gebhart/patrepeval huggingface dataset:
Dual function of the tRNA(m5U54)methyltransferase in tRNA maturation (2002)

A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalyzed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. In this study, we identified four different strains with mutant forms of tRNA(Ser)CGA. The absence of the TRM2 gene in these strains decreased the stability of tRNA(Ser)CGA and induced lethality. Two alleles of TRM2 encoding catalytically inactive tRNA(m5U54)methyltransferases were able to stabilize tRNA(Ser)CGA in one of the mutants, revealing a role for the Trm2 protein per se in tRNA maturation. Other tRNA modification enzymes interacting with tRNA(Ser)CGA in the maturation process, such as Pus4p, Trm1 p, and Trm3p were essential or important for growth of the tRNA(Ser)CGA mutants. Moreover, Lhp1p, a protein binding RNA polymerase III transcripts, was required to stabilize the mutant tRNAs. Based on our results, we suggest that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.
Clinical relevance of circulating mucosal-associated invariant T cell levels and their anti-cancer activity in patients with mucosal-associated cancer (2016)

Mucosal-associated invariant T (MAIT) cells are an antimicrobial MR1-restricted T cell subset and play an important role in immune defense response to bacteria. However, little is known about the role of MAIT cells in cancer. The aims of this study were to examine the level and function of MAIT cells in cancer patients and to evaluate the clinical relevance of MAIT cell levels. Ninety-nine patients with cancer and 20 healthy controls were included in this study. Circulating MAIT cell levels were significantly reduced in patients with mucosal-associated cancers (MACs), such as gastric, colon and lung cancers, but their capacities for IFN-γ, IL-17, or TNF-α production were preserved. This MAIT cell deficiency was significantly correlated with N staging and carcinoembryonic antigen level. Percentages of MAIT cells were significantly higher in cancer tissue than in peripheral blood and immunofluorescent labeling showed MAIT cell infiltration into colon cancer tissues. Circulating MAIT cells exhibited high levels of CCR6 and CXCR6, and their corresponding chemokines, such as CCL20 and CXCL16, were strongly expressed in colon cancer tissues. Activated MAIT cells not only had lymphokine-activated killer activity, but they also had direct cytotoxicity on K562 cells via degranulation of granzyme B and perforin. This study primarily demonstrates that circulating MAIT cells are reduced in MAC patients due to migration to mucosal cancer tissues and they have the potential to kill cancer cells. In addition, this circulating MAIT cell deficiency is related to the degree of cancer progression in mucosal tissues.
Neurotoxin Treatments for Urinary Incontinence in Subjects With Spinal Cord Injury or Multiple Sclerosis: A Systematic Review of Effectiveness and Adverse Effects (2008)

Neurotoxins may improve refractive UI in adults with SCI or MS, although trial results were inconsistent. Trials were small in size and relatively short in duration. Further studies are needed to determine the efficacy and tolerability of long-term application.
Some Dihalo-(trifluoromethyl)-benzenes (1951)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSome Dihalo-(trifluoromethyl)-benzenesE. T. McBee, O. R. Pierce, R. D. Lowery, and E. RapkinCite this: J. Am. Chem. Soc. 1951, 73, 8, 3932–3934Publication Date (Print):August 1, 1951Publication History Published online1 May 2002Published inissue 1 August 1951https://pubs.acs.org/doi/10.1021/ja01152a111https://doi.org/10.1021/ja01152a111research-articleACS PublicationsRequest reuse permissionsArticle Views332Altmetric-Citations9LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The su(Hw) Insulator Can Disrupt Enhancer-Promoter Interactions When Located More than 20 Kilobases Away from the <i>Drosophila</i> achaete-scute Complex (1999)

