gebhart/patrepeval huggingface dataset:
Evaluation of a Universal Real-Time Polymerase Chain Reaction for Detection of Amniotic Fluid Infection in Premature Rupture of Membranes (2011)

Managing preterm rupture of membranes (PPROM) is a balance between benefits of prolonging gestation and the risks of perinatal infection. This study evaluates a real-time polymerase chain reaction (PCR) for the detection of amniotic fluid infection and neonatal complications by amniocentesis following PPROM. A total of 61 singleton pregnancies with PPROM were analyzed retrospectively, including histopathologic examination of the placenta and neonatal complications. The real-time PCR detects a highly conserved sequence of the bacterial 16S ribosomal DNA, and its efficacy was compared with standard tests including amniotic fluid glucose concentration, lactate dehydrogenase level, and maternal white cells count and C-reactive protein levels. Sensitivity and specificity were similar for PCR (64% and 85%) and standard tests (58% and 80%). However, the PCR technique has the additional advantage of possible identification of the bacteria through sequencing and has a much better positive predictive value in the occurrence of neonatal complications (60% for PCR versus 35% for standard tests). The latency period between premature rupture of the membranes and delivery was not related to the incidence of histopathologic signs of infection in the placenta or the umbilical cord and was inversely related to the incidence of neonatal complications.
Pneumatic conveyor dynamic models for a pulverized coal plant (2012)

This article describes new advanced non-linear dynamic models for pulverized coal injection (PCI) plant into blast furnaces. A complete new approach for modelling is developed for the actual state-of-art PCI injection station. These models take into account all the physical dynamic laws and pneumatic conveyor variables allied to a modern updated digital control system (DCS). The models were constructed to operate in real time for the same DCS that controls the industrial PCI plant. Process validations include pressure and modern mass flow meter specially designed to check the models. New verification variables allowed by these equipments shows the functionality of the dynamic model-based, thermal, pressure profile and the particle velocity models. The models can be used mainly to improve coal flow stability control by means of modern control strategies and to prevent clogging lance caused by low coal particle speed and high solid to gas ratio.
How retrotransposons shape genome regulation (2016)

Retrotransposons are mutagenic units able to move within the genome. Despite many defenses deployed by the host to suppress potentially harmful activities of retrotransposons, these genetic units have found ways to meld with normal cellular functions through processes of exaptation and domestication. The same host mechanisms targeting transposon mobility allow for expansion and rewiring of gene regulatory networks on an evolutionary time scale. Recent works demonstrating retrotransposon activity during development, cell differentiation and neurogenesis shed new light on unexpected activities of transposable elements. Moreover, new technological advances illuminated subtler nuances of the complex relationship between retrotransposons and the host genome, clarifying the role of retroelements in evolution, development and impact on human disease.
Transmissive concentrator multijunction solar cells with over 47% in-band power conversion efficiency (2016)

Transmissive concentrator multijunction (TCMJ) solar cells with over 47% in-band power conversion efficiency (PCE) have been designed and realized. These TCMJ solar cells have been characterized under 1 sun and concentrated 500 sun solar spectra, showing that the PCE for in-band light (photon energies above the cell's lowest bandgap) can reach up to 47.6% (29.5% for the full solar spectrum). Temperature coefficients of electrical parameters (Voc, Jsc, fill factor) have been derived from measurements within the temperature range of 20 °C–130 °C, showing linear variations versus temperature change. Optical measurements demonstrate that the cells show 76.5% solar-weighted optical transmission for the out-of-band light (photon energy below the cell's lowest bandgap). This TCMJ solar cell exhibits promising spectrum splitting capability, which has the potential for use in hybrid photovoltaic-solar thermal applications.
Use of Antisense Oligonucleotides in Functional Genomics and Target Validation (2004)

