gebhart/patrepeval huggingface dataset:
The C Terminus of Annexin II Mediates Binding to F-actin (2001)

Annexin II heterotetramer (AIIt) is a multifunctional Ca(2+)-binding protein composed of two 11-kDa subunits and two annexin II subunits. The annexin II subunit contains the binding sites for anionic phospholipids, heparin, and F-actin, whereas the p11 subunit provides a regulatory function. The F-actin-binding site is presently unknown. In the present study we have utilized site-directed mutagenesis to create annexin II mutants with truncations in the C terminus of the molecule. Interestingly, a mutant annexin II lacking its C-terminal 16, 13, or 9 amino acids was unable to bind to F-actin but still retained its ability to interact with both anionic phospholipids and heparin. Recombinant AIIt, composed of wild-type p11 subunits and the mutant annexin II subunits, was also unable to bundle F-actin. This loss of F-actin bundling activity was directly attributable to the inability of mutant AIIt to bind F-actin. These results establish for the first time that the annexin II C-terminal amino acid residues, LLYLCGGDD, participate in F-actin binding.
Free-space information transfer using light beams carrying orbital angular momentum (2004)

We demonstrate the transfer of information encoded as orbital angular momentum (OAM) states of a light beam. The transmitter and receiver units are based on spatial light modulators, which prepare or measure a laser beam in one of eight pure OAM states. We show that the information encoded in this way is resistant to eavesdropping in the sense that any attempt to sample the beam away from its axis will be subject to an angular restriction and a lateral offset, both of which result in inherent uncertainty in the measurement. This gives an experimental insight into the effects of aperturing and misalignment of the beam on the OAM measurement and demonstrates the uncertainty relationship for OAM.
Chorismate Synthase: An Attractive Target For Drug Development Against Orphan Diseases (2007)

The increase in incidence of infectious diseases worldwide, particularly in developing countries, is worrying. Each year, 14 million people are killed by infectious diseases, mainly HIV/AIDS, respiratory infections, malaria and tuberculosis.. Despite the great burden in the poor countries, drug discovery to treat tropical diseases has come to a standstill. There is no interest by the pharmaceutical industry in drug development against the major diseases of the poor countries, since the financial return cannot be guaranteed. This has created an urgent need for new therapeutics to neglected diseases. A possible approach has been the exploitation of the inhibition of unique targets, vital to the pathogen such as the shikimate pathway enzymes, which are present in bacteria, fungi and apicomplexan parasites but are absent in mammals. The chorismate synthase (CS) catalyses the seventh step in this pathway, the conversion of 5-enolpyruvylshikimate-3-phosphate to chorismate. The strict requirement for a reduced flavin mononucleotide and the anti 1,4 elimination are both unusual aspects which make CS reaction unique among flavin-dependent enzymes, representing an important target for the chemotherapeutic agents development. In this review we present the main biochemical features of CS from bacterial and fungal sources and their difference from the apicomplexan CS. The CS mechanisms proposed are discussed and compared with structural data. The CS structures of some organisms are compared and their distinct features analyzed. Some known CS inhibitors are presented and the main characteristics are discussed. The structural and kinetics data reviewed here can be useful for the design of inhibitors.
CRD-BP: a c-Myc mRNA stabilizing protein with an oncofetal pattern of expression. (2003)

