gebhart/patrepeval huggingface dataset:
Electrorheological fluid-actuated microfluidic pump (2006)

The authors report the design and implementation of an electrorheological (ER) fluid-actuated microfluidic pump, with programmable digital control. Our microfluidic pump has a multilayered structure fabricated on polydimethylsiloxane by soft-lithographic technique. The ER microfluidic pump exhibits good performance at high pumping frequencies and uniform liquid flow characteristics. It can be easily integrated with other microfluidic components. The programmable control also gives the device flexibility in its operations.
Boron migration due to annealing in CoFeB/MgO/CoFeB interfaces: A combined hard x-ray photoelectron spectroscopy and x-ray absorption studies (2011)

We report the hard x-ray photo-electron spectroscopy (HAXPES) and near edge x-ray absorption fine structure (NEXAFS) of CoFeB|MgO|CoFeB interfaces as a function of annealing time. Upon annealing, the oxidation state of B changes from predominantly elemental (0 valence) boron in the as deposited sample to higher oxidation in annealed samples as evident from HAXPES spectra. The NEXAFS spectroscopy results showed that upon heating, B species migrate towards the MgO and interact with it. A comparison of the tunnel junction NEXAFS signature with some standards suggests that the B forms a 3-fold coordinated boron compound in the MgO environment and 4-fold coordinated boron resembling Kotoite mineral in the CoFe/MgO interface.
Aminooxypentane-RANTES Induces CCR5 Internalization but Inhibits Recycling: A Novel Inhibitory Mechanism of HIV Infectivity (1998)

CCR5, a chemokine receptor expressed on T cells and macrophages, is the principal coreceptor for M-tropic HIV-1 strains. Recently, we described an NH2-terminal modification of the CCR5 ligand regulated on activation, normal T cell expressed and secreted (RANTES), aminooxypentane-RANTES (AOP-RANTES), that showed potent inhibition of macrophage infection by HIV-1 under conditions where RANTES was barely effective. To investigate the mechanism of AOP-RANTES inhibition of HIV infectivity we examined the surface expression of CCR5 using a monoclonal anti-CCR5 antibody, MC-1. We demonstrate that AOP-RANTES rapidly caused >90% decrease in cell surface expression of CCR5 on lymphocytes, monocytes/ macrophages, and CCR5 transfected Chinese hamster ovary (CHO) cells. RANTES also caused a loss of cell surface CCR5, although its effect was less than with AOP-RANTES. Significantly, AOP-RANTES inhibited recycling of internalized CCR5 to the cell surface, whereas RANTES did not. When peripheral blood mononuclear cells are cultured for prolonged periods of time in the presence of RANTES, CCR5 expression is comparable to that seen on cells treated with control medium, whereas there is no CCR5 surface expression on cells cultured in the presence of AOP-RANTES. Immunofluorescence indicated that both AOP-RANTES and RANTES induced downmodulation of cell surface CCR5, and that the receptor was redistributed into endocytic organelles containing the transferrin receptor. When RANTES was removed, the internalized receptor was recycled to the cell surface; however, the receptor internalized in the presence of AOP-RANTES was retained in endosomes. Using human osteosarcoma (GHOST) 34/CCR5 cells, the potency of AOP-RANTES and RANTES to inhibit infection by the M-tropic HIV-1 strain, SF 162, correlated with the degree of downregulation of CCR5 induced by the two chemokines. These differences between AOP-RANTES and RANTES in their effect on receptor downregulation and recycling suggest a mechanism for the potent inhibition of HIV infection by AOP-RANTES. Moreover, these results support the notion that receptor internalization and inhibition of receptor recycling present new targets for therapeutic agents to prevent HIV infection.
Platelet Concentrates Stored in Synthetic Medium after Filtration (1992)

Platelet concentrates prepared from pooled buffy coats (BCPC) were stored in Plasma-Lyte A, a glucose-free synthetic medium, after leukocyte depletion by filtration through Pall PL 50, and compared to paired unfiltered BCPC stored in the same medium. Each pair of BCPC units was prepared from a pool of 10 buffy coats split into two identical units. Platelet and leukocyte counts per unit of BCPC were 2.70 +/- 0.19 x 10(11) and 3.8 +/- 2.8 x 10(6) (filtered BCPC), 2.59 +/- 0.27 x 10(11) and 79 +/- 56 x 10(6) (control BCPC), respectively. Filtration procedures did not affect in vitro parameters of platelet quality and function such as osmotic reversal, ATP release and aggregation in response to collagen and ADP during 15-day storage. A similar decrease of platelet membrane glycoprotein Ib and a similar rise of activation markers GMP-140, gp 53 and platelet-bound fibrinogen were observed during storage of filtered and control BCPC. Our study indicates that storage of BCPC after filtration is feasible and that a reduction in leukocyte content by filtration to mean cell counts of less than five millions per unit has probably no effect on platelet storage lesion.
Vemurafenib acts as an aryl hydrocarbon receptor antagonist: Implications for inflammatory cutaneous adverse events (2019)

