gebhart/patrepeval huggingface dataset:
LPS receptor (CD14): a receptor for phagocytosis of Alzheimer's amyloid peptide (2005)

The amyloid beta peptide 42 (Abeta(42)) plays a key role in neurotoxicity in Alzheimer's disease. Mononuclear phagocytes, i.e. microglia, have the potential to clear Abeta by phagocytosis. Recently, the lipopolysaccharide (LPS) receptor CD14 was shown to mediate phagocytosis of bacterial components and furthermore to contribute to neuroinflammation in Alzheimer's disease. Here, we investigated whether this key innate immunity receptor can interact with Abeta(42) and mediate phagocytosis of this peptide. Using flow cytometry, confocal microscopy and two-photon fluorescence lifetime imaging (FLIM) combined with fluorescence resonance energy transfer (FRET), we demonstrated a direct molecular interaction in the range of a few nanometers between Abeta(42) and CD14 in human CD14-transfected Chinese hamster ovary cells. Investigations using cells that were genetically deficient for this receptor showed that in <30 minutes exogenous Abeta(42) added to cultured primary microglial cells was phagocytosed into the cytoplasmic compartment in a CD14-dependent manner. This phagocytosis occurred at Abeta(42) concentration ranges that were considerably lower than the threshold to activate a cellular inflammatory reaction. In contrast, there was no association of CD14 to microglial internalization of microbeads. In complementary clinical experiments, we detected a pronounced CD14 immunoreactivity on parenchymal microglia spatially correlated to characteristic Alzheimer's disease lesion sites in brain sections of Alzheimer's disease patients but not in brain sections of control subjects. By showing a close interaction between CD14 and Abeta(42), demonstrating a direct role of CD14 in Abeta(42) phagocytosis, and detecting CD14-specific staining in brains of Alzheimer's disease patients, our results indicate a role of the LPS receptor in the pathophysiology of Alzheimer's disease, which could be of therapeutic relevance.
Urine in Clinical Proteomics (2008)

Urine has become one of the most attractive biofluids in clinical proteomics as it can be obtained non-invasively in large quantities and is stable compared with other biofluids. The urinary proteome has been studied by almost any proteomics technology, but mass spectrometry-based urinary protein and peptide profiling has emerged as most suitable for clinical application. After a period of descriptive urinary proteomics the field is moving out of the discovery phase into an era of validation of urinary biomarkers in larger prospective studies. Although mainly due to the site of production of urine, the majority of these studies apply to the kidney and the urinary tract, but recent data show that analysis of the urinary proteome can also be highly informative on non-urogenital diseases and used in their classification. Despite this progress in urinary biomarker discovery, the contribution of urinary proteomics to the understanding of the pathophysiology of disease upon analysis of the urinary proteome is still modest mainly because of problems associated to sequence identification of the biomarkers. Until now, research has focused on the highly abundant urinary proteins and peptides, but analysis of the less abundant and naturally existing urinary proteins and peptides still remains a challenge. In conclusion, urine has evolved as one of the most attractive body fluids in clinical proteomics with potentially a rapid application in the clinic.
Glass-reinforced Polyimide Composites based on Poly(4-furanyl-butan-2-one) (1992)

A novel approach was used to develop a matrix resin for processable poiyimide-glass-fibre composites. Furfural-acetone (FAC) resin, poly(4-Furanyl butan-2-one), and various bismaleimides were polymerized at 140 + 10 and 180+ 10 + C by in situ Diels-Alder intermolecular reaction into moderately thermally stable and highly cross-linked polyimide-glass-fibre composites without the evolution oQf by-products. The fabricated composites (i.e. laminates) were characterized by their chemical resistance and mechanical properties
Dynamic imaging of coherent sources: Studying neural interactions in the human brain (2001)

