gebhart/patrepeval huggingface dataset:
Therapeutic prospects for spinocerebellar ataxia type 2 and 3 (2009)

Spinocerebellar ataxia type 2 (SCA2) and type 3 (SCA3) are autosomal-dominant neurodegenerative disorders. SCA2 primarily affects cerebellar Purkinje neurons. SCA3 primarily affects dentate and pontine nuclei and substantia nigra. Both disorders belong to a class of polyglutamine (polyQ) expansion disorders. SCA2 is caused by a polyQ expansion in the amino-terminal region of a cytosolic protein ataxin-2 (Atxn2). SCA3 is caused by a polyQ expansion in the carboxy-terminal portion of a cytosolic protein ataxin-3 (Atxn3). Both disorders are found worldwide, but SCA2 is common among people of Cuban decent and SCA3 is common among people of Portuguese decent. No effective treatment exist for SCA2, SCA3 or any other polyQ-expansion disorder. Based on anecdotal evidence, a number of small scale clinical trials have been attempted previously for SCA2 and SCA3. These trials were underpowered and did not yield any promising results so far. A number of pathogenic mechanisms have been proposed to explain neuronal dysfunction and degeneration in SCA2 and SCA3. Knockdown of mutant Atxn2 and Atxn3 protein by RNAi or similar approach is most promising avenue of therapeutic development in the long term, but translation of this approach to clinic faces very serious technical challenges. Recent preclinical studies in SCA2 and SCA3 genetic mouse model suggested that abnormal neuronal calcium (Ca<sup>2+</sup>) signaling may play an important role in SCA2 and SCA3 pathology. These studies also suggested that dantrolene and other Ca<sup>2+</sup> signaling inhibitors and stabilizers may have a therapeutic value for treatment of SCA2 and SCA3. Controlled clinical evaluation of dantrolene, memantine, riluzole, dihydropyridines, CoQ10, creatine or other Ca<sup>2+</sup> blockers and stabilizers in SCA2 and SCA3 patients is necessary to test clinical importance of these ideas. The EUROSCA consortium provides a potential framework for such clinical evaluation.
Biosynthesis of terpenoids: YgbB protein converts 4-diphosphocytidyl-2C-methyl- d -erythritol 2-phosphate to 2C-methyl- d -erythritol 2,4-cyclodiphosphate (2000)

In many microorganisms, the putative orthologs of the Escherichia coli ygbB gene are tightly linked or fused to putative orthologs of ygbP, which has been shown earlier to be involved in terpenoid biosynthesis. The ygbB gene of E. coli was expressed in a recombinant E. coli strain and was shown to direct the synthesis of a soluble, 17-kDa polypeptide. The recombinant protein was found to convert 4-diphosphocytidyl-2C-methyl-D-erythritol 2-phosphate into 2C-methyl-D-erythritol 2,4-cyclodiphosphate and CMP. The structure of the reaction product was established by NMR spectroscopy using (13)C-labeled substrate samples. The enzyme-catalyzed reaction requires Mn(2+) or Mg(2+) but no other cofactors. Radioactivity from [2-(14)C]2C-methyl-D-erythritol 2,4-cyclodiphosphate was diverted efficiently to carotenoids by isolated chromoplasts from Capsicum annuum and, thus, was established as an intermediate in the deoxyxylulose phosphate pathway of isoprenoid biosynthesis. YgbB protein also was found to convert 4-diphosphocytidyl-2C-methyl-D-erythritol into 2C-methyl-D-erythritol 3,4-cyclophosphate. This compound does not serve as substrate for the formation of carotenoids by isolated chromoplasts and is assumed to be an in vitro product without metabolic relevance.
Forkhead Transcription Factors Are Critical Effectors of Cell Death and Cell Cycle Arrest Downstream of PTEN (2000)

PTEN acts as a tumor suppressor, at least in part, by antagonizing phosphoinositide 3-kinase (PI3K)/Akt signaling. Here we show that Forkhead transcription factors FKHRL1 and FKHR, substrates of the Akt kinase, are aberrantly localized to the cytoplasm and cannot activate transcription in PTEN-deficient cells. Restoration of PTEN function restores FKHR to the nucleus and restores transcriptional activation. Expression of a constitutively active form of FKHR that cannot be phosphorylated by Akt produces the same effect as reconstitution of PTEN on PTEN-deficient tumor cells. Specifically, activated FKHR induces apoptosis in cells that undergo PTEN-mediated cell death and induces G(1) arrest in cells that undergo PTEN-mediated cell cycle arrest. Furthermore, both PTEN and constitutively active FKHR induce p27(KIP1) protein but not p21. These data suggest that Forkhead transcription factors are critical effectors of PTEN-mediated tumor suppression.
Molecular modelling of a sequence-specific DNA-binding agent based on the pyrrolo[2, 1-c][1,4]benzodiazepines (1999)

