gebhart/patrepeval huggingface dataset:
The three major immediate-early transcripts of bovine herpesvirus 1 arise from two divergent and spliced transcription units (1991)

Among 54 transcripts expressed in a temporal cascade during lytic infection with bovine herpesvirus 1, we have previously identified three major immediate-early (IE) RNAs, IER4.2 (4.2 kb), IER2.9 (2.9 kb), and IER1.7 (1.6 to 1.8 kb depending on the virus strain) transcribed from the HindIII C genome region (U. V. Wirth, K. Gunkel, M. Engels, and M. Schwyzer, J. Virol. 63:4882-4889, 1989). Northern (RNA) blot, S1 nuclease protection, and primer extension analysis used in the present study demonstrated that all three IE transcripts were spliced and originated from two divergent transcription units with start sites located in the inverted repeat. Transcription unit 1 encoded two alternative spliced transcripts, IER4.2 and IER2.9, with a common exon 1 located at 0.797 to 0.795 map units (m.u.) and an exon 2 for IER4.2 (0.792 to 0.762 m.u.) in the inverted repeat; exon 2 for IER2.9 (0.754 to 0.738 m.u.) was located in the unique long sequence and transcribed in antisense orientation to latency-related RNA. Transcription unit 2 (0.818 to 0.836 m.u.), further characterized by cDNA cloning, encoded the spliced IER1.7 with three exons in the inverted repeat. Additional minor IE transcripts were interpreted as unspliced precursors and splicing variants. With regard to the number and layout of IE genes, bovine herpesvirus 1 occupies an intermediate position between pseudorabies virus and equine herpesvirus 1 on the one hand and varicella-zoster virus and herpes simplex virus type 1 on the other.
MyD88, an Adapter Protein Involved in Interleukin-1 Signaling (1998)

MyD88 has a modular organization, an N-terminal death domain (DD) related to the cytoplasmic signaling domains found in many members of the tumor necrosis factor receptor (TNF-R) superfamily, and a C-terminal Toll domain similar to that found in the expanding family of Toll/interleukin-1-like receptors (IL-1R). This dual domain structure, together with the following observations, supports a role for MyD88 as an adapter in IL-1 signal transduction; MyD88 forms homodimers in vivo through DD-DD and Toll-Toll interactions. Overexpression of MyD88 induces activation of the c-Jun N-terminal kinase (JNK) and the transcription factor NF-kappaB through its DD. A point mutation in MyD88, MyD88-lpr (F56N), which prevents dimerization of the DD, also blocks induction of these activities. MyD88-induced NF-kappaB activation is inhibited by the dominant negative versions of TRAF6 and IRAK, which also inhibit IL-1-induced NF-kappaB activation. Overexpression of MyD88-lpr or MyD88-Toll (expressing only the Toll domain) acted to inhibit IL-1-induced NF-kappaB and JNK activation in a 293 cell line overexpressing the IL-1RI. MyD88 coimmunoprecipitates with the IL-1R signaling complex in an IL-1-dependent manner.
Heparan sulfate: growth control with a restricted sequence menu (2001)

The growth and differentiation of cells and their organization into organs and tissues are complex processes, largely determined by the concerted actions of the ECM and small, soluble “effector” proteins in the pericellular milieu. Cells respond to the instructive potential of their microenvironment by means of specialized plasma membrane receptors, which elicit intracellular signals when activated by cognate ECM or soluble peptide ligands. In many receptor systems, ligand binds first to an abundant, low-affinity receptor, which draws the ligand onto the cell surface and then transfers it to a second, high-affinity receptor that transduces the appropriate signal into the cell. The most common and widely acting low-affinity receptors are the heparan sulfate proteoglycans (HSPGs), which play central roles in the reception and modulation of a wide range of growth factors, morphogens, and chemokines (1–3). They also act in combination with membrane integrins to control cell adhesion and migration in the ECM (4).

