Finally, the hot media topic of the safety of mobile phones receives due attention, including details of how the human body interacts with the electromagnetic fields of these devices.Its logical development and extensive range of diagrams, figures, and photographs make this handbook easy to follow and provide a clear understanding of design techniques and the performance of finished products. Its unique, comprehensive coverage written by top experts in their fields promises tomake the Handbook of Antennas in Wireless Communications the standard reference for the field.
Desaturation of oleoyl groups in envelope membranes from spinach chloroplasts. (1990)

Envelope membranes isolated from chloroplasts of spinach (Spinacia oleracea) desaturate oleoyl groups in monogalactosyl diacylglycerol to linoleoyl groups. The desaturation requires NADPH in combination with ferredoxin and is not restricted to monogalactosyl diacylglycerol, since it is also observed in biosynthetic intermediates as, for example, in phosphatidic acid. This indicates a certain degree of unspecificity of the oleate desaturase in isolated envelope membranes. Lipid desaturation is another important function of chloroplast envelopes.
AMP-activated protein kinase mediates mitochondrial fission in response to energy stress (2016)

Mitochondria undergo fragmentation in response to electron transport chain (ETC) poisons and mitochondrial DNA-linked disease mutations, yet how these stimuli mechanistically connect to the mitochondrial fission and fusion machinery is poorly understood. We found that the energy-sensing adenosine monophosphate (AMP)-activated protein kinase (AMPK) is genetically required for cells to undergo rapid mitochondrial fragmentation after treatment with ETC inhibitors. Moreover, direct pharmacological activation of AMPK was sufficient to rapidly promote mitochondrial fragmentation even in the absence of mitochondrial stress. A screen for substrates of AMPK identified mitochondrial fission factor (MFF), a mitochondrial outer-membrane receptor for DRP1, the cytoplasmic guanosine triphosphatase that catalyzes mitochondrial fission. Nonphosphorylatable and phosphomimetic alleles of the AMPK sites in MFF revealed that it is a key effector of AMPK-mediated mitochondrial fission.
Critically-evaluated propagation rate coefficients in free radical polymerizationsII. Alkyl methacrylkates (Technical Report) (1998)

Abstract
Stream processing platforms for analyzing big dynamic data (2016)

Abstract Nowadays, data is produced in every aspect of our lives, leading to a massive amount of information generated every second. However, this vast amount is often too large to be stored and for many applications the information contained in these data streams is only useful when it is fresh. Batch processing platforms like Hadoop MapReduce do not fit these needs as they require to collect data on disk and process it repeatedly. Therefore, modern data processing engines combine the scalability of distributed architectures with the one-pass semantics of traditional stream engines. In this paper, we survey the current state of the art in scalable stream processing from a user perspective. We examine and describe their architecture, execution model, programming interface, and data analysis support as well as discuss the challenges and limitations of their APIs. In this connection, we introduce Piglet, an extended Pig Latin language and code generator that compiles (extended) Pig Latin code into programs for various data processing platforms. Thereby, we discuss the mapping to platform-specic concepts in order to provide a uniform view.
Optimizing arbovirus surveillance using risk mapping and coverage modelling (2019)

Diseases carried by mosquitoes and other arthropods endanger human health globally. Though costly, surveillance efforts are vital for disease control and prevention This paper describes an approach for strategically configuring targeted disease surveillance sites across a study area. The methodology combines risk index mapping and spatial optimization modelling. The risk index is used to identify demand for surveillance, and the maximum covering location problem is used to select a specified number of candidate surveillance sites that covers the maximum amount of risk. The approach is demonstrated using a case study where optimal locations for sentinel surveillance sites are selected for the purposes of detecting eastern equine encephalitis virus in a county in the state of Florida. Optimal sentinel sites were selected under a number of scenarios that modelled different target populations (horses or humans), coverage distances (0.5, 1.0, and 1.5 km), and numbers of sites to select (1–12). Sentinel site selections for the horse and human models displayed different spatial patterns, with horse sites located largely in the west-central region and human ones in the north-central. Minor amounts of spatial overlap between the horse and human sites were observed, especially as coverage distances and numbers of sites were increased. Additionally, a near linear increase in risk coverage was observed as sites were incrementally added to the scenarios. This finding suggests that the number of sentinel sites within the ranges explored should be based on the maximum that can be funded, since they provide similar levels of benefit.
Abstract 4794: Preclinical evaluation of WX-0593, a potent orally active ALK inhibitor (2018)

