gebhart/patrepeval huggingface dataset:
Engineering Specificity for Folate into Dihydrofolate Reductase from Escherichia coli (1996)

Despite several similarities in structure and kinetic behavior, the bacterial and vertebrate forms of the enzyme dihydrofolate reductase (DHFR) exhibit differential specificity for folate. In particular, avian DHFR is 400 times more specific for folate than the Escherichia coli reductase. We proposed to enhance the specificity of the E. coli reductase for folate by incorporating discrete elements of vertebrate secondary structure. Two vertebrate loop mutants, VLI and VLII containing 3-7 additional amino acid insertions, were constructed and characterized by using steady-state kinetics, spectrofluorimetric determination of ligand equilibrium dissociation constants, and circular dichroism spectroscopy. Remarkably, the VLI and VLII mutants are kinetically similar to wild-type E. coli reductase when dihydrofolate is the substrate, although VLII exhibits prolonged kinetic hysteresis. Moreover, the VLI dihydrofolate reductase is the first mutant form of E. coli DHFR to display enhanced specificity for folate [(kcat/Km)mutant/(kcat/Km)wt = 13]. A glycine-alanine loop (GAL) mutant was also constructed to test the design principles for the VLI mutant. In this mutant of the VLI reductase, all of the residues from positions 50 to 60, except the strictly conserved amino acids Leu-57 and Arg-60, were converted to either glycine or alanine. A detailed kinetic comparison of the GAL and wild-type reductases revealed that the mutations weaken the binding by both cofactor and substrate by up to 20-fold, but under saturating conditions the enzyme exhibits a kcat value nearly identical to that of the wild type. The rate of hydride transfer is reduced by a factor of 30, with a compensating increase in the dissociation rate for tetrahydrofolate. Although key stabilizing interactions have been sacrificed (it shows no activity toward folate), the maintenance of the correct register between key residues preserves the activity of the enzyme toward its natural substrate. Collectively, neither specific proximal point site mutations nor larger, more distal secondary structural substitutions are sufficient to confer a specificity for folate reduction that matches that observed with the avian enzyme. This is consistent with the hypothesis that the entire protein structure must contribute extensively to the enzyme's specificity.
Immune response to human papillomavirus type 16 E6 gene in a live vaccinia vector (1994)

Immunization of mice with a recombinant vaccinia virus expressing the human papillomavirus type 16 (HPV-16) E6 gene elicits specific antibody, proliferative and cytotoxic T lymphocyte responses. T and B cell epitopes were mapped by using synthetic peptides. This study provides the background to future investigation aimed at developing prophylactic and therapeutic vaccines against HPV-16 infection and cervical cancer.
Expression of Heat Shock Protein 27 in Human Atherosclerotic Plaques and Increased Plasma Level of Heat Shock Protein 27 in Patients With Acute Coronary Syndrome (2006)

In the atherosclerotic lesion, Hsp27 expression is increased in the normal-appearing vessel adjacent to atherosclerotic plaque, whereas levels in the plaque itself are significantly decreased. Both plaque and adjacent artery show decreased Hsp27 phosphorylation compared with reference vessel. In ACS, plasma Hsp27 and Hsp70 are increased, and levels of Hsp27 correlate with Hsp70, C-reactive protein, and CD40L levels.
Secure anonymous database search (2009)

There exist many large collections of private data that must be protected on behalf of the entities that hold them or the clients they serve. However, there are also often many legitimate reasons for sharing that data in a controlled manner. How can two parties decide to share data without prior knowledge of what data they have? For example, two intelligence agencies might be willing to cooperate by sharing documents about a specific case, and need a way of determining which documents might be of interest to each other. We introduce and address the problem of allowing such entities to search each other's data securely and anonymously. We aim to protect the content of the queries, as well as the content of documents unrelated to those queries, while concealing the identity of the participants. Although there exist systems for solving similar problems, to our knowledge we are the first to address this specific need and also the first to present a secure anonymous search system that is practical for real-time querying. In order to achieve this in an efficient manner, we make use of Bloom filters [5], definitions of security for deterministic encryption [22] that we adapt and instantiate in the private key setting and of a novel encryption primitive, reroutable encryption.
A highly conserved family of inactivated archaeal B family DNA polymerases (2008)

