gebhart/patrepeval huggingface dataset:
Chemical and physical processes for integrated temperature control in microfluidic devices (2003)

Microfluidic devices are a promising new tool for studying and optimizing (bio)chemical reactions and analyses. Many (bio)chemical reactions require accurate temperature control, such as for example thermocycling for PCR. Here, a new integrated temperature control system for microfluidic devices is presented, using chemical and physical processes to locally regulate temperature. In demonstration experiments, the evaporation of acetone was used as an endothermic process to cool a microchannel. Additionally, heating of a microchannel was achieved by dissolution of concentrated sulfuric acid in water as an exothermic process. Localization of the contact area of two flows in a microfluidic channel allows control of the position and the magnitude of the thermal effect.
Polymer-Supported Lipid Bilayers on Benzophenone-Modified Substrates (2000)

Solid-supported lipid membranes are important for their roles in fundamental biophysical research as well as in applications such as biosensors. In our study, lipopolymers containing alkyl side chains were synthesized and a mixture of the lipopolymer and free lipids was preorganized at the air-water interface and then transferred to a solid substrate using the Langmuir-Blodgett technique. A photochemical reaction between a substrate-functionalized benzophenone and C-H bonds on the lipopolymer was used to attach the lipopolymers to the substrate. The final assembly of the membrane was completed by vesicle fusion. Langmuir film experiments at the air-water interface indicate tighter molecular packing for the lipopolymers with 28 mol % alkyl side chains than for the ones with 22 mol %. Atomic force microscopy images point to phase separation of lipopolymers on the substrates due to their dewetting from hydrophobic surfaces. However, a mixture of lipopolymers and free lipids formed a smooth film on the same substrate. After the addition of the second lipid layer on the lipopolymer/free lipid layer, the fluorescence images of the polymer-supported bilayer suggested that the distal lipid layer is homogeneous on the micrometer scale. The relaxation of the fluorescent probe lipids was analyzed after application of an electric field to determine their diffusion coefficient; the distal lipid layer was mobile with an average diffusion coefficient of approximately 0.1 microm(2)/s. Moreover, the immobile fraction of the lipids in the distal layer was estimated to be around 15%.
REGULATION OF COLLECTING DUCT Na+ REABSORPTION BY ANP 31–67 (1995)

1. The bulk of studies of the actions of atrial natriuretic peptides (ANP) have focussed on the carboxyterminal derivative (ANP 99-126) of the prohormone (ANP 1-126), but recent evidence indicates that an additional peptide derived from ANP 1-126, namely, ANP 31-67 also circulates, and has natriuretic actions. 2. The effects of ANP 31-67 on inner medullary collecting duct (IMCD) Na+ transport have been examined in freshly prepared suspensions of rabbit IMCD cells. Like ANP 99-126, ANP 31-67 reduces Na+ transport in these cells. 3. However, unlike ANP 99-126, this effect is not mediated by cGMP, and does not result from inhibition of apical Na+ channels. Rather, ANP 31-67 inhibits basolateral Na/K-ATPase, probably via the stimulation of PGE2 synthesis. 4. These results are discussed in the context of other natriuretic substances (interleukin 1 and endothelin), which also inhibit Na+ reabsorption by PGE2-mediated inhibition of Na/K-ATPase.
Measurement of Caspase Activity in Cells Undergoing Apoptosis (2004)

Cysteine proteases of the caspase family play key roles in the execution of apoptosis and in the maturation of proinflammatory cytokines. During apoptosis signaling, the latent forms of caspase precursors undergo rapid proteolytic processing and activation. Thus, the measurement of caspase activation provides a quick and convenient mean to assess apoptosis. This chapter outlines the various commonly used assays for determining caspase activity in cultured cells or tissue extracts.
Simultaneous synthesis of DNA and specialized cellular products by differentiating cartilage cells in vitro. (1967)

