gebhart/patrepeval huggingface dataset:
Mitochondrial Dysfunction in the Elderly: Possible Role in Insulin Resistance (2003)

Insulin resistance is a major factor in the pathogenesis of type 2 diabetes in the elderly. To investigate how insulin resistance arises, we studied healthy, lean, elderly and young participants matched for lean body mass and fat mass. Elderly study participants were markedly insulin-resistant as compared with young controls, and this resistance was attributable to reduced insulin-stimulated muscle glucose metabolism. These changes were associated with increased fat accumulation in muscle and liver tissue assessed by 1H nuclear magnetic resonance (NMR) spectroscopy, and with a approximately 40% reduction in mitochondrial oxidative and phosphorylation activity, as assessed by in vivo 13C/31P NMR spectroscopy. These data support the hypothesis that an age-associated decline in mitochondrial function contributes to insulin resistance in the elderly.
Allergic and irritant contact dermatitis (2009)

Irritant and allergic contact dermatitis are common inflammatory skin diseases induced by repeated skin contact with low molecular weight chemicals, called xenobiotics or haptens. Although both diseases may have similar clinical presentations, they can be differentiated on pathophysiological grounds. Irritant contact dermatitis (ICD) is a non-specific inflammatory dermatitis brought about by activation of the innate immune system by the pro-inflammatory properties of chemicals. Allergic contact dermatitis (ACD) corresponds to a delayed-type hypersensitivity response with a skin inflammation mediated by hapten-specific T cells. Recent progress in the pathophysiology of chemical-induced skin inflammation has shown that ICD and ACD are closely associated and that the best way to prevent ACD is to develop strategies to avoid ICD. The immunological diagnosis of ICD or ACD requires investigation of the presence (ACD) or absence (ICD) of antigen-specific T cells. The detection of T cells can be performed in the skin (collected from ACD lesions or positive patch tests) and/or in the blood, particularly by using the enzyme-linked immunospot assay (ELISPOT). This method, recently developed in ACD to metals, offers a new biological tool enabling the immunobiological diagnosis of ACD.
이익관리수단에 관한 연구 (2004)

본 연구는 한국 상장기업들이 이익관리를 할 때 어느 수단을 이용하는지를 실증적으로 연구하였다. 이를 위하여 1995년부터 2001년까지의 기업-년자료 2,895개를 발생액의 정도에 따라 각각 이익증가집단, 중간집단 및 이익감소집단으로 구분하여 이익관리수단에 어떤 체계적인 차이가 있는지를 분석하였다. 본 연구에서는 영업활동으로 인한 현금흐름과 함께 회계이익을 구성하는 발생액을 3단계에 걸쳐 체계적으로 구분하였으며, 기업들이 보고이익을 증가하거나 감소시킬 때 어느 수단을 활용하는지를 검토하였다. 실증분석결과 보고이익증가집단과 보고이익감소집단 간에는 기업들이 활용하는 이익관리수단에 상당한 차이가 있는 것으로 나타났다. 구체적으로 보면 이익증가집단은 자산처분차익을 주로 활용하는 반면, 이익감소집단은 대손상각비와 자산처분차손을 주로 활용하는 것으로 나타났다.
The effect of hydrogen plasma on the properties of a-Si:H/a-Si1-xNx:H superlattices (1988)

Abstract A hydrogen plasma introduced during the interrupting interval when alternating two gases affects the properties of a-Si:H/a-Si1-xNx:H superlattices resulting in the creation of fewer interface defects than the superlattices prepared without the hydrogen plasma.
Recovering high dynamic range radiance maps from photographs (2008)

We present a method of recovering high dynamic range radiance maps from photographs taken with conventional imaging equipment. In our method, multiple photographs of the scene are taken with different amounts of exposure. Our algorithm uses these differently exposed photographs to recover the response function of the imaging process, up to factor of scale, using the assumption of reciprocity. With the known response function, the algorithm can fuse the multiple photographs into a single, high dynamic range radiance map whose pixel values are proportional to the true radiance values in the scene. We demonstrate our method on images acquired with both photochemical and digital imaging processes. We discuss how this work is applicable in many areas of computer graphics involving digitized photographs, including image-based modeling, image compositing, and image processing. Lastly, we demonstrate a few applications of having high dynamic range radiance maps, such as synthesizing realistic motion blur and simulating the response of the human visual system.
DUX4-induced gene expression is the major molecular signature in FSHD skeletal muscle (2014)

