gebhart/patrepeval huggingface dataset:
Blocking the Rac1-TRPC5 pathway protects human podocytes (2020)

Abstract Podocyte injury and the appearance of proteinuria are key features of several progressive kidney diseases. Genetic deletion or selective inhibition of TRPC5 channels with small-molecule inhibitors protects podocytes in rodent models of disease, but less is known about the human relevance and translatability of TRPC5 inhibition. Here, we investigate the effect of TRPC5 inhibition in puromycin aminonucleoside (PAN)-treated human iPSC-derived podocytes and kidney organoids. We first established that systemic administration of the TRPC5-specific blocker AC1903 was sufficient to protect podocyte cytoskeletal proteins and suppress proteinuria in PAN-induced nephrosis in rats, an established model of podocyte injury and progressive kidney disease. PAN treatment also triggered the Rac1-TRPC5 injury pathway in human iPSC-derived podocytes and kidney organoids. TRPC5 current was recorded in human iPSC-derived podocytes, and was blocked by AC1903. The TRPC5 blocker also reversed the effects of PAN-induced injury in human podocytes in both 2D and 3D culture systems. Taken together, these results revealed the relevance of the TRPC5-Rac1 pathway in human kidney tissue highlighting the potential of this therapeutic strategy for patients.
Planar reflectionless filters (2019)

The harmful effects that standing waves may have on an electronic system are well known. The symptoms of standing waves are less direct when they occur out-of-band, but the negative impact they have on system performance is no less real or important. Problems that arise from stop-band mismatches are in some ways even more troublesome than those in-band because they are too often not fully appreciated until after the first prototype is built, by which time some critical design and packaging decisions have already been made. Reflectionless filters provide a safeguard against these concerns. This chapter looks at reflectionless network topology, scaled prototype parameter tables, planar lumped-element implementations, delta-wye transformation for reduced impedance, non-canonical filter responses, transmission-line reflectionless filters, Chebyshev and Zolotarev type I filters.
Colony-stimulating factor (CSF) 1 receptor blockade reduces inflammation in human and murine models of rheumatoid arthritis (2016)

Simultaneous inhibition of CSF1R interactions with both CSF-1 and IL-34 suppresses inflammatory activation of RA synovial tissue and pathology in CIA, suggesting a novel therapeutic strategy for RA.
Abstract 395: Chemokine ligand 7 expression in liver metastasis of colorectal cancer (2011)

Abstract The main cause of death for colorectal cancer (CRC) patients is the development of metastatic lesions at sites distant from the primary tumor. Therefore, it is important to find biomarkers that are related to the metastasis and to study the possible mechanism. Recent data have shown that soluble attractant molecules called chemokines support the metastasis of certain cancers to certain organs. To identify molecular regulators that are differentially expressed in liver metastasis of CRC, PCR array was performed and CCL7 showed remarkable overexpression in liver metastatic tumor tissues. To validate the result of PCR array, 30 patients with primary CRC and liver metastases were selected. Immunohistochemistry and real-time PCR analysis showed that CCL7 was expressed in normal colonic epithelium and the expression was higher in liver metastases than in primary CRC. CCR1, CCR2, and CCR3, receptors of CCL7, were not expressed in normal colonic epithelium nor colon and metastatic cancer, but expressed in normal hepatocytes and stroma by immunohistochemical staining. Real-time PCR showed that the expressions of CCR1, CCR2, and CCR3 were also higher in liver metastases than in primary CRC. There would be chemokine/chemokine receptors interactions between CCL7 and its receptors in liver, which supply the environment for metastatic colon cancer cells to survive and proliferate in liver. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 395. doi:10.1158/1538-7445.AM2011-395
The epitope associated with the binding of the capsular polysaccharide of the group B meningococcus and of Escherichia coli K1 to a human monoclonal macroglobulin, IgMNOV. (1988)