Taken together, we obtained no hint of an underlying sensitization against vemurafenib but found evidence suggesting that vemurafenib enhances proinflammatory responses by inhibition of canonical AhR signaling. Our findings contribute to our understanding of the central role of the AhR in skin inflammation and may point toward a potential role for topical AhR agonists in supportive cancer care.
Chronic Lung Injury in Preterm Lambs: Disordered Respiratory Tract Development (1999)

The cause of chronic lung disease of early infancy, often called bronchopulmonary dysplasia (BPD), remains unclear, partly because large-animal models that reliably reproduce BPD have not been available. We developed a model of BPD in lambs that are delivered prematurely and ventilated for 3 to 4 wk after birth to determine whether the histopathology of chronic lung injury in premature lambs mimics that which occurs in preterm infants who die with BPD, and to compare two ventilation strategies to test the hypothesis that differences in tidal volume (VT) influence histopathologic outcome. The two ventilation strategies were slow, deep ventilation (20 breaths/min, 15 +/- 2 ml/kg body weight VT; n = 5) or rapid, shallow ventilation (60 breaths/min, 6 +/- 1 ml/kg body weight VT; n = 5). Lambs were delivered at 125 +/- 4 d gestation (term = 147 d), treated with surfactant, and mechanically ventilated with sufficient supplemental oxygen to maintain normal arterial oxygenation (60 to 90 mm Hg). Quantitative histologic analysis revealed lung structural abnormalities for both groups of experimental lambs compared with lungs of control term lambs that were < 1 d old (matched for developmental age; n = 5) or 3 to 4 wk old (matched for postnatal age; n = 5). Compared with control lambs, chronically ventilated preterm lambs had pulmonary histopathology characterized by nonuniform inflation patterns, impaired alveolar formation, abnormal abundance of elastin, increased muscularization of terminal bronchioles, and inflammation and edema. Slow, deep ventilation was associated with less atelectasis, less alveolar formation, and more elastin when compared with rapid, shallow ventilation. We conclude that prolonged mechanical ventilation of preterm lambs disrupts lung development and produces pulmonary histopathologic changes that are very similar to those that are seen in the lungs of preterm infants who die with BPD. This chronic lung disease is not prevented by surfactant replacement at birth, does not appear to require arterial hyperoxia, and is influenced by VT.
A hybrid training mechanism for applying neural networks to web-based applications (2005)

This paper proposes a hybrid training neural network and applying it to the accuracy counter (AC) developed previously. The neural network is used for detecting the cheating model for abnormal browsing behaviors performed by users in the conflicting environment. The most significant issue, training, should be taken into consideration while we are applying the neural network to Web-based applications such as the accuracy counter. Therefore, we design a hybrid Web based training mechanism for neural networks to deal with this kind of training problem. Finally, we also find out that the AC's block rate for detecting the abnormal browsing behaviors is increasing from 61% (rule-based) to 76% (neural networks with hybrid training mechanism) in the efficient and acceptable training period.
A Square Root Inverse Filter for Efficient Vision-aided Inertial Navigation on Mobile Devices (2015)

In this paper, we present a square-root inverse sliding window filter (SR-ISWF) for vision-aided inertial navigation systems (VINS). While regular inverse filters suffer from numerical issues, employing their square-root equivalent enables the usage of single-precision number representations, thus achieving considerable speed ups as compared to doubleprecision alternatives on resource-constrained mobile platforms. Besides a detailed description of the SR-ISWF for VINS, which focuses on the numerical procedures that enable exploiting the problem's structure for gaining in efficiency, this paper presents a thorough validation of the algorithm's processing requirements and achieved accuracy. In particular, experiments are conducted using a commercial-grade cell phone, where the proposed algorithm is shown to achieve the same level of estimation accuracy, when compared to state-of-the-art VINS algorithms, with significantly higher speed.
Stability, clearance, and disposition of intraventricularly administered oligodeoxynucleotides: implications for therapeutic application within the central nervous system. (1993)

