gebhart/patrepeval huggingface dataset:
Sensing of Alzheimer’s Disease and Multiple Sclerosis Using Nano-Bio Interfaces (2017)

It is well understood that patients with different diseases may have a variety of specific proteins (e.g., type, amount, and configuration) in their plasmas. When nanoparticles (NPs) are exposed to these plasmas, the resulting coronas may incorporate some of the disease-specific proteins. Using gold (Au) NPs with different surface properties and corona composition, we have developed a technology for the discrimination and detection of two neurodegenerative diseases, Alzheimer's disease (AD) and multiple sclerosis (MS). Applying a variety of techniques, including UV-visible spectra, colorimetric response analyses and liquid chromatography-tandem mass spectrometry, we found the corona-NP complexes, obtained from different human serums, had distinct protein composition, including some specific proteins that are known as AD and MS biomarkers. The colorimetric responses, analyzed by chemometrics and statistical methods, demonstrate promising capabilities of the technology to unambiguously identify and discriminate AD and MS. The developed colorimetric technology might enable a simple, inexpensive and rapid detection/discrimination of neurodegenerative diseases.
Rare occurrence of DNMT3A mutations in myelodysplastic syndromes (2011)

Gene mutations and epigenetic changes have been shown to play significant roles in the pathogenesis of myelodysplastic syndromes. Recently, mutations in DNMT3A were identified in 22.1% of patients with acute myeloid leukemia. In this study, we analyzed the frequency and clinical impact of DNMT3A mutations in a cohort of 193 patients with myelodysplastic syndromes. Mutations in DNMT3A were found in 2.6% of patients. The majority of mutations were heterozygous missense mutations affecting codon R882. Patients with DNMT3A mutations were found to have a higher rate of transformation to acute myeloid leukemia. When assessing the global methylation levels in patients with mutated versus unmutated DNMT3A and healthy controls no difference in global DNA methylation levels between the two groups was seen. Our data show that in patients with myelodysplastic syndromes, DNMT3A mutations occur at a low frequency and may be a risk factor for leukemia progression.
Adenylosuccinate lyase deficiency (2014)

Adenylosuccinate lyase ADSL) deficiency is a defect of purine metabolism affecting purinosome assembly and reducing metabolite fluxes through purine de novo synthesis and purine nucleotide recycling pathways. Biochemically this defect manifests by the presence in the biologic fluids of two dephosphorylated substrates of ADSL enzyme: succinylaminoimidazole carboxamide riboside (SAICAr) and succinyladenosine (S-Ado). More than 80 individuals with ADSL deficiency have been identified, but incidence of the disease remains unknown. The disorder shows a wide spectrum of symptoms from slowly to rapidly progressing forms. The fatal neonatal form has onset from birth and presents with fatal neonatal encephalopathy with a lack of spontaneous movement, respiratory failure, and intractable seizures resulting in early death within the first weeks of life. Patients with type I (severe form) present with a purely neurologic clinical picture characterized by severe psychomotor retardation, microcephaly, early onset of seizures, and autistic features. A more slowly progressing form has also been described (type II, moderate or mild form), as having later onset, usually within the first years of life, slight to moderate psychomotor retardation and transient contact disturbances. Diagnosis is facilitated by demonstration of SAICAr and S-Ado in extracellular fluids such as plasma, cerebrospinal fluid and/or followed by genomic and/or cDNA sequencing and characterization of mutant proteins. Over 50 ADSL mutations have been identified and their effects on protein biogenesis, structural stability and activity as well as on purinosome assembly were characterized. To date there is no specific and effective therapy for ADSL deficiency.
Genetic homogeneity of autoimmune polyglandular disease type I. (1996)

