gebhart/patrepeval huggingface dataset:
Adaptive bolus-based targeted glucose regulation of hyperglycaemia in critical care (2004)

Tight regulation of blood glucose can significantly reduce mortality in critical illness. Critically ill patients are extremely diverse in the dynamics of their hyperglycaemia. Hence, responses can vary significantly, due to variations in insulin levels, effective insulin utilization, glucose absorption and other factors. Consequently, fixed protocols and sliding scales can result in error, given this large variation in patient dynamics. A two-compartment glucose-insulin system model that accounts for time-varying insulin sensitivity and endogenous glucose removal, along with two different saturation kinetics, is developed and tested in preliminary proof-of-concept clinical trials for adaptive control of blood glucose levels. The adaptive control algorithm developed in this research monitors the physiological status of a critically ill patient, allowing real-time, tight glycaemic regulation. The bolus-based insulin administration provides a safe approach to glucose level management. The ability to track changing physiological status and account for insulin transport and effect saturation enabled targeted stepwise reduction in glycaemic levels in three test cases.
Pathophysiology of Acetam inophen Overdosage Toxicity: Implications for Management (1978)

Acute acetaminophen intoxication was studied in the dog to characterize pathogenesis and in the mouse as a model for antidotal research. In the dog, overt toxicity was manifested principally by cyanosis, facial and paw edema, gastrointestinal disturbance, and coma. Typical laboratory findings were methemoglobinemia, hemoconcentration, leukocytosis, and hepatic centrolobular necrosis. In the mouse, physical signs of acetaminophen overdose appeared to be central in origin; sequelae included anemia, leukopenia, thrombocytopenia, and hepatic centrolobular necrosis. The antidotal profile of acetylcysteine in mice was characterized. When acetylcysteine therapy was instituted early (one hour after acetaminophen overdose), it conferred dose-related protection from lethality coupled with hepatoprotection, as judged from transaminase activity. When acetylcysteine therapy was instituted relatively late (4 1/2 hours after acetaminophen overdose), its beneficial effect on survival persisted but was unaccompanied by distinct hepatoprotection, indicating that SGPT activity was an unreliable prognostic indicator. Acetylcysteine was well tolerated in mice even when administered in the presence of preexisting acetaminophen-induced liver damage.
RNA-seq analysis of glucose fermentation by the natural Isopropanol producer Clostridium beijerinckii DSM6423 (2018)

Purpose: C. beijerinckii DSM 6423 is the most cited natural IpOH producer. Improving the natural production of this strain through a targeted approach required a full sequencing and characterization of its genome, together with transcriptomic analyses of its own regulations.The goals of this study are then to evaluate the transcriptional profile (RNA-Seq) of C. beijerinckii DSM6423, a natural isopropanol producer, during a fermentation of glucose in controlled bioreactors. Methods: A RNA-Seq approach was chosen in order to have a timelapse study of DSM 6423 throughout the fermentation process. Three independent duplicate fermentations of DSM 6423 were carried out in bioreactors on three different weeks, showing good reproducibility. On each cultivation, five biomass samples were collected for RNA-Seq analyses.and DNA was eliminated after DNAse I treatment (AM1906, Invitrogen). The 15 resulting RNA samples were sequenced and analyzed using the previously reconstructed genome of DSM 6423. Results: Using a data analysis workflow (TAMARA) developed by the Genoscope platform of Evry, we were able to highlight the transcriptional regulation along the fermentation by calculating the transcription profiles of each gene, using the 3h sample as reference. Clustering was performed using CAST algorithm revealed 8 clusters containing 953 genes and corresponding to genes up-regulated at 6, 8, 11 or 24 hours and gene down-regulated at 6, 8, 11 or 24 hours. Conclusion: Such analyses were carried out in this study and provide useful data to better understand the genetic background and the physiological specificities of C. beijerinckii DSM6423 isopropanol producer. Notably, this work is the first omic study of a natural IBE producer. The data gathered needs time for proper exploitation, but a better understanding of the metabolic pathways and various genes involved opens the door for future targeted approaches.
Methods and devices for measuring arterial stiffness in humans (2008)

Atherosclerosis and arteriosclerosis are the common pathologic causes of such cardiovascular diseases as myocardial infarction,cerebral apoplexy,and so on.Early detecting the changes of artery's malfunction and proper treatment can effectively help to prevent those mortal diseases or slow down the its procedure.This review analyses currently used methods and devices evaluating the arterial stiffness.Three main methods and instruments which based upon analysis of pulse transit time,wave contour of the arterial pulse,and direct measurement of arterial geometry and pressure,which correspond to the evaluation of regional,local and systemic stiffness of body region are discussed.They are used in clinical laboratory and/or in clinical treatment particular attention is given to the reproducibility of each device.

