gebhart/patrepeval huggingface dataset:
Crystallization of Old Yellow Enzyme Illustrates an Effective Strategy for Increasing Protein Crystal Size (1993)

Old Yellow Enzyme (OYE) was the first flavoenzyme discovered, and has been widely used as a model flavoenzyme. Three crystal forms have been grown from natural protease-nicked OYE and one has been grown from intact recombinant OYE. The recombinant OYE crystals are best suited for structure determination and grow from a solution containing polyethylene glycol and MgCl2. They belong to space group P4(3)2(1)2 with unit cell dimensions a = b = 142.88 A, c = 43.01 A and have a single OYE chain per asymmetric unit. In order to optimize the production of large single crystals, we have carried out a systematic study of crystal size versus drop volume. Crystallographic lore holds that the volume of the medium in which the crystals are grown should have a significant effect on the final size of the crystals produced. However, a systematic investigation of the degree to which the volume of the crystallization sample affects the final size of the crystals has not been reported. In order to investigate this phenomenon, drops were set up in both hanging and sandwich geometry at a variety of drop volumes, but otherwise identical crystallization conditions. A 60-fold increase in drop volume produced a 730-fold increase in crystal volume, and a simultaneous increase in the effective diffraction limit of the crystals from near 2.5 A to well beyond 2.0 A resolution. The dramatic crystal volume increase appears to be due both to the increased amount of protein and the slower equilibration rates associated with larger drops. Our results also emphasize that the quality of diffraction data may often be limited by crystal size rather than intrinsic crystal order even in the case of reasonably sized (200 to 400 microns) crystals.
Large uterine myoma with erythropoietin messenger RNA and erythrocytosis (2000)

Erythropoietin production by myomata might cause erythrocytosis in myomatous erythrocytosis syndrome.
Cold shock damage is due to lipid phase transitions in cell membranes: A demonstration using sperm as a model (1993)

When cells are cooled to temperatures above the freezing point of water at rates greater than a few degrees per minute, they sustain irreversible injury. Reduction of this "cold shock" damage could increase the survival of animals and plants at low environmental temperatures and improve the cryopreservation of plant and animal cells. Leakage of solutes across membranes, associated with thermotropic phase transitions in membrane lipids, is thought to be responsible, but this hypothesis has not been tested directly. Using Fourier transform infrared spectroscopy (FTIR), we measured the lipid phase transitions in intact, living sperm, the animal cell in which cold shock has been studied most extensively. A shift in the CH2 absorbance peaks indicates the transition from liquid-crystalline to gel phase. The phase transition in sperm membranes occurred at a lower temperature for a marine shrimp than for the pig. In each case, potassium leakage, which is a hallmark of cold shock damage, increased abruptly near the end of the phase transition. Human sperm are quite resistant to cold shock, and an abrupt lipid phase transition was not detected. This phase behavior is typical of membranes containing a high proportion of cholesterol, and human sperm have an unusually high sterol content. High cholesterol levels are known to stabilize membranes during cooling. Overall, the lipid phase behavior was consistent with the temperature range over which cooling was damaging for pig and shrimp sperm, and the with the extent of damage produced in pig and human sperm. This is the first direct evidence that cold shock results from lipid phase transitions in cell membranes.
Fast drug-receptor mapping by site-directed distances: a novel method of predicting new pharmacological leads (1991)

The searching and characterization of large chemical databases has recently provoked much interest, particularly with respect to the question of whether any of the compounds in the database could serve as new leads to a compound of pharmacological interest. This paper introduces a fast and novel method of determining whether any of a given series of compounds are able, on geometrical grounds, to interact with an active site of interest. The C program written to implement the method is able to make a qualitative prediction for a given compound in about 1 s per structure (for drug-sized molecules), while still permitting the compound complete conformational freedom. However, the algorithm is sufficiently flexible to permit distance constraints to be placed on the molecules while docking. The test system studied was a family of Baker's triazines docking into the active site of dihydrofolate reductase (DHFR), as defined by a methotrexate/NADPH complex.
Hydrogen-Bonded Complexes of Aromatic Crown Ethers with (9-Anthracenyl)methylammonium Derivatives. Supramolecular Photochemistry and Photophysics. pH-Controllable Supramolecular Switching (1997)