The question arises as to how the structure and properties of the HSPGs enable them to fulfill such diverse and fundamental roles. These issues are the subject of intense experimental study, and a growing body of data has been published on the protein recognition properties of HSPGs and their association with signaling receptor complexes. However, more questions are being raised than problems solved by these analyses, perhaps as a result of the unusual properties of the HS chains that determine the majority of the interactions of PGs with external proteins. HS polysaccharides display a versatility in conformation and orientation of functional groups that permits them to employ different modes of binding with any individual protein or protein complex. Here, I argue that this versatility could offset the need for the controlled synthesis of a vast repertoire of defined sequences for exclusive binding of individual proteins.
Pervanadate [peroxide(s) of vanadate] mimics insulin action in rat adipocytes via activation of the insulin receptor tyrosine kinase (1989)

Both vanadate and hydrogen peroxide (H2O2) are known to have insulin-mimetic effects. We previously reported that the mixture of vanadate plus H2O2 results in the generation of a peroxide(s) of vanadate, which strongly enhances IGF-II binding to rat adipocytes (Kadota et al., 1987b). We now report that pervanadate mimics insulin in isolated rat adipocytes to (1) stimulate lipogenesis, (2) inhibit epinephrine-stimulated lipolysis, and (3) stimulate protein synthesis. The efficacy of pervanadate is comparable to that of insulin. However, it is 10(2)-10(3) times more potent than vanadate alone. Exposure of intact rat adipocytes to pervanadate was found to activate the WGA-purified insulin receptor tyrosine kinase assayed with the exogenous substrate poly(Glu80/Tyr20) in a dose-dependent manner to a maximum of 1464% of control at 10(-3) M compared with a maximum insulin effect of 1046% at 10(-6) M. In contrast, in vitro assayed autophosphorylation of the WGA-purified extract was increased 3-fold after exposure of intact cells to insulin but not significantly increased after pervanadate. Furthermore, high concentrations of pervanadate (10(-5) M) inhibited subsequent in vitro added insulin-stimulated autophosphorylation. In vitro addition of pervanadate to WGA-purified receptors could not stimulate autophosphorylation or exogenous tyrosine kinase activity and did not inhibit insulin-stimulated autophosphorylation. Labeling of intact adipocytes with [32P]orthophosphate followed by exposure to 10(-4) M pervanadate increased insulin receptor beta-subunit phosphorylation (7.9 +/- 3.0)-fold, while 10(-7) M insulin and 10(-4) vanadate increased labeling (5.3 +/- 1.8)- and (1.1 +/- 0.2)-fold, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)
Vibronic Fine Structure Found in the Blue Luminescence from Silicon Nanocolloids (1999)

Well-isolated vibronic fine structures are observed on the ultraviolet-visible photoluminescence spectrum from suspended silicon nanometer-sized particles in an organic fluid. Progression analyses of these structures and IR data show that these structures come from various local vibrational modes that couple with the localized electronic state of surface chemical species related to oxygen.
Surface-Confined Nanoparticles as Substrates for Photopolymerizable Self-Assembled Monolayers (1999)

Constraints on substrate size and shape are minimized in the fully solution-based approach to surface fabrication reported here. It is shown that not only is it possible to prepare self-assembled monolayers of a diacetylene compound on colloidal gold nanoparticles that are adsorbed onto supported organic films, but also subsequent polymerization yields highly conjugated poly(diacetylene). The ability to fabricate nanosized gold particles coated with conjugated polymers holds interesting possibilities for applications in nonlinear optics and electronics.
A gene expression fingerprint of C. elegans embryonic motor neurons (2005)

We have described a microarray-based method, MAPCeL, for profiling gene expression in specific C. elegans motor neurons and provide evidence that this approach can reveal candidate genes for key roles in the differentiation and function of these cells. These methods can now be applied to generate a gene expression map of the C. elegans nervous system.
The effect on sero-viral transcript by inhibiting transmission of hepatitis B virus from mother to infant (2006)

Objective
To further investigate the preventive effects on different intervention approaches on mother-infant vertical transmission of hepatitis B virus(HBV). To investigate the characteristics and clinical significance of HBV transcripts(RNA)in transmitting from mother to infant.


Methods
91 cases chronic HBsAg/HBeAg-carriers in pregnancy were divided into two groups. 61 cases received anti-HBV immunoglobulin injections and levamisole liniment since the 26th week of gestation ; 30 control cases did not receive the treatment. The viral DNA and different types of transcripts in the sera were detected using PCR and RT-PCR, respectively. Representative amplification products were cloned and sequenced. The serum viral nucleic acids extracted from pairs of mother and infant were analyzed using PCR and RT-PCR targeted to the HBV protein-encoding region. Reaction specificity was confirmed by Southern blotting.


