gebhart/patrepeval huggingface dataset:
Endothelium independent relaxation of human coronary arteries by 17 -oestradiol in vitro (1993)

17 beta-Oestradiol produced an endothelium independent relaxation of precontracted human coronary arteries in vitro, and this effect was associated with an increase in both cyclic AMP and the cyclic GMP content. This direct relaxant effect of oestrogens on coronary arteries may contribute to the beneficial effects of oestrogen replacement therapy in postmenopausal women.
Syntheses of Basic Phenolalkyl Ethers (Further Report. VIII) (1949)

Basic phenol alkyl ethers were synthesized by the condensation of methyl 3-allyl-4-hydroxyphenyl ether and methyl 4-allyl-5-hydroxyphenyl ether with β-diethylamino-ethyl chloride. Application of magnesium-ethyl bromide on diethylamino-acetone gives 1-diethylamino-2-methylbutanol-(2) which was changed to 1-diethylamino-2-methyl-2-chlorobutane. Condensation of C-allylguaiacol to the latter gave (β-diethylamino-α-methyl-α-ethyl)-ethyl 2-methoxy-6-allylphenyl ether.
Increased SARS-CoV-2 Infection, Protease, and Inflammatory Responses in Chronic Obstructive Pulmonary Disease Primary Bronchial Epithelial Cells Defined with Single-Cell RNA Sequencing (2022)

<b>Rationale:</b> Patients with chronic obstructive pulmonary disease (COPD) develop more severe coronavirus disease (COVID-19); however, it is unclear whether they are more susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and what mechanisms are responsible for severe disease. <b>Objectives:</b> To determine whether SARS-CoV-2 inoculated primary bronchial epithelial cells (pBECs) from patients with COPD support greater infection and elucidate the effects and mechanisms involved. <b>Methods:</b> We performed single-cell RNA sequencing analysis on differentiated pBECs from healthy subjects and patients with COPD 7 days after SARS-CoV-2 inoculation. We correlated changes with viral titers, proinflammatory responses, and IFN production. <b>Measurements and Main Results:</b> Single-cell RNA sequencing revealed that COPD pBECs had 24-fold greater infection than healthy cells, which was supported by plaque assays. Club/goblet and basal cells were the predominant populations infected and expressed mRNAs involved in viral replication. Proteases involved in SARS-CoV-2 entry/infection (<i>TMPRSS2</i> and <i>CTSB</i>) were increased, and protease inhibitors (<i>serpins</i>) were downregulated more so in COPD. Inflammatory cytokines linked to COPD exacerbations and severe COVID-19 were increased, whereas IFN responses were blunted. Coexpression analysis revealed a prominent population of club/goblet cells with high type 1/2 IFN responses that were important drivers of immune responses to infection in both healthy and COPD pBECs. Therapeutic inhibition of proteases and inflammatory imbalances reduced viral titers and cytokine responses, particularly in COPD pBECs. <b>Conclusions:</b> COPD pBECs are more susceptible to SARS-CoV-2 infection because of increases in coreceptor expression and protease imbalances and have greater inflammatory responses. A prominent cluster of IFN-responsive club/goblet cells emerges during infection, which may be important drivers of immunity. Therapeutic interventions suppress SARS-CoV-2 replication and consequent inflammation.
Evaluation of antimycobacterial activity of medicinal plants used by Malian traditional medicine practitioners to treat tuberculosis (2021)

Global Tuberculosis (TB) control is facing major challenges such as occurrence of multidrug-resistant (MDR) and extensively drug-resistant tuberculosis (XDR). The current TB drugs are getting less effective and associated with side effects limiting their use, especially with MDR and XDR infected patients. In Mali, many medicinal plants are used against various diseases including bacterial infections. The study aimed at studying the antimycobacterial activities of 60 extracts from 22 Malian medicinal. The antibacterial activity against Mycobacterium tuberculosis H37Rv was assessed employing micro-broth dilution method. Out of 60 extracts evaluated, eleven from nine different plants were found to be active against H37Rv strain. The minimal inhibitory concentrations (MICs) ranked from 125 μg/mL to 1250 μg/mL. The most active extracts (125 μg/mL) were represented by ethanolic extract of Saba senegalensis and Vitellaria paradoxa leaves, dichloromethane extract of Cola cordifolia leaves, Strychnos spinosa and Ximenia Americana roots. Ethanolic extract of Zizyphus mauritiana, Guiera senegalensis and methanolic extract of Anthocleista djalonensis also prevented the growth of H37Rv at 250 μg/mL. The results suggest that Saba senegalensis, Vitellaria paradoxa, Cola cordifolia, Strychnos spinosa and Ximenia Americana could be potential sources of antimycobacterial molecules
New Technique for Measuring ( pi-Meter ) Indicated Mean Effective Pressure (1959)

