gebhart/patrepeval huggingface dataset:
I-Shaped Microchannel Array Chip for Parallel Electrophoretic Analyses (2007)

We demonstrate electrophoresis in I-shaped microchannels with a new design and operation principle. Unlike the conventional T- or cross-shaped microchannels, the simple I-shaped design makes it straightforward to integrate parallel microchannels with electrodes onto a microchip. The operation of the I-shaped microchannels has been enabled by the autonomous solution filling technique, which exploits the high gas solubility in poly(dimethylsiloxane) (PDMS). We fabricated an I-shaped microchannel array (IMA) chip by integrating 12 independent microchannels and 2 electrodes onto a 3 cm x 2 cm area in a PDMS-glass hybrid microchip. For autonomous regulation of stable sample plugs in all the microchannels, we discovered that O2 plasma treatment of the PDMS-made reservoirs is effective. On the IMA chip, size-dependent separation of double-stranded (ds) DNA and sequence-specific separation of single-stranded DNA were achieved. Specifically, 10 fragments in a 100-1000-bp dsDNA ladder were separated using hydroxyethylcellulose as a sieving matrix within a separation length of 2 mm, and polymerase chain reaction products of the wild-type K-ras gene and its point mutant were separated using a probe DNA-poly(dimethylacrylamide) conjugate on the basis of affinity capillary electrophoresis. The IMA chip presented here opens up a new possibility of large-scale integration of microchannels for high-throughput electrophoretic analyses.
Lipids Significantly Reduced by Diets Containing Barley in Moderately Hypercholesterolemic Men (2004)

Increasing soluble fiber through consumption of barley in a healthy diet can reduce cardiovascular risk factors.
High-Precision Catalysts:  Regioselective Hydroformylation of Internal Alkenes by Encapsulated Rhodium Complexes (2006)

We report the formation of high-precision catalysts using encapsulated rhodium complexes. In the current example, the encapsulated rhodium catalyst shows unprecedented high selectivity in the rhodium-catalyzed hydroformylation of internal alkenes, forming predominantly one of the branched aldehydes. This catalyst system is the first example that is able to discriminate between carbon atoms C3 and C4 in trans-3-octene.
An approach to extracting the target text line from a document image captured by a pen scanner (2004)

In this paper, we present a new approach to extracting the target text line from a document image captured by a pen scanner. Given the binary image, a set of possible text lines are first formed by nearest-neighbor grouping of connected components (CC). They are then refined by text line merging and adding the missed CCs. The possible target text line is identified by using a geometric feature based score function and fed to an OCR engine for character recognition. If the recognition result is confident enough, the target text line is accepted. Otherwise, all the remaining text lines are fed to the OCR engine to verify whether an alternative target text line exists or the whole image should be rejected. The effectiveness of the above approach is confirmed by experiments on a testing database consisting of 117 document images captured by C-Pen and ScanEye pen scanners.
A GATA binding site is involved in the regulation of 15‐lipoxygenase‐1 expression in human colorectal carcinoma cell line, Caco‐2 (2000)

The data presented implicate a GATA binding site in the transcriptional regulation of 15-lipoxygenase-1 (15-LO-1) gene expression in human colorectal carcinoma Caco-2 cells. High expression of GATA-6 mRNA and protein was observed, while GATA-4 mRNA was expressed at a very low level in Caco-2 cells. The expression of GATA-6 was down-regulated, while 15-LO-1 expression was dramatically up-regulated after treatment with sodium butyrate (NaBT). A study using an electrophoretic mobility shift assay indicated that a GATA binding site of the 15-LO-1 promoter region binds to GATA proteins present in both undifferentiated and, to a lesser extent, NaBT-treated (differentiated) Caco-2 cells. Moreover, that DNA binding shift band was disrupted after the addition of GATA-6 antibody in a supershift assay in the absence of NaBT, suggesting that GATA-6 is bound to the GATA binding site of the 15-LO-1 promoter in undifferentiated cells. In contrast, the addition of GATA-6 antibody did not affect the DNA binding ability in NaBT-induced differentiated cells. On the other hand, mutation of the GATA site of the 15-LO-1 promoter decreased the transactivation of the 15-LO-1 promoter as measured by luciferase activity in both FBS and NaBT cultured cells, indicating an unknown GATA binding protein to up-regulate 15-LO-1 expression. These implicate the GATA site at -240 of the proximal region of the 15-LO-1 promoter in the basic transcription of 15-LO-1 gene expression in Caco-2 cells, with GATA-6 acting to repress 15-LO-1 expression.
Temporal Trends in Rates of Patient Harm Resulting from Medical Care (2010)

