gebhart/patrepeval huggingface dataset:
Matrix metalloproteinases and inhibitors in cartilage tissue engineering (2011)

Inhibiting matrix metalloproteinase (MMP) activity has been considered as a potential therapeutic treatment that may modify the outcome for osteoarthritis (OA), a disease governed by abnormalities in the balance between MMPs and their inhibitors. Due to unexpected tissue fibrosis in early-phase clinical trials with some MMP inhibitors, possible divergent effects of inhibiting MMP activity on different cells are hypothesized. Therefore, we evaluated the effects of MMP inhibition on cells relevant to cartilage tissue engineering by culturing them in vitro in poly(ethylene glycol) diacrylate hydrogels to create 3D representations of cartilage tissue while allowing for local and direct administration of inhibitors. Mesenchymal stem cells demonstrated an inhibitor concentration-dependent decrease in extracellular matrix (ECM) deposition, while normal chondrocytes were mainly affected at the highest concentration of inhibitors. In contrast, the concomitant treatment of chondrocytes from patients with OA resulted in an increase in glycosaminoglycan content only in the presence of both inhibitors and anabolic growth factors. The observed upregulation of bone markers, however, indicates a delicate balance that must be addressed to therapeutically treat OA chondrocytes to stimulate more ECM production without errant bone formation. In conclusion, this study suggests that MMPs have complex interactions in both pathobiology and homeostasis.
In Vitro and In Vivo Evaluation of Alexa Fluor 680-Bombesin[7–14]NH2 Peptide Conjugate, a High-Affinity Fluorescent Probe with High Selectivity for the Gastrin-Releasing Peptide Receptor (2007)

Gastrin-releasing peptide (GRP) receptors are overexpressed on several types of human cancer cells, including breast, prostate, small cell lung, and pancreatic cancers. Bombesin (BBN), a 14-amino acid peptide that is an analogue of human GRP, binds to GRP receptors with very high affinity and specificity. The aim of this study was to develop a new fluorescent probe based on BBN having high tumor uptake and optimal pharmacokinetics for specific targeting and optical imaging of human breast cancer tissue. In this study, solid-phase peptide synthesis was used to produce H(2)N-glycylglycylglycine-BBN[7-14]NH(2) peptide with the following general sequence: H(2)N-G-G-G-Q-W-A-V-G-H-L-M-(NH(2)). This conjugate was purified by reversed-phase high-performance liquid chromatography and characterized by electrospray-ionization mass spectra. The fluorescent probe Alexa Fluor 680-G-G-G-BBN[7-14]NH(2) conjugate was prepared by reaction of Alexa Fluor 680 succinimidyl ester to H(2)N-G-G-G-BBN[7-14]NH(2) in dimethylformamide (DMF). In vitro competitive binding assays, using (125)I-Tyr(4)-BBN as the radiolabeling gold standard, demonstrated an inhibitory concentration 50% value of 7.7 +/- 1.4 nM in human T-47D breast cancer cells. Confocal fluorescence microscopy images of Alexa Fluor 680-G-G-G-BBN[7-14]NH(2) in human T-47D breast cancer cells indicated specific uptake, internalization, and receptor blocking of the fluorescent bioprobe in vitro. In vivo investigations in SCID mice bearing xenografted T-47D breast cancer lesions demonstrated the ability of this new conjugate to specifically target tumor tissue with high selectivity and affinity.
Hydrogen storage in liquid organic heterocycles (2008)

Hydrogen storage in liquid organic heterocycles is feasible thermodynamically and is attractive in terms of simplicity, safety, scalability, heat management and economy, but extensive catalyst development is needed to bring it to fruition.
A Novel Fuel Performance Index for LTC Engines Based on Operating Envelopes in Light-Duty Driving Cycle Simulations (2014)