Functional connectivity between cortical areas may appear as correlated time behavior of neural activity. It has been suggested that merging of separate features into a single percept ("binding") is associated with coherent gamma band activity across the cortical areas involved. Therefore, it would be of utmost interest to image cortico-cortical coherence in the working human brain. The frequency specificity and transient nature of these interactions requires time-sensitive tools such as magneto- or electroencephalography (MEG/EEG). Coherence between signals of sensors covering different scalp areas is commonly taken as a measure of functional coupling. However, this approach provides vague information on the actual cortical areas involved, owing to the complex relation between the active brain areas and the sensor recordings. We propose a solution to the crucial issue of proceeding beyond the MEG sensor level to estimate coherences between cortical areas. Dynamic imaging of coherent sources (DICS) uses a spatial filter to localize coherent brain regions and provides the time courses of their activity. Reference points for the computation of neural coupling may be based on brain areas of maximum power or other physiologically meaningful information, or they may be estimated starting from sensor coherences. The performance of DICS is evaluated with simulated data and illustrated with recordings of spontaneous activity in a healthy subject and a parkinsonian patient. Methods for estimating functional connectivities between brain areas will facilitate characterization of cortical networks involved in sensory, motor, or cognitive tasks and will allow investigation of pathological connectivities in neurological disorders.
Study of a hammerhead ribozyme containing 2'-modified adenosine residues (1991)

The improved synthesis of 2'-fluoro-2'-deoxyadenosine (2'-FA) starting from adenosine is described. This compound was converted to the phosphoramidite and incorporated into a hammerhead ribozyme RNA with the use of automated RNA synthesis techniques. Ribozymes containing 2'-deoxy-adenosine (2'-dA) were prepared in a similar manner. A kinetic rate comparison of the unmodified ribozyme with two ribozymes that had every adenosine replaced with 2'FA or 2'-dA revealed a large decrease in catalytic efficiency (kcat/Km) for the modified ribozymes resulting from a drop in kcat. The kinetic analysis of a number of partially substituted 2'-FA or 2'-dA containing hammerheads revealed that the decrease in activity was not associated with any particular residue but was the result of the accumulation of modified nucleosides within the structure.
Inhibition of Adipocyte Differentiation by HIV Protease Inhibitors (1999)

Patients with AIDS who are receiving therapy with HIV protease inhibitors have been widely reported to be afflicted with a syndrome characterized by lipodystrophy (fat redistribution favoring the accumulation of abdominal and cervical adipose tissue), hyperlipidemia, and insulin resistance. HIV protease inhibitors have been suggested to have a direct role in modulating adipocyte differentiation. To address this hypothesis, several HIV protease inhibitors were studied for their ability to either augment or inhibit the differentiation of murine 3T3-L1 preadipocytes. Dose-responsive inhibition of adipogenesis by several protease inhibitors was noted as measured by reduced triglyceride accumulation and attenuated induction of three differentiation marker genes -- aP2, lipoprotein lipase, and Adipo Q. Potential mechanisms for altered adipocyte function, including direct binding to PPARgamma or inhibition of PPARgamma-mediated gene transcription were effectively excluded.
Successful engraftment of human postnatal thymus in severe combined immune deficient (SCID) mice: differential engraftment of thymic components with irradiation versus anti-asialo GM-1 immunosuppressive regimens. (1991)

To develop a model of human thymus growth in vivo, we have implanted postnatal human thymus under the renal capsule of severe combined immune deficient (SCID) mice and assayed for graft survival and graft characteristics 1-3 mo after engraftment. Three groups of SCID mice were engrafted with postnatal human thymus: untreated SCID mice, SCID mice pretreated with 400 cGy of gamma irradiation 1-5 d before engraftment, and SCID mice treated with intraperitoneal anti-asialo GM-1 antiserum every 4-5 d during engraftment. In the untreated group of SCID mice, only 37% of grafts survived and consisted of human thymic microenvironment components and human immature thymocytes. Irradiation of SCID mice before engraftment improved survival of human thymic grafts to 83%, but these grafts were largely devoid of thymocytes and contained only thymic microenvironment components with large numbers of thymic macrophages. Treatment of SCID mice with anti-asialo GM-1 antiserum throughout the engraftment period also promoted human thymus engraftment (70%) and induced SCID B cell Ig production (SCID[Ig+]) in 38% of animals. In SCID(Ig-) anti-asialo GM-1-treated mice, the human thymic grafts were similar in content to those in untreated SCID mice. However, in anti-asialo GM-1-treated animals with grafts that became SCID(Ig+), all animals were found to have mouse-human chimeric grafts in that the human thymic microenvironment (human fibroblasts, thymic epithelium, vessels) was colonized by murine T cells. These data demonstrate that human postnatal thymus will grow as xenografts in SCID mice, and that the components of human thymus that engraft are dependent on the immunosuppressive regimen used in recipient mice. A striking finding in this study was the induction of T and B lymphopoiesis in SCID mice by abrogation of NK cell activity with in vivo anti-asialo GM-1 treatment. These data strongly suggest that asialo GM-1+ NK cells and/or macrophages play a role in mediation of suppression of lymphopoiesis in SCID mice.
Small-Molecule Reagents for Cellular Pull-Down Experiments (2008)