With the completion of sequencing of the human genome, a great deal of interest has been shifted toward functional genomics-based research for identification of novel drug targets for treatment of various diseases. The major challenge facing the pharmaceutical industry is to identify disease-causing genes and elucidate additional roles for genes of known functions. Gene functionalization and target validation are probably the most important steps involved in identifying novel potential drug targets. This review focuses on recent advances in antisense technology and its use for rapid identification and validation of new drug targets. The significance and applicability of this technology as a beginning of the drug discovery process are underscored by relevant cell culture-based assays and positive correlation in specific animal disease models. Some of the antisense inhibitors used to validate gene targets are themselves being developed as drugs. The current clinical trials based on such leads that were identified in a very short time further substantiate the importance of antisense technology-based functional genomics as an integral part of target validation and drug target identification.
The feasibility of using thermal strain imaging to regulate energy delivery during intracardiac radio-frequency ablation (2011)

A method is introduced to monitor cardiac ablative therapy by examining slope changes in the thermal strain curve caused by speed of sound variations with temperature. The sound speed of water-bearing tissue such as cardiac muscle increases with temperature. However, at temperatures above about 50°C, there is no further increase in the sound speed and the temperature coefficient may become slightly negative. For ablation therapy, an irreversible injury to tissue and a complete heart block occurs in the range of 48 to 50°C for a short period in accordance with the well-known Arrhenius equation. Using these two properties, we propose a potential tool to detect the moment when tissue damage occurs by using the reduced slope in the thermal strain curve as a function of heating time. We have illustrated the feasibility of this method initially using porcine myocardium in vitro. The method was further demonstrated in vivo, using a specially equipped ablation tip and an 11-MHz microlinear intracardiac echocardiography (ICE) array mounted on the tip of a catheter. The thermal strain curves showed a plateau, strongly suggesting that the temperature reached at least 50°C.
Allogeneic NK Cell Therapy After Autologous Stem Cell Transplant: Results of a Phase I Study (2010)

Abstract Abstract 4299 Previous reports have shown that infusion of NK cells from a MHC mismatched donor can mediate an anti-leukemic effect in the recipient of an allogeneic hematopoietic stem cell transplant (HSCT). In this phase I study, we infused increasing numbers of allogeneic NK-cell enriched mononuclear cells (NK-MNC) from a MHC haplo-mismatched relative into patients who had recently undergone autologous stem cell transplant. We sought to determine whether infusion of mismatched, allogeneic NK-MNC cells was safe without concern for GvHD or graft rejection, and also whether cell collection, processing and patient treatment could feasibly be performed at different cities across the US. MNC were obtained by apheresis from healthy haploidentical relatives by one steady-state leukapheresis of 2–4 hours on day 1, and were sent by air courier to the PACT* cell processing facility (University of Minnesota) where immunomagnetic depletion of CD3 cells (Miltenyi CliniMACS) was performed. The CD3-depleted cells were then cultured in X-VIVO 15, without gentamicin and phenol red (Cambrex BioScience, Walkersville, Maryland), supplemented with 1000 U/mL IL-2 (Chiron Corporation, Emeryville, CA) and 10% human heat-inactivated AB serum (Valley Biomedical Products and Services, Inc., Winchester, VA) in VueLife™Teflon® (FEP) bags (American Fluoroseal Corporation, Gaithersburg, MD). The resulting NK-MNC products were then returned by air courier at approximately body temperature to Boston for infusion on day 3. Twelve patients (age range: 27–63) within 49–191 days (median 106 days) after autologous HSCT were treated at four different dose levels of NK-MNC: 105, 106, 107 and 2×107 NK-MNC/kg. No logistical transport issues between Boston and the processing facility in Minnesota occurred. Release criteria (&lt; 5 × 105 CD3+ cells/kg, &gt; 20% CD3-/CD56+ cells, viability &gt;70%, Gram stain – no organisms) were met in all but one case. Side effects after infusion occurred only at the higher dose level of NK-MNC infusion: rigors (n=2) and muscle aches (n=1), responsive to meperidine. None of the patients required discontinuation of NK-MNC infusion. No GvHD or marrow suppression occurred. Chimerism analysis (STR-PCR) from leukocytes on peripheral blood samples collected 24 hours after the NK-MSC infusion failed to detect donor-derived NK-MNC in the recipients (sensitivity: 3 %). Given these results, we conclude that long-distance transport of manipulated NK-MNC products between treatment and processing centers is feasible and reliable, clearly supporting the premise of PACT, and that CD3-depleted allogeneic NK-MNC from a MHC-mismatched relative can be safely administered to recipients of a recent autologous HSCT. This project has been funded in part by the National Heart, Lung, and Blood Institute, National Institutes of Health, under the University of Minnesota Contract [] N01-HB-37164 and HHSN268201000008C *PACT: Production Assistance for Cellular Therapies Disclosures: No relevant conflicts of interest to declare.
Corrosion Characterization of Resistance Spot Welded Aluminum and Steel Couple (2019)