Facioscapulohumeral dystrophy (FSHD) is caused by decreased epigenetic repression of the D4Z4 macrosatellite array and recent studies have shown that this results in the expression of low levels of the DUX4 mRNA in skeletal muscle. Several other mechanisms have been suggested for FSHD pathophysiology and it remains unknown whether DUX4 expression can account for most of the molecular changes seen in FSHD. Since DUX4 is a transcription factor, we used RNA-seq to measure gene expression in muscle cells transduced with DUX4, and in muscle cells and biopsies from control and FSHD individuals. We show that DUX4 target gene expression is the major molecular signature in FSHD muscle together with a gene expression signature consistent with an immune cell infiltration. In addition, one unaffected individual without a known FSHD-causing mutation showed the expression of DUX4 target genes. This individual has a sibling with FSHD and also without a known FSHD-causing mutation, suggesting the presence of an unidentified modifier locus for DUX4 expression and FSHD. These findings demonstrate that the expression of DUX4 accounts for the majority of the gene expression changes in FSHD skeletal muscle together with an immune cell infiltration.
Human IL-3/GM-CSF knock-in mice support human alveolar macrophage development and human immune responses in the lung (2011)

Mice with a functional human immune system have the potential to allow in vivo studies of human infectious diseases and to enable vaccine testing. To this end, mice need to fully support the development of human immune cells, allow infection with human pathogens, and be capable of mounting effective human immune responses. A major limitation of humanized mice is the poor development and function of human myeloid cells and the absence of human immune responses at mucosal surfaces, such as the lung. To overcome this, we generated human IL-3/GM-CSF knock-in (hIL-3/GM-CSF KI) mice. These mice faithfully expressed human GM-CSF and IL-3 and developed pulmonary alveolar proteinosis because of elimination of mouse GM-CSF. We demonstrate that hIL-3/GM-CSF KI mice engrafted with human CD34(+) hematopoietic cells had improved human myeloid cell reconstitution in the lung. In particular, hIL-3/GM-CSF KI mice supported the development of human alveolar macrophages that partially rescued the pulmonary alveolar proteinosis syndrome. Moreover, human alveolar macrophages mounted correlates of a human innate immune response against influenza virus. The hIL-3/GM-CSF KI mice represent a unique mouse model that permits the study of human mucosal immune responses to lung pathogens.
Improvement of in‐gel digestion protocol for peptide mass fingerprinting by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (2001)

Abstract High‐sensitivity, high‐throughput analysis of proteins for proteomics studies is usually performed by polyacrylamide gel electrophoresis in combination with mass spectrometry. However, the quality of the data obtained depends on the in‐gel digestion procedure employed. This work describes an improvement in the in‐gel digestion efficiency for matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) analysis. A dramatic improvement in the coverage of tryptic peptides was observed when n‐octyl glucoside was added to the buffer. Whole cell extracted proteins from S. cerevisiae were separated by two‐dimensional gel electrophoresis and stained with silver. Protein spots were identified using our improved in‐gel digestion method and MALDI‐TOFMS. In addition, the mass spectra obtained by using the matrix α‐cyano‐4‐hydroxycinnamic acid (CHCA) were compared with those obtained using 2,5‐dihydroxybenzoic acid (DHB). The DHB matrix usually gave more peaks, which led to higher sequence coverage and, consequently, to higher confidence in protein identification. This improved in‐gel digestion protocol is simple and useful for protein identification by MALDI‐TOFMS. Copyright © 2001 John Wiley &amp; Sons, Ltd.
Quantum Dot DNA Bioconjugates: Attachment Chemistry Strongly Influences the Resulting Composite Architecture (2010)

