gebhart/patrepeval huggingface dataset:
Characterization of Crosslinked Gel Kinetics and Gel Strength Using NMR (2004)

Abstract Highly crosslinked gels are used in high-permeability reservoirs to achieve good fluid-loss control during well completion and workover operations. Crosslinked gels are also commonly used for shutting off unwanted gas and/or water influx into production wells, and for improving the conformance of the near wellbore injection profile in naturally fractured or in high-permeability reservoirs. In all such applications, the appropriate design of the gel treatment is critical to ensure an efficient gel placement. One important variable of the gel application design is the rheology of the gel system for establishing the crosslinking kinetics and the gel strength after gelation is complete. Rheology of gels and gelation rates are commonly determined by rheological methods or in a qualitative mode through bottle testing using a well-known gel strength code (i.e., the Sydansk&s Code). The rheological measurements can be both time consuming and expensive, while bottle testing can lead to an inconsistent gel description as a result of the subjective nature of the gel strength code. This paper describes the use of low field nuclear magnetic resonance (NMR0 to monitor gelation rates and to characterize gel strength. This technique provides fast and accurate gel strength characterization and gelation monitoring. Through calibration with polymer concentration, crosslinker concentration, aging of gels, and the effect of brine, it is possible to predict NMR parameters. This then allows for a standardized method for the rheological categorization of gels. The results of this work present the correlation between the NMR spectra, rheological measurements, and the qualitative codification of gel strength.
Transferrin Serves As a Mediator to Deliver Organometallic Ruthenium(II) Anticancer Complexes into Cells (2013)

We report herein a systematic study on interactions of organometallic ruthenium(II) anticancer complex [(η(6)-arene)Ru(en)Cl](+) (arene = p-cymene (1) or biphenyl (2), en = ethylenediamine) with human transferrin (hTf) and the effects of the hTf-ligation on the bioavailability of these complexes with cisplatin as a reference. Incubated with a 5-fold excess of complex 1, 2, or cisplatin, 1 mol of diferric hTf (holo-hTf) attached 0.62 mol of 1, 1.01 mol of 2, or 2.14 mol of cisplatin. Mass spectrometry revealed that both ruthenium complexes coordinated to N-donors His242, His273, His578, and His606, whereas cisplatin bound to O donors Tyr136 and Tyr317 and S-donor Met256 in addition to His273 and His578 on the surface of both apo- and holo-hTf. Moreover, cisplatin could bind to Thr457 within the C-lobe iron binding cleft of apo-hTf. Neither ruthenium nor platinum binding interfered with the recognition of holo-hTf by the transferrin receptor (TfR). The ruthenated/platinated holo-hTf complexes could be internalized via TfR-mediated endocytosis at a similar rate to that of holo-hTf itself. Moreover, the binding to holo-hTf well preserved the bioavailability of the ruthenium complexes, and the hTf-bound 1 and 2 showed a similar cytotoxicity toward the human breast cancer cell line MCF-7 to those of the complexes themselves. However, the conjugation with holo-hTf significantly reduced the cellular uptake of cisplatin and the amount of platinated DNA adducts formed intracellularly, leading to dramatic reduction of cisplatin cytotoxicity toward MCF-7. These findings suggest that hTf can serve as a mediator for the targeting delivery of Ru(arene) anticancer complexes while deactivating cisplatin.
Cadherins regulate aggregation of pancreatic β-cells in vivo (1996)

It is thought that the cadherin protein family of cell adhesion molecules regulates morphogenetic events in multicellular organisms. In this study we have investigated the importance of beta-cell cadherins for cell-cell interactions mediating the organization of endocrine cells into pancreatic islets of Langerhans. To interfere with endogenous cadherin activity in beta-cells during pancreatic development, we overexpressed a dominant negative mutant of mouse E-cadherin, lacking nearly all extracellular amino acids, in pancreatic beta-cells in transgenic mice. Expression of the truncated E-cadherin receptor displaced both E- and N-cadherin from pancreatic beta-cells. As a result, the initial clustering of beta-cells, which normally begins at 13.5-14.5 days postcoitum, was perturbed. Consequently, the clustering of endocrine cells into islets, which normally begins at 17.5-18 days postcoitum, was abrogated. Instead, transgenic beta-cells were found dispersed in the tissue as individual cells, while alpha-cells selectively aggregated into islet-like clusters devoid of beta-cells. Furthermore, expression of truncated E-cadherin in beta-cells resulted in an accumulation of beta-catenin in the cytoplasm. Thus, we have for the first time shown in vivo that cadherins regulate adhesive properties of beta-cells which are essential for the aggregation of endocrine cells into islets.
Chemical and Immunological Properties and Amino Acid Sequences of Three Lysozymes from Peking-Duck Egg White (1982)

