gebhart/patrepeval huggingface dataset:
Effects of protein, mucin, and human tears on adherence of Pseudomonas aeruginosa to hydrophilic contact lenses (1988)

Pseudomonas aeruginosa isolated from a corneal ulcer was examined for its ability to adhere to hydrophilic contact lenses with adsorbed organic films. Generally, adherence was enhanced by mucin, lactoferrin, lysozyme, immunoglobulin A, bovine serum albumin, and a mixture of these macromolecules. The water content of the lenses also influenced bacterial adherence and protein adsorption. Adherence to lenses coated with human tear films was more complex; both enhanced and inhibited adherence were observed on lenses obtained from different individuals.
Effect of amyloid on memory and non-memory decline from preclinical to clinical Alzheimer’s disease (2013)

High amyloid has been associated with substantial episodic memory decline over 18 and 36 months in healthy older adults and individuals with mild cognitive impairment. However, the nature and magnitude of amyloid-related memory and non-memory change from the preclinical to the clinical stages of Alzheimer's disease has not been evaluated over the same time interval. Healthy older adults (n = 320), individuals with mild cognitive impairment (n = 57) and individuals with Alzheimer's disease (n = 36) enrolled in the Australian Imaging, Biomarkers and Lifestyle study underwent at least one positron emission tomography neuroimaging scan for amyloid. Cognitive assessments were conducted at baseline, and 18- and 36-month follow-up assessments. Compared with amyloid-negative healthy older adults, amyloid-positive healthy older adults, and amyloid-positive individuals with mild cognitive impairment and Alzheimer's disease showed moderate and equivalent decline in verbal and visual episodic memory over 36 months (d's = 0.47-0.51). Relative to amyloid-negative healthy older adults, amyloid-positive healthy older adults showed no decline in non-memory functions, but amyloid-positive individuals with mild cognitive impairment showed additional moderate decline in language, attention and visuospatial function (d's = 0.47-1.12), and amyloid-positive individuals with Alzheimer's disease showed large decline in all aspects of memory and non-memory function (d's = 0.73-2.28). Amyloid negative individuals with mild cognitive impairment did not show any cognitive decline over 36 months. When non-demented individuals (i.e. healthy older adults and adults with mild cognitive impairment) were further dichotomized, high amyloid-positive non-demented individuals showed a greater rate of decline in episodic memory and language when compared with low amyloid positive non-demented individuals. Memory decline does not plateau with increasing disease severity, and decline in non-memory functions increases in amyloid-positive individuals with mild cognitive impairment and Alzheimer's disease. The combined detection of amyloid positivity and objectively-defined decline in memory are reliable indicators of early Alzheimer's disease, and the detection of decline in non-memory functions in amyloid-positive individuals with mild cognitive impairment may assist in determining the level of disease severity in these individuals. Further, these results suggest that grouping amyloid data into at least two categories of abnormality may be useful in determining the disease risk level in non-demented individuals.
Generalized Born Model Based on a Surface Integral Formulation (1998)

We have derived a surface-area-based version of the generalized Born model (S-GB) as a well-defined approximation to the boundary element formulation of the Poisson−Boltzmann (PB) equation. The relationship of the surface area methodology to the volume-integration-based approach of Still and co-workers is elucidated. On the basis of insights obtained from these results, we then develop empirical correction schemes which yield significant improvements in accuracy, as compared to the uncorrected GB model, in reproducing accurate solutions of the Poisson−Boltzmann equation. A large suite of energetic comparisons of GB, corrected S-GB, and PB for multiple conformations of peptides and proteins is presented.
Hemodynamic and oxygen transport patterns in surviving and nonsurviving postoperative patients (1985)

Invasive hemodynamic monitoring was performed on 220 critically ill surgical patients judged by clinical evaluation to have a high likelihood of surgical complications or death. Patients with markedly abnormal preoperative hemodynamic values were excluded from analysis. Data were separated into preoperative, intraoperative and postoperative time intervals and the mean value of each variable for each patient at each time period was computed. In comparison to survivors, the nonsurvivors generally had: (a) reduced myocardial performance as judged by lower cardiac index and left ventricular stroke work in the presence of high right and left ventricular filling pressures, (b) reduced pulmonary function (increased alveolar-arterial oxygen content difference and pulmonary shunt fraction), (c) pulmonary vasoconstriction (increased pulmonary artery pressure and pulmonary vascular resistance), and (d) decreased oxygen delivery despite maintenance of normal arterial blood gases and comparable hemoglobin values. Both survivors and nonsurvivors had vital signs usually within the normal range (until the terminal state of nonsurvivors).
Towards low-cost flexible substrates for nanoplasmonic sensing (2012)

