gebhart/patrepeval huggingface dataset:
Carbon Microelectrodes with a Renewable Surface (2010)

Electrode fouling decreases sensitivity and can be a substantial limitation in electrochemical experiments. In this work we describe an electrochemical procedure that constantly renews the surface of a carbon microelectrode using periodic triangle voltage excursions to an extended anodic potential at a scan rate of 400 V s(-1). This methodology allows for the regeneration of an electrochemically active surface and restores electrode sensitivity degraded by irreversible adsorption of chemical species. We show that repeated voltammetric sweeps to moderate potentials in aqueous solution causes oxidative etching of carbon thereby constantly renewing the electrochemically active surface. Oxidative etching was established by tracking surface-localized fluorine atoms with XPS, by monitoring changes in carbon surface morphology with AFM on pyrolyzed photoresist films, and also by optical and electron microscopy. The use of waveforms with extended anodic potentials showed substantial increases in sensitivity toward the detection of catechols. This enhancement arose from the adsorption of the catechol moiety that could be maintained with a constant regeneration of the electrode surface. We also demonstrate that application of the extended waveform could restore the sensitivity of carbon microelectrodes diminished by irreversible adsorption (electrode fouling) of byproducts resulting from the electrooxidation and polymerization of tyramine. Overall, this work brings new insight into the factors that affect electrochemical processes at carbon electrodes and provides a simple method to remove or reduce fouling problems associated with many electrochemical experiments.
Scalable Production of Embryonic Stem Cell-Derived Cells (2004)

Embryonic stem (ES) cells have the ability to self-renew as well as differentiate into any cell type in the body. These traits make ES cells an attractive "raw material" for a variety of cell-based technologies. However, uncontrolled cell aggregation in ES cell differentiation culture inhibits cell proliferation and differentiation and thwarts the use of stirred suspension bioreactors. Encapsulation of ES cells in agarose microdrops prevents physical interaction between developing embryoid bodies (EBs) that, in turn, prevents EB agglomeration. This enables use of stirred suspension bioreactors that can generate large numbers of ES-derived cells under controlled conditions.
Embedding secret information into a dithered multi-level image (2002)

A coding scheme for secretly embedding character information into a dithered multilevel image is presented. This scheme inputs both a monotone image and secret information, which is converted to binary sequences, and it outputs a single dithered image. This image contains the character data of about 2 kByte in a dithered bilevel image 3 kByte in a dithered three-level image of 256*256 pixels, and it appears to be an ordinary dithered image. This scheme is available for storing a picture in a database or communication system with secret information.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Vaccination With Messenger RNA (2006)

As an alternative to DNA-based vaccines, messenger RNA (mRNA)-based vaccines present additional safety features: no persistence, no integration in the genome, no induction of autoantibodies. Moreover, mRNA which are generated by in vitro transcription, are easy to produce in large amounts and very high purity. This feature facilitates the good manufacturing practices process and guaranties batch-to-batch reproducibility. Vaccination can be achieved by several delivery methods including direct injection of naked mRNA, injection of mRNA encapsulated in liposomes Gene Gun delivery of mRNA loaded on gold beads or in vitro transfection of the mRNA in cells followed by re-injection of the cells into the patients. Two of these technologies are being evaluated in human clinical trials: (1) in vitro mRNA-transfection of dendritic cells to be adoptively transferred and (2) direct injection of globin-stabilized mRNA. This chapter describes the production of mRNA and the preparation of the two types of mRNA-based vaccines tested in humans.
On‐line reaction monitoring by extractive electrospray ionisation (2011)

The design and development of a novel extractive electrospray ionisation (EESI) device for on-line reaction monitoring is described. The EESI apparatus uses a secondary, grounded nebuliser to produce an analyte aerosol and a Venturi pump is then used to transfer a sample of the aerosol to an electrospray source where it is ionised. The EESI apparatus was then tested with a variety of small, organic molecules to assess sensitivity, linearity and dynamic range. The performance of the technique will depend on the mass spectrometer used for the experiments; in the configurations used here it has a usable dynamic range of around 3.5 orders of magnitude with a linear range of around 2.5 orders of magnitude and is capable of analysing species present down to low µg/mL with signal-to-noise ratio greater than 2.5. The use of EESI for reaction monitoring was validated using a series of mock reaction mixtures and then used to monitor the base hydrolysis of ethyl salicylate to salicylic acid.
A Review of Computational Models of Transcranial Electrical Stimulation (2013)