Affinity purification of interacting proteins from cellular extracts is a powerful technique for identifying the cellular targets of small molecules. Affinity matrix-based small-molecule reagents are usually prepared by conjugating small molecules of interest to a solid support such as agarose. This protocol describes an efficient and robust method to immobilize small molecules containing a primary alcohol, a common functional group in small molecules, especially in small molecules prepared using diversity-oriented synthesis. This method comprises one element of a systematic approach to the target identification problem in chemical biology.
Cardiorespiratory Patterns in Complicated and Uncomplicated Septic Shock (1971)

From the Department of Surgery, The Mount Sinai School of Medicine of the City University of New York, New York City
DNASE1L3Mutations in Hypocomplementemic Urticarial Vasculitis Syndrome (2013)

These results show that HUVS is caused by mutations in DNASE1L3, encoding an endonuclease that previously has been associated with SLE.
Current Developments in the Tissue Engineering of Autologous Heart Valves: Moving Towards Clinical Use (2010)

The use of tissue-engineering methods to create autologous heart valve constructs has the potential to overcome the fundamental drawbacks of more traditional valve prostheses. Traditional mechanical valves, while durable, increase the risk for endocarditis and thrombogenesis, and require the recipient to continue lifelong anticoagulant therapy. Homograft or xenograft heart valve prostheses are associated with immune reaction and progressive deterioration with limited durability. Most importantly, neither option is capable of growth and remodeling in vivo and both options place the patient at risk for valve-related complications and reoperation. These shortcomings have prompted the application of tissue-engineering techniques to create fully autologous heart valve replacements. Future clinically efficacious tissue-engineered autologous valves should be nonthrombogenic, biocompatible, capable of growth and remodeling in vivo, implantable with current surgical techniques, hemodynamically perfect, durable for the patient's life and most importantly, significantly improve quality of life for the patient. In order to meet these expectations, the nature of the ideal biochemical milieu for conditioning an autologous heart valve will need to be elucidated. In addition, standardized criteria by which to quantitatively evaluate a tissue-engineered heart valve, as well as noninvasive analytical techniques for use in long-term animal models, will be required. This article highlights the advances, challenges and future clinical prospects in the field of tissue engineering of autologous heart valves, focusing on progress made by studies that have investigated a fully autologous, tissue-engineered pulmonary valve replacement in vivo.
Isolation and Partial Characterization of an Adhesin from Candida albicans (1987)

Candida albicans produces extracellular polymeric material (EP) which contains a mannoprotein adhesin. EP isolated from culture supernatants of C. albicans GDH 2346 consisted of a mixture of glycoprotein components and inhibited yeast adhesion to buccal epithelial cells by up to 60%. Partial purification of the adhesin was achieved by a two-step procedure involving chromatography of EP on concanavalin A-Sepharose and DEAE-cellulose. The purified adhesin inhibited adhesion to buccal cells 30 times more efficiently (on a weight basis) than unfractionated EP. Pretreatment of EP with heat, dithiothreitol or proteolytic enzymes either partially or completely destroyed its ability to inhibit adhesion, whereas pretreatment with sodium periodate or alpha-mannosidase had little or no effect. These results suggest that the protein portion of the mannoprotein adhesin is more important than the carbohydrate moiety in mediating yeast attachment to buccal epithelial cells.
Phase 1 study of atrasentan (ABT627), novel endothelin receptor-A antagonist, in Japanese patients with hormone refractory prostate cancer (2006)