A considerable body of literature has accumulated in recent years which indicates that differentiating cells do not synthesize DNA at the same time that they are ac- tively expressing their differentiated properties.1-7Exceptions to this pattern have been claimed for maintenance of specialized function by certain tumor cells in vitro.12Several tissues (e.g., pancreas, mammary gland) exhibit a pattern of growth in which a stem cell line which undergoes rapid divisions throws off daughter cells which only express their differentiation after divisions have stopped or slowed considerably.While this may be the case in muscle and many glandular tissues, it may not be the rule in tissues such as pigmented retina, cartilage, and cardiac mus- cle.In these tissues, expression of function does not appear to be incompatible with rapid growth.In fact, cardiac myoblasts have been shown to divide in tissue cul- ture while beating; presumably, mitotic divisions are taking place in beating cells in the heart after its differentiation into a functional organ.9The data presented here demonstrate that, at least in the case of chick embryo chondrocytes, a considerable population of differentiated cells can undergo rapid nuclear DNA synthesis, rapid increase in number, and synthesis of specific cellular products simultaneously.
Two-dimensional apodized silicon photonic phased arrays (2014)

In this Letter, we demonstrate an 8×8 apodized silicon photonic phased array where the emission from each of 64 nanoantennas was tailored to exhibit Gaussian-shaped intensity distributions in the near field so that the sidelobes of the generated far-field optical beam were suppressed compared to that of a uniform phased array. With the aid of the 72 thermo-optic phase tuners directly integrated within the phased array, we dynamically shaped the generated optical beam in the far field in a variety of ways.
Open-Surface Digital Microfluidics (2008)

Open-surface digital microfluidics refers to droplet manipulations in an open surface. Different chemical/ biological reaction protocols can easily be demonstrated in the same device by reprogramming the order of droplet manipulations. While continuous-flow or liquid-plug microfluidics within microchannels have inherently limited programmability, there is no limit of reprogrammability in open-surface digital microfluidics. Three different mechanisms for droplet manipulations are addressed in this mini-review: electrowetting-on-dielectric, magnetofluidics and wire-guide manipulations. Brief theories of surface tension and work of adhesion are addressed. Potential applications are addressed as well as their complications.
Response to Hays et al and McHorney and Cohen: Practical Implications of Item Response Theory and Computerized Adaptive Testing (2000)

*From QualityMetric, Inc, Lincoln, Rhode Island. †From the Health Assessment Lab, Boston, Massachusetts. ‡From the National Institute of Occupational Health, Copenhagen, Denmark. Preparation of this article and data collection costs for the 1999 National Headache Impact Survey were supported by Glaxo Wellcome. Address correspondence to: John E. Ware, Jr, PhD, QualityMetric, Inc, 640 George Washington Hwy, Lincoln, RI 02865. E-Mail: [email protected]
Construction of irregular LDPC codes with low error floors (2004)

This work explains the relationship between cycles, stopping sets, and dependent columns of the parity check matrix of low-density parity-check (LDPC) codes. Furthermore, it discusses how these structures limit LDPC code performance under belief propagation decoding. A new metric called extrinsic message degree (EMD) measures cycle connectivity in bipartite graph. Using an easily computed estimate of EMD, we propose a Viterbi-like algorithm that selectively avoids cycles and increases stopping set size. This algorithm yields codes with error floors that are orders of magnitude below those of girth-conditional codes.
Stack caching for interpreters (1995)

An interpreter can spend a significant part of its execution time on accessing arguments of virtual machine instructions. This paper explores two methods to reduce this overhead for virtual stack machines by caching top-of-stack values in (real machine) registers. The dynamic method is based on having, for every possible state of the cache, one specialized version of the whole interpreter; the execution of an instruction usually changes the state of the cache and the next instruction is executed in the version corresponding to the new state. In the static method a state machine that keeps track of the cache state is added to the compiler. Common instructions exist in specialized versions for several states, but it is not necessary to have a version of every instruction for every cache state. Stack manipulation instructions are optimized away.
Effects of Prolonged Intensive Lipid-Lowering Therapy on the Characteristics of Carotid Atherosclerotic Plaques In Vivo by MRI (2001)