Transcranial electrical stimulation (tES), which includes transcranial direct current stimulation (tDCS) and electroconvulsive therapy (ECT), has played an important role in the treatment of various psychiatric disorders. Decades of empirical research and clinical experience have led to new and improved brain stimulation techniques, but the mechanisms underlying treatment efficacy and side effects are poorly understood. As part of the ongoing research effort in tES, the value of computational models of transcranial electric current flow has been increasingly recognized, and a proliferation of modeling studies have been published. The complexity of these tES models ranges from simple sphere-based models of the head to high-resolution anatomical reconstructions based on head-image scans. This review provides an up-to-date description and comparison of existing computational models of tES (primarily tDCS and ECT), focusing on the modeling approaches adopted in previous studies and their significant finding.
A Versatile Integrated Circuit for the Acquisition of Biopotentials (2007)

Electrically active cells in the body produce a wide variety of voltage signals that are useful for medical diagnosis and scientific investigation. These biopotentials span a wide range of amplitudes and frequencies. We have developed a versatile front-end integrated circuit that can be used to amplify many types of bioelectrical signals. The 0.6-μm CMOS chip contains 16 fully-differential amplifiers with gains of 46 dB, 2μV <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</sub> input-referred noise, and bandwidths programmable from 10 Hz to 10kHz.
Arginine vasopressin in 316 patients with advanced vasodilatory shock* (2005)

Supplementary AVP infusion improved cardiocirculatory function in advanced vasodilatory shock, but an increase in liver enzymes and bilirubin, and a decrease in platelet count occurred during AVP therapy, particularly during simultaneous hemofiltration. Initiation of AVP infusion before norepinephrine requirements exceeding 0.6 microg x kg x min may improve outcome.
MagR：揭开“第六感”之谜？ (2015)

从司南到航海罗盘,再到装有磁强计的智能手机,聪明的人类发明出了各种各样的工具,利用磁场来辨别方向。制造指南针这样的事情人类固然没有其他动物能够胜任,但自然选择将堪称神奇的磁场感应能力放进了许多动物的体内。研究显示,帝王蝶、龙虾、信鸽等动物都能感知磁场。然而,要阐明这些动物自带的＂指南针＂在哪里、怎样发挥作用,可比在路上找得着北困难多了。为了解释动物们感受磁场的机制,科学家提出了各种可能的模型。
PipeLayer: A Pipelined ReRAM-Based Accelerator for Deep Learning (2017)

Convolution neural networks (CNNs) are the heart of deep learning applications. Recent works PRIME [1] and ISAAC [2] demonstrated the promise of using resistive random access memory (ReRAM) to perform neural computations in memory. We found that training cannot be efficiently supported with the current schemes. First, they do not consider weight update and complex data dependency in training procedure. Second, ISAAC attempts to increase system throughput with a very deep pipeline. It is only beneficial when a large number of consecutive images can be fed into the architecture. In training, the notion of batch (e.g. 64) limits the number of images can be processed consecutively, because the images in the next batch need to be processed based on the updated weights. Third, the deep pipeline in ISAAC is vulnerable to pipeline bubbles and execution stall. In this paper, we present PipeLayer, a ReRAM-based PIM accelerator for CNNs that support both training and testing. We analyze data dependency and weight update in training algorithms and propose efficient pipeline to exploit inter-layer parallelism. To exploit intra-layer parallelism, we propose highly parallel design based on the notion of parallelism granularity and weight replication. With these design choices, PipeLayer enables the highly pipelined execution of both training and testing, without introducing the potential stalls in previous work. The experiment results show that, PipeLayer achieves the speedups of 42.45x compared with GPU platform on average. The average energy saving of PipeLayer compared with GPU implementation is 7.17x.
The Effect of L-Carnitine on Myocardial Protection in Cold Cardioplegia Followed by Reperfusion (1994)