Three lysozymes (DLs-1, -2, and -3) were purified from Peking-duck egg white by adsorption on CM-Sephadex C-25 resin, followed by CM-Sephadex C-25 and Sephadex G-50 column chromatographies. The three enzymes each moved as a single band, but showed different electrophoretic mobilities, on disc-polyacrylamide gel electrophoresis at pH 4.1. Final yields of DL-1, DL-2, DL-3 were 18.2%, 22.0%, and 6.0%, respectively, from the crude material adsorbed on CM-Sephadex resin. The enzymatic activities of DL-1, DL-2, and DL-3 were 1.53, 1.52, and 1.34 times that of hen egg white lysozyme, respectively, using Micrococcus lysodeikticus cell wall as a substrate at pH 6.2 and 37 degrees C. All the DLs lacked histidine and their amino acid compositions differed from each other by a few amino acid exchanges. The amino acid sequences of DL-2 and DL-3 differed from that of DL-1 by two displacements (Ser-37 to Gly and Gly-71 to Arg) and three displacements (Pro-79 to Arg in addition to the same substitutions), respectively. In comparison with Duck II and Duck III lysozymes from Kaki-duck (Hermann and Jollès (1970) Biochim. Biophys. Acta 200, 178-179; Hermann et al. (1971) Eur. J. Biochem. 24, 12-17) as regards amino acid sequences, Duck II is identical to DL-1 except for one displacement of Gln-57 in DL-1 to Glu in Duck II, while Duck III is rather different from our three lysozymes. All DLs gave single precipitin lines with any rabbit antisera against DLs and each precipitin line fused completely with that of any of the DLs in Ouchterlony double diffusion tests. However, the radiobinding inhibition assay showed that some anti-DL antisera clearly discriminated fine differences among the three DLs. The displacement at residue 79 (Pro in equilibrium Arg) gave the clearest immunological difference among the three kinds of displacements found in DLs.
[Isolation of human thrombin by affinity chromatography with silicate to be used in the preparation of biological glue]. (1990)

At present the preparations of fibrin glue used a thrombin from equine or bovine origin. In order to remove the problems of antigenicity we developed a method of purification from acidified plasma. We used one affinity chromatography on benzamidine-Spherodex and compared three methods of elution: non specific (sodium chloride gradient) and biospecific competitors (arginin methylester or benzamidin). The yield is evaluated between 64 and 84% and the purification factor close to 160. The obtained thrombin is better than animal thrombin in the preparations of fibrin glue.
A Noise-Shaping Time-to-Digital Converter Using Switched-Ring Oscillators—Analysis, Design, and Measurement Techniques (2014)

A high-resolution time-to-digital converter (TDC) using switched-ring oscillators (SROs) is presented. Leveraging oversampling and noise shaping, the proposed SRO-TDC achieves high resolution without the need for calibration. Ring oscillators are switched between two frequencies to achieve noise shaping of the quantization error in an open-loop manner. By decoupling the sampling clock and input carrier frequencies, SRO-TDC is capable of operating at high oversampling ratios (OSRs). This paper also discusses different noise sources and quantization/device noise tradeoffs in noise-shaping TDCs and presents techniques to characterize TDC linearity, range, and noise performance. Fabricated in 90 nm CMOS technology, the proposed TDC operates over a wide range of input carrier frequencies (0.6-750 MHz) and sampling rates (50-750 MS/s). At 500 MS/s and 80 MHz carrier frequency, it achieves an integrated noise of 315 fs in a 1 MHz bandwidth while consuming 1.5 mW from a 1 V supply. The SRO-TDC occupies an active die area of only 0.02 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Optimization methods for brain-like intelligent control (2002)

