gebhart/patrepeval huggingface dataset:
P2Y Receptor-mediated Inhibition of Tumor Necrosis Factor α-stimulated Stress-activated Protein Kinase Activity in EAhy926 Endothelial Cells (2000)

In the EAhy926 endothelial cell line, UTP, ATP, and forskolin, but not UDP and epidermal growth factor, inhibited tumor necrosis factor alpha (TNFalpha)- and sorbitol stimulation of the stress-activated protein kinases, JNK, and p38 mitogen-activated protein (MAP) kinase, and MAPKAP kinase-2, the downstream target of p38 MAP kinase. In NCT2544 keratinocytes, UTP and a proteinase-activated receptor-2 agonist caused similar inhibition, but in 13121N1 cells, transfected with the human P2Y(2) or P2Y(4) receptor, UTP stimulated JNK and p38 MAP kinase activities. This suggests that the effects mediated by P2Y receptors are cell-specific. The inhibitory effects of UTP were not due to induction of MAP kinase phosphatase-1, but were manifest upstream in the pathway at the level of MEK-4. The inhibitory effect of UTP was insensitive to the MEK-1 inhibitor PD 098059, changes in intracellular Ca(2+) levels, or pertussis toxin. Acute phorbol 12-myristate 13-acetate pretreatment also inhibited TNFalpha-stimulated SAP kinase activity, while chronic pretreatment reversed the effects of UTP. Furthermore, the protein kinase C inhibitors Ro318220 and Go6983 reversed the inhibitory action of UTP, but GF109203X was ineffective. These results indicate a novel mechanism of cross-talk regulation between P2Y receptors and TNFalpha-stimulated SAP kinase pathways in endothelial cells, mediated by Ca(2+)-independent isoforms of protein kinase C.
Silicon(IV) Phthalocyanine-Decorated Cyclodextrin Vesicles as a Self-Assembled Phototherapeutic Agent against MRSA (2016)

The host-guest complexation of a tailored Si(IV) phthalocyanine with supramolecular β-cyclodextrin vesicles (CDV) was studied, revealing a reduced aggregation of the photoactive center upon binding to the CDV, even in aqueous environments. For this purpose, a photosensitizing unit axially decorated with one adamantyl group and one pyridinium moiety on the other side was obtained by two successive click reactions on a bis-azido-functionalized derivative of Si(IV) phthalocyanine. To evaluate its potential as a photosensitizer against antibiotic-resistant bacteria, comparative studies of the photophysical properties including absorption and emission spectroscopy, lifetimes as well as fluorescence and singlet oxygen quantum yields were determined for the Si(IV) phthalocyanine alone and upon self-assembly on the CDV surface. In vitro phototoxicity against the methicillin-resistant Staphylococcus aureus (MRSA) USA300 was evaluated, showing an almost complete inactivation.
A Model for Range Estimation and Energy-Efficient Routing of Electric Vehicles in Real-World Conditions (2019)

This paper presents an integrated model for energy consumption and range estimation, capable of energy-efficient routing. This integrated model predicts the energy consumption on all road segments in the road network and applies shortest path algorithms to calculate energy-efficient routes. A temperature-dependent model of the battery internal resistance based on real-world data translates the energy consumption prediction into driving range. The graph representation of the road network is transformed from a node-based graph to an edge-based graph to allow cost allocation of one edge based on the characteristics of the preceding edge. The integrated model is used to perform an analysis of energy-efficient routes for a real-life scenario. The analysis showed that the energy-optimal route is different from the time- and distance-optimal route with energy-efficiency gains up to 37% for the chosen scenario. The energy-efficient route tends to lean toward a distance-optimal route in the case of low auxiliary consumption and to lean toward a time-optimal route in the case of high auxiliary consumption. The energy-efficient route generation is tested in real life for one case of the chosen scenario. The measured results showed a good match with the predicted values for the energy consumption with a 9% mean relative error and preserved the ranking of all routes in terms of the travel distance, travel time, and energy consumption. The proposed integrated model is a functional model for energy consumption in real-life that differentiates many energy consumption influencing factors and produces energy-efficient routes with good accuracy.
A Comparative Study of Flows Through Funnel-Shaped Bottlenecks Placed in the Middle and Corner (2022)