We studied the effect of exogenous L-carnitine on myocardial viability and carnitine uptake following ischemia-reperfusion in isolated rat hearts. Hearts were subjected to hypothermic cardioplegia at 26 degrees C for 80 minutes with and without carnitine 10 mmol/L added to the perfusate and cardioplegic solution [Groups I (n = 9) and II (n = 14), respectively]. Additionally, to study myocardial carnitine uptake, hearts were subjected to global ischemia at 20 degrees C [Group III (n = 6) and IV (n = 6)] and at 37 degrees C [Group V (n = 6) and VI (n = 6)] with and without carnitine 10 mmol/L added to the perfusate. All hearts received normothermic reperfusion, and Krebs-Henseleit solution was used as the perfusate in all groups. Postischemic aortic flow, expressed as the percentage of pre-ischemic flow, morphometric scores of myocardial mitochondria, and the myocardial concentration of adenosine triphosphate at the end of reperfusion were significantly higher in Group I than in Group II. In hearts treated with L-carnitine both at 20 degrees C and 37 degrees C the myocardial concentrations of carnitine fractions (free, short-acyl, and long-acyl) increased significantly compared to those in hearts without L-carnitine treatment. The myocardial concentration of free carnitine at the end of reperfusion was significantly higher in Group III than at pre-ischemia. These results suggest that exogenous L-carnitine is incorporated into cellular metabolism, even in hypothermic cardioplegia, improving cardiac function and preserving the myocardial adenosine triphosphate concentration.
Stability and Compatibility of Recombinant Adeno-Associated Virus Under Conditions Commonly Encountered in Human Gene Therapy Trials (2015)

Recombinant adeno-associated virus (rAAV) vectors are rapidly becoming the first choice for human gene therapy studies, as clinical efficacy has been demonstrated in several human trials and proof-of-concept data have been demonstrated for correction of many others. When moving into human use under the auspices of an FDA Investigational New Drug (IND) application, it is necessary to demonstrate the stability of vector material under various conditions of storage, dilution, and administration when used in humans. Limited data are currently available in the literature regarding vector compatibility and stability, leading most IND sponsors to repeat all necessary studies. The current study addresses this issue with an rAAV vector (rAAV1-CB-chAATmyc) containing AAV2-inverted terminal repeat sequences packaged into an AAV1 capsid. Aliquots of vector were exposed to a variety of temperatures, diluents, container constituents, and other environmental conditions, and its functional biological activity (after these various treatments) was assessed by measuring transgene expression after intramuscular injection in mice. rAAV was found to be remarkably stable at temperatures ranging from 4°C to 55°C (with only partial loss of potency after 20 min at 70°C), at pH ranging from 5.5 to 8.5, after contact with mouse or human serum (with or without complement depletion) or with gadolinium and after contact with glass, polystyrene, polyethylene, polypropylene, and stainless steel. The only exposure resulting in near-total loss of vector activity (10,000-fold loss) was UV exposure for 10 min. The stability of rAAV1 preparations bodes well for future dissemination of this therapeutic modality.
Noise in MRI (1996)

This study analyzes the signal-to-noise ratio (SNR) in magnetic resonance imaging. The factors that determine the SNR are derived starting from basic principles. The SNR, for a given object, is shown to be proportional to the voxel volume and the square root of the acquisition time. The noise generated by the body is derived using a cylindrical model and is shown to be proportional to the square of the radius and the square root of the length.
Anti-inflammatory effects of topically applied dimethyl sulfoxide gel on endotoxin-induced synovitis in horses (1998)

Topically applied DMSO penetrated into synovial fluid in sufficient quantities to be detected and to decrease joint inflammation.
Intrinsic RNA (guanine-7) methyltransferase activity of the vaccinia virus capping enzyme D1 subunit is stimulated by the D12 subunit. Identification of amino acid residues in the D1 protein required for subunit association and methyl group transfer. (1994)