The fine structure of the combining site of human mAb IgMNOV to poly-alpha(2----8)linked NeuNAc, the epitope of the group B meningococcal and E. coli K1 polysaccharides, has been probed using RIA and ELISA. Inhibition by oligomers ranging from 2 to 12 residues was used to assay binding to IgMNOV by group B meningococcal polysaccharide preparations (GBMP) or by poly(A). The inhibitory properties of the oligomers were almost identical in both assays of the binding of GBMP to horse IgM (H46). This evidence and the finding that both GBMP and poly(A) precipitated IgMNOV equally per unit weight indicated that the epitope of poly(A) must mimic an equivalent epitope on GBMP despite the absence of any apparent common structural features in the two molecules. Unlike most carbohydrate-anticarbohydrate systems in which the site is saturated by oligomers of up to six or seven sugars, all the anti-alpha(2----8)NeuNAc systems above required much larger oligomers. Because these oligomers are larger than the maximum size of an antibody site the epitope must be conformationally controlled, and this has been confirmed by nuclear magnetic resonance spectroscopy. However, despite the above similarities, GBMP and poly(A) were differentiated in that only GBMP bound to H46. Smaller linear molecules obtained by delipidating the GBMP, as well as periodate-oxidized GBMP with its nonreducing end oxidized or linked covalently to BSA, bound to and precipitated IgMNOV and H46. This showed that, despite their differences, terminal nonreducing ends were not involved and that both epitopes were located in the conformationally controlled inner residues of the GBMP. The difference thus must reside in the ability of IgMNOV and H46 to recognize different structural aspects of the same conformationally controlled inner residues. The ELISA data indicate that both IgMNOV and H46 have groove-type sites that bind exclusively to an epitope located on the acidic side of the inner residues. The differences determining the ability of IgMNOV and the failure of H46 to cross-react with poly(A), poly(I), and denatured DNA, may depend on differences in the degree of protonation required by each antibody, and this may be clarified by a study of the effects of pH on the precipitin behavior of IgMNOV and H46.
Rapid Detection of Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae from Urine Samples by Use of the ESBL NDP Test (2014)

From June to September 2012, 500 urine samples were recovered from patients with urinary tract infections (UTI) due to Gram-negative bacilli (≥ 10(4) leukocytes/ml and ≥ 10(5) Gram-negative isolates/ml) who visited the University hospital Bicêtre (France). They were challenged with extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E) using the rapid diagnostic ESBL NDP test. Results of the ESBL NDP test were compared to the results of the double-disc susceptibility test (DDST) performed on solid-agar plates and molecular identification of the β-lactamase genes. Among the 450 nonduplicate urine samples, 11.3% were positive for ESBL-E by using the DDST, the ESBL determinants being mostly of the CTX-M type (CTX-M-15) according to molecular testing. Results of the ESBL NDP test were obtained within 15 min. The sensitivity and specificity of the ESBL NDP test were 98% and 99.8%, respectively, whereas the positive and negative predictive values of this test were 98% and 99.8%, respectively. A perfect correlation between cefotaxime resistance and positivity of the ESBL NDP test was observed. Therefore, the ESBL NDP test offers a powerful tool for a rapid identification of ESBL-E and associated resistance to expanded-spectrum cephalosporins. It may be useful in particular for guiding first-line antibiotic therapy.
<title>Fast subword permutation instructions based on butterfly network</title> (1999)

Many contemporary microprocessor architectures incorporate multimedia extensions to accelerate media-rich applications using subword arithmetic. While these extensions significantly improve the performance of most multimedia applications, the lack of subword rearrangement support potentially limits performance gain. Several means of adding architectural support for subword rearrangement were proposed and implemented but none of them provide a fully general solution. In this paper, a new class of permutation instructions based on the butterfly interconnection network is proposed to address the general subword rearrangement problem. It can be used to perform arbitrary permutation (without repetition) of n subwords within log n cycles regardless of the subword size. The instruction coding and the low-level implementation for the instructions are quite simple. An algorithm is also given to derive an instruction sequence for any arbitrary permutation.
Diode laser for abdominal tissue cauterization (1999)