A widespread and highly conserved family of apparently inactivated derivatives of archaeal B-family DNA polymerases is described. Phylogenetic analysis shows that the inactivated forms comprise a distinct clade among archaeal B-family polymerases and that, within this clade, Euryarchaea and Crenarchaea are clearly separated from each other and from a small group of bacterial homologs. These findings are compatible with an ancient duplication of the DNA polymerase gene followed by inactivation and parallel loss in some of the lineages although contribution of horizontal gene transfer cannot be ruled out. The inactivated derivative of the archaeal DNA polymerase could form a complex with the active paralog and play a structural role in DNA replication.
Letrozole normalizes serum testosterone in severely obese men with hypogonadotropic hypogonadism (2005)

Short-term Letrozole treatment normalized serum testosterone levels in all obese men. The clinical significance of this intervention remains to be established in controlled, long-term studies.
Chromosomal localization of a single copy gene by in situ hybridization ‐ human β globin genes on the short arm of chromosome 11 (1981)

1. The localization of the beta globin genes by in situ hybridization to fixed chromosomes is described. 2. The probe used was a [3H]cRNA copy of a genomic clone containing in total 4.4 kb of DNA and including the beta globin gene. 3. The evidence for the localization of the gene comes from three pieces of data. (a) Chromosome 11 is labelled to double the extent expected if the grains were randomly distributed, (b) the extra grains above background are clustered on the short arm of 11 close to the centromere, and (c) the absolute number of grains observed is very close to that predicted for a probe of that length by comparison with ribosomal genes. The localization is in agreement with that obtained by other methods. 4. This method could be extended to any gene for which a genomic clone containing at least 5 kb of single copy DNA is available.
Inositol Polyphosphate 1-Phosphatase Is a Novel Antihypertrophic Factor (2002)

Activation of G(q)-coupled alpha(1)-adrenergic receptors leads to hypertrophic growth of neonatal rat ventricular cardiomyocytes that is associated with increased expression of hypertrophy-related genes, including atrial natriuretic peptide (ANP) and myosin light chain-2 (MLC), as well as increased ribosome synthesis. The role of inositol phosphates in signaling pathways involved in these changes in gene expression was examined by overexpressing inositol phosphate-metabolizing enzymes and determining effects on ANP, MLC, and 45 S ribosomal gene expression following co-transfection of appropriate reporter gene constructs. Overexpression of enzymes that metabolize inositol 1,4,5-trisphosphate did not reduce ANP or MLC responses, but overexpression of the enzyme primarily responsible for metabolism of inositol 4,5-bisphosphate (Ins(1,4)P(2)), inositol polyphosphate 1-phosphatase (INPP), reduced ANP and MLC responses associated with alpha(1)-adrenergic receptor-mediated hypertrophy. Similarly overexpressed INPP reduced ANP and MLC responses associated with contraction-induced hypertrophy. In addition, overexpression of INPP reduced the increase in ribosomal DNA transcription associated with both hypertrophic models. Hypertrophied cells from both cell models as well as ventricular tissue from mouse hearts hypertrophied by pressure overload in vivo contained heightened levels of Ins(1,4)P(2), suggesting reduced INPP activity in three different models of hypertrophy. These studies provide evidence for an involvement of Ins(1,4)P(2) in hypertrophic signaling pathways in ventricular myocytes.
Immunohistochemical Markers for Quantitative Studies of Neurons and Glia in Human Neocortex (2007)

Reproducible visualization of neurons and glia in human brain is essential for quantitative studies of the cellular changes in neurological disease. However, immunohistochemistry in human brain specimens is often compromised because of prolonged fixation. To select cell lineage-specific antibodies for quantitative studies of neurons and the major types of glia, we used 29 different antibodies, different epitope retrieval methods, and different detection systems to stain tissue arrays of formalin-fixed human brain. The screening pointed at CD45/leukocyte common antigen (LCA), CD68(KP1), 2',3' cyclic nucleotide phosphatase (CNPase), glial fibrillary acidic protein (GFAP), HLA-DR, Ki67, neuronal nuclei (NeuN), p25alpha-antigen, and S100beta as candidates for future cell counting purposes, because these markers visualized specific neuronal and glial cell bodies. However, significant negative correlation between staining result and formalin fixation was observed by blinded scoring of staining for CD45/LCA, CNPase, GFAP, and NeuN in brain specimens fixed by immersion and stored up to 10 years in 4% formalin solution at room temperature, independent of donor sex and postmortem interval. In contrast, improved preservation of NeuN and CNPase staining, and full preservation of GFAP and CD45/LCA staining in tissue fixed by perfusion and stored for up to 3 years in 0.1% paraformaldehyde solution at 4C, indicated that immunohistochemistry can be performed in well-preserved biobank material.
The interaction of pH, bile, and Helicobacter pylori may explain duodenal ulcer. (1996)