We report experiments in the rat demonstrating the feasibility of intraventricular administration of oligodeoxynucleotides (ODNs) as a regional treatment approach to disorders within the central nervous system (CNS). Although we find little intrinsic nuclease activity in cerebrospinal fluid (CSF), phosphodiester ODNs are rapidly degraded by brain-associated alpha-exonuclease activity. Phosphorothioate ODNs, however, appear resistant to degradation in the CNS and, after intraventricular administration, we find they are cleared in a manner consistent with CSF bulk flow. Continuous infusion of ODN at 1.5 nmol/hr by miniosmotic pump can maintain micromolar concentrations of intact phosphorothioate ODN in CSF for at least 1 week without obvious neurologic or systemic toxicity. After infusion, extensive brain penetration and marked cellular uptake, especially by astrocytic cells, is demonstrated.
Involvement of the protein of Xenopus vasa homolog (Xenopus vasa‐like gene 1, XVLG1) in the differentiation of primordial germ cells (1997)

In order to understand the role of the protein of Xenopus vasa homolog (Xenopus vasa-like gene 1, XVLG1) in germ line cells, an attempt was made to perturb the function of the protein with the anti-vasa antibody 2L-13. The 2L-13 or the control antibody was microinjected with a lineage tracer (FITC-dextran-lysine, FDL) into single vegetal blastomeres containing the germ plasm of Xenopus 32-cell embryos, the descendants of which were destined to differentiate into a small number of primordial germ cells (PGC) and a large number of somatic cells, mostly of endodermal tissues at the tadpole stage. No significant effect of the injection of the antibodies on FDL-labeled, presumptive PGC (pPGC) was observed in embryos until stage 37/38. However, FDL-labeled PGC were not observed in almost all the 2L-13 antibody-injected tadpoles, although a similar number of labeled somatic cells were always present. As 2L-13 antibody specifically reacts with XVLG1 protein in the embryos by immunoblotting, the present results suggest that the antibody perturbed the function of XVLG1 protein in the pPGC, resulting in failure of PGC differentiation at the tadpole stage.
Overcoming Acquired BRAF Inhibitor Resistance in Melanoma via Targeted Inhibition of Hsp90 with Ganetespib (2014)

Abstract Activating BRAF kinase mutations serve as oncogenic drivers in over half of all melanomas, a feature that has been exploited in the development of new molecularly targeted approaches to treat this disease. Selective BRAFV600E inhibitors, such as vemurafenib, typically induce initial, profound tumor regressions within this group of patients; however, durable responses have been hampered by the emergence of drug resistance. Here, we examined the activity of ganetespib, a small-molecule inhibitor of Hsp90, in melanoma lines harboring the BRAFV600E mutation. Ganetespib exposure resulted in the loss of mutant BRAF expression and depletion of mitogen-activated protein kinase and AKT signaling, resulting in greater in vitro potency and antitumor efficacy compared with targeted BRAF and MAP–ERK kinase (MEK) inhibitors. Dual targeting of Hsp90 and BRAFV600E provided combinatorial benefit in vemurafenib-sensitive melanoma cells in vitro and in vivo. Importantly, ganetespib overcame mechanisms of intrinsic and acquired resistance to vemurafenib, the latter of which was characterized by reactivation of extracellular signal-regulated kinase (ERK) signaling. Continued suppression of BRAFV600E by vemurafenib potentiated sensitivity to MEK inhibitors after acquired resistance had been established. Ganetespib treatment reduced, but not abolished, elevations in steady-state ERK activity. Profiling studies revealed that the addition of a MEK inhibitor could completely abrogate ERK reactivation in the resistant phenotype, with ganetespib displaying superior combinatorial activity over vemurafenib. Moreover, ganetespib plus the MEK inhibitor TAK-733 induced tumor regressions in vemurafenib-resistant xenografts. Overall these data highlight the potential of ganetespib as a single-agent or combination treatment in BRAFV600E-driven melanoma, particularly as a strategy to overcome acquired resistance to selective BRAF inhibitors. Mol Cancer Ther; 13(2); 353–63. ©2014 AACR.
Thermal conductivity of IR-opacified silica aerogel powders between 10 K and 275 K (1995)

