gebhart/patrepeval huggingface dataset:
Analysis of genome-wide copy number variation in Irish and Dutch ALS populations (2008)

Amyotrophic lateral sclerosis (ALS) is an unrelenting neurodegenerative condition characterized by adult-onset loss of motor neurons. Genetic risk factors have been implicated in ALS susceptibility. Copy number variants (CNVs) account for more inter-individual genetic variation than SNPs and have the capacity to alter gene dose and phenotype. We sought to identify the contribution both of commonly polymorphic CNVs and rare ALS-specific CNVs to sporadic ALS (SALS). Using high-density genome-wide data from 408 Irish individuals and 868 Dutch individuals and the QuantiSNP CNV-detection algorithm, we showed that no common CNV locus is significantly associated with ALS risk. However, we identified 39 recurrent CNV loci and 16 replicated ALS-specific gene dose alterations that occur exclusively in patients with ALS and do not occur in more than 11 000 previously identified CNVs in the Database of Genomic Variation. Ataxin genes and the hereditary haemochromatosis locus were implicated along with ENSG00000176605, an uncharacterized gene on chromosome 14. Our data support the hypothesis that multiple rare CNVs may contribute risk for SALS. Future work should seek to profile the contribution of CNVs located in regions not covered on the present SNP platforms.
Suppression of miR-184 in malignant gliomas upregulates SND1 and promotes tumor aggressiveness (2014)

Our study is the first to show a novel regulatory role of SND1, a direct target of miR-184, in glioma progression, suggesting that the miR-184/SND1 axis may be a useful diagnostic and therapeutic tool for malignant glioma.
A multi-institutional phase II study of BMS-182248-01 (BR96-doxorubicin conjugate) administered every 21 days in patients with advanced gastric adenocarcinoma. (2001)

Although BMS-182248-01 represents a novel approach of monoclonal antibody conjugated with an active chemotherapy agent, delivered intracellularly, it was ineffective in patients with gastric carcinoma whose tumors carried LewisY antigen.
RF2b, a rice bZIP transcription activator, interacts with RF2a and is involved in symptom development of rice tungro disease (2004)

The phloem-specific promoter of rice tungro bacilliform virus (RTBV) is regulated in part by sequence-specific DNA-binding proteins that bind to Box II, an essential cis element. Previous studies demonstrated that the bZIP protein RF2a is involved in transcriptional regulation of the RTBV promoter. Here we report the identification and functional characterization of a second bZIP protein, RF2b. RF2b, identified by its interaction with RF2a, binds to Box II in in vitro assays as a homodimer and as RF2a/RF2b heterodimers. Like RF2a, RF2b activates the RTBV promoter in transient assays and in transgenic tobacco plants. Both RF2a and RF2b are predominantly expressed in vascular tissues. However, RF2a and RF2b have different DNA-binding affinities to Box II, show distinctive expression patterns in different rice organs, and exhibit different patterns of subcellular localization. Furthermore, transgenic rice plants with reduced levels of RF2b exhibit a disease-like phenotype. We propose that the regulation of phloem-specific expression of the RTBV promoter and potentially the control of RTBV replication are mainly achieved via interactions of the Box II cis element with multiple host factors, including RF2a and RF2b. We also propose that quenching/titration of these and perhaps other transcription factors by RTBV is involved in the development of the symptoms of rice tungro disease.
Degradable Self-Assembling Dendrons for Gene Delivery: Experimental and Theoretical Insights into the Barriers to Cellular Uptake (2011)

