gebhart/patrepeval huggingface dataset:
Neuronal c-Abl Overexpression Leads to Neuronal Loss and Neuroinflammation in the Mouse Forebrain (2011)

Several immunocytochemical studies have revealed that Abelson tyrosine kinase (c-Abl) is associated with both neuritic plaques and neurofibrillary tangles in the brains of patients with Alzheimer's disease (AD). Additionally, c-Abl has been shown to phosphorylate tau on tyrosine 394. The activity of c-Abl is also involved in the control of the cell cycle and apoptosis. To examine the consequences of c-Abl activation in the adult brain, we have constructed two lines of transgenic mice expressing either a constitutively active form of c-Abl (AblPP/tTA mice) or its sister protein, Arg (ArgPP/tTA mice), with a neuron-specific promoter (CamKIIα) regulated by doxycycline (Tet-Off). Expression of active c-Abl in adult mouse forebrain neurons results in severe neurodegeneration, particularly in the CA1 region of the hippocampus. Neuronal loss was preceded and accompanied by substantial microgliosis and astrocyctosis. Despite careful examination, no c-Abl expression is found in glial cells, indicating that neuronal c-Abl expression is responsible for the gliosis. In contrast, ArgPP/tTA mice have no evidence of neuronal loss or gliosis, even though protein expression and kinase activity levels are similar to those in the AblPP/tTA mice. Given the evidence of c-Abl activation in the human AD brain combined with the pathological phenotype of AblPP/tTA mice, it is likely that aberrant c-Abl activity may play a role in neurodegenerative disease.
Casting Metal Nanowires Within Discrete Self-Assembled Peptide Nanotubes (2003)

Tubular nanostructures are suggested to have a wide range of applications in nanotechnology. We report our observation of the self-assembly of a very short peptide, the Alzheimer's beta-amyloid diphenylalanine structural motif, into discrete and stiff nanotubes. Reduction of ionic silver within the nanotubes, followed by enzymatic degradation of the peptide backbone, resulted in the production of discrete nanowires with a long persistence length. The same dipeptide building block, made of D-phenylalanine, resulted in the production of enzymatically stable nanotubes.
Impaired Cognitive Function in Women with Congenital Adrenal Hyperplasia (2006)

Impaired cognitive function was observed in patients with CAH, especially in salt-wasting CAH. These intriguing findings may reflect adverse effects of hyponatremic episodes, suboptimal postnatal hormone replacement therapy or prenatal adrenal androgen excess, and the potential psychosocial consequences of the disorder.
Broadband dual-frequency operation of circular patch antennas and arrays with a pair of L-shaped slots (2003)

By embedding properly arranged L-shaped slots in a circular patch, a novel broadband dual-frequency design is proposed and experimentally studied. With the use of an L-strip microstrip line for feeding the proposed antenna, the impedance bandwidths, determined from 10 dB return loss, of two operating bands can reach about 7.0% to 12.5% for the lower band and 18.9% to 21.5% for the higher band. Operating frequencies across the obtained lower and higher bands are of the same polarization planes, and have a tunable frequency ratio between the center frequencies of the two operating bands ranging from about 1.31-1.61. The application of the proposed antenna to the design of a 2 /spl times/ 2 broadband dual-frequency patch antenna array is also demonstrated. Details of the proposed broadband dual-frequency design are described, and experimental results of the constructed prototypes are presented and discussed.
Circumstances and Mechanisms of Inhibition of Translation by Secondary Structure in Eucaryotic mRNAs (1989)