In a study of 10 North Carolina hospitals, we found that harms remain common, with little evidence of widespread improvement. Further efforts are needed to translate effective safety interventions into routine practice and to monitor health care safety over time. (Funded by the Rx Foundation.).
Changes in extracellular space size and geometry in APP23 transgenic mice: A model of Alzheimer's disease (2005)

Diffusion parameters of the extracellular space (ECS) are changed in many brain pathologies, disturbing synaptic as well as extrasynaptic "volume" transmission, which is based on the diffusion of neuroactive substances in the ECS. Amyloid deposition, neuronal loss, and disturbed synaptic transmission are considered to be the main causes of Alzheimer's disease dementia. We studied diffusion parameters in the cerebral cortex of transgenic APP23 mice, which develop a pathology similar to Alzheimer's disease. The real-time tetramethylammonium (TMA) method and diffusion-weighted MRI were used to measure the ECS volume fraction (alpha = ECS volume/total tissue volume) and the apparent diffusion coefficients (ADCs) of TMA (ADC(TMA)), diffusing exclusively in the ECS and of water (ADC(W)). Measurements were performed in vivo in 6-, 8-, and 17- to 25-month-old hemizygous APP23 male and female mice and age-matched controls. In all 6- to 8-month-old APP23 mice, the mean ECS volume fraction, ADC(TMA), and ADC(W) were not significantly different from age-matched controls (alpha = 0.20 +/- 0.01; ADC(TMA), 580 +/- 16 microm(2).s(-1); ADC(W), 618 +/- 19 microm(2).s(-1)). Aging in 17- to 25-month-old controls was accompanied by a decrease in ECS volume fraction and ADC(W), significantly greater in females than in males, but no changes in ADC(TMA). ECS volume fraction increased (0.22 +/- 0.01) and ADC(TMA) decreased (560 +/- 7 microm(2).s(-1)) in aged APP23 mice. The impaired navigation observed in these animals in the Morris water maze correlated with their plaque load, which was twice as high in females (20%) as in males (10%) and may, together with changed ECS diffusion properties, account for the impaired extrasynaptic transmission and spatial cognition observed in old transgenic females.
TLR and NKG2D Signaling Pathways Mediate CS-Induced Pulmonary Pathologies (2013)

Long-term exposure to cigarette smoke (CS) can have deleterious effects on lung epithelial cells including cell death and the initiation of inflammatory responses. CS-induced cell injury can elaborate cell surface signals and cellular byproducts that stimulate immune system surveillance. Our previous work has shown that the expression of ligands for the cytotoxic lymphocyte activating receptor NKG2D is enhanced in patients with COPD and that the induction of these ligands in a mouse model can replicate COPD pathologies. Here, we extend these findings to demonstrate a role for the NKG2D receptor in CS-induced pathophysiology and provide evidence linking nucleic acid-sensing endosomal toll-like receptor (TLR) signaling to COPD pathology through NKG2D activation. Specifically, we show that mice deficient in NKG2D exhibit attenuated pulmonary inflammation and airspace enlargement in a model of CS-induced emphysema. Additionally, we show that CS exposure induces the release of free nucleic acids in the bronchoalveolar lavage and that direct exposure of mouse lung epithelial cells to cigarette smoke extract similarly induces functional nucleic acids as assessed by TLR3, 7, and 9 reporter cell lines. We demonstrate that exposure of mouse lung epithelial cells to TLR ligands stimulates the surface expression of RAET1, a ligand for NKG2D, and that mice deficient in TLR3/7/9 receptor signaling do not exhibit CS-induced NK cell hyperresponsiveness and airspace enlargement. The findings indicate that CS-induced airway injury stimulates TLR signaling by endogenous nucleic acids leading to elevated NKG2D ligand expression. Activation of these pathways plays a major role in the altered NK cell function, pulmonary inflammation and remodeling related to long-term CS exposure.
PCR‐mediated seamless gene deletion and marker recycling in Saccharomyces cerevisiae (2006)