Key words: 
Arterial stiffness; Measurement; Device
Neuropathology and immune biomarker discovery in a rat model of Alzheimer's disease, TgF344‐AD, with controlled cortical injury model of traumatic brain injury (2020)

Abstract Background Individuals with a history of traumatic brain injury (TBI) have a higher risk of developing Alzheimer’s disease (AD) and AD‐related dementias (ADRD), such as chronic traumatic encephalopathy (CTE). However, the relationship(s) between TBI, AD, and CTE remain poorly understood and markedly understudied. Because transgenic mouse models of AD that develop amyloidosis do not readily develop pathological tauopathy that is commonly found in ADRD, we used the TgF344‐AD transgenic rat model of AD in which amyloid deposition drives endogenous tauopathy and neurodegeneration for our TBI studies. Method We used the closed‐head controlled cortical impact (CCI) model of TBI, performed either once (1X‐CCI) or twice over two weeks (2X‐CCI) in both 6‐ and 12‐month‐old TgF344‐AD and wild‐type (F344) rats to investigate the effects of TBI on acute and chronic neuroinflammation, on blood brain barrier (BBB) integrity, and on ADRD‐associated neuropathology. Whole brains and terminal blood draws were collected at different time points following the 1X‐ or 2X‐CCI TBI procedures at 3, 15, 30, 60, and 120 days after the final CCI procedure. Thus, the tissue collection ages of animals across the project allow for TBI‐induced ADRD‐related pathological analyses at 6, 7, 8, 10, 12, 13, 14, and 16 months of age. MRI scans were conducted at 30‐days post‐CCI to examine BBB leakage and chronic inflammation, with subsequent post‐mortem histochemical confirmation. Terminal blood draw samples were used for complete blood cell counts with differential and multiple biomarker analyses. Result This project is ongoing, but interim analyses reveal chronic neutrophil percentages remaining consistent in both TgF344‐AD and wild‐type 12‐month‐old cohorts undergoing either 1X‐ or 2X‐CCI at all post‐injury time points. Also, the upright time for the animals does not appear to differ based on impact type or genotype so far. However, histochemical pathological analyses of the 12‐month‐old AD rats have demonstrated changes in Aβ pathology and astrogliosis markers. MRI analyses have not yet been completed. Conclusion We are continuing to carry out detailed analyses of changes in ADRD‐related pathology and blood biomarkers. These animal models should help provide an increased understanding of chronic neuroinflammation and other pathological mechanisms associated with TBI and risk for ADRD.
Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IκBα through a phosphoenzyme intermediate (2023)

Rapid and high-fidelity phosphorylation of serine residues at positions 32 and 36 of IκBα by IKK2, a prototypical Ser/Thr kinase, is critical for canonical NF-κB activation. Here, we report that IKK2 not only phosphorylates substrate serine residues and autophosphorylates its own activation loop, but also autophosphorylates at a tyrosine residue proximal to the active site and is, therefore, a dual-specificity kinase. We observed that mutation of Y169, an autophosphorylatable tyrosine located at the DFG+1 (DLG in IKK1) position, to phenylalanine renders IKK2 incapable of catalyzing phosphorylation at S32 within its IκBα substrate. We also observed that mutation of the phylogenetically conserved ATP-contacting residue K44 in IKK2 to methionine converts IKK2 to an enzyme that no longer catalyzes specific phosphorylation of IκBα at S32 or S36, but rather directs phosphorylation of IκBα at other residues. Lastly, we report evidence of a phospho-relay from autophosphorylated IKK2 to IκBα in the presence of ADP. These observations suggest an unusual evolution of IKK2, in which autophosphorylation of tyrosine(s) in the activation loop, and the conserved ATP-contacting K44 residue provide its signal-responsive substrate specificity and ensure fidelity during NF-κB activation.
Solubility prediction, solvate and cocrystal screening as tools for rational crystal engineering (2015)