Autoimmune polyglandular disease type I (APECED) is an autosomal recessive autoimmune disease (MIM 240300) characterized by hypoparathyroidism, primary adrenocortical failure, and chronic mucocutaneous candidiasis. The disease is highly prevalent in two isolated populations, the Finnish population and the Iranian Jewish one. Sporadic cases have been identified in many other countries, including almost all European countries. The APECED locus has previously been assigned to chromosome 21q22.3 by linkage analyses in 14 Finnish families. Locus heterogeneity is a highly relevant question in this disease affecting multiple tissues and with great phenotypic diversity. To solve this matter, we performed linkage and haplotype analyses on APECED families rising from different populations. Six microsatellite markers on the critical chromosomal region of 2.6 cM on 21q22.3 were analyzed. Pairwise linkage analyses revealed significant LOD scores for all these markers, maximum LOD score being 10.23. The obtained haplotype data and the geographic distribution of the great-grandparents of the Finnish APECED patients suggest the presence of one major, relatively old mutation responsible for approximately 90% of the Finnish cases. Similar evidence for one founder mutation was also found in analyses of Iranian Jewish APECED haplotypes. These haplotypes, however, differed totally from the Finnish ones. The linkage analyses in 21 non-Finnish APECED families originating from several European countries provided independent evidence for linkage to the same chromosomal region on 21q22.3 and revealed no evidence for locus heterogeneity. The haplotype analyses of APECED chromosomes suggest that in different populations APECED is due to a spectrum of mutations in a still unknown gene on chromosome 21.
Rab7 Associates with Early Endosomes to Mediate Sorting and Transport of Semliki Forest Virus to Late Endosomes (2005)

Semliki forest virus (SFV) is internalized by clathrin-mediated endocytosis, and transported via early endosomes to late endosomes and lysosomes. The intracellular pathway taken by individual fluorescently labeled SFV particles was followed using immunofluorescence in untransfected cells, and by video-enhanced, triple-color fluorescence microscopy in live cells transfected with GFP- and RFP-tagged Rab5, Rab7, Rab4, and Arf1. The viruses progressed from Rab5-positive early endosomes to a population of early endosomes (about 10% of total) that contained both Rab5 and Rab7. SFV were sequestered in the Rab7 domains, and they were sorted away from the early endosomes when these domains detached as separate transport carriers devoid of Rab5, Rab4, EEA1, Arf1, and transferrin. The process was independent of Arf1 and the acidic pH in early endosomes. Nocodazole treatment showed that the release of transport carriers was assisted by microtubules. Expression of constitutively inactive Rab7T22N resulted in accumulation of SFV in early endosomes. We concluded that Rab7 is recruited to early endosomes, where it forms distinct domains that mediate cargo sorting as well as the formation of late-endosome-targeted transport vesicles.
The condensation of diphenylphosphinic azide with substituted acetonitriles ‐ Formation of phosphorylated tetrazolines (1968)

Abstract The condensation between diphenylphosphinic azide and several substituted phenylacetonitriles was investigated. Rather than a substituted aminotriazole, a phosphorylated tetrazoline (IX) was isolated from several reactions. In addition, a phosphorylated nitrile (X) and a phosphorylated eniminonitrile (XI) were found. N ‐Acylation of IX, followed by warming, lead to a phosphorylated oxadiazoline (XX). Structural assignments are based on UV, IR, and NMR spectral data and chemical degradative evidence. A brief analysis of the results is presented.
Enhanced secretion through the Shigella flexneri Mxi‐Spa translocon leads to assembly of extracellular proteins into macromolecular structures (1995)

Genes required for entry of Shigella flexneri into epithelial cells in vitro are clustered in two adjacent loci, one of which encodes secretory proteins, the IpaA-D proteins, and the other their dedicated secretion apparatus, the Mxi-Spa translocon. Ipa secretion, which is induced upon contact of bacteria with epithelial cells, is prevented during growth in vitro. Here, we show that ipaB and ipaD mutations lead to enhanced secretion of a set of about 15 proteins. These extracellular proteins and some Ipas associate in organized structures consisting of extended sheets. Growth of the wild-type strain in the presence of Congo red is shown to induce protein secretion through the Mxi-Spa translocon. Cultures grown to stationary phase in the presence of Congo red contain extracellular filaments whose composition and morphology are similar to those produced by the hypersecreting ipaB and ipaD mutants.
Synthesis and characterization of 3‐aryl‐2‐(polystyryl)cyclopropenones via cyclopropenium ion substitution on polystyrene (1995)