Upon exiting buildings, theatres, and stadiums, which house a great number of people, egress points can act as bottlenecks, resulting in crowded exits and decreased flows. Most studies investigating flow have been conducted in either narrow bottlenecks (doors) or funnel shape bottlenecks, with the latter investigating bottlenecks placed in the middle of the walkway. This study investigates, for the first time, crowd flow through funnel-shaped bottlenecks placed in the corner of the walkway and makes comparisons with similar bottlenecks of the same length, entrance and exit width placed in the middle of the walkway. The entry width and exit width of the bottlenecks were 3 m and 1 m respectively, with lengths varying from 1 m to 4 m; they continued into a 10 m corridor. Ninety-four participants of various ages were observed moving through each of the configurations. The results indicated that using funnel-shaped bottlenecks in the middle of the walkway increased the flow rate significantly compared to the corner in bottlenecks with 2 m and 3 m lengths. This is contrary to what some other researchers have found for narrow bottlenecks placed in the middle and corner of a wall, although it is recognised that the configuration of funnel-shaped bottlenecks makes the comparison more complex and further work is required in this area. Notwithstanding these results are considered valuable for consideration when designing egress points and corridors in complex buildings such as metro and train stations.
A 1H n.m.r. study of the role of the glutamate moiety in the binding of methotrexate to Lactobacillus casei dihydrofolate reductase (1984)

The binding of a series of amide derivatives of methotrexate to Lactobacillus casei dihydrofolate reductase has been studied by inhibition constant measurements and by 1H n.m.r. spectroscopy. Amide modification of the alpha-carboxylate of methotrexate was found to prevent interaction of the gamma-carboxylate with the imidazole of His 28. Estimates of the contributions to the binding energy from the alpha-carboxylate-Arg 57 and gamma-carboxylate-His 28 interactions have been made from a combination of inhibition and n.m.r. data.
Potential assessment of lung samples by X-ray histology (XRH) during surgery (2020)

More than 25,000 operations to remove all or part of a patient’s lung take place in Europe each year. The full extent and type of changes in lung structure due to disease may not be evident until surgery is underway. Immediate microanatomical assessment of removed tissue can guide and inform the surgical team.&lt;br/&gt;We explored the feasibility of using micro-computed tomography (µCT) based X-ray histology (XRH) for timely 3D histological imaging during surgery. Key criteria include (1) visualisation of relevant microanatomical structures (2) results in less than 20 minutes during the operation (3) rapid and effective presentation of the data-rich 3D images and (4) compatibility with current intra-operative and post-operative pathology protocols.&lt;br/&gt;For protocol development, pig lung was used as it is similar in size and structure to human lung. Using optimised µCT scan conditions at our XRH facility in Southampton, consistent 3D imaging of fresh, unfixed peripheral lung samples was demonstrated (n=6), providing relevant microanatomical information in less than 10 minutes (Fig 1). Snap freezing and/or air-inflation of lung samples were also feasible within the time required. Both required additional preparation steps and could lead to over-inflation or affect preparation for routine wax histology, respectively. Short scan times minimised the impact of sample movement on image quality. A system for rapid, automated generation of user-friendly reports was developed. This brings together images and sample details for assessment, patient records and clinical team discussions. To streamline the integration of XRH with existing protocols, we scanned samples in standard containers used to transfer surgical samples to the pathology lab. This allows fast, non-invasive, non-contact scanning in a sealed container, reducing sample handling and avoiding contamination.&lt;br/&gt;The rapid XRH data were judged to be of potential diagnostic quality by pathologists. This approach provides opportunities for future research and diagnostic use.
Synergistic neuroprotection by coffee components eicosanoyl-5-hydroxytryptamide and caffeine in models of Parkinson's disease and DLB (2018)