High-resolution magnetic resonance imaging (MRI) with flow suppression not only provides useful information on luminal and wall areas of the carotid artery but also can identify the principal tissue components of the carotid atherosclerotic plaque. The effects of intensive lipid-lowering therapy on these MRI tissue characteristics were examined in patients with coronary disease (CAD). Eight CAD patients who have been receiving intensive lipid-lowering treatment (niacin 2.5 g/d, lovastatin 40 mg/d, and colestipol 20 g/d) for 10 years in the Familial Atherosclerosis Treatment Study (FATS) follow-up were randomly selected from among 60 such treated patients. Eight CAD patients who were matched to the treated patients for age (+/-3 years), baseline low density lipoprotein (+/-5 mg/dL), and triglycerides (+/-50 mg/dL) but who had never been treated with lipid-lowering drugs were selected as controls. For each of these 32 carotid arteries, luminal and plaque areas were measured by planimetry, in a blinded protocol, from the magnetic resonance image that showed most plaque. Fibrous tissue, calcium, and lipid deposits were identified on the basis of established criteria. Plaque composition was estimated as a fraction of total planimetered area. Patients treated with 10-year intensive lipid-lowering therapy, compared with control subjects, had significantly lower low density lipoprotein cholesterol levels (84 versus 158 mg/dL, respectively; P<0.001) and higher high density lipoprotein cholesterol levels (51 versus 37 mg/dL, respectively; P<0.001). As a group, treated patients, compared with untreated control subjects, had a smaller core lipid area (0.7 versus 10.2 mm(2), respectively; P=0.01) and lipid composition (1% versus 17%, respectively). Group differences in luminal area (55 [treated] versus 44 [control] mm(2), P=NS) and plaque area (58 [treated] versus 64 [control] mm(2), P=NS) tended to favor treatment. MRI appears useful for estimating carotid plaque size and composition. Hyperlipidemic CAD patients frequently (97%) have at least moderate (>/=40% area stenosis) carotid plaque. In this case-control study, prolonged intensive lipid-lowering therapy is associated with a markedly decreased lipid content, a characteristic of clinically stable plaques.
Snake-based brain white matter fiber reconstruction (2014)

Diffusion tensor imaging (DTI) is a tractography algorithm that provides the only means of mapping white matter fibers. Furthermore, because of its wealth of applications, diffusion MRI tractography is gaining importance in clinical and neuroscience research. This paper presents a novel brain white matter fiber reconstruction method based on the snake model by minimizing the energy function, which is composed of both external energy and internal energy. Internal energy represents the assembly of the interaction potential between connected segments, whereas external energy represents the differences between predicted DTI signals and measured DTI signals. Through comparing the proposed method with other tractography algorithms in the Fiber Cup test, the present method was shown to perform superiorly to the majority of the other methods. In fact, the proposed test performed the third best out of the ten available methods, which demonstrates that present method can accurately formulate the brain white matter fiber reconstruction.
Transactivation of vimentin by beta-catenin in human breast cancer cells. (2003)

The cytoplasmic and nuclear redistribution of beta-catenin and the de novo expression of vimentin are frequently involved in the epithelial-to-mesenchymal transition associated with increased invasive/migratory properties of epithelial cells. Because beta-catenin can act as a coactivator of transcription through its binding to the T-cell factor (TCF)/lymphoid enhancer factor 1 transcription factor family, we have explored the possibility that beta-catenin/TCF could directly transactivate vimentin. We first compared vimentin expression in relation with the localization of beta-catenin in eight breast cancer cell lines displaying various degrees of invasiveness and in a model of cell migration using human mammary MCF10A cells. We could thus show a cytoplasmic and/or nuclear distribution of beta-catenin in invasive/migratory cells expressing vimentin, but not in noninvasive/stationary vimentin-negative cell lines. In addition, the human vimentin promoter was found to be up-regulated by beta-catenin and TCF-4 cotransfection. Varying with the cellular background, a diminution of this up-regulation was observed when the putative beta-catenin/TCF binding site of the vimentin promoter was mutated. Our results therefore demonstrate that the vimentin promoter is a target of the beta-catenin/TCF pathway and strongly suggest an implication of this regulation in epithelial cell migration/invasion.
NF-κB activation (2000)

