gebhart/patrepeval huggingface dataset:
Gabapentin: A Stereochemically Constrained γ Amino Acid Residue in Hybrid Peptide Design (2009)

Nature has used the all-alpha-polypeptide backbone of proteins to create a remarkable diversity of folded structures. Sequential patterns of 20 distinct amino acids, which differ only in their side chains, determine the shape and form of proteins. Our understanding of these specific secondary structures is over half a century old and is based primarily on the fundamental elements: the Pauling alpha-helix and beta-sheet. Researchers can also generate structural diversity through the synthesis of polypeptide chains containing homologated (omega) amino acid residues, which contain a variable number of backbone atoms. However, incorporating amino acids with more atoms within the backbone introduces additional torsional freedom into the structure, which can complicate the structural analysis. Fortunately, gabapentin (Gpn), a readily available bulk drug, is an achiral beta,beta-disubstituted gamma amino acid residue that contains a cyclohexyl ring at the C(beta) carbon atom, which dramatically limits the range of torsion angles that can be obtained about the flanking C-C bonds. Limiting conformational flexibility also has the desirable effect of increasing peptide crystallinity, which permits unambiguous structural characterization by X-ray diffraction methods. This Account describes studies carried out in our laboratory that establish Gpn as a valuable residue in the design of specifically folded hybrid peptide structures. The insertion of additional atoms into polypeptide backbones facilitates the formation of intramolecular hydrogen bonds whose directionality is opposite to that observed in canonical alpha-peptide helices. If hybrid structures mimic proteins and biologically active peptides, the proteolytic stability conferred by unusual backbones can be a major advantage in the area of medicinal chemistry. We have demonstrated a variety of internally hydrogen-bonded structures in the solid state for Gpn-containing peptides, including the characterization of the C(7) and C(9) hydrogen bonds, which can lead to ribbons in homo-oligomeric sequences. In hybrid alphagamma sequences, distinct C(12) hydrogen-bonded turn structures support formation of peptide helices and hairpins in longer sequences. Some peptides that include the Gpn residue have hydrogen-bond directionality that matches alpha-peptide helices, while others have the opposite directionality. We expect that expansion of the polypeptide backbone will lead to new classes of foldamer structures, which are thus far unknown to the world of alpha-polypeptides. The diversity of internally hydrogen-bonded structures observed in hybrid sequences containing Gpn shows promise for the rational design of novel peptide structures incorporating hybrid backbones.
Geomorphology from space: A global overview of regional landforms (1987)

This book, Geomorphology from Space: A Global Overview of Regional Landforms, was published by NASA STIF as a successor to the two earlier works on the same subject: Mission to Earth: LANDSAT views the Earth, and ERTS-1: A New Window on Our Planet. The purpose of the book is threefold: first, to serve as a stimulant in rekindling interest in descriptive geomorphology and landforms analysis at the regional scale; second, to introduce the community of geologists, geographers, and others who analyze the Earth's surficial forms to the practical value of space-acquired remotely sensed data in carrying out their research and applications; and third, to foster more scientific collaboration between geomorphologists who are studying the Earth's landforms and astrogeologists who analyze landforms on other planets and moons in the solar system, thereby strengthening the growing field of comparative planetology.
Transketolase-Mediated Synthesis of 4-Deoxy-D-fructose 6-Phosphate by Epoxide Hydrolase-Catalysed Resolution of 1,1-Diethoxy-3,4-epoxybutane (1999)

4-Deoxy-D-fructose 6-phosphate is synthesised from nonnatural sources in four steps, including two enzymatic reactions. (3S)-1,1-Diethoxy-3,4-epoxybutane is first obtained by epoxide hydrolase-catalysed resolution. Opening of this epoxide by inorganic phosphate leads to 2-deoxy-D-erythrose 4-phosphate. In the last step, transketolase transfers a hydroxyacetyl group from L-erythrulose onto this aldehyde, controlling the second asymmetric center.
Metabolic Programming of MEST DNA Methylation by Intrauterine Exposure to Gestational Diabetes Mellitus (2012)