Hyperphosphorylated α-synuclein in Lewy bodies and Lewy neurites is a characteristic neuropathological feature of Parkinson's disease (PD) and Dementia with Lewy bodies (DLB). The catalytic subunit of the specific phosphatase, protein phosphatase 2A (PP2A) that dephosphorylates α-synuclein, is hypomethylated in these brains, thereby impeding the assembly of the active trimeric holoenzyme and reducing phosphatase activity. This phosphatase deficiency contributes to the accumulation of hyperphosphorylated α-synuclein, which tends to fibrillize more than unmodified α-synuclein. Eicosanoyl-5-hydroxytryptamide (EHT), a fatty acid derivative of serotonin found in coffee, inhibits the PP2A methylesterase so as to maintain PP2A in a highly active methylated state and mitigates the phenotype of α-synuclein transgenic (Syn<sup>Tg</sup>) mice. Considering epidemiologic and experimental evidence suggesting protective effects of caffeine in PD, we sought, in the present study, to test whether there is synergy between EHT and caffeine in models of α-synucleinopathy. Coadministration of these two compounds orally for 6 mo at doses that were individually ineffective in Syn<sup>Tg</sup> mice and in a striatal α-synuclein preformed fibril inoculation model resulted in reduced accumulation of phosphorylated α-synuclein, preserved neuronal integrity and function, diminished neuroinflammation, and improved behavioral performance. These indices were associated with increased levels of methylated PP2A in brain tissue. A similar profile of greater PP2A methylation and cytoprotection was found in SH-SY5Y cells cotreated with EHT and caffeine, but not with each compound alone. These findings suggest that these two components of coffee have synergistic effects in protecting the brain against α-synuclein-mediated toxicity through maintenance of PP2A in an active state.
Cu/Fe/O=PPh3-Catalyzed Etherification for the Synthesis of Aryl 3-Benzo[b]thienyl Ethers (2018)

Cu/Fe-cocatalyzed cross-coupling reactions between 3-bromobenzo[b]thiophene and hydroxyaryls are described herein. The combination of Cu and Fe catalysts is important for the progress of the reactions, and the use of triphenylphosphine oxide as a ligand suppresses the dehalogenation of 3-bromobenzo[b]thiophene, and promptly facilitates the reaction. The obtained aryl benzo[b]thienyl ethers can be converted to pextended thienobenzofuran derivatives via Pd-catalyzed dehydrogenative cyclizations.
Data from Quantification of T- and B-cell Immune Receptor Distribution Diversity Characterizes Immune Cell Infiltration and Lymphocyte Heterogeneity in Clear Cell Renal Cell Carcinoma (2023)

&lt;div&gt;Abstract&lt;p&gt;Immune-modulating systemic therapies are often used to treat advanced cancer such as metastatic clear cell renal cell carcinoma (ccRCC). Used alone, sequence-based biomarkers neither accurately capture patient dynamics nor the tumor immune microenvironment. To better understand the tumor ecology of this immune microenvironment, we quantified tumor infiltration across three distinct ccRCC patient tumor cohorts using complementarity determining region-3 (CDR3) sequence recovery counts in tumor-infiltrating lymphocytes and a generalized diversity index (GDI) for CDR3 sequence distributions. GDI can be understood as a curve over a continuum of diversity scales that allows sensitive characterization of distributions to capture sample richness, evenness, and subsampling uncertainty, along with other important metrics that characterize tumor heterogeneity. For example, richness quantified the total unique sequence count, while evenness quantified similarities across sequence frequencies. Significant differences in receptor sequence diversity across gender and race revealed that patients with larger and more clinically aggressive tumors had increased richness of recovered tumoral CDR3 sequences, specifically in those from T-cell receptor alpha and B-cell immunoglobulin lambda light chain. The GDI inflection point (IP) allowed for a novel and robust measure of distribution evenness. High IP values were associated with improved overall survival, suggesting that normal-like sequence distributions lead to better outcomes. These results propose a new quantitative tool that can be used to better characterize patient-specific differences related to immune cell infiltration, and to identify unique characteristics of tumor-infiltrating lymphocyte heterogeneity in ccRCC and other malignancies.&lt;/p&gt;Significance:&lt;p&gt;Assessment of tumor-infiltrating T-cell and B-cell diversity in renal cell carcinoma advances the understanding of tumor-immune system interactions, linking tumor immune ecology with tumor burden, aggressiveness, and patient survival.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Krishna and Hakimi, p. 764&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Comparison of Commercial ELISA Blood Tests for Early Pregnancy Detection in Dairy Cows (2010)