Results
The seropositivity rates for HBsAg, viral DNA and full-length and trucated transcripts in babies from the treatment and reference groups were3. 3%, 3. 3%, 47. 5% and 6. 7%, 13. 3%, 70. 0%, with the first three parameters, rather than the last one, being significantly reduced in the former group than those in the latter.


Conclusion
The intervention therapy with immunoglobulin injections and levamisole liniment during pregnancy seems preventive on the vertical transmission of HBsAg, HBV DNA and full-length transcripts, rather than that of the truncated viral RNA moleicues obviously reduced transcripts. Compared with HBV DNA and HBV gene expressing products, trRNA might be a earlier detectable serum maker for identifying HBV infection profile accurately in infnats, which was associated closely with their mothers' expression of trRNA.


Key words: 
preventive intervention; hepatitis B virus; levamisole liniment; HBV immunoglobulin; viral transcript
The Complexation of Tetracycline and Anhydrotetracycline with Mg2+ and Ca2+:  A Spectroscopic Study (1998)

Steady-state absorption and emission, circular dichroism (CD), and time-of-flight secondary-ion-mass-spectroscopic (TOF−SIMS) measurements were performed to study the complexation of tetracycline (TC) and anhydrotetracycline (AHTC) with Mg2+ and Ca2+ ions, respectively, in aqueous solutions at pH 8.02. The results obtained suggest that Ca2+ forms a 1:2 ligand:metal complex with TC via chelation through O10−O11 and O12−O1 and induces thereby the extended conformation A of TC, which is stabilized through hydrogen bonding between the deprotonated dimethylamino nitrogen, N4, and OH12a. pH titrations provide evidence that N4 deprotonates in the presence of a 164-fold molar excess of Ca2+ at approximately pH ⩾ 7.7 (cTC = 2.1 × 10-5 M). In contrast to Ca2+, Mg2+ binds to N4−O3 and thereby stabilizes the twisted conformation B of TC. TOF−SIMS measurements indicate that a 1:2 ligand:metal complex is formed in addition to the 1:1 complex. The Mg2+-induced increase in the fluorescence intensity and the observed changes in the absorption spectra provide evidence that the other Mg2+ ion binds to the BCD ring system through the deprotonated O11. In contrast to TC, which adopts the twisted conformation B in aqueous solution at pH 8.02, AHTC exhibits the extended conformation A due to slightly lower deprotonation constants. In the presence of Mg2+, however, the conformational equilibrium is shifted toward the twisted conformation B due to binding of Mg2+ to N4. TOF−SIMS measurements suggest that a 2:2 ligand:metal complex is formed. AHTC remains in conformation A upon addition of Ca2+; complexation through O10 can be excluded on the basis of absorption spectroscopic data.
Demonstration of a role for α-synuclein as a functional microtubule-associated protein (2004)

Alpha-synuclein is a major constituent of pathological intracellular inclusion bodies, a common feature of several neurodegenerative diseases. Two missense mutations in the alpha-synuclein gene have been identified in confirmed autosomal-dominant familial Parkinson's disease, which segregate with the illness. However, the physiological function of alpha-synuclein remains unknown. After biochemical investigations we have revealed tubulin to be an alpha-synuclein associated/binding protein. Here, we show that alpha-synuclein induces polymerization of purified tubulin into microtubules. Mutant forms of alpha-synuclein lose this potential. The binding site of alpha-synuclein to tubulin is identified, and co-localization of alpha-synuclein with microtubules is shown in cultured cells. To our knowledge, this is the first demonstration of microtubule-polymerizing activity of alpha-synuclein. Now we can see a striking resemblance between alpha-synuclein and tau: both have the same physiological function and pathological features, making abnormal structures in diseased brains known as synucleinopathies and tauopathies. The discovery of a physiological role for alpha-synuclein may provide a new dimension in researches into the mechanisms of alpha-synuclein-associated neurodegenerative diseases.
Fluctuations in microvascular blood flow parameters caused by hemodynamic mechanisms (1994)