Plasmonic nanostructures have played a significant role in the field of nanotechnology due to their unprecedented ability to concentrate light at the nanometre scale, which renders them precious for various sensing applications. The adsorption of plasmonic nanoparticles and nanostructures onto solid substrates in a controlled manner is a crucial process for the fabrication of nanoplasmonic devices, in which the nanoparticles amplify the electromagnetic fields for enhanced device performance. In this perspective article we summarize recent developments in the fabrication of flexible nanoplasmonic devices for sensing applications based on surface enhanced Raman scattering (SERS) and localized surface plasmon resonance (LSPR) shifts. We introduce different types of flexible substrates such as filter paper, free-standing nanofibres, elastomers, plastics, carbon nanotubes and graphene, for the fabrication of low-cost flexible nanoplasmonic devices. Various techniques are described that allow impregnation of such flexible substrates with plasmonic nanoparticles, including solution processes, physical vapour deposition and lithographic techniques. From the discussion in this Perspective, it is clear that highly sensitive and reproducible flexible plasmonic devices can currently be fabricated on a large scale at relatively low-cost, toward real-world applications in diagnostics and detection.
The role of the DNA mismatch repair system in the cytotoxicity of the topoisomerase inhibitors camptothecin and etoposide to human colorectal cancer cells. (2001)

The DNA mismatch repair (MMR) system is involved in the correction of base/base mismatches and insertion/deletion loops arising during replication. In addition, some of the MMR components participate in recombination and double-strand break repair as well as cell cycle regulation and apoptosis. The inactivation of MMR genes, usually hMSH2 or hMLH1, is associated with human colorectal cancers and is responsible for the characteristic microsatellite instability (MSI)+ phenotype of these tumors. Because MMR is assumed to modulate cytotoxicity to various chemotherapeutic agents that act upon DNA, our objectives have been to define its possible involvement in the cytotoxicity of topoisomerase inhibitors. We have shown that colorectal cancer cell lines defective in DNA MMR exhibit an increased sensitivity to both camptothecin, a topoisomerase I inhibitor, and etoposide, a topoisomerase II inhibitor. Sensitivity to these drugs cannot be predicted by measuring endogenous levels of topoisomerase I and II. Our results also indicate that neither p53 status, nor cell cycle alterations correlate with the sensitivity of colorectal cancer cells to topoisomerase inhibitors. On the other hand, our data showing that resistance to these drugs can be achieved by the functional complementation of hMLH1 in an hMLH1-defective cell line have allowed us to establish that MMR is a critical determinant for chemosensitivity. Interestingly, our observations provide the rationale for the better responsiveness of MSI+ tumors to CPT-11, a camptothecin derivative, which we have observed in patients with metastatic colorectal cancers.
Salinity Decreases Nitrite Reductase Gene Diversity in Denitrifying Bacteria of Wastewater Treatment Systems (2004)

Investigation of the diversity of nirK and nirS in denitrifying bacteria revealed that salinity decreased the diversity in a nitrate-containing saline wastewater treatment system. The predominant nirS clone was related to nirS derived from marine bacteria, and the predominant nirK clone was related to nirK of the genus ALCALIGENES:
Reduced fear expression after lesions of the ventral hippocampus (2002)

The hippocampus has a critical role in several fundamental memory operations, including the conditioning of fear to contextual information. We show that the hippocampus is necessary also for unconditioned fear, and that the involved circuitry is at the ventral pole of the hippocampus. Rats with selective hippocampal lesions failed to avoid open arms in an elevated plus-maze and had decreased neuroendocrine stress responses during confinement to a brightly lit chamber. These effects were reproduced by lesions of the ventral half of the hippocampus, but not by damage to the dorsal three-quarters of the hippocampus or the amygdala. Ventral lesions failed to impair contextual fear conditioning or spatial navigation, suggesting that the ventral hippocampus may specifically influence some types of defensive fear-related behavior.
Nanoscale Squeezing in Elastomeric Nanochannels for Single Chromatin Linearization (2012)

