gebhart/patrepeval huggingface dataset:
Depletion of High‐density Lipoprotein and Appearance of Triglyceride‐rich Low‐density Lipoprotein in a Japanese Patient With FIC1 Deficiency Manifesting Benign Recurrent Intrahepatic Cholestasis (2007)

The present study showed an appearance of triglyceride-rich LDL due to suppressions of LCAT and HTGL activities and a depletion of HDL that is not able to be explained by lipoprotein regulators or FXR in our patient.
Molecular Cloning and Immunologic Reactivity of a Novel Low Molecular Mass Antigen of Mycobacterium tuberculosis (1998)

Polypeptide Ags present in the culture filtrate of Mycobacterium tuberculosis were purified and evaluated for their ability to stimulate PBMC from purified protein derivative (PPD)-positive healthy donors. One such Ag, which elicited strong proliferation and IFN-gamma production, was further characterized. The N-terminal amino acid sequence of this polypeptide was determined and used to design oligonucleotides for screening a recombinant M. tuberculosis genomic DNA library. The gene (Mtb 8.4) corresponding to the identified polypeptide was cloned, sequenced, and expressed in Escherichia coli. The predicted m.w. of the recombinant protein without its signal peptide was 8.4 kDa. By Southern analysis, the DNA encoding this mycobacterial protein was found in the M. tuberculosis substrains H37Rv, H37Ra, Erdman, and "C" strain, as well as in certain other mycobacterial species, including Mycobacterium avium and Mycobacterium bovis BCG (bacillus Calmette-Guerin, Pasteur). The Mtb 8.4 gene appears to be absent from the environmental mycobacterial species examined thus far, including Mycobacterium smegmatis, Mycobacterium gordonae, Mycobacterium chelonae, Mycobacterium fortuitum, and Mycobacterium scrofulaceum. Recombinant Mtb 8.4 Ag induced significant proliferation as well as production of IFN-gamma, IL-10, and TNF-alpha, but not IL-5, from human PBMC isolated from PPD-positive healthy donors. Mtb 8.4 did not stimulate PBMC from PPD-negative donors. Furthermore, immunogenicity studies in mice indicate that Mtb 8.4 elicits a Th1 cytokine profile, which is considered important for protective immunity to tuberculosis. Collectively, these results demonstrate that Mtb 8.4 is an immunodominant T cell Ag of M. tuberculosis.
Diversity, functionality, and stability of the T cell repertoire derived in vivo from a single human T cell precursor (2000)

In this report, we have analyzed the human T cell repertoire derived in vivo from a single T cell precursor. A unique case of X-linked severe combined immunodeficiency in which a reverse mutation occurred in an early T cell precursor was analyzed to this end. It was determined that at least 1,000 T cell clones with unique T cell receptor-beta sequences were generated from this precursor. This diversity seems to be stable over time and provides protection from infections in vivo. A similar estimation was obtained in an in vitro murine model of T cell generation from a single cell precursor. Overall, our results document the large diversity potential of T cell precursors and provide a rationale for gene therapy of the block of T cell development.
Automatic detection and classification of acoustic breathing cycles (2014)

This paper focuses on respiratory phase detection and classification without the help of the airflow measurements. Instead of using the airflow measurements to identify breathing phases, the proposed work depends on advanced digital signal processing techniques to process the acoustic signal of respiration that was collected using a microphone placed in front of the subject's nose. The recorded signal is processed using the voiced-unvoiced algorithm to differentiate between the voiced period and the unvoiced (silence) period. The desired features are extracted from each voiced phase. Finally, support vector machine is used to distinguish between the inspiration and the expiration phases according to the extracted features. The signals were recorded from a number of subjects who do not have a history of pulmonary diseases. The proposed method has achieved an accuracy of 95% when tested on the subjects.
The Role of Mesenchymal Stem Cells in the Regenerative Wound Healing Phenotype (2012)

Regenerative medicine and novel wound therapies using autologous stem cells holds great promise for clinical management of difficult wounds. The ideal candidate stem cells can be used to repopulate the wound bed to mediate appropriate epidermal and dermal regeneration and promote efficient wound repair, while modulating the immune system to prevent infection.
Engineering of the mRNA-interfering complementary RNA immune system against viral infection. (1986)

