gebhart/patrepeval huggingface dataset:
Application of HVJ-liposome mediated gene transfer in lung transplantation—distribution and transfection efficiency in the lung (2005)

Our results suggest that the repeated transtracheal gene transfection using HVJ-liposome may have benefits for treatment of problems after lung transplantation. In addition, gene transfer using a flushing solution during harvest may provide an opportunity for gene manipulation in the setting of lung transplantation.
Biosynthesis. Part 26. Synthetic studies on structural modification of late biosynthetic precursors for colchicine (1983)

The latter part of the natural pathway to colchicine is known to involve conversion of a phenethyltetra-hydroisoquinoline (2) by phenol oxidation into a dienone (O-methylandrocymbine)(4), the dienone subsequently undergoing ring-expansion to generate the tropolone system. Synthetic routes are here described which yield the isoquinoline and dienone structures in modified forms (16), (17), and (38), all having a C-methyl group introduced adjacent to the nitrogen atom. An alternative approach for synthesis of the dienone, involving conversion of a phenanthrene into a dibenzocycloheptene, is also explored.Incorporation experiments on Colchicium autumnale plants using labelled isoquinolines (16a) and (17a) show that they are not converted enzymically into tropolone alkaloids nor is the former significantly cyclised in the plants to the C-methylated dienone (38). Clearly, at least one of the enzymes required for the late biosynthetic stages is highly sensitive to structural change close to the nitrogen atom.
ICESat observations of Arctic sea ice: A first look (2004)

Analysis of near‐coincident ICESat and RADARSAT imagery shows that the retrieved elevations from the laser altimeter are sensitive to new openings (containing thin ice or open water) in the sea ice cover as well as to surface relief of old and first‐year ice. The precision of the elevation estimates, measured over relatively flat sea ice, is ∼2 cm. Using the thickness of thin‐ice in recent openings to estimate sea level references, we obtain the sea‐ice freeboard along the altimeter tracks. This step is necessitated by the large uncertainties in the sea surface topography compared to that required for accurate determination of freeboard. Unknown snow depth introduces the largest uncertainty in the conversion of freeboard to ice thickness. Surface roughness is also derived, for the first time, from the variability of successive elevation estimates along the altimeter track. Overall, these ICESat measurements provide an unprecedented view of the Arctic Ocean ice cover at length scales at and above the spatial dimension of the altimeter footprint of ∼70 m.
Charge dependent behavior of PNA/DNA/PNA triplexes in the gas phase (2006)

Intact noncovalent complexes were studied in the gas phase using negative ion nano-ESI mass spectrometry. Among various noncovalent systems studied in the gas phase, the interaction of DNA strands with peptide nucleic acids (PNAs) presents a strong interest as biologically relevant systems. PNAs originally described by Nielsen are used as DNA mimics as possible medical agents by imprisoning DNA single strands into stable noncovalent complexes. Two types of PNAs were investigated in the PNA/DNA multiplex: the original Nielsen's PNA and a modified backbone PNA by the introduction of syn- and anti-(aminoethyl)thiazolidine rings. We first investigated the stoichiometry of PNA/DNA multiplexes formed in solution and observed them in the gas phase via qualitative kinetics of complementary strand associations. It resulted in observing PNA2/DNA triplexes (ts) as the multiply deprotonated species, most stable in both the solution and gas phase. Second, charge-dependant decompositions of these species were undertaken under low-energy collision conditions. It appears that covalent bond cleavages (base releasing or skeleton cleavage) occur from lower ts charge states rather than ts unzipping, which takes place from higher charge states. This behavior can be explained by considering the presence of zwitterions depending on the charge state. They result in strong salt-bridge interactions between the positively charged PNA side chain and the negatively charged DNA backbone. We propose a general model to clearly display the involved patterns in the noncovalent triplex decompositions. Third, the relative stability of three PNA2/DNA complexes was scrutinized in the gas phase by acquiring the breakdown curves of their ts(6-) form, corresponding to the ts unzipping. The chemical structures of the studied PNAs were chosen in order to evidence the possible influence of backbone stereochemistry on the rigidity of PNA2/DNA complexes. It provided significantly different stabilities via V(m) measurements. The relative gas-phase stability order obtained was compared to that found in solution by Chassaing et al., and shows qualitative agreement.
Triptolide, A Novel Immunosuppressive and Anti-Inflammatory Agent Purified from a Chinese Herb Tripterygium Wilfordii Hook F (2001)