The Coding Region Determinant-Binding Protein (CRD-BP) is an RRM and KH-domain-containing protein that recognizes specifically at least three RNAs. It binds to one of the two c-myc mRNA instability elements, to the 5'Un Translated Region (UTR) of the leader 3 IGF-II mRNA and to the oncofetal H19 RNA. CRD-BP has been assigned a role in stabilizing c-myc mRNA by preventing its endonucleolytic cleavage and in repressing the translation of the leader 3 IGF-II mRNA, the major embryonic species of this message. CRD-BP is normally expressed only in fetal tissues. However, its expression is detected in primary tumors and transformed cell lines of different origins. The vast majority of colon (80%) and breast (60%) tumors and sarcomas (73%) express CRD-BP whereas in other tumor types, for example prostate carcinomas, its expression is rare. CRD-BP expression has also been detected in benign tumors such as breast fibroadenomas, meningiomas and other benign mesenchymal tumors, implying a role for this gene in abnormal cell proliferation. In breast carcinomas, CRD-BP expression and or gene copy number gains in the region encompassing the c-myc locus were detected in approximately 75% of tumors, implying that the deregulated expression of c-myc may be more widespread than previously believed. Infiltrated lymph nodes, corresponding to CRD-BP-positive primary tumors, were also found positive indicating that monitoring for CRD-BP could prove useful for the detection and monitoring of disseminated disease.
A Staphylococcus aureus capsular polysaccharide (CP) vaccine and CP-specific antibodies protect mice against bacterial challenge (1996)

The efficacy of capsular polysaccharide (CP)-specific antibodies elicited by active immunization with vaccines composed of Staphylococcus aureus types 5 and 8 CP linked to Pseudomonas aeruginosa exoprotein A or with immune immunoglobulin G (I-IgG) obtained from vaccinated plasma donors was tested in lethal and sublethal bacterial mouse challenge models. A dose of 2 x 10(5) CFU of S. aureus type 5 CP per mouse administered intraperitoneally (i.p.) with 5% hog mucin was found to cause 80 to 100% mortality in BALB/c mice within 2 to 5 days. Mice passively immunized i.p. 24 h earlier or subcutaneously 48 h earlier with 0.5 ml of I-IgG showed significantly higher average survival rates than animals receiving standard IgG or saline (P < 0.01) following the bacterial challenge. Animals actively immunized with the monovalent type 5 CP-P. aeruginosa exoprotein A conjugate showed a survival rate of 73% compared with 13% in phosphate-buffered saline-immunized animals. The prechallenge geometric mean titer of type 5 CP antibodies in animals that died was significantly (P < 0.05) lower than that of animals which survived the challenge (95.7 versus 223.6 micrograms/ml, respectively). The IgG was further evaluated in mice challenged i.p. with a sublethal dose of 5 x 10(4) CFU per mouse. Serial blood counts were performed on surviving animals at 6, 12, 24, and 48 h. Surviving animals were sacrificed at 72 h, and bacterial counts were performed on their kidneys, livers, and peritoneal lavage fluids. Animals receiving I-IgG had lower bacterial counts in blood samples and lower bacterial densities in kidneys, livers, and peritoneal lavage samples than mice immunized with standard IgG (P < 0.05). These data suggest that S. aureus type 5 CP antibodies induced by active immunization or administered by passive immunization confer protection against S. aureus infections.
Exaggerated platelet reactivity in major depression (1996)

Depressed patients exhibit enhanced baseline platelet activation and responsiveness in comparison with normal subjects. Heightened susceptibility to platelet activation may be a mechanism by which depression is a significant risk factor for ischemic heart and cerebrovascular disease and/or mortality after myocardial infarction.
The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution (2017)

The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.
Carboxyl Ester Lipase (Bile Salt-Stimulated Lipase), Colipase, Lipase, and Phospholipase A2Levels in Pancreatic Enzyme Supplements (1997)

PES differ considerably in their content of lipolytic enzymes. CEL activities were relatively low and COL and PLA2 activities high compared with normal duodenal content. The manufacturing procedure can be improved to increase the lipolytic activity in PES in a broader meaning. It seems to be most important to increase the amount of CEL. From these in vitro data we advocate a more careful decision in the choice of PES for each patient, depending on the total clinical picture. Money can be saved without disadvantage to the patient.
Biological and Biomechanical Effects of Fibrin Injection Into Porcine Intervertebral Discs (2011)