This paper uses a combined experimental and theoretical approach to gain unique insight into gene delivery. We report the synthesis and investigation of a new family of second-generation dendrons with four triamine surface ligands capable of binding to DNA, degradable aliphatic-ester dendritic scaffolds, and hydrophobic units at their focal points. Dendron self-assembly significantly enhances DNA binding as monitored by a range of experimental methods and confirmed by multiscale modeling. Cellular uptake studies indicate that some of these dendrons are highly effective at transporting DNA into cells (ca. 10 times better than poly(ethyleneimine), PEI). However, levels of transgene expression are relatively low (ca. 10% of PEI). This indicates that these dendrons cannot navigate all of the intracellular barriers to gene delivery. The addition of chloroquine indicates that endosomal escape is not the limiting factor in this case, and it is shown, both experimentally and theoretically, that gene delivery can be correlated with the ability of the dendron assemblies to release DNA. Mass spectrometric assays demonstrate that the dendrons, as intended, do degrade under biologically relevant conditions over a period of hours. Multiscale modeling of degraded dendron structures suggests that complete dendron degradation would be required for DNA release. Importantly, in the presence of the lower pH associated with endosomes, or when bound to DNA, complete degradation of these dendrons becomes ineffective on the transfection time scale-we propose this explains the poor transfection performance of these dendrons. As such, this paper demonstrates that taking this kind of multidisciplinary approach can yield a fundamental insight into the way in which dendrons can navigate barriers to cellular uptake. Lessons learned from this work will inform future dendron design for enhanced gene delivery.
Leukotriene C: a slow-reacting substance from murine mastocytoma cells. (1979)

Murine mastocytoma cells treated with calcium ionophore A23187 produced a slow-reacting substance (SRS) that caused guinea pig ileum to contract. The response was reversed by the SRS antagonist FPL 55712. On the basis of isotope incorporation experiments, spectroscopy, and chemical degradations, the SRS was identified as a cysteine-containing derivative of 5-hydroxy-7,9,11,14-icosatetraenoic acid. This amino acid was attached in thioether linkage at C-6. The SRS is structurally related to previously identified epoxy and dihydroxy metabolites of arachidonic acid in leukocytes. A common feature is the presence of a conjugated triene, and the name "leukotriene" has been introduced to designate these compounds. Leukotriene A (5,6-epoxy-7,9,11,14-icosatetraenoic acid) is an intermediate in the formation of leukotriene B (5,12-dihydroxy-6,8,10,14-icosatetraenoic acid) and is proposed to be a precursor also of leukotriene C, which is the SRS identified here.
Flexible ligand docking using conformational ensembles (1998)

Molecular docking algorithms suggest possible structures for molecular complexes. They are used to model biological function and to discover potential ligands. A present challenge for docking algorithms is the treatment of molecular flexibility. Here, the rigid body program, DOCK, is modified to allow it to rapidly fit multiple conformations of ligands. Conformations of a given molecule are pre-calculated in the same frame of reference, so that each conformer shares a common rigid fragment with all other conformations. The ligand conformers are then docked together, as an ensemble, into a receptor binding site. This takes advantage of the redundancy present in differing conformers of the same molecule. The algorithm was tested using three organic ligand protein systems and two protein-protein systems. Both the bound and unbound conformations of the receptors were used. The ligand ensemble method found conformations that resembled those determined in X-ray crystal structures (RMS values typically less than 1.5 A). To test the method's usefulness for inhibitor discovery, multi-compound and multi-conformer databases were screened for compounds known to bind to dihydrofolate reductase and compounds known to bind to thymidylate synthase. In both cases, known inhibitors and substrates were identified in conformations resembling those observed experimentally. The ligand ensemble method was 100-fold faster than docking a single conformation at a time and was able to screen a database of over 34 million conformations from 117,000 molecules in one to four CPU days on a workstation.
Serology of Chlamydia in Relation to Asthma and Bronchial Hyperresponsiveness (1996)

Antibodies to the 3 strains of chlamydia were measured in the sera of 197 subjects; 122 with asthma-related symptoms and 75 from the general population. The subjects underwent a structured interview, spirometry, a methacholine provocation test and skin-prick tests. For chlamydia antibodies, IgG titer values of > or = 1:512 and/or IgM > or = 1:16 were regarded as evidence of a current or recent infection while IgG levels < 1:512 and > 1:32 were regarded as indicative of a previous infection. For Chlamydia pneumoniae, a relationship was found between current or recent infection and wheezing (odds ratio (OR) 6.0, confidence intervals (CI) 1.3-28) and also between IgA antibodies and bronchial hyperresponsiveness (BHR) (OR 3.3, CI 1.3-8.3). For Chlamydia trachomatis, serological signs of a previous infection were found significantly more often in subjects who reported having had asthma at some time: (OR 3.2, CI 1.4-7.1), asthma during the last year (OR 3.2, CI 1.4-7.1), wheezing during the last year (OR 4.2, CI 1.6-6.6) and in those who had BHR (OR 2.7, CI 1.2-6.1). We conclude that a relationship may exist between Chlamydia pneumoniae and Chlamydia trachomatis infections and asthma-related symptoms and BHR.
Transmembrane Movement of Exogenous Long-Chain Fatty Acids: Proteins, Enzymes, and Vectorial Esterification (2003)

