gebhart/patrepeval huggingface dataset:
Atypical phenylketonuria due to biopterin deficiency. Early treatment with tetrahydrobiopterin and neurotransmitter precursors, trials of monotherapy. (1982)

This report presents the first case where an infant with tetrahydrobiopterin deficiency has been identified by screening of newborns with hyperphenylalaninemia for tetrahydrobiopterin deficiency. Therapy with L-Dopa, 5-hydroxytryptophan, Carbidopa and tetrahydrobiopterin was started at the age of seven weeks while the child received a normal diet. At that time already muscular hypotonia was observed. The girl, now 2 1/2 years old, shows slight muscular hypotonia and hypomotility, short periods of hypertonic extension of the limbs, and retardation of sensomotor and mental development of about 6-8 months. Monotherapy with tetrahydrobiopterin dihydrochloride, 20-40 mg/kg b.w., diminished the muscular hypotonia. The effect lasted however for only about 1 day. While urinary serotonin and phenylalanine remained normal for at least 3 days and neopterin was only slightly elevated, urinary free dopamine however remained low. Similar results were obtained after 1',2'-diacetyl tetrahydrobiopterin dihydrochloride administration, 20 mg/kg b.w.
Tyrosine kinase inhibitor STI571 potentiates the pharmacologic activity of retinoic acid in acute promyelocytic leukemia cells: effects on the degradation of RARα and PML-RARα (2001)

Abstract The 2-phenylaminopyrimidine derivative STI571 is a selective inhibitor of c-Abl, c-kit, and platelet-derived growth factor–receptor tyrosine kinases and is presently in phase II-III clinical studies. Here, this study reports on a novel pharmacologic activity of the compound, ie, enhancement of the cyto-differentiating, growth-inhibitory, and apoptogenic actions of all-trans-retinoic acid (ATRA). Whereas STI571 is not a cytodifferentiating agent by itself, the compound interacts with ATRA and enhances the myeloid maturation program set in motion by the retinoid in the PML-RARα+ acute promyelocytic leukemia NB4 and the PML-RARα− myeloblastic HL60 and U937 cell lines. In addition, STI571 relieves the cyto-differentiation block observed in the ATRA-resistant cell lines, NB4.R1, NB4.306, and NB4.007. In NB4 promyelocytes, a RARα agonist, but not an RXR agonist, can substitute for ATRA and interact with STI571. By contrast, STI571 is unique among c-Abl–specific tyrosine kinase inhibitors in modulating the pharmacologic activity of ATRA. In NB4 cells, enhanced cyto-differentiation results in increased up-regulation of the expression of a number of genes coding for myeloid differentiation markers, including CD11b, CD11c, and some of the components of the nicotinamide adenine dinucleotide phosphate–oxidase enzymatic complex. All this is accompanied by inhibition of c-Abl tyrosine phosphorylation and retardation of the retinoid-dependent degradation of PML-RARα and RARα. Stabilization of the 2 retinoic acid receptors is likely to be the result of augmented and accelerated inhibition of the proteasome-dependent proteolytic activity observed on ATRA treatment.
Bacterial Adherence: Adhesin-Receptor Interactions Mediating the Attachment of Bacteria to Mucosal Surfaces (1981)

Recent studies have indicated that the attachment of bacteria to mucosal surfaces is the initial event in the pathogenesis of most infectious diseases due to bacteria in animals and humans. An understanding of the mechanisms of attachment and a definition of the adhesive molecules on the surfaces of bacteria (adhesins) as well as those on host cell membranes (receptors) have suggested new approaches to the prevention of serious bacterial infections: (1) application of purified adhesion or receptor materials or their analogues as competitive inhibitors of bacterial adherence; (2) administration of sublethal concentrations of antibiotics that suppress the formation and expression of bacterial adhesins; and (3) development of vaccines against bacterial surface components involved in adhesion to mucosal surfaces. Progress has already been made in the development of antiadhesive vaccines directed against the fimbrial adhesins of several human bacterial pathogens.
A survey of the genetics of stomach, liver, and adipose gene expression from a morbidly obese cohort (2011)