This paper describes a novel nanofluidic phenomenon where untethered DNA and chromatin are linearized by rapidly narrowing an elastomeric nanochannel filled with solutions of the biopolymers. This nanoscale squeezing procedure generates hydrodynamic flows while also confining the biopolymers into smaller and smaller volumes. The unique features of this technique enable full linearization then trapping of biopolymers such as DNA. The versatility of the method is also demonstrated by analysis of chromatin stretchability and mapping of histone states using single strands of chromatin.
[Effect of fagopyrum cymosum rootin on clonal formation of four human tumor cells]. (1993)

The effects of fagopyrum cymosum rootin on four human tumor cells in vitro were observed in comparison with 5-Fu. It was found that the clonal formations of four human tumor cells were markedly inhibited and the inhibition rates were positively proportional to concentration. At the concentration of 12.5 micrograms/ml, inhibition rates were GLC 98.7%, Hela 53.8%, SGC 65.4% and KB 82.1%.
Tumor-infiltrating myeloid-derived suppressor cells are pleiotropic-inflamed monocytes/macrophages that bear M1- and M2-type characteristics (2008)

Here, tumor-infiltrating CD11b(+) myelomonocytoid cells in murine colon adenocarcinoma-38 and GL261 murine glioma were phenotypically characterized. Over 90% were of the CD11b(+)F4/80(+) monocyte/macrophage lineage. They also had a myeloid-derived suppressor cell (MDSC) phenotype, as they suppressed the proliferation of activated splenic CD8(+) T cells and had a CD11b(+)CD11c(+)Gr-1(low)IL-4Ralpha(+) phenotype. In addition, the cells expressed CX(3)CR1 and CCR2 simultaneously, which are the markers of an inflammatory monocyte. The MDSCs expressed CD206, CXCL10, IL-1beta, and TNF-alpha mRNAs. They also simultaneously expressed CXCL10 and CD206 proteins, which are typical, classical (M1) and alternative (M2) macrophage activation markers, respectively. Peritoneal exudate cells (PECs) strongly expressed CD36, CD206, and TGF-beta mRNA, which is characteristic of deactivated monocytes. The MDSCs also secreted TGF-beta, and in vitro culture of MDSCs and PECs with anti-TGF-beta antibody recovered their ability to secrete NO. However, as a result of secretion of proinflammatory cytokines, MDSCs could not be categorized into deactivated monocyte/macrophages. Thus, tumor-infiltrating MDSCs bear pleiotropic characteristics of M1 and M2 monocytes/macrophages. Furthermore, CD206 expression by tumor-infiltrating MDSCs appears to be regulated by an autocrine mechanism that involves TGF-beta.
Quantum walks on complex networks with connection instabilities and community structure (2011)

A continuous-time quantum walk is investigated on complex networks with the characteristic property of community structure, which is shared by most real-world networks. Motivated by the prospect of viable quantum networks, I focus on the effects of network instabilities in the form of broken links, and examine the response of the quantum walk to such failures. It is shown that the reconfiguration of the quantum walk is determined by the community structure of the network. In this context, quantum walks based on the adjacency and Laplacian matrices of the network are compared, and their responses to link failures is analyzed.
Effects of hydroxyapatite implants on primary mineralization during rat tibial healing: Biochemical and morphometric analyses (1993)