The unique properties provided by hybrid semiconductor quantum dot (QD) bioconjugates continue to stimulate interest for many applications ranging from biosensing to energy harvesting. Understanding both the structure and function of these composite materials is an important component in their development. Here, we compare the architecture that results from using two common self-assembly chemistries to attach DNA to QDs. DNA modified to display either a terminal biotin or an oligohistidine peptidyl sequence was assembled to streptavidin/amphiphilic polymer- or PEG-functionalized QDs, respectively. A series of complementary acceptor dye-labeled DNA were hybridized to different positions on the DNA in each QD configuration and the separation distances between the QD donor and each dye-acceptor probed with Förster resonance energy transfer (FRET). The polyhistidine self-assembly yielded QD-DNA bioconjugates where predicted and experimental separation distances matched reasonably well. Although displaying efficient FRET, data from QD-DNA bioconjugates assembled using biotin-streptavidin chemistry did not match any predicted separation distances. Modeling based upon known QD and DNA structures along with the linkage chemistry and FRET-derived distances was used to simulate each QD-DNA structure and provide insight into the underlying architecture. Although displaying some rotational freedom, the DNA modified with the polyhistidine assembles to the QD with its structure extended out from the QD-PEG surface as predicted. In contrast, the random orientation of streptavidin on the QD surface resulted in DNA with a wide variety of possible orientations relative to the QD which cannot be controlled during assembly. These results suggest that if a particular QD biocomposite structure is desired, for example, random versus oriented, the type of bioconjugation chemistry utilized will be a key influencing factor.
High-Sensitivity Quantitative PCR Platform (2003)

Real-time PCR methods have become widely used within the past few years. However, real-time PCR is rarely used to study chronic diseases with low pathogen loads, presumably because of insufficient sensitivity. In this report, we developed an integrated nucleic acid isolation and real-time PCR platform that vastly improved the sensitivity of the quantitative detection of the intracellular bacterium, Chlamydia spp., by fluorescence resonance energy transfer real-time PCR. Determinants of the overall detection sensitivity were analyzed by extracting nucleic acids from bovine milk specimens spiked with low amounts of chlamydial organisms. Nucleic acids were optimally preserved and recovered by collection in guanidinium stabilization buffer, binding to a matrix of glass fiber fleece, and elution in low volume. Step-down thermal cycling and an excess of hot-start Taq polymerase vastly improved the robustness and sensitivity of the real-time PCR while essentially maintaining 100% specificity. The amplification of Chlamydia 23S rRNA allowed for the differentiation of chlamydial species and was more robust at low target numbers than amplification of the omp1 gene. The best combined method detected single targets per a 100-microL specimen equivalent in a 5-microL real-time PCR input. In an initial application, this high-sensitivity real-time PCR platform demonstrated a high prevalence of chlamydial infection in cattle.
Design of an 8&#x2013;40 GHz antenna for the wideband instrument for snow measurements (WISM) (2015)

Measurement of land surface snow remains a significant challenge in the remote sensing arena. Developing the tools needed to remotely measure Snow Water Equivalent (SWE) is an important priority. The Wideband Instrument for Snow Measurements (WISM) is being developed to address this need. WISM is an airborne instrument comprised of a dual-frequency (X- and Ku-band) Synthetic Aperture Radar (SAR) and dual-frequency (K- and Ka-band) radiometer. A unique feature of this instrument is that all measurement bands share a common antenna aperture consisting of an array-feed reflector that covers the entire bandwidth. This paper covers the design and fabrication of the wideband array feed, which is based on tightly coupled dipole arrays. Implementation using a relatively new multi-layer microfabrication process results in a small, 6×6-element, dual-linear polarized array with beamformer that operates from 8 to 40 GHz.
From colloidal-silica sols to aerogels and xerogels (1992)

By destabilization of quasi-monodisperse silica sols, fractal clusters can be obtained. Solvent evacuation gives a porous solid with fractal structure. Structural investigations of these colloidal aerogels by small-angle neutron scattering are presented, and compared to similar observations in concentrated sols and xerogels. An investigation of the vibrational modes of these materials by inelastic neutron scattering gives clear evidence of a strong non-Debye contribution in the low-frequency regime.
Benefit-risk assessment of tumour necrosis factor antagonists in the treatment of psoriasis (2010)

These analyses demonstrated that, during the initial year of treatment, the likelihood of success with anti-TNF therapy for psoriasis was several orders of magnitude greater than the likelihood of serious toxicity.
Adaptive beam steering implemented in a ferroelectric liquid-crystal spatial-light-modulator free-space, fiber-optic switch (2002)