To map the genetics of gene expression in metabolically relevant tissues and investigate the diversity of expression SNPs (eSNPs) in multiple tissues from the same individual, we collected four tissues from approximately 1000 patients undergoing Roux-en-Y gastric bypass (RYGB) and clinical traits associated with their weight loss and co-morbidities. We then performed high-throughput genotyping and gene expression profiling and carried out a genome-wide association analyses for more than 100,000 gene expression traits representing four metabolically relevant tissues: liver, omental adipose, subcutaneous adipose, and stomach. We successfully identified 24,531 eSNPs corresponding to about 10,000 distinct genes. This represents the greatest number of eSNPs identified to our knowledge by any study to date and the first study to identify eSNPs from stomach tissue. We then demonstrate how these eSNPs provide a high-quality disease map for each tissue in morbidly obese patients to not only inform genetic associations identified in this cohort, but in previously published genome-wide association studies as well. These data can aid in elucidating the key networks associated with morbid obesity, response to RYGB, and disease as a whole.
Sequence independent interferon‐α induction by multimerized phosphodiester DNA depends on spatial regulation of Toll‐like receptor‐9 activation in plasmacytoid dendritic cells (2008)

Single-stranded versus multimeric phosphorothioate-modified CpG oligodeoxynucleotides (ODNs) undergo differential endosomal trafficking upon uptake into plasmacytoid dendritic cells (pDCs), correlating with Toll-like receptor-9-dependent pDC maturation/activation (single-stranded B-type CpG ODN) or interferon-alpha (IFN-alpha) induction (multimeric A-type CpG ODN), respectively. As was recently shown, IFN-alpha production, other than by CpG ODNs, can also be induced in a sequence-independent manner by phosphodiester (PD) ODNs multimerized by 3' poly-guanosine (poly-G) tails. We investigate here the type of endosomal trafficking responsible for IFN-alpha induction by natural PD ODN ligands. We show that 3' extension with poly-G tails leads to multimerization of single-stranded PD ODNs and to enhanced cellular uptake into pDCs. While monomeric PD ODNs, which induce CpG-dependent Toll-like receptor-9 stimulation and pDC maturation/activation, localized to late endosomal/lysosomal compartments, the poly-G multimerized PD ODNs, which induce CpG-independent IFN-alpha production, located to vesicles with a distinct, 'early' endosomal phenotype. We conclude that poly-G-mediated multimerization of natural PD ODNs allows for sequence-independent, Toll-like receptor-9-dependent IFN-alpha induction in pDCs by combining three distinct effects: relative protection of sensitive PD ODNs from extracellular and intracellular DNase degradation, enhanced cellular uptake and preferential early endosomal compartmentation.
Loss of the Malignant Phenotype of Human Neuroblastoma Cells by a Catalytically Inactive Dominant-Negative hTERT Mutant (2012)

Telomerase, a ribonucleoprotein complex mainly composed of the reverse transcriptase catalytic subunit (human telomerase reverse transcriptase, hTERT) and the RNA component (hTR), is a key enzyme of cancer progression. That aggressive stage 4-neuroblastoma expressed high levels of telomerase activity, whereas favorable tumors had no or little telomerase expression and activity, prompted us to investigate the role of this enzyme in this tumor model of altered proliferation, neuronal differentiation, and apoptosis. A human MYCN-amplified neuroblastoma cell line (IGR-N-91) was engineered to stably express either the normal hTERT protein (WT-hTERT) or a catalytically inactive dominant-negative mutant of this protein (DN-hTERT). We showed that DN-hTERT expression inhibited the endogenous hTERT in the malignant neuroblasts without telomere shortening nor loss of in vitro proliferative capacity. Importantly, DN-hTERT expression induced major changes in cell morphology of neuroblasts that switched them from a neuronal to a substrate adherent phenotype, which was more prone to apoptosis and lost their tumorigenic properties in nude mice. These biologic effects arose from modifications in the expression of genes involved in both apoptosis and neuroblastoma biology. Taken together these results highlighted the functional relevance of noncanonical functions of hTERT in the determination of neuroblast cell fate. Therefore, our results envision new therapeutic strategies for metastatic neuroblastoma therapeutic management.
MRI detection of glycogen in vivo by using chemical exchange saturation transfer imaging (glycoCEST) (2007)