The placement of Bio-Oss Collagen in the fresh extraction wound obviously delayed socket healing. Thus, after 2 weeks of tissue repair, only minute amounts of newly formed bone occurred in the apical and lateral borders of the grafted sockets, while large amounts of woven bone had formed in most parts of the non-grafted sites.
RNA Interference and Heterochromatin Assembly (2011)

In most eukaryotes, histone and DNA modifications are responsible for the silencing of genes integrated in heterochromatic sequences, as well as the silencing of pericentromeric repeats and transposable elements themselves. But the mechanisms that guide these modifications to heterochromatin during the cell cycle have been elusive. RNA interference takes advantage of heterochromatic transcription to process small RNAs and recruit enzymes required for both histone and DNA modifications, and is one such mechanism that has been identified. The processes are best understood in fission yeast and plants, but recent work in mammalian cells, especially in the germline, suggests these mechanisms may be highly conserved.
Mass Spectrometric detection of SARS-CoV-2 virus in scrapings of the epithelium of the nasopharynx of infected patients via Nucleocapsid N protein (2020)

ABSTRACT Detection of viral RNA by PCR is currently the main diagnostic tool for COVID-19 [1]. The PCR-based test, however, shows limited sensitivity, especially at early and late stages of the disease development [2,3], and is relatively time consuming. Fast and reliable complementary methods for detecting the viral infection would be of help in the current pandemia conditions. Mass-spectrometry is one of such possibilities. We have developed a mass-spectrometry based method for the detection of the SARS CoV-2 virus in nasopharynx epithelial swabs, based on the detection of the viral nucleocapsid N protein. The N protein of the SARS-COV-2 virus, the most abundant protein in the virion, is the best candidate for mass-spectrometric detection of the infection, and MS-based detection of several peptides from the SARS-COoV-2 nucleoprotein has been reported earlier by the Sinz group [4]. Our approach shows confident identification of the N protein in patient samples even with the lowest viral loads and a much simpler preparation procedure. Our main protocol consists of virus inactivation by heating and adding of isopropanol, and tryptic digestion of the proteins sedimented from the swabs followed by MS analysis. A set of unique peptides, produced as a result of proteolysis of the nucleocapsid phosphoprotein of SARS-CoV-2, is detected. The obtained results can further be used to create fast parallel mass-spectrometric approaches for the detection of the virus in the nasopharyngeal mucosa, saliva, sputum and other physiological fluids.
Cloning and Analysis of the Genes Encoding the Type IIS Restriction-Modification System HphI from Haemophilus Parahaemolyticus (1996)

The genomic region encoding the type IIS restriction-modification (R-M) system HphI (enzymes recognizing the asymmetric sequence 5'-GGTGA-3'/5'-TCACC-3') from Haemophilus parahaemolyticus were cloned into Escherichia coli and sequenced. Sequence analysis of the R-M HphI system revealed three adjacent genes aligned in the same orientation: a cytosine 5 methyltransferase (gene hphIMC), an adenine N6 methyltransferase (hphIMA) and the HphI restriction endonuclease (gene hphIR). Either methyltransferase is capable of protecting plasmid DNA in vivo against the action of the cognate restriction endonuclease. hphIMA methylation renders plasmid DNA resistant to R.Hindill at overlapping sites, suggesting that the adenine methyltransferase modifies the 3'-terminal A residue on the GGTGA strand. Strong homology was found between the N-terminal part of the m6A methyltransferasease and an unidentified reading frame interrupted by an incomplete gaIE gene of Neisseria meningitidis. The HphI R-M genes are flanked by a copy of a 56 bp direct nucleotide repeat on each side. Similar sequences have also been identified in the non-coding regions of H.influenzae Rd DNA. Possible involvement of the repeat sequences in the mobility of the HphI R-M system is discussed.
Patterning of epitaxial VO2microstructures by a high-temperature lift-off process (2014)