This paper defines a more restricted class of designs, to be called "brain-like intelligent control". The paper explains the definition and concepts behind it, describes benefits in control engineering, emphasizing stability, mentions 4 groups who have implemented such designs, for the first time, since late 1993, and discusses the brain as a member of this class, one which suggests features to be sought in future research. These designs involve approximate dynamic programming-dynamic programming approximated in generic ways to make it affordable on large-scale nonlinear control problems. These designs are based on learning. They permit a neural net implementation-like the brain but do not require it. They include some but not all "reinforcement learning" or "adaptive critic" designs.
SILCA: Fast-Yet-Accurate Time-Domain Simulation of VLSI Circuits with Strong Parasitic Coupling Effects (2003)

We propose a new circuit analysis method, namely Semi-Implicit Linear-Centric Analysis (SILCA), for efficient SPICE-accurate transient simulation of deep-submicron VLSI circuits with strong parasitic coupling effects introduced by interconnect lines, common substrate, power/ground networks, etc. SILCA is based on two linear-centric techniques. First, a new semi-implicit iterative numerical integration scheme is developed, which applies dynamic time step control accounting for stiff systems and meanwhile keeps constant equivalent conductance for capacitor/inductor companion models. Its convergence and stability properties are characterized. Second, to achieve constant linearized conductance for nonlinear devices during nonlinear iteration process, a successive variable chord method is introduced as an alternative of the Newton-Raphson method and the rank-one update technique is implemented for fast LU factorization. With these techniques, SILCA reduces the number and cost of required LU factorizations dramatically. Experimental results on substrate and power/ground networks have demonstrated that SILCA yields SPICE-like accuracy with an over 80X reduction in LU factorization cost, and an about 20X overall CPU time speedup over SPICE3 for circuits with tens of thousands elements, and the efficiency increases further with the size of a circuit.
Sample Path Derivatives for (s, S) Inventory Systems (1994)

for (s, S) inventory systems, we derive sample path derivatives of performance measures with respect to the two parameters s and S. These derivatives yield derivative estimators which can be estimated from a single sample path or simulation of the inventory system, in some cases not even requiring actual knowledge of the underlying demand distribution. Such derivative estimates would be useful in sensitivity analysis or in gradient-based optimization techniques. We consider the nondiscounted periodic review system with general independent and identically distributed (i.i.d.) continuous demands, full backlogging, and general holding and shortage costs. For the infinite horizon model, consistency proofs are given for some special cases, although we argue why the estimators should be correct for the more general case.
Gait abnormalities in peroneal nerve paralysis and their corrections by orthoses: a biomechanical study. (1986)

Stroke, brain injury, incomplete spinal cord injuries, and peripheral neuropathies frequently result in dysfunction of the foot dorsiflexors and evertors. A controlled examination of aspects of these disabilities was conducted with normal volunteers who underwent a temporary peroneal nerve block. The effects of peroneal nerve paralysis were analyzed to quantitatively describe the resulting gait abnormalities and to assess the effectiveness of orthoses in restoring a normal gait pattern. Kinematic and kinetic measurements were made during normal ambulation, ambulation with a right peroneal nerve paralysis, and ambulation with a paralysis and an ankle-foot orthosis (AFO) with three different adjustments: a posterior stop set in 5 degrees plantarflexion, a posterior stop set in 5 degrees dorsiflexion, and spring-assisted dorsiflexion. The peroneal paralysis produced abnormalities during both the stance and swing phases of gait. During early stance there was a decrease in the length of the heelstrike phase and a reduction in the peak plantarflexion moment (p less than 0.01). During midstance there was an increase in the range of inversion-eversion achieved suggesting medial-lateral instability (p less than 0.01). The second vertical force peak and the aft-shear force peak were reduced (p less than 0.05) as were the peak dorsiflexion moment and the opposite steplength (p less than 0.01). These reductions are believed to be due to medial-lateral instability during pushoff. Subjects demonstrated a steppage gait during swing phase and increased inversion just prior to heelstrike (p less than 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)
Far Infrared Therapy Inhibits Vascular Endothelial Inflammation via the Induction of Heme Oxygenase-1 (2008)

These results demonstrate that FIR therapy exerts a potent antiinflammatory effect via the induction of HO-1. The ability of FIR therapy to inhibit inflammation may play a critical role in preserving blood flow and patency of AVFs in hemodialysis patients.
The Stratus architecture (2002)