COSMO-RS theory can be applied to a range of physico-chemical properties, which are of interest in rational crystal engineering. Most notably, in combination with experimental reference data, accurate quantitative solubility predictions in any solvent or solvent mixture are possible. Additionally, COSMO-RS can be extended to the prediction of cocrystal formation, which results in considerable predictive accuracy concerning coformer screening. In a recent variant costly quantum chemical calculations are avoided resulting in a significant speed-up and ease-of-use.
Preparation of Polypyrrole/Polymer Electrolyte Composites with Concentration Gradient of Polypyrrole as Cathode/Electrolyte Material for Lithium Secondary Battery (1999)

Polypyrrole/ion-conducting polymer electrolyte composites are prepared by in situ electro-polymerization of pyrrole in polymer electrolyte matrix. The existence of the concentration gradient of PPy is characterized at the PPy/polymer electrolyte interface and this concentration gradient leads to the facile electron transfer due to the fast counterion-transport across the interface.
Partitioning and First Flush of Metals in Urban Roadway Storm Water (1997)

Storm water runoff from urban roadways often contains significant quantities of metal elements and solids. These anthropogenic constituents are generated mainly from traffic-related activities. Metal elements partition into dissolved and particulate-bound fractions as a function of pH, pavement residence time, and solids concentration. Lateral pavement sheet flow from an experimental field site on a heavily traveled urban highway in Cincinnati was sampled during five rainfall runoff events in 1995. Results indicate that Zn, Cd, and Cu are mainly in dissolved form while Pb, Fe, and Al are mainly particulate-bound. Dissolved fractions of Zn, Cd, and Cu exhibited a strong first flush in lateral pavement sheet flow. Pb exhibited a weak first flush for all events. Event mean concentrations of Zn, Cd, and Cu exceed surface water quality discharge standards. Findings from this study will assist in the development of effective control strategies for the immobilization of metal elements and solids in urban runoff.
Observation and simulation of motion and deformation for impact-loaded metal cylinders (2017)

Complementary gas-gun experiments and computational simulations have examined the time-resolved motion and post-mortem deformation of cylindrical metal samples subjected to impact loading. The effect of propagation distance on a compressive waveform generated in a sample by planar impact at one end was determined using a velocity interferometer to track the longitudinal motion at the center of the opposing rear (i.e., free) surface. Samples (25.4-mm diameter) were fabricated from aluminum (types 6061 and 7075), copper (OFHC = oxygen free, high conductivity), stainless steel (type 316), and cobalt alloy L-605 (AMS 5759; also referenced as Haynes®25 alloy). For each material, waveforms obtained for a 25.4-mm long cylinder corresponded to two-dimensional strain at the measurement point. The wave-profile data have been analyzed to (i) establish key dynamic material modeling parameters, (ii) assess the functionality of the Sierra Solid Mechanics-Presto (Sierra/SM) code, and (iii) identify the need for additional testing, material modeling, and/or code development. The results of subsequent simulations have been compared to benchmark recovery experiments that showed the residual plastic deformation incurred by cylinders following end, side, and corner impacts.
Low efficacy of a Bacillus thuringiensis (Berl.) formulation in Controlling the diamondback moth, Plutella xylostella (L.), in the Philippines (1988)