The ability of H. pylori to grow in the presence of taurine-conjugated bile acids and the precipitation of glycine but not taurine bile acid conjugates by acid may provide one missing link among inhibition of H. pylori by bile, acid secretion, ability of antisecretory therapy to accelerate ulcer healing, and the ability of H. pylori to colonize the duodenal bulb of ulcer patients, leading to duodenal ulcer. These data also explain the disparate results of previous investigations of the effect of bile reflux in the stomach on the presence of H. pylori.
Photothermal-Induced Self-Healable and Reconfigurable Shape Memory Bio-Based Elastomer with Recyclable Ability (2018)

Photothermal-induced self-healable and shape memory materials have drawn much attention due to the rapidly growing technical applications and environmental requirements. As epoxy natural rubber (ENR) is a kind of bio-based elastomer with good mechanical properties, weather resistance, and air impermeability, it is of great significance to incorporate ENR with recyclable, photothermal-induced self-healable and shape memory properties. In this study, we report a simple method to cross-link ENR with dodecanedioic acids (DAs) through esterification reaction, and during the cross-linking process, a little aniline trimer (ACAT, a kind of oligoaniline) was added at the same time. Then, the ENR-DA-ACAT vitrimers that were covalently cross-linked with recyclable, self-healable, and multiple responsive properties were obtained, which also possessed various functions. As a result of the transesterification reactions at elevated temperatures, the ENR-based vitrimers possess the ability to be reprocessed and self-healed, and the mechanical properties could be maintained even after three consecutive breaking/mold pressing cycles. Besides, the vitrimer is also responsive to near-infrared (NIR) light and pH with the introduction of ACAT, and we also find that ACAT can be used as a catalyst to accelerate the transesterification reaction. Moreover, it is demonstrated that the ENR-DA-ACAT vitrimer could also be used to construct the reconfigurable shape memory polymer; the shape fixing ratio and shape recovery ratio are both above 95% in the reconfiguration process, and the multistage shape memory performance can also be achieved by NIR irradiation, which will potentially lead to a wide application for ENR in the field of actuators.
Quantitative assays based on the use of replicatable hybridization probes. (1989)

Amplifiable hybridization probes--molecules with a probe sequence embedded within the sequence of a replicatable RNA--will promote the development of sensitive clinical assays. To demonstrate their utility, we prepared a recombinant RNA that contained a 30-nucleotide-long probe complementary to a conserved region of the pol gene in human immunodeficiency virus type 1 (HIV-1) mRNA. Test samples were prepared, each containing a different number of HIV-1 transcripts that served as simulated HIV-1 mRNA targets. Hybridizations were carried out in a solution containing the chaotropic salt, guanidine thiocyanate. Probe-target hybrids were isolated by reversible target capture on paramagnetic particles. The probes were then released from their targets and amplified by incubation with the RNA-directed RNA polymerase, Q beta replicase (EC 2.7.7.48). The replicase copied the probes in an exponential manner: after each round of copying, the number of RNA molecules doubled. The amount of RNA synthesized in each reaction (approximately 50 ng) was sufficient to measure without using radioisotopes. Kinetic analysis of the reactions demonstrated that the number of HIV-1 targets originally present in each sample could be determined by measuring the time it took to synthesize a particular amount of RNA (the longer the synthesis took, the fewer the number of targets originally present). The results suggest that clinical assays involving replicatable hybridization probes will be simple, accurate, sensitive, and automatable.
Ueber die Oxydation des Cymols und das sogenannte Nitrocymol (1886)

A. Bladin: Ueber die Oxydation des Cymols und das sogenannte Nitrocymol
C–C Chemokines Released by Lipopolysaccharide (LPS)-stimulated Human Macrophages Suppress HIV-1 Infection in Both Macrophages and T Cells (1997)