Active alignment of a 1 x 8 free-space optical switch was studied experimentally. Optical signals, carried on single-mode fibers, were switched by a ferroelectric liquid-crystal-on-silicon spatial light modulator. Continuous measurement of the in-coupled power to the fibers provided feedback for the switch control. The switch automatically located and locked to the output fibers. An advantage with adaptive switches of a similar kind is relaxed geometrical tolerances in the switch assembly. Further, such switches can adapt to possible geometrical changes and light wavelength drift during operation.
The Paris System for Reporting Urinary Cytology: The Quest to Develop a Standardized Terminology (2016)

The main purpose of urine cytology is to detect high-grade urothelial carcinoma. With this principle in mind, The Paris System (TPS) Working Group, composed of cytopathologists, surgical pathologists, and urologists, has proposed and published a standardized reporting system that includes specific diagnostic categories and cytomorphologic criteria for the reliable diagnosis of high-grade urothelial carcinoma. This paper outlines the essential elements of TPS and the process that led to the formation and rationale of the reporting system. TPS Working Group, organized at the 2013 International Congress of Cytology, conceived a standardized platform on which to base cytologic interpretation of urine samples. The widespread dissemination of this approach to cytologic examination and reporting of urologic samples and the scheme's universal acceptance by pathologists and urologists is critical for its success. For urologists, understanding the diagnostic criteria, their clinical implications, and limitations of TPS is essential if they are to utilize urine cytology and noninvasive ancillary tests in a thoughtful and practical manner. This is the first international/inclusive attempt at standardizing urinary cytology. The success of TPS will depend on the pathology and urology communities working collectively to improve this seminal paradigm shift, and optimize the impact on patient care.
Cryptosporidiosis Facilitated by Murine Retroviral Infection with LP-BM5 (1991)

LP-BM5 murine leukemia virus infection caused alterations in splenic T cell subsets in adult C57BL/6 female mice. Prolonged infection resulted in increased immunosuppression and a concomitant decreased resistance to Cryptosporidium parvum infection. Significant Cryptosporidium colonization of the intestinal villi was seen 10 days after oral challenge in mice infected with murine retrovirus for 3 months but not in non-virally infected controls. Parasite numbers per villus of retrovirally infected mice were 20-fold higher than in controls, which showed only occasional parasites. Feces from most virally infected mice but none from controls contained oocysts. Cryptosporidium infection in mice after 4 and 5 months of retroviral infection was accompanied by severe immunosuppression and parasite levels 50-5000 times higher than in controls. A high level of infection persisted 21 days after Cryptosporidium challenge in virally infected mice, while controls cleared their transient and marginal infection. These results further characterize LP-BM5 infection as a murine model of retrovirally induced acquired immune deficiency.
The requirement for lymphocyte function-associated antigen 1 in homotypic leukocyte adhesion stimulated by phorbol ester. (1986)

Lymphocytes become adherent and aggregate after stimulation with phorbol esters such as PMA. Time-lapse video showed that aggregating cells were motile and exhibited vigorous pseudopodial movements. Adhesion sites were initiated between pseudopodia of neighboring cells, and then moved to the uropod. PMA-stimulated aggregation by EBV-transformed B cell lines, SKW-3 (a T cell line), differentiated U937 (a monocytic line), and blood lymphocytes was inhibited by mAbs to LFA-1. A number of different mAb to the LFA-1 alpha and beta subunits and F(ab')2 and Fab' fragments inhibited aggregation. Furthermore, lymphoblasts from normal individuals, but not from LFA-1-deficient patients, aggregated in response to PMA. These findings suggest LFA-1 is critically involved in stimulated lymphocyte adhesion. LFA-1 expression was not increased by PMA stimulation, showing that other mechanisms regulate LFA-1-dependent adherence. LFA-1-deficient patient cells were able to coaggregate with LFA-1+ cells, showing that aggregation is not mediated by like-like interactions between LFA-1 molecules on opposite cells. Aggregation was Mg+2-dependent, inhibited by cytochalasin B, and was reversed when LFA-1 mAb was added to preformed aggregates. Previous findings suggesting that LFA-1 is important in a wide variety of leukocyte functions are elucidated by this work, which shows that LFA-1 is a general leukocyte cell adhesion molecule, the activity of which is regulated by cell activation.
Large-Scale Hierarchical Organization of Nanowire Arrays for Integrated Nanosystems (2003)