Abstract Neem ( Azadirachta indica ) seed kernel extracts were evaluated in cabbage fields in the Philippines for their ability to control the diamondback moth, Plutella xylostella (L.). The extracts were compared to synthetic insecticides and a Bacillus thuringiensis (Berl.) formulation ( thuricide hp ). The B.t . treatments (1 kg prod./ha) showed low efficacy in controlling P. xylostella . The assumption that this was due to higher UV‐radiation in the trial area could not be confirmed in a corresponding field experiment. Possible development of B.t . resistance in P. xylostella populations is discussed. Zusammenfassung über die geringe Wirksamkeit einer Bacillus thuringiensis (Berl.) Formulierung bei der Bekämpfung von Plutella xylostella auf den Philippinen Extrakte aus Niemsamen ( Azadirachta indica ) wurden In Kohlfeldern auf den Philippinen im Hinblick auf ihre Eignung zur Bekämpfung der Kohlmotte Plutella xylostella (L.) untersucht. Die Extrakte wurden mit synthetischen Insektiziden und einer Bacillus thuringiensis (Berl.)‐ Formulierung ( thuricide hp ) verglichen. Die B.t .‐Behandlungen zeigten einen geringen Bekämpfungseffekt bei P. xylostella . Die Annahme, daß dies auf stärkere UV‐Einstrahlung im Versuchsgebiet zurückzuführen sein könnte, ließ sich in einem entsprechend angelegten Feldversuch nicht bestätigen. Die mögliche Resistenzentwicklung gegen B.t . bei P. xylostella wird diskutiert.
Quantum computation by coupled quantum dot system and controlled NOT operation (1999)

A quantum computer based on an asymmetric coupled dot system has been proposed and shown to operate as the controlled NOT gate. The basic idea is (1) the electron is localized in one of the asymmetric coupled dots. (2)The electron transfer takes place from one dot to the other when the energy-levels of the coupled dots are set close. (3)The Coulomb interaction between the coupled dots mutually affects the energy levels of the other coupled dots. The proposed system can be realized by developing the technology of the single electron memory using Si nanocrystals and the direct combination of the quantum circuit and the conventional circuit is possible.
"Blackfeet Belong to the Mountains": Blackfeet Relationships with the Glacier National Park Landscape and Institution (2008)

National Parks are home to many landscapes of great significance to Native American peoples. The eastern half of Glacier National Park is considered a homeland by the Blackfeet people, and has historically been very important to their material, cultural, and spiritual well-being. This relationship, like those of many other Native peoples, has been severely disrupted by the establishment and presence of the national park, resulting in prolonged conflict between tribes and parks. Blackfeet relationships with this cultural landscape require interaction and engagement in order to realize the full extent of its benefits. Often, these practices serve distinct material needs, however, the nature of Blackfeet relationships with the landscape are such that material, cultural, and spiritual needs are often interconnected. By restricting subsistence uses of the landscape, the national park simultaneously restricts these other intangible values which are important to Blackfeet cultural identity. Conflict between the Blackfeet and Glacier is, however, much more complex than simply a struggle over the material benefits of the park landscape, whether for subsistence or economic reasons. Many Blackfeet support the national park for its role in protecting this significant landscape, particularly as a landscape representative of an authentic Blackfeet identity. Conflict is influenced by tension between the benefits of park protection and the negative effects the park has on Blackfeet well-being. Tension is also fueled by the symbolism of the park, which is viewed by Blackfeet as part of a larger historical land and cultural dispossession by the federal government. Blackfeet are forced to navigate this terrain of hope and loss when dealing with the national park, for the park landscape embodies both an opportunity for cultural renewal, as well as a real sense of limitation and loss. Blackfeet interview participants describe perspectives which identify both significant opportunities for cooperation and collaboration with the National Park Service, as well as obstacles which continue to fuel conflict.
New carbasugars from Streptomyces lincolnensis (2009)

Two new carbasugars (9 and 10) were isolated from Streptomyces lincolnensis DSM 40355 along with streptol (valienol, 8), gabosine I (valienone, 14), and glucosylglycerate. The reported (1)H and (13)C assignments are based on 1D ((1)H, (13)C, 1D-TOCSY, homodecoupling) and 2D (gCOSY, J-resolved, TOCSY, ROESY, gHSQC, gHMBC) NMR techniques and electrospray ionization FT mass spectrometry (ESI FTMS).
PSFNET: ultrafast generation of PSF-modelled-like PET images using deep convolutional neural network (2019)