Repeated gene manipulations can be performed in yeast by excision of an introduced marker. Cassette modules containing a marker flanked by two direct repeat sequences of hisG or loxP have often been used for marker recycling, but these leave one copy of the repeats in the chromosome after excision. Genomic copies of a repeat can cause increased mistargeting of constructs containing the same repeats or unexpected chromosomal rearrangements via intra- or interchromosomal recombinations. Here, we describe a novel marker recycling procedure that leaves no scar in the genome, which we have designated seamless gene deletion. A 40 base sequence derived from an adjacent region to the targeted locus was placed in an integrating construct to generate direct repeats after integration. Seamless HIS3 deletion was achieved via a PCR fragment that consisted of a URA3 marker attached to a 40 base repeat-generating sequence flanked by HIS3 targeting sequences at both ends. Transformation of the designed construct resulted in his3 disruption and the generation of 40 base direct repeats on both sides of URA3 in the targeted locus. The resulting his3::URA3 disruptants were plated on 5-fluoroorotic acid medium to select for URA3 loss. All the selected colonies had lost URA3 precisely by recombination between the repeats, resulting in his3 deletion without any extraneous sequences left behind in the chromosome.
DEVELOPMENTAL CYCLES AND BIOLOGY OF PATHOGENIC TRYPANOSOMES (1985)

Journal Article DEVELOPMENTAL CYCLES AND BIOLOGY OF PATHOGENIC TRYPANOSOMES Get access Keith Vickerman Keith Vickerman Department of Zoology, University of Glasgow Search for other works by this author on: Oxford Academic PubMed Google Scholar British Medical Bulletin, Volume 41, Issue 2, 1985, Pages 105–114, https://doi.org/10.1093/oxfordjournals.bmb.a072036 Published: 01 June 1985
Detection of human cytomegalovirus in clinical specimens by centrifugation culture with a nonhuman cell line (1992)

The sensitivities of MRC-5 and mink lung (ML) cells in centrifugation culture were compared simultaneously for the detection of cytomegalovirus (CMV) IE antigen (immediate-early antigen) from clinical specimens. Of 413 samples assayed, 51 (12%) were positive for CMV by both centrifugation and standard cell culture. At 20 h postinoculation (p.i.), 46 of 51 (90.2%) CMV-positive specimens were detected in ML cells. At 40 h p.i., 50 of 51 (98.0%) CMV-positive specimens were detected in ML cells, compared with 48 of 51 (94.0%) in MRC-5 cells. There was no significant difference in the detection of CMV in either cell line by centrifugation culture. However, in 19 of 23 positive samples that had countable foci at 20 h p.i., there was a 25% increase in the number of positive foci observed for ML cells compared with MRC-5 cells. Less toxicity was also noted for ML cells than for MRC cells, particularly in viral blood specimens. These data suggest that ML cells are comparable to MRC-5 cells for the rapid detection of CMV by centrifugation culture.
Plasma membrane-associated tumor necrosis factor. A non-integral membrane protein possibly bound to its own receptor. (1988)

Purified plasma membranes from LPS-activated human blood monocytes produced significant lysis and growth inhibition of the TNF-sensitive L929 murine fibroblast cell line. Unactivated human monocyte plasma membranes did not display either activity. Anti-TNF serum specifically inhibited the anti-tumor activity of activated monocyte membranes whereas anti-IL-1 serum or non-specific rabbit serum decreased neither the lysis nor growth inhibition of L929 cells. Membrane-associated TNF did not behave as an integral protein as it could be eluted from the plasma membranes by either high salt or low pH treatment. Plasma membranes cleared of membrane-associated TNF by high salt treatment were able to bind TNF, and this binding was specifically inhibited by preincubation of rTNF with specific anti-TNF serum. Western blot analysis of plasma membranes showed a membrane-associated TNF with a m. w. of approximately 17 kDa present only in the activated monocytes. When the plasma membranes were preincubated with the cross-linker agent dissuccinimidyl suberate, Western blot analysis revealed the presence of a TNF-binding protein with a Mr of approximately 102 kDa. These studies indicate that unlike IL-1, membrane-associated TNF is not an integral membrane protein and that TNF may be associated with the monocyte membrane by occupying the TNF R.
Views to nature: Effects on attention (1995)