Here we report that the su(Hw) insulator may not necessarily separate promoters from enhancers to allow inhibition of transcription by the su(Hw) protein. For this purpose we used the strains of Drosophila melanogaster which carry inversion of the region containing the yellow gene and the achaete-scute complex (AS-C). Despite the reverse orientation of the region, the AS-C enhancers continue to activate achaete and scute gene expression. The su(Hw) insulator, located more than 20 kb away from the inversion, facilitates strong suppression of achaete and scute gene expression, although is does not separate the promoters from the AS-C enhancers.
Equilibrium and Kinetics of Rotamer Interconversion in Immunosuppressant Prodigiosin Derivatives in Solution (1999)

The equilibrium and relative rate of rotamer interconversion around the bond joining the 2,2'-bipyrrolyl and pyrromethene moieties in a synthetic analogue of immunosuppressant prodigiosin are investigated as a function of pHapp in a water/acetonitrile mixture (1/1 by volume). Two chromatographically separable isomeric forms are obtained in acid solutions (pHapp < 4), whereas rapid interconversion occurs above neutrality. Furthermore, pH modulates the conformational preference of the molecule according to nitrogen protonation on the three pyrrole rings system (pKa = 7.2). At high pHapp (neutral form), the same conformer that is observed in pure acetonitrile prevails, whereas the other one is preferred by the protonated form. The nuclear magnetic resonance data indicate that the structures of the two conformers mainly differ in the value of the torsion angle around the aforementioned C-C bond. Kinetic and equilibrium data are quantitatively interpreted with a cyclic mechanism including two protonation (pKa1 = 8.23 +/- 0.03, pKa2 = 5. 4 +/- 0.2) and two conformational rearrangement steps. A molecular interpretation of the observed behavior includes, for the preferred conformer at low pH, formation of a new hydrogen bond between the exocyclic oxygen and the neighboring pyrrole NH upon protonation of the three pyrrole rings system.
Flail chest as a marker for significant injuries. (1994)

The records of 92 patients with flail chest injury treated at a Level I trauma center were analyzed retrospectively. Associated intrathoracic injuries included pulmonary contusion (46 percent) and pneumothorax or hemothorax, or both (70 percent). The incidence of great vessel, tracheobronchial and diaphragmatic injuries was no different from that of a control population with simple rib fractures. Adult respiratory distress syndrome developed in 27 percent of patients with flail chest; 69 percent of all patients required ventilation (mean duration, 22 days). Mean length of hospital stay was 24 days. The mortality rate was 33 percent. We conclude that flail chest serves as a marker of significant intrathoracic injury, highly associated with pulmonary contusion, but even more so with pneumothorax or hemothorax. Flail chest does not seem to be a marker for great vessel, tracheobronchial, or diaphragmatic injuries. The majority of patients (more than two-thirds) will require mechanical ventilation for prolonged periods. Of paramount importance is the recognition of flail chest as a marker of high kinetic energy absorption, resulting in life-threatening thoracic as well as nonthoracic injuries.
Performance Test of Autonomous Vehicle Lidar Sensors Under Different Weather Conditions (2020)

This paper intends to analyze the Light Detection and Ranging (Lidar) sensor performance on detecting pedestrians under different weather conditions. Lidar sensor is the key sensor in autonomous vehicles, which can provide high-resolution object information. Thus, it is important to analyze the performance of Lidar. This paper involves an autonomous bus operating several pedestrian detection tests in a parking lot at the University at Buffalo. By comparing the pedestrian detection results on rainy days with the results on sunny days, the evidence shows that the rain can cause unstable performance and even failures of Lidar sensors to detect pedestrians in time. After analyzing the test data, three logit models are built to estimate the probability of Lidar detection failure. The rainy weather still plays an important role in affecting Lidar detection performance. Moreover, the distance between a vehicle and a pedestrian, as well as the autonomous vehicle velocity, are also important. This paper can provide a way to improve the Lidar detection performance in autonomous vehicles.
Isolation, Characterization and Differentiation Potential of Chicken Spermatogonial Stem Cell Derived Embryoid Bodies (2015)