Vaccinia virus mRNA capping enzyme, a heterodimer of virus-encoded D1 and D12 subunits, catalyzes three steps in the synthesis of the m7GpppN cap. By expressing portions of the subunits in bacteria, singly and together, we have localized the RNA (guanine-7) methyltransferase domain to a 305-amino acid carboxyl-terminal segment of the D1 polypeptide (residues 540-844) complexed with the D12 protein. We find that the purified carboxyl D1 protein has a weak intrinsic methyltransferase activity, indicating that the catalytic center resides within this subunit. The basal level of activity can be stimulated 100-fold by addition of purified D12 protein, which is itself catalytically inert. The carboxyl region of D1 forms a heterodimer with the D12 subunit in vivo and in vitro. Analysis of alanine substitution mutants of the D1 protein identifies amino acid residues important for subunit interaction. Our results suggest that subunit heterodimerization is necessary, but not sufficient, for full methyltransferase activity. A mutation of vicinal positions His-682-Tyr-683 that specifically affects catalytic activity but not subunit interaction implicates these residues as constituents of the active site.
Conformational Reorganization of the Four-helix Bundle of Human Apolipoprotein E in Binding to Phospholipid (2000)

Conformational reorganization of the amino-terminal four-helix bundle (22-kDa fragment) of apolipoprotein E (apoE) in binding to the phospholipid dimyristoylphosphatidylcholine (DMPC) to form discoidal particles was investigated by introducing single, double, and triple interhelical disulfide bonds to restrict the opening of the bundle. Interaction of apoE with DMPC was assessed by vesicle disruption, turbidimetric clearing, and gel filtration assays. The results indicate that the formation of apoE·DMPC discoidal particles occurs in a series of steps. A triple disulfide mutant, in which all four helices were tethered, did not form complexes but could release encapsulated 5-(6)-carboxylfluorescein from DMPC vesicles, indicating that the initial interaction does not involve major reorganization of the helical bundle. Initial interaction is followed by the opening of the four-helix bundle to expose the hydrophobic faces of the amphipathic helices. In this step, helices 1 and 2 and helices 3 and 4 preferentially remain paired, since these disulfide-linked mutants bound to DMPC in a manner similar to that of the 22-kDa fragment of apoE4. In contrast, mutants in which helices 2 and 3 and/or helices 1 and 4 paired bound poorly to DMPC. However, all single and double helical pairings resulted in the formation of larger discs than were formed by the 22-kDa fragment, indicating that further reorganization of the helices occurs following the initial opening of the four-helix bundle in which the protein assumes its final lipid-bound conformation. In support of this rearrangement, reducing the disulfide bonds converted the large disulfide mutant discs to normal size.
Purification and N-terminal analysis of urease from Helicobacter pylori (1990)

Urease of Helicobacter pylori (formerly Campylobacter pylori) is believed to represent a critical virulence determinant for this species. Ammonia generated by hydrolysis of urea may protect the acid-sensitive bacterium as it colonizes human gastric mucosa. An H. pylori strain, cultured from a gastric biopsy of a patient with complaints of abdominal pain and a history of peptic ulcer disease, was isolated on selective medium and cultured in Mueller-Hinton broth supplemented with 4% fetal calf serum. Whole cells were ruptured by French pressure cell lysis, and soluble protein was chromatographed on DEAE-Sepharose, phenyl-Sepharose, Mono-Q, and Superose 6 resins. Purified urease represented 6% of the soluble protein of crude extract, was estimated to have a native molecular size of 550 kilodaltons (kDa), and was composed of two distinct subunits of apparent molecular sizes of 66 and 29.5 kDa. On the basis of subunit size, a 1:1 subunit ratio as measured by scanning densitometry of Coomassie blue-stained sodium dodecyl sulfate-polyacrylamide gels, and estimated native molecular size, the data are consistent with a stoichiometry of (29.5 kDa-66 kDa)6 for the structure of the native enzyme. Km for urea was estimated at 0.2 mM. By N-terminal analysis, the 29.5-kDa subunit of H. pylori urease was found to share significant amino acid sequence similarity with the smallest of three subunits of the Proteus mirabilis and Morganella morganii ureases, as well as to the amino terminus of the unique jack bean subunit. The 66-kDa subunit also shared up to 80% similarity with the largest of three subunits of P. mirabilis, M. morganii, and Klebsiella aerogenes ureases and to internal sequences (amino acids 271 to 285) of the jack bean urease subunit. Thus, the amino acid sequence is conserved among ureases with one, two, and three distinct subunits, suggesting a common ancestral urease gene. Also, urease subunits of M. morganii and jack bean were specifically recognized by antisera raised against the 66-kDa subunit of H. pylori urease, demonstrating that at least some antigenic determinants were conserved among ureases from different species.
Salivary histatin 5: dependence of sequence, chain length, and helical conformation for candidacidal activity. (1990)