Human immunodeficiency virus-1 (HIV-1) expression in monocyte-derived macrophages (MDM) infected in vitro is known to be inhibited by lipopolysaccharide (LPS). However, the mechanisms are incompletely understood. We show here that HIV-1 suppression is mediated by soluble factors released by MDM stimulated with physiologically significant concentrations of LPS. LPS-conditioned supernatants from MDM inhibited HIV-1 replication in both MDM and T cells. Depletion of C-C chemokines (RANTES, MIP-1 alpha, and MIP-1 beta) neutralized the ability of LPS-conditioned supernatants to inhibit HIV-1 replication in MDM. A combination of recombinant C-C chemokines blocked HIV-1 infection as effectively as LPS. Here, we report an inhibitory effect of C-C chemokines on HIV replication in primary macrophages. Our results raise the possibility that monocytes may play a dual role in HIV infection: while representing a reservoir for the virus, they may contribute to the containment of the infection by releasing factors that suppress HIV replication not only in monocytes but also in T lymphocytes.
Structure–Efficiency Relationship of [1,2,4]Triazol-3-ylamines as Novel Nicotinamide Isosteres that Inhibit Tankyrases (2013)

Tankyrases 1 and 2 are members of the poly(ADP-ribose) polymerase (PARP) family of enzymes that modulate Wnt pathway signaling. While amide- and lactam-based nicotinamide mimetics that inhibit tankyrase activity, such as XAV939, are well-known, herein we report the discovery and evaluation of a novel nicotinamide isostere that demonstrates selectivity over other PARP family members. We demonstrate the utilization of lipophilic efficiency-based structure-efficiency relationships (SER) to rapidly drive the evaluation of this series. These efforts led to a series of selective, cell-active compounds with solubility, physicochemical, and in vitro properties suitable for further optimization.
Ray space factorization for from-region visibility (2003)

From-region visibility culling is considered harder than from-point visibility culling, since it is inherently four-dimensional. We present a conservative occlusion culling method based on factorizing the 4D visibility problem into horizontal and vertical components. The visibility of the two components is solved asymmetrically: the horizontal component is based on a parameterization of the ray space, and the visibility of the vertical component is solved by incrementally merging umbrae. The technique is designed so that the horizontal and vertical operations can be efficiently realized together by modern graphics hardware. Similar to image-based from-point methods, we use an occlusion map to encode visibility; however, the image-space occlusion map is in the ray space rather than in the primal space. Our results show that the culling time and the size of the computed potentially visible set depend on the size of the viewcell. For moderate viewcells, conservative occlusion culling of large urban scenes takes less than a second, and the size of the potentially visible set is only about two times larger than the size of the exact visible set.
Past, present and future role of polyurethanes for surgical implants (1980)

Polyurethanes, which were once thought to be unstable when used in the body, are now occupying a dominant place in the armamentarium of the biomedical researcher. This paper discusses the history of this class of biomaterials, its chemical structure relevant to long-term surgical implants, physiological acceptability based on standard animal tests, the effects of some modifications, and possible areas of future developments with promising but yet untested formulations.
Co-delivery of platelet-derived growth factor (PDGF-BB) and bone morphogenic protein (BMP-2) coated onto heparinized titanium for improving osteoblast function and osteointegration (2013)

The aim of this study was to improve osteoblast function by delivering two growth factors, PDGF-BB and BMP-2, incorporated onto heparinized titanium (Hep-Ti) substrate. To achieve co-delivery of PDGF-BB and BMP-2, the surface of anodized Ti was immobilized with heparin, and then the two growth factors were coated onto the Hep-Ti surface. Incorporation of the two growth factors onto Hep-Ti was evaluated by SEM and XPS. Incorporated PDGF-BB and BMP-2 were released from the Hep-Ti substrate in a sustained manner. In vitro studies revealed that osteoblasts grown on PDGF-BB- and BMP-2-immobilized Hep-Ti increased ALP activity, calcium deposition, osteocalcin and osteopontin levels as compared to those grown on PDGF-BB alone- or BMP-2 alone-immobilized Hep-Ti. These results suggested that co-delivery of PDGF-BB and BMP-2 using Hep-Ti substrate will be a promising material for the enhancement of osteoblast function and osteointegration.
Functional Notch signaling is required for BMP4-induced inhibition of myogenic differentiation (2003)