The thermal conductivity of evacuated pure and opacified silica aerogel powders was measured in a guarded hot plate apparatus for temperatures from 10 K up to 275 K and external loads from 1.5*104 Pa to 105 Pa. Infrared optical measurements of the extinction give the possibility to separate contributions from solid thermal conduction and radiative thermal transport. Measured thermal conductivities range from 29 to 80*10-6 W m-1 K-1 at a temperature of 15 K and from 0.9 to 3.1*10-3 W m-1 K-1 at a temperature of 250 K. The solid thermal conductivities lambda powder of the powders were compared with those of the monolithic silica aerogel ( lambda monolith) the powder grains consist of. The ratio g'= lambda monolith/ lambda powder was found to be temperature independent in the investigated temperature range. Thus g' can be interpreted as a geometrically induced reduction factor. The mean thermal conductivities averaged over the application temperatures range from 0.7 to 2.2*10-3 W m-1 K-1 for boundary temperatures of 77.6 and 290 K and from 0.5 to 1.8*10-3 W m-1 K-1 for boundary temperatures of 20.4 and 290 K. The investigated silica aerogel powders show a large improvement potential for cryogenic thermal powder insulations. They are well suited to substitute expanded Perlite as cryo insulation.
Natural antibodies to IFN-gamma in man and their increase during viral infection. (1990)

Abstract Natural antibodies to IFN-gamma were found in healthy individuals ranging from newborn babies to adults and, at higher levels, in patients suffering from different viral infections. During a viral infection, the titer of anti-IFN-gamma antibodies was observed to be correlated with the stage of the disease. Antibodies specific to IFN-gamma were affinity purified both from sera taken from healthy individuals and sera from viral-infected patients, by using a rIFN-gamma-coupled CNBr-activated Sepharose 4B column. The antibodies were found to be of the IgG class, and maintained their ability to bind rIFN-gamma. They were then tested for neutralizing activity and none of the IgG preparations we analyzed impaired the antiviral activity of rIFN-gamma. This finding suggests that the antigenic determinants recognized by these antibodies on the IFN-gamma molecule are located outside the site, on the IFN-gamma molecule, responsible for its antiviral activity.
Rapid screening of T‐cell receptor (TCR) variable gene usage by multiplex PCR: Application for assessment of clonal composition (1999)

The selection of various T-cell receptor (TCR) gene families and complex rearrangements during intra-thymic differentiation provide the basis for the expression of antigen specificity by mature T cells. TCR beta variable (TCRBV) transcripts can be identified by RT-PCR, but multiple reactions are required to detect all genes of the TCRBV subfamilies. We describe here a multiplex PCR method that amplifies 46 functional genes comparing 23 TCRBV families in 5 reactions where each reaction contains 4 to 7 specific primers together with a single fluorescence-tagged TCR beta constant region primer. Between 8 and 10 distinct subtypes within each of the 23 TCRBV families can be identified by analysis of the CDR3 length. Multiplex PCR products isolated from agarose gels can be subjected to direct sequencing for confirmation and definitive clonotyping if necessary. The data illustrated here show that the multiplex PCR technique is useful for screening TCRBV usage and can be easily adapted for analysis of clonal composition in T-cell populations.
Buck or Boost Tracking Power Converter (2004)

A cascade of buck and boost converter is presented here. The control operates in a manner that the converter is either in buck or boost (BOB) mode on a cycle by cycle basis. It transitions between the modes seamlessly to provide a tracking power conversion function for modulating the power supply of a variable envelope radio frequency (RF) power amplifier. The control algorithm and its implementation using switched capacitor circuits is described. Simulation and measured experimental results including converter efficiency, tracking accuracy, and spectrum at the output of the RF power amplifier are provided. This control technique allows seamless transition between the buck and boost modes while tracking RF envelopes with bandwidth greater than 100 kHz, and maintaining extreme accuracy and extremely low ripple. The efficiency of this converter operating at 1.68 MHz is close to 90% over a wide range of conversion ratios. The area of the power converter is extremely small allowing this to be integrated into a cellular telephone. The controller was integrated as part of a larger power management IC as well as a discrete IC.
FGF signaling network in the gastrointestinal tract (Review) (2006)