Histatin 5 (Asp1-Ser-His-Ala4-Lys-Arg-His-His8-Gly-Tyr-Lys-Arg12-Lys-Ph e-His-Glu16-Lys-His - His-Ser20-His-Arg-Gly-Tyr24), one of the basic histidine-rich peptides present in human parotid saliva and several of its fragments, 1-16 (N16), 9-24 (C16), 11-24 (C14), 13-24 (C12), 15-24 (C10), and 7-16 (M10), were synthesized by solid-phase procedures. Native histatin 5 from human parotid saliva was also purified. Their antifungal activities on two strains of Candida albicans have been studied and their conformational preferences both in aqueous and non-aqueous solutions examined by circular dichroism. The synthetic histatin 5, C16, and C14 peptides were highly active and inhibited the growth of C. albicans. The candidacidal activity data of synthetic histatin 5 were comparable to the values of the native histatin 5 isolated from parotid saliva and those reported previously, although the assay system used and the strains examined were different. The C16 fragment was as active as the whole peptide itself, whereas the N16 fragment was far less active than C14, suggesting that the sequence at the C-terminal is important for its fungicidal activity. An increase in the chain length of the C-terminal sequence from 12 to 16 residues increased the candidacidal activity, thereby indicating that a peptide chain length of at least 12 residues is necessary to elicit optimum biological activity. The CD spectra of these linear peptides showed that they are structurally more flexible, and they adopt different conformations depending on the solvent environment. CD studies provided evidence that histatin 5 and the longer fragments, C16, N16, and C14 preferred alpha-helical conformations in non-aqueous solvents such as trifluoroethanol and methanol, while in water and pH 7.4 phosphate buffers, they favored random coil structures. The shorter sequences seemed to adopt either turn structures or unordered structures both in aqueous and non-aqueous solutions. It appears that the sequence at the C-terminal of histatin 5 with a minimum chain length of 14 residues and alpha-helical conformation are the important structural requirements for appreciable candidacidal activity.
Modified Array-based Comparative Genomic Hybridization Detects Cryptic and Variant PML-RARA Rearrangements in Acute Promyelocytic Leukemia Lacking Classic Translocations (2013)

Acute promyelocytic leukemia (APL) is typically defined at the molecular level by a reciprocal translocation of the promyelocytic leukemia (PML) and retinoic acid receptor α (RARA) genes. An accurate diagnosis of APL is critical for appropriate choice of therapy and prognostic assessment. Cryptic and variant rearrangements in APL are discoverable by a variety of molecular methods including fluorescence in situ hybridization (FISH), reverse transcriptase polymerase chain reaction, or gene sequencing. Rare reports of FISH-negative APL harboring cryptic rearrangements of PML-RARA detected by reverse transcriptase polymerase chain reaction or sequencing have been described. Here, we describe the detection of cryptic or variant PML-RARA rearrangements by translocation-based comparative genomic hybridization (tCGH), a recently described modification of traditional CGH technology that facilitates the detection of balanced translocations by means of the linear amplification of a potential translocation breakpoint region(s), in 2 unusual cases of APL. One tumor lacked detectable t(15;17) by karyotype and FISH, and the other tumor lacked the typical morphologic and immunophenotypic features of APL and had a variant 3-way translocation involving PML and RARA. PML-RARA translocations were identified by tCGH in both cases providing confirmation of the diagnosis of APL. These data emphasize the benefit of using complementary molecular methods including tCGH for detecting cryptic and variant PML-RARA translocations in unusual cases of APL.