The (9-anthracenyl)methylammonium and (9-anthracenyl)benzylammonium tetrakis(hexafluorophosphate) salts give hydrogen-bonded complexes in CH2Cl2 with aromatic crown ethers containing dibenzo (DB) or dinaphtho (DN) units. The association constants vary from 3 × 103 to 1 × 106 M-1 in CH2Cl2, depending on the specific ammonium cation and crown ether involved. In a number of cases, pseudorotaxane-like geometries for the complexes are demonstrated by (a) 1H NMR spectroscopy in solution, (b) X-ray crystallography in the solid state, and (c) mass spectrometry in the gas phase. The results obtained by absorption, emission, and excitation spectroscopy and excited lifetimes show that, as a consequence of the hydrogen bond driven recognition process, the anthracene chromophoric unit interacts with the aromatic units of the crown ethers. In the complexes involving the DB18C6, DB24C8, and DB30C10 macrocycles, the interaction leads to the complete quenching of the fluorescence of the dialkoxybenzene moieties and parallels sensitization of the anthracene fluorescence. In the complexes of 1/5-DN38C10, both the crown and the anthracene fluorescence are completely quenched, most likely by an energy-transfer cascade involving the triplet state of the dialkoxynaphthalene moiety. In the complexes of 2/3-DN30C10, the interaction between the anthracene moiety and the naphthalene rings of the crown ether is relatively strong, as indicated by the perturbation of the absorption bands, the disappearance of the fluorescence bands of the naphthalene- and anthracene-type chromophoric units, and the appearance of a new, broad fluorescence band. The complexes can also be formed by addition of CF3COOH or CF3SO3H to CH2Cl2 solutions containing crown ether and amine. The association process between DB24C8 and (9-anthracenyl)benzylammonium salt can be reversed quantitatively upon addition of a suitable base and the complex can be formed again after treatment with acid.
Nerve growth factor treatment of adult rats selectively enhances innervation of urinogenital tract rather than vascular smooth muscle (1995)

Following treatment of adult rats with nerve growth factor (0.5 mg/rat, three times a week for 3 weeks), the innervation of cardiovascular and urinogenital tract smooth muscle was investigated using immunoassay and immunohistochemical techniques. Substance P and calcitonin gene-related peptide levels were increased in the vas deferens, but not in the atria or femoral artery. Neuropeptide Y and vasoactive intestinal polypeptide levels were unchanged. In penile tissues, there was a marked increase in the density of substance P-, calcitonin gene-related peptide-, neuropeptide Y-, tyrosine hydroxylase- and vasoactive intestinal polypeptide-containing nerves innervating the urethra and in SP-containing nerves in the tunica with little changes in the innervation of the deep dorsal vein and artery and corpus cavernosum. In the bladder, there was increased innervation of the detrusor by neuropeptide Y- and vasoactive intestinal polypeptide-containing nerves, but a decrease in innervation by substance P-containing nerves in the trigone. There were no changes in the density of innervation of the femoral artery after nerve growth factor treatment. Thus, in the mature rat, sensory and sympathetic nerve innervating urinogenital tract smooth muscle appear to be more responsive to exogenous nerve growth factor than those innervating cardiovascular smooth muscle. This may reflect an ongoing requirement of plasticity of innervation in the urinogenital tract of the sexually mature animal.
Selective uptake of HDL cholesteryl esters is active in transgenic mice expressing human apolipoprotein A-I. (1995)

The direct non-endocytotic uptake of cholesteryl esters (CE) from high density lipoprotein (HDL) plays a major role in HDL CE metabolism in rats and rabbits. In vitro evidence indicates it may also play such a role in humans. However, a study in mice (tracing the CE and apoA-I moieties of HDL) concluded that, while selective uptake played a role in normal animals, it did not in transgenic mice which express predominantly human apoA-I (Chajek-Shaul et al., 1991. Proc. Natl. Acad. Sci. USA. 88: 6731-6735);thus human apoA-I was apparently unable to support selective uptake. These conclusions rested on plasma decay data that represent a composite of all tissue and which may obscure tissue-specific factors. Thus we reexamined the matter by measuring the rates of uptake of HDL components by individual tissues using intracellularly trapped tracers. Plasma decay data were much as reported in the referenced study. Nonetheless the fractional rate of uptake of HDL CE was greater than that of apoA-I in adrenal gland and liver, indicating selective uptake. Kidney took up apoA-I tracer at a greater fractional rate than CE tracer, apparently by filtration and reabsorption of free apoA-I, and this uptake was at a greater fractional rate in the transgenic mice than in normal mice. Thus, the lack of evidence for selective uptake in the plasma decay data of the transgenic mice was explained by a higher rate of renal uptake of apoA-I and not by a diminished rate of selective uptake in other tissues.(ABSTRACT TRUNCATED AT 250 WORDS)
Progressive Supranuclear Palsy and Corticobasal Degeneration: Pathophysiology and Treatment Options (2016)