Triptolide is a diterpenoid triepoxide purified from a Chinese herb Tripterygium Wilfordii Hook F (TWHF). TWHF has been used in traditional Chinese medicine for more than two thousand years. However, its potential value was recognized by the western medicine only after investigators observed the effectiveness of TWHF in the treatment of leprosy and rheumatoid arthritis. Triptolide has been identified as the major component responsible for the immunosuppressive and anti-inflammatory effects of TWHF. Triptolide inhibits both Ca(2+)-dependent and Ca(2+)-independent pathways and affects T cell activation through inhibition of interleukin-2 transcription at a site different from the target of cyclosporin A. Triptolide also has inhibitory effects on a variety of proinflammatory cytokines and mediators and on the expression of adhesion molecules by endothelial cells. Triptolide is effective for the treatment of a variety of autoimmune diseases and in prevention of allograft rejection and graft-versus-host disease in both animals and humans. Moreover, triptolide possesses antitumor and male anti-fertility effect. However, the toxicities of triptolide may be associated with renal, cardiac, hematopoietic and reproductive systems. Currently available data suggest that triptolide is a promising immunosuppressive and anti-inflammatory agent and should be explored further in autoimmune diseases and transplantation.
The alpha 2(VIII) collagen gene. A novel member of the short chain collagen family located on the human chromosome 1. (1991)

Type VIII collagen is a major component of Descemet's membrane, the specialized basement membrane of corneal endothelial cells. Sequence analysis of a cDNA isolated from a library made with mRNA from rabbit corneal endothelial cells has indicated that type VIII molecules contain a polypeptide chain, alpha 1(VIII), consisting of a short triple-helical domain of 454 amino acid residues flanked by non-triple-helical domains of 117 and 173 amino acid residues at the amino and carboxyl ends, respectively (Yamaguchi, N., Benya, P. D., van der Rest, M., and Ninomiya, Y. (1989) J. Biol. Chem. 264, 16022-16029). The sequence of alpha 1(VIII) is strikingly similar to that of alpha 1(X) collagen, a product of hypertrophic chondrocytes. Also, characterization of the alpha 1(VIII) and alpha 1(X) collagen genes has shown that they are quite similar in their exon organization. It has been concluded, therefore, that they are homologous members of a distinct subclass of collagen genes (Yamaguchi, N., Mayne, R., and Ninomiya, Y. (1991) J. Biol. Chem. 266, 4508-4513). We have given this subclass the name short chain collagens because of the relatively small size of the triple-helical domain. In the present study, we report on the identification and characterization of a collagen gene encoding a polypeptide which is co-expressed with the alpha 1(VIII) chain in corneal endothelial cells. This collagen chain contains a triple-helical and a carboxyl non-triple-helical domain encoded by a single, large exon both in mice and humans. We conclude, therefore, that the genes encodes a novel member of the short chain collagen family, and we have given this chain the designation alpha 2(VIII) collagen. By in situ hybridization we demonstrate that the alpha 2(VIII) gene is located in the p32.3-p34.3 region of the short arm of chromosome 1.
Semantic localization and mapping in robot vision (2016)