This paper describes in vitro experiments with two types of intramolecular duplex structures that inhibit translation in cis by preventing the formation of an initiation complex or by causing the complex to be abortive. One stem-loop structure (delta G = -30 kcal/mol) prevented mRNA from engaging 40S subunits when the hairpin occurred 12 nucleotides (nt) from the cap but had no deleterious effect when it was repositioned 52 nt from the cap. This result confirms prior in vivo evidence that the 40S subunit-factor complex, once bound to mRNA, has considerable ability to penetrate secondary structure. Consequently, translation is most sensitive to secondary structure at the entry site for ribosomes, i.e., the 5' end of the mRNA. The second stem-loop structure (hp7; delta G = -61 kcal/mol, located 72 nt from the cap) was too stable to be unwound by 40S ribosomes, hp7 did not prevent a 40S ribosomal subunit from binding but caused the 40S subunit to stall on the 5' side of the hairpin, exactly as the scanning model predicts. Control experiments revealed that 80S elongating ribosomes could disrupt duplex structures, such as hp7, that were too stable to be penetrated by the scanning 40S ribosome-factor complex. A third type of base-paired structure shown to inhibit translation in vivo involves a long-range interaction between the 5' and 3' noncoding sequences.
Diels-Alder Reactions of 6-Hydroxy-2H-pyran-3(6H)-ones with Cyclopentadiene and Its Application for the Synthesis of New Skeletal Oxa-Cage Compounds (2001)

The 2(5H)-furanone and 3(6H)-pyranone structures are frequently found in natural products, which have a broad range of biological activities. In addition, furanones and pyranones have served as versatile intermediates in the synthesis of a variety of products. 1 Recently, we envisioned that studies on the synthesis and chemistry of heterocyclic cage compounds can greatly expand the scopes and utilities of cage compounds.2 As part of a program that involves the synthesis, chemistry, and applications of heterocyclic cage compounds, we report here the Diels-Alder reactions of 6-hydroxy2H-pyran-3(6H)-ones 1 and 2 with cyclopentadiene and the application of the cycloadducts for the synthesis of oxa-cage compounds 3-6 with new skeleton. Compound 6 is a potential new chiral amino-alcohol.
Identifying suspicious activities through DNS failure graph analysis (2010)

As a key approach to securing large networks, existing anomaly detection techniques focus primarily on network traffic data. However, the sheer volume of such data often renders detailed analysis very expensive and reduces the effectiveness of these tools. In this paper, we propose a light-weight anomaly detection approach based on unproductive DNS traffic, namely, the failed DNS queries, with a novel tool - DNS failure graphs. A DNS failure graph captures the interactions between hosts and failed domain names. We apply a graph decomposition algorithm based on the tri-nonnegative matrix factorization technique to iteratively extract coherent co-clusters (dense subgraphs) from DNS failure graphs. By analyzing the co-clusters in the daily DNS failure graphs from a 3-month DNS trace captured at a large campus network, we find these co-clusters represent a variety of anomalous activities, e.g., spamming, trojans, bots, etc.. In addition, these activities often exhibit distinguishable subgraph structures. By exploring the temporal properties of the co-clusters, we show our method can identify new anomalies that likely correspond to unreported domain-flux bots.
Sites of Rhinovirus Recovery After Point Inoculation of the Upper Airway (1986)

Spread of rhinovirus infection in the nose was studied after point inoculation of 25 microL of rhinovirus suspension either under the right inferior turbinate via the test duct (26 volunteers) or onto the posterior nasopharyngeal wall (through the mouth under direct vision) (six volunteers). Epithelial brush samples obtained daily from the anterior and posterior portions of the inferior turbinate in both nasal cavities and the nasopharynx were cultured for rhinovirus. Point inoculation of rhinovirus produced a high infection rate, but the entire nasal lining was not infected at the time of peak symptoms. Virus was usually first detected at the nasopharyngeal site, with subsequent spread of infection anteriorly to one or both inferior turbinates. Spread to the left turbinate was not detected in seven of 17 volunteers during the first five days after right eye inoculation. Virus recovery from the mucosa declined by day 16 and ceased by day 21.
Cytochrome o as a terminal oxidase and receptor for aerotaxis in Salmonella typhimurium (1984)

Cytochrome o was the only oxidase of the electron transport system that was present in exponentially growing Salmonella typhimurium ST1. Identification of cytochrome o was made by the (CO-reduced)-minus-(reduced) difference spectra and by the photochemical action spectrum of the relief, by light, of CO-inhibited respiration. Cytochrome o also functioned as the receptor for chemotaxis to oxygen (aerotaxis). The concentration of oxygen that elicits the maximum response for aerotaxis (0.7 microM) was similar to the Km for respiration (0.74 microM), and both aerotaxis and respiration were blocked 5 mM KCN.
Transforming growth factor‐beta 1, 2, 3 and receptor type I and II in diabetic foot ulcers (2002)