Abstract Human, murine and monkey spermatogonial stem cells (SSCs) have the capability to undergo self-renewal and differentiation into different body cell types in vitro, which are expected to serve as a powerful tool and resource for the developmental biology and regenerative medicine. We have successfully isolated and characterized the chicken SSCs from 3-day-old chicken testicular cells. The pluripotency was using Periodic Acid-Schiff (PAS ) staining or alkaline phosphatase staining, and antibodies to stage-specific embryonic antigens. In suspension culture conditions SSCs formed embryoid bodies (EBs) like embryonic stem (ES) cells. Subsequently EB differentiated into osteoblasts, adipocytes and most importantly into cardiomyocytes under induced differentiation conditions. The differentiation potential of EBs into cardiomyocyte-like cells was confirmed by using antibodies against sarcomeric α-actinin, cardiac troponin T and connexin 43. Cardiomyocytes-like cells were also confirmed by RT-PCR analysis for several cardiac cell genes like GATA-4, Nkx2-5, α-MHC, and ANF. We have successfully established an in vitro differentiation system for chicken SSCs into different body cells such as osteoblasts, adipocytes and cardiomyocytes. The most significant finding of this study is the differentiation potential of chicken SSCs into cardiomyocytes. Our findings may have implication in developmental biology and regenerative medicine by using chicken as the most potential animal model.
Clean Nanotube Unzipping by Abrupt Thermal Expansion of Molecular Nitrogen: Graphene Nanoribbons with Atomically Smooth Edges (2012)

We report a novel physicochemical route to produce highly crystalline nitrogen-doped graphene nanoribbons. The technique consists of an abrupt N(2) gas expansion within the hollow core of nitrogen-doped multiwalled carbon nanotubes (CN(x)-MWNTs) when exposed to a fast thermal shock. The multiwalled nanotube unzipping mechanism is rationalized using molecular dynamics and density functional theory simulations, which highlight the importance of open-ended nanotubes in promoting the efficient introduction of N(2) molecules by capillary action within tubes and surface defects, thus triggering an efficient and atomically smooth unzipping. The so-produced nanoribbons could be few-layered (from graphene bilayer onward) and could exhibit both crystalline zigzag and armchair edges. In contrast to methods developed previously, our technique presents various advantages: (1) the tubes are not heavily oxidized; (2) the method yields sharp atomic edges within the resulting nanoribbons; (3) the technique could be scaled up for the bulk production of crystalline nanoribbons from available MWNT sources; and (4) this route could eventually be used to unzip other types of carbon nanotubes or intercalated layered materials such as BN, MoS(2), WS(2), etc.
Combined hyperthermia and chlorophyll-based photodynamic therapy: tumour growth and metabolic microenvironment (2003)

The effects of combined and simultaneously applied localised 43 degrees C hyperthermia (HT) and an antivascular bacteriochlorophyll-serine-based photodynamic therapy (Bchl-ser-PDT) on tumour growth and several microenvironmental parameters were examined. Rats bearing DS-sarcomas were allocated to treatment groups: (i) sham-treatment (control), (ii) Bchl-ser-PDT (20 mg kg(-1) i.v.), (iii) localised HT, (iv) Bchl-ser-PDT+HT. The light source used was an infrared-A irradiator, which, by use of appropriate filters, delivered the different ranges of wavelengths required. Following treatment, tumour volume was monitored. The greatest tumour growth inhibition was seen with Bchl-ser-PDT+HT, and subsequent experiments identified the pathophysiological basis for this effect. Red blood cell flux in tumour microvessels declined rapidly upon Bchl-ser-PDT+HT, reaching approximately 10% of initial values by the end of treatment. Similarly, tumour oxygenation worsened, reaching almost anoxic levels by the end of the treatment period. Assessment of metabolic parameters showed a pronounced increase in lactate levels and a decrease in ATP concentrations after combined treatment. The results presented suggest that vascular collapse and flow stasis resulting in a deterioration of tumour oxygenation and a switch from oxidative to glycolytic glucose turnover are key elements in the tumour eradication seen with this novel approach in which an antivascular PDT and HT are combined and simultaneously applied.
Effect of Epithelial Sodium Channel Blockade on the Myogenic Response of Rat Juxtamedullary Afferent Arterioles (2009)