Abstract The corrosion resistance of resistance spot welded (RSW) Al-steel couples of varying combinations of 6016-T4 aluminum alloys and steel substrates, including with and without adhesive at the faying interface has been successfully evaluated, and compared to corresponding self-pierce riveted (SPR) couples. The corrosion resistance of resistance spot welded Al-steel couples has performed well in cyclic corrosion testing (GMW 17026) and the results are comparable to or better than that of self-pierce riveted couples. SPR couples are more susceptible to galvanic corrosion than resistance spot-welded couples based upon experimentally measured electrochemical potentials from actual joints. The presence of adhesive acts significantly to reduce galvanic corrosion between aluminum alloy and steel substrates, and moreover tensile lap-shear strength significantly increased with structural adhesive for both RSW and SPR joining systems. However, despite the presence of adhesive the lap-shear strength was reduced by more than 50% after cyclic corrosion testing to strength levels comparable to the lap-shear strength of couples having no adhesive and tested in ambient conditions.
The Effect of Initial State Estimates on Just-in-Time Adaptive Disturbanc Estimation (2014)

Run-to-Run control algorithms for high-mix semiconductor processes typically require that the initial product state estimates have sufficient accuracy for satisfactory control. In this paper, we use historical process data and apply single observation just-in-time adaptive disturbance estimation (JADE) to find the initial product state estimates. Single observation JADE with random selection, high-frequency sampling, and exclusion of the earliest data from the average is shown to provide satisfactory initial product state estimates. The effect of initial state estimate accuracy is demonstrated by several simulation and industrial data examples. We also provide a method to estimate relative confidence between individual product state estimates, information that may be used to determine assignment of process error between the tool and product state.
Commensal bacteria weaken the intestinal barrier by suppressing epithelial neuropilin-1 and Hedgehog signaling (2023)

The gut microbiota influences intestinal barrier integrity through mechanisms that are incompletely understood. Here we show that the commensal microbiota weakens the intestinal barrier by suppressing epithelial neuropilin-1 (NRP1) and Hedgehog (Hh) signaling. Microbial colonization of germ-free mice dampens signaling of the intestinal Hh pathway through epithelial Toll-like receptor (TLR)-2, resulting in decreased epithelial NRP1 protein levels. Following activation via TLR2/TLR6, epithelial NRP1, a positive-feedback regulator of Hh signaling, is lysosomally degraded. Conversely, elevated epithelial NRP1 levels in germ-free mice are associated with a strengthened gut barrier. Functionally, intestinal epithelial cell-specific Nrp1 deficiency (Nrp1<sup>ΔIEC</sup>) results in decreased Hh pathway activity and a weakened gut barrier. In addition, Nrp1<sup>ΔIEC</sup> mice have a reduced density of capillary networks in their small intestinal villus structures. Collectively, our results reveal a role for the commensal microbiota and epithelial NRP1 signaling in the regulation of intestinal barrier function through postnatal control of Hh signaling.
Development of an in vitro model of dysbiotic colonic conditions of IBS-D patients (2021)

Session 3: New approaches to study the gut microbiome : Communications P 127
TATA-binding protein activates transcription when upstream of a GCN4-binding site in a novel yeast promoter. (1992)