Fibroblast growth factor (FGF) signals are transduced through FGF receptors (FGFRs) and FRS2/FRS3- SHP2 (PTPN11)-GRB2 docking protein complex to SOS-RAS-RAF-MAPKK-MAPK signaling cascade and GAB1/GAB2-PI3K-PDK-AKT/aPKC signaling cascade. The RAS approximately MAPK signaling cascade is implicated in cell growth and differentiation, the PI3K approximately AKT signaling cascade in cell survival and cell fate determination, and the PI3K approximately aPKC signaling cascade in cell polarity control. FGF18, FGF20 and SPRY4 are potent targets of the canonical WNT signaling pathway in the gastrointestinal tract. SPRY4 is the FGF signaling inhibitor functioning as negative feedback apparatus for the WNT/FGF-dependent epithelial proliferation. Recombinant FGF7 and FGF20 proteins are applicable for treatment of chemotherapy/radiation-induced mucosal injury, while recombinant FGF2 protein and FGF4 expression vector are applicable for therapeutic angiogenesis. Helicobacter pylori, a causative pathogen for peptic ulcer diseases, chronic atrophic gastritis and gastric cancer, injects bacterial proteins into gastric epithelial cells by using Type IV secretion system, which leads to FGF signaling activation through FGF2 upregulation as well as CagA-dependent SHP2 activation. FGFR2 gene is preferentially amplified and overexpressed in diffuse-type gastric cancer. PD173074 is a small-molecule inhibitor for FGFR, while RO4396686 and SU6668 are small-molecule inhibitors for FGFR and other tyrosine kinases. Cocktail therapy using multiple protein kinase inhibitors could enhance the therapeutic effects for gastrointestinal cancer through the reduction of recurrence associated with somatic mutations of drug-target genes. Single nucleotide polymorphism (SNP) and copy number polymorphism (CNP) of genes encoding FGF signaling molecules will be identified as novel risk factors of gastrointestinal cancer. Personalized prevention and personalized medicine based on the combination of genetic screening and novel therapeutic agents could dramatically improve the prognosis of cancer patients.
Video browsing system based on compressed domain feature extraction (2000)

We present a video browsing system that dynamically extracts features and other content-description (meta-data) from compressed video. We devise a description scheme for a video browsing system that combines color and motion descriptors extracted in the compressed domain. The extraction is fast and enables our proposed dynamic feature extraction based video browsing system. We examine the tradeoff between fast feature extraction and accuracy of matching to arrive at a combination of color and motion descriptors that is easy to extract and provides accurate matching.
Multiple Diverse Circoviruses Infect Farm Animals and Are Commonly Found in Human and Chimpanzee Feces (2009)

Circoviruses are known to infect birds and pigs and can cause a wide range of severe symptoms with significant economic impact. Using viral metagenomics, we identified circovirus-like DNA sequences and characterized 15 circular viral DNA genomes in stool samples from humans in Pakistan, Nigeria, Tunisia, and the United States and from wild chimpanzees. Distinct genomic features and phylogenetic analysis indicate that some viral genomes were part of a previously unrecognized genus in the Circoviridae family we tentatively named "Cyclovirus" whose genetic diversity is comparable to that of all the known species in the Circovirus genus. Circoviridae detection in the stools of U.S. adults was limited to porcine circoviruses which were also found in most U.S. pork products. To determine whether the divergent cycloviruses found in non-U.S. human stools were of dietary origin, we genetically compared them to the cycloviruses in muscle tissue samples of commonly eaten farm animals in Pakistan and Nigeria. Limited genetic overlap between cycloviruses in human stool samples and local cow, goat, sheep, camel, and chicken meat samples indicated that the majority of the 25 Cyclovirus species identified might be human viruses. We show that the genetic diversity of small circular DNA viral genomes in various mammals, including humans, is significantly larger than previously recognized, and frequent exposure through meat consumption and contact with animal or human feces provides ample opportunities for cyclovirus transmission. Determining the role of cycloviruses, found in 7 to 17% of non-U.S. human stools and 3 to 55% of non-U.S. meat samples tested, in both human and animal diseases is now facilitated by knowledge of their genomes.
Cyanohydrin as an Anchoring Group for Potent and Selective Inhibitors of Enterovirus 71 3C Protease (2015)

Cyanohydrin derivatives as enterovirus 71 (EV71) 3C protease (3C(pro)) inhibitors have been synthesized and assayed for their biochemical and antiviral activities. Compared with the reported inhibitors, cyanohydrins (1S,2S,2'S,5S)-16 and (1R,2S,2'S,5S)-16 exhibited significantly improved activity and attractive selectivity profiles against other proteases, which were a result of the specific interactions between the cyanohydrin moiety and the catalytic site of 3C(pro). Cyanohydrin as an anchoring group with high selectivity and excellent inhibitory activity represents a useful choice for cysteine protease inhibitors.