There are currently no disease-modifying treatments for progressive supranuclear palsy (PSP) or corticobasal degeneration (CBD), and no approved pharmacological or therapeutic treatments that are effective in controlling their symptoms. The use of most pharmacological treatment options are based on experience in other disorders or from non-randomized historical controls, case series, or expert opinion. Levodopa may provide some improvement in symptoms of Parkinsonism (specifically bradykinesia and rigidity) in PSP and CBD; however, evidence is conflicting and where present, benefits are often negligible and short lived. In fact, "poor" response to levodopa forms part of the NINDS-SPSP criteria for the diagnosis of PSP and consensus criteria for the diagnosis of CBD (Lang Mov Disord. 20 Suppl 1:S83-91, 2005; Litvan et al. Neurology. 48:119-25, 1997; Armstrong et al. Neurology. 80(5):496-503, 2013). There is some evidence that intrasalivery gland botulinum toxin is useful in managing problematic sialorrhea and that intramuscular botulinum toxin and baclofen are helpful in reducing dystonia, including blepharospasm. Benzodiazepines may also be useful in managing dystonia. Myoclonus may be managed using levetiracetam and benzodiazepines. Pharmacological agents licensed for Alzheimer's disease (such as acetylcholinesterase inhibitors and N-Methyl-D-aspartate receptor antagonists) have been used off-label in PSP, CBD, and other tauopathies with the aim of improving cognition; however, there is limited evidence that they are effective and risk of adverse effects may outweigh benefits. The use of atypical antipsychotics for behavioural symptoms is not recommended in the elderly or those with demetia associated conditions and most antipsychotics will worsen Parkinsonism. Antidepressants may be useful for behavioral symptoms and depression but are often poorly tolerated due to adverse effects. In the absence of an effective drug treatment to target the underlying cause of CBD and PSP, management should focus on optimizing quality of life, relieving symptoms and assisting patients with their activities of daily living (ADL). Patients should be managed by a multidisciplinary team consisting of neurologists, physiotherapists (PT), occupational therapists (OT), speech and language therapists (SALT), dieticians, ophthalmologists, psychologists, and palliative care specialists.
Characterization of the Precursor of Prostate-specific Antigen (1997)

The precursor or zymogen form of prostate-specific antigen (pro-PSA) is composed of 244 amino acid residues including an amino-terminal propiece of 7 amino acids. Recombinant pro-PSA was expressed in Escherichia coli, isolated from inclusion bodies, refolded, and purified. The zymogen was readily activated by trypsin at a weight ratio of 50:1 to generate PSA, a serine protease that cleaves the chromogenic chymotrypsin substrate 3-carbomethoxypropionyl-L-arginyl-L-prolyl-L-tyrosine-p-nitroanili ne- HCl (S-2586). In this activation, the amino-terminal propiece Ala-Pro-Leu-Ile-Leu-Ser-Arg was released by cleavage at the Arg-Ile peptide bond. The recombinant pro-PSA was also activated by recombinant human glandular kallikrein, another prostate-specific serine protease, as well as by a partially purified protease(s) from seminal plasma. The recombinant PSA was inhibited by alpha1-antichymotrypsin, forming an equimolar complex with a molecular mass of approximately 100 kDa. The recombinant PSA failed to activate single chain urokinase-type plasminogen activator, in contrast to the recombinant hK2, which readily activated single chain urokinase-type plasminogen activator. These results indicate that pro-PSA is converted to an active serine protease by minor proteolysis analogous to the activation of many of the proteases present in blood, pancreas, and other tissues. Furthermore, PSA is probably generated by a cascade system involving a series of precursor proteins. These proteins may interact in a stepwise manner similar to the generation of plasmin during fibrinolysis or thrombin during blood coagulation.
Vasopressin in septic shock: Clinical equipoise mandates a time for restraint * (2003)