Epigenetic processes are primary candidates when searching for mechanisms that can stably modulate gene expression and metabolic pathways according to early life conditions. To test the effects of gestational diabetes mellitus (GDM) on the epigenome of the next generation, cord blood and placenta tissue were obtained from 88 newborns of mothers with dietetically treated GDM, 98 with insulin-dependent GDM, and 65 without GDM. Bisulfite pyrosequencing was used to compare the methylation levels of seven imprinted genes involved in prenatal and postnatal growth, four genes involved in energy metabolism, one anti-inflammatory gene, one tumor suppressor gene, one pluripotency gene, and two repetitive DNA families. The maternally imprinted MEST gene, the nonimprinted glucocorticoid receptor NR3C1 gene, and interspersed ALU repeats showed significantly decreased methylation levels (4-7 percentage points for MEST, 1-2 for NR3C1, and one for ALUs) in both GDM groups, compared with controls, in both analyzed tissues. Significantly decreased blood MEST methylation (3 percentage points) also was observed in adults with morbid obesity compared with normal-weight controls. Our results support the idea that intrauterine exposure to GDM has long-lasting effects on the epigenome of the offspring. Specifically, epigenetic malprogramming of MEST may contribute to obesity predisposition throughout life.
Smooth Muscle Cell of the Canine Prostate in Spontaneous Benign Hyperplasia, Steroid Induced Hyperplasia and Estrogen or Tamoxifen Treated Dogs (1983)

Human benign prostatic hyperplasia is a predominantly stromal hyperplasia with accumulation of connective tissue. The main ultrastructural finding, which may be causal, is an activation of the smooth muscle cells, as seen by an increase of the volume density of the organelles within these cells. The dog is widely used as an animal model for human prostatic hyperplasia in spite of several differences. In this work the smooth muscle cells of the spontaneous and steroid-induced (by treating castrates with dihydrotestosterone and estradiol) prostatic hyperplasia of dogs were analysed by electron microscopical morphometry, and compared to estrogen or tamoxifen (antiestrogen) treated dogs as well as to untreated or castrated control dogs. The results clearly show that the prostatic smooth muscle cells of the dog can be activated by estrogen as well as tamoxifen, which proves the estrogenic side activity of the latter. In marked contrast to that, neither in the spontaneous nor in the steroid-induced prostatic hyperplasia could an activation of the smooth muscle cells be found. This is a most important difference from human benign prostatic hyperplasia, which limits the use of this animal model, and it might even be the explanation of the different reaction of human and canine prostatic hyperplasia to therapeutic hormonal manipulations.
The cdk2 kinase is required for the G1-to-S transition in mammalian cells. (1993)

In the cell cycle of fission and budding yeast, the p34cdc2/CDC28 kinase is required for both the G1-to-S and G2-to-M phase transitions. In vertebrates, the homologous p34cdc2 kinase is required for G2-to-M phase transitions but appears to be dispensable for DNA synthesis. We have investigated the function of a related kinase, p33cdk2, using serum-stimulated quiescent human fibroblasts. While the p33cdk2 protein was expressed at constant levels throughout the cell cycle, p33cdk2 kinase activity was first detected a few hours prior to the onset of DNA synthesis. Microinjection of anti-p33cdk2 antibodies blocked cells from entering S phase. Pre-adsorption of these antibodies with cdk2 protein abrogated their blocking effect suggesting that the G1 arrest caused by these antibodies is cdk2-specific. These results indicate that p33cdk2 is required for the G1-to-S phase transition in mammalian cells. We also show evidence to suggest that the cyclin E/p33cdk2 complex is likely to be required for entry into S phase since the timing of the cyclin E-associated kinase activity was coincident with that of p33cdk2 and preclearing of either component abolished the majority of the histone H1 kinase activity present in the lysates harvested from the late G1.
The biosynthesis of shikimate metabolites (1999) (2001)

Covering: 1999. Previous review: 2000, 17, 269.
Antisense Oligonucleotide Down-Regulation of E-Cadherin in the Yolk Sac and Cranial Neural Tube Malformations1 (1995)

