gebhart/patrepeval huggingface dataset:
Picornavirus internal ribosome entry segments: comparison of translation efficiency and the requirements for optimal internal initiation of translationin vitro (1995)

On the basis of primary sequence comparisons and secondary structure predictions, picornavirus internal ribosome entry segments (IRESes) have been divided into three groups (entero- and rhinoviruses; cardio- and and aphthoviruses; and hepatitis A virus). Here, we describe a detailed comparison of the ability of IRESes from each group to direct internal initiation of translation in vitro using a single dicistronic mRNA (the only variable being the IRES inserted into the dicistronic region). We studied the influence of various parameters on the capacity of six different picornaviral IRESes, and the non-picornaviral hepatitis C virus IRES, to direct internal initiation of translation: salt concentration, the addition of HeLa cell proteins to rabbit reticulocyte lysate translation reactions, the presence of foot-and-mouth disease virus Lb or human rhinovirus 2A proteinase. On the basis of the characteristics of IRES-driven translation in vitro, the picornaviral IRESes can be classified in a similar manner to when sequence homologies are considered. IRESes from each of the three groups responded differently to all of the parameters tested, indicating that while all of these elements can direct internal ribosome entry, the functional requirements for efficient IRES activity vary dramatically. In the individual optimal conditions for translation initiation, the best IRESes were those from the cardio- and aphthoviruses, followed by those from the enteroviruses, which exhibited up to 70% of the efficiency of the EMCV element in directing internal initiation of translation.
New mouse models for chronic Cryptosporidium infection in immunodeficient hosts (1990)

Cryptosporidium sp. causes fulminant diarrhea and chronic infection in immunocompromised, particularly human immunodeficiency virus-infected, persons. The lack of in vitro cultivation and a suitable animal model has limited development of effective treatment. We describe two new mouse models of chronic symptomatic cryptosporidiosis in adult athymic mice and in T-cell subset-depleted mice. A progressive infection, fatal within 4 months, occurred in most adult athymic mice; a few developed stable infections. Symptoms included dehydration, weight loss, intermittent diarrhea, and jaundice. Pathologic abnormalities and organisms localized in the intestine in stable infections but involved the hepatobiliary tree and pancreas in others. Lymphoid cells from histocompatible, Cryptosporidium sp.-immune mice cured infected nude mice. Identical infections occurred in neonatally infected BALB/c mice treated with anti-CD4 monoclonal antibodies alone or also with anti-CD8 monoclonal antibodies; the mice were cured when the monoclonal antibody treatments were stopped. These models will be useful in definition of the immune defects that permit chronic cryptosporidiosis to develop and in assessment of treatment modalities.
Pancreatic Stem Cells (2009)

From the discovery of Pdx1, the first “master gene” of pancreatic development, to the most recent findings on the role of microRNAs in beta cell homeostasis, the last fifteen years have seen an unprec
Influence of Surface Roughness on Superhydrophobicity (2006)

Superhydrophobic surfaces, with a liquid contact angle theta greater than 150 degrees , have important practical applications ranging from self-cleaning window glasses, paints, and fabrics to low-friction surfaces. Many biological surfaces, such as the lotus leaf, have a hierarchically structured surface roughness which is optimized for superhydrophobicity through natural selection. Here we present a molecular dynamics study of liquid droplets in contact with self-affine fractal surfaces. Our results indicate that the contact angle for nanodroplets depends strongly on the root-mean-square surface roughness amplitude but is nearly independent of the fractal dimension D(f) of the surface.
Coronary thrombolysis with Desmodus salivary plasminogen activator in dogs. Fast and persistent recanalization by intravenous bolus administration. (1994)

In a canine coronary thrombosis model, DSPA exhibited higher potency and recanalized coronary arteries faster and with a lower incidence of reocclusion than TPA. Its properties may translate into a higher efficacy in patients compared with available thrombolytic agents. The long half-life of DSPA may allow for single bolus administration in the treatment of acute myocardial infarction.
Graphic Rule for Drug Metabolism Systems (2010)