The processes that govern the regulated transport of long-chain fatty acids across the plasma membrane are quite distinct compared to counterparts involved in the transport of hydrophilic solutes such as sugars and amino acids. These differences stem from the unique physical and chemical properties of long-chain fatty acids. To date, several distinct classes of proteins have been shown to participate in the transport of exogenous long-chain fatty acids across the membrane. More recent work is consistent with the hypothesis that in addition to the role played by proteins in this process, there is a diffusional component which must also be considered. Central to the development of this hypothesis are the appropriate experimental systems, which can be manipulated using the tools of molecular genetics. Escherichia coli and Saccharomyces cerevisiae are ideally suited as model systems to study this process in that both (i) exhibit saturable long-chain fatty acid transport at low ligand concentrations, (ii) have specific membrane-bound and membrane-associated proteins that are components of the transport apparatus, and (iii) can be easily manipulated using the tools of molecular genetics. In both systems, central players in the process of fatty acid transport are fatty acid transport proteins (FadL or Fat1p) and fatty acyl coenzyme A (CoA) synthetase (FACS; fatty acid CoA ligase [AMP forming] [EC 6.2.1.3]). FACS appears to function in concert with FadL (bacteria) or Fat1p (yeast) in the conversion of the free fatty acid to CoA thioesters concomitant with transport, thereby rendering this process unidirectional. This process of trapping transported fatty acids represents one fundamental mechanism operational in the transport of exogenous fatty acids.
The prevalence and characteristics of migraine in a population-based cohort (1999)

The prevalence of migraine is higher then previously reported. The coexistence of migraine with and without aura occurs frequently and has implications for future studies on the genetics of migraine.
Outer membrane protein B1, an iron-repressible protein conserved in the outer membrane of Moraxella (Branhamella) catarrhalis, binds human transferrin (1996)

Moraxella (Branhamella) catarrhalis is a gram-negative human mucosal pathogen, which primarily causes otitis media in young children. However, this bacterium is also a common cause of lower respiratory tract infections in adults with underlying lung disease. Our previous data have shown that M. catarrhalis expresses iron-repressible outer membrane proteins in response to iron limitation. We have extended these observations to demonstrate that one of these proteins, termed outer membrane protein (OMP) B1, binds human transferrin. Using a newly developed monoclonal antibody to OMP B1, we determined that this protein is conserved in the iron-stressed outer membranes of all clinical isolates of M. catarrhalis tested to date. Furthermore, our data have confirmed that children infected with M. catarrhalis have immunoglobulin G antibodies to OMP B1 in their convalescent sera. These current data suggest that OMP B1 is immunogenic and expressed in vivo and may be involved in an iron uptake mechanism utilized by M. catarrhalis.
Self-biased high-bandwidth low-jitter 1-to-4096 multiplier clock generator PLL (2003)

A self-biased phase-locked loop (PLL) uses a sampled feedforward filter network and a multistage inverse-linear programmable current mirror for constant loop dynamics that scale with reference frequency and are independent of multiplication factor, output frequency, process, voltage, and temperature. The PLL achieves a multiplication range of 1-4096 with less than 1.7% output jitter. Fabricated in 0.13-μm CMOS, the area is 0.182mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and the supply is 1.5 V.
Direct Sequence Data from Heterogeneous Creatine Kinase (43 kDa) by High-Resolution Tandem Mass Spectrometry (1995)

Isoelectric focusing separation of recombinant rabbit muscle creatine kinase (CK) and its 282Cys-->282Ser mutant shows the presence of three and two isoforms, respectively, that exhibit equivalent enzymatic activity. Electrospray ionization coupled with Fourier-transform mass spectrometry (10(5) resolving power) of both CKs indicates that their major components are within +/- 2 Da of the M(r) value predicted from the cDNA sequences of these mixtures. Dissociation of (M + nH)n+ gives no evidence that the components of either CK are isomers; the masses of the 51 fragment ions correlate completely (+/- 1 Da) with the values predicted from the cDNA sequence and confirm the identities of 21 of the 380 amino acids and the 282Cys-->282Ser replacement in the mutant. The results are consistent with one or two steps of post-translational amidation/deamidation (NH2-->OH, 16 Da-->17 Da), each of which would produce only a 1 Da difference in M(r), with the fragment masses indicating that at least one modification occurs between residues 212 and 282.
Relaxin, a Pregnancy Hormone, Is a Functional Endothelin-1 Antagonist (2003)