We have developed a mathematical model of microvascular network blood flow in which the nonlinear flow properties of blood and the nonuniform axial distribution of red blood cells in each vessel, as well as disproportionate cell partitioning at bifurcations, are all accounted for. The movements of red blood cells in the network are tracked; hence, the model is able to simulate temporal variations in local flow parameters in the network due to hemodynamic mechanisms. The model was applied to four rat mesenteric networks for which the topology, boundary conditions, blood velocity, and discharge hematocrit (Hctd) had been measured for each branch. Temporal variations in Hctd and blood velocity after simulation convergence were predicted. In some cases of the three vessels connected to a node, Hctd of one vessel fluctuates in a simple periodic form, Hctd of the second one oscillates in a more complex periodic form, whereas the Hctd of the third one does not oscillate at all. These variations were obtained with constant flow boundary conditions and, therefore, are due to hemodynamic factors alone. The temporal variations in flow parameters predicted by the model simulations are caused by hemorheological mechanisms and would be superimposed on variations caused by other mechanisms (e.g., vasomotion). The frequencies of the predicted fluctuations in blood velocity are in qualitative agreement with observed in vivo variations in dual-slit velocity in the arterioles of the cremaster muscle of anesthetized Golden hamster.
Investigating by CD the molecular mechanism of elasticity of elastomeric proteins (2008)

Elastomeric proteins are widespread in the animal kingdom, and their main function is to confer elasticity and resilience to organs and tissues. Besides common functional properties, elastomeric proteins share a common sequence design. They are usually constituted by repetitive sequences with a high content of glycine residues. From a conformational point of view, all the elastomeric proteins since now analyzed show a dynamic equilibria between folded (mainly beta-turns) and extended (polyproline II and beta-strands) conformations that could be at the origin of the high entropy of the relaxed state. As a matter of fact, elastin, lamprin, abductin, as well as the PEVK domain of titin share the same conformational ensemble, thus pointing to a common molecular mechanism as the origin of elasticity. CD spectroscopy represents the proper spectroscopic technique to be used overall because of its particular sensitivity to the presence of PPII structure. Its use in the molecular studies of elastin, abductin, and lamprin as well as the recently analyzed protein resilin will be presented.
Vehicle Speed Estimation Using Accelerometer and Wheel Speed Measurements (2002)

&lt;div class="htmlview paragraph"&gt;This paper treats the problem of estimating the longitudinal velocity of a braking vehicle using measurements from an accelerometer and wheel speed data from standard antilock braking wheel speed sensors. We develop and experimentally test three velocity estimation algorithms of increasing complexity. The algorithm that works the best gives peak errors of less than 3 percent even when the accelerometer signal is significantly biased.&lt;/div&gt;
Captopril Inhibits Capillary Degeneration in the Early Stages of Diabetic Retinopathy (2007)

Inhibition of the renin-angiotensin system can block retinal capillary degeneration and inflammation in the early stages of diabetic retinopathy.
Paracrine Systems in the Cardioprotective Effect of Angiotensin-Converting Enzyme Inhibitors on Myocardial Ischemia/Reperfusion Injury in Rats (1996)

After transient episodes of ischemia, benefits of thrombolytic or angioplastic therapy may be limited by reperfusion injury. Angiotensin-converting enzyme inhibitors protect the heart against ischemia/reperfusion injury, an effect mediated by kinins. We examined whether the protective effect of the angiotensin-converting enzyme inhibitor ramiprilat on myocardial ischemia/reperfusion is due to kinin stimulation of prostaglandin and/or nitric oxide release. The left anterior descending coronary artery of Lewis inbred rats was occluded for 30 minutes, followed by 120 minutes of reperfusion. Immediately before reperfusion rats were treated with vehicle, ramiprilat, or the angiotensin II type 1 receptor antagonist losartan. We tested whether pretreatment with the kinin receptor antagonist Hoe 140, the nitric oxide synthase inhibitor NG-nitro-L-arginine methyl ester, or the cyclooxygenase inhibitor indomethacin blocked the effect of ramiprilat on infarct size and reperfusion arrhythmias. In controls, infarct size as a percentage of the area at risk was 79 +/- 3%; ramiprilat reduced this to 49 +/- 4% (P < .001), but losartan had little effect (74 +/- 6%, P = NS). Pretreatment with Hoe 140, NG-nitro-L-arginine methyl ester, or indomethacin abolished the beneficial effect of ramiprilat. Compared with the 30-minute ischemia/120-minute reperfusion group, nonreperfused hearts with 30 minutes of ischemia had significantly smaller infarct size as a percentage of the area at risk, whereas in the 150-minute ischemia group it was significantly larger. This suggests that reperfusion caused a significant part of the myocardial injury, but it also suggests that compared with prolonged ischemia, reperfusion salvaged some of the myocardium. Ventricular arrhythmias mirrored the changes in infarct size. Thus, angiotensin-converting enzyme inhibitors protect the myocardium against ischemia/reperfusion injury and arrhythmias; these beneficial effects are mediated primarily by a kinin-prostaglandin-nitric oxide pathway, not inhibition of angiotensin II formation.
A Recessive Variant of the Romano-Ward Long-QT Syndrome? (1998)