St. Paul’s Hospital and the University of British Columbia McDonald Research Laboratories/The iCAPTURE Centre Vancouver, BC, Canada *See also p. 2646.
DSP implementations of sophisticated speech codecs (1988)

Hardware implementation aspects of sophisticated speech codecs are addressed. The major points discussed are approaches to implementation of the sophisticated speech codecs, requirements for DSP (digital signal-processing) implementation of the codecs, such as the type of arithmetic processing and the necessity of bit-level specifications, and codec implementation and DSP programming techniques for three specific coding algorithms: 32-kb/s ADPCM (adaptive digital pulse code modulation), 64-kb/s (7 kHz) SB (subband)-ADPCM, and 16-kb/s APC-AB (adaptive predictive coding with adaptive but allocation) codecs.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Trans-splicing with the group I intron ribozyme from Azoarcus (2013)

Group I introns are ribozymes (catalytic RNAs) that excise themselves from RNA primary transcripts by catalyzing two successive transesterification reactions. These cis-splicing ribozymes can be converted into trans-splicing ribozymes, which can modify the sequence of a separate substrate RNA, both in vitro and in vivo. Previous work on trans-splicing ribozymes has mostly focused on the 16S rRNA group I intron ribozyme from Tetrahymena thermophila. Here, we test the trans-splicing potential of the tRNA(Ile) group I intron ribozyme from the bacterium Azoarcus. This ribozyme is only half the size of the Tetrahymena ribozyme and folds faster into its active conformation in vitro. Our results showed that in vitro, the Azoarcus and Tetrahymena ribozymes favored the same set of splice sites on a substrate RNA. Both ribozymes showed the same trans-splicing efficiency when containing their individually optimized 5' terminus. In contrast to the previously optimized 5'-terminal design of the Tetrahymena ribozyme, the Azoarcus ribozyme was most efficient with a trans-splicing design that resembled the secondary structure context of the natural cis-splicing Azoarcus ribozyme, which includes base-pairing between the substrate 5' portion and the ribozyme 3' exon. These results suggested preferred trans-splicing interactions for the Azoarcus ribozyme under near-physiological in vitro conditions. Despite the high activity in vitro, however, the splicing efficiency of the Azoarcus ribozyme in Escherichia coli cells was significantly below that of the Tetrahymena ribozyme.
A unique family of Mrr-like modification-dependent restriction endonucleases (2010)

Mrr superfamily of homologous genes in microbial genomes restricts modified DNA in vivo. However, their biochemical properties in vitro have remained obscure. Here, we report the experimental characterization of MspJI, a remote homolog of Escherichia coli's Mrr and show it is a DNA modification-dependent restriction endonuclease. Our results suggest MspJI recognizes (m)CNNR (R = G/A) sites and cleaves DNA at fixed distances (N(12)/N(16)) away from the modified cytosine at the 3' side (or N(9)/N(13) from R). Besides 5-methylcytosine, MspJI also recognizes 5-hydroxymethylcytosine but is blocked by 5-glucosylhydroxymethylcytosine. Several other close homologs of MspJI show similar modification-dependent endonuclease activity and display substrate preferences different from MspJI. A unique feature of these modification-dependent enzymes is that they are able to extract small DNA fragments containing modified sites on genomic DNA, for example ∼32 bp around symmetrically methylated CG sites and ∼31 bp around methylated CNG sites. The digested fragments can be directly selected for high-throughput sequencing to map the location of the modification on the genomic DNA. The MspJI enzyme family, with their different recognition specificities and cleavage properties, provides a basis on which many future methods can build to decode the epigenomes of different organisms.
The TRANSPARENT TESTA16 Locus Encodes the ARABIDOPSIS BSISTER MADS Domain Protein and Is Required for Proper Development and Pigmentation of the Seed Coat (2002)