The bone morphogenetic protein (BMP) and Notch signaling pathways are crucial for cellular differentiation. In many cases, the two pathways act similarly; for example, to inhibit myogenic differentiation. It is not known whether this inhibition is caused by distinct mechanisms or by an interplay between Notch and BMP signaling. Here we demonstrate that functional Notch signaling is required for BMP4-mediated block of differentiation of muscle stem cells, i.e. satellite cells and the myogenic cell line C2C12. Addition of BMP4 during induction of differentiation dramatically reduced the number of differentiated satellite and C2C12 cells. Differentiation was substantially restored in BMP4-treated cultures by blocking Notch signaling using either the gamma-secretase inhibitor L-685,458 or by introduction of a dominant-negative version of the Notch signal mediator CSL. BMP4 addition to C2C12 cells increased transcription of two immediate Notch responsive genes, Hes1 and Hey1, an effect that was abrogated by L-685,458. A 3 kb Hey1-promoter reporter construct was synergistically activated by the Notch 1 intracellular domain (Notch 1 ICD) and BMP4. The BMP4 mediator SMAD1 mimicked BMP activation of the Hey1 promoter. A synthetic Notch-responsive promoter containing no SMAD1 binding sites responded to SMAD1, indicating that DNA-binding activity of SMAD1 is not required for activation. Accordingly, Notch 1 ICD and SMAD1 interacted in binding experiments in vitro. Thus, the data presented here provide evidence for a direct interaction between the Notch and BMP signaling pathways, and indicate that Notch has a crucial role in the execution of certain aspects of BMP-mediated differentiation control.
Ectopic Expression ofTsi1in Transgenic Hot Pepper Plants Enhances Host Resistance to Viral, Bacterial, and Oomycete Pathogens (2002)

In many plants, including hot pepper plants, productivity is greatly affected by pathogen attack. We reported previously that tobacco stress-induced gene 1 (Tsi1) may play an important role in regulating stress responsive genes and pathogenesis-related (PR) genes. In this study, we demonstrated that overexpression of Tsi1 gene in transgenic hot pepper plants induced constitutive expression of several PR genes in the absence of stress or pathogen treatment. The transgenic hot pepper plants expressing Tsi1 exhibited resistance to Pepper mild mottle virus (PMMV) and Cucumber mosaic virus (CMV). Furthermore, these transgenic plants showed increased resistance to a bacterial pathogen, Xanthomonas campestris pv. vesicatoria and also an oomycete pathogen, Phytophthora capsici. These results suggested that ectopic expression of Tsi1 in transgenic hot pepper plants enhanced the resistance of the plants to various pathogens, including viruses, bacteria, and oomycete. These results suggest that using transcriptional regulatory protein genes may contribute to developing broad-spectrum resistance in crop plants.
Identification and synthesis of a recognition signal for the attachment of glycosaminoglycans to proteins. (1987)

Comparison of the amino acid sequences of three different proteoglycan core proteins reveals a 12-amino acid sequence that is about 50% homologous among these proteoglycans. In each of the proteoglycans, this sequence surrounds the serine-glycine dipeptide in which the serine is known or presumed to be substituted with a chondroitin/dermatan sulfate glycosaminoglycan chain. Peptides containing this sequence from two proteoglycans were examined for their ability to serve as acceptors for xylosyltransferase, the enzyme that begins the assembly of glycosaminoglycan chains. Those peptides corresponding to amino acid sequences known to contain glycosaminoglycan-substituted serine residues in the protein were efficient xylosyltransferase acceptors, whereas peptides from sequences with no glycosaminoglycan-substituted serine residues were not. Amino acid substitutions at four critical sites in the acceptor peptides showed that single substitutions could completely abolish acceptor activity or greatly reduce it. The results suggest that the proteoglycan recognition consensus sequence for the attachment of glycosaminoglycans to core proteins consists of acidic amino acids closely followed by the tetrapeptide Ser-Gly-Xaa-Gly, where Xaa is any amino acid. The signal appears to be contained in the primary sequence information. In this regard it resembles a number of other signals for protein processing and intracellular routing.