The mechanotransduction mechanism underlying the myogenic response is poorly understood, but evidence implicates participation of epithelial sodium channel (ENaC)-like proteins. Therefore, the role of ENaC on the afferent arteriolar myogenic response was investigated in vitro using the blood-perfused juxtamedullary nephron technique. Papillectomy was used to isolate myogenic influences by eliminating tubuloglomerular feedback signals. Autoregulatory responses were assessed by manipulating perfusion pressure in 30-mm Hg steps. Under control conditions, arteriolar diameter increased by 15% from 13.0+/-1.3 to 14.7+/-1.2 microm (P<0.05) after reducing perfusion pressure from 100 to 70 mm Hg. Diameter decreased to 11.3+/-1.1 and 10.6+/-1.0 microm after increasing pressure to 130 and 160 mm Hg (88+/-1 and 81+/-2% of control diameter, P<0.05), respectively. Pressure-mediated autoregulatory responses were significantly inhibited by superfusion of 10 micromol/L amiloride (102+/-2, 97+/-4, and 94+/-3% of control diameter), or 10 micromol/L benzamil (106+/-5, 100+/-3, and 103+/-3% of control diameter), and when perfusing with blood containing 5 micromol/L amiloride (106+/-2, 97+/-4, and 97+/-4% of control diameter). Vasoconstrictor responses to 55 mmol/L KCl were preserved as diameters decreased by 67+/-4, 55+/-8, and 60+/-4% in afferent arterioles superfused with amiloride or benzamil, and perfused with amiloride, respectively. These responses were similar to responses obtained from control afferent arterioles (64+/-6%, P>0.05). Immunofluorescence revealed expression of the alpha, beta, and gamma subunits of ENaC in freshly isolated preglomerular microvascular smooth muscle cells. These results demonstrate that selective ENaC inhibitors attenuate afferent arteriolar myogenic responses and suggest that ENaC may function as mechanosensitive ion channels initiating pressure-dependent myogenic responses in rat juxtamedullary afferent arterioles.
ChemInform Abstract: OXIDATIVE ADDITION OF 1,3‐DICARBONYL COMPOUNDS TO OLEFINS IN THE PRESENCE OF THE MANGANESE(III) ACETATE/LITHIUM CHLORIDE SYSTEM AND SYNTHESIS OF FUNCTIONALLY SUBSTITUTED CYCLOPROPANES (1984)

Abstract Acetylaceton (I) als 1,3‐Dicarbonylverbindung reagiert in Gegenwart des Systems Mn(OAc)3/LiCl mit den Olefinen (II) unter oxidativer Anlagerung, wobei als Hauptprodukte die Verbindungen (III) entstehen.
POLYNUCLEOTIDES. I. MOLECULAR PROPERTIES AND CONFIGURATIONS OF POLYRIBOADENYLIC ACID IN SOLUTION<sup>1</sup> (1957)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPOLYNUCLEOTIDES. I. MOLECULAR PROPERTIES AND CONFIGURATIONS OF POLYRIBOADENYLIC ACID IN SOLUTION1Jacques R. Fresco and Paul DotyCite this: J. Am. Chem. Soc. 1957, 79, 14, 3928–3929Publication Date (Print):July 1, 1957Publication History Published online1 May 2002Published inissue 1 July 1957https://pubs.acs.org/doi/10.1021/ja01571a089https://doi.org/10.1021/ja01571a089research-articleACS PublicationsRequest reuse permissionsArticle Views124Altmetric-Citations158LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Intestinal Absorption of Low Permeability Drugs: A Transporter- and Enzyme- Targeted Approach. (2010)