Detection of glycogen in vivo would have utility in the study of normal physiology and many disorders. Presently, the only magnetic resonance (MR) method available to study glycogen metabolism in vivo is (13)C MR spectroscopy, but this technology is not routinely available on standard clinical scanners. Here, we show that glycogen can be detected indirectly through the water signal by using selective radio frequency (RF) saturation of the hydroxyl protons in the 0.5- to 1.5-ppm frequency range downfield from water. The resulting saturated spins are rapidly transferred to water protons via chemical exchange, leading to partial saturation of the water signal, a process now known as chemical exchange saturation transfer. This effect is demonstrated in glycogen phantoms at magnetic field strengths of 4.7 and 9.4 T, showing improved detection at higher field in adherence with MR exchange theory. Difference images obtained during RF irradiation at 1.0 ppm upfield and downfield of the water signal showed that glycogen metabolism could be followed in isolated, perfused mouse livers at 4.7 T before and after administration of glucagon. Glycogen breakdown was confirmed by measuring effluent glucose and, in separate experiments, by (13)C NMR spectroscopy. This approach opens the way to image the distribution of tissue glycogen in vivo and to monitor its metabolism rapidly and noninvasively with MRI.
A study on the human mitochondrial RNA polymerase activity points to existence of a transcription factor B‐like protein (2001)

In the present work, the RNA polymerase activity of the human mitochondrial RNA polymerase mature protein (h-mtRPOLm) is shown, and its molecular activity calculated (2.1+/-0.9 min(-1)). An activity analysis of h-mtRPOLm and deleted versions of it has demonstrated that the entire recombinant protein is required for this activity. In addition, h-mtRPOLm alone or in presence of the known mitochondrial transcription factors (human mitochondrial transcription factor A and/or human mitochondrial transcription termination factor) is not able to initiate transcription from the specific human mitochondrial promoters pointing to the existence of a human mitochondrial transcription factor B-like protein.
Functional brain abnormalities in young adults at genetic risk for late-onset Alzheimer's dementia (2003)

Fluorodeoxyglucose positron emission tomography (PET) studies have found that patients with Alzheimer's dementia (AD) have abnormally low rates of cerebral glucose metabolism in posterior cingulate, parietal, temporal, and prefrontal cortex. We previously found that cognitively normal, late-middle-aged carriers of the apolipoprotein E epsilon4 allele, a common susceptibility gene for late-onset Alzheimer's dementia, have abnormally low rates of glucose metabolism in the same brain regions as patients with probable AD. We now consider whether epsilon4 carriers have these regional brain abnormalities as relatively young adults. Apolipoprotein E genotypes were established in normal volunteers 20-39 years of age. Clinical ratings, neuropsychological tests, magnetic resonance imaging, and PET were performed in 12 epsilon4 heterozygotes, all with the epsilon3/epsilon4 genotype, and 15 noncarriers of the epsilon4 allele, 12 of whom were individually matched for sex, age, and educational level. An automated algorithm was used to generate an aggregate surface-projection map that compared regional PET measurements in the two groups. The young adult epsilon4 carriers and noncarriers did not differ significantly in their sex, age, educational level, clinical ratings, or neuropsychological test scores. Like previously studied patients with probable AD and late-middle-aged epsilon4 carriers, the young epsilon4 carriers had abnormally low rates of glucose metabolism bilaterally in the posterior cingulate, parietal, temporal, and prefrontal cortex. Carriers of a common Alzheimer's susceptibility gene have functional brain abnormalities in young adulthood, several decades before the possible onset of dementia.
DRPM: dynamic speed control for power management in server class disks (2004)

A large portion of the power budget in server environments goes into the I/O subsystem - the disk array in particular. Traditional approaches to disk power management involve completely stopping the disk rotation, which can take a considerable amount of time, making them less useful in cases where idle times between disk requests may not be long enough to outweigh the overheads. We present a new approach called DRPM to modulate disk speed (RPM) dynamically, and gives a practical implementation to exploit this mechanism. Extensive simulations with different workload and hardware parameters show that DRPM can provide significant energy savings without compromising much on performance. We also discuss practical issues when implementing DRPM on server disks.
Distinct Exocytotic Responses of Intact and Permeabilised Chromaffin Cells After Cleavage of the 25‐kDa Synaptosomal‐Associated Protein (SNAP‐25) or Synaptobrevin by Botulinum Toxin A or B (1996)