Creation of an artificial mRNA-interfering complementary RNA (micRNA) immune system, utilizing anti-sense RNAs to inhibit viral gene expression, has been shown to be an effective way to prevent viral infection. In the RNA coliphage SP, the gene for the maturation protein was found to be the best target for this type of immune system; mRNA-interfering complementary RNAs specific to the genes for coat protein and replicase were less effective in preventing infection. The greatest inhibitory effect was observed with a 240-base sequence encompassing the 24-base noncoding region of the maturation gene plus the 216-base coding sequence. Significantly, even a 19-base sequence covering only the Shine-Dalgarno sequence (ribosome-binding region) without the coding region exerted a strong inhibitory effect on phage proliferation. In contrast to the highly specific action against phage SP exhibited by the longer mRNA-interfering complementary RNA, the specificity with the shorter mRNA-interfering complementary RNA was broadened to phages Q beta and GA as well as SP, all of which are classified in the different groups of RNA coliphages. Therefore, this type of anti-viral reagent may be designed to have a particular breadth of specificity, thus increasing its value in various research and possibly clinical applications.
DNA Transport in Hierarchically-Structured Colloidal-Nanoparticle Porous-Wall Nanochannels (2008)

We report a simple approach to the formation of 3D colloidal nanoparticle structures incorporating enclosed mesoscopic structures through a simple process of spin-coating-driven directed self-assembly onto lithographically defined polymer templates. Removal of the buried polymer patterns by high temperature calcination results in the formation of hierarchically enclosed channels, continuous networks, isolated cavities, and multilayered structures with high stability and environmental resistance. These channels are used to investigate the transport of DNA molecules in constrained geometries.
Construction of a novel phagemid to produce custom DNA origami scaffolds (2018)

DNA origami, a method for constructing nanoscale objects, relies on a long single strand of DNA to act as the 'scaffold' to template assembly of numerous short DNA oligonucleotide 'staples'. The ability to generate custom scaffold sequences can greatly benefit DNA origami design processes. Custom scaffold sequences can provide better control of the overall size of the final object and better control of low-level structural details, such as locations of specific base pairs within an object. Filamentous bacteriophages and related phagemids can work well as sources of custom scaffold DNA. However, scaffolds derived from phages require inclusion of multi-kilobase DNA sequences in order to grow in host bacteria, and those sequences cannot be altered or removed. These fixed-sequence regions constrain the design possibilities of DNA origami. Here, we report the construction of a novel phagemid, pScaf, to produce scaffolds that have a custom sequence with a much smaller fixed region of 393 bases. We used pScaf to generate new scaffolds ranging in size from 1512 to 10 080 bases and demonstrated their use in various DNA origami shapes and assemblies. We anticipate our pScaf phagemid will enhance development of the DNA origami method and its future applications.
Copolymerization of CO2 and Epoxides Catalyzed by Metal Salen Complexes (2004)

The design of efficient metal catalysts for the selective coupling of epoxides and carbon dioxide to afford completely alternating copolymers has made significant gains over the past decade. Hence, it is becoming increasingly clear that this "greener" route to polycarbonates has the potential to supplement or supplant current processes for the production of these important thermoplastics, which involve the condensation polymerization of diols and phosgene or organic carbonates. On the basis of the experiences in our laboratory, this Account summarizes our efforts at optimizing (salen)CrIIIX catalysts for the selective formation of polycarbonates from alicyclic and aliphatic epoxides with CO2. An iterative catalyst design process is employed in which the salen ligand, initiator, cocatalyst, and reaction conditions are systematically varied, with the reaction rates and product selectivity being monitored by in situ infrared spectroscopy.
Interaction of 92-kDa type IV collagenase with the tissue inhibitor of metalloproteinases prevents dimerization, complex formation with interstitial collagenase, and activation of the proenzyme with stromelysin. (1992)

Secreted metalloproteases initiating proteolytic degradation of collagens and proteoglycans play a critical role in remodeling of the connective tissue. Activation of the secreted proenzymes and interaction with their specific inhibitors TIMP and TIMP-2 are responsible for regulation of enzyme activity in extracellular space. We have previously demonstrated that 92- and 72-kDa Type IV procollagenases, in contrast to interstitial collagenase (ClI), form specific complexes with TIMP and the related inhibitor TIMP-2, respectively. The physiologic significance of the proenzyme-inhibitor complex and the mechanism of activation of Type IV collagenases remained unclear. Here, we demonstrate that in the absence of TIMP, 92-kDa Type IV procollagenase (92T4Cl) can form a covalent homodimer and a novel complex with ClI. In the presence of TIMP, the formation of a 92T4Cl proenzyme complex with TIMP prevents dimerization, formation of the complex with ClI, and activation of the 92T4Cl proenzyme by stromelysin, a related metalloprotease. The proenzyme homodimer is unable to form a complex with TIMP. All TIMP-free forms of the proenzyme can be activated by stromelysin. The 92T4Cl-ClI complex can be activated to yield a complex active against both gelatin and fibrillar Type I collagen, suggesting a mechanism for cooperative action of two enzymes in reducing collagen fibrils to small peptides under physiologic conditions.
Adding redundant features for CRFs-based sentence sentiment classification (2008)