The growing field of oxide-electronics demands adequate fabrication methods that do not impair the material?s beneficial properties. To this end, we present a modified lift-off lithography method replacing the conventional polymer mask with an AlOx based mask. It can sustain the high-temperature and reactive gasses conditions commonly needed for oxide deposition, and is effectively wet-etched in dilute NaOH solutions. Here we demonstrate patterning of VO2 films. With its metal?insulator transition (MIT) near room temperature, it is attractive for various applications including sensors and transistors. But patterning is challenging since its properties are very sensitive to fabrication processes. We demonstrate patterning of 3 ?m wide VO2 electrodes and show they preserve the MIT magnitude and epitaxial growth of the non-patterned films. Some thinning of the VO2 is also observed. This process can be useful for patterning other materials that require harsh deposition conditions, and are resilient to low NaOH concentrations.
Comparison of Growth and Differentiation of Fetal and Adult Rhesus Monkey Mesenchymal Stem Cells (2006)

The goal of this study was to compare the growth and differentiation potential of fetal and adult rhesus monkey (Macaca mulatta) mesenchymal stem cells (rhMSCs). rhMSCs were obtained from healthy early third-trimester fetal (n = 3) and adult (n = 3) rhesus monkey bone marrow. Fetal rhMSCs were plated at 10, 50, 100, or 1,000 cells/cm(2) in medium containing 10% or 20% infant monkey serum (IMS) or fetal bovine serum (FBS). Fetal rhMSCs grown at 1,000 cells/cm(2) in 20% FBS showed faster growth rates and differentiation toward adipogenic, chondrogenic, and osteogenic lineages when compared to other culture conditions and to adult cells (p < 0.05). Fetal rhMSC showed higher population doubling times (11.3 +/- 0.5) when compared to adult cells (7.3 +/- 0.8) during the first three passages. Adult rhMSC did not grow beyond the third passage under all culture conditions, including those supplemented with insulin-like growth factor (IGF)-I, IGF-II, platelet-derived growth factor (PDGF), and fibroblast growth factor-2 (FGF-2). After the third passage, adult rhMSC cultures were observed with large syncytia and with evidence of apoptosis. Cells obtained from these cultures tested positive for simian foamy virus (SFV) by PCR, RT-PCR, and immunofluorescent assay. Adult rhMSCs cultured with 10 microM tenofovir, an antiviral agent, showed normal growth and differentiation for over 20 population doublings. These findings suggest that: (1) fetal rhMSCs possess greater self-renewal and differentiation potential when compared to adult cells; and (2) SFV can inhibit proliferation of adult rhMSCs in culture, whereas the addition of tenofovir can successfully suppress SFV replication in vitro and result in resumed growth.
In vivo biocompatibility testing of peek polymer for a spinal implant system: A study in rabbits (2002)

We are developing a new spinal implant system (SIS) without fusion (bone graft). This SIS is made from two materials, metal and polyetheretherketone (PEEK) polymer. The Food and Drug Administration recommended testing in vivo, in an animal model, whether the PEEK polymer could be used in a SIS without any harm of wear debris to the nervous tissue (spinal cord and nerve roots). The objective was to evaluate the biological response of the spinal cord and nerve roots (dura mater) to PEEK polymer particles. Twenty-four female New Zealand white rabbits were used. The rabbits were divided into three groups: test (n = 12), control (n = 9), and sham (n = 3). During the surgery, the test group received the PEEK particle injections (5 x 10(7) particles per site, lumbar and thoracic), while the control group received only the vehicle (0.9% saline solution). The sham group had the same surgical approach without injection. In each group, the rabbits were euthanized at 1, 4, and 12 weeks postsurgery. The macroscopic and semiquantitative histologic analyses of the spinal cords (dura mater) showed normal vascularization and particle adherence to the connective tissue especially at the injection sites. Neither necrosis nor swelling of the dura mater and nerve roots was observed. The PEEK polymer is harmless to the spinal cord; thus it might be used as component in the spinal implant system.
Comparative effectiveness of intensity modulated radiation therapy to 3-dimensional conformal radiation in locally advanced lung cancer: pathological and clinical outcomes (2019)