The CHARMm force field was used for the first time to model the tricyclic pyrrolobenzodiazepine (PBD) ring system. This system forms the core of the well known sequence-selective DNA-interactive anthramycin-type antitumour antibiotics. The results agreed with previous results obtained using the AMBER and X-PLOR force fields. The simple family member DC-81 preferentially binds in the 5S orientation with S-stereochemistry at the C11 position of the PBD and with the A-ring of the molecule oriented towards the 5′ end of the covalently bound strand. The modelling studies and energetic analyses also support the observation that the molecules have a sequence preference for the purine-guanine-purine motif.
A molecular analysis of NKT cells: identification of a class-I restricted T cell-associated molecule (CRTAM) (2000)

cDNA library subtraction techniques were used to identify transcripts expressed by activated mouse alphabetaTCR+ CD4-CD8- (double-negative; DN) T cells, a subset of natural killer T (NKT) cells. The most frequent cDNAs identified included the chemokines TCA3, macrophage inflammatory protein-1alpha (MIP-1alpha), MIP-1beta, and lymphotactin (LPTN), the cytokines interleukin-4 (IL-4) and interferon-gamma (IFN-gamma), and a granzyme. We also identified a new member of the immunoglobulin superfamily (Ig-SF). This molecule was designated class I-restricted T cell-associated molecule (CRTAM) as a result of its restricted expression pattern in T cells. Human CRTAM was also identified, and shares the same expression pattern as the mouse molecule. LPTN and CRTAM exhibit the same expression pattern in T cells, suggesting the existence of a gene expression program common to class I-MHC-restricted T cells.
CLoning of equine interleukin 1 alpha and equine interleukin 1 beta and determination of their full-length cDNA sequences. (1998)

Results establish a basis for studying the roles of interleukin 1 in healthy and diseased joints in horses.
The Raw microprocessor: a computational fabric for software circuits and general-purpose programs (2002)

Wire delay is emerging as the natural limiter to microprocessor scalability. A new architectural approach could solve this problem, as well as deliver unprecedented performance, energy efficiency and cost effectiveness. The Raw microprocessor research prototype uses a scalable instruction set architecture to attack the emerging wire-delay problem by providing a parallel, software interface to the gate, wire and pin resources of the chip. An architecture that has direct, first-class analogs to all of these physical resources will ultimately let programmers achieve the maximum amount of performance and energy efficiency in the face of wire delay.
Anatomical and physiological properties of ipsilaterally projecting spinothalamic neurons in the second cervical segment of the cat's spinal cord (1978)

Anatomical and electrophysiological methods were used to investigate the projections and response properties of neurons in the second cervical (C2) spinal segment of the cat giving origin to a previously undescribed projection to the ipsilateral thalamus. The method of retrograde axonal transport of horseradish peroxidase (HRP) was used to identify neurons in C2 giving rise to thalamic projections. Following large (3.0 microliter) thalamic HRP injections, a large number of labeled neurons was observed in lateral laminae VII-VIII of C2 ipsilateral to the injections. They occurred as small clusters of cells along the longitudinal axis of C2. Labeled neurons were also observed contralaterally in the lateral cervical nucleus, dorsal horn (especially medial lamina VI), and loosely distributed in the ventral horn. The ipsilaterally projecting neurons were also labeled following small (0.2--0.5 microliter) HRP injections restricted to individual spinothalamic terminal zones (intralaminar nuclei, ventrobasal complex-nucleus ventralis lateralis border zone, medial division of the posterior nuclei), indicating that as a group they project widely throughout the thalamus. Single unit recording methods were used to obtain complementary information on the functional properties of these neurons. The antidromic stimulation method was applied to identify units in C2 projecting to the ipsilateral thalamus in anesthetized, paralyzed cats. Three categories of ipsilaterally projecting C2 units were identified: (1) units not driven by any type of natural stimulation; (2) units having large cutaneous receptive fields (RFs) and wide dynamic response ranges ("widefield"), and (3) units with smaller RFs and varied properties ("other"). Widefield units with bilaterally symmetrical and asymmetrical RFs were observed. Co-stimulation of different portions of an excitatory RF produced summation of the unit response. Inhibitory RF components were identified in one-third of the widefield units. Unit recordings after spinal tract lesions revealed that the afferent input passed via the ipsilateral lateral and/or ventral funiculi. Widefield unit responses to somatosensory stimuli could be inhibited by dorsal column conditioning stimulation. Several "other" units resembled widefield units, while a second group had small RFs restricted to the C2 dermatome. Possible functional roles of the projecting C2 neurons in somatosensory and non-specific systems are discussed.
Macrophage activation induces formation of the anti-inflammatory lipid cholesteryl-nitrolinoleate (2008)