Low-temperature combustion (LTC) engine concepts such as homogeneous charge compression ignition (HCCI) offer the potential of improved efficiency and reduced emissions of NOx and particulates. However, engines can only successfully operate in HCCI mode for limited operating ranges that vary depending on the fuel composition. Unfortunately, traditional ratings such as octane number poorly predict the autoignition behavior of fuels in such engine modes, and metrics recently proposed for HCCI engines have areas of improvement when wide ranges of fuels are considered. In this study, a new index for ranking fuel suitability for LTC engines was defined, based on the fraction of potential fuel savings achieved in the FTP-75 light-duty vehicle driving cycle. Driving cycle simulations were performed using a typical light-duty passenger vehicle, providing pairs of engine speed and load points. Separately, single-zone naturally aspirated HCCI engine simulations were performed for a variety of fuels in order to determine the operating envelopes for each. These results were combined to determine the varying improvement in fuel economy offered by fuels, forming the basis for a fuel performance index. Results showed that, in general, lower octane fuels performed better, resulting in higher LTC fuel index values; however, octane number alone did not predict fuel performance.
Comparison of Agar Dilution to Broth Microdilution for Testing In Vitro Activity of Cefiderocol against Gram-Negative Bacilli (2020)

Cefiderocol (CFDC) is a siderophore cephalosporin with activity against Gram-negative bacterial species that are resistant to carbapenems and other drugs. The MICs of CFDC were determined for 610 Gram-negative bacilli, including 302 multinational <i>Enterobacterales</i> isolates with characterized mechanisms of beta-lactam resistance, 180 clinical isolates from the Mayo Clinic and Mayo Clinic Laboratories not characterized for specific resistance mechanisms, and 128 isolates with CFDC MICs of ≥8 μg/ml obtained from International Health Management Associates, Inc. (IHMA, Schaumburg, IL). Broth microdilution using standard cation-adjusted Mueller-Hinton broth (BMD) and iron-depleted cation-adjusted Mueller-Hinton broth (ID-BMD), and agar dilution (AD) using standard Mueller-Hinton agar were performed according to Clinical and Laboratory Standards Institute (CLSI) guidelines. MICs were interpreted according to the investigational CLSI, FDA, and EUCAST breakpoints, and results were compared. MICs inhibiting 50 and 90% of organisms (MIC<sub>50</sub> and MIC<sub>90</sub>, respectively), essential agreement (EA), categorical agreement (CA), and error of different types were determined. Results showed considerable discordance between AD and ID-BMD. CFDC showed low EA and CA rates and high error rates for AD in comparison to ID-BMD. Overall, this study does not support use of standard AD for determining CFDC MICs.
Production of recombinant SERA proteins of Plasmodium falciparum in Escherichia coli by using synthetic genes (1996)

We expressed two regions of the serine repeat antigen (SERA) protein of Plasmodium falciparum in Escherichia coli by synthesizing the genes with a changed codon usage. One of the synthetic gene sequences encodes amino acid residues 17-382 (SE47') and the other encodes amino acid residues 586-802 (SE50A). The products produced by the synthetic gene sequences in E. coli accounted for 15-30% of the total bacterial protein. Antisera against both the purified gene products prepared in rats inhibited malaria parasite growth in vitro. The anti-SE47' serum was significantly more inhibitory than the anti-SE50A serum. The described methods provide a large scale preparation of recombinant antigens for improving and producing malaria vaccine.
Polymorphic Toxins and Their Immunity Proteins: Diversity, Evolution, and Mechanisms of Delivery (2020)

All bacteria must compete for growth niches and other limited environmental resources. These existential battles are waged at several levels, but one common strategy entails the transfer of growth-inhibitory protein toxins between competing cells. These antibacterial effectors are invariably encoded with immunity proteins that protect cells from intoxication by neighboring siblings. Several effector classes have been described, each designed to breach the cell envelope of target bacteria. Although effector architectures and export pathways tend to be clade specific, phylogenetically distant species often deploy closely related toxin domains. Thus, diverse competition systems are linked through a common reservoir of toxin-immunity pairs that is shared via horizontal gene transfer. These toxin-immunity protein pairs are extraordinarily diverse in sequence, and this polymorphism underpins an important mechanism of self/nonself discrimination in bacteria. This review focuses on the structures, functions, and delivery mechanisms of polymorphic toxin effectors that mediate bacterial competition.
Almanacs, Astrology, and the Stationers’ Company (1996)