Using graphic rules to deal with kinetic systems is an elegant approach by combining the graph representation (schematic representation) and rigorous mathematical derivation. It bears the following advantages: (1) providing an intuitive picture or illuminative insights; (2) helping grasp the key points from complicated details; (3) greatly simplifying many tedious, laborious, and error-prone calculations; and (4) able to double-check the final results. In this mini review, the non-steady state graphic rule in enzyme-catalyzed kinetics and protein-folding kinetics was extended to cover drug-metabolic systems. As a demonstration, a step-by-step illustration is presented showing how to use the graphic rule to derive the concentrations of the parent drug and its metabolites vs. time for the seliciclib, vildagliptin, and cyclin-dependent kinase inhibitor (AG-024322) metabolic systems, respectively. It can be seen from these paradigms that the graphic rule is particularly useful to analyze complicated drug metabolic systems and ensure the correctness of the derived results. Meanwhile, the intuitive feature of graphic representation may facilitate analyzing and classifying drug metabolic systems; e.g., according to their directed graphs, the metabolism of seliciclib and the metabolism of vildagliptin can be categorized as 0-->5 mechanism while that of AG-024322 as 0-->4-->3 mechanism.
A New and Direct Trifluoromethoxylation of Aliphatic Substrates with 2,4‐Dinitro(trifluoromethoxy)benzene (2010)

Abstract The reaction of tetrabutylammonium triphenyldifluorosilicate with 2,4‐dinitro(trifluoromethoxy)benzene, in acetonitrile and under microwave irradiation, generates a trifluoromethoxide anion which is able to substitute activated bromides (benzyl bromide, cinnamyl bromide), as well as, to some extent, alkyl iodides. Aliphatic trifluoromethyl ethers are thus formed. This is the first example of the nucleophilic displacement of the trifluoromethoxy group from an activated aromatic ring.
CAR-3, a monoclonal antibody-defined antigen expressed on human carcinomas. (1985)

Several monoclonal antibodies were raised against the human epidermoid carcinoma line A 431. The antibody produced by clone AR-3, when tested in enzyme-linked immunosorbent assay, was found to react with the cell line used as immunogen, the human gastric carcinoma line KATO III, the colon carcinoma line HT29, and the ovarian carcinoma line SW626. This monoclonal antibody was found unreactive when tested on human peripheral blood leukocytes or on a number of normal or neoplastic cell lines. The antibody precipitated a high-molecular-weight glycosylated component. When tested on paraffin sections by the avidin:biotin: peroxidase method, the AR-3 antibody stained pancreatic (6:7), gastric (11:14), ovarian (5:6), colon (4:8), endometrial (4:6), and cervical (4:7) carcinomas. A small minority of carcinomas of other organs was also stained. Sarcomas, lymphomas, and other tumors of nonepithelial origin were constantly negative. Staining of some normal epithelial cells was also observed. Among the fetal tissue tested, the antibody reacted with pancreatic ducts and the small intestine. The antibody recognized metastatic carcinoma cells in peritoneal effusions. On the basis of its tissue distribution, the antigenic determinant defined by the AR-3 monoclonal antibody was called CAR-3. The monoclonal AR-3 did not cross-react with partially purified preparations of carcinoembryonic antigen, gastrointestinal carcinoma antigen, or the human milk fat globule antigen. The AR-3 MAb appear, thus, to broaden the number of available reagents for histopathological diagnosis of carcinomas.
PLEDS: A Personalized Entity Detection System Based on Web Log Mining Techniques (2008)

With the expansion of the internet, many specialized, high-profile sites have become available that bring very technical subject matter to readers with non-technical backgrounds. While the theme of these sites may be of interest to these readers, the posts themselves may contain terms that non-experts may be unfamiliar with and may wish to know more about. We developed PLEDS, a personalized entity detection system which identifies interesting entities and provides related information for individual users by mining web logs and query logs. The experimental results of a systemic user study shows that with PLEDS's aid, users can experience the benefits of an enriched internet surfing experience.
Interstitial fluid: Exchange of macromolecules between plasma and skin interstitium (1981)