This dissertation is the investigation of a prodrug strategy for increased oral absorption via transport by hPEPT1 and activation by hVACVase. L-Valine, L-isoleucine and L-phenylalanine esters of a guanidino-containing model compound [3-(hydroxymethyl)phenyl]guanidine (3-HPG) were synthesized and evaluated for the feasibility of this prodrug approach to guanidino-containing drugs. In HeLa/hPEPT1 cells, Val-3-HPG and Ile-3-HPG exhibited high affinity to hPEPT1 (IC50: 0.65 mM and 0.63 mM, respectively), and all three L-amino acid esters showed higher uptake (2.6- to 9-fold) than the parent compound 3-HPG. Val-3-HPG and Ile-3-HPG demonstrated remarkable Caco-2 permeability enhancement, and Val-3-HPG exhibited comparable permeability to valacyclovir. The low permeability of D-Val-3-HPG and the inhibition studies indicated that hPEPT1 was the predominant transporter responsible for Val-3-HPG permeability. In rat perfusion studies, Val-3-HPG and Ile-3-HPG permeabilities were significantly higher than 3-HPG, and exceeded/matched the high-permeability standard metoprolol, respectively. In HeLa and Caco-2 cell homogenates, the hydrolysis of amino acid esters was faster than in the corresponding buffer, indicating predominant enzymatic activation. All the L-amino acid 3-HPG esters were found to be good substrates of hVACVase, and exhibited higher specificity constants than that for valacyclovir (kcat/Km in mM-1•s-1: Val-3-HPG, 3370; Ile-3-HPG, 1580; Phe-3-HPG, 1660; valacyclovir, 850), presumably resulting from high binding affinity to hVACVase as well as favorable leaving group lability. The results in this study suggested that the leaving group had an effect on both binding and specific activity of hVACVase-catalyzed prodrug activation. hVACVase is an ideal target for α-amino acid ester prodrugs with relatively labile leaving groups but is unable to activate amide prodrugs.
Structural relationship between the mammalian Fe(III)‐Fe(II) and the Fe(III)‐Zn(II) plant purple acid phosphatases (1995)

The primary structure of uteroferrin (Uf), a 35 kDa monomeric mammalian purple acid phosphatase (PAP) containing a Fe(III)-Fe(II) center, has been compared with the sequence of the homodimeric 111 kDa Fe(III)-Zn(II) kidney bean purple acid phosphatase (KBPAP). The alignment suggests that the amino acid residues ligating the dimetal center are identical in Uf and KBPAP, although the geometry of the coordination sphere might slightly differ. Secondary structure predictions indicate that Uf contains two beta alpha beta alpha beta motifs thus resembling the folding topology of the plant enzyme. Guided by the recently determined X-ray structure of KBPAP a tentative model for the mammalian PAP can be constructed.
WebTelop: dynamic TV-content augmentation by using Web pages (2003)

In this paper, we propose a method for dynamic integration of TV-program content and related Web content and demonstrate our prototype system called WebTelop. The primary source of information in WebTelop is the TV-program content. Web pages related to the TV-program content are retrieved automatically in real time and are used to augment the TV-program content in the form of captions. Our method enables: (1) real time integration of TV-program content with Web-page content, (2) information retrieval for TVprogram content augmentation based on the topic structures of the TV programs and Web pages, and (3) the use of a virtual character agent to help users navigate through the related Web pages of the TV programs.
Outcome of Pregnancy in Patients with Organic Heart Disease in Taiwan (1993)

A total of 122 pregnancies in 101 women with organic heart disease were reviewed. The incidence of organic heart disease in pregnant women was 0.25%. The ratio of rheumatic to congenital heart disease was 1.0 to 1.5. In the congenital heart disease group, IUGR was more frequent in the cyanotic group as were preterm births. Patients with cyanotic lesions had a significantly higher maternal mortality rate than those with acyanotic lesions. The cyanotic group without surgical correction had a significantly higher maternal mortality rate and more IUGR than those with correction. Congestive heart failure was the most common maternal complication, with a rate of 38.1%. The patients with good cardiac status control during pregnancy developed less IUGR, had fewer preterm births, less maternal morbidity and less maternal mortality than those in poor condition. Patients in functional classes I and II before pregnancy carried less risk of maternal morbidity than those in classes III and IV.