Botulinum neurotoxin (BoNT) types A and B are Zn2+-requiring endoproteases which potently block neurotransmitter release by cleavage of a 25-kDa synaptosomal-associated protein (SNAP-25) and synaptobrevin, respectively. Synaptobrevin is important for the exocystosis of catecholamines from dense-core granules and evidence is presented here for the involvement of SNAP-25 in this process in neuroendocrine cells. The effects of BoNT/A and BoNT/B on regulated secretion were compared in intact bovine chromaffin cells to investigate the consequences of cleavage of the different targets. Catecholamine secretion elicited by Ba2+, by elevated K+ concentrations or by nicotine was prevented by each toxin. A very good correlation was observed between the extents of SNAP-25 cleavage or synaptobrevin cleavage and inhibition of secretion by BoNT/A or BoNT/B, respectively, which indicates the importance of SNAP-25 and synaptobrevin in regulated exocytosis. Despite truncation of almost the entire SNAP-25 pool by exposure of the cells to BoNT/A, a residual fraction of secretion persisted that was induced by 20microM Ca2+ (and to a lesser extent by 1 mM Ba2+) following permeabilisation. Addition of more BoNT/A failed to reduce this level of secretion. Inclusion of Mg.ATP, which greatly enhanced secretion from permeabilised cells, was required for Ca2+-stimulated or Ba2+-stimulated BoNT/A-resistant secretion. Furthermore, synaptobrevin is essential for this response because the response was not observed in BoNT/B treated cells. In view of the ability of BoNT/E to abolish secretion from permeabilised cells and to delete 26 amino acids from the C-terminus of SNAP-25, it can be deduced that cleavage of only nine residues by BoNT/A does not prevent the resultant truncated form exhibiting attenuated activity under the conditions created by permeabilisation. This identification of a novel component of secretion from permeabilised cells should facilitate investigation of the functional interaction of SNAP-25 with other proteins involved in regulated exocytosis.
Persistent Systemic Production of Human Factor IX in Mice by Skeletal Myoblast-Mediated Gene Transfer: Feasibility of Repeat Application to Obtain Therapeutic Levels (1997)

Abstract Myoblast-mediated gene transfer and its repeated applications were tested for achieving a long-term stable systemic production of human factor IX (hFIX) at a therapeutic level in SCID mice. Primary skeletal myoblasts were stably transfected with a hFIX expression plasmid vector, pdLMe4βAhIXm1, which contains a hFIX minigene under the control of a β-actin promoter with muscle creatine kinase enhancers. Myotubes derived from the myoblasts produced 1,750 ng hFIX/106 cells/24 hours in culture. hFIX secretion by the myoblasts and thereof derived myotubes were equally efficient, and myotubes were shown to have a sufficient secretory capacity to handle a substantially elevated production of hFIX. After intramuscular injection of 5, 10, and 20 × 106 myoblasts, SCID mice stably produced hFIX into the systemic circulation proportional to the number of implanted cells, and the expression levels were maintained for at least up to 10 months (end of the experiment). Additional cell injections administered to animals that originally received 10 × 106 cells approximately 2 months later elevated the systemic hFIX levels to an average of 182 ± 21 ng/mL, a therapeutic level, which persisted for at least 8 months (end of the experiment). These results indicate that long-term, stable systemic production of hFIX at therapeutic levels can be achieved by repeated application of myoblast-mediated gene transfer.
Manganese Superoxide Dismutase (Sod2) and Redox-Control of Signaling Events That Drive Metastasis (2011)

Manganese superoxide dismutase (Sod2) has emerged as a key enzyme with a dual role in tumorigenic progression. Early studies were primarily directed at defining the tumor suppressive function of Sod2 based on its low level expression in many tumor types. It is now commonly held that loss of Sod2 expression is likely an early event in tumor progression allowing for further propagation of the tumorigenic phenotype resulting from steady state increases in free radical production. Increases in free radical load have also been linked to defects in mitochondrial function and metastatic disease progression. It was initially believed that Sod2 loss may propagate metastatic disease progression, in reality both epidemiologic and experimental evidence indicate that Sod2 levels increase in many tumor types as they progress from early stage non-invasive disease to late stage metastatic disease. Sod2 overexpression in many instances enhances the metastatic phenotype that is reversed by efficient H(2)O(2) scavenging. This review evaluates the many sequelae associated with increases in Sod2 that impinge on the metastatic phenotype. The ability to use Sod2 to modulate the cellular redox-environment has allowed for the identification of redox-responsive signaling events that drive malignancy, such as invasion, migration and prolonged tumor cell survival. Further studies of these redox-driven events will help in the development of targeted therapeutic strategies to efficiently restrict redox-signaling essential for malignant progression.
Steroid Hormones: A Practical Approach (1989)