An overview is given of the architecture of the Stratus fault-tolerant computer systems, which were the first to use hardware alone to provide fault tolerance in the commercial marketplace. The power subsystem, system boards, and off-board I/O interface buses are examined in some detail. Recovery scenarios and the Stratus service approach are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Fluorescence-guided Tumor Visualization Using the Tumor Paint BLZ-100 (2014)

Objective: Intraoperatively delineating between normal tissue and tumorous tissue in real time ensures near-complete tumor resection. Recently, this has been shown by using targeted fluorescent agents that bind to tumor cells, conjugated to a fluorophore that can be detected with fluorescence imaging methods. One promising tumor ligand for in vivo fluorescence imaging is chlorotoxin (CTX), which has been conjugated to indocyanine green (ICG), and named BLZ-100. In conjunction with BLZ-100, we are nearing completion of developing and optimizing an imaging system (SIRIS) for in-vivo imaging of BLZ-100 for use in surgical resections of gliomas. Methods: BLZ-100 concentrations were prepared in a 5% intralipid solution. The concentrations tested ranged from 1 µMolar to 100 picoMolar. Serial dilutions of ICG were prepared in aqueous concentrations ranging from 3.23 mM to 66.1 pM. The tray was imaged using the commercial Zeiss Pentero surgical microscope and SIRIS. Finally, BLZ-100 was injected in animals implanted with intracranial human glioblastoma cells 48 hours prior to euthanasia. Fluorescence imaging was performed by SIRIS, a camera system developed that simultaneously acquires both white light and NIR images, while combining these images via super-imposition on a high-definition (HD) video monitor. Results: The NIR imaging system developed (SIRIS) is capable of visualizing concentrations of ICG down to 1 nM and BLZ-100 to well below 1 nM (extinction at 100 pM). Glioma and medulloblastoma implanted in mouse brains demonstrated that BLZ-100 has a high affinity for both tumor types compared to normal brain where there is no measurable fluorescence. Conclusions: We have developed a camera system for NIR detection of fluorescence tumor ligands, and demonstrated the utility of this camera for detecting BLZ-100 both in vivo and in vitro. The system is designed to permit simultaneous tumor resection and NIR visualization, and has been developed as an ergonomic and surgeon-friendly device.
An Automated Method to Calibrate Industrial Robots Using a Virtual Closed Kinematic Chain (2007)

This paper describes an industrial robot calibration algorithm called the virtual closed kinematic chain method. Current robot kinematic calibration methods use measurements of position and orientation of the end effector. The accuracy of these measurements is limited by the resolution of the measuring equipment. In the proposed method, a laser pointer tool, attached to the robot's end effector, aims at a constant but unknown location on a fixed object, effectively creating a virtual 7 DOFs closed kinematic chain. As a result, small variations in position and orientation of the end effector are magnified on the distant object. Hence, the resolution of observations is improved, increasing the accuracy of joint angle measurements that are required to calibrate the robot. The method is verified using both simulation and real experiments. It is also shown in simulation that the method can be automated by a feedback system that can be implemented in real time. The accuracy of the robot after using the proposed calibration procedure is measured by aiming at an arbitrary fixed point and measuring the mean and standard deviation of the radius of spread of the projected points. The mean and standard deviation of the radius of spread were improved from 5.64 and 1.89 mm to 1.05 and 0.587 mm, respectively.
Optimization of a gene electrotransfer procedure for efficient intradermal immunization with an hTERT-based DNA vaccine in mice (2014)

DNA vaccination consists in administering an antigen-encoding plasmid in order to trigger a specific immune response. This specific vaccine strategy is of particular interest to fight against various infectious diseases and cancer. Gene electrotransfer is the most efficient and safest non-viral gene transfer procedure and specific electrical parameters have been developed for several target tissues. Here, a gene electrotransfer protocol into the skin has been optimized in mice for efficient intradermal immunization against the well-known telomerase tumor antigen. First, the luciferase reporter gene was used to evaluate gene electrotransfer efficiency into the skin as a function of the electrical parameters and electrodes, either non-invasive or invasive. In a second time, these parameters were tested for their potency to generate specific cellular CD8 immune responses against telomerase epitopes. These CD8 T-cells were fully functional as they secreted IFNγ and were endowed with specific cytotoxic activity towards target cells. This simple and optimized procedure for efficient gene electrotransfer into the skin using the telomerase antigen is to be used in cancer patients for the phase 1 clinical evaluation of a therapeutic cancer DNA vaccine called INVAC-1.
Predicting the Binding Mode of 2-Hydroxypropyl-β-cyclodextrin to Cholesterol by Means of the MD Simulation and the 3D-RISM-KH Theory (2018)