We have recently demonstrated that relaxin (RLX) acts as compensatory mediator in human heart failure. RLX inhibits the stimulation of endothelin-1, the most potent vasoconstrictor in heart failure. Upregulation of the endothelin type-B receptor (ET(B)), which mediates endothelin-1 clearance and endothelial release of NO, represents a pivotal mode of RLX action. However, signal transduction and abundance of this phenomenon are unknown. Therefore, we investigated RLX-induced regulation of ET(B) in human umbilical vein endothelial, epithelial (HeLa), and vascular smooth muscle cells. In human umbilical vein endothelial cells and HeLa cells, but not in human vascular smooth muscle cells, RLX upregulated ET(B) expression and activated extracellular signal-regulated kinase-1/2 (ERK-1/2) and nuclear factor-kappaB (NF-kappaB), a transcription factor. PD-98059, a selective inhibitor of the mitogen-activated protein kinase kinase-1 (MEK-1)-ERK-1/2 pathway, abolished ERK-1/2 and NF-kappaB activation and ET(B) upregulation. NF-kappaB inhibition also prevented RLX-mediated ET(B) stimulation. In NF-kappaB-luciferase reporter assays, we demonstrated complete inhibition of RLX-induced NF-kappaB activation in cells transfected with dominant-negative Raf-1, MEK-1, or ERK-1/2 constructs, whereas dominant-negative Ras had no effect. In rat aorta and mesenteric artery, RLX pretreatment, in an ET(B)-dependent fashion, mitigated the maximum contractile response to endothelin-1, by 38+/-4% and 43+/-6%, and the endothelin-1 sensitivity (-log[EC(50)]: aorta, 8.2+/-0.2 for vehicle versus 7.2+/-0.2 for RLX; mesenteric artery, 8.0+/-0.2 for vehicle versus 7.1+/-0.1 for RLX). RLX pretreatment augmented the dilator effect of the ET(B) agonist endothelin-3 by 100+/-8% and 133+/-13%. In conclusion, RLX stimulates endothelial and epithelial ET(B) via a Ras-independent Raf-1-MEK-1-ERK-1/2 pathway that activates NF-kappaB. On vascular smooth muscle cells, ET(B), a contributor to endothelin-mediated vasoconstriction, remains unaffected. This renders RLX a functional endothelin-1 antagonist.
Release of platelet-activating factor (PAF) and accelerated healing induced by a PAF antagonist in an animal model of chronic colitis (1988)

The role of platelet-activating factor as a mediator of inflammation was examined using a rat model of colitis. Release of platelet-activating factor by samples of colonic tissue, as measured by bioassay, was determined at various times after induction of inflammation by intracolonic administration of trinitrobenzene sulfonic acid. At the same times, colonic damage was scored and the extent of neutrophil infiltration was assessed by measuring tissue levels of myeloperoxidase activity. Platelet-activating factor release from normal colon averaged 46 +/- 17 pg/g, while not being detectable in samples taken 24 h after induction of inflammation, a time when neutrophil infiltration was maximal. However, substantial release of platelet-activating factor (12-16 times control levels; p less than 0.05) was observed in samples from rats sacrificed 1-3 weeks after induction of inflammation. In a second series of experiments, the effects of treatment with BN52021, a specific platelet-activating factor receptor antagonist, were assessed using this model. Treatment with BN52021 during either the 1st or 2nd weeks after induction of colitis resulted in significant (p less than 0.05) reductions of colonic damage scores and the wet weight of the distal colon. These results demonstrate that platelet-activating factor release is significantly elevated during the chronic phase of colitis in this animal model, and that inhibition of the action of platelet-activating factor, through receptor antagonism, leads to a significant reduction of colonic inflammation and ulceration. These observations are therefore consistent with a role for platelet-activating factor as an inflammatory mediator in chronic inflammation of the rat colon.
Quantitative analysis of vascular endothelial growth factor in primary breast cancer (1996)