This study validates the real-world effectiveness of IMRT compared to 3DCRT.
Sanctis A–C: Three Racemic Procyanidin Analogues from The Lichen Parmotrema sancti‐angelii (2018)

The phytochemical investigation of the lichen Parmotrema sancti‐angelii afforded three racemic compounds, sanctis A–C, which feature an original dibenzo‐2,8‐dioxabicyclo[3.3.1]nonane scaffold. These compounds were structurally characterized by extensive NMR spectroscopy analyses, comparison between experimental and theoretical NMR spectroscopic data, and X‐ray crystallography. These metabolites are similar to procyanidin A and display a methyl group instead of a pendant aromatic ring at C‐9, a so far unprecedented structural feature. A biosynthetic route to sanctis A–C is proposed.
Determining influences of different stirring methods for encapsulating stearic acid with SiO2 shell for thermal energy storage applications (2022)

ABSTRACT Stearic acid was encapsulated successfully with SiO2 shell in nanoscale by in situ emulsion interfacial hydrolysis and poly-condensation techniques. The influence of using different mixing techniques on these techniques was investigated. Morphologic, thermal and crystal structure analysis results show that the ultrasonic mixing technique is suggested for synthesis of SiO2 nanocapsules. Ultrasonic vibrations lead to more homogeneous covering of the oil droplets without residuals by effectively orienting SiO2 molecules during polymerization.
Panta Rhei benchmark dataset: socio-hydrological data of paired events of floods and droughts (2023)

Abstract. As the adverse impacts of hydrological extremes increase in many regions of the world, a better understanding of the drivers of changes in risk and impacts is essential for effective flood and drought risk management and climate adaptation. However, there is currently a lack of comprehensive, empirical data about the processes, interactions, and feedbacks in complex human–water systems leading to flood and drought impacts. Here we present a benchmark dataset containing socio-hydrological data of paired events, i.e. two floods or two droughts that occurred in the same area. The 45 paired events occurred in 42 different study areas and cover a wide range of socio-economic and hydro-climatic conditions. The dataset is unique in covering both floods and droughts, in the number of cases assessed and in the quantity of socio-hydrological data. The benchmark dataset comprises (1) detailed review-style reports about the events and key processes between the two events of a pair; (2) the key data table containing variables that assess the indicators which characterize management shortcomings, hazard, exposure, vulnerability, and impacts of all events; and (3) a table of the indicators of change that indicate the differences between the first and second event of a pair. The advantages of the dataset are that it enables comparative analyses across all the paired events based on the indicators of change and allows for detailed context- and location-specific assessments based on the extensive data and reports of the individual study areas. The dataset can be used by the scientific community for exploratory data analyses, e.g. focused on causal links between risk management; changes in hazard, exposure and vulnerability; and flood or drought impacts. The data can also be used for the development, calibration, and validation of socio-hydrological models. The dataset is available to the public through the GFZ Data Services (Kreibich et al., 2023, https://doi.org/10.5880/GFZ.4.4.2023.001).
Cluster Boosted Tree Classifier for Multi-View, Multi-Pose Object Detection (2007)

Detection of object of a known class is a fundamental problem of computer vision. The appearance of objects can change greatly due to illumination, view point, and articulation. For object classes with large intra-class variation, some divide-and-conquer strategy is necessary. Tree structured classifier models have been used for multi-view multi- pose object detection in previous work. This paper proposes a boosting based learning method, called Cluster Boosted Tree (CBT), to automatically construct tree structured object detectors. Instead of using predefined intra-class sub- categorization based on domain knowledge, we divide the sample space by unsupervised clustering based on discriminative image features selected by boosting algorithm. The sub-categorization information of the leaf nodes is sent back to refine their ancestors' classification functions. We compare our approach with previous related methods on several public data sets. The results show that our approach outperforms the state-of-the-art methods.
Iron increases the susceptibility of multiple myeloma cells to bortezomib (2012)