The objective of the present study was to compare two commercially available blood-based pregnancy tests, namely BioPRYN, an ELISA for pregnancy-specific protein B (PSPB), and an ELISA for pregnancy-associated glycoprotein (PAG), for early pregnancy diagnosis in dairy cattle using transrectal ultrasonography as a gold standard. Transrectal ultrasonography was conducted 26-58 days after artificial insemination (AI) in 197 cattle from 19 farms. Concurrently, a blood sample was collected for determination of serum PSPB and PAG. Transrectal palpation was performed approximately 120 days after AI to verify that pregnancy was maintained. For PSPB and PAG, there were no significant differences (P>0.05) in sensitivity (98.0 and 97.8%), specificity (97.1 and 91.2%), positive predictive values (99.3 and 97.8%), negative predictive values (91.9 and 91.2%) and accuracy (97.8 and 96.4%). In conclusion, the two blood pregnancy assays were equally efficacious and were highly accurate (based on transrectal ultrasonography as the gold standard).
Comment on Sobczyk, M.K.; Gaunt, T.R. The Effect of Circulating Zinc, Selenium, Copper and Vitamin K1 on COVID-19 Outcomes: A Mendelian Randomization Study. Nutrients 2022, 14, 233 (2022)

Sobczyk and Gaunt genetically predicted circulating zinc, selenium, copper, and vitamin K<sub>1</sub> levels-instead of directly measuring nutrients in blood-and hypothesized that these levels would associate with SARS-CoV-2 infection and COVID-19 severity [...].
Recovery of Indigestible Fiber from Feces of Sheep and Cattle on Forage Diets (1986)

Experiment 1
Proton magnetic resonance spectra of the atropisomers of ortho‐hexaphenylene (1973)

Abstract The structures of the atropisomers of o ‐hexaphenylene are confirmed by their proton magnetic resonance spectra. The centrosymmetrical isomer 1a gives rise to an AA′BB′ spectrum, whereas the helical isomer 1b displays an AA′BB′ spectrum for two of its aromatic rings and an ABCD for the remaining four rings. Long‐range coupling between the AA′BB′ and ABCD parts of 1b leads to a tentative assignment of the protons. An analysis of the spectrum of o ‐tetraphenylene ( 2 ) is also given.
3D multiple attenuation and depth imaging of ocean‐bottom seismic data (2007)

In 3D Ocean Bottom seismic surveys (3D‐OBS) both pressure and vertical particle velocity is recorded. This presents the opportunity to decompose the recorded wavefields in up‐ and downgoing components and apply to 3D common receivers gathers a designature/demultiple algorithm to attenuate free surface multiples. This single processing step replaces several steps in conventional processing usually encompassing tau‐p predictive deconvolution and Radon demultiple. Using a 3D‐OBS data set from the Gullfaks Sør field in the North Sea, the new 3D designature/demultiple approach, together with 3D common receiver depth migration, is shown to result in seismic images of better quality than by the traditional processing sequence.
Psychosocial Impact of COVID-19 Pandemic in Elderly Psychiatric Patients: a Longitudinal Study (2021)

The study was designed to investigate the impact of the Coronavirus Disease 2019 (COVID-19) pandemic on mental health and perceived psychosocial support for elderly psychiatric patients in a longitudinal design. n = 32 patients with affective or anxiety disorders aged ≥60 years were included. Telephone interviews were conducted in April/May 2020 (T1) and August 2020 (T2). The psychosocial impact (PSI) of the pandemic and psychopathology were measured. Changes between T1 and T2 were examined. Patients' psychosocial support system six months before the pandemic and at T1/T2 was assessed. We found a significant positive correlation between general PSI and depression as well as severity of illness. General PSI differed significantly depending on social contact. Neither general PSI nor psychopathology changed significantly between T1 and T2. At T1, patients' psychosocial support systems were reduced as compared to six months before. Patients reported an increase in psychosocial support between T1 and T2 and high demand for additional support (sports, arts/occupational therapy, physiotherapy, psychotherapy). Elderly psychiatric patients show a negative PSI of the pandemic. They are likely to suffer from an impaired psychosocial situation, emphasizing the importance of developing concepts for sufficient psychosocial support during a pandemic.
4-(Phenylaminomethylene)isoquinoline-1,3(2H,4H)-diones as Potent and Selective Inhibitors of the Cyclin-Dependent Kinase 4 (CDK4) (2008)