1369 Aim: PET imaging suffers from a limited spatial resolution and the resulting partial volume effect (PVE). Implementation of PSF modeling within iterative reconstruction (accounting for the point spread function of the PET system) attempts to compensate for the degradation of spatial resolution and to reduce PVE. We aimed to generate PSF-modelled-like higher-resolution PET images using deep convolutional neural network, as an ultrafast alternative to conventional PSF-modeled image reconstructions.
 Methods: Ninety-one patient’s data with brain PET were used in this study. Data were randomly partitioned into 70, 10 and 11 patients for the training, test, and external validation sets, respectively. PSFNET consists of encoder and decoder networks where the encoder converts non-PSF images to feature vectors and the decoder reconstructs the PSF-like image with end to end learning. Quality of the synthesized images were quantitatively assessed by mean absolute error (MAE), root mean square error (RSME), peak signal-to-noise ratio (PSNR), and structural Similarity index metrics (SSIM). Image quantification was assessed using SUV bias map and joint histogram of pixel-wise SUV correlation between generated images (PSFNET) and reference (PSF images).
 Results: With respect to reference original PSF images MAE, RMSE, PSNR and SSIM values were 0.0036±0.0015 [0.0008-0.010], 0.012±0.0043 [0.004-0.032], 38.23±2.71 [29.78-46.63], 0.992±0.008 [0.89-0.99] and 0.0033±0.0011 [0.0007-0.012], 0.011±0.0041 [0.004-0.029], 39.21±3.41 [32.48-47.13], 0.994±0.003 [0.92-0.99] for the test set and external validation set. Pixel wise SUV correlation (Pearson correlation, R2) between PSFNET images and reference PSF image was 0.99± 0.01 and 0.98± 0.05 for the test set and external validation set. Relative error (%) of SUV was -5.12±1.01 [-6.02-1.4] and -5.02±2.13 [-6.52-2.1] for the test set and external validation set respectively.
 Conclusions: This study has identified the possibility of generating PSF-modelled-like PET images using deep convolutional neural network modeling. The proposed deep convolutional neural network method shows promise for generation of high-resolution PET images in the context of improved quantitative analysis.
Dgcr8 and Dicer are essential for sex chromosome integrity during meiosis in males (2015)

Small RNAs play crucial roles in regulating gene expression during mammalian meiosis. To investigate the function of microRNAs (miRNAs) and small interfering RNAs (siRNAs) during meiosis in males, we generated germ-cell-specific conditional deletions of Dgcr8 and Dicer in mice. Analysis of spermatocytes from both conditional knockout lines revealed that there were frequent chromosomal fusions during meiosis, always involving one or both sex chromosomes. RNA sequencing indicates upregulation of Atm in spermatocytes from miRNA-deficient mice, and immunofluorescence imaging demonstrates an increased abundance of activated ATM kinase and mislocalization of phosphorylated MDC1, an ATM phosphorylation substrate. The Atm 3'UTR contains many potential microRNA target sites, and, notably, target sites for several miRNAs depleted in both conditional knockout mice were highly effective at promoting repression. RNF8, a telomere-associated protein whose localization is controlled by the MDC1-ATM kinase cascade, normally associates with the sex chromosomes during pachytene, but in both conditional knockouts redistributed to the autosomes. Taken together, these results suggest that Atm dysregulation in microRNA-deficient germ lines contributes to the redistribution of proteins involved in chromosomal stability from the sex chromosomes to the autosomes, resulting in sex chromosome fusions during meiotic prophase I.
On-line rheological measurement of a binary mixture polymer/sc-CO2 in an extruder (2011)

International audience
Recording active-seismic ground rotations using induction-coil magnetometers (2018)

Most of the current rotational sensing technology is not geared toward the recording of seismic rotations’ amplitudes and frequencies. There are few instruments that are designed for rotational seismology, and the technology for building them is currently being developed. There are no mass industrial producers of seismic rotation sensors as there are for geophones, and only one current sensor model can be deployed on the ocean bottom. We reviewed some current rotational-seismic acquisition technologies, and developed a new method of recording rotations using an existing, robust and field-deployable technology that had seen extensive use in large exploration surveys: induction-coil magnetometers. We conducted an active seismic experiment, in which we found that magnetometers could be used to record seismic rotations. We converted the magnetometer data to rotation-rate data, and validated them by comparing the waveforms and amplitudes with rotation rates recorded by electrokinetic rotation sensors.
Clomiphene, Metformin, or Both for Infertility in the Polycystic Ovary Syndrome (2007)

Clomiphene is superior to metformin in achieving live birth in infertile women with the polycystic ovary syndrome, although multiple birth is a complication. (ClinicalTrials.gov number, NCT00068861 [ClinicalTrials.gov].).