gebhart/patrepeval huggingface dataset:
Speckle Reduction in OCT using Massively-Parallel Detection and Frequency-Domain Ranging (2006)

Speckle noise significantly limits the information content provided by coherent optical imaging methods such as optical coherence tomography and its recent derivative, optical frequency-domain imaging (OFDI). In this paper, we demonstrate a novel OFDI system that simultaneously acquires hundreds of angularly resolved images, which can be compounded to reduce speckle noise. The system comprises an InGaAs line-scan camera and an interferometer, configured so that the elements of the detector array simultaneously capture light spanning a backscattering angular range of 32 degrees. On successive read-outs of the array, the wavelength of the laser source was stepped through a range of 130 nm centered at 1295 nm to concurrently generate 400 angle-resolved OFDI images. A theory of angle-resolved OFDI and the design equations of the system are presented. Incoherent averaging of the angle-resolved data is shown to yield substantial speckle reduction (as high as an 8 dB SNR improvement) in images of a tissue phantom and esophageal tissue ex vivo.
Depolarizing stimulation upregulates GA‐binding protein in neurons: a transcription factor involved in the bigenomic expression of cytochrome oxidase subunits (2000)

Neurons are unique in having dendrites that extend far away from their cell bodies. Mitochondria located in the dendrites can be separated from the nucleus for long distances. The mechanism of bigenomic coordination is of particular importance to cytochrome oxidase (CO), which has subunits that are encoded in both the nuclear and mitochondrial DNA. GA-binding protein (GABP) is a transcription factor that is required for the promoter activity of mitochondrial transcription factor A as well as several nuclear-encoded CO subunits. Thus, GABP may play a key role in coordinating the transcription of both mitochondrial and nuclear-encoded subunits of CO. The goal of the present study was to determine if GABP was expressed in neurons and whether and how it responded to increased neuronal activity. Using primary neuronal cultures, the beta-subunit of GABP was localized immunocytochemically to both the cytoplasm and the nucleus, whereas the alpha-subunit was expressed mainly in the nucleus. In KCl-treated cultures, immunoreactivity for both alpha- and beta-subunits was significantly increased in the nucleus compared with untreated sister cultures. The induction of GABP preceded that of CO gene expression from the two genomes, which, in turn, preceded that of CO activity. Thus, our data suggest that neuronal activity regulates subunit concentrations of GABP in the nucleus, and GABP may be a critical sensor of changes in neuronal activity. Our data are also consistent with the postulated role of GABP as a coordinator of both mitochondrial and nuclear transcription for subunits of CO in neurons.
Exopolysaccharide from Bifidobacterium longum subsp. longum 35624™ modulates murine allergic airway responses (2018)

Interactions between the host and the microbiota are thought to significantly influence immunological tolerance mechanisms at mucosal sites. We recently described that the loss of an exopolysaccharide (EPS) from Bifidobacterium longum 35624™ eliminated its protective effects in colitis and respiratory allergy murine models. Our goal was to investigate the immune response to purified EPS from B. longum 35624, determine if it has protective effects within the lung and identify the protective mechanisms. Isolated EPS from B. longum 35624 cultures was used for in vitro, ex vivo and in vivo studies. Human monocyte-derived dendritic cells (MDDCs) were used to investigate in vitro immunological responses to EPS. Cytokine secretion, expression of surface markers and signalling pathways were examined. The ovalbumin (OVA) respiratory allergy murine model was used to evaluate the in vivo immunomodulatory potential of EPS. In addition, interleukin (IL)-10 knockout (KO) mice and anti-Toll-like receptor (TLR)-2 blocking antibody were used to examine the underlying protective mechanisms of intranasal EPS administration. Stimulation of human MDDCs with EPS resulted in IL-10 secretion, but not proinflammatory cytokines. IL-10 secretion was TLR-2-dependent. Eosinophil recruitment to the lungs was significantly decreased by EPS intranasal exposure, which was associated with decreased expression of the Th2-associated markers C-C motif chemokine 11 (CCL11), C-C chemokine receptor type 3 (CCR3), IL-4 and IL-13. TLR-2-mediated IL-10 secretion was shown to be required for the reduction in eosinophils and Th2 cytokines. EPS-treatment reduced eosinophil recruitment within the lung in a respiratory inflammation mouse model, which is both TLR-2 and IL-10 mediated. EPS can be considered as a novel molecule potentially reducing the severity of chronic eosinophil-related airway disorders.
Database-aware semantically-smart storage (2005)