The cyclin-dependent kinases (CDKs), as complexes with their respective partners, the cyclins, are critical regulators of cell cycle progression. Because aberrant regulations of CDK4/cyclin D1 lead to uncontrolled cell proliferation, a hallmark of cancer, small-molecule inhibitors of CDK4/cyclin D1 are attractive as prospective antitumor agents. The series of 4-(phenylaminomethylene)isoquinoline-1,3(2H,4H)-dione derivatives reported here represents a novel class of potent inhibitors that selectively inhibit CDK4 over CDK2 and CDK1 activities. In the headpiece of the 4-(phenylaminomethylene)isoquinoline-1,3(2H,4H)-dione, a basic amine substituent is required on the aniline ring for the CDK4 inhibitory activity. The inhibitory activity is further enhanced when an aryl or heteroaryl substituent is introduced at the C-6 position of the isoquinoline-1,3(2H,4H)-dione core. We present here SAR data and a CDK4 mimic model that explains the binding, potency, and selectivity of our CDK4 selective inhibitors.
A Multiplexed Luciferase-based Screening Platform for Interrogating Cancer-associated Signal Transduction in Cultured Cells (2013)

Genome-scale interrogation of gene function using RNA interference (RNAi) holds tremendous promise for the rapid identification of chemically tractable cancer cell vulnerabilities. Limiting the potential of this technology is the inability to rapidly delineate the mechanistic basis of phenotypic outcomes and thus inform the development of molecularly targeted therapeutic strategies. We outline here methods to deconstruct cellular phenotypes induced by RNAi-mediated gene targeting using multiplexed reporter systems that allow monitoring of key cancer cell-associated processes. This high-content screening methodology is versatile and can be readily adapted for the screening of other types of large molecular libraries.
DBD regeneration of GAC loaded with acid orange 7 (2009)

Abstract Activated carbon (AC) has been widely used as adsorbent in various industrial applications, such as purification of water in sewage facilities and filtration of air in toxicity‐treating factories. However, after exhaustion, AC should be regenerated and reused because of the limited resources for AC production and additional secondary pollution of spent‐carbon dumped into water or soil. In this study, a process for regenerating AC based on high active species (O 3 , ·OH, HO 2 , O 2 , ·RO, etc.) generated by dielectric barrier discharge (DBD) oxidation was proposed. The regeneration of granular‐activated carbon (GAC) exhausted with azo dye acid orange 7 was investigated to assay this method. The influences of the parameters, such as treatment time, electric field and gas kind, on the readsorption rate were studied systematically. The results of structural properties of GAC analyses showed that the surface area, the micropore area, external surface area, micropore volume and total volume of GAC after three cycles DBD treatment decreased to different extent. The adsorption isotherms indicated that the regeneration efficiency was about 81% after three times DBD plasma regeneration cycles, which confirmed the reuse feasibility of the regenerated GAC. Copyright © 2009 Curtin University of Technology and John Wiley &amp; Sons, Ltd.
Linking lineage diversification to climate and habitat heterogeneity: phylogeography of the southern African shrew Myosorex varius (2011)

Aim The phylogeographical patterning of taxa distributed in the Cape Floristic Region (CFR) of southern Africa has received much recent attention. Few studies, however, have focused on taxa with broad ecological requirements, such as the South African endemic shrew Myosorex varius (Soricidae). The species is considered a generalist and is distributed throughout the CFR and the grasslands of South Africa. Our aims were: (1) to investigate the fine-scale phylogeographical structure of M. varius through comprehensive spatial sampling across the entire distribution; and (2) to determine if the distribution of genetic structuring was correlated with environmental factors such as seasonal rainfall regimes. Location South Africa. Methods The phylogeographical structure of M. varius was determined by making use of 1029 sequenced characters derived from two independent markers (the mitochondrial hypervariable control region and an intron of a nuclear gene, signal transducer and activator of transcription 5A – STAT). Bayesian analysis of population structure (baps) and spatial genetic landscapes were used to describe broad-scale patterns of genetic diversity across the entire distribution of M. varius. Results Several geographically correlated lineages were detected within the species. The northern lineage comprised all individuals collected from the grassland and savanna habitats of South Africa and, although genetically diverse, did not show any significant geographically correlated substructure. The southern lineage, represented by individuals collected from the Western and Eastern Cape provinces of South Africa, displayed considerably more phylogeographical partitioning, with populations of M. varius in this region subdivided into western and eastern CFR groupings. Main conclusions Contrary to expectations, this study recovered high levels of spatial genetic structuring within the southern African generalist shrew species M. varius. This phylogeographical structure is consistent with that proposed by previous studies on other unrelated taxa, and this study contributes significantly to the growing body of work highlighting the importance of rainfall and associated vegetation types as factors influencing biodiversity patterns in the region.