In this paper, we present a novel method based on CRF's in response to the two special characteristics of "contextual dependency" and "label redundancy" in sentence sentiment classification. We try to capture the contextual constraints on sentence sentiment using CRFs. Through introducing redundant labels into the original sentimental label set and organizing all labels into a hierarchy, our method can add redundant features into training for capturing the label redundancy. The experimental results prove that our method outperforms the traditional methods like NB, SVM, MaxEnt and standard chain CRFs. In comparison with the cascaded model, our method can effectively alleviate the error propagation among different layers and obtain better performance in each layer.
Genetic Immunization Against the Human Thyrotropin Receptor Causes Thyroiditis and Allows Production of Monoclonal Antibodies Recognizing the Native Receptor (1998)

The generation of Abs recognizing the native structure of the human thyrotropin receptor (hTSHR) has been difficult because there is currently no method allowing the purification of correctly folded Ag in the amounts required by classical immunization protocols. The majority of Abs made against the hTSHR react preferentially with denatured molecules. We report that a humoral response against the native hTSHR, compatible with mAb production, is elicited in mice by immunization with a DNA construct encoding the receptor. BALB/c mice were inoculated in the anterior tibialis muscle with 100 microg of plasmid DNA harboring the hTSHR cDNA. Eleven weeks after the first injection, 10 mice of 14 showed by FACS analysis a strong IgG response against the hTSHR expressed at the surface of Chinese hamster ovary cells. A clear TSH-binding inhibiting Ig and thyrotropin-blocking Ab activity (competition with TSH binding and TSH activity, respectively) was demonstrated in the majority of sera tested. One serum exhibited a clear stimulating activity. Despite the maintenance of normal circulating free T4 levels in all mice, these bioactivities persisted until 18 wk, in which mice were sacrificed, their thyroids were examined histologically, and spleens from two animals were used for mAb production. All mice displayed a severe lymphocytic infiltration of their thyroids, composed mostly of activated B cells. Three mAbs were produced against conformational epitopes of the hTSHR. We conclude that genetic immunization is an efficient method of generating Abs recognizing the native structure of the hTSHR and a new way of inducing thyroiditis in mice murine.
Protein folding/refolding analysis by mass spectrometry. Scrambling of disulphide bridges in insulin (1990)

In this paper we present a protocol that allows a dynamic analysis of disulphide-bridge formation, based on freezing the intermediates by acid/acetone precipitation, followed by digestion with pepsin and direct fast-atom-bombardment mass-spectrometric analysis. A rapid definition of the exact nature of disulphide bridges formed can be obtained via a definitive assignment of disulphide-linked peptides according to their unique mass values. With the use of an appropriate thiol concentration, scrambling of the native disulphide bonds in bovine insulin occurs, and the process is catalysed by protein disulphide-isomerase (EC 5.3.4.1). The disruption of native and the formation of new disulphide bonds can be monitored as described above, and interestingly B-chain dimers containing Cys-B7-Cys-B7 and Cys-B7-Cys-B19 bonds are detected.
Factorial Hidden Markov Models. (1996)

Hidden Markov models (HMMs) have proven to be one of the most widely used tools for learning probabilistic models of time series data.In an HMM, information about the past is conveyed through a single discrete variable-the hidden state.We discuss a generalization of HMMs in which this state is factored into multiple state variables and is therefore represented in a distributed manner.We describe an exact algorithm for inferring the posterior probabilities of the hidden state variables given the observations, and relate it to the forward-backward algorithm for HMMs and to algorithms for more general graphical models.Due to the combinatorial nature of the hidden state representation, this exact algorithm is intractable.As in other intractable systems, approximate inference can be carried out using Gibbs sampling or variational methods.Within the variational framework, we present a structured approximation in which the the state variables are decoupled, yielding a tractable algorithm for learning the parameters of the model.Empirical comparisons suggest that these approximations are efficient and provide accurate alternatives to the exact methods.Finally, we use the structured approximation to model Bach's chorales and show that factorial HMMs can capture statistical structure in this data set which an unconstrained HMM cannot.
Hexagonal pore arrays with a 50–420 nm interpore distance formed by self-organization in anodic alumina (1998)

Self-organized hexagonal pore arrays with a 50–420 nm interpore distance in anodic alumina have been obtained by anodizing aluminum in oxalic, sulfuric, and phosphoric acid solutions. Hexagonally ordered pore arrays with distances as large as 420 nm were obtained under a constant anodic potential in phosphoric acid. By comparison of the ordered pore formation in the three types of electrolyte, it was found that the ordered pore arrays show a polycrystalline structure of a few micrometers in size. The interpore distance increases linearly with anodic potential, and the relationship obtained from disordered porous anodic alumina also fits for periodic pore arrangements. The best ordered periodic arrangements are observed when the volume expansion of the aluminum during oxidation is about 1.4 which is independent of the electrolyte. The formation mechanism of ordered arrays is consistent with a previously proposed mechanical stress model, i.e., the repulsive forces between neighboring pores at the metal/oxide interface promote the formation of hexagonally ordered pores during the oxidation process.
An Attentional Framework for Stereo Vision (2005)