Screening for seed pigmentation phenotypes in Arabidopsis led to the isolation of three allelic yellow-seeded mutants, which defined the novel TRANSPARENT TESTA16 (TT16) locus. Cloning of TT16 was performed by T-DNA tagging and confirmed by genetic complementation and sequencing of two mutant alleles. TT16 encodes the ARABIDOPSIS BSISTER (ABS) MADS domain protein. ABS belongs to the recently identified "B-sister" (B(S)) clade, which contains genes of unknown function that are expressed mainly in female organs. Phylogenetic analyses using a maximum parsimony approach confirmed that TT16/ABS and related proteins form a monophyletic group. TT16/ABS was expressed mainly in the ovule, as are the other members of the B(S) clade. TT16/ABS is necessary for BANYULS expression and proanthocyanidin accumulation in the endothelium of the seed coat, with the exception of the chalazal-micropylar area. In addition, mutant phenotype and ectopic expression analyses suggested that TT16/ABS also is involved in the specification of endothelial cells. Nevertheless, TT16/ABS apparently is not required for proper ovule function. We report the functional characterization of a member of the B(S) MADS box gene subfamily, demonstrating its involvement in endothelial cell specification as well as in the increasingly complex genetic control of flavonoid biosynthesis in the Arabidopsis seed coat.
Determination of heme in microorganisms using HPLC-MS/MS and cobalt(III) protoporphyrin IX inhibition of heme acquisition in Escherichia coli (2017)

One of the main threats to the achievements in modern medicine is antimicrobial resistance. Molecular targeting of bacterial acquisition mechanisms of heme has been suggested to be an alternative to antibiotics. In the present study, HPLC-MS/MS combined with a simple clean-up based on liquid-liquid extraction has been developed and evaluated for simultaneous determination of heme and porphyrin heme precursors in microorganisms. Experimental design was used to optimize the extraction parameters, to obtain a method with high recovery, low matrix effects, and high precision. The effects of additives in the culture medium on the biosynthesis of heme were studied using Escherichia coli as a model microorganism. 5-Aminolaevulinic acid and hemin increased the heme concentration in E. coli by a factor of 1.5 and 4.5, respectively. Addition of 5-aminolaevulinic acid bypassed the E. coli negative feedback control of heme biosynthesis, which led to high amounts of intracellular porphyrins. The high heme concentration obtained when hemin was used as a culture additive shows that E. coli has an uptake of heme from its surroundings. In contrast, addition of cobalt protoporphyrin IX to the growth medium reduced the amount of heme in E. coli, demonstrating this compound's ability to mimic real heme and inhibit the heme acquisition mechanisms.
Soluble fumarate reductase isoenzymes fromSaccharomyces cerevisiaeare required for anaerobic growth (1998)

In Saccharomyces cerevisiae, the cytosolic and promitochondrial isoenzymes of fumarate reductase are encoded by the FRDS and OSM1 genes, respectively. The product of the OSM1 gene is reported to be required for growth in hypertonic medium. Simultaneous disruption of the FRDS and OSM1 genes resulted in the inability of the yeasts to grow anaerobically on glucose as a carbon source, and disruption of the OSM1 gene caused poor growth under anaerobic conditions. However, the disruption of both the FRDS and/or OSM1 genes had no effect on aerobic growth or growth under hypertonic conditions. These results suggest that the fumarate reductase isoenzymes in Saccharomyces cerevisiae are essential for anaerobic growth but not for growth under hypertonic conditions.
Area time trade-offs in micro-grain VLSI array architectures (1994)

We study the relative performance of three different massively parallel fine-grain, VLSI, control-flow architectures. The processor architectures being considered are: an associative memory architecture, a Mux-based SIMD architecture and a modification of the Mux-based architecture using RAMs making it suitable for systolic MIMD/MISD computation. All three architectures are organized as two-dimensional, near-neighbor mesh connected, array of processors. All three are very similar in their construction, and in their control and data-flow requirements. The custom hardware for all three architectures was built using the same technology. We compare and contrast the performance of these three VLSI architectures for a select set of applications. To evaluate the computational power of the three architectures we use the area time product, AT, as the metric. The three designs are known to perform well in their niche applications and we find that for non-niche applications all three designs are comparable in power to within a small constant factor. The performance of the Mux-based SIMD architecture is better in general than the other two in terms of speed though the associative architecture is found to out-perform the SIMD architecture for certain numeric applications like the FFT and matrix multiplication in the AT sense.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>