Recent research has demonstrated the potential benefits of building storage arrays that understand the file systems above them. Such disk systems use knowledge of file system structures and operations to improve performance, availability, and even security in ways that are precluded in a traditional storage system architecture.In this paper, we study the applicability of semantically smart disk technology underneath database management systems. For three case studies, we analyze the differences when building database-aware storage. We find that semantically-smart disk systems can be successfully applied underneath a database, but that new techniques, such as log snooping and explicit access statistics, are needed.
TOR Regulates Cell Death Induced by Telomere Dysfunction in Budding Yeast (2008)

Telomere dysfunction is known to induce growth arrest (senescence) and cell death. However, the regulation of the senescence-death process is poorly understood. Here using a yeast dysfunctional telomere model cdc13-1, which carries a temperature sensitive-mutant telomere binding protein Cdc13p, we demonstrate that inhibition of TOR (Target of Rapamycin), a central regulator of nutrient pathways for cell growth, prevents cell death, but not growth arrest, induced by inactivation of Cdc13-1p. This function of TOR is novel and separable from its G1 inhibition function, and not associated with alterations in the telomere length, the amount of G-tails, and the telomere position effect (TPE) in cdc13-1 cells. Furthermore, antioxidants were also shown to prevent cell death initiated by inactivation of cdc13-1. Moreover, inhibition of TOR was also shown to prevent cell death induced by inactivation of telomerase in an est1 mutant. Interestingly, rapamycin did not prevent cell death induced by DNA damaging agents such as etoposide and UV. In the aggregate, our results suggest that the TOR signaling pathway is specifically involved in the regulation of cell death initiated by telomere dysfunction.
Study on the Preparation and Solution Property of Fluorine-Containing Oligomeric Surfactants by the Use of Nitrogen-Containing Perfluorocarboxylic Acids (1999)

フルオロァルキル基として, 鎖状あるいは環状の数種類のペルフルオロ (ジアルキルアミノ) 基を有するオリゴマー型のフッ素系界面活性化合物をペルフルオロ (ジアルキルアミノ) 基置換ペルフルオロカルボン酸フルオリドと重合度の異なるポリエチレンイミンを反応させることにより合成した。これらの化合物では, ペルフルオロ (ジアルキルアミノ) 基鎖がイミノ基に対して, 0.4～2.2%導入された。ペルフルオロジアルキルアミノ基鎖の導入率が比較的高い試料では, 対応する含窒素ペルフルオロカルボン酸アルカリ金属塩単独と同程度の表面張力低下能を示した。
Structured Learning and Prediction in Computer Vision (2010)

Powerful statistical models that can be learned efficiently from large amounts of data are currently revolutionizing computer vision. These models possess a rich internal structure reflecting task-specific relations and constraints. Structured Learning and Prediction in Computer Vision introduces the reader to the most popular classes of structured models in computer vision. The focus is on discrete undirected graphical models which are covered in detail together with a description of algorithms for both probabilistic inference and maximum a posteriori inference. It also discusses separately recently successful techniques for prediction in general structured models. The second part of Structured Learning and Prediction in Computer Vision describes methods for parameter learning, distinguishing the classic maximum likelihood based methods from the more recent prediction-based parameter learning methods. It highlights developments to enhance current models and discusses kernelized models and latent variable models. Throughout Structured Learning and Prediction in Computer Vision the main text is interleaved with successful computer vision applications of the explained techniques. For convenience the reader can find a summary of the notation used at the end of the book.
ChemInform Abstract: POLYCYCLIC TRIARYLDIOXYPHOSPHORANES OF EXTREME STABILITY (1978)