It has been found that a cyclodextrin derivative, 2-hydroxypropyl-β-cyclodextrin (HPβCD), has reasonable therapeutic effect on Niemann-Pick disease type C, which is caused by abnormal accumulation of unesterified cholesterol and glycolipids in the lysosomes and shortage of esterified cholesterol in other cellular compartments. We study the binding affinity and mode of HPβCD with cholesterol to elucidate the possible mechanism of HPβCD for removing cholesterol from the lysosomes. The dominant binding mode of HPβCD with cholesterol is found based on the molecular dynamics simulation and a statistical mechanics theory of liquids, or the three-dimensional reference interaction site model theory with Kovalenko-Hirata closure relation. We examine the two types of complexes between HPβCD and cholesterol, namely, one-to-one (1:1) and two-to-one (2:1). It is predicted that the 1:1 complex makes two or three types of stable binding mode in solution, in which the βCD ring tends to be located at the edge of the steroid skeleton. For the 2:1 complex, there are four different types of the complex conceivable, depending on the orientation between the two HPβCDs: head-to-head (HH), head-to-tail (HT), tail-to-head (TH), and tail-to-tail (TT). The HT and HH cyclodextrin dimers show higher affinity to cholesterol compared to the other dimers and to all the binding modes of 1:1 complexes. The physical reason why the HT and HH dimers have higher affinity compared to the other complexes is discussed based on the consistency with the 1:1 complex. On the one hand, in case of the HT and HH dimers, the position of each CD in the dimer along the cholesterol chain comes right on or close to one of the positions where a single CD makes a stable complex. On the other hand, one of the CD molecules is located on unstable region along the cholesterol chain, for the case of TH and TT dimers.
[Influences of chronic stress on central nervous systems]. (2000)

Chronic mild or moderate stress elicits an adaptive change in central nervous systems that function to maintain homeostasis. The principal components of stress response are the extrahypothalamic corticotropin-releasing hormone (CRH) and the locus coeruleus (LC)-norepinephrine (NE) systems. CRH is known to produce various stress-, anxiety- and arousal-associated behaviors in animals. Moreover, CRH causes an increase in the firing rate and activity of tyrosine hydroxylase in the LC, and NE release in LC projection areas. It is thought that chronic inescapable and unpredictable stress can result in a sustained dysregulation of both CRH neuronal activity and LC-NE systems. One may hypothesize that the NE-CRH interaction occurs in the terminal projection of forebrain NE systems, the hypothalamic paraventricular nucleus (PVN), the bed nucleus of the stria terminalis (BNST) and the central nucleus of the amygdala (CeA) where NE stimulates CRH release. Such CRH-NE-CRH feed-forward systems elicit progressive augmentation of stress responsivity with repeated exposure. The beta-adrenergic receptor down-regulation is induced by acute and chronic exposure to moderate and predictable stress, implying an adaptation to stress. However, chronic unpredictable (variable) stress (CVS), a model for depression, up-regulated the beta-AR. In our laboratory, we found that concurrent treatment with the selective serotonin reuptake inhibitor (SSRI) citalopram caused beta-R down-regulation in the frontal cortex of rats treated with CVS for 14 days. As previously reported by the authors, an increase in 5-HT availability plays a role in preserving beta-R down-regulation by NE potentiating agents. In depressed patients, hyperactivation of the CRH-NE systems caused by the CRH-NE feed-forward system is thought to be involved in generating anxiety, sympathetic activation and hyperarousal. Moreover, a decrease in the 5-HT turnover in depressed patients has been reported. Accordingly, it is proposed that an increase in 5-HT availability by SSRI might contribute to normalize beta-R down-regulation as an adaptive regulatory mechanism against excessive CRH-NE neurotransmission under a "stressful" situation.