FS facilitated structural, compositional, and mechanical repair of the surgically damaged IVD. These FS-derived benefits are likely due to its conductive scaffold properties and metabolically active constituents such as thrombin, factor XIII, and aprotinin acetate.
Validation of a five reagent immunohistochemistry assay for prognostication of estrogen-receptor expressing breast cancer (2006)

10081 Background: We have previously reported the translation of gene expression data into a five reagent polyclonal antibody immunohistochemistry assay targeting p53, SLC7A5, NDRG1, HTF9C, and CEACAM5 whose staining results are combined using a Cox proportional hazard model for prognostication of estrogen receptor expressing breast cancer. Monoclonal antibodies targeting these genes have now been obtained and or produced. Methods: Paraffin blocks from 229 patients seen at the University of Alabama at Birmingham Clinical Cancer Center were assembled into tissue arrays and clinical follow-up data was collected by chart review. Immunohistochemical stains were performed and cases scored as positive or negative with the five monoclonal antibody assay. In order to further test the assays predictive value for assessing outcome, the prospectively defined Cox proportional hazard model and high, moderate, and low risk cutoffs were applied to the staining results on the estrogen receptor positive (ER+) patients for whom a assessment of death due to disease (DOD) and staining results for all five biomarkers were available. Results: The Kaplan-Meier estimates of outcome confirmed that the Cox model distinguished ER+ patients with poor outcomes. The five antisera algorithm identified high risk patients with a five year estimate of DOD of 41% compared to 20% for moderate and 9% for good (p=0.006) (79 patients total). In ER+ node negative patients the model identified high risk patients with a five year estimate of DOD of 50% compared to 18% for moderate and 5% for good (p=0.01) (40 patients total). The prognosticator was independent of age, pathological stage, and tumor size. Conclusions: A panel of five antibodies can significantly improve upon traditional prognosticators in predicting outcome for estrogen receptor positive breast cancer patients. This represents the third independent validation study performed on cohorts from different institutions. Retrospective studies on clinical trial cohorts and prospective studies should be performed to further establish the utility of this test in identifying early stage breast cancer patients at high risk for recurrence. [Table: see text]
Production of porous Calcium Phosphate (CaP) ceramics with aligned pores using ceramic/camphene-based co-extrusion (2015)

Aligned porous CaP ceramic scaffolds with considerably enhanced mechanical properties and tailorable porosity would find very useful applications as the bone scaffold.
Isolation and analysis of arc repressor mutants: Evidence for an unusual mechanism of DNA binding (1986)

We have isolated 64 different missense mutations at 36 out of 53 residue positions in the Arc repressor of bacteriophage P22. Many of the mutant proteins with substitutions in the C-terminal 40 residues of Arc have reduced intracellular levels and probably have altered structures or stabilities. Mutations in the N-terminal ten residues of Arc cause large decreases in operator DNA binding affinity without affecting the ability of Arc to fold into a stable three-dimensional structure. We argue that these N-terminal residues are important for operator recognition but that they are not part of a conventional helix-turn-helix DNA binding structure. These results suggest that Arc may use a new mechanism for sequence specific DNA binding.
70% TMR at Room Temperature for SDT Sandwich Junctions With CoFeB as Free and Reference Layers (2004)

Spin dependent tunneling (SDT) wafers were deposited using dc magnetron sputtering. SDT junctions were patterned and connected with one layer of metal lines using photolithography techniques. These junctions have a typical stack structure of Si(100)-Si/sub 3/N/sub 4/-Ru-CoFeB-Al/sub 2/O/sub 3/-CoFeB-Ru-FeCo-CrMnPt with the antiferromagnet CrMnPt layers for pinning at the top. High-resolution transmission electron microscopy (HRTEM) reveals that the CoFeB has an amorphous structure and a smooth interface with the Al/sub 2/O/sub 3/ tunnel barrier. Although it is difficult to pin the amorphous CoFeB directly from the top, the use of a synthetic antiferromagnet (SAF) pinned layer structure allows sufficient rigidity of the reference CoFeB layer. The tunnel junctions were annealed at 250/spl deg/C for 1 h and tested for magneto-transport properties with tunnel magnetoresistive (TMR) values as high as 70.4% at room temperature, which is the highest value ever reported for such a sandwich structure. This TMR value translates to a spin polarization of 51% for CoFeB, which is likely to be higher at lower temperatures. These junctions also have a low coercivity (Hc) and a low parallel coupling field (Hcoupl). The combination of a high TMR, a low Hc, and a low Hcoupl is ideal for magnetic field sensor applications.
A fair protocol for signing contracts (1990)