In the gal-his3 hybrid promoter, his3-GG1, GCN4 stimulates transcription at the position normally occupied by a TATA element. This expression requires two elements within gal1-10 sequences, a REB1-binding site and a second element, Z, which resides 20 base pairs upstream of the GCN4-binding site. No obvious TATA element is present in this promoter. To characterize the function of Z, we replaced it with short random oligonucleotides and selected for expression in vivo. Fourteen elements were identified and classified into groups based upon sequence and phenotypic similarities. Group 1 elements contained functional TATA sequences that were essential for activity. TATA elements can thus function when positioned upstream of a GCN4-binding site. The Group 2 elements activated transcription poorly when used as conventional TATA elements; however, mutational analyses demonstrated that their activity required TATA-like sequences. These TATA-like sequences bound the yeast TATA-binding protein (TBP) poorly in vitro but function in vivo as TBP interaction sites based upon two criteria. First mutations that improved their TATA character correspondingly improved function and second their activity could be enhanced in the presence of an altered binding specificity mutant of TBP. Furthermore, the Group 2 elements enabled the identification of mutations outside of the TATA-like core that contribute to transcriptional activation without adversely affecting TBP binding. The finding that low affinity TBP-binding sites can be used at unconventional positions suggests that many "TATA-less" promoters contain a cryptic interaction site for TBP.
On-line implementation of nonlinear parameter estimation for the Space Shuttle main engine (1992)

We investigate the performance of a nonlinear estimation scheme applied to the estimation of several parameters in a performance model of the Space Shuttle Main Engine. The nonlinear estimator is based upon the extended Kalman filter which has been augmented to provide estimates of several key performance variables. The estimated parameters are directly related to the efficiency of both the low pressure and high pressure fuel turbopumps. Decreases in the parameter estimates may be interpreted as degradations in turbine and/or pump efficiencies which can be useful measures for an online health monitoring algorithm. This paper extends previous work which has focused on off-line parameter estimation by investigating the filter's on-line potential from a computational standpoint. ln addition, we examine the robustness of the algorithm to unmodeled dynamics. The filter uses a reduced-order model of the engine that includes only fuel-side dynamics. The on-line results produced during this study are comparable to off-line results generated previously. The results show that the parameter estimates are sensitive to dynamics not included in the filter model. Off-line results using an extended Kalman filter with a full order engine model to address the robustness problems of the reduced-order model are also presented.
Review of Hemoglobin-Induced Myocardial Lesions (2004)

Over 100 preclinical studies in several small and large animal species were performed to evaluate the safety and efficacy of diaspirin cross-linked hemoglobin (DCLHb; Baxter Healthcare Corp.) as an oxygen therapeutic. During the preclinical evaluation of DCLHb, myocardial lesions were observed following the administration of DCLHb to certain species. These lesions were characterized as minimal to moderate, focal-to-multifocal myocardial degeneration and/or necrosis that were scored using a severity scale of minimal to marked in relative severity. The lesions were typically observed 24-48 h after single topload infusions of DCLHb into rhesus monkeys or pigs at doses as low as 200 or 700 mg/kg, respectively. Dogs, sheep, and rats did not develop these lesions after single-dose administrations of DCLHb. The left ventricular myocardium, typically near the base of or including the papillary muscles, was the most severely affected region, followed by the intraventricular septum and the right ventricle. The left and right atria were usually not affected. In a study in rhesus monkeys, morphometric analysis revealed that these lesions comprised less than 3% of the total myocardium. Although increases in serum enzyme activities (AST, CK, LDH) were observed after infusion of DCLHb, myocardial-related isoenzymes did not increase. ECG analysis and echocardiography were not altered by these lesions, and there was no observable adverse effect on myocardial function. Polymerization of DCLHb reduced, but did not eliminate, the incidence and severity of the lesions. However, infusion of hemoglobin solutions with reduced reaction rates with nitric oxide (NO) resulted in a significant decrease in lesion incidence and severity, while administration of L-NAME, an NO synthase inhibitor, resulted in the appearance of lesions that were indistinguishable from those induced by hemoglobin, suggesting that reduction in normal NO levels is an important mechanistic factor. Overall, the presence of myocardial lesions represents a histopathologic finding that must be considered during the preclinical testing and development of new HBOCs.
Pharmacological characterization of repeated administration of the first generation abused synthetic cannabinoid CP47,497 (2016)