The cadherins are a family of calcium-dependent cell adhesion molecules that are regulated both spatially and temporally during development. Epithelial cadherin (E-cadherin) is present in epithelial cells in both the embryo and yolk sac during organogenesis. The consequences of disrupting the expression of E-cadherin at this stage of development are poorly understood. We report here our studies on the effects of antisense oligonucleotides on E-cadherin in the rat whole embryo culture system. Four 18-base single strand phosphorothioate oligodeoxynucleotides (AS-oligos), complementary to various regions of the mouse E-cadherin cDNA sequence, were dissolved in saline and injected into the amniotic cavities of 5-7 somite rat embryos; a sense (S-oligo) to oligo-1, an 18-base random sequence oligo (C-oligo), and PBS were used as controls. Embryos were cultured for up to 45 h; embryo morphology and the relative concentrations of E-cadherin protein were examined. All six oligonucleotides (AS-oligos and control oligos) induced malformations when amounts ranging from 25 to 50 pmol of oligonucleotide were injected per embryo. The malformations induced by all the oligos included craniofacial hypoplasia, an enlarged pericardium, twisted spinal cord, swelling of the rhombencephalon, and underdeveloped forelimb. Injection of AS-oligo-1, a sequence starting at the tenth base downstream from the translation initiation codon (ATG), resulted in malformed embryos with a high incidence of cranial neural tube malformations. The effects of AS-oligo-1 on the relative abundance of E- and neural (N)-cadherin proteins were examined by Western blot analysis. In the AS-oligo-1-exposed malformed embryos, the relative abundance of E- and N-cadherin proteins was not altered up to 24 h after injection; E- and N-cadherin concentrations in the embryo were decreased at 45 h postinjection. In contrast, the relative abundance of the E-cadherin protein in the yolk sac was reduced at 1-2 h after injection of AS oligo-1 and returned to control levels by 4 h. S-oligo-1 did not induce any change in the relative abundance of E- or N-cadherins. Thus, there was a tissue-specific and temporary "knockdown" of E-cadherin expression in the yolk sac of embryos exposed to antisense (AS-oligo-1); the down-regulation of yolk sac E-cadherin appears to lead to the induction of neural tube defects in the embryo. The exposure of whole embryos in culture to antisense oligonucleotides provides a model system in which the roles of developmentally important molecules and their spatial and temporal contributions to embryogenesis can be elucidated.
Focal dilation and paradoxical collapse of cortical fissures and sulci in patients with normal-pressure hydrocephalus (1998)

This study demonstrates that focal fissural and sulcal dilation may represent reservoirs of cerebrospinal fluid analogous to the ventricular system. Patients should not be denied a shunting procedure solely on the basis of focally dilated fissures of sulci.
Direct contacts between extracellular membrane-proximal domains are required for VEGF receptor activation and cell signaling (2010)

Structural analyses of the extracellular region of stem cell factor (SCF) receptor (also designated KIT) in complex with SCF revealed a sequence motif in a loop in the fourth Ig-like domain (D4) that is responsible for forming homotypic receptor contacts and for ligand-induced KIT activation and cell signaling. An identical motif was identified in the most membrane-proximal seventh Ig-like domain (D7) of vascular endothelial growth factor receptor 1 (VEGFR1), VEGFR2, and VEGFR3. In this report we demonstrate that ligand-induced tyrosine autophosphorylation and cell signaling via VEGFR1 or VEGFR2 harboring mutations in critical residues (Arg726 or Asp731) in D7 are strongly impaired. We also describe the crystal structure of D7 of VEGFR2 to a resolution of 2.7 A. The structure shows that homotypic D7 contacts are mediated by salt bridges and van der Waals contacts formed between Arg726 of one protomer and Asp731 of the other protomer. The structure of D7 dimer is very similar to the structure of D4 dimers seen in the crystal structure of KIT extracellular region in complex with SCF. The high similarity between VEGFR D7 and KIT D4 in both structure and function provides further evidence for common ancestral origins of type III and type V RTKs. It also reveals a conserved mechanism for RTK activation and a novel target for pharmacological intervention of pathologically activated RTKs.
Dynamic Ray Scheduling to Improve Ray Coherence and Bandwidth Utilization (2007)