Nitroalkene derivatives of fatty acids act as adaptive, anti-inflammatory signalling mediators, based on their high-affinity PPARgamma (peroxisome-proliferator-activated receptor gamma) ligand activity and electrophilic reactivity with proteins, including transcription factors. Although free or esterified lipid nitroalkene derivatives have been detected in human plasma and urine, their generation by inflammatory stimuli has not been reported. In the present study, we show increased nitration of cholesteryl-linoleate by activated murine J774.1 macrophages, yielding the mononitrated nitroalkene CLNO2 (cholesteryl-nitrolinoleate). CLNO2 levels were found to increase approximately 20-fold 24 h after macrophage activation with Escherichia coli lipopolysaccharide plus interferon-gamma; this response was concurrent with an increase in the expression of NOS2 (inducible nitric oxide synthase) and was inhibited by the (*)NO (nitric oxide) inhibitor L-NAME (N(G)-nitro-L-arginine methyl ester). Macrophage (J774.1 and bone-marrow-derived cells) inflammatory responses were suppressed when activated in the presence of CLNO2 or LNO2 (nitrolinoleate). This included: (i) inhibition of NOS2 expression and cytokine secretion through PPARgamma and *NO-independent mechanisms; (ii) induction of haem oxygenase-1 expression; and (iii) inhibition of NF-kappaB (nuclear factor kappaB) activation. Overall, these results suggest that lipid nitration occurs as part of the response of macrophages to inflammatory stimuli involving NOS2 induction and that these by-products of nitro-oxidative reactions may act as novel adaptive down-regulators of inflammatory responses.
Mechanisms of Angiogenesis (1987)

Macrophage polarization refers to how macrophages have been activated at a given point in space and time. Polarization is not fixed, as macrophages are sufficiently plastic to integrate multiple signals, such as those from microbes, damaged tissues, and ...Read More
Pulse Combustion: Tailpipe Exit Jet Characteristics* (1993)

Abstract A preliminary study of the convective transfer rates of scalar quantities in a strongly oscillating free jet (+70 m/s to -50 m/s at 100 Hz generated by a pulse combustor) has been performed. This work is described in two parts: This paper discusses the free jet character, whereas the companion paper discusses the impinging jet characteristics associated with the convective heat transfer rate to a plate normal to the jet axis. In this paper the essential differences between the steady and oscillating jets are described. Rayleigh temperature measurements and flow visualizations (schlieren photography and laser Mie scattering) were used to quantify the jet characteristics. The method of vortex dynamics was used to model the vorticity and velocity fields of the pulsating jet. The modeling results support the conclusions drawn from experimental data. The steady jet exhibited typical axial and radial temperature profiles for an axisymmetric jet and, hence, it had typical decay rates. The character of the oscillating jet was dominated by the formation of toroidal vortex elements during the positive velocity portion of the cycle. The entrainment of ambient fluid and, hence, the mixing of this fluid with that of the jet was an order of magnitude greater for the oscillating jet than for the steady jet. Thus, the temperature decay rate was also an order of magnitude higher than that of the steady jet. The high peak velocities, finer scale of turbulence, and the coherent toroidal vortex of the oscillating jet are believed to be responsible for the improved scalar transport.
Long, abundantly expressed non-coding transcripts are altered in cancer (2007)