Fluid was collected from blisters developed by suction on the abdominal skin in ten normal volunteers. During the same study the transcapillary escape rate of intravenously injected 131I-albumin and 125I-IgG together with the accumulation of these tracers in the blister fluid was measured. The ratios between the concentrations of endogenous albumin, transferrin, IgG and alpha 2-macroglobulin in the blister fluid (Cb) and serum (Cs) correlated directly with the free diffusion coefficients indicating that the sieving properties of the vascular endothelium remained intact during the suction. The ratios of intravascular to total masses of the four endogenous proteins calculated from plasma volume, Cs, Cb and extracellular fluid volume determined with inulin and Cb were very similar to those obtained in long-term metabolic turnover studies. The ratio between the accumulated IgG and albumin tracers in the blister fluid (0.80) was identical with the Cb/Cs ratio between endogenous IgG and albumin (0.78) but higher than the ratio between the IgG and albumin escape rates from the total microvasculature (0.58). From the protein tracer determinations it cannot be definitely excluded that suction increases the microvascular escape rates. If the distribution volume of inulin equates that of albumin in steady-state it can, however, be concluded from the data given on the endogenous plasma protein, that blister fluid from the abdominal skin corresponds to average interstitial tissue fluid.
Detection of colorectal carcinoma by emission-computerized tomography after injection of 123I-labeled Fab or F(ab')2 fragments from monoclonal anti-carcinoembryonic antigen antibodies. (1986)

This clinical study was based on experimental results obtained in nude mice grafted with human colon carcinoma, showing that injected 131I-labeled F(ab')2 and Fab fragments from high affinity anti-carcinoembryonic antigen (CEA) monoclonal antibodies (MAb) gave markedly higher ratios of tumor to normal tissue localization than intact MAb. 31 patients with known colorectal carcinoma, including 10 primary tumors, 13 local tumor recurrences, and 21 metastatic involvements, were injected with 123I-labeled F(ab')2 (n = 14) or Fab (n = 17) fragments from MAb anti-CEA. The patients were examined by emission-computerized tomography (ECT) at 6, 24, and sometimes 48 h after injection using a rotating dual head scintillation camera. All 23 primary tumors and local recurrences except one were clearly visualized on at least two sections of different tomographic planes. Interestingly, nine of these patients had almost normal circulating CEA levels, and three of the visualized tumors weighed only 3-5 g. Among 19 known metastatic tumor involvements, 14 were correctly localized by ECT. Two additional liver and several bone metastases were discovered by immunoscintigraphy. Altogether, 86% of the tumor sites were detected, 82% with F(ab')2 and 89% with Fab fragments. The contrast of the tumor images obtained with Fab fragments suggests that this improved method of immunoscintigraphy has the potential to detect early tumor recurrences and thus to increase the survival of patients. The results of this retrospective study, however, should be confirmed in a prospective study before this method can be recommended for the routine diagnosis of cancer.
Septic encephalopathy. Evidence for altered phenylalanine metabolism and comparison with hepatic encephalopathy (1990)

We elected to test the hypothesis that the metabolic encephalopathy associated with systemic sepsis may have a pathogenesis that is similar to hepatic encepathology, ie, as the consequence of hepatic dysfunction that induces alterations in synthesis of catecholic and noncatecholic neurotransmitters. Eleven patients with septic encephalopathy were compared with nine patients with septic encephalopathy and nine normal controls with respect to blood and cerebrospinal fluid (CSF) amino acid profile, phenylethylamine and its metabolite phenylacetic acid, and blood ammonia. Blood and CSF levels of phenylacetic acid increased markedly in septic and hepatic encephalopathy while CSF phenylethylamine levels were not increased in either condition, presumably due to rapid turnover. The CSF concentrations of all the aromatic amino acids were increased in hepatic encephalopathy, whereas in the patients with sepsis, only phenylalanine levels were increased. Evidence of stimulated neutral amino acid transport into brain was demonstrated in hepatic not septic encephalopathy and appeared to correlate with the CSF glutamine concentration. Blood ammonia levels were increased in hepatic but not in septic encephalopathy. Our data support the hypothesis that metabolites of phenylethylamine contribute to encephalopathy in systemic sepsis and hepatic failure; however, the entities differ in other respects.
Partial sequence at 2BC region of HAV isolated from stool of acute sporadic HAV patients. (2002)