Abstract Die Phosphorane (Ia‐d), (If) und (II) mit [1,2]‐Oxaphospholo[4,3,2‐hi][2,1]benzoxaphosphol‐Gerüst sind im Gegensatz zu ihren acyclischen Analogen konstitutiv wie auch konformativ sehr beständig, was sich bereits in ihrer unerwartet bereitwilligen Bildung aus z.B. Phosphinoxid‐Vorstufen wie (VII) äußert.
Purification and characterization of hepatocyte growth factor from injured liver of carbon tetrachloride-treated rats. (1991)

A hepatocyte growth factor (HGF)-like substance that strongly stimulated DNA synthesis of adult rat hepatocytes in primary culture was found to increase markedly in liver of rats treated with carbon tetrachloride (CCl4). This increase of HGF-like activity was time- and dose-dependent, and 36 h after a dose of CCl4 of 0.2 ml per 100 g body weight the activity was about 20-times the normal level. The extent of induction of HGF-like factor correlated well with the extent of liver damage. The HGF-like factor was purified to homogeneity from the liver of CCl4-treated rats by a four-step procedure. The purified HGF-like factor had a molecular weight of 82-85 kDa, as estimated by SDS-PAGE, and was a heterodimer composed of a large subunit of about 69 kDa and a small subunit of 34 kDa linked by disulfide bridges. This factor had similar biological and chemical properties to HGF purified from rat platelets. Moreover, the N-terminal amino acid sequence of its 34-kDa subunit was identical to that of the small subunit of rat HGF. These findings indicate that the HGF-like factor in damaged liver of CCl4-treated rats is HGF and that liver itself can produce HGF when injured.
Detecting Colorectal Cancer in Stool With the Use of Multiple Genetic Targets (2001)

We were able to detect the majority of colorectal cancers by analyzing stool DNA for just three genetic markers. Additional work is needed to determine the specificity of these genetic tests for detecting colorectal neoplasia in asymptomatic patients and to more precisely estimate the prevalence of the mutations and sensitivity of the assay.
Identification and characterization by antisense oligonucleotides of exon and intron sequences required for splicing. (1994)

Certain thalassemic human beta-globin pre-mRNAs carry mutations that generate aberrant splice sites and/or activate cryptic splice sites, providing a convenient and clinically relevant system to study splice site selection. Antisense 2'-O-methyl oligoribonucleotides were used to block a number of sequences in these pre-mRNAs and were tested for their ability to inhibit splicing in vitro or to affect the ratio between aberrantly and correctly spliced products. By this approach, it was found that (i) up to 19 nucleotides upstream from the branch point adenosine are involved in proper recognition and functioning of the branch point sequence; (ii) whereas at least 25 nucleotides of exon sequences at both 3' and 5' ends are required for splicing, this requirement does not extend past the 5' splice site sequence of the intron; and (iii) improving the 5' splice site of the internal exon to match the consensus sequence strongly decreases the accessibility of the upstream 3' splice site to antisense 2'-O-methyl oligoribonucleotides. This result most likely reflects changes in the strength of interactions near the 3' splice site in response to improvement of the 5' splice site and further supports the existence of communication between these sites across the exon.
Inter‐individual and intra‐individual variability of ethanol concentration‐time profiles: comparison of ethanol ingestion before or after an evening meal. (1995)

1. The magnitude of the variability of ethanol absorption is an important factor for studies that seek to determine the significance of potential interactions between ethanol and drugs. The aim of this study was to determine the extent of inter- and intra-individual variability of ethanol concentration-time profiles in fasted and fed subjects. 2. Twenty-four healthy male subjects were randomized to receive ethanol 0.3 g kg-1 before an evening meal on two study days and ethanol 0.3 g kg-1 after an evening meal on two study days. Plasma ethanol concentrations were measured at intervals from 0-240 min. 3. There were significant differences in the mean area under the ethanol concentration-time curve (AUC), the mean peak ethanol concentration (Cmax), the mean ethanol elimination slope and the time to peak ethanol concentration between the fed and fasted subjects. There were no significant differences between the first and second study days for either fed or fasting subjects for all parameters. 4. There was no statistically significant difference in inter- or intra-subject variance between fed and fasted studies although the coefficients of variation (standard deviation expressed as a percentage of the mean) for the differences between the first and second study day were higher for fed studies. 5. The large inter- and intra-individual variability of alcohol absorption for both fasted and fed subjects must be considered in the design of alcohol-drug interaction studies.
Peptide‐binding specificity of the prosurfactant protein C Brichos domain analyzed by electrospray ionization mass spectrometry (2009)