Two parties, A and B, want to sign a contract C over a communication network. To do so, they must simultaneously exchange their commitments to C. Since simultaneous exchange is usually impossible in practice, protocols are needed to approximate simultaneity by exchanging partial commitments in piece-by-piece manner. During such a protocol, one party or another may have a slight advantage; a fair protocol keeps this advantage within acceptable limits. A new protocol is proposed. It is fair in the sense that, at any stage in its execution, the conditional probability that one party cannot commit both parties to the contract given that the other party can, is close to zero. This is true even if A and B have vastly different computing powers and is proved under very weak cryptographic assumptions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Thin-film growth modeling (1987)

Early 2-D film growth models qualitatively exhibited several effects commonly observed in conventionally deposited thin films, notably columnar microstructures. A model of this type under study at the Optical Sciences Center simulates the growth of films with dimensions as large as an optical wavelength.
A Keratin Peptide Inhibits Mannose-Binding Lectin (2001)

Complement plays a significant role in mediating endothelial injury following oxidative stress. We have previously demonstrated that the lectin complement pathway (LCP), which is initiated by deposition of the mannose-binding lectin (MBL), is largely responsible for activating complement on endothelial cells following periods of oxidative stress. Identifying functional inhibitors that block MBL binding will be useful in characterizing the role of the LCP in disease models. The human cytokeratin peptide SFGSGFGGGY has been identified as a molecular mimic of N-acetyl-D-glucosamine (GlcNAc), a known ligand of MBL. Thus, we hypothesized that this peptide would specifically bind to MBL and functionally inhibit the LCP on endothelial cells following oxidative stress. Using a BIAcore 3000 optical biosensor, competition experiments were performed to demonstrate that the peptide SFGSGFGGGY inhibits binding of purified recombinant human MBL to GlcNAc in a concentration-dependent manner. Solution affinity data generated by BIAcore indicate this peptide binds to MBL with an affinity (K(D)) of 5 x 10(-5) mol/L. Pretreatment of human serum (30%) with the GlcNAc-mimicking peptide (10-50 microg/ml) significantly attenuated MBL and C3 deposition on human endothelial cells subjected to oxidative stress in a dose-dependent manner, as demonstrated by cell surface ELISA and confocal microscopy. Additionally, this decapeptide sequence attenuated complement-dependent VCAM-1 expression following oxidative stress. These data indicate that a short peptide sequence that mimics GlcNAc can specifically bind to MBL and functionally inhibit the proinflammatory action of the LCP on oxidatively stressed endothelial cells.
Acutely-dissociated Schwann cells used in tendon autografts for bridging nerve defects in rats: A new principle for tissue engineering in nerve reconstruction (2005)

A new method of acute dissociation of Schwann cells was used to study the effect of addition of such cells to a tendon autograft--a recently-described graft material--on peripheral nerve regeneration in rats. Autologous Schwann cells were obtained from enzymatic dissociation of predegenerated nerves. The tendon autografts were supplied with Schwann cells through brief in vitro coincubation. Schwann cell-free tendon autografts were used as controls. Axonal outgrowth was measured immunohistochemically after four, seven, and 10 days. At seven days, outgrowth was significantly longer in the pretreated autografts. The use of acutely-dissociated Schwann cells is a new approach to tissue engineering in nerve reconstruction, and may abolish the need for time-consuming culture of Schwann cells.
P-glycoprotein: a major determinant of rifampicin-inducible expression of cytochrome P4503A in mice and humans. (1996)