Recent studies with tiling arrays have revealed more genomic transcription than previously anticipated. Whole new groups of non-coding transcripts (NCTs) have been detected. Some of these NCTs, including miRNAs, can regulate gene expression. To date, most known NCTs studied have been relatively short, but several important regulatory NCTs, including XIST, MALAT-1, BC1 and BC200, are considerably larger in length and represent a novel class of long, non-coding RNA species. Whole-genome tiling arrays were utilized to identify novel long NCTs across the entire human genome. Our results have identified a new group of long (>400 nt), abundantly expressed NCTs and have found that a subset of these are also highly evolutionarily conserved. In this report, we have begun to characterize 15 long, conserved NCTs. Quantitative real-time RT-PCR was used to analyze their expression in different normal human tissue and also in breast and ovarian cancers. We found altered expression of many of these NCTs in both cancer types. In addition, several of these NCTs have consistent mutations when sequences of normal samples were compared with a panel of cancer-derived cell lines. One NCT was found to be consistently mutated in a panel of endometrial cancers compared with matched normal blood. These NCTs were among the most abundantly expressed transcripts detected. There are probably many long, conserved NCTs, albeit with lower levels of expression. Although the function of these NCTs is currently unknown, our study indicates that they may play an important function in both normal cells and in cancer development.
An integrated architecture for surveillance and monitoring in an archaeological site (2005)

This paper describes an on-going work aimed at designing and deploying a system for the surveillance and monitoring of an archaeological site, namely the "Valley of the Temples" in Agrigento, Italy. Given the relevance of the site from an artistical and historical point of view, it is important to protect the monuments from malicious or simply incautious behavior; however, the vastity of the area to be monitored and the vague definition of its boundaries make it unpractical to provide extensive coverage through traditional sensors or similar devices. We describe the design of an architecture for the surveillance of the site and for the monitoring of the visitors' behavior consisting in an integrated framework of networked sensors and cameras. Information will be collected by a minimal set of cameras deployed only at critical spots and coupled with higher-performance wireless sensor nodes. Both sets of devices will be supported by more densely deployed lower-cost wireless sensor so that the system will fulfill the concurrent goals of being minimally intrusive and remaining both responsive and efficient. Sensed data will be processed locally whenever possible and convenient, or otherwise sent to a central intelligent unit that will perform further and more sophisticated analyses using a reasoning system, will infer a higher level representation of the outdoor environment, and finally will be able to fine-tune the action of remote devices.
Heat shock protein derived from a non‐autologous tumour can be used as an anti‐tumour vaccine (2003)

Antigenic cross-reactivity between certain tumours has allowed the development of more widely applicable, major histocompatibility complex-disparate (allogeneic) whole-cell vaccines. This principle should also allow heat shock proteins (hsp) derived from certain tumours (and carrying cross-reactive antigens) to be used as vaccines to generate anti-tumour immunity in a range of cancer patients. Here, hsp70 derived from gp70-antigen+ B16 melanoma generated cytotoxic-T-lymphocyte-mediated immune protection in BALB/c mice against challenge with gp70-antigen+ CT26 colorectal tumour cells. Using ovalbumin as a model tumour antigen, it is shown that hsp70 enhances peptide re-presentation by dendritic cells via class I over equimolar whole ovalbumin antigen. However, while transfection of tumour cells with inducible hsp70 increases hsp yield from tumours, it does not enhance antigen recognition via purified hsp70 nor via whole cells or their lysate.
Phosphate-enhanced transfection of cationic lipid-complexed mRNA and plasmid DNA (1998)

Cationic lipid-mediated gene transfer has been shown to be a competent albeit inefficient mechanism of promoting cellular gene transfer. One way to improve the efficacy of cationic lipid-mediated transgene expression is to optimize conditions for complex formation between the lipids and nucleic acids. In this report we describe the beneficial effects of using phosphate buffer to precondition lipofectin (a 1:1 (w/w) mixture of N-[1-(2,3-dioleyloxy)propyl]-n,n, n-trimethylammonium chloride (DOTMA), and dioleoyl phosphatidylethanolamine (DOPE)) prior to complexing with plasmid DNA or mRNA. Under such optimized conditions we studied the kinetics of DNA- and RNA-mediated transgene expression in a human osteosarcoma cell line (HOS). Preincubation of lipofectin in phosphate buffer resulted in up to 26- and 56-fold increases in luciferase expression from plasmid DNA and mRNA, respectively. Addition of chloroquine (50 microM), which enhanced plasmid-mediated gene delivery 3-fold, was synergistic with phosphate resulting in an additional 46-fold increase in luciferase expression. The preincubation with phosphate shortened both the time required for cellular uptake and the time to achieve maximal transgene expression. Optimal transfection was achieved in the presence of 30-80 mM phosphate, at pH 5.6-6.8 under which the phosphate anion is divalent. The effect of phosphate anion was specific in that monovalent Cl- and acetate anions were not stimulatory. These results demonstrate that divalent phosphate anion plays a stimulatory role during complex formation and transfection when cationic lipids come in contact with negatively charged nucleic acids and cell membranes. These findings delineate specific conditions which dramatically enhance transfection efficiency for both DNA and mRNA, and provide an effective procedure for gene transfection studies.
Evidence that DNA-A of a geminivirus associated with severe cassava mosaic disease in Uganda has arisen by interspecific recombination. (1997)