More than 20 hepatitis A virus (HAV) strains that can be distinguished from each other are known till now. In the present study, a cytopathic strain of HAV (HA-10) was isolated in Egypt from stool of acute sporadic cases. The isolated strain showed CPE in early stages of adaptation in cell culture. Accordingly, the first step in the work was to confirm the presence of HAV, the second step was to prove that no enteric virus is associated with the isolate and finally to try to know the reason for that rapid adaptation in cell culture. So, RT-PCR was carried out for different regions of the viral RNA (5'ntr, VP1, VP1/2A, 2B and 2B/2C) also, enterovirus primers (5'ntr) were used. Reference HAV strains such as HM-175, HAS-15, MBB and 18F were used for comparison. Segment of 2BC region of the viral RNA was sequenced and compared with the nucleotide sequence of the reference HAV strains at the same region. The results revealed that HA-10 isolate react with all HAV primers and similar in this behavior with 18F and HM-175 strains. The nucleotide sequencing showed that there are 16 mutations in HA-10, two of them in 2B and the others in 2C region which may explain the reason for the highly adaptation of HA-10 isolate than 18F. As a result of this study, HA-10 may give us a highlight on HAV replication and also, the isolated strain may be useful for vaccine development.
Template-prime-dependent turnover of (Sp)-dATP alpha S by T4 DNA polymerase. The stereochemistry of the associated 3' goes to 5'-exonuclease. (1982)

T4 DNA polymerase converts (Sp)-2'-deoxyadenosine 5'-O-(1-thio[1-18O2]triphosphate) to 2'-deoxyadenosine 5'-O-[18O]-phosphorothioate in the presence of poly(d(A-T).poly(d(A-T)) template-primer. Control experiments involving either omitting the poly(d(A-T)).poly(d(A-T) template-primer or employing the (Rp)-2'-deoxyadenosine 5'-O-(1-thiotriphosphate) diastereomer showed no reaction. It is assumed, therefore, that this conversion as in the P--O case involves incorporation of the thionucleotide into the poly(d(A-T)) followed by hydrolysis resulting from the 3' goes to 5'-exonuclease activity. The 2'-deoxyadenosine 5'-O-[18O] phosphorothioate was converted to (Sp)-2'-deoxyadenosine 5'-O-(1-thio[1-18O]triphosphate), with no change in the configuration at P alpha by using the coupled adenylate kinase-pyruvate kinase enzyme system. A 31P NMR spectrum of the product showed that the 18O was entirely in the nonbridging position, indicating an overall retention in the net turnover process (i.e. incorporation followed by excision). Since the incorporation process involves an inversion of configuration around the phosphorus (Romaniuk, P. J., and Eckstein, F. (1982) J. Biol. Chem. 257, 7684-7688), it must be inferred that the 3' goes to 5'-exonuclease activity of T4 polymerase proceeds with inversion of configuration at the phosphorus atom, most simply via a direct displacement mechanism. This finding represents the first example of phosphodiester hydrolysis catalyzed by an exonuclease that does not involve a covalent phosphoryl-enzyme intermediate (Knowles, J. R. (1980) Annu. Rev. Biochem. 49, 877-919).
Novel Hollow Polymer Shells by Colloid-Templated Assembly of Polyelectrolytes (1998)