14602 Background: Endothelin (ET)-1 and its primary receptor, the ET A receptor, contribute to tumor cell growth, survival, angiogenesis and invasion. Atrasentan is a highly potent, selective ET A receptor antagonist. This study assessed safety and pharmacokinetics (PK) in Japanese patients with hormone refractory prostate cancer. Methods: This open-label, single-center Phase I trial evaluated the safety and PK of escalating oral atrasentan doses (2.5, 10 or 20 mg) given daily on day 1 and day 4 through 27 (except day 2 and 3). Dose-limiting toxicity (DLT) was defined as Grade 3 or greater adverse events related to study drug. Results: Eighteen patients, aged 54–74 (median; 66) were treated in cohorts of 6 patients each. The compliance of all patients was 100%. The most common toxicities were rhinitis, peripheral edema, headache, hypotension and anemia, all of which were well tolerated. These events were consistent with the anticipated vasodilatory effects or with a hemodilution effect of the study drug. DLTs were not observed. Atrasentan was rapidly absorbed following oral administration of 2.5 to 20 mg, maximum plasma concentrations averaged from 0.4 to 0.8 hours. After peaking, plasma concentrations declined bi-exponentially with a terminal half-life of approximately 25 hours. In the 10 mg dosing group, the steady-state maximum plasma concentration (C max ) and the area under the curve (AUC 0–24h ) averaged 135.5 ng/mL and 533 ng h/mL, respectively. The C max and AUC values generally increased linearly with increasing dose after single- and multiple-dose administration. Compared to baseline, PSA decreased 50% or more in 1 patient (20 mg) and increased 25% or more in 10 patients (2.5 mg;2, 10 mg;5, 20 mg;3). The PSA of the remaining 7 patients (2.5 mg;4, 10 mg;1, 20 mg;2) ranged from &lt; 25% increase to &lt; 50% decrease. Fourteen patients continued on study drug in an extension study. Conclusions: Atrasentan is well tolerated, with no dose-limiting adverse events observed up to 20 mg in Japanese patients. The main adverse events are consistent with the vasodilatory effect of the drug. PK are linear and dose-proportional; the half-life is appropriate for once-daily dosing. No significant financial relationships to disclose.
Bioequivalence, dose-proportionality, and pharmacokinetics of naltrexone after oral administration. (1984)

Healthy male volunteers (N = 24) participated in a four-way crossover study to compare the rate and extent of absorption of naltrexone after administration of 50 mg tablets as 50, 100, and 200 mg doses and a 10 mg/ml reference syrup. A high-performance liquid chromatographic method was employed to measure naltrexone and 6-beta-naltrexol in plasma and urine. Compared to the syrup, the 50 mg tablets were absorbed more slowly but equally well. There was excellent linearity between the administered dose and the area under the plasma concentration-time profile, as well as total urinary recovery of both drug and metabolite. The mean half-lives for naltrexone and beta-naltrexol were approximately 4 and 12 hours, respectively. The fraction of drug reaching the systemic circulation was estimated to be 5% of the administered dose because of extensive first-pass metabolism. Less than 1% of the dose was excreted in the urine as naltrexone after 48 hours, while 25% was recovered as unconjugated beta-naltrexol. The renal clearance of naltrexone and beta-naltrexol was approximately 127 ml/min and 283 ml/min, respectively. The total systemic clearance for naltrexone was approximately 94 L/hr.
An invariant traffic sign recognition system based on sequential color processing and geometrical transformation (2002)

One of the most noteworthy problems associated with conventional pattern recognition methods is that it is not easy to extract feature vectors from images which are not translation, rotation, and scale change invariant in outdoor noisy environments. This paper describes the development of an invariant traffic sign recognition system capable of tolerating the above variations. The signs are restricted to three types of warning signs and are all of red color. The developed method is insensitive to brightness changes as well as invariant to translation, rotation, scale change, and noise. The architecture of this system is based upon neural network supervised learning after geometrical transformations have been applied. The performance of this system is compared with other invariant approaches in terms of the percentage of correct decisions in outdoor noisy environments.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
IgE to Cross-Reactive Carbohydrate Determinants: Analysis of the Distribution and Appraisal of the in vivo and in vitro Reactivity (2002)