Abstract Taken as a whole, the Stationers' Company almanacs catered for more than just the cottage-dweller. At least some of the evidence for a predominantly low social level of readership comes from the pen of Charles Knight, in whose interests it was to make such a clear-cut distinction seem possible. By constructing a picture of a newly literate, impressionable workforce corrupted by the ‘trash’ of almanacs, he lent urgency to his own plans to produce a respectable replacement. The potential divisiveness of popular reading for popular audiences was replaced by the mass discourse of an idealized ‘society of the text’, a readership whose utilitarian values would acknowledge the grand narrative of useful knowledge.
Maximum-likelihood estimation for frequency-modulated continuous-wave laser ranging using photon-counting detectors (2013)

We analyze the minimum achievable mean-square error in frequency-modulated continuous-wave range estimation of a single stationary target when photon-counting detectors are employed. Starting from the probability density function for the photon-arrival times in photodetectors with subunity quantum efficiency, dark counts, and dead time, we derive the Cramér-Rao bound and highlight three important asymptotic regimes. We then derive the maximum-likelihood (ML) estimator for arbitrary frequency modulation. Simulation of the ML estimator shows that its performance approaches the standard quantum limit only when the mean received photons are between two thresholds. We provide analytic approximations to these thresholds for linear frequency modulation. We also compare the ML estimator's performance to conventional Fourier transform (FT) frequency estimation, showing that they are equivalent if the reference arm is much stronger than the target return, but that when the reference field is weak the FT estimator is suboptimal by approximately a factor of √2 in root-mean-square error. Finally, we report on a proof-of-concept experiment in which the ML estimator achieves this theoretically predicted improvement over the FT estimator.
The long-term fate of CO 2 in the subsurface: natural analogues for CO 2 storage (2004)

Abstract CO 2 is a common gas in geological systems so that planned storage of CO 2 in the subsurface may do no more than mimic nature. Natural CO 2 has a wide number of sources that can be at least partly identified by carbon stable isotope geochemistry. Three pairs of case studies with different reservoir characteristics and CO 2 contents have been examined to assess the natural impact of adding CO 2 to geological systems. Carbonate minerals partially dissolve when CO 2 is added simply because the CO 2 dissolves in water and forms an acidic solution. Therefore, carbonate minerals in the subsurface are not capable of sequestering secondary CO 2 . The addition of CO 2 to a pure quartz sandstone (or a sandstone in which the supply of reactive aluminosilicate minerals has been exhausted by excess natural CO 2 addition) will have no consequences: the CO 2 will simply saturate the water and then build up as a separate gas phase. The addition of CO 2 to carbonate cemented sandstone without reactive aluminosilicate minerals will induce a degree of carbonate mineral dissolution but no solid phase sequestration of the added CO 2 . When CO 2 is naturally added to sandstones it will induce combined aluminosilicate dissolution and carbonate cementation if the aluminosilicate minerals contain calcium or magnesium (or possibly iron). Examination of a CO 2 -filled porous sandstone with abundant reactive aluminosilicate minerals that received a huge CO 2 charge about 8000 to 100 000 years ago reveals minimal evidence of solid phase sequestration of the added CO 2 . This indicates that either dissolution of reactive aluminosilicates or precipitation of carbonate minerals is relatively slow. It is very likely that the slow dissolution of reactive aluminosilicates is the rate-limiting step. Solid phase sequestration of CO 2 occurs only when reactive aluminosilicates are present in a rock and when the system has had many tens to hundreds of thousands of years to equilibrate. The two critical aspects of the behaviour of CO 2 when injected into the subsurface are (1) that the rock must contain reactive Ca and Mg aluminosilicates and (2) that reaction to produce carbonate minerals is extremely slow on a human timescale. The reactive minerals include anorthite, zeolite, smectite and other Fe- and Mg-clay minerals. Such minerals are absent from clean sandstones and limestones but are present in ‘dirty’ standstones (lithic arenites which are mineralogically immature) and some mudstones. The analysis of geological analogues shows that injection of CO 2 into carbonate-bearing rocks that do not contain reactive minerals will induce dissolution of the carbonate, whether it is a matrix cement, rock fragment, fault seal or part of a top-sealing mudstone.
Diagnostic and therapeutic role of endoscopic ultrasound in children’s pancreaticobiliary disorders (2017)