Binding sites for the transcriptional regulatory factor nuclear factor kappa B (NF-kappaB) are present in the promoter regions of many of the proinflammatory cytokines and immunoregulatory mediators important in inducing acute inflammatory responses associated with critical illnesses. Because increased activation of NF-kappaB leads to enhanced expression of these proinflammatory mediators, NF-kappaB activation may be a central event in the development of multiple organ dysfunction associated with infection, blood loss, and ischemia-reperfusion injury. NF-kappaB is normally retained in the cytoplasm through its association with the inhibitory molecule I kappaB. Phosphorylation, ubiquination, and proteolysis of I kappaB allows NF-kappaB to translocate to the nucleus and induce transcription, once associated with the transcriptional cofactor CBP. The transcriptional activity of NF-kappaB can be regulated at multiple steps, including the amount of I kappaB present, NF-kappaB subunit composition, and competition for CBP binding. Because of the central role that NF-kappaB occupies in modulating immunoregulatory responses, further understanding of its regulation will be important in designing future therapies able to prevent or minimize acute inflammatory injury associated with critical illness.
Inhibition of T cell signaling by immunophilin-ligand complexes correlates with loss of calcineurin phosphatase activity (1992)

Calcineurin, a Ca2+, calmodulin-dependent protein phosphatase, was recently found to bind with high affinity to two different immunosuppressant binding proteins (immunophilins) with absolute dependence on the presence of the immunosuppressants FK506 or cyclosporin A (CsA) [Liu et al. (1991) Cell 66, 807-815]. The binding affinities of the immunophilin-drug complexes toward calcineurin and the stoichiometry of the resultant multimeric complexes have now been determined, and structural elements of FK506, CsA, and calcineurin that are critical for mediating their interactions have been identified. Analogues of FK506 (FK520, FK523, 15-O-demethyl-FK520) and CsA (MeBm2t1-CsA and MeAla6-CsA) whose affinities for their cognate immunophilins do not correlate with their immunosuppressive activities have been prepared and evaluated in biochemical and cellular assays. We demonstrate a strong correlation between the ability of these analogues, when bound to their immunophilins, to inhibit the phosphatase activity of calcineurin and their ability to inhibit transcriptional activation by NF-AT, a T cell specific transcription factor that regulates IL-2 gene synthesis in human T cells. In addition, FKBP-FK506 and CyP-CsA do not inhibit members of the PP1, PP2A, and PP2C classes of serine/threonine phosphatases. These data suggest that calcineurin is the relevant cellular target of these immunosuppressive agents and is involved in Ca(2+)-dependent signal transduction pathways in, among others, T cells and mast cells.
[Laryngeal reinnervation by nerve-muscle multipedicle transfer]. (1996)

Abductive ability was restored by means of a modified nerve-muscle pedicle technique, utilizing nerve-muscle multipedicle and multipoint implantation in seventeen dogs. The results showed that the procedure was superior to traditional Tucker's technique in functional recovery, electrophysiological activity and muscle strength which was also demonstrated by histochemical studies. There was little difference between double and three nerve-muscle pedicle transfer. The procedure has been used in three patients with bilateral vocal cord paralysis. Return of spontaneous abduction in the operated side in two patients was noted after eight and twelve weeks after surgery. All patients have achieved sufficient airway without the need of tracheotomy. Electromyography confirmed the reinnervation of posterior cricoarytenoid muscle.
Interwell Tracer Tests: Lessons Learned From Past Field Studies (2005)

Abstract The application of interwell tracer tests is becoming increasingly important to the petroleum industry. Interwell tracer tests, as a proven and efficient tool, have been used to investigate reservoir flow performance and reservoir properties that control gas and water displacement processes. Tracer data have been used to reduce uncertainties attributed to well-to-well communications, vertical and horizontal flow, and residual oil saturation. This paper describes the development of interwell tracer tests in the petroleum industry, from the first qualitative tracer test in the 1950s to the latest quantitative tracer test in the 2000s. The results of our study indicate that poor sampling is the most frequently encountered problem that leads to a failure tracer test and only a small number of interwell tracer tests have employed the advanced numerical modeling methods to analyze the test data. In addition, the interwell tracer tests in the petroleum industry are not well studied as hydrology industry. Therefore, the interwell tracer tests interpretation methods deserve to be paid more attention, so that petroleum engineers can take better advantage of the costly interwell tracer tests.
The cartoon animation filter (2006)