Integration of human semantics plays an increasing role in robotics tasks such as mapping, localization and detection. Increased use of semantics serves multiple purposes, including giving computers the ability to process and present data containing human meaningful concepts, allowing computers to employ human reasoning to accomplish tasks.\nThis dissertation presents three solutions which incorporate semantics onto visual data in order to address these problems. First, on the problem of constructing topological maps from sequence of images. The proposed solution includes a novel image similarity score which uses dynamic programming to match images using both appearance and relative positions of local features simultaneously. An MRF is constructed to model the probability of loop-closures and a locally optimal labeling is found using Loopy-BP. The recovered loop closures are then used to generate a topological map. Results are presented on four urban sequences and one indoor sequence.\nThe second system uses video and annotated maps to solve localization. Data association is achieved through detection of object classes, annotated in prior maps, rather than through detection of visual features. To avoid the caveats of object recognition, a new representation of query images is introduced consisting of a vector of detection scores for each object class. Using soft object detections, hypotheses about pose are refined through particle filtering. Experiments include both small office spaces, and a large open urban rail station with semantically ambiguous places. This approach showcases a representation that is both robust and can exploit the plethora of existing prior maps for GPS-denied environments while avoiding the data association problems encountered when matching point clouds or visual features.\nFinally, a purely vision-based approach for constructing semantic maps given camera pose and simple object exemplar images. Object response heatmaps are combined with known pose to back-project detection information onto the world. These update the world model, integrating information over time as the camera moves. The approach avoids making hard decisions on object recognition, and aggregates evidence about objects in the world coordinate system.\nThese solutions simultaneously showcase the contribution of semantics in robotics and provide state of the art solutions to these fundamental problems.
The Surgeon's Third Hand an Interactive Robotic C-Arm Fluoroscope (2006)

Experiments with this world's first fully robotized C-arm show very promising results. Movements in the image plane, longbone images, data acquisition for 3D reconstruction, and landmark based positioning were successfully implemented and tested. The next version of our C-arm will overcome mechanical problems such as lacking positioning accuracy and mechanical deformation. The value of an every-day OR-device can be increased by simple means. The workflow can be optimized and mistakes can be prevented. Operation time is saved and radiation dose for patient and staff is minimized. The experiences of this study have already been transferred to other systems such as OR microscope (Knopp et al. 2004) and showed similar promising results. Chances are that the number of such robot- assisted systems in the OR will increase soon.
Hydrogel Cell Cultures (2007)

Three-dimensional synthetic gels that mimic the extracellular matrix provide a promising tool for studying cell interactions.
MiR‐485‐3p modulates neural stem cell differentiation and proliferation via regulating TRIP6 expression (2019)

Recent references have showed crucial roles of several miRNAs in neural stem cell differentiation and proliferation. However, the expression and role of miR-485-3p remains unknown. In our reference, we indicated that miR-485-3p expression was down-regulated during NSCs differentiation to neural and astrocytes cell. In addition, the TRIP6 expression was up-regulated during NSCs differentiation to neural and astrocytes cell. We carried out the dual-luciferase reporter and found that overexpression of miR-485-3p decreased the luciferase activity of pmirGLO-TRIP6-wt but not the pmirGLO-TRIP6-mut. Ectopic expression of miR-485-3p decreased the expression of TRIP6 in NSC. Ectopic miR-485-3p expression suppressed the cell growth of NSCs and inhibited nestin expression of NSCs. Moreover, elevated expression of miR-485-3p decreased the ki-67 and cyclin D1 expression in NSCs. Furthermore, we indicated that miR-485-3p reduced proliferation and induced differentiation of NSCs via targeting TRIP6 expression. These data suggested that a crucial role of miR-485-3p in self-proliferation and differentiation of NSCs. Thus, altering miR-485-3p and TRIP6 modulation may be one promising therapy for treating with neurodegenerative and neurogenesis diseases.
Characterization and application of two novel monoclonal antibodies against human OX40: costimulation of T cells and expression on tumor as well as normal gland tissues (2006)

OX40, a membrane-bound molecule of the tumor-necrosis-factor-receptor superfamily, is a critical costimulatory receptor during the immune response. Here, we newly generated two specific mouse antihuman OX40 monoclonal antibodies (mAbs) (2G2 and 1F7), whose specificities are quite different from the available OX40 mAb (ACT35) by competition assay. It was also found that both mAbs could enhance the proliferation, activation and differentiation of T lymphocytes primed by anti-CD3 mAb. These results evidenced that both were functional antihuman OX40 mAbs. Furthermore, stained by 2G2 and 1F7, FCM and immunohistochemistry detected the constitutive expression of OX40 on tumor cell lines from epithelium, breast cancer and glioma tissues. Meanwhile, the non-tumor tissues (thyroid gland, stomach gland) were also found OX40 expression. These results suggested that OX40 is not only expressed in activated T cells, but also in some tumors as well as normal gland tissues. Such expression pattern indicated that OX40 may be a valuable surface antigen in unveiling its expression and function outside the immune system. Briefly, these novel antibodies may contribute to the evaluation of the mechanism of tumor metastasis and eventually shed light on further study of tumor immunotherapy and autoimmune diseases.
CD25+CD4+ regulatory T cells generated by exposure to a model protein antigen prevent allograft rejection: antigen-specific reactivation in vivo is critical for bystander regulation (2005)