The assembly of nanowires and nanotubes into arrays patterned on multiple length scales is critical to the realization of integrated electronic and photonic nanotechnologies. A general and efficient solution-based method for controlling organization and hierarchy of nanowire structures over large areas has been developed. Nanowires were aligned with controlled nanometer to micrometer scale pitch using the Langmuir−Blodgett technique and transferred to planar substrates in a layer-by-layer process to form parallel and crossed nanowire structures. The parallel and crossed nanowire structures were efficiently patterned into repeating arrays of controlled dimensions and pitch using photolithography to yield hierarchical structures with order defined from the nanometer through centimeter length scales. In addition, electrical transport studies show that reliable electrical contacts can be made to the hierarchical nanowire arrays prepared by this method. This solution-based process offers a flexible pathway for bottom-up assembly of virtually any nanowire material into highly integrated and hierarchically organized nanodevices needed for a broad range of functional nanosystems.
Comparative study of two typing methods,hsp65 PRA and ITS sequencing, revealed a possible evolutionary link betweenMycobacterium kansasiitype I and II isolates (2005)

One hundred and ninety-eight clinical isolates of Mycobacterium kansasii collected between 2003 and 2004 in Japan were genotyped by PCR and restriction enzyme analysis (PRA) and 16S-23S internal transcribed spacer (ITS) sequencing. The results demonstrated that clinical isolates of M. kansasii in Japan are almost exclusively of the type I PRA genotype, as is the case in other countries. Although the results of subtyping using the 16S-23S ITS sequence were generally consistent with subtyping using hsp65 PRA, four strains showed a discrepancy between the two methods. Sequence analysis of the hsp65, gyrB and 16S rRNA genes and the ITS sequence of the four strains suggests that they branched from type II and could be considered an ancestral strain of the type I strain. The newly recognized strains were designated as intermediate type I.
Tempering by Subsampling (2014)

In this paper we demonstrate that tempering Markov chain Monte Carlo samplers for Bayesian models by recursively subsampling observations without replacement can improve the performance of baseline samplers in terms of effective sample size per computation. We present two tempering by subsampling algorithms, subsampled parallel tempering and subsampled tempered transitions. We provide an asymptotic analysis of the computational cost of tempering by subsampling, verify that tempering by subsampling costs less than traditional tempering, and demonstrate both algorithms on Bayesian approaches to learning the mean of a high dimensional multivariate Normal and estimating Gaussian process hyperparameters.
TNFR1 mediates the radioprotective effects of lipopolysaccharide in the mouse intestine (2004)

LPS is radioprotective in the mouse small intestine through a mechanism that includes the synthesis of cyclooxygenase-2 (COX-2) and PGE2. The goal of this study was to identify the intermediate steps in this process. We used wild-type (WT) C57BL/6 mice and knockouts for tumor necrosis factor receptors 1 and 2 (TNFR1-/-, TNFR2-/-) and recombination-activating gene 1-/- mice. Mice were given parenteral LPS and then subjected to 12 Gy total body gamma irradiation. The number of surviving intestinal crypts was assessed 3.5 days after irradiation using a clonogenic assay. Crypt cell apoptosis was assessed by histology. Parenteral administration of LPS induced COX-2 expression, PGE2 production, and radioprotection in WT and TNFR2-/- mice but not in TNFR1-/- mice. TNFR1-/- mice were radioprotected by administration of exogenous 16,16-dimethyl PGE2. Immunohistochemical studies localized TNFR1 and COX-2 expression to subeptihelial fibroblasts and villus epithelial cells. Radiation-induced apoptosis was reduced by pretreatment with LPS in WT and TNFR2-/- mice but not in TNFR1-/- mice. In the absence of LPS, crypt survival was elevated in TNFR1-/- when compared with WT mice. These findings demonstrate that TNFR1 function is required for LPS-induced radioprotection in C57BL/6 mice and define an essential role for TNFR1 function in the induction of COX-2 expression and PGE2 production in this process. The immunolocalization of TNFR1 and COX-2 expression to subepithelial fibroblasts following LPS administration suggests that this cell type plays an intermediate role in LPS-induced radioprotection in the intestine.