Abstract Electrophilic substitution of cyclopropenium ions on aromatic polymers offers a unique opportunity to introduce polar functionality in a controlled manner to conventional, nonpolar polymers. Phenylcyclopropenone substituted polystyrene with predictable chemical composition and narrow molecular weight distribution were prepared. Size exclusion chromatography (SEC) analysis demonstrated the absence of branching or crosslinking in these functionalized polystyrenes during electrophilic substitution of the parent homopolymer. 13 C‐NMR confirmed that the degree of phenylcyclopropenone substitution was both highly efficient and predictable over a broad compositional range. The glass transition temperature ( T g ) of the polymers was found to vary linearly with mole % phenylcyclopropenone substitution of the polystyrene. Thermal gravimetric analysis (TGA) indicated that thermal decarbonylation of the appended cyclopropenones occurred at approximately 180°C. Weight loss vs. temperature profiles correlated reasonably well with levels of substitution based on 13 C‐NMR analysis, confirming that decarbonylation of the calculated cyclopropenone substituents was the predominant thermal decomposition pathway. © 1995 John Wiley &amp; Sons, Inc.
Linking age-related changes in skeletal muscle mass and composition with metabolism and disease. (2006)

Skeletal muscle (SM) plays a central role in many biological functions, such as movement and metabolism, and alterations in SM mass and composition can have a marked influence on health and disease. The purpose of this review was to examine and characterize age-related changes in SM mass and composition and to link these changes to corresponding changes in metabolism and disease. It can be concluded from several studies that SM mass decreases with advancing age in both men and women. The age-related reduction in SM, also known as sarcopenia, is related to a corresponding reduction in SM strength, and if left untreated, sarcopenia may lead to functional impairment and physical disability. An emerging body of evidence also suggests that age-related changes in the composition of SM, particularly the accumulation of lipids within SM fibers, may lead to metabolic disorders such as insulin resistance.
Boholmycin, a new aminoglycoside antibiotic. I. Production, isolation and properties. (1988)

A novel aminoglycoside antibiotic, boholmycin, was produced by Streptomyces hygroscopicus H617-25 isolated from a soil sample collected in Bohol Island, the Philippines. It has a pseudotetrasaccharide structure composed of a heptose, two aminosugars and dicarbamoyl-scyllo-inositol. Intrinsic antibacterial activity of boholmycin is weak but it exhibits broad spectrum activity against Gram-positive and Gram-negative bacteria including aminoglycoside-resistant strains. Boholmycin is non-toxic in mice at 1,000 mg/kg intravenously.
Dexamethasone selectively increases sodium‐dependent alanine transport across neonatal piglet intestine. (1987)

1. Lysine and alanine uptake by pig enterocytes has been measured in piglet mid intestine both during normal development and 3 days after injection of dexamethasone and epidermal growth factor (EGF) into 3-day-old animals. 2. Alanine uptake measured in the presence of sodium increased markedly during the first 4 weeks of post-natal life. Similar effects on alanine uptake could be produced through injection of dexamethasone, but not EGF, into 3-day-old piglets. Alanine uptake measured in the absence of sodium and lysine uptake measured in the presence of sodium remained unchanged during development and unaffected by injection of dexamethasone or EGF. 3. Enterocytes capable of transporting alanine in the presence of sodium were found, by quantitative autoradiography, to cover the top 400 micron of the villus in 6-day-old and 3-4-week-old control pigs. Alanine concentrations in villus tip enterocytes in 3-4-week-old pigs were four times those found in 6-day-old animals. Qualitative examination of selected villi, however, showed alanine uptake taking place over a considerably greater area of villus surface in 6-day-old compared with 3-4-week-old animals. 4. Injection of dexamethasone and EGF into 3-day-old piglets caused an increase in crypt depth without apparent change in crypt cell proliferation. The rate at which enterocytes migrated out of the crypt and the length of individual villi also remained unchanged by dexamethasone or EGF injection. 5. Dexamethasone produces its effect on alanine uptake by acting on older enterocytes present on the upper part of the villus. These enterocytes can be shown, by calculations based on enterocyte migration rate, to have already been present on the villus at the time the pig was born. 6. The above findings are discussed in relation to the ability of villus as well as crypt enterocytes to change their programme of differentiation in response to external stimuli. The particular ability of dexamethasone to induce system A type carrier function is further discussed in relation to normal changes found to occur during neonatal development. It is finally suggested, as a working hypothesis, that endogenous glucagon might act as the final mediator of both developmentally controlled and dexamethasone-induced changes in amino acid transport.
Immunohistochemistry of Terrien's and Mooren's Corneal Degeneration (1991)