This study is based on a theoretical view which suggests that under increased demands for attention, individuals' capacity to direct attention may become fatigued. Once fatigued, attentional restoration must occur in order to return to an effectively functioning state. An attention-restoring experience can be as simple as looking at nature. The purpose of this study was to explore whether university dormitory residents with more natural views from their windows would score better than those with less natural views on tests of directed attention. Views from dormitory windows of 72 undergraduate students were categorized into four groups ranging from all natural to all built. The capacity to direct attention was measured using a battery of objective and subjective measures. Natural views were associated with better performance on attentional measures, providing support for the proposed theoretical view.
Mechanism of N-Acetylgalactosamine Binding to a C-type Animal Lectin Carbohydrate-recognition Domain (1998)

The mammalian hepatic asialoglycoprotein receptor, a member of the C-type animal lectin family, displays preferential binding to N-acetylgalactosamine compared with galactose. The structural basis for selective binding to N-acetylgalactosamine has been investigated. Regions of the carbohydrate-recognition domain of the receptor believed to be important in preferential binding to N-acetylgalactosamine have been inserted into the homologous carbohydrate-recognition domain of a mannose-binding protein mutant that was previously altered to bind galactose. Introduction of a single histidine residue corresponding to residue 256 of the hepatic asialoglycoprotein receptor was found to cause a 14-fold increase in the relative affinity for N-acetylgalactosamine compared with galactose. The relative ability of various acyl derivatives of galactosamine to compete for binding to this modified carbohydrate-recognition domain suggest that it is a good model for the natural N-acetylgalactosamine binding site of the asialoglycoprotein receptor. Crystallographic analysis of this mutant carbohydrate-recognition domain in complex with N-acetylgalactosamine reveals a direct interaction between the inserted histidine residue and the methyl group of the N-acetyl substituent of the sugar. Evidence for the role of the side chain at position 208 of the receptor in positioning this key histidine residue was obtained from structural analysis and mutagenesis experiments. The corresponding serine residue in the modified carbohydrate-recognition domain of mannose-binding protein forms a hydrogen bond to the imidazole side chain. When this serine residue is changed to valine, loss in selectivity for N-acetylgalactosamine is observed. The structure of this mutant reveals that the beta-branched valine side chain interacts directly with the histidine side chain, resulting in an altered imidazole ring orientation.
Constraint Management Methodology for Conceptual Design Tradeoff Studies (1996)

Abstract This paper presents a constraint management methodology, which facilitates tradeoff studies during conceptual design. This approach represents design models as constraints between variables, and uses the resulting constraint network to automatically derive computational procedures for performing user-specified tradeoff studies. By decomposing large constraint networks into smaller pieces that can be solved robustly, this approach can solve extremely large systems of non-linear equations present in practical system models. Design Sheet is a software implementation of this methodology; it allows the designer to interactively develop models, flexibly define tradeoff studies, and quickly explore large areas of design space to study how the different performance and cost criteria tradeoff with respect to one another. Design Sheet has been used on practical applications ranging from the system-level design of spacecraft using combined performance and cost models to the preliminary design of automotive bearings. This paper demonstrates the unique capabilities of Design Sheet in performing design tradeoff studies, using a thermal imaging system performance model developed for the DARPA MADE program.
Intraoperative optical coherence tomography and ab interno trabecular meshwork surgery with the Trabectome (2017)

The iOCT can be used to objectify the immediate success of the surgical procedure, ie, the removal of the trabecular meshwork, of ab interno trabeculotomy with the Trabectome. The procedure itself cannot be captured sufficiently via iOCT.
Void Formation Induced Electrical Switching in Phase-Change Nanowires (2008)