These findings provide the first evidence for a recessive form of the Romano-Ward long-QT syndrome and indicate that homozygous mutations on KVLQT1 do not invariably produce the Jervell and Lange-Nielsen syndrome. The implications of this observation prompt a reconsideration of the penetrance of different mutations responsible for LQTS and suggest that mild mutations in LQTS genes may be present among the general population and may predispose to drug-induced ventricular arrhythmias.
Effects of conventional and a novel colonic‐release bile acid sequestrant, A3384, on fibroblast growth factor 19 and bile acid metabolism in healthy volunteers and patients with bile acid diarrhoea (2016)

Serum FGF19 was suppressed and bile acid production up-regulated on conventional bile acid sequestrants, but not with A3384. This colonic-release formulation of colestyramine produced symptomatic benefit in patients with BAD.
Anatomy of an Endogenous Antagonist: Relationship between Agouti-Related Protein and Proopiomelanocortin in Brain (1999)

Agouti-related protein (AGRP) is a recently discovered orexigenic neuropeptide that inhibits the binding and action of alpha-melanocyte-stimulating hormone derived from proopiomelanocortin (POMC) at the melanocortin 3 receptor (MC3R) and melanocortin 4 receptor (MC4R) and has been proposed to function primarily as an endogenous melanocortin antagonist. To better understand the interplay between the AGRP and melanocortin signaling systems, we compared their nerve fiber distributions with each other by immunohistochemistry and their perikarya distribution with MC3R and MC4R by double in situ hybridization. Although deriving from distinct cell groups, AGRP and melanocortin terminals project to identical brain areas. Both AGRP and melanocortin neurons selectively express the MC3R, which provides a neuroanatomical basis for a dual-input circuit with biological amplification and feedback inhibition. These studies highlight a broader complexity in POMC-mediated behavior in the brain.
Simultaneous gene expression analysis of steady-state and actively translated mRNA populations from osteosarcoma MG-63 cells in response to IL-1 via an open expression analysis platform (2003)

Pro-inflammatory cytokines play a key role in various forms of metabolic bone diseases, including osteopenia and osteoporosis. Human MG-63 cells treated with IL-1alpha were used as a model system to identify potential marker genes that are differentially expressed. This study is designed to quantitate gene expression of actively translated mRNAs as compared to the steady-state mRNA population. Both steady-state mRNAs and actively translated mRNAs from control MG-63 cells and MG-63 cells treated with IL-1alpha were isolated and converted to cDNA. The gene expression analysis from these samples was then quantitated with an open expression analysis platform with no requirement for a priori knowledge of sequence information. As a result, many differentially regulated genes were discovered via IL-1alpha treatment. Some of the genes have been described previously as playing important roles in the regulation of inflammation and cell adhesion. These comparisons provided a panoramic overview of gene expression at both the total transcript and post-transcriptional levels. In addition, the quantitation of actively translated mRNAs associated with polysomes also provided a better estimation of protein expression levels. This methodology allows for the identification of genes acutely regulated during translation. Furthermore, the process may aid in the identification of new drug targets or biomarkers.
High-Resolution Profiling of Fetal DNA Clearance from Maternal Plasma by Massively Parallel Sequencing (2013)

MPS of maternal plasma and urinary DNA permits high-resolution study of the clearance profile of circulating fetal DNA.