Lamellar keratoplasty specimens from a patient with Terrien's marginal degeneration and a patient with Mooren's ulcer were compared using routine histopathologic and immunohistochemical staining with an avidin-biotin-peroxidase complex. Less than 25% of the resident cells in the Terrien's marginal degeneration specimen expressed major histocompatibility class II antigens compared with 75% to 100% of the resident cells in the Mooren's ulcer specimen. The ratio of CD4 cells (T-helper/inducer) to CD8 cells (T-suppressor/cytotoxic cells) in the Terrien's marginal degeneration specimen was almost 1:1 compared with 24:1 in the Mooren's ulcer specimen. In addition, less than 5% of the infiltrating cells from the Terrien's marginal degeneration specimen stained positive for CD22 (B cells), compared with 25% to 50% from the Mooren's ulcer specimen. These data may help explain why Terrien's marginal degeneration runs a more benign course than does Mooren's ulcer and provides a rationale for the use of immunosuppressive drugs to treat Mooren's ulcer.
Effects of Thickened Feeding on Gastroesophageal Reflux in Infants: A Placebo-Controlled Crossover Study Using Intraluminal Impedance (2003)

Thickened feeding has a significant effect on the reduction of regurgitation frequency and amount in otherwise healthy infants. This effect is caused by a reduction in the number of nonacid (pH >4) GER episodes, but also because of a decrease of mean reflux height reached in the esophagus. However, the occurrence of acid GER is not reduced. The combination of IMP and pH monitoring allows the complete registration and description of these GER episodes. Thickening of formula feedings with carob bean gum is an efficient therapy for uncomplicated GER in infants.
Induction of L-phenylalanine ammonia-lyase during utilization of phenylalanine as a carbon or nitrogen source in Rhodotorula glutinis (1981)

Rhodotorula glutinis is a convenient source of L-phenylalanine ammonia-lyase, an enzyme that is useful as a biochemical reagent in the assay of L-phenylalanine. There have been previous descriptions of induced lyase production in complex medium where induction occurs late in exponential growth, suggesting a role in secondary metabolism such as is the case in higher plants. A higher specific activity of L-phenylalanine ammonia-lyase (sixfold higher than a complex medium) can be obtained during midexponential growth in a defined medium containing L-phenylalanine as the sole source of carbon. L-Phenylalanine will also induce lyase synthesis during exponential growth in minimal in which L-phenylalanine is the sole source of nitrogen. The appearance of lyase in complex medium supplemented with L-phenylalanine is probably triggered fortuitously by exhaustion late in growth of a prime source of nitrogen. In this study, R. glutinis appeared to express a single lyase enzyme, regardless of whether induction was nitrogen signaled or carbon signaled. Thin-layer chromatographic analysis of ether extracts prepared from cultures induced with doubly labeled (U-14C; ring-4-3H) L-phenylalanine provided evidence of a catabolic sequence containing cinnamic acid, benzoic acid, and 4-hydroxybenzoic acid as degradative intermediates. 3,4-Dihydroxybenzoic acid was not identified as a catabolic intermediate.
Role of the JNK signal transduction pathway in inflammatory bowel disease (2008)

The c-Jun NH2-terminal Kinase (JNK) pathway represents one sub-group of the mitogen-activated protein (MAP) kinases which plays an important role in various inflammatory diseases states, including inflammatory bowel disease (IBD). Significant progress towards understanding the function of the JNK signaling pathway has been achieved during the past few years. Blockade of the JNK pathway with JNK inhibitors in animal models of IBD lead to resolution of intestinal inflammation. Current data suggest specific JNK inhibitors hold promise as novel therapies in IBD.
Tyr-503 of β-galactosidase (Escherichia coli) plays an important role in degalactosylation (1999)