The lack of TGF-beta1 up-regulation in both diabetic foot ulcers and venous ulcers may explain the impaired healing in these chronic wounds, and could represent a general pattern for chronicity.
Imbibition in Porous Membranes of Complex Shape: Quasi-stationary Flow in Thin Rectangular Segments (2009)

The sustained liquid flow of a typical lateral flow assay can be mimicked by two-dimensional shaped, thin porous membranes, specifically rectangular membranes appended to circular sectors. In designing these fan-shaped devices, we have been aided by analytical equations and finite-element simulations. We show both mathematically and experimentally how a continuous increase in unwetted pore volume causes a deviation from traditional imbibition, and leads to quasi-stationary flow in the rectangular element. These results are both theoretically and practically important because they indicate how medical diagnostic test strips may be fabricated without incorporating an absorbent pad.
Decreased α-Methylacyl CoA Racemase Expression in Localized Prostate Cancer is Associated with an Increased Rate of Biochemical Recurrence and Cancer-Specific Death (2005)

Alpha-methylacyl CoA racemase (AMACR) is overexpressed in prostate cancer relative to benign prostatic tissue. AMACR expression is highest in localized prostate cancer and decreases in metastatic prostate cancer. Herein, we explored the use of AMACR as a biomarker for aggressive prostate cancer. AMACR protein expression was determined by immunohistochemistry using an image analysis system on two localized prostate cancer cohorts consisting of 204 men treated by radical prostatectomy and 188 men followed expectantly. The end points for the cohorts were time to prostate-specific antigen (PSA) failure (i.e., elevation >0.2 ng/mL) and time to prostate cancer death in the watchful waiting cohort. Using a regression tree method, optimal AMACR protein expression cut-points were determined to best differentiate prostate cancer outcome in each of the cohorts separately. Cox proportional hazard models were then employed to examine the effect of the AMACR cut-point on prostate cancer outcome, and adjusted for clinical variables. Lower AMACR tissue expression was associated with worse prostate cancer outcome, independent of clinical variables (hazard ratio, 3.7 for PSA failure; P = 0.018; hazard ratio, 4.1 for prostate cancer death, P = 0.0006). Among those with both low AMACR expression and high Gleason score, the risk of prostate cancer death was 18-fold higher (P = 0.006). The AMACR cut-point developed using prostate cancer-specific death as the end point predicted PSA failures independent of Gleason score, PSA, and margin status. This is the first study to show that AMACR expression is significantly associated with prostate cancer progression and suggests that not all surrogate end points may be optimal to define biomarkers of aggressive prostate cancer.
Vertebral Body and Posterior Element Morphology (1988)

Multiple morphologic parameters were studied in 50 normal adult vertebral columns ranging in age from 20 to 40 years at the time of death. Posterior element morphology is highly variable and largely unpredictable. Minimum pedicle diameters ranged from 1.8 mm at T6 to 6.4 mm at L5, and did not correlate with any more readily measured vertebral dimensions. Penetration of 5 mm screw threads through pedicle cortex can be expected to occur routinely in the lower thoracic spine, and in a lesser but significant number of lumbar vertebrae.
A buyer's guide to electromagnetic tracking systems for clinical applications (2008)

When choosing an Electromagnetic Tracking System (EMTS) for image-guided procedures, it is desirable for the system to be usable for different procedures and environments. Several factors influence this choice. To date, the only factors that have been studied extensively, are the accuracy and the susceptibility of electromagnetic tracking systems to distortions caused by ferromagnetic materials. In this paper we provide a holistic overview of the factors that should be taken into account when choosing an EMTS. These factors include: the system's refresh rate, the number of sensors that need to be tracked, the size of the navigated region, system interaction with the environment, can the sensors be embedded into the tools and provide the desired transformation data, and tracking accuracy and robustness. We evaluate the Aurora EMTS (Northern Digital Inc., Waterloo, Ontario, Canada) and the 3D Guidance EMTS with the flat-panel and the short-range field generators (Ascension Technology Corp., Burlington, Vermont, USA) in three clinical environments. We show that these systems are applicable to specific procedures or in specific environments, but that, no single system is currently optimal for all environments and procedures we evaluated.
Design of hierarchical self-healing ring networks (2002)