Background and Objectives: The diagnostic role of endoscopic ultrasound (EUS) in children has been demonstrated only recently. Data on the technique’s therapeutic indications remain scarce. We evaluated diagnostic and interventional EUS indications, safety, and impact in children with pancreaticobiliary disorders. Patients and Methods: We retrospectively reviewed our single pediatric center experience covering a 14-year period. Results: Between January 2000 and 2014, 52 EUS procedures were performed on 48 children (mean age 12 years) with pancreaticobiliary disorders for suspected biliary obstruction (n = 20/52), acute/chronic pancreatitis (n = 20), pancreatic mass (n = 3), pancreatic blunt trauma (n = 7), and ampullary adenoma (n = 2). Positive impact of EUS was observed in 51/52 procedures (98%), precluding using endoscopic retrograde cholangiopancreatography (ERCP) (n = 9), focusing on endotherapy (n = 21), or reorienting therapy toward surgery (n = 7). EUS-guided fine needle aspiration was carried out on 12 patients. Thirteen therapeutic EUS procedures were conducted, nine of which were combined EUS-ERCP procedures (three EUS-guided pseudocyst drainage, one EUS-guided transgastric biliary drainage of a metastatic rhabdomyosarcoma). Conclusions: We report on a large pediatric EUS series for diagnostic and therapeutic pancreaticobiliary disorders, showing a significant impact of diagnostic EUS and affording insights into novel EUS and combined EUS-ERCP therapeutic applications. We suggest considering EUS as a diagnostic and therapeutic tool in the management of pediatric biliopancreatic diseases.
The growth of malignant and nonmalignant human cells is modulated by a human placental extract. (1999)

Our data seem to suggest that in FD both stimulating and inhibitory growth-factors coexist, the activity of which are greatly influenced by the culture conditions used.
Indoor Emissions as a Primary Source of Airborne Allergenic Fungal Particles in Classrooms (2015)

This study quantifies the influence of ventilation and indoor emissions on concentrations and particle sizes of airborne indoor allergenic fungal taxa and further examines geographical variability, each of which may affect personal exposures to allergenic fungi. Quantitative PCR and multiplexed DNA sequencing were employed to count and identify allergenic fungal aerosol particles indoors and outdoors in seven school classrooms in four different countries. Quantitative diversity analysis was combined with building characterization and mass balance modeling to apportion source contributions of indoor allergenic airborne fungal particles. Mass balance calculations indicate that 70% of indoor fungal aerosol particles and 80% of airborne allergenic fungal taxa were associated with indoor emissions; on average, 81% of allergenic fungi from indoor sources originated from occupant-generated emissions. Principal coordinate analysis revealed geographical variations in fungal communities among sites in China, Europe, and North America (p < 0.05, analysis of similarity), demonstrating that geography may also affect personal exposures to allergenic fungi. Indoor emissions including those released with occupancy contribute more substantially to allergenic fungal exposures in classrooms sampled than do outdoor contributions from ventilation. The results suggest that design and maintenance of buildings to control indoor emissions may enable reduced indoor inhalation exposures to fungal allergens.
Differences between Mean-Field Dynamics andN-Particle Quantum Dynamics as a Signature of Entanglement (2008)

A Bose-Einstein condensate in a tilted double-well potential under the influence of time-periodic potential differences is investigated in the regime where the mean-field (Gross-Pitaevskii) dynamics become chaotic. For some parameters near stable regions, even averaging over several condensate oscillations does not remove the differences between mean-field and N-particle results. While introducing decoherence via piecewise deterministic processes reduces those differences, they are due to the emergence of mesoscopic entangled states in the chaotic regime.
Ipragliflozin improves mitochondrial abnormalities in renal tubules induced by a high‐fat diet (2018)