The performance of full-featured ray tracers has historically been limited by the hardware's floating point computational power. However, next generation multi-threaded multi-core architectures promise to provide sufficient CPU throughput to support real time frame rates. In such systems, limited memory system performance in terms of both on-chip cache and DRAM-to-cache bandwidth is likely to bound overall system performance. This paper presents a novel ray tracing algorithm that both improves cache utilization and reduces DRAM-to-cache bandwidth usage. The key insight is to view ray traversal as a scheduling problem, which allows our algorithm to match ray traversal computations and intersection computations with available system resources. Using a detailed simulator, we show that our algorithm significantly reduces the amount of data brought into the cache in exchange for the small overhead of maintaining the ray schedule. Moreover, our algorithm creates units of work that are more amenable to parallelization than traditional Whitted-style ray tracers.
The Puromycin Route to Assess Stereo- and Regiochemical Constraints on Peptide Bond Formation in Eukaryotic Ribosomes (2003)

We synthesized a series of puromycin analogues to probe the chemical specificity of the ribosome in an intact eukaryotic translation system. These studies reveal that both d-enantiomers and beta-amino acid analogues can be incorporated into protein, and provide a quantitative means to rank natural and unnatural residues. Modeling of a d-amino acid analogue into the 50S ribosomal subunit indicates that steric clash may provide part of the chiral discrimination. The data presented provide one metric of the chiral and regiospecificity of mammalian ribosomes.
Association of Human Immunodeficiency Virus Type 1 Vif with RNA and Its Role in Reverse Transcription (2000)

The vif gene of human immunodeficiency virus type 1 (HIV-1) is essential for viral replication, although the functional target of Vif remains elusive. HIV-1 vif mutant virions derived from nonpermissive H9 cells displayed no significant differences in the amount, ratio, or integrity of their protein composition relative to an isogenic wild-type virion. The amounts of the virion-associated viral genomic RNA and tRNA(3)(Lys) were additionally present at normal levels in vif mutant virions. We demonstrate that Vif associates with RNA in vitro as well as with viral genomic RNA in virus-infected cells. A functionally conserved lentivirus Vif motif was found in the double-stranded RNA binding domain of Xenopus laevis, Xlrbpa. The natural intravirion reverse transcriptase products were markedly reduced in vif mutant virions. Moreover, purified vif mutant genomic RNA-primer tRNA complexes displayed severe defects in the initiation of reverse transcription with recombinant reverse transcriptase. These data point to a novel role for Vif in the regulation of efficient reverse transcription through modulation of the virion nucleic acid components.
Amyloid β inhibits retinoic acid synthesis exacerbating Alzheimer disease pathology which can be attenuated by an retinoic acid receptor α agonist (2013)

The retinoic acid receptor (RAR) α system plays a key role in the adult brain, participating in the homeostatic control of synaptic plasticity, essential for memory function. Here we show that RARα signalling is down-regulated by amyloid beta (Aβ), which inhibits the synthesis of the endogenous ligand, retinoic acid (RA). This results in the counteraction of a variety of RARα-activated pathways that are key in the aetiopathology of Alzheimer's disease (AD) but which can be reversed by an RARα agonist. RARα signalling improves cognition in the Tg2576 mice, it has an anti-inflammatory effect and promotes Aβ clearance by increasing insulin degrading enzyme and neprilysin activity in both microglia and neurons. In addition, RARα signalling prevents tau phosphorylation. Therefore, stimulation of the RARα signalling pathway using a synthetic agonist, by both clearing Aβ and counteracting some of its toxic effects, offers therapeutic potential for the treatment of AD.
The Mechanism of N-Terminal Acetylation of Protein (1985)