We have developed a new device to effectively and quickly stop bleeding. The new device uses a small, 5 W diode laser to heat-up the tip of a modified medical forceps. The laser beam is totally contained within a protective enclosure, satisfying the requirements for a Class I laser system, which eliminates the need to protective eyewear. The new device is used in a manner similar to that of a bipolar electrocautery device. After visual location, the bleeding site or local vessel(s) is grabbed and clamped with the tips of the forceps-like instrument. The laser is then activated for a duration of typically 5 sec or until traditional visual or auditory clues such as local blubbling and popping indicate that the targeted site is effectively cauterized. When the laser is activated, the tip of the instrument, thus providing hemostasis. The new device was evaluated in animal models and compared with the monopolar and bipolar electrocautery, and also with the recently developed ultrasound technology. It has new been in clinical trials for abdominal surgery since September 1997.
A three-dimensional, polarization-insensitive superconducting nanowire avalanche photodetector (2012)

We demonstrate an approach to improving the detection efficiency, removing the polarization dependence, and increasing the signal-to-noise ratio of conventional superconducting nanowire single photon detectors (SNSPDs) by vertically stacking two WSi SNSPDs and electrically connecting them in parallel, forming a three-dimensional superconducting nanowire avalanche photodetector. We measure a peak system detection efficiency of 87.7% ± 0.5% and a polarization dependence of less than 2%, representing nearly an order of magnitude improvement in both system detection efficiency and reduction of polarization dependence compared to conventional SNSPDs.
Silicon nitride cantilevers with oxidation-sharpened silicon tips for atomic force microscopy (2002)

High-resolution atomic force microscopy (AFM) of soft or fragile samples requires a cantilever with a low spring constant and a sharp tip. We have developed a novel process for making such cantilevers from silicon nitride with oxidation-sharpened silicon tips. First, we made and sharpened silicon tips on a silicon wafer. Next, we deposited a thin film of silicon nitride over the tips and etched it to define nitride cantilevers and to remove it from the tips so that they protruded through the cantilevers. Finally, we etched from the back side to release the cantilevers by removing the silicon substrate. We characterized the resulting cantilevers by imaging them with a scanning electron microscope, by measuring their thermal noise spectra, and by using them to image a test sample in contact mode. A representative cantilever had a spring constant of /spl sim/0.06 N/m, and the tip had a radius of 9.2 nm and a cone angle of 36/spl deg/ over 3 /spl mu/m of tip length. These cantilevers are capable of higher resolution imaging than commercially available nitride cantilevers with oxidation-sharpened nitride tips, and they are especially useful for imaging large vertical features.
A Floating-Gate-Based Field-Programmable Analog Array (2010)

A field-programmable analog array (FPAA) with 32 computational analog blocks (CABs) and occupying 3 × 3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in 0.35-μm CMOS is presented. Each CAB has a wide variety of subcircuits ranging in granularity from multipliers and programmable offset wide-linear-range Gm blocks to nMOS and pMOS transistors. The programmable interconnects and circuit elements in the CAB are implemented using floating-gate (FG) transistors, the total number of which exceeds fifty thousand. Using FG devices eliminates the need for SRAM to store configuration bits since the switch stores its own configuration. This system exhibits significant performance enhancements over its predecessor in terms of achievable dynamic range (> 9 b of FG voltage) and speed (≈ 20 gates/s) of accurate FG current programming and isolation between ON and OFF switches. An improved routing fabric has been designed that includes nearest neighbor connections to minimize the penalty on bandwidth due to routing parasitic. A maximum bandwidth of 57 MHz through the switch matrix and around 5 MHz for a first-order low-pass filter is achievable on this chip, the limitation being a “program” mode switch that will be rectified in the next chip. Programming performance improved drastically by implementing the entire algorithm on-chip with an SPI digital interface. Measured results of the individual subcircuits and two system examples including an AM receiver and a speech processor are presented.
Stannyl Derivatives of Naphthalene Diimides and Their Use in Oligomer Synthesis (2012)