The P-glycoprotein (Pgp) efflux pump can influence the hepatocellular concentration of xenobiotics that are modulators and substrates of cytochrome P4503A (CYP3A). We tested the hypothesis that Pgp is a determinant of drug-inducible expression of CYP3A. The magnitude of CYP3A induction by rifampicin was compared in the human parental colon carcinoma cell line LS 180/WT (wild type) and in two derivative clones overexpressing the human multidrug resistance gene MDR1 (also designated PGY1) because of either drug selection (LS 180/ADR) or transfection with MDRI cDNA (LS 180/MDR). In both MDR1 cDNA-overexpressing clones, rifampicin induction of CYP3A mRNA and protein was decreased and required greater rifampicin concentrations compared with parental cells. The role of Pgp in regulation of CYP3A expression in vivo was analyzed in mice carrying a targeted disruption of the mdr1a mouse gene. Oral treatment with increasing doses of rifampicin resulted in elevated drug levels in the livers of mdr1a (-/-) mice compared with mdr1a (+/+) mice at all doses. Consistent with the enhanced accumulation of rifampicin in mdr1a (-/-) mice, lower doses of rifampicin were required for induction of CYP3A proteins, and the magnitude of CYP3A induction was greater at all doses of rifampicin in mdr1a (-/-) mice compared with mdr1a (+/+) mice. We conclude that Pgp-mediated transport is a critical element influencing the CYP3A inductive response.
Recent Advances in the Development of Adenovirus- and Poxvirus- Vectored Tuberculosis Vaccines (2005)

Tuberculosis vaccine research began with the search for a vaccine that might be better than, and thus could replace, the current Bacillus Calmette Guérin (BCG) vaccine. Over the last fifteen years or so, intense research effort has led to the identification of a number of novel tuberculosis (TB) vaccines which can be divided into 4 categories: genetically modified mycobacteria, protein, plasmid DNA and viral. However, it is increasingly believed that the current BCG vaccine will continue to be used as a childhood vaccine and that more effort should be directed to developing appropriate boosting vaccines. Mounting evidence suggests that recombinant genetic vaccines, particularly recombinant viral vaccines, are effective in boosting immune activation and protection by BCG vaccination. Since modified vaccinia virus Ankara (MVA)- and adenovirus-vectored TB vaccines have been most extensively studied, this review will focus on recent advances in the development and applications of these two viral TB vaccines.
Monovalent antibody design and mechanism of action of onartuzumab, a MET antagonist with anti-tumor activity as a therapeutic agent (2013)

Binding of hepatocyte growth factor (HGF) to the receptor tyrosine kinase MET is implicated in the malignant process of multiple cancers, making disruption of this interaction a promising therapeutic strategy. However, targeting MET with bivalent antibodies can mimic HGF agonism via receptor dimerization. To address this limitation, we have developed onartuzumab, an Escherichia coli-derived, humanized, and affinity-matured monovalent monoclonal antibody against MET, generated using the knob-into-hole technology that enables the antibody to engage the receptor in a one-to-one fashion. Onartuzumab potently inhibits HGF binding and receptor phosphorylation and signaling and has antibody-like pharmacokinetics and antitumor activity. Biochemical data and a crystal structure of a ternary complex of onartuzumab antigen-binding fragment bound to a MET extracellular domain fragment, consisting of the MET Sema domain fused to the adjacent Plexins, Semaphorins, Integrins domain (MET Sema-PSI), and the HGF β-chain demonstrate that onartuzumab acts specifically by blocking HGF α-chain (but not β-chain) binding to MET. These data suggest a likely binding site of the HGF α-chain on MET, which when dimerized leads to MET signaling. Onartuzumab, therefore, represents the founding member of a class of therapeutic monovalent antibodies that overcomes limitations of antibody bivalency for targets impacted by antibody crosslinking.