Abstract Objective: ALK is a tyrosine kinase belonging to the insulin receptor super-family. The constitutively active ALK fusions are oncogenic and linked with multiple types of human cancer. The EML4-ALK fusion has been proven to be the driver of approximately 5% of NSCLC patients. We disclose here for the first time a novel ALK inhibitor WX-0593 and its preclinical evaluation data in preclinical models of ALK driven NSCLC. Method: The enzyme activities of WX-0593 for ALKWT, ALKL1196M, ALKC1156Y and EGFRL858R/T790M were measured with corresponding kinase assays. The anti-proliferative activity was evaluated in Karpas-299, Ba/F3, Ba/F3 (EML4-ALK-WT), Ba/F3 (EML4-ALK-L1196M), Ba/F3 (EML4-ALK-C1156Y), and NCI-H1975 cell lines. The specific effect (PD) of WX-0593 on ALK signaling was analyzed in NCI-H3122 cells. Antitumor activity of WX-0593 was evaluated in three patient-derived xenograft (PDX) models of NSCLC (LU-01-0015, LU-01-0319, and crizotinib resistant LU-01-0319R) and one cell-derived xenograft (CDX) model of NSCLC (NCI-H3122). PKPD was assessed by western blot analysis of the treated tumor tissues for p-ALK (Tyr1604), p-STAT3 (Tyr705), p-STAT5 (Tyr694), p-AKT, and p-ERK. Result: WX-0593 displayed potent enzymatic activities for ALKWT, ALKL1196M, ALKC1156Y and EGFRL858R/T790M with IC50 of 5.38, 9.26, 9.28, and 16.74 nM respectively. It also showed expected anti-proliferative activity in six cell lines, Karpas-299, Ba/F3, Ba/F3 (EML4-ALK-WT), Ba/F3 (EML4- ALK-L1196M), Ba/F3 (EML4-ALK-C1156Y), and NCI-H1975, with IC50 of 4.5, 2208, 4, 9.5, 9, and 508 nM, respectively. Western blot study in NCI-H3122 cells showed that WX-0593 could fully inhibit p-ALK, p-ERK,p-STAT5 at 11.1 nM and p-AKT at 100 nM. WX-0593 significantly inhibited tumor growth at all doses tested (P&amp;lt;0.001) in the LU-01-0015 (HIP1-ALK), LU-01-0319 (EML4-ALK), and LU-01-0319R NSCLC PDX models as well as in the NCI-H3122 CDX model. Western blot analysis of the tumor samples showed that WX-0593 inhibited p-ALK (Tyr1604), p-STAT3 (Tyr705), p-STAT5 (Tyr694), p-AKT, and p-ERK, indicating that the tumor growth inhibition was mediated by inhibition of ALK signaling. Conclusion: We have identified a potent orally active second generation ALK inhibitor, WX-0593. It can inhibit the activity of both wide type and crizotinib resistant ALK and showed strong antitumor activity in in vitro and in vivo preclinical models. These results are considered highly promising and warrant moving the compound forward to clinical investigation. Citation Format: Liu Xile, Charles Z Ding, Weifeng Mao, Yuxin Qin, Shansong Zheng, Yingying Yang, Qingmei Zheng, Long Zhang, Shuyong Zhao. Preclinical evaluation of WX-0593, a potent orally active ALK inhibitor [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4794.
A novel method for quantitative analysis of recombinant secreted proteins using two‐dimensional electrophoresis (1998)

We describe a two-dimensional polyacrylamide gel electrophoresis (2-D PAGE)-based approach for detecting and quantifying secreted recombinant proteins in media conditioned by baby hamster kidney (BHK) cells. Seven secreted proteins were analyzed in this system: leptin, thrombopoietin, thrombin, glycoprotein 130, soluble interleukin-2 receptor, and two novel sequences obtained from sequence database searches. BHK cells transfected with plasmids encoding each of these proteins, and cells transfected with empty plasmids (control cells), were metabolically labeled and the resulting conditioned media were analyzed by 2-D PAGE. Gel images derived from cells expressing recombinant proteins were compared with images from control cells in order to identify spots corresponding to the expressed proteins. All seven of the test proteins were successfully detected using this method. The sensitivity of the system was evaluated by diluting samples derived from high-expressing clones with conditioned media from control cells. The sensitivity of detection was protein-dependent, but recombinant proteins expressed at levels as low as 10 ng/mL could be detected. Quantification of recombinant protein levels was achieved by measuring spot intensities using phosphorimager analysis. The intensity of spots corresponding to recombinant proteins were compared with the spot intensity of an endogenous BHK protein which had been calibrated to a known standard. Estimates of the levels of expressed protein determined using this technique correlated with the levels determined using standard affinity assays. We conclude that this system provides a reliable method for quantifying levels of protein expression when specific assays are unavailable.
Elevated Coding Mutation Rate During the Reprogramming of Human Somatic Cells into Induced Pluripotent Stem Cells (2011)