Multiple myeloma is a malignant still incurable plasma cell disorder. Pharmacological treatment based on proteasome inhibition has improved patient outcome; however, bortezomib-resistance remains a major clinical problem. Inhibition of proteasome functionality affects cellular iron homeostasis and iron is a potent inducer of reactive oxygen species and cell death, unless safely stored in ferritin. We explored the potential role of iron in bortezomib-resistance. We analyzed iron proteins, oxidative status and cell viability in 7 multiple myeloma cell lines and in plasma cells from 5 patients. Cells were treated with increasing bortezomib concentrations with or without iron supplementation. We reduced ferritin levels by both shRNA technology and by drug-induced iron starvation. Multiple myeloma cell lines are characterized by distinct ferritin levels, which directly correlate with bortezomib resistance. We observed that iron supplementation upon bortezomib promotes protein oxidation and cell death, and that iron toxicity inversely correlates with basal ferritin levels. Bortezomib prevents ferritin upregulation in response to iron, thus limiting the ability to buffer reactive oxygen species. Consequently, reduction of basal ferritin levels increases both bortezomib sensitivity and iron toxicity. In patients' cells, we confirmed that bortezomib prevents ferritin increase, that iron supplementation upon bortezomib increases cell death and that ferritin reduction overcomes bortezomib resistance. Bortezomib affects iron homeostasis, sensitizing cells to oxidative damage. Modulation of iron status is a strategy worth exploring to improve the efficacy of proteasome inhibition therapies.
Analytical Technique for Allocating Production to Subzones to Evaluate Prospect Candidates in the Terminal Zone of Fault Blocks III and IV, Wilmington Field, CA (2005)

Abstract The analytical technique integrated the 3D geologic model, reservoir and production and injection information into a single Project database for a study area that comprised 109 acres in Fault Blocks III and IV in the Wilmington Oil Field, California. The result was the creation of a new reservoir evaluation tool that enables the user to quickly evaluate reservoir performance and potential development well locations. It provided a "snapshot" picture of well production or injection on a subzone basis for any selected time interval without using a simulator. The Project database is flexible because it utilizes whatever well, reservoir characterization, production and geologic information that are available to provide a more robust analysis than typical cumulative production and injection bubble maps. An empirical mathematical algorithm was created to allocate the commingled total well fluid production to subzones. The algorithm allocated subzone production based on: 1) fraction of completed interval open in each subzone; 2) net sand weighted-value; and 3) flow capability (KH) weighted-value. The subzone flow capability (subzone KH) was calculated by multiplying the subzone average core air-permeability by the net sand thickness for each subzone. The allocation algorithm was developed for single fluid flow and not for fractional fluid flow. Fluid flow trends were identified by analysis of the produced oil and water volumes, WORs and water injection volumes tracked over selected time intervals and well completions. Volumetric analysis was used to estimate remaining oil in-place for each subzone and drainage areas. Pseudo oil saturation maps were generated to visually site and evaluate infill waterflood development well prospects. The validity of the allocation algorithm was confirmed by the reasonable agreement found between the measured and predicted percent injection splits. This reservoir evaluation-screening project demonstrated the potential for a field-wide application to identify and prioritize drilling prospects.
Protective Effect of 3-Aminobenzamide, an Inhibitor of Poly (ADP-Ribose) Synthetase, against Laryngeal Injury in Rats (1999)

The effect of 3-aminobenzamide, an inhibitor of poly (ADP-ribose) synthetase activity, was evaluated in a rat model of laryngeal injury induced by endotracheal intubation for 1 h. At 1 h after extubation, the laryngeal damage was characterized by areas of mucosal necrosis, submucosal edema, swelling of subglottic glands, and submucosal infiltration of inflammatory cells. Activity of myeloperoxidase, a marker of neutrophil infiltration, was also markedly increased into the damaged tissue. Immunohistochemistry for nitrotyrosine, an index of nitrosative stress, showed an intense staining in the inflamed larynx. Treatment with 3-aminobenzamide (10 mg/kg intraperitoneally) significantly reduced the appearance of mucosal damage and was associated with a significant reduction of tissue myeloperoxidase activity and nitrotyrosine immunoreactivity in the larynx. The results of this study suggest that poly (ADP-ribose) synthetase may play a role in the inflammatory process after laryngeal intubation and extubation, and administration of 3-aminobenzamide may be a beneficial therapeutic approach.