N alpha-acetylation is almost exclusively restricted to eukaryotic structural proteins. As a rule it is a post-initiational process, requiring the presence of the enzyme N alpha-acetyltransferase and the acetyl donor acetylcoenzyme A. N alpha-acetyltransferases appear to have a narrow substrate specificity, which is very similar for enzymes from different tissues and species. Amino acids predominantly present at the N terminus of N alpha-acetylated proteins are alanine, serine, and methionine. The occurrence of these residues is apparently a prerequisite for acetylation. The region following these amino acids is also important. If methionine is at the N terminus, the second position is always occupied by a strongly hydrophilic amino acid. Two- and three-dimensional structural characteristics of the protein do not seem to play a major role in N alpha-acetylation. Up to now the exact function for N alpha-acetylation is not known.
Rapid evaluation of topoisomerase inhibitors: Caffeine inhibition of topoisomerases in vivo (1990)

Caffeine was found to inhibit both type I and type II topoisomerases in vivo as judged by its effects on replicating simian virus 40 (SV40) chromosomes. The study was facilitated by the use of a rapid filter assay for the detection and characterization of topoisomerase inhibitors. The assay, which requires neither purified enzymes nor substrates, was able to identify both antagonists and poisons of type I and type II topoisomerases.
Binding of Pramipexole to Extrastriatal Dopamine D2/D3 Receptors in the Human Brain: A Positron Emission Tomography Study Using 11C-FLB 457 (2011)

The purpose of this study was to determine the binding sites of pramipexole in extrastriatal dopaminergic regions because its antidepressive effects have been speculated to occur by activating the dopamine D(2) receptor subfamily in extrastriatal areas. Dynamic positron emission tomography (PET) scanning using (11)C-FLB 457 for quantification of D(2)/D(3) receptor subtype was performed on 15 healthy volunteers. Each subject underwent two PET scans before and after receiving a single dose of pramipexole (0, 0.125, or 0.25 mg). The study demonstrated that pramipexole significantly binds to D(2)/D(3) receptors in the prefrontal cortex, amygdala, and medial and lateral thalamus at a dose of 0.25 mg. These regions have been indicated to have some relation to depression and may be part of the target sites where pramipexole exerts its antidepressive effects.
Healthy ageing of cloned sheep (2016)

The health of cloned animals generated by somatic-cell nuclear transfer (SCNT) has been of concern since its inception; however, there are no detailed assessments of late-onset, non-communicable diseases. Here we report that SCNT has no obvious detrimental long-term health effects in a cohort of 13 cloned sheep. We perform musculoskeletal assessments, metabolic tests and blood pressure measurements in 13 aged (7-9 years old) cloned sheep, including four derived from the cell line that gave rise to Dolly. We also perform radiological examinations of all main joints, including the knees, the joint most affected by osteoarthritis in Dolly, and compare all health parameters to groups of 5-and 6-year-old sheep, and published reference ranges. Despite their advanced age, these clones are euglycaemic, insulin sensitive and normotensive. Importantly, we observe no clinical signs of degenerative joint disease apart from mild, or in one case moderate, osteoarthritis in some animals. Our study is the first to assess the long-term health outcomes of SCNT in large animals.
Investigation and management of the hepatic glycogen storage diseases. (2015)

The glycogen storage diseases (GSD) comprise a group of disorders that involve the disruption of metabolism of glycogen. Glycogen is stored in various organs including skeletal muscle, the kidneys and liver. The liver stores glycogen to supply the rest of the body with glucose when required. Therefore, disruption of this process can lead to hypoglycaemia. If glycogen is not broken down effectively, this can lead to hepatomegaly. Glycogen synthase deficiency leads to impaired glycogen synthesis and consequently the liver is small. Glycogen brancher deficiency can lead to abnormal glycogen being stored in the liver leading to a quite different disorder of progressive liver dysfunction. Understanding the physiology of GSD I, III, VI and IX guides dietary treatments and the provision of appropriate amounts and types of carbohydrates. There has been recent re-emergence in the literature of the use of ketones in therapy, either in the form of the salt D,L-3-hydroxybutyrate or medium chain triglyceride (MCT). High protein diets have also been advocated. Alternative waxy maize based starches seem to show promising early data of efficacy. There are many complications of each of these disorders and they need to be prospectively surveyed and managed. Liver and kidney transplantation is still indicated in severe refractory disease.