The quantitation of intratumoral VFGF levels seems to be useful for assessing the activity of tumor angiogenesis.
Amino Acids and Peptides; XLIII1. Dehydroamino Acids; XVIII2. Synthesis of Dehydroamino Acids and Amino Acids fromN-Acyl-2-(dialkyloxyphosphinyl)-glycin Esters; II (1984)

Synthese de deshydroaminoacides (I) et deshydropeptides (II) par condensation d'aldehydes avec des N-acyl- et N-alcoxycarbonyl-dialcoxyphosphoryl glycinates de methyle. Hydrogenation enantioselective de (I) et (II)
Biotin-responsive basal ganglia disease-linked mutations inhibit thiamine transport via hTHTR2: biotin is not a substrate for hTHTR2 (2006)

The water-soluble micronutrient thiamine is required for normal tissue growth and development in humans. Thiamine is accumulated into cells through the activity of two cell surface thiamine transporters (hTHTR1 and hTHTR2), which are differentially targeted in polarized tissues. Mutational dysfunction of hTHTR1 is associated with the clinical condition of thiamine-responsive megaloblastic anemia: the symptoms of which are alleviated by thiamine supplementation. Recently, two hTHTR2 mutants (G23V, T422A) have been discovered in clinical kindreds manifesting biotin-responsive basal ganglia disease (BBGD): the symptoms of which are alleviated by biotin administration. Why then does mutation of a specific thiamine transporter isoform precipitate a disorder correctable by exogenous biotin? To investigate the suggestion that hTHTR2 can physiologically function as a biotin transporter, we examined 1) the cell biological basis of hTHTR2 dysfunction associated with the G23V and T422A mutations and 2) the substrate specificity of hTHTR2 and these clinically relevant mutants. We show that the G23V and T422A mutants both abrogate thiamine transport activity rather than targeting of hTHTR2 to the cell surface. Furthermore, biotin accumulation was not detectable in cells overexpressing either the full length hTHTR2 or the clinically relevant hTHTR2 mutants, yet was demonstrable in the same assay using cells overexpressing the human sodium-dependent multivitamin transporter, a known biotin transporter. These results cast doubt on the most parsimonious explanation for the BBGD phenotype, namely that hTHTR2 is a physiological biotin transporter.
Differentiation of [3H]phencyclidine and ( + )‐[3H]SKF‐10,047 binding sites in rat cerebral cortex (1985)

The potency of a series of opioid and non-opioid psychotomimetic drugs to inhibit the specific binding of [3H]PCP and (+)-[3H]SKF-10,047 to rat cerebral cortical membranes was examined. (+)-PCMP, the 3-methylpiperidino analog of PCP, was a potent inhibitor of the specific binding of both ligands. All of the other 12 compounds examined, however, displayed a 3-277-fold selectivity for either [3H]PCP or (+)-[3H]SKF-10,047 binding. These results suggest that although these opioid and non-opioid psychotomimetics bind to both sites, most have significantly different affinities. The binding sites for [3H]PCP appear to be distinct from the 'sigma' binding sites labeled with (+)-[3H]SKF-10,047.
Electric field effects in hyperexcitable neural tissue: A review (2003)

Uniform electric fields applied to neural tissue can modulate neuronal excitability with a threshold value of about 1 mV mm(-1) in normal physiological conditions. However, electric fields could have a lower threshold in conditions where field sensitivity is enhanced, such as those simulating epilepsy. Uniform electrical fields were applied to hippocampal brain slices exposed to picrotoxin, high potassium or low calcium solutions. The results in the low calcium medium show that neuronal activity can be completely blocked in 10% of the 30 slices tested with a field amplitude of 1 mV mm(-1). These results suggest that the threshold for this effect is clearly smaller than 1 mV mm(-1). The hypothesis that the extracellular resistance could affect the sensitivity to the electrical fields was tested by measuring the effect of the osmolarity of the extracellular solution on the efficacy of the field. A 10% decrease in osmolarity resulted in a 56% decrease (n = 4) in the minimum field required for full suppression. A 14% in osmolarity produced an 81% increase in the minimum field required for full suppression. These results show that the extracellular volume can modulate the efficacy of the field and could lower the threshold field amplitudes to values lower than approximately 1 mmV mm(-1).