Mutations in human induced pluripotent stem cells (iPSCs) pose a risk for their clinical use due to preferential reprogramming of mutated founder cell and selection of mutations during maintenance of iPSCs in cell culture. It is unknown, however, if mutations in iPSCs are due to stress associated with oncogene expression during reprogramming. We performed whole exome sequencing of human foreskin fibroblasts and their derived iPSCs at two different passages. We found that in vitro passaging contributed 7% to the iPSC coding point mutation load, and ultradeep amplicon sequencing revealed that 19% of the mutations preexist as rare mutations in the parental fibroblasts suggesting that the remaining 74% of the mutations were acquired during cellular reprogramming. Simulation suggests that the mutation intensity during reprogramming is ninefold higher than the background mutation rate in culture. Thus the factor induced reprogramming stress contributes to a significant proportion of the mutation load of iPSCs.
Synchronized Multi-list User Interfaces for Fashion Catalogs (2023)

Several online catalogs use carousels to present thematic lists of products, based on different optimization criteria. While this makes it possible to search for items according to diverse relevance perspectives, it hardly supports an integrated evaluation, which is key to critical consuming behavior. To address this issue, we propose a synchronized multi-list model that (i) enriches item presentation by visualizing its evaluation and (ii) enables the user to simultaneously center the carousels of the multi-list on the item in her/his focus of attention, showing its ranking in each list. This type of visualization is aimed at enhancing the transparency of results by enabling the user to simultaneously compare products across all the evaluation criteria applied within the multi-list.
A fast reconstruction algorithm for deterministic compressive sensing using second order reed-muller codes (2008)

This paper proposes a deterministic compressed sensing matrix that comes by design with a very fast reconstruction algorithm, in the sense that its complexity depends only on the number of measurements n and not on the signal dimension N. The matrix construction is based on the second order Reed- Muller codes and associated functions. This matrix does not have RIP uniformly with respect to all k-sparse vectors, but it acts as a near isometry on k-sparse vectors with very high probability.
Discovery of Potent 3,5-Diphenyl-1,2,4-oxadiazole Sphingosine-1-phosphate-1 (S1P1) Receptor Agonists with Exceptional Selectivity against S1P2 and S1P3 (2005)

A class of 3,5-diphenyl-1,2,4-oxadiazole based compounds have been identified as potent sphingosine-1-phosphate-1 (S1P1) receptor agonists with minimal affinity for the S1P2 and S1P3 receptor subtypes. Analogue 26 (S1P1 IC50 = 0.6 nM) has an excellent pharmacokinetics profile in the rat and dog and is efficacious in a rat skin transplant model, indicating that S1P3 receptor agonism is not a component of immunosuppressive efficacy.
Anticoagulation increases alveolar hemorrhage in mice infected with influenza A (2016)

Influenza A virus infection is a common respiratory tract infection. Alveolar hemorrhage has been reported in patients with influenza pneumonia and in mice infected with influenza A. In this study, we investigated the effect of two anticoagulants on alveolar hemorrhage after influenza A virus (IAV) infection of wild-type mice. Wild-type mice were anticoagulated with either warfarin or the direct thrombin inhibitor dabigatran etexilate and then infected with a mouse-adapted influenza virus (A/Puerto Rico/8/34 H1N1). Alveolar hemorrhage was assessed by measuring hemoglobin levels in the bronchoalveolar lavage fluid (BALF). We also measured vascular permeability and viral genomes in the lung, as well as white blood cells, inflammatory mediators, and protein in BALF Survival and body weight were monitored for 14 days after influenza A infection. In infected mice receiving either warfarin or dabigatran etexilate we observed decreased activation of coagulation in the BALF and increased alveolar hemorrhage. Warfarin but not dabigatran etexilate increased vascular permeability and mortality of influenza A-infected mice. Anticoagulation did not affect levels of influenza A genomes, white blood cells, inflammatory mediators, or protein in the BALF Our study indicates that systemic anticoagulation increases alveolar hemorrhage in influenza A-infected mice.