The design of hierarchical self-healing ring (HSHR) networks is considered. It is shown that the enumeration method, which finds the optimal configuration of HSHR at any given number of levels and given number of nodes on its single self-healing rings, minimizing total capacity required, can only be used for small networks due to the complexity. A heuristic algorithm to solve the near-optimal topology construction in HSHR networks is proposed. Numerical results show that the performance of the heuristic is satisfactory.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
One-Third-the-Sites Transition-State Inhibitors for Purine Nucleoside Phosphorylase (1998)

Genetic defects in human purine nucleoside phosphorylase cause T-cell deficiency as the major phenotype. It has been proposed that efficient inhibitors of the enzyme might intervene in disorders of T-cell function. Compounds with features of the transition-state structure of purine nucleoside phosphorylase were synthesized and tested as inhibitors. The transition-state structure for purine nucleoside phosphorylase is characterized by (1) an elevated pKa at N7 of the purine ring for protonation or favorable H-bond interaction with the enzyme and (2) oxocarbenium ion formation in the ribosyl ring (Kline, P. C., and Schramm, V. L. (1995) Biochemistry 34, 1153-1162). Both features have been incorporated into the stable transition-state analogues, (1S)-1-(9-deazahypoxanthin-9-yl)-1,4-dideoxy-1,4-imino-D-ribitol (immucillin-H) and (1S)-1-(9-deazaguanin-9-yl)-1,4-dideoxy-1, 4-imino-D-ribitol (immucillin-G). Both inhibitors exhibit slow-onset tight-binding inhibition of calf spleen and human erythrocyte purine nucleoside phosphorylase. The inhibitors exhibit equilibrium dissociation constants (Ki) from 23 to 72 pM and are the most powerful inhibitors reported for the enzyme. Complete inhibition of the homotrimeric enzyme occurs at one mole of inhibitor per mole of enzymic trimer. Binding of the transition-state inhibitor at one site per trimer prevents inhibitor binding at the remaining two sites of the homotrimer. A mechanism of sequential catalysis at each subunit, similar to that of F1 ATPase, is supported by these results. Slow inhibitor dissociation (e.g., t1/2 of 4.8 h) suggests that these compounds will have favorable pharmacologic properties. Interaction of transition-state inhibitors with purine nucleoside phosphorylase is different from reactant-state (substrate and product analogue) inhibitors of the enzyme which bind equally to all subunits of the homotrimer.
A Novel Near-Infrared Fluorescence Sensor for Detection of Thrombin Activation in Blood (2002)

Thrombosis is an important pathophysiologic component of many cardiovascular diseases. Thrombin, a serine protease, plays a central role in thrombosis formation. Detection and imaging of thrombin activity may thus be of considerable biomedical interest. The goal of this study was to design, synthesize, and characterize a novel thrombin-activated near-infrared fluorescence (NIRF) probe. The probe consisted of a thrombin-cleavable peptide spacer (...D-Phe-Pip-Arg...; Pip=pipecolic acid) and contained a terminal fluorescence reporter which was quenched when conjugated to a biocompatible delivery vehicle. A control peptide spacer was synthesized that differed by one amino acid. Following thrombin addition, the probe was activated within minutes. The NIRF signal increased by a factor of 27-fold within 20 minutes, and was inhibited by hirudin, a specific thrombin inhibitor. NIRF optical imaging experiments confirmed rapid activation of the probe in both buffer and human blood. The control probe showed minimal activation in all experiments. In addition to potentially furthering our understanding of thrombin regulation in vivo, the thrombin-activated near-infrared probe may have broad clinical application to the diagnosis of arterial and venous thrombosis.
Phagosome-Lysosome Fusion and Cyclic Adenosine 3': 5'-Monophosphate in Macrophages Infected with Mycobacterium microti, Mycobacterium bovis BCG or Mycobacterium lepraemurium (1979)