Substitutions for Tyr-503 of beta-galactosidase caused large decreases of the activity. Both the galactosylation (k2) and degalactosylation (k3) rates were decreased. Substitutions by residues without transferable protons, caused k3 to decrease much more than k2 while substitutions with residues having transferable protons, caused approximately equal decreases of k2 and k3. Several lines of evidence showed this. The Km values of the substituted enzymes were much smaller than those for the wild type if the substituted amino acid residues did not have transferable protons; this was not the case when the substituted residues had transferable protons. Inhibition studies showed that the Km values were not small because of small Ks values but were small because of relatively small k3 values (compared with the k2 values). The conclusion that the k3 values are small relative to k2 upon substitution with residues without transferable protons is also based upon other studies: studies indicating that the reaction rates were similar with different substrates, studies in the presence of alcohol acceptors, studies showing that the rate of inactivation by 2,4-dinitrophenyl-2-deoxy-2-F-beta-D-galactopyranoside decreased much less than the rate of reactivation; studies on burst kinetics, and pH studies. The data suggest that Tyr-503 may be important for the degalactosylation reaction because of its ability to transfer protons and thereby facilitate cleavage of the transient covalent bond between galactose and Glu-537.
Multiple Organ Dysfunction Score (1995)

This multiple organ dysfunction score, constructed using simple physiologic measures of dysfunction in six organ systems, mirrors organ dysfunction as the intensivist sees it and correlates strongly with the ultimate risk of ICU mortality and hospital mortality. The variable, delta Multiple Organ Dysfunction Score, reflects organ dysfunction developing during the ICU stay, which therefore is potentially amenable to therapeutic manipulation. (ABSTRACT TRUNCATED)
Serum Uric Acid (2006)

Serum uric acid was first noted to be associated with increased BP by Frederick Mohamed in the 1870s. Although the link was rediscovered periodically over the years, it generally was dismissed as a surrogate marker for decreased renal function that led to increased uric acid and increased risk for hypertension and cardiovascular (CV) disease. Recently, however, several lines of evidence suggest that increased serum uric acid may be a significant modifiable risk factor. Increased serum uric acid is associated with increased risk for future hypertension in several large longitudinal clinical trials as well as an independent risk factor for poor CV prognosis. Animal model experiments demonstrate that increased serum uric acid causes increased BP that initially is reversible but becomes irreversible, salt sensitive, and uric acid independent over time. The mechanisms include the direct action of uric acid on smooth muscle and vascular endothelial cells. Finally, in adolescents with new-onset essential hypertension, the prevalence of elevated serum uric acid is >90%, and preliminary clinical trial evidence suggests that agents that lower serum uric acid may lower BP in this select population. Although the investigations are still preliminary, serum uric acid represents a possible new and intriguing target for the reduction of morbidity and mortality associated with hypertension and CV disease.
Highly efficient heritable plant genome engineering using Cas9 orthologues from Streptococcus thermophilus and Staphylococcus aureus (2015)

The application of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system of Streptococcus pyogenes (SpCas9) is currently revolutionizing genome engineering in plants. However, synthetic plant biology will require more complex manipulations of genomes and transcriptomes. The simultaneous addressing of different specific genomic sites with independent enzyme activities within the same cell is a key to this issue. Such approaches can be achieved by the adaptation of additional bacterial orthologues of the CRISPR/Cas system for use in plant cells. Here, we show that codon-optimised Cas9 orthologues from Streptococcus thermophilus (St1Cas9) and Staphylococcus aureus (SaCas9) can both be used to induce error-prone non-homologous end-joining-mediated targeted mutagenesis in the model plant Arabidopsis thaliana at frequencies at least comparable to those that have previously been reported for the S. pyogenes CRISPR/Cas system. Stable inheritance of the induced targeted mutations of the ADH1 gene was demonstrated for both St1Cas9- and SaCas9-based systems at high frequencies. We were also able to demonstrate that the SaCas9 and SpCas9 proteins enhance homologous recombination via the induction of double-strand breaks only in the presence of their species-specific single guide (sg) RNAs. These proteins are not prone to inter-species interference with heterologous sgRNA expression constructs. Thus, the CRISPR/Cas systems of S. pyogenes and S. aureus should be appropriate for simultaneously addressing different sequence motifs with different enzyme activities in the same plant cell.
Virion stiffness regulates immature HIV-1 entry (2013)

This linkage between particle stiffness and viral entry activity illustrates a novel level of regulation for viral replication, providing the first evidence for a biological role of virion physical properties and suggesting a new inhibitory strategy.