The C-terminal domain of lung surfactant protein C (CTC) precursor (proSP-C) is involved in folding of the transmembrane segment of proSP-C. CTC includes a Brichos domain with homologs in cancer- and dementia-associated proteins. Mutations in the Brichos domain cause misfolding of proSP-C and hence amyloid fibril formation in interstitial lung disease. Electrospray ionization mass spectrometry (ESI-MS) with collision-induced dissociation (CID) experiments was applied to study non-covalent interactions between human recombinant CTC or its Brichos domain, and SP-C analogs, homotripeptides and peptides designed to model amyloid fibril formation. The results show that the Brichos domain contains the peptide-binding function of CTC. In titration experiments, apparent dissociation constants (KD) were in the micromolar range where triple-valine showed the lowest KD and triple-tyrosine the highest. Non-hydrophobic peptides failed to form complexes with Brichos. CID revealed that complexes with aromatic peptide ligands are more stable in the gas phase than complexes with non-aromatic ligands. The Brichos domain was also shown to bind fibril-forming peptides containing aromatic/hydrophobic residues.
<title>Dual-wavelength interferometer for testing projection lenses</title> (1995)

A custom-built phase shifting interferometer is described for measuring the wavefront quality of Ultratech Stepper 1X projection lenses over a field of 25 mm X 50 mm using wavelengths of 363.8 nm (for i-line systems) and 442.0 nm (for gh-systems). Over an N.A. of 0.42 the wavefront is determined at 240 X 240 points with a calibrated accuracy of (lambda) /20 peak-to-valley (at (lambda) equals 363.8 nm). The interferometer is an unequal path Twyman-Green interferometer with an Argon-laser and a HeCd-laser as light sources. The interferometer test system is integrated on a 10 ft X 4 ft vibration isolation table together with an xy-stage to position the projection lens at different field points. The safe handling of the projection lens is supported by a load/unload mechanism on the table. The measurement wavefront maps at various field points of the tested projection lens are used to optimize the state of alignment of the projection lens.
Oppression and Privilege: Toward a Relational Conceptualization of Race (1996)

In this paper I bring together this diverse literature into what I call a relational model—one that focuses on both the oppressive and the privileging aspects of race. Using the concepts of white privilege and white supremacy to show how race implicates everyone, this paradigm provides a more realistic account of race and its effects on people's lives. After outlining this model in contrast to the traditional view, I focus on issues involved in teaching about race as a relation: preparing to teach about race from this model, taking it into the classroom, and dealing with white students' reactions to this conceptualization.
Cationic liposomes as non‐viral carriers of gene medicines: Resolved issues, open questions, and future promises (2006)

The clinical success of gene therapy is critically dependent on the development of efficient and safe gene delivery reagents, popularly known as "transfection vectors." The transfection vectors commonly used in gene therapy are mainly of two types: viral and non-viral. The efficiencies of viral transfection vectors are, in general, superior to their non-viral counterparts. However, the myriads of potentially adverse immunogenic aftermaths associated with the use of viral vectors are increasingly making the non-viral gene delivery reagents as the vectors of choice. Among the existing arsenal of non-viral gene delivery reagents, the distinct advantages associated with the use of cationic transfection lipids include their: (a) robust manufacture; (b) ease in handling and preparation techniques; (c) ability to inject large lipid:DNA complexes; and (d) low immunogenic response. The present review highlights the major achievements in the area of designing efficacious cationic transfection lipids, some of the more recent advances in the field of cationic liposomes-mediated gene transfer and targeted gene delivery, some unresolved issues and challenges in liposomal gene delivery, and future promises of cationic liposomes as gene-carriers in non-viral gene therapy.
Antibody‐Conjugated Nanoparticles for Biomedical Applications (2009)