The effect of 40- to 60-mesh hydroxyapatite (HA) granules (Calcitek, Inc., Carlsbad, CA) on the process of primary mineralization during bone healing was examined following insertion of the HA granules into rat tibial bone after marrow ablation. Response to HA was assessed by monitoring morphometric and biochemical changes in matrix vesicles, which are extracellular organelles associated with initial calcification. Following insertion of HA, matrix vesicle-enriched membranes (MVEMs) were isolated from the tissue adjacent to the implant and from the endosteum of the contralateral limb at 3, 6, 14, and 21 days and from a nonimplanted control group (t = 0). MVEM alkaline phosphatase- and phospholipase A2-specific activities were increased on days 6 (peak) and 14; phosphatidylserine content was also elevated on days 6 and 14 (peak). Comparable changes were seen in the contralateral limb but at lesser magnitudes. Morphological changes were observed as well. The number of matrix vesicles/micron2 matrix increased on days 6 (peak) and 14. The mean diameter of the matrix vesicles was elevated on days 6 (peak), 14, and 21. Mean distance from the calcifying front increased on day 6 but was decreased on days 14 and 21. These results indicated that HA behaves like bone-bonding implants in that there is a stimulation of matrix vesicle enzymes, increased phosphatidylserine content, and increase numbers of matrix vesicles. However, the increases occur only after 6 days postimplantation, indicating a delay in response when compared to normal healing. This delay is confirmed by the morphometric measurements. HA causes a reduction in the response associated with marrow ablation. In addition, the effects of HA are comparable locally and systemically but with different intensity. These observations suggest that osteogenic cells are able to compensate for the inhibitory effects of HA and primary calcification involves normal matrix vesicle production and maturation, if somewhat delayed and reduced in magnitude. The ability to support primary mineral formation may contribute to the successful bonding of HA with surrounding osseous tissue.
Comparison of readout characteristics between magnetooptic transfer heads and magnetic heads (1989)

The readout characteristics of a magnetooptic transfer (MOT) head were compared with those of a magnetic head. Magnetic recording/readout was done on a CrO/sub 2/ flexible disk by using a head with a track width of 5 mu m. A Bi-substituted garnet film with a domain width of 1.2 mu m and an He-Ne laser spot focused down to 3 mu m were used as the MOT head. Readout waveforms from both heads were surprisingly similar. The maximum carrier-to-noise ratio obtained was 50 dB (bandwidth: 30 kHz) for both heads. Experimental data for off-track and crosstalk characteristics demonstrated that the MOT head was suitable for use as a high-track-density readout head. The potential advantages of multitrack readout using MOT heads are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Requirement of nickel metabolism proteins HypA and HypB for full activity of both hydrogenase and urease in <i>Helicobacter pylori</i> (2001)

The nickel-containing enzymes hydrogenase and urease require accessory proteins in order to incorporate properly the nickel atom(s) into the active sites. The Helicobacter pylori genome contains the full complement of both urease and hydrogenase accessory proteins. Two of these, the hydrogenase accessory proteins HypA (encoded by hypA) and HypB (encoded by hypB), are required for the full activity of both the hydrogenase and the urease enzymes in H. pylori. Under normal growth conditions, hydrogenase activity is abolished in strains in which either hypA (HypA:kan) or hypB (HypB:kan) have been interrupted by a kanamycin resistance cassette. Urease activity in these strains is 40 (HypA:kan)- and 200 (HypB:kan)-fold lower than for the wild-type (wt) strain 43504. Nickel supplementation in the growth media restored urease activity to almost wt levels. Hydrogenase activity was restored to a lesser extent, as has been observed for hyp mutants in other (H(2)-oxidizing) bacteria. Expression levels of UreB (the urease large subunit) were not affected by inactivation of either hypA or hypB, as determined by immunoblotting. Urease activity was not affected by lesions in the genes for either the hydrogenase accessory proteins HypD or HypF or the hydrogenase large subunit structural gene, indicating that the urease deficiency was not caused by lack of hydrogenase activity. When crude extracts of wt, HypA:kan and HypB:kan were separated by anion exchange chromatography, the urease-containing fractions of the mutant strains contained about four (HypA:kan)- and five (HypB:kan)-fold less nickel than did the urease from wt, indicating that the lack of urease activity in these strains results from a nickel deficiency in the urease enzyme.
Concentration of autoantibodies to native 60‐kd ro/ss‐a and denatured 52‐kd ro/ss‐a in eluates from the heart of a child who died with congenital complete heart block (1994)

These findings indicate a major role for anti-native 60-kd Ro/SS-A in the immunopathogenesis of CCHB.
Deep brain stimulation of the subthalamic nucleus reestablishes neuronal information transmission in the 6-OHDA rat model of parkinsonism (2014)