2-Stannyl and 2,6-distannyl naphthalene diimides (NDIs) can be synthesized through the palladium-catalyzed reaction of the appropriate bromo derivatives with hexabutylditin. The utility of these precursors in palladium catalyzed cross-coupling reactions is demonstrated by the synthesis of bi- and ter-NDI derivatives, UV-vis, cyclic voltammetry, and n-channel organic field-effect transistor data for which are compared to those of the monomeric parent NDI.
Attenuation of Infectious Bronchitis Virus in Eggs Results in Different Patterns of Genomic Variation across Multiple Replicates (2019)

The gammacoronavirus infectious bronchitis virus (IBV) causes an acute, highly contagious respiratory disease of poultry. Live attenuated vaccines are traditionally generated by serial passage of a virulent strain in embryonated chicken eggs; however, the molecular mechanism of attenuation is unknown. M41-CK, a virulent lab-adapted strain of IBV, was egg passaged over 100 times in four parallel independent replicates. All four final egg-passaged viruses were attenuated <i>in vivo</i> and exhibited similar growth phenotypes in adult chicken kidney cells and <i>ex vivo</i> tracheal organ cultures. The virus populations were sequenced by 454 pyrosequencing at the end of passaging, and the results showed that overall sequence diversity in the IBV population increased but the four replicates only had between 11 and 17 consensus-level single nucleotide polymorphisms (SNPs). Although hot spots of variation were identified in spike and nucleocapsid structural proteins as well as the 3' untranslated region, each attenuated virus possessed a different pattern of genomic variation. Overall, only a small number of consensus-level SNPs were acquired during egg passage, leaving a potentially short route back to virulence. These results highlight the unpredictable nature of attenuation by serial egg passage and the need to develop mechanisms to rationally attenuate IBV for the next generation of effective vaccines.<b>IMPORTANCE</b> Infectious bronchitis remains a major problem in the global poultry industry, despite the existence of many different vaccines. IBV vaccines are currently developed by serial passage of a virulent strain on embryonated hen's eggs until attenuation; however, little is known about the evolution of the viral population during the process of attenuation. High-throughput sequencing of four replicates of a serially egg-passaged IBV revealed a different pattern of genomic variation in each attenuated replicate and few consensus-level SNPs. This raises concerns that only a small number of genomic mutations are required to revert to a virulent phenotype, which may result in vaccine breakdown in the field. The observed hot spots of variation in the attenuated viruses have the potential to be used in the rational attenuation of virulent IBV for next-generation vaccine design.
Total disc replacement using a tissue-engineered intervertebral disc in vivo: new animal model and initial results (2010)

This study demonstrates for the first time that tissue-engineered composite IVDs with circumferentially aligned collagen fibrils survive and integrate with surrounding vertebral bodies when placed in the rat spine for up to 6 months. Tissue-engineered composite IVDs restored function to the rat spine as indicated by maintenance of disc height and vertebral alignment. A significant finding was that maintenance of the composite structure in group III was observed, with increased proteoglycan staining in the nucleus pulposus region (Figure 4d-f). Proteoglycan and collagen matrix as well as disc height preservation and positive T2 signals in MRI are promising parameters and indicate functionality of the implants.
The use of lignosulfonic acid in the synthesis of water‐dispersible polyaniline (2008)

Abstract Polyaniline was synthesized in the presence of lignosulfonic acid to yield a product (LIGNO‐PANI) that is water‐dispersible. Several samples ranging from 0 to 70% lignosulfonate (LS) were prepared. These samples were then evaluated for differences in dispersibility and conductivity. As the percent of LS in the samples was increased, the water‐dispersibility of the LIGNO‐PANI also increased. The particle size of the samples as well as the conductivity of the samples decreased with increasing percentages of LS in the samples. After extensive washings, however, the conductivity remained fairly constant (∼ 0.4 S/cm) regardless of the amount of LS in the samples. Additionally, elemental analysis, TGA, and IR data were used to demonstrate that the LS is grafted to polyaniline during the synthesis of LIGNO‐PANI. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci 2008
Effects of cationic porphyrins as G-quadruplex interactive agents in human tumor cells. (1999)

