gebhart/patrepeval huggingface dataset:
Material parameter estimation with terahertz time-domain spectroscopy (2001)

Imaging systems based on terahertz (THz) time-domain spectroscopy offer a range of unique modalities owing to the broad bandwidth, subpicosecond duration, and phase-sensitive detection of the THz pulses. Furthermore, the possibility exists for combining spectroscopic characterization or identification with imaging because the radiation is broadband in nature. To achieve this, we require novel methods for real-time analysis of THz waveforms. This paper describes a robust algorithm for extracting material parameters from measured THz waveforms. Our algorithm simultaneously obtains both the thickness and the complex refractive index of an unknown sample under certain conditions. In contrast, most spectroscopic transmission measurements require knowledge of the samples thickness for an accurate determination of its optical parameters. Our approach relies on a model-based estimation, a gradient descent search, and the total variation measure. We explore the limits of this technique and compare the results with literature data for optical parameters of several different materials. 2001 Optical Society of America
Cutting Edge: Activation of STING in T Cells Induces Type I IFN Responses and Cell Death (2017)

Stimulator of interferon genes (STING) was initially described as a sensor of intracellular bacterial and viral DNA and a promising adjuvant target in innate immune cells; more recently STING has also been shown to detect endogenous DNA and play a role in tumor immunity and autoimmune disease development. Thus far STING has been studied in macrophages and dendritic cells. In this study, to our knowledge we provide the first evidence of STING activation in T cells, in which STING agonists not only provoke type I IFN production and IFN-stimulated gene expression, mirroring the response of innate cells, but are also capable of activating cell stress and death pathways. Our results suggest a re-evaluation of STING agonist-based therapies may be necessary to identify the possible effects on the T cell compartment. Conversely, the effects of STING on T cells could potentially be harnessed for therapeutic applications.
PD-L1 has distinct functions in hematopoietic and nonhematopoietic cells in regulating T cell responses during chronic infection in mice (2010)

The inhibitory receptor programmed death 1 (PD-1) is upregulated on antigen-specific CD8+ T cells during persistent viral infections. Interaction with PD-1 ligand 1 (PD-L1) contributes to functional exhaustion of responding T cells and may limit immunopathology during infection. PD-L1 is expressed on both hematopoietic and nonhematopoietic cells in tissues. However, the exact roles of PD-L1 on hematopoietic versus nonhematopoietic cells in modulating immune responses are unclear. Here we used bone marrow chimeric mice to examine the effects of PD-L1 deficiency in hematopoietic or nonhematopoietic cells during lymphocytic choriomeningitis virus clone 13 (LCMV CL-13) infection. We found that PD-L1 expression on hematopoietic cells inhibited CD8+ T cell numbers and function after LCMV CL-13 infection. In contrast, PD-L1 expression on nonhematopoietic cells limited viral clearance and immunopathology in infected tissues. Together, these data demonstrate that there are distinct roles for PD-L1 on hematopoietic and nonhematopoietic cells in regulating CD8+ T cell responses and viral clearance during chronic viral infection.
Myoblast differentiation of human mesenchymal stem cells on graphene oxide and electrospun graphene oxide–polymer composite fibrous meshes: importance of graphene oxide conductivity and dielectric constant on their biocompatibility (2015)

Recently graphene and graphene based composites are emerging as better materials to fabricate scaffolds. Addition of graphene oxide (GO) nanoplatelets (GOnPs) in bioactive polymers was found to enhance its conductivity (σ) and, dielectric permittivity (ϵ) along with biocompatibility. In this paper, human cord blood derived mesenchymal stem cells (CB-hMSCs) were differentiated to skeletal muscle cells (hSkMCs) on spin coated thin GO sheets composed of GOnPs and on electrospun fibrous meshes of GO-PCL (poly-caprolactone) composite. Both substrates exhibited excellent myoblast differentiations and promoted self-alignedmyotubesformation similar to natural orientation. σ, ϵ, microstructural and vibration spectroscopic studies were carried out for the characterizations of GO sheet and the composite scaffolds. Significantly enhanced values of both σ and ϵ of the GO-PCL composite were considered to provide favourable cues for the formation of superior multinucleated myotubes on the electrospun meshes compared to those on thin GO sheets. The present results demonstrated that both substrates might be used as potential candidates for CB-hMSCs differentiation and proliferation for human skeletal muscle tissue regeneration.
A Biocatalytic Route to Highly Enantioenriched β‐Hydroxydioxinones (2017)

A novel biocatalytic system to access a wide variety of β-hydroxydioxinones from β-ketodioxinones employing commercial engineered ketoreductases has been developed. This practical system provides a remarkably straightforward solution to limitations in accessing certain chemical scaffolds common in β-hydroxydioxinones that are of great interest due to their diversification capabilities. A few highlights of this system are that it is high yielding, highly enantioselective, and chromatography-free. We have demonstrated both a wide substrate scope and a high degree of scalability.
Region-based color image indexing and retrieval (2002)

A region-based color image indexing and retrieval algorithm is presented. As a basis for the indexing, a novel K-Means segmentation algorithm is used, modified so as to take into account the coherence of the regions. A new color distance is also defined for this algorithm. Based on the extracted regions, characteristic features are estimated using color, texture and shape information. An important and unique aspect of the algorithm is that, in the context of similarity-based querying, the user is allowed to view the internal representation of the submitted image and the query results. Experimental results demonstrate the performance of the algorithm. The development of an intelligent image content-based search engine for the World-Wide Web is also presented, as a direct application of the presented algorithm.
Deconstructing Pluripotency (2008)

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Basic fibroblast growth factor enhances nerve growth factor receptor gene promoter activity in human neuroblastoma cell line CHP100. (1992)

The human neuroblastoma cell line CHP100 provides a useful model system in which to study the molecular mechanisms of transcriptional regulation of the low-affinity nerve growth factor receptor (NGFR) gene during neuronal development. Basic fibroblast growth factor (bFGF) induced morphological changes in CHP100 cells, including flattening of cell bodies and neurite outgrowth. bFGF also increased p75NGFR immunoreactivity, as assessed by immunocytochemistry, and increased p75NGFR mRNA levels, as assessed by Northern (RNA) blot analysis. A chimeric gene consisting of 6.7 kb of the 5'-flanking region of the human NGFR gene linked to the chloramphenicol acetyltransferase gene was constructed. In stable transformants of CHP100 cells, 10 ng of bFGF per ml induced an eightfold increase in chloramphenicol acetyltransferase activity. These results indicate that upstream elements of the NGFR gene mediate transcriptional regulation by bFGF.
Cellular Binding of Soluble CD14 Requires Lipopolysaccharide (LPS) and LPS-binding Protein (1997)

The stimulation of nonmyeloid cells by lipopolysaccharide (LPS) is mediated by the serum protein, soluble CD14 (sCD14). We have examined the interaction of sCD14 with whole cells using a biologically active radiolabeled sCD14 molecule as a ligand. Specific binding of sCD14 to nonmyeloid cells is detected only when it is first incubated with both LPS and the serum LPS-binding protein (LBP). Through the use of an anti-CD14 monoclonal antibody, we demonstrate that sCD14 must interact with LPS in order for cellular binding to occur. Although LBP is traditionally known to function as a catalyst in the transfer of LPS to sCD14, our results reveal that LBP is actually a physical part of sCD14-containing, cell-associating complexes. The LPS- and LBP-dependent cell surface binding of sCD14 appears to be distinct from events leading to cell stimulation, since certain anti-CD14 and anti-LBP monoclonal antibodies have different effects on cellular binding versus cellular activation. Bound sCD14 is internalized, indicating that the LBP- and LPS-dependent binding of sCD14 may represent a novel general mechanism by which nonmyeloid cells clear LPS.
Deletion of clustered O-linked carbohydrates does not impair function of low density lipoprotein receptor in transfected fibroblasts. (1986)

A single exon in the gene for the receptor for plasma low density lipoprotein (LDL) encodes a region of clustered serine and threonine residues that is immediately external to the membrane-spanning sequence. This region has been proposed as the site of clustered O-linked carbohydrate chains. In the current studies we have deleted the 144 base pairs (48 amino acids) that encode this serine- and threonine-rich region from the cDNA for the human LDL receptor. Upon transfection into receptor-deficient hamster fibroblasts, this mutated cDNA encoded a shortened receptor that no longer showed an anomalously high molecular weight on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Labeling with [3H]glucosamine confirmed the lack of clustered O-linked sugars and further revealed that the shortened receptor and the normal receptor both contained isolated O-linked carbohydrate chains attached to the NH2-terminal portion of the protein. The ratio of clustered to isolated O-linked sugar chains in the normal receptor was estimated to be approximately 4-6 to 1. Despite the loss of clustered O-linked carbohydrate, the LDL receptor encoded by the deletion-bearing cDNA bound and internalized LDL normally. It also recycled normally and exhibited a normal half-life. We conclude that: 1) the serine- and threonine-rich region of the LDL receptor is the site for addition of clustered O-linked carbohydrates; 2) the receptor contains a small number of isolated chains of O-linked carbohydrates in addition to the clustered chains; and 3) the clustered O-linked carbohydrates are not essential for LDL receptor function in cultured hamster fibroblasts.
Becker muscular dystrophy (2013)

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Characterization of human immunodeficiency virus type 1 Vif particle incorporation (1996)

The human immunodeficiency virus type 1 (HIV-1) Vif protein is necessary at the time of viral particle formation yet functionally manifests its effect after virions enter target cells. This suggests that Vif either acts on another viral protein or is itself incorporated into particles. In this study, we have examined the latter possibility. We confirm our previous observation that Vif is incorporated into human immunodeficiency virus type 1 virions at a ratio of approximately 1 molecule of Vif for every 75 to 220 molecules of p24, or 7 to 20 molecules per virion. Furthermore, we demonstrate that the relative concentration of Vif is much lower in particles than in infected cells, whereas the opposite is observed for the main virus components. The viral envelope, Nef, Vpr, Vpu, protease, reverse transcriptase, integrase, nucleocapsid, and p6gag proteins as well as the viral genomic RNA are dispensable for Vif packaging. Furthermore, mutating several highly conserved residues (H-108, C-114, C-133, L-145, and Q-146) or deleting the C-terminal 18 amino acids of Vif, either of which severely impairs Vif function, does not abolish its incorporation into virions. Finally, Vif can be packaged into murine leukemia virus particles. On the basis of these data, we conclude that the specificity of Vif incorporation into virions remains an open question.
A Communication Architecture For IVHS (1992)

This paper documents the development of a communications architecture for Intelligent Vehicle Highway Systems (IVHS) being studied by the California PATH Program. The authors use a layered architecture based on the OSI 7- layer reference model.
In Vivo Osteogenic Potential of Human Adipose-Derived Stem Cells/Poly Lactide-Co-Glycolic Acid Constructs for Bone Regeneration in a Rat Critical-Sized Calvarial Defect Model (2007)

Recent studies suggest that human adipose tissue contains pluripotent stem cells, which are similar to bone marrow-derived stem cells. The objective of the present study was to assess the effect in bone regenerating capability of human adipose-derived stem cells (ADSCs) cultured in osteogenic media layered over poly lactide-co-glycolic acid (PLGA) and implanted in a critical nude rat calvarial defect. Twenty-seven nude rats were randomized into 3 groups (n = 9): 1) PLGA alone (control), 2) PLGA with undifferentiated ADSCs, and 3) PLGA with differentiated ADSCs. These 3 groups were divided into 9 subgroups (n = 3) according to in vitro pre-cultured periods (day 1 pre-culture (Group1), day 7 pre-culture (Group2), and day 14 pre-culture (Group3)) before implantation. An 8 mm critical-size circular calvarial defect was made in each nude rat. Specimens were harvested at 12 weeks post-implantation and evaluated radiographically and histologically. Radiodensitometric analysis revealed significantly higher bone growth in implants pre-cultured in osteogenic media for 14 days for Group 3. Histomorphometric analysis demonstrated that Groups 2 and 3 had bone formation filling 35% to 72% of the area of the defect after transplantation with cells that had been pre-cultured for 14 days. Constructs with differentiated ADSCs (Group 3) had noticeably more maximal and robust bone tissue regeneration than constructs with undifferentiated ADSCs (Group 2). These data provide evidence that constructs or implants made of PLGA and osteogenically differentiated ADSCs pre-cultured for 14 days before transplantation have better, more-robust bone regeneration capability in critical-sized skeletal defects than constructs with undifferentiated ADSCs. Human adipose derived stem cells can therefore be used as seed cells to construct tissue-engineered bone.
Binary Arithmetic Coding System with Adaptive Probability Estimation by "Virtual Sliding Window" (2006)

Virtual Sliding Window" algorithm presented in this paper is an adaptive mechanism for estimating the probability of ones at the output of binary non-stationary sources. It is based on "Imaginary sliding window" idea proposed by B. Ryabko. The proposed algorithm was used as an alternative adaptation mechanism in Context-Based Adaptive Binary Arithmetic Coding (CABAC) - an entropy coding scheme of H.264/AVC standard for video compression. The "virtual sliding window" algorithm was integrated into an open-source codec supporting H. 264/AVC standard. Comparison of the "virtual sliding window" algorithm with the original adaptation mechanism from CABAC is presented. Test results for standard video sequences are included. These results indicate that using the proposed algorithm improves rate-distortion performance compared to the original CABAC adaptation mechanism. Besides improvement in rate-distortion performances the "Virtual Sliding Window" algorithm has one more advantage. CABAC uses a finite state machine (FSM) for estimation of the probability of ones at the output of a binary source. Transitions for FSM are defined by a table stored in memory. The disadvantage of CABAC consists in frequent reference to this table (one time for every binary symbol encoding), which is critical for DSP implementation. The "Virtual Sliding Window" algorithm allows to avoid using the table of transitions 1.
Intraocular retinal transplants. (1985)

Embryonic rat retinae transplanted into the anterior chamber of adult rat eyes of the same or different strain survive and grow. Light and electron microscopic studies show that the transplants undergo histogenetic differentiation, resulting in the development of mature inner and outer layer neurons and Müller glial cells. Vascular connections develop between the host iris and the retinal transplant. These initial observations indicate that retinal transplantation to a recipient eye is a procedure which offers ample opportunities for the study of problems related to neural development, retinal plasticity and repair.
Effectiveness of vagus nerve stimulation in epilepsy patients (2004)

A retrospective review of the safety, tolerability, and efficacy of vagus nerve stimulation (VNS) in 48 patients with intractable partial epilepsy was performed. Side effects were few and mild to moderate. Mean seizure frequency decreased by 26% after 1 year, 30% after 5 years, and 52% after 12 years with VNS treatment.
A Micro Ionizer for Portable Mass Spectrometers using Double-gated Isolated Vertically Aligned Carbon Nanofiber Arrays (2007)

We report micro-fabricated double-gated vertically aligned carbon nanofiber (CNF) arrays for ionization of gasses in low power portable mass spectrometers. The devices can be operated in one of two modes - electron impact ionization (EII ) or field ionization (FI). When operated as electron impact ionizer, power dissipation was reduced from >1 W typical of thermionic emission based electron impact ionizers to <100 mW. When operated as a field ionizer, the turn-on voltage for field ionization is reduced from 5-10 kV typical of ungated ionizers to 350 V.
Voltammetry at linear gold and platinum microelectrode arrays produced by lithographic techniques (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTVoltammetry at linear gold and platinum microelectrode arrays produced by lithographic techniquesWolfgang. Thormann, Peter. Van den Bosch, and Alan M. BondCite this: Anal. Chem. 1985, 57, 14, 2764–2770Publication Date (Print):December 1, 1985Publication History Published online1 May 2002Published inissue 1 December 1985https://pubs.acs.org/doi/10.1021/ac00291a007https://doi.org/10.1021/ac00291a007research-articleACS PublicationsRequest reuse permissionsArticle Views417Altmetric-Citations74LEARN 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
Metorphamide: isolation, structure, and biologic activity of an amidated opioid octapeptide from bovine brain. (1983)

Acid acetone extracts of caudate nucleus from bovine brain were found to contain an amidated opioid octapeptide with the following structure: Tyr-Gly-Gly-Phe-Met-Arg-Arg-Val-NH2. The peptide has been named metorphamide. Bovine metorphamide appears to be derived by proteolytic cleavage from proenkephalin, the common precursor to [Met5]enkephalin and [Leu5]enkephalin. The cleavage within the precursor giving rise to the carboxyl terminus of metorphamide occurs at a single arginine residue and is followed by transformation of a carboxyl-terminal glycine into an amide group. Metorphamide was detected in bovine caudate nucleus extracts by radioimmunoassay, and it was purified to homogeneity by gel filtration and reversed-phase high performance liquid chromatography. Amino acid composition analysis and automated Edman degradation in the gas-phase sequencer confirmed the postulated amino acid sequence. Carboxyl-terminal amidation of bovine metorphamide was shown by stability to carboxypeptidase A digestion and full crossreactivity in a radioimmunoassay that required the carboxyl-terminal amide as part of the recognition site. A synthetic replicate of metorphamide as well as several synthetic analogs were tested for opioid activity in several bioassays and binding assays, and metorphamide was found to have a high mu-binding activity. Metorphamide is the only known naturally occurring opioid peptide that has a high mu-binding activity. The kappa-binding activity is approximately equal to 50% that of the mu-binding activity, but delta-binding activity is negligible.
Magnetic nanoparticles: synthesis, functionalization, and applications in bioimaging and magnetic energy storage (2009)

This tutorial review summarizes the recent advances in the chemical synthesis and potential applications of monodisperse magnetic nanoparticles. After a brief introduction to nanomagnetism, the review focuses on recent developments in solution phase syntheses of monodisperse MFe(2)O(4), Co, Fe, CoFe, FePt and SmCo(5) nanoparticles. The review further outlines the surface, structural, and magnetic properties of these nanoparticles for biomedicine and magnetic energy storage applications.
Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys (2014)

The exploration of microbial communities by sequencing 16S rRNA genes has expanded with low-cost, high-throughput sequencing instruments. Illumina-based 16S rRNA gene sequencing has recently gained popularity over 454 pyrosequencing due to its lower costs, higher accuracy and greater throughput. Although recent reports suggest that Illumina and 454 pyrosequencing provide similar beta diversity measures, it remains to be demonstrated that pre-existing 454 pyrosequencing workflows can transfer directly from 454 to Illumina MiSeq sequencing by simply changing the sequencing adapters of the primers. In this study, we modified 454 pyrosequencing primers targeting the V4-V5 hyper-variable regions of the 16S rRNA gene to be compatible with Illumina sequencers. Microbial communities from cows, humans, leeches, mice, sewage, and termites and a mock community were analyzed by 454 and MiSeq sequencing of the V4-V5 region and MiSeq sequencing of the V4 region. Our analysis revealed that reference-based OTU clustering alone introduced biases compared to de novo clustering, preventing certain taxa from being observed in some samples. Based on this we devised and recommend an analysis pipeline that includes read merging, contaminant filtering, and reference-based clustering followed by de novo OTU clustering, which produces diversity measures consistent with de novo OTU clustering analysis. Low levels of dataset contamination with Illumina sequencing were discovered that could affect analyses that require highly sensitive approaches. While moving to Illumina-based sequencing platforms promises to provide deeper insights into the breadth and function of microbial diversity, our results show that care must be taken to ensure that sequencing and processing artifacts do not obscure true microbial diversity.
Overexpression of WDR62 is associated with centrosome amplification in human ovarian cancer (2013)

Our findings suggest that WDR62 overexpression is related to centrosome amplification in ovarian cancer. It may be a novel useful differentiation biomarker and a potential therapy target for OC. Further assessment of WDR62 expression is highly warranted in large, prospective studies.