The necessity and utility of visual attention are discussed in the context of stereo vision in machines and primates. Specific problems that arise in this domain including binocular rivalry, and the deployment of attention in three-dimensional space are considered. Necessary conditions are outlined for achieving appropriate attentional behaviour in both the aforementioned domains. In this light, we outline classes of existing computational models of attention and discuss their applicability for realizing binocular attention. Finally, a stereo attention framework is presented by considering the tenets of an existing attentional architecture that extends naturally to the binocular domain, in conjunction with the connectivity of units involved in achieving stereo vision.
Two-photon laser precision microfabrication and its applications to micro-nano devices and systems (2003)

Two-photon absorption (TPA) provides the ability to confine photochemical and physical reactions to the order of laser wavelength in three dimensions. For applying TPA to laser precision microfabrication, we proposed a two-photon photopolymerization technique, by which photonic crystals and various micromachines with near-diffraction-limit features have been produced. Here we show that the diffraction limit was exceeded by utilizing nonlinear laser-matter interaction processes, and spatial resolutions far smaller than the diffraction limit were achieved. The super resolution, combined with other technologies newly developed by us including three-dimensional imaging of voxels, rapid surface profile scanning, device functionalization and its mechanical driving with a laser trapping force, and dye-doping polymerization for three-dimensional microdiagnosis, makes the technique quite compelling for nanophotonic and optical microelectromechanical (MEMS) applications.
Proteolytic Cleavage of the Fusion Protein but Not Membrane Fusion Is Required for Measles Virus-Induced Immunosuppression In Vitro (2000)

Immunosuppression induced by measles virus (MV) is associated with unresponsiveness of peripheral blood lymphocytes (PBL) to mitogenic stimulation ex vivo and in vitro. In mixed lymphocyte cultures and in an experimental animal model, the expression of the MV glycoproteins on the surface of UV-inactivated MV particles, MV-infected cells, or cells transfected to coexpress the MV fusion (F) and the hemagglutinin (H) proteins was found to be necessary and sufficient for this phenomenon. We now show that MV fusion-inhibitory peptides do not interfere with the induction of immunosuppression in vitro, indicating that MV F-H-mediated fusion is essentially not involved in this process. Proteolytic cleavage of MV F(0) protein by cellular proteases, such as furin, into the F(1)-F(2) subunits is, however, an absolute requirement, since (i) the inhibitory activity of MV-infected BJAB cells was significantly impaired in the presence of a furin-inhibitory peptide and (ii) cells expressing or viruses containing uncleaved F(0) proteins revealed a strongly reduced inhibitory activity which was improved following trypsin treatment. The low inhibitory activity of effector structures containing mainly F(0) proteins was not due to an impaired F(0)-H interaction, since both surface expression and cocapping efficiencies were similar to those found with the authentic MV F and H proteins. These results indicate that the fusogenic activity of the MV F-H complexes can be uncoupled from their immunosuppressive activity and that the immunosuppressive domains of these proteins are exposed only after proteolytic activation of the MV F(0) protein.
Research on Network Traffic Identification Based on Improved BP Neural Network (2013)

Traffic identification is a key task for any Internet Service Providers (ISP) or network administrators. Neural network is an important research method on traffic classification, this paper introduces the important methods of traffic classification,through study on Principal Component Analysis(PCA) and BP neural network. An improved BP neural network to identify traffic is proposed and M OORE SET is used as dataset, meanwhile, building N OC SET dataset based on CERNET(China Education and Research Network).the experiment results show that the accuracy rate of traffic classification based on the improved BP neural network model is relatively high.Finally,this paper analyzes packet sampling impact on traffic identification.
Effects of Oral Administration of Type II Collagen on Rheumatoid Arthritis (1993)

Rheumatoid arthritis is an inflammatory synovial disease thought to involve T cells reacting to an antigen within the joint. Type II collagen is the major protein in articular cartilage and is a potential autoantigen in this disease. Oral tolerization to autoantigens suppresses animal models of T cell-mediated autoimmune disease, including two models of rheumatoid arthritis. In this randomized, double-blind trial involving 60 patients with severe, active rheumatoid arthritis, a decrease in the number of swollen joints and tender joints occurred in subjects fed chicken type II collagen for 3 months but not in those that received a placebo. Four patients in the collagen group had complete remission of the disease. No side effects were evident. These data demonstrate clinical efficacy of an oral tolerization approach for rheumatoid arthritis.