SGLT2 inhibition might act directly on tubular cells and protect kidney tubular cells from mitochondrial damage by metabolic insults regardless of blood glucose levels or improvement in bodyweight reduction.
Strategies to Maximize Patient Participation in Clinical Trials (2017)

Despite considerable interest and success in oncology drug development, the minority of patients with cancer diagnoses enroll in clinical trials. Multiple obstacles account for this low enrollment rate. An improvement in patient participation in clinical trials could increase patient access to novel and potentially promising agents, provide faster trial results, and, with implementation of rational eligibility criteria, allow for a better understanding of the drug’s safety and efficacy in a heterogeneous population. We present barriers and potential solutions to maximize patient participation, including a review of the ASCO and Friends of Cancer Research (FoCR) Modernizing Eligibility Criteria Project, U.S. Food and Drug Administration (FDA) regulatory considerations, an industry perspective, and a patient perspective.
Cell-Specific Expression of the Human Parathyroid Hormone Gene in Rat Pituitary Cells (1986)

The promoter region of the human parathyroid hormone gene was fused to the Escherichia coli neo gene and introduced into GH4C1 rat pituitary and human HeLa cells. Both TATA boxes of the human parathyroid hormone gene accurately directed transcription in GH4C1 cells; the parathyroid hormone promoter was inactive in HeLa cells.
The Application of Advanced Wellbore Monitoring in Coal Seam Gas for Continuous Inflow Profiling (2014)

Abstract This paper describes the application of down-hole monitoring technologies to a coal seam gas (CSG) field located in the Bowen Basin in Queensland, Australia. The monitoring technology includes both conventional bottom-hole pressure sensing and the newer, fibre optic-based Distributed Temperature Sensing (DTS). As one of the first applications of DTS in a low permeability CSG well we will review the method of installation, data gathered and application of this data for monitoring production from multiple intervals in a single coal seam. The coals in the Bowen Basin region are characteristically of low permeability, and multi-seam hydraulically fractured wells are commonly deployed as a result. All wells require artificial lift; as a result, water is produced up the tubing string, generally with the assistance of a Progressing Cavity Pump (PCP), whilst gas flows up the annulus. Whilst this is an economic method of evaluating the performance of multiple formations simultaneously, the key limitation of this practice for appraisal purposes is that only total, commingled production for each phase is measured at surface. Given the requirement for artificial lift, production logging techniques are currently unavailable to assist in this multi-seam production allocation, meaning that typically, a reservoir simulation history-matching process is required to estimate the relative performance of individual formations based upon regional trends derived from core measurements or static well logs, often with little justification to adjust parameters outside certain ranges. Any unexpected changes in these reservoir parameters (gas content, permeability, etc.) or completion properties (perforation / stimulation effectiveness) between layers can give rise to dramatic differences in production contribution, which may impact the assessment of which formations (or collection thereof) are prospective targets for further development. DTS allows the measurement of a continuous flow profile during desorption and subsequent production. This allows for better understanding of any such heterogeneity between production intervals, and an improved understanding of the reasons for production variation both at start-up and over time. This paper will present DTS data acquired over the initial stages of the well life and show how the thermal behaviour changes over time with production. We will discuss how the thermal profile is related to the well production rate, and describe some of the complexity involved in the inversion process when converting a thermal profile to a production profile. This inversion is especially complex as a typical CSG well is completed with artificial lift and has flow in both the tubing and annulus. This creates separate, but coupled, thermal responses in the tubing and annulus. The well performance and thermal behaviour also depends on the liquid level in the annulus, which is itself controlled by the rate of the PCP.
Matrices de microgouttes pour l’analyse de globules rouges uniques (2012)

La micro-fluidique a le potentiel pour révolutionner la pratique des sciences de la santé à travers la miniaturisation et l’intégration des briques élémentaires des laboratoires de biologie. Ces nouvelles technologies, en cours de développement, permettront d’intégrer sur une puce unique des opérations qui nécessitent actuellement des robots, des instruments de mesure coûteux, en plus des heures de travail pour le personnel de laboratoire. On parle donc de Laboratoires sur puce, ou « Lab on a chip » en anglais, qui visent à automatiser et à standardiser les opérations du laboratoire de biologie.