Nanoscience and Nanotechnology have found their way into the fields of Biotechnology and Medicine. Nanoparticles by themselves offer specific physicochemical properties that they do not exhibit in bulk form, where materials show constant physical properties regardless of size. Antibodies are nanosize biological products that are part of the specific immune system. In addition to their own properties as pathogens or toxin neutralizers, as well as in the recruitment of immune elements (complement, improving phagocytosis, cytotoxicity antibody dependent by natural killer cells, etc.), they could carry several elements (toxins, drugs, fluorochroms, or even nanoparticles, etc.) and be used in several diagnostic procedures, or even in therapy to destroy a specific target. The conjugation of antibodies to nanoparticles can generate a product that combines the properties of both. For example, they can combine the small size of nanoparticles and their special thermal, imaging, drug carrier, or magnetic characteristics with the abilities of antibodies, such as specific and selective recognition. The hybrid product will show versatility and specificity. In this review, we analyse both antibodies and nanoparticles, focusing especially on the recent developments for antibody‐conjugated nanoparticles, offering the researcher an overview of the different applications and possibilities of these hybrid carriers.
A Laboratory Investigation of Cementing Horizontal Wells (1988)

Summary Obtaining a successful cement job will remain one of the most important factors to the productive life of any well and will be especially critical for horizontal-well completions. Achieving a high mud-displacement efficiency under highly deviated or horizontal-well conditions requires that special attention be given to the many aspects of drilling/completion practices—e.g., drill-fluid systems and properties and casing and hole sizes—to obtain optimum mud displacement and cementing results. A study of factors affecting mud-displacement efficiency focused on cementing an ultralow-permeability formation that is being evaluated as a subject for horizontal completion. Realistic laboratory testing was conducted on a large-scale test model that has been used for many years to evaluate factors influencing drilling-fluid-displacement efficiency. Factors evaluated for this study included influence of hole and pipe sizes, pipe centralization, displacement rates, and spacer systems. Findings from this study provided specific recommendations for low-permeability reservoirs that also can be applied to horizontally drilled wells. Various techniques for cementing horizontal wells will be discussed and general recommendations will be given.
The COOH Terminus of the Amelogenin, LRAP, Is Oriented Next to the Hydroxyapatite Surface (2004)

The organic matrix in forming enamel consists largely of the amelogenin protein self-assembled into nanospheres that are necessary to guide the formation of the unusually long and highly ordered hydroxyapatite (HAP) crystallites that constitute enamel. Despite its ability to direct crystal growth, the interaction of the amelogenin protein with HAP is unknown. However, the demonstration of growth restricted to the c-axis suggests a specific protein-crystal interaction, and the charged COOH terminus is often implicated in this function. To elucidate whether the COOH terminus is important in the binding and orientation of amelogenin onto HAP, we have used solid state NMR to determine the orientation of the COOH terminus of an amelogenin splice variant, LRAP (leucine-rich amelogenin protein), which contains the charged COOH terminus of the full protein, on the HAP surface. These experiments demonstrate that the methyl 13C-labeled side chain of Ala46 is 8.0 A from the HAP surface under hydrated conditions, for the protein with and without phosphorylation. The experimental results provide direct evidence orienting the charged COOH-terminal region of the amelogenin protein on the HAP surface, optimized to exert control on developing enamel crystals.
Benzocycloalkyl amines as novel C-termini for HIV protease inhibitors (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBenzocycloalkyl amines as novel C-termini for HIV protease inhibitorsTerry A. Lyle, Catherine M. Wiscount, James P. Guare, Wayne J. Thompson, Paul S. Anderson, Paul L. Darke, Joan A. Zugay, Emilio A. Emini, William A. Schleif, and Cite this: J. Med. Chem. 1991, 34, 3, 1228–1230Publication Date (Print):March 1, 1991Publication History Published online1 May 2002Published inissue 1 March 1991https://pubs.acs.org/doi/10.1021/jm00107a051https://doi.org/10.1021/jm00107a051research-articleACS PublicationsRequest reuse permissionsArticle Views373Altmetric-Citations85LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts