gebhart/patrepeval huggingface dataset:
Cell‐free translation systems for protein engineering (2006)

Cell-free translation systems have developed significantly over the last two decades and improvements in yield have resulted in their use for protein production in the laboratory. These systems have protein engineering applications, such as the production of proteins containing unnatural amino acids and development of proteins exhibiting novel functions. Recently, it has been suggested that cell-free translation systems might be used as the fundamental basis for cell-like systems. We review recent progress in the field of cell-free translation systems and describe their use as tools for protein production and engineering.
Continuously distributed magnetization profile for millimeter-scale elastomeric undulatory swimming (2014)

We have developed a millimeter-scale magnetically driven swimming robot for untethered motion at mid to low Reynolds numbers. The robot is propelled by continuous undulatory deformation, which is enabled by the distributed magnetization profile of a flexible sheet. We demonstrate control of a prototype device and measure deformation and speed as a function of magnetic field strength and frequency. Experimental results are compared with simple magnetoelastic and fluid propulsion models. The presented mechanism provides an efficient remote actuation method at the millimeter scale that may be suitable for further scaling down in size for micro-robotics applications in biotechnology and healthcare.
Pseudo-immortalization of postnatal cochlear progenitor cells yields a scalable cell line capable of transcriptionally regulating mature hair cell genes (2015)

The mammalian cochlea is a highly specialized organ within the inner ear. Sensory hair cells (HC) in the cochlea detect and transduce sound waves into electrical impulses that are sent to the brain. Studies of the molecular pathways regulating HC formation are hindered by the very sparse nature of HCs, where only ~3300 are found within an entire mouse cochlea. Current cell lines mimic certain aspects of HCs but lack terminal HC marker expression. Here we successfully "pseudo-immortalized" cochlear progenitor cells using the "conditional reprogramming" technique. These cells, termed "Conditionally Reprogrammed Otic Stem Cells" (CR-OSC), are able to bypass the senescence inherent to cochlear progenitor cells without genetic alterations, allowing for the generation of over 15 million cells from a single cochlea. These cells can be differentiated and up-regulate both early and terminal differentiation genes associated with HCs, including the terminal HC differentiation marker prestin. CR-OSCs also respond to known HC cues, including upregulation of HC genes in response to Atoh1 overexpression, and upregulation of prestin expression after thyroid hormone application. Overall, we describe the creation of a HC line capable of regulated expression of HC genes that can easily be recreated in any laboratory from any mouse of interest.
Superinfection of Cats with Feline Immunodeficiency Virus Subtypes A and B (1994)

The ability of feline immunodeficiency virus (FIV) isolates from subtypes A and B to superinfect cats and cell cultures was tested. Three specific pathogen-free (SPF) cats were first inoculated with 10 ID50 of subtype B virus (FIVBang) and 30 weeks later inoculated with 100 ID50 of subtype A virus (FIVPet). On the basis of subtype-specific PCR analysis, both FIV subtypes were detected in the peripheral blood lymphocytes (PBLs) of two of three cats from 9 to 30 weeks following the second inoculation. Only the first virus was detected in the bone marrow (BM) cells of these two cats until 30 weeks following the second inoculation, at which time the second virus was finally detected in their BM cells. Both cats developed significant virus-neutralizing (VN) antibodies to the second virus by 15 weeks following the second inoculation; but only one cat had high VN titers to the first virus, which remained at the same level even after the second inoculation. The two control cats inoculated with only the second virus developed VN titers specifically to the second virus and were consistently PCR positive for the virus in PBLs and BM cells starting 9 weeks postinoculation. Thus a delay in BM infection with the second virus was observed in the two superinfected cats. In contrast, one of three cats had neither VN antibodies to the second virus nor PCR signal of the second virus in its PBLs, BM, and lymph node throughout the 30 weeks of study and it appeared to be resistant to superinfection.(ABSTRACT TRUNCATED AT 250 WORDS)
Agonist Anti-GITR Monoclonal Antibody Induces Melanoma Tumor Immunity in Mice by Altering Regulatory T Cell Stability and Intra-Tumor Accumulation (2010)

In vivo GITR ligation has previously been shown to augment T-cell-mediated anti-tumor immunity, yet the underlying mechanisms of this activity, particularly its in vivo effects on CD4+ foxp3+ regulatory T cells (Tregs), have not been fully elucidated. In order to translate this immunotherapeutic approach to the clinic it is important gain better understanding of its mechanism(s) of action. Utilizing the agonist anti-GITR monoclonal antibody DTA-1, we found that in vivo GITR ligation modulates regulatory T cells (Tregs) directly during induction of melanoma tumor immunity. As a monotherapy, DTA-1 induced regression of small established B16 melanoma tumors. Although DTA-1 did not alter systemic Treg frequencies nor abrogate the intrinsic suppressive activity of Tregs within the tumor-draining lymph node, intra-tumor Treg accumulation was significantly impaired. This resulted in a greater Teff:Treg ratio and enhanced tumor-specific CD8+ T-cell activity. The decreased intra-tumor Treg accumulation was due both to impaired infiltration, coupled with DTA-1-induced loss of foxp3 expression in intra-tumor Tregs. Histological analysis of B16 tumors grown in Foxp3-GFP mice showed that the majority of GFP+ cells had lost Foxp3 expression. These "unstable" Tregs were absent in IgG-treated tumors and in DTA-1 treated TDLN, demonstrating a tumor-specific effect. Impairment of Treg infiltration was lost if Tregs were GITR(-/-), and the protective effects of DTA-1 were reduced in reconstituted RAG1(-/-) mice if either the Treg or Teff subset were GITR-negative and absent if both were negative. Our results demonstrate that DTA-1 modulates both Teffs and Tregs during effective tumor treatment. The data suggest that DTA-1 prevents intra-tumor Treg accumulation by altering their stability, and as a result of the loss of foxp3 expression, may modify their intra-tumor suppressive capacity. These findings provide further support for the continued development of agonist anti-GITR mAbs as an immunotherapeutic strategy for cancer.
Pathogenesis of Canine Bordetellosis (1977)

Bordetella bronchiseptica produced tracheobronchitis when administered in aerosol to specific pathogen-free dogs. Clinical signs appeared to be directly related to numbers of bacteria in the trachea. Electron microscopic examination revealed that each bacterium was close to one or more tracheal cilia and that a fibrillar material was radiating from the bacterial cell wall. B. bronchiseptica required 14 weeks to be cleared from the tracheas of infected dogs; in contrast, other organisms commonly isolated from the respiratory tracts of dogs were cleared within one to three days. Strains of high and low in vitro passage and strains representing three different morphotypes were of equal pathogenicity. Local immunity was observed after infection and appeared to be of primary importance in recovery from the infection. Presumably this response involves prevention of bacterial attachment and reattachment to cilia.
IDH1 and IDH2 mutation studies in 1473 patients with chronic-, fibrotic- or blast-phase essential thrombocythemia, polycythemia vera or myelofibrosis (2010)

In a multi-institutional collaborative project, 1473 patients with myeloproliferative neoplasms (MPN) were screened for isocitrate dehydrogenase 1 (IDH1)/IDH2 mutations: 594 essential thrombocythemia (ET), 421 polycythemia vera (PV), 312 primary myelofibrosis (PMF), 95 post-PV/ET MF and 51 blast-phase MPN. A total of 38 IDH mutations (18 IDH1-R132, 19 IDH2-R140 and 1 IDH2-R172) were detected: 5 (0.8%) ET, 8 (1.9%) PV, 13 (4.2%) PMF, 1 (1%) post-PV/ET MF and 11 (21.6%) blast-phase MPN (P<0.01). Mutant IDH was documented in the presence or absence of JAK2, MPL and TET2 mutations, with similar mutational frequencies. However, IDH-mutated patients were more likely to be nullizygous for JAK2 46/1 haplotype, especially in PMF (P=0.04), and less likely to display complex karyotype, in blast-phase disease (P<0.01). In chronic-phase PMF, JAK2 46/1 haplotype nullizygosity (P<0.01; hazard ratio (HR) 2.9, 95% confidence interval (CI) 1.7-5.2), but not IDH mutational status (P=0.55; HR 1.3, 95% CI 0.5-3.4), had an adverse effect on survival. This was confirmed by multivariable analysis. In contrast, in both blast-phase PMF (P=0.04) and blast-phase MPN (P=0.01), the presence of an IDH mutation predicted worse survival. The current study clarifies disease- and stage-specific IDH mutation incidence and prognostic relevance in MPN and provides additional evidence for the biological effect of distinct JAK2 haplotypes.
FcεRI cross‐linking‐induced actin assembly mediates calcium signalling in RBL‐2H3 mast cells (2002)

1. To determine the role of actin assembly in the Ca(2+) signalling of mast cells activated by cross-linking of FcepsilonRI, we examined the effects of cytochalasin D, an inhibitor of actin polymerization. 2. In the RBL-2H3 cells, F-actin content was increased by sensitization with anti-dinitrophenol (DNP) IgE. In these cells, cytochalasin D induced oscillatory increases in cytosolic Ca(2+) ([Ca(2+)](i)); these increase were inhibited by jasplakinolide, a stabilizer of actin filaments. 3. In the IgE-sensitized RBL-2H3 cells, DNP-human serum albumin (DNP-HSA) augmented actin assembly. DNP-HSA also increased the production of IP(3), [Ca(2+)](i) and degranulation. Cytochalasin D enhanced all of these DNP-HSA-induced effects. 4. In a Ca(2+)-free solution, DNP-HSA induced a transient increase in [Ca(2+)](i), and this increase was accelerated by cytochalasin D. After cessation of the DNP-HSA-induced Ca(2+) release, the re-addition of Ca(2+) induced a sustained increase in [Ca(2+)](i) through capacitative Ca(2+) entry (CCE), and this increase was enhanced by cytochalasin D. 5 The effect of cytochalasin D in enhancing the CCE activity was prevented by xestospongin C. 6. In contrast, neither the Ca(2+) release nor the CCE activation that was induced by thapsigargin was affected by cytochalasin D. 7. These results suggest that actin de-polymerization stimulates the FcepsilonRI-mediated signalling to augment the release of Ca(2+) from the endoplasmic reticulum in RBL-2H3 cells.
Investigation of Experimental Factors That Underlie BRCA1/2 mRNA Isoform Expression Variation: Recommendations for Utilizing Targeted RNA Sequencing to Evaluate Potential Spliceogenic Variants (2018)

PCR-based RNA splicing assays are commonly used in diagnostic and research settings to assess the potential effects of variants of uncertain clinical significance in <i>BRCA1</i> and <i>BRCA2</i>. The Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium completed a multicentre investigation to evaluate differences in assay design and the integrity of published data, raising a number of methodological questions associated with cell culture conditions and PCR-based protocols. We utilized targeted RNA-seq to re-assess <i>BRCA1</i> and <i>BRCA2</i> mRNA isoform expression patterns in lymphoblastoid cell lines (LCLs) previously used in the multicentre ENIGMA study. Capture of the targeted cDNA sequences was carried out using 34 <i>BRCA1</i> and 28 <i>BRCA2</i> oligonucleotides from the Illumina Truseq Targeted RNA Expression platform. Our results show that targeted RNA-seq analysis of LCLs overcomes many of the methodology limitations associated with PCR-based assays leading us to make the following observations and recommendations: (1) technical replicates (<i>n</i> > 2) of variant carriers to capture methodology induced variability associated with RNA-seq assays, (2) LCLs can undergo multiple freeze/thaw cycles and can be cultured up to 2 weeks without noticeably influencing isoform expression levels, (3) nonsense-mediated decay inhibitors are essential prior to splicing assays for comprehensive mRNA isoform detection, (4) quantitative assessment of exon:exon junction levels across <i>BRCA1</i> and <i>BRCA2</i> can help distinguish between normal and aberrant isoform expression patterns. Experimentally derived recommendations from this study will facilitate the application of targeted RNA-seq platforms for the quantitation of <i>BRCA1</i> and <i>BRCA2</i> mRNA aberrations associated with sequence variants of uncertain clinical significance.
CpG Oligodeoxynucleotides Act as Adjuvants for Pneumococcal Polysaccharide-Protein Conjugate Vaccines and Enhance Antipolysaccharide Immunoglobulin G2a (IgG2a) and IgG3 Antibodies (2000)

Pneumococcal polysaccharide-protein conjugate vaccines elicit antipolysaccharide antibodies, but multiple doses are required to achieve protective antibody levels in children. In addition, the immunogenicity of experimental multivalent pneumococcal conjugate vaccines varies with different polysaccharide serotypes. One strategy to improve these vaccines is to incorporate an adjuvant to enhance their immunogenicity. Synthetic oligodeoxynucleotides containing unmethylated CpG motifs (CpG ODN) are adjuvants that promote T-cell and T-dependent antibody responses to protein antigens, but it has been unclear whether CpG ODN can enhance polysaccharide-specific antibody responses. The present studies demonstrate significant adjuvant activity of CpG ODN for antibody responses against Streptococcus pneumoniae polysaccharide types 19F and 6B induced by conjugates of 19F and 6B with the protein carrier CRM(197). BALB/c ByJ mice were injected with 19F-CRM(197) or 6B-CRM(197) with or without CpG ODN, and sera were tested for anti-19F or anti-6B antibodies by enzyme-linked immunosorbent assay. The polysaccharide-specific antibody response to 19F-CRM(197) alone was predominantly of the immunoglobulin G1 (IgG1) and IgM isotypes, but addition of CpG ODN markedly increased geometric mean titers of total anti-19F antibody (23-fold), anti-19F IgG2a (26-fold), and anti-19F IgG3 (>246-fold). The polysaccharide-specific antibody response to 6B-CRM(197) alone consisted only of IgM, but addition of CpG ODN induced high titers of anti-6B IgG1 (>78-fold increase), anti-6B IgG2a (>54-fold increase), and anti-6B IgG3 (>3,162-fold increase). CpG ODN also increased anti-CRM(197) IgG2a and IgG3. Adjuvant effects were not observed with control non-CpG ODN. Thus, CpG ODN significantly enhance antipolysaccharide IgG responses (especially IgG2a and IgG3) induced by these glycoconjugate vaccines.
Generalisation of flying capacitor-based active-neutral-point-clamped multilevel converter using voltage-level modulation (2012)

A generalised n-level flying capacitor (FC)-based active-neutral-point-clamped (ANPC) voltage source converter is discussed in this study. The converter is based on the arrangement of a three-level ANPC cell and a number of two-level cells creating an n-level line-to-neutral voltage waveform. The converter is operated under a phase-shifted carrier (PSC) pulse-width modulation (PWM) technique. The mathematical model for the DC-link capacitors&apos; voltage behaviour of the three-phase converter is also presented. It is shown through simulations that the voltage of the FCs can naturally balance to the required level to generate the required waveforms. Selected results are included in the study to support the analysis. Moreover, experimental results taken from a single-phase seven-level FC-based ANPC converter prototype are also presented to verify the theoretical considerations.
Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits (2012)

It is well-established that synapse formation involves highly selective chemospecific mechanisms, but how neuron arbors are positioned before synapse formation remains unclear. Using 3D reconstructions of 298 neocortical cells of different types (including nest basket, small basket, large basket, bitufted, pyramidal, and Martinotti cells), we constructed a structural model of a cortical microcircuit, in which cells of different types were independently and randomly placed. We compared the positions of physical appositions resulting from the incidental overlap of axonal and dendritic arbors in the model (statistical structural connectivity) with the positions of putative functional synapses (functional synaptic connectivity) in 90 synaptic connections reconstructed from cortical slice preparations. Overall, we found that statistical connectivity predicted an average of 74 ± 2.7% (mean ± SEM) synapse location distributions for nine types of cortical connections. This finding suggests that chemospecific attractive and repulsive mechanisms generally do not result in pairwise-specific connectivity. In some cases, however, the predicted distributions do not match precisely, indicating that chemospecific steering and aligning of the arbors may occur for some types of connections. This finding suggests that random alignment of axonal and dendritic arbors provides a sufficient foundation for specific functional connectivity to emerge in local neural microcircuits.
Factors XI and XII as Targets for New Anticoagulants (2017)

Compared with vitamin K antagonists, the direct oral anticoagulants (DOACs) are simpler to administer and are associated with less intracranial bleeding. Nonetheless, even with the DOACs, bleeding still occurs and many patients with atrial fibrillation fail to receive anticoagulant thromboprophylaxis because of the fear of bleeding. Therefore, there is an urgent need for safer anticoagulants. Recent investigations into the biochemistry of hemostasis and thrombosis have identified new targets for development of novel anticoagulants. Using data from complementary sources, including epidemiological studies and investigations in various animal models, the contact pathway has emerged as a potential mediator of thrombosis that plays a minor part in hemostasis. Consequently, factor (F) XII of the contact system and FXI in the intrinsic pathway have been identified as potentially safer targets of anticoagulation than thrombin or FXa. However, further studies are needed to identify which is the better target for the appropriate indication. This review highlights the evidence for focusing on FXI and FXII and examines the novel approaches directed at these new targets. These emerging strategies should address current unmet medical needs and provide new avenues by which to improve anticoagulant therapy by reducing the risk of bleeding.
Environment‐specific amino acid substitution tables: Tertiary templates and prediction of protein folds (1992)

The local environment of an amino acid in a folded protein determines the acceptability of mutations at that position. In order to characterize and quantify these structural constraints, we have made a comparative analysis of families of homologous proteins. Residues in each structure are classified according to amino acid type, secondary structure, accessibility of the side chain, and existence of hydrogen bonds from the side chains. Analysis of the pattern of observed substitutions as a function of local environment shows that there are distinct patterns, especially for buried polar residues. The substitution data tables are available on diskette with Protein Science. Given the fold of a protein, one is able to predict sequences compatible with the fold (profiles or templates) and potentially to discriminate between a correctly folded and misfolded protein. Conversely, analysis of residue variation across a family of aligned sequences in terms of substitution profiles can allow prediction of secondary structure or tertiary environment.
Enhanced B Cell Expansion, Survival, and Humoral Responses by Targeting Death Receptor 6 (2002)

Targeted disruption of death receptor (DR)6 results in enhanced CD4(+) T cell expansion and T helper cell type 2 differentiation after stimulation. Similar to T cells, DR6 is expressed on resting B cells but is down-regulated upon activation. We examined DR6(-/-) B cell responses both in vitro and in vivo. In vitro, DR6(-/-) B cells undergo increased proliferation in response to anti-immunoglobulin M, anti-CD40, and lipopolysaccharide. This hyperproliferative response was due, at least in part, to both increased cell division and reduced cell apoptosis when compared with wild-type B cells. Consistent with these observations, increased nuclear levels and activity of nuclear factor kappaB transcription factor, c-Rel, and elevated Bcl-x(l) expression were observed in DR6(-/-) B cells upon stimulation. In addition, DR6(-/-) B cells exhibited higher surface levels of CD86 upon activation and were more effective as antigen-presenting cells in an allogeneic T cell proliferation response. DR6(-/-) mice exhibited enhanced germinal center formation and increased titers of immunoglobulins to T-dependent as well as T-independent type I and II antigens. This is the first demonstration of a regulatory role of DR6 in the activation and function of B cells.
The efficacy of the semi-blind approach of transversus abdominis plane block on postoperative analgesia in patients undergoing inguinal hernia repair: a prospective randomized double-blind study (2013)

Semi-blind TAP block provided effective analgesia, reducing total 24-hour postoperative analgesic consumption and morphine requirement in patients undergoing elective unilateral inguinal hernia repair.
Subdivision surfaces in character animation (1998)

Article Free Access Share on Subdivision surfaces in character animation Authors: Tony DeRose Pixar Animation Studios Pixar Animation StudiosView Profile , Michael Kass Pixar Animation Studios Pixar Animation StudiosView Profile , Tien Truong Pixar Animation Studios Pixar Animation StudiosView Profile Authors Info & Claims SIGGRAPH '98: Proceedings of the 25th annual conference on Computer graphics and interactive techniquesJuly 1998 Pages 85–94https://doi.org/10.1145/280814.280826Online:24 July 1998Publication History 338citation4,650DownloadsMetricsTotal Citations338Total Downloads4,650Last 12 Months161Last 6 weeks34 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Protective effect of Gingko biloba extract against doxorubicin-induced cardiotoxicity in mice. (2002)

Doxorubicin (DXR) causes dose dependent cardiotoxicity in experimental animals and in humans. In chronic doxorubicin cardiotoxicity model mice, the role of G. biloba extract (Gbe) which has an antioxidant property, was investigated. Doxorubicin treated animals showed higher mortality (68%), increased ascites, marked bradycardia, prolongation of ST and QT intervals and widening of QRS complex. Myocardial SOD and glutathione peroxidase activity were decreased and lipid peroxidation was increased. Ultrastructure of heart of DXR treated animals showed loss of myofibrils, swelling of mitochondria, vacuolization of mitochondria. G. biloba extract significantly protected the mice from cardiotoxic effects of doxorubicin as evidenced by lowered mortality, ascites, myocardial lipid peroxidation, normalization of antioxidant enzymes, reversal of ECG changes and minimal ultrastructural damage of the heart. The results indicate that administration of G. biloba extract protected mice from doxorubicin-induced cardiotoxicity.