Geminivirus isolates associated with the epidemic of severe cassava mosaic disease in Uganda were studied and compared with virus isolates from the part of Uganda outside the epidemic area, and with African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV). Isolates of a novel type [the Uganda variant (UgV)] were detected in severely affected plants from the epidemic area, whereas those from plants outside the epidemic area were typical of ACMV. The complete nucleotide sequences of DNA-A of UgV (2799 nt) and of a Tanzanian isolate of EACMV (2801 nt) were determined and are extremely similar, except for the coat protein (CP) gene. The CP gene of UgV has three distinct regions: the 5' 219 nt are 99% identical to EACMV (only 79% to ACMV); the following 459 nt are 99% identical to ACMV (75% to EACMV); and the 3' 93 nt are 98% identical to EACMV (76% to ACMV). UgV DNA-A therefore is considered to have arisen by interspecific recombination of EACMV and ACMV. Despite the hybrid nature of their CP, UgV isolates were indistinguishable from ACMV in tests with 20 monoclonal antibodies (MAbs), including seven which reacted with ACMV but not EACMV. The discontinuous epitopes detected by these seven MAbs must involve amino acids which lie in the central part of the CP (residues 74-226) and which differ in ACMV and EACMV. UgV isolates were detected in severely mosaic-affected plants from all 11 widely separated locations sampled. The probable role of recombination in geminivirus evolution in the short to medium term is discussed.
Bombardolides:  New Antifungal and Antibacterial γ-Lactones from the Coprophilous Fungus Bombardioidea anartia (2001)

Chemical studies of organic extracts from cultures of the coprophilous fungus Bombardioidea anartia have led to the discovery of bombardolides A−D (1−4), a series of new antifungal and antibacterial metabolites. Three of these metabolites (1−3) were obtained as inseparable pairs of geometric isomers. A new 3-substituted phenol (5) and the known compound asterriquinone B4 were also encountered. The structures of compounds 1−5 were determined by analysis of NMR and MS data.
Ornithine Aminotransferase, A Potential Target for the Treatment of Hyperammonemias (2000)

Ornithine-delta-aminotransferase (OAT) (EC 2.6.1.13) is a pyridoxal-5' phosphate dependent mitochondrial matrix enzyme. It controls the L-ornithine (Orn) level in tissues by catalysing the transfer of the delta-amino group of Orn to 2-oxoglutarate. The products of this reaction are L-glutamate-gamma-semialdehyde and L-glutamate. Among the compounds known to inhibit (or inactivate) OAT, only L-canaline and (SS)-5-(fluoromethyl)ornithine [(SS)-5FMOrn] are selective for OAT. Treatment of laboratory animals with 5FMOrn causes a dramatic accumulation of Orn in most tissues and organs, and the enhanced formation of urea due to saturation of ornithine:carbamoyltransferase with its substrate. The enhancement of urea formation by increased endogenous levels of Orn is comparable with that produced by large doses of Orn and arginine, a treatment known to enhance the detoxification of ammonia. However, protection to lethal doses of ammonium salts by exogenous Orn is rapidly fading. In contrast, inactivation of OAT by a small dose of 5FMOrn renders a long-lasting protective effect against various forms of hyperammonemic states. Among these the reduction of ammonia concentrations in blood and tissues, and the reduction of the pathologic excretion of orotic acid to normal levels in mice with hereditary defects of the urea cycle, were most impressive. In human hereditary OAT deficiency the elevated intraocular concentrations of Orn are considered to be a cause of gyrate atrophy. This is presumably the reason, why OAT has not been considered as a therapeutically useful target. Chronic inactivation of OAT by repeated administration of 5FMOrn, caused elevated intraocular Orn concentrations, but this treatment had no effect on the function and histology of the visual system, or the behaviour of adult mice. The confirmation of this and related observations in higher species will show, whether OAT inactivation has potentials in the treatment of hyperammonemic states.