When ingested by mouse peritoneal macrophage monolayers, live Mycobacterium microti caused a sustained increase in monolayer cyclic AMP content and fusion of lysosomes with the bacterium-containing phagosomes was impaired. Ingested live M. bovis BCG caused a transient increase in cyclic AMP and the defect in phagolysosome formation was less pronounced. Dead mycobacteria and live M. lepraemurium neither enhanced monolayer cyclic AMP content nor inhibited phagolysosome formation. Mycobacterium microti and BCG exceeded M. lepraemurium in cyclic AMP-synthesizing activity in vitro but the question of whether bacterial cyclic AMP contributed substantially to the increments in infected macrophages was not resolved. Antibody-coated BCG retained the ability to synthesize cyclic AMP and to enhance monolayer cyclic AMP but lost the ability to inhibit phagolysosome formation in macrophages, The observations are discussed in terms of possible control of phagolysosome formation by cyclic nucleotides.
Model-based estimates of risks of disease transmission and economic costs of seven injection devices in sub-Saharan Africa. (2002)

Despite their nominal purchase and usage costs, conventional needles and syringes carry a hidden but huge burden of iatrogenic disease. Alternative injection devices for the millions of injections administered annually in sub-Saharan Africa would be of value and should be considered by policy-makers in procurement decisions.
The preparation and some properties of hyaluronic acid from human umbilical cord (1948)

Research Article| January 01 1948 The preparation and some properties of hyaluronic acid from human umbilical cord Z. Hadidian; Z. Hadidian 1The Worcester Foundation for Experimental Biology, Shrewsbury, Massachusetts, and the Department of Physiology, Tufts Medical School Search for other works by this author on: This Site PubMed Google Scholar N. W. Pirie N. W. Pirie * 1The Worcester Foundation for Experimental Biology, Shrewsbury, Massachusetts, and the Department of Physiology, Tufts Medical School Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1948) 42 (2): 260–265. https://doi.org/10.1042/bj0420260 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation Z. Hadidian, N. W. Pirie; The preparation and some properties of hyaluronic acid from human umbilical cord. Biochem J 1 January 1948; 42 (2): 260–265. doi: https://doi.org/10.1042/bj0420260 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1948 CAMBRIDGE UNIVERSITY PRESS1948 Article PDF first page preview Close Modal You do not currently have access to this content.
Phosphodiesterase7 Inhibition Activates Adult Neurogenesis in Hippocampus and Subventricular Zone In Vitro and In Vivo (2016)

The phosphodiesterase 7 (PDE7) enzyme is one of the enzymes responsible for controlling intracellular levels of cyclic adenosine 3',5'-monophosphate in the immune and central nervous system. We have previously shown that inhibitors of this enzyme are potent neuroprotective and anti-inflammatory agents. In addition, we also demonstrated that PDE7 inhibition induces endogenous neuroregenerative processes toward a dopaminergic phenotype. Here, we show that PDE7 inhibition controls stem cell expansion in the subgranular zone of the dentate gyrus of the hippocampus (SGZ) and the subventricular zone (SVZ) in the adult rat brain. Neurospheres cultures obtained from SGZ and SVZ of adult rats treated with PDE7 inhibitors presented an increased proliferation and neuronal differentiation compared to control cultures. PDE7 inhibitors treatment of neurospheres cultures also resulted in an increase of the levels of phosphorylated cAMP response element binding protein, suggesting that their effects were indeed mediated through the activation of the cAMP/PKA signaling pathway. In addition, adult rats orally treated with S14, a specific inhibitor of PDE7, presented elevated numbers of proliferating progenitor cells, and migrating precursors in the SGZ and the SVZ. Moreover, long-term treatment with this PDE7 inhibitor shows a significant increase in newly generated neurons in the olfactory bulb and the hippocampus. Also a better performance in memory tests was observed in S14 treated rats, suggesting a functional relevance for the S14-induced increase in SGZ neurogenesis. Taken together, our results indicate for the first time that inhibition of PDE7 directly regulates proliferation, migration and differentiation of neural stem cells, improving spatial learning and memory tasks. Stem Cells 2017;35:458-472.