&lt;i&gt;Background:&lt;/i&gt; IgE to cross-reacting carbohydrate determinants has already been described by several authors, but their function and distribution are still a matter of debate. In previous studies we showed how the presence of IgE to bromelain could be a useful and simple marker of the presence of IgE to carbohydrate epitopes. &lt;i&gt;Methods:&lt;/i&gt; A survey of 1,831 subjects with a suspected allergic respiratory disease has been carried out by detecting IgE to bromelain. Data were analysed on the basis of demographical and allergological parameters. To find out whether a glycoprotein is capable of triggering an allergic reaction, 1,076 subjects were also skin tested with several purified molecules bearing carbohydrate side chains differing in number, composition and complexity. &lt;i&gt;Results:&lt;/i&gt; An overall prevalence of 23% of positive IgE to cross-reacting carbohydrate determinants was recorded. Prevalence varied when subsets of non-allergic (5%), non-pollen-allergic (10%), and pollen-allergic (31%) subjects were considered. Prevalence further increased in subsets with multiple pollen sensitization (71%), and with a previous pollen immunotherapy course (46%), whereas minor differences were found in gender and age distribution. Almost all the allergenic extracts recorded negative in the skin test gave a positive IgE test in vitro. A higher correlation was found mainly with plant-derived allergenic extracts, whereas a lower one was recorded with mites and fungi. Horseradish peroxidase was the only glycoprotein capable of exerting a positive skin test in 21% of the subjects with IgE to cross-reacting carbohydrate determinants, 80% of them having IgE to the HRP molecule. &lt;i&gt;Conclusions:&lt;/i&gt; IgE to cross-reacting carbohydrate determinants are common among the allergic population and the binding to skin test negative allergenic extracts further confirms their poor biological activity. Further studies on horseradish peroxidase should be carried out to define the role of the glycan side chains in its allergenic activity.
Acoustic radiation force on a spherical particle in a viscous heat-conducting fluid. III. Force on a liquid drop (1997)

The general expression derived in Part I of this work [J. Acoust. Soc. Am. 101, 713–721 (1997)] for the acoustic radiation force exerted by a sound field on a spherical particle in a viscous heat-conducting fluid is applied here to a liquid drop. To demonstrate dissipative effects clearly, two limiting cases are studied. In both cases, the sound wavelength is taken to be much larger than other characteristic parameters of the system, such as the drop radius and the viscous and thermal wavelengths both outside and inside the drop. Within this assumption, two reverse situations are considered, in the first of which the dissipative effects are assumed to be weak, and in the second, to be strong. For each of these two cases, three types of incident wave are dealt with: a plane traveling wave, a plane standing wave, and a diverging spherical wave. Emphasis is given to the thermal effects on the radiation force. These are found to be greatest in the traveling and spherical waves, while in the standing wave, for both limiting cases, the thermal effects only give rise to small corrections to the leading terms due to compressibility and viscosity.
SKP2 attenuates autophagy through Beclin1-ubiquitination and its inhibition reduces MERS-Coronavirus infection (2019)

Autophagy is an essential cellular process affecting virus infections and other diseases and Beclin1 (BECN1) is one of its key regulators. Here, we identified S-phase kinase-associated protein 2 (SKP2) as E3 ligase that executes lysine-48-linked poly-ubiquitination of BECN1, thus promoting its proteasomal degradation. SKP2 activity is regulated by phosphorylation in a hetero-complex involving FKBP51, PHLPP, AKT1, and BECN1. Genetic or pharmacological inhibition of SKP2 decreases BECN1 ubiquitination, decreases BECN1 degradation and enhances autophagic flux. Middle East respiratory syndrome coronavirus (MERS-CoV) multiplication results in reduced BECN1 levels and blocks the fusion of autophagosomes and lysosomes. Inhibitors of SKP2 not only enhance autophagy but also reduce the replication of MERS-CoV up to 28,000-fold. The SKP2-BECN1 link constitutes a promising target for host-directed antiviral drugs and possibly other autophagy-sensitive conditions.
Effects of isoniazid on the proliferation and cytokine production of bladder cancer cells in vitro induced by bacille Calmette‐Guérin (1997)

Assuming an essential role of (tumour) epithelial cells in the local immune response induced by BCG, these in vitro results suggest that the administration of isoniazid does not interfere with this part of the mechanisms by which BCG operates.