The importance of CD25(+)CD4(+) regulatory T (Treg) cells in the control of immune responses is established, but their antigen specificity in vivo remains unclear. Understanding Treg-cell specificity requirements will be important if their potential is to be developed for immunotherapy. Pretreatment of recipient mice with donor alloantigen plus anti-CD4 antibody generates CD25(+)CD4(+) Treg cells with the capacity to prevent skin allograft rejection in adoptive transfer recipients. Here we demonstrate that, although this regulation can be antigen-specific, reactivation with the original tolerizing alloantigen allows the Treg cells to suppress rejection of third-party allografts. Aware of the limitations of alloantigen pretreatment, we asked whether graft-protective Treg cells could be generated against unrelated, nongraft antigens. We demonstrate that bystander regulation also extends to CD25(+)CD4(+) Treg cells generated in vivo by exposure to nominal antigens under anti-CD4 antibody cover. Providing these Treg cells are reexposed to the tolerizing antigens before adoptive transfer, they prevent the rejection of fully allogeneic skin grafts. That this might form the basis of a clinically relevant tolerance induction strategy is demonstrated by the fact that, when combined with subtherapeutic anti-CD8 antibody, Treg cells generated in response to nongraft antigens facilitate the acceptance of cardiac allografts in primary recipients.
Recent Trends in Survival From Out-of-Hospital Cardiac Arrest in the United States (2014)

Data drawn from a large subset of U.S communities suggest that rates of survival from out-of-hospital cardiac arrest have improved among sites participating in a performance improvement registry.
The action of phenylmethylsulfonyl fluoride on human acetylcholinesterase, chymotyrpsin and trypsin. (1969)

In view of the prevalent clinical impression that acute hemorrhagic pancreatitis involves autodigestion of the pancreas by prematurely activated pancreatic proteolytic enzymes and of reports in the literature that phenylmethylsulfonyl fluoride (PMSF) and related compounds inactivate trypsin and chymotrypsin (from bovine tissues) without affecting acetylcholinesterase (from electriceel), we have studied the action of PMSF on human enzymes and its toxicity in vivo. PMSF rapidly inactivates purified chymotrypsin from human pancreas, although human trypsin is less susceptible to inhibition by PMSF. In contrast to the insensitivity of acetylcholinesterase from electric eels to PMSF, which was confirmed, the enzyme from human erythrocytes is rapidly inhibited by low concentrations of PMSF. This appears to be the first major difference detected between acetylcholinesterases from mammalian sources and from the electric eel. C 14 -labeled PMSF penetrates human red cells rapidly and inhibits acetylcholinesterase in situ. The labeled inhibitor also penetrates freely through the blood-brain barrier. Despite these suggestions of potential toxicity, PMSF had no discernible effect on synaptic transmission at the neuromuscular junction in the isolated rat diaphragm preparation, and its systemic toxicity when administered to mice i. p. was rather low (LD5O = 200 mg/kg).
Comparisons of the F and HN gene sequences of different strains of bovine parainfluenza virus type 3: relationship to phenotype and pathogenicity. (1996)

The genes for the F and HN glycoprotein of a pathogenic field isolate of bovine parainfluenza virus type 3 (BPIV3) were isolated, converted to cDNA, and sequenced using dideoxynucleotides. The resulting nucleotide sequences were converted to protein sequence and were compared to previously sequenced glycoprotein genes with amino acid differences in the glycoproteins of isolates expressing different phenotypes. The HN glycoprotein, involved in the attachment and release of the virus, and the F glycoprotein, involved in penetration and spread of the virus, have been shown to affect pathogenicity of the virus and are the immunodominant proteins of the virus. Both the F and HN proteins have been shown to be required for syncytium formation. Our results suggest that BPIV3 viruses that exhibit greater syncytium-inducing activity in vitro have greater pathogenicity in vivo. By determining which epitopes are involved in syncytium formation and comparing the sequences and enzymatic activities of different strains of virus, it may be possible to design subunit vaccines that protect against disease.
Characterization of parathyroid hormone receptors in canine renal cortical plasma membranes using a radioiodinated sulfur-free hormone analogue. Correlation of binding with adenylate cyclase activity. (1979)