We present the "Cartoon Animation Filter", a simple filter that takes an arbitrary input motion signal and modulates it in such a way that the output motion is more "alive" or "animated". The filter adds a smoothed, inverted, and (sometimes) time shifted version of the second derivative (the acceleration) of the signal back into the original signal. Almost all parameters of the filter are automated. The user only needs to set the desired strength of the filter. The beauty of the animation filter lies in its simplicity and generality. We apply the filter to motions ranging from hand drawn trajectories, to simple animations within PowerPoint presentations, to motion captured DOF curves, to video segmentation results. Experimental results show that the filtered motion exhibits anticipation, follow-through, exaggeration and squash-and-stretch effects which are not present in the original input motion data.
Characterization of murine CD70 by molecular cloning and mAb (1998)

CD27, a member of the tumor necrosis factor (TNF) receptor family, has been implicated in T cell activation, T cell development and T-dependent antibody production by B cells. Its ligand CD70 has been identified only in humans, and, thus, physiological and pathological roles of the CD70-CD27 interaction remain to be determined in an experimental animal system. In the present study, we identified murine (m) CD70 by molecular cloning, and characterized its expression and function by generating an anti-mCD70 mAb. The mCD70 cDNA encoded a type II transmembrane glycoprotein of the TNF family, having 56.5% identity to the human CD70 amino acid sequence. The mCd70 gene was assigned in the central region of chromosome 17. To explore the expression and function of mCD70, we generated cDNA transfectants and anti-mCD70 mAb (FR70), which inhibited binding of a murine CD27-Fc fusion protein (mCD27-Ig) to mCD70 transfectants. FR70, as well as mCD27-Ig, immunoprecipitated a 30-33 kDa surface protein from A20 and mCD70-P815 cells but not from P815 cells. The mCD70 transfectants exhibited a potent co-stimulatory activity for anti-CD3-stimulated T cell proliferation, which was blocked by FR70 far more efficiently than mCD27-Ig. FR70 also abrogated the CD28-independent co-stimulatory activity of A20 cells. The expression of mCD70 was detected on splenic T cells after stimulation with anti-CD3 and anti-CD28 mAb, and on splenic B cells after stimulation with anti-CD40 mAb. Cross-linking of surface Ig by anti-IgM mAb did not induce the mCD70 expression but enhanced the anti-CD40-induced mCD70 expression on splenic B cells. These results suggest a contribution of CD70 to murine T-B cognate interaction as proposed in the human system. FR70 will be useful for further investigating the physiological and pathological roles of the CD70-CD27 interaction in T cell development, T-dependent antibody production and various disease models in the murine system.
Toward Understanding the Lithium Transport Mechanism in Garnet-type Solid Electrolytes: Li+ Ion Exchanges and Their Mobility at Octahedral/Tetrahedral Sites (2015)

The cubic garnet-type solid electrolyte Li7La3Zr2O12 with aliovalent doping exhibits a high ionic conductivity, reaching up to ∼10–3 S/cm at room temperature. Fully understanding the Li+ transport mechanism including Li+ mobility at different sites is a key topic in this field, and Li7–2x–3yAlyLa3Zr2–xWxO12 (0 ≤ x ≤ 1) are selected as target electrolytes. X-ray and neutron diffraction as well as ac impedance results show that a low amount of aliovalent substitution of Zr with W does not obviously affect the crystal structure and the activation energy of Li+ ion jumping, but it does noticeably vary the distribution of Li+ ions, electrostatic attraction/repulsion, and crystal defects, which increase the lithium jump rate and the creation energy of mobile Li+ ions. For the first time, high-resolution NMR results show evidence that the 24d, 96h, and 48g sites can be well-resolved. In addition, ionic exchange between the 24d and 96h sites is clearly observed, demonstrating a lithium transport route of 24d–96h–48g–96h–24d. The lithium mobility at the 24d sites is found to dominate the total ionic conductivity of the samples, with diffusion coefficients of 10–9 m2 s–1 and 10–12 m2 s–1 at the octahedral and tetrahedral sites, respectively.
Antibody-dependent Enhancement of Plaque Formation on Cell Lines of Macrophage Origin -- A Sensitive Assay for Antiviral Antibody (1981)

An assay for antiviral antibody based on antibody-dependent plaque enhancement (ADPE) in the macrophage cell line P388D1 is described which is as sensitive as, or more sensitive than a radioimmune assay. The method is applicable to a range of Togaviridae and Bunyaviridae although not to Picornaviridae and Herpesviridae. The variables affecting the assay are investigated.