Pathophysiological activity of basal ganglia neurons accompanies the motor symptoms of Parkinson's disease. High-frequency (>90 Hz) deep brain stimulation (DBS) reduces parkinsonian symptoms, but the mechanisms remain unclear. We hypothesize that parkinsonism-associated electrophysiological changes constitute an increase in neuronal firing pattern disorder and a concomitant decrease in information transmission through the ventral basal ganglia, and that effective DBS alleviates symptoms by decreasing neuronal disorder while simultaneously increasing information transfer through the same regions. We tested these hypotheses in the freely behaving, 6-hydroxydopamine-lesioned rat model of hemiparkinsonism. Following the onset of parkinsonism, mean neuronal firing rates were unchanged, despite a significant increase in firing pattern disorder (i.e., neuronal entropy), in both the globus pallidus and substantia nigra pars reticulata. This increase in neuronal entropy was reversed by symptom-alleviating DBS. Whereas increases in signal entropy are most commonly indicative of similar increases in information transmission, directed information through both regions was substantially reduced (>70%) following the onset of parkinsonism. Again, this decrease in information transmission was partially reversed by DBS. Together, these results suggest that the parkinsonian basal ganglia are rife with entropic activity and incapable of functional information transmission. Furthermore, they indicate that symptom-alleviating DBS works by lowering the entropic noise floor, enabling more information-rich signal propagation. In this view, the symptoms of parkinsonism may be more a default mode, normally overridden by healthy basal ganglia information. When that information is abolished by parkinsonian pathophysiology, hypokinetic symptoms emerge.
A novel synthetic aperture technique for breast tomography with toroidal arrays (2009)

Ultrasound is commonly used as an adjunct to mammography for diagnostic evaluation of suspicions arising from breast cancer screening. As an alternative to conventional sonography that uses hand-held transducers, toroidal array probes that encircle the breast immersed in a water bath have been investigated for ultrasound tomography. This paper introduces a new method for three-dimensional synthetic aperture diffraction tomography that maximizes the resolution in the scanning direction and provides quantitative reconstructions of the acoustic properties of the object. The method is validated by means of numerical simulations.
Why Do We Use 600 mg of Rifampicin in Tuberculosis Treatment? (2011)

The 600-mg once daily dose of rifampicin plays a key role in tuberculosis treatment. The evidence underpinning this dose is scant. A review of the historical literature identified 3 strands of reasoning. The first is the pharmacokinetic argument: The 600-mg dose yields serum drug concentrations well above the minimum inhibitory concentration of rifampicin against Mycobacterium tuberculosis. The second is the argument that adverse events may be dose related. The third is the economic argument: Rifampicin was prohibitively expensive at the time of its introduction. Recent in vitro, animal, and early bactericidal activity studies suggest that the 600-mg once daily dose is at the lower end of the dose-response curve, refuting the pharmacokinetic argument. The reduced cost and the lack of evidence of toxicity at higher daily doses remove the other arguments. To optimize tuberculosis treatment, the clinical value of higher doses of rifampicin should be tested in clinical trials.
ACOUSTICS2008/1857 Critical-band compression method of speech enhancement for elderly people: Investigation of syllable and word intelligibility (2008)

Auditory filters for the hearing impaired tend to be wider than those of normal hearing people. Thus, the frequency selectivity decreases because of increased masking eects [Glasberg and Moore, J. Acoust. Soc. Am., 79(4), 1020-1033, 1986]. We have developed a method, called ”critical-band compression,” in which the critical band is compressed along the frequency axis [Yasu et al., Handbook of the International Hearing Aid Research Conference (IHCON), 55, Lake Tahoe, 2004]. We investigated whether our method improves syllable and word intelligibility. Thirty one elderly people participated in experiments. First, we measured the auditory filter bandwidth using a notched noise method [Patterson, J. Acoust. Soc. Am., 59(3), 640-654, 1976]. Second, we conducted syllable and word intelligibility tests. The compression rates of critical-band compression were set to 0% for the original, and 25%, 50%, and 75%. The results were that the percentages of correct responses were almost the same at 0%, 25% and 50% compression rates for syllable and word intelligibility. A significant correlation was not obtained between the compression rate of processing and the auditory filter bandwidth. [Work supported by JSPS.KAKENHI (16203041) and Sophia University Open Research Center from MEXT.]