Section I: Introduction and metabolism Section II: Sampling and extraction Section III: Physio-chemical methods Section IV: Pharmacological and immunoassays Section V: Enzymology and lipid peroxidation Section VI: Related techniques Appendix: Eicosanoids: structure, availability, storage and stability Abbreviations Introduction to the eicosanoids Metabolism of prostaglandins and lipoxygenase products: relevance for eicosanoid assay Tissue sampling and preparation Extraction of eicosanoids from biological samples Thin-layer chromatography (including radio thin-layer chromatography and autoradiography of prostaglandins and related compounds High pressure liquid chromatography in the analysis of arachidonic acid metabolites Gas chromatography and mass spectrometry of eicosanoids Measurement of prostaglandins, thromboxanes and leukotrienes by smooth muscle bioassay Aggregometry techniques for prostanoid study and evaluation Radioimmunoassay of eicosanoids Enzyme immunoassay Cyclo-oxygenases: measurement, purification and properties Lipoxygenases: measurement, characterization and properties Lipid peroxidation Quantitative measurement of arachidonic acid in tissues or fluids Methods in prostanoid receptor classification Paf-acether (platelet-activating factor) Appendix Index
Mechanism of the cardioprotective effect of transforming growth factor beta 1 in feline myocardial ischemia and reperfusion. (1993)

We studied the effects of transforming growth factor beta 1 (TGF-beta 1) in a feline model of myocardial ischemia (1.5 hr) and reperfusion (4.5 hr). Myocardial ischemia followed by reperfusion resulted in severe myocardial injury, endothelial dysfunction, high cardiac myeloperoxidase activity indicative of neutrophil accumulation in the ischemic myocardium, and significant neutrophil adherence to the ischemic coronary endothelium. In contrast, intravenous administration of TGF-beta 1 (20 micrograms/kg) 30 min prior to reperfusion significantly attenuated myocardial necrosis (13.8% +/- 3.5% vs. 32.2% +/- 2.9% of area-at-risk, P < 0.01) and attenuated endothelial dysfunction (P < 0.01) associated with ischemia-reperfusion. Moreover, myeloperoxidase activity in the ischemic myocardium was significantly lower than vehicle controls (0.2 +/- 0.1 vs. 1.7 +/- 0.3 units/100 mg of tissue, P < 0.01) and neutrophil adherence to ischemic coronary endothelium was significantly (P < 0.01) attenuated in TGF-beta 1-treated cats. These results demonstrate that TGF-beta 1 exerts a significant cardioprotective effect in a feline model of myocardial ischemia and reperfusion. The mechanism of this protective effect appears to relate to endothelial preservation by TGF-beta 1 inhibiting circulating neutrophils from adhering to the endothelium, a critical step in neutrophil-induced reperfusion injury.
Non-Abelian anyons and topological quantum computation (2008)

Topological quantum computation has emerged as one of the most exciting approaches to constructing a fault-tolerant quantum computer. The proposal relies on the existence of topological states of matter whose quasiparticle excitations are neither bosons nor fermions, but are particles known as non-Abelian anyons, meaning that they obey non-Abelian braiding statistics. Quantum information is stored in states with multiple quasiparticles, which have a topological degeneracy. The unitary gate operations that are necessary for quantum computation are carried out by braiding quasiparticles and then measuring the multiquasiparticle states. The fault tolerance of a topological quantum computer arises from the nonlocal encoding of the quasiparticle states, which makes them immune to errors caused by local perturbations. To date, the only such topological states thought to have been found in nature are fractional quantum Hall states, most prominently the $\ensuremath{\nu}=5∕2$ state, although several other prospective candidates have been proposed in systems as disparate as ultracold atoms in optical lattices and thin-film superconductors. In this review article, current research in this field is described, focusing on the general theoretical concepts of non-Abelian statistics as it relates to topological quantum computation, on understanding non-Abelian quantum Hall states, on proposed experiments to detect non-Abelian anyons, and on proposed architectures for a topological quantum computer. Both the mathematical underpinnings of topological quantum computation and the physics of the subject are addressed, using the $\ensuremath{\nu}=5∕2$ fractional quantum Hall state as the archetype of a non-Abelian topological state enabling fault-tolerant quantum computation.