A series of in vivo and in vitro assays were conducted to characterize the pharmacological effects of the first generation abused synthetic cannabinoid CP47,497, a racemic bicyclic cannabinoid that is similar in structure to the potent, high-efficacy synthetic cannabinoid CP55,940. CP47,497 was less efficacious than CP55,940 in activating G-proteins and dose-dependently produced common CB1 receptor-dependent pharmacological effects (i.e. catalepsy, hypothermia, antinociception, and hypolocomotion). CP47,497 also substituted for Δ9-tetrahydrocannabinol (THC) in the mouse drug discrimination, indicating that both drugs elicited a similar interceptive stimulus. The pharmacological effects of CP47,497 underwent tolerance following repeated administration and showed cross-tolerance following repeated THC administration, further suggesting a common cannabimimetic mechanism of action. Finally, the CB1 receptor antagonist rimonabant precipitated similar magnitudes of somatic withdrawal responses in mice treated repeatedly with THC or CP47,497. Taken together, these data verify the acute cannabimimetic effects of CP47,497, and indicate tolerance and dependence following repeated administration. The assays used here provide a straightforward approach to characterize the emerging next generation of abused synthetic cannabinoids.
Development of a bioartificial pancreas: I. Long‐term propagation and basal and induced secretion from entrapped βTC3 cell cultures (1999)

Bioartificial pancreatic constructs based on immunoisolated, insulin-secreting cells have the potential for providing effective, long-term treatment of type I (insulin-dependent) diabetes. Use of insulinoma cells, which can be amplified in culture, relaxes the tissue availability limitation that exists with normal pancreatic islet transplantations. We have adopted mouse insulinoma βTC3 cells entrapped in calcium alginate/poly-L-lysine/alginate (APA) beads as our model system for a bioartificial pancreas, and we have characterized the effects of long-term propagation and of glucose concentration step changes on the bioenergetic status and on the metabolic and secretory activities of the entrapped cells. Cell bioenergetics were evaluated nonivasively by phosphorus-31 nuclear magnetic resonance (31P NMR) spectroscopy, and metabolic and secretory parameters by assaying cell culture medium. Data indicate that net cell growth occurred between days 3 and 10 of the experiment, resulting in an approximate doubling of the overall metabolic and secretory rates and of the intracellular metabolite levels. Concurrently, a reorganization of cell distribution within the beads was observed. Following this growth period, the measured metabolic and secretory parameters remained constant with time. During glucose step changes in the perfusion medium from a high concentration of 12 to 15 mM to 0 mM for 4.5 h to the same high glucose concentration, the oxygen consumption rate was not affected, whereas insulin secretion was always glucose-responsive. Intracellular nucleotide triphosphates did not change during 0 mM glucose episodes performed early in culture history, but they declined by 20% during episodes performed later in the experiment. It is concluded that the system of APA-entrapped βTC3 cells exhibits several of the desirable characteristics of a bioartificial pancreas device, and that a correlation between ATP and the rate of insulin secretion from βTC3 cells exists for only a domain of culture conditions. These findings have significant implications in tissue engineering a long-term functional bioartificial endocrine pancreas, in developing noninvasive methods for assessing construct function postimplantation, and in the biochemical processes associated with insulin secretion. © 1999 John Wiley & Sons, Inc. Biotechnol Bioeng 66: 219–230, 1999.
Journal Club: Depression before and after diagnosis with amyotrophic lateral sclerosis (2016)

The prevalence of depression among individuals with amyotrophic lateral sclerosis (ALS) is reported to be up to 44%, depending on the assessment methodology.1 Depression negatively affects quality of life in ALS, and psychological stress is related to poorer survival among individuals with ALS.2