The abbreviations used are: PTH, parathyroid hormone; bPTH, bovine parathyroid hormone; Nle, norleucine; ACTH, adrenocorticotropin. ' Compounds with limited NHZ-terminal modifications, such as bPTH-(2-34), have shown discordant results between
Wnt signaling induces differentiation of progenitor cells in organotypic keratinocyte cultures (2007)

These results are consistent with the phenotypes reported for transgenic mice engineered to have gain or loss of function of Wnt signaling in skin, which would recommend our culture model as an accurate one for molecular analysis. Since it is known that canonical ligands are expressed in skin, it is likely that this pathway normally regulates the balance of growth and differentiation, and suggests it could be important to pathogenesis.
Large TCR Diversity of Virus-Specific CD8 T Cells Provides the Mechanistic Basis for Massive TCR Renewal after Antigen Exposure (2011)

Ex vivo analysis of virus-specific CD8 T cell populations by anchored PCR has shown that the CD8 TCR repertoire was less oligoclonal (seven to nine clonotypes per individual epitope) than previously thought. In the current study, TCR diversity was investigated by assessing both the overall TCR β-chain variable regions usage as well as the CDR3 regions in ex vivo-isolated CMV- and EBV-specific CD8 T cells from 27 healthy donors. The average number of clonotypes specific to most single viral epitopes comprised between 14 and 77. Changes in the CD8 TCR repertoire were also longitudinally assessed under conditions of HIV-1 chronic infection (i.e., in patients with suppressed virus replication and after treatment interruption and Ag re-exposure). The results showed that a large renewal (≤ 80%) of the TRB repertoire occurred after Ag re-exposure and was eventually associated with an increased T cell recognition functional avidity. These results demonstrate that the global CD8 TCR repertoire is much more diverse (≤ 9-fold) than previously estimated and provide the mechanistic basis for supporting massive repertoire renewal during chronic virus infection and Ag re-exposure.
Co-expression of EGFRvIII with ErbB-2 enhances tumorigenesis: EGFRvIII mediated constitutively activated and sustained signaling pathways, whereas EGF-induced a transient effect on EGFR-mediated signaling pathways (2008)

Elevated levels of epidermal growth factor receptor (EGFR) have been detected in a variety of human cancers. Several reports have demonstrated that the Type III EGF receptor deletion-mutant (EGFRvIII) is frequently detected in various human cancers, including breast cancer. We generated and characterized monoclonal antibody against EGFRvIII. We demonstrated that 29% of DCIS, 40% of primary invasive breast cancers and 54% of metastatic lymph nodes express EGFRvIII by immunohistochemical analysis with two monoclonal antibodies. High levels of EGFRvIII expression were detected in about 5% of primary breast cancer and 27% of metastatic lymph-nodes. Furthermore, in the positive samples, the normal mammary gland exhibited negative staining for EGFRvIII, while the tumor cells were positive. The frequency of EGFRvIII expression correlated with breast cancer progression. We also showed that, despite the absence of gene amplification of EGFR in breast carcinoma cells, EGFRvIII was phosphorylated in breast cancer. In addition, approximately 40% of ErbB-2 positive primary breast tumors were found to co-express EGFRvIII. Even more striking is that 75% (3/4) of ErbB-2 positive metastatic lymph node specimens co-expressed with EGFRvIII. Co-expression of EGFRvIII with ErbB-2 in 32D cells amplified downstream signaling cascades and significantly enhanced tumorigenesis in vivo. Furthermore, EGFRvIII mediated constitutively activated and sustained downstream signaling pathways, whereas EGF-ligand induced a transient effect on wt-EGFR-mediated downstream signaling pathways.