Solid-state structural transformation coupled with an electronic property change is an important mechanism for nonvolatile information storage technologies, such as phase-change memories. Here we exploit phase-change GeTe single-nanowire devices combined with ex situ and in situ transmission electron microscopy to correlate directly nanoscale structural transformations with electrical switching and discover surprising results. Instead of crystalline-amorphous transformation, the dominant switching mechanism during multiple cycling appears to be the opening and closing of voids in the nanowires due to material migration, which offers a new mechanism for memory. During switching, composition change and the formation of banded structural defects are observed in addition to the expected crystal-amorphous transformation. Our method and results are important to phase-change memories specifically, but also to any device whose operation relies on a small scale structural transformation.
Reviewing perineal colostomy (1978)

The Journal of Wound, Ostomy and Continence Nursing (JWOCN) is the premier publication for wound, ostomy and continence practice and research. The Journal’s mission is to publish current best evidence and original research to guide the delivery of expert health care. The WOCN Society is a professional nursing society which supports its members by promoting educational, clinical and research opportunities to advance the practice and guide the delivery of expert health care to individuals with wounds, ostomies and continence care needs.
Shape-Controlled Synthesis and Shape-Induced Texture of MnFe2O4 Nanoparticles (2004)

Monodisperse MnFe2O4 nanoparticles with cubelike and polyhedron shapes were synthesized by reaction of Fe(acac)3 and Mn(acac)2 with 1,2-hexadecanediol, oleic acid, and oleylamine. Controlled evaporation of the particle dispersion led to nanoparticle superlattices. The crystal orientation of the particle in the assembly depends on the shape of the particles, with particles in a cubelike shape showing (100) texture and those in the polyhedron shape exhibiting (110) texture.
Cytokine induction by lipopolysaccharide (LPS) corresponds to lethal toxicity and is inhibited by nontoxic Rhodobacter capsulatus LPS (1990)

Many pathological effects of gram-negative bacteria are produced by their cell wall-derived lipopolysaccharides (LPSs). Differing pathogenicity of gram-negative LPSs, however, may depend on their capacities to induce cytokines. Thus, we studied the lethal toxicity of four nonenterobacterial LPSs and compared it with their capacity to induce mononuclear cell (MNC)-derived interleukin-1 (IL-1), interleukin-6 (IL-6), and tumor necrosis factor (TNF). Unstimulated MNC did not release these cytokines. LPS from the phototrophic strain Rhodobacter capsulatus 37b4 elaborated little toxicity in galactosamine-treated mice (10 micrograms of LPS per mouse was the 100% lethal dose [LD100]) and induced IL-1 and IL-6 release only at high concentrations (10 to 50 micrograms of LPS per ml). R. capsulatus LPS failed to induce TNF activity even at the highest concentration tested (100 micrograms of LPS per ml). In contrast, LPS derived from Pseudomonas diminuta NCTC 8545 or the nodulating species Bradyrhizobium lupini DSM 30140 and Rhizobium meliloti 10406 expressed lethal toxicity (LD100, 1,000, 100, and 10 ng per mouse, respectively) and induced IL-1 or IL-6 (10 to 100, 10, and 1 ng of LPS per ml, respectively) at concentrations 1,000- to 10,000-fold lower than effective levels of R. capsulatus LPS. LPSs from P. diminuta, B. lupini, and R. meliloti also stimulated TNF production and release. MNC accumulated cell-associated IL-1 activities under circumstances in which released activity was readily detected. The cells contained only scant IL-6 activity, indicating release of this mediator rather than intracellular accumulation. Antisera to the respective cytokines inactivated biological activities of the samples selectively. The R. capsulatus LPS inhibited cytokine induction by LPS from P. diminuta, B. lupini, and R. meliloti in coincubation experiments. These results show that the in vivo lethality of the LPSs tested correlates with the induction of monocyte-derived cytokines in vitro. The results of this study suggest that the different lethality of various LPSs from gram-negative bacteria may be due to the differential ability of these LPSs to induce cytokine production.