A series of cationic porphyrins has been identified as G-quadruplex interactive agents (QIAs) that stabilize telomeric G-quadruplex DNA and thereby inhibit human telomerase; 50% inhibition of telomerase activity was achieved in HeLa cell-free extract at porphyrin concentrations in the range < or = 50 microM. Cytotoxicity of the porphyrins in vitro was assessed in normal human cells (fibroblast and breast) and human tumor cells representing models selected for high telomerase activity and short telomeres (breast carcinoma, prostate, and lymphoma). In general, the cytotoxicity (EC50, effective concentration for 50% inhibition of cell proliferation) against normal and tumor cells was > 50 microM. The porphyrins were readily absorbed into tumor cell nuclei in culture. Inhibition of telomerase activity in MCF7 cells by subcytotoxic concentrations of TMPyP4 showed time and concentration dependence at 1-100 microM TMPyP4 over 15 days in culture (10 population doubling times). The inhibition of telomerase activity was paralleled by a cell growth arrest in G2-M. These results suggest that relevant biological effects of porphyrins can be achieved at concentrations that do not have general cytotoxic effects on cells. Moreover, the data support the concept that a rational, structure-based approach is possible to design novel telomere-interactive agents with application to a selective and specific anticancer therapy.
EUV Spectral Purity Filter for Full IR-to-VUV Out-of-Band Rejection, With IR Power Recycling (2015)

A plasma light source for EUV lithography can be spectrally filtered by a phase-Fresnel collector mirror to reject all out-of-band radiation in the IR-to-VUV spectral range, leaving only pure EUV in the filtered output. EUV collection efficiency is not significantly compromised, and EUV conversion efficiency can be enhanced by recycling rejected or uncollected IR back to the plasma via retroreflection. Introduction A phase-Fresnel optic is a grating-type surface (reflecting or transmitting) with a sawtooth profile similar to a Fresnel lens, which preserves optical phase coherence between Fresnel facets at a particular “blaze” wavelength. [Ref. 1] This paper discusses the application of phase-Fresnel spectral filters for extreme ultraviolet (EUV) lithography using a laser-produced plasma (LLP) source, which requires elimination or separation of the infrared (IR) drive-laser radiation from the EUV. Ideally, the full out-of-band spectrum from the deep IR to the vacuum ultraviolet (VUV) should be eliminated in the EUV collection optics. [Ref’s. 2, 3] One type of filter that has been developed for lithography is an LPP collection mirror with a lamellar (rectangular-section) diffraction grating on its surface, which is designed to extinguish the zero-order IR radiation at the 10.6μm laser wavelength. [Ref’s. 4-8] The IR radiation is scattered into first and higher diffraction orders, and an aperture at the collector’s intermediate focus (IF) blocks the scattered IR while transmitting the focused EUV radiation beam. The EUV beam is substantially unaffected by the grating because its wavelength (13.5 nm) is much smaller than the grating period (which is of order 1 mm). In a variation of this process, one of the grating’s first diffraction orders in the IR is directed back (“recycled”) to the plasma source to improve conversion efficiency. [Ref. 9] A limitation of spectral filtering via diffractive IR scattering is that it only eliminates outof-band radiation at one or very few design wavelengths. Also, power recycling is limited by the grating diffraction efficiency. An alternative LPP filtering mechanism discussed in this paper similarly rejects IR by diverting it into a ring or halo around the IF aperture, but not via diffractive scattering. Instead, the collection mirror shape is configured to reflect the specularly reflected IR away from the focus, and a blazed phase-Fresnel grating on the mirror surface diffracts the 13.5-nm EUV toward the focus. The grating dimensions are too small to significantly affect the IR, and complete rejection of unwanted radiation can be achieved over the full IR-to-VUV spectral range. Moreover, efficient power recycling can be achieved by retroreflecting the rejected IR (and also uncollected IR) back to the plasma.