Exact control of the film thickness of polyelectrolyte shells (a transmission electron microscopy image is shown) is achieved by colloid-templated consecutive adsorption of polyanions and polycations followed by decomposition of the templating core. Possible areas of application for these shells range from the pharmaceutical, food, cosmetic, and paint industries to catalysis and microcrystallization.
Effects of Preexisting Immunity on the Response to Herpes Simplex-Based Oncolytic Viral Therapy (2000)

Herpes simplex viruses (HSV) type 1 are the basis of a number of anticancer strategies that have proven efficacious in animal models. They are natural human pathogens and the majority of adults have anti-HSV immunity. The current study examined the effect of preexisting immunity on the response to herpes-based oncolytic viral treatment of hepatic metastatic cancer in a murine model designed to simulate a clinical approach likely to be utilized for nonneurological tumors. Specifically, the anticancer effects of NV1020 or G207, two multimutated HSV-1 oncolytic viruses, were tested in immunocompetent mice previously immunized with a wild-type herpes simplex type 1 virus. Mice were documented to have humoral as well as cell-mediated immunity to HSV-1. Tumor response to oncolytic therapy was not measurably abrogated by immunity to HSV at the doses tested. The influence of route of viral administration was also tested in models of regional hepatic arterial and intravenous therapy. Route of viral administration influenced efficacy, as virus delivered intravenously produced some detectable attenuation while hepatic arterial therapy remained unaffected. These results demonstrate that when given at appropriate doses and in reasonable proximity to tumor targets, HSV-based oncolytic therapy can still be expected to be effective treatment for patients with hepatic malignancies.
DREAM: A Component Framework for Constructing Resource-Aware, Configurable Middleware (2005)

DREAM (dynamic reflective asynchronous middleware) is a software framework for building asynchronous middleware from components, which we can assemble statically or dynamically (at deployment time or at runtime). DREAM's component library and set of tools lets us build, configure, and deploy middleware that implements various asynchronous communication paradigms, including message-passing, event-reaction, and publish-subscribe. We show how to use our framework to dynamically control resource consumption and concurrency. The performance of dynamically configurable MOMs built with the DREAM framework compares favorably to monolithic, functionally equivalent middleware
Stable lines of transgenic zebrafish exhibit reproducible patterns of transgene expression (1990)

To study the frequency of germ-line transformation and to examine the reproducibility of tissue-specific transgene expression, we produced several lines of transgenic zebrafish expressing a recombinant chloramphenicol acetyltransferase (CAT) gene. Supercoiled plasmids containing both Rous sarcoma virus and SV-40 promoter sequences upstream of the CAT coding region were injected into zebrafish embryos prior to first cleavage. CAT activity could be detected in batches of injected embryos as early as 8 h and up to at least 12 days post-fertilization. Approximately 18% of injected fish raised to maturity exhibited CAT activity in their fins, and approximately 5% of injected fish became stable germ-line transformants. Breeding studies indicated that although transgenic founder fish were frequently germ-line mosaics, transgenic individuals of subsequent generations were fully hemizygous for the transgene marker. The transgenes present in the F1 progeny of four independent lines were relatively well expressed in fin and skin, while lower levels of expression were observed in heart, gill and muscle. Little or no CAT expression was observed in the brain, liver and gonad. A monoclonal antibody directed against the CAT gene product consistently revealed variegated patterns of CAT expression in ectodermally derived fin epidermal cells in three of these lines. These results show that it is possible to efficiently produce stable germ-line transformants of the zebrafish and to observe reproducible tissue-specific patterns of transgene expression in this organism. Possible mechanisms for the variegated expression observed within tissues are also considered.
Molecular mechanisms of apoptosis in the cells of the immune system in human aging (2005)

Aging is associated with progressive decline in immune functions and increased frequency of infections, autoimmunity, and cancer. Among immune functions, a decline in T-cell functions during aging predominates. In this review, I discuss the molecular signaling of three distinct pathways of apoptosis, namely the death receptor pathway, the mitochondrial pathway, and the most recently described endoplasmic reticulum stress pathway, and the relative sensitivity of naive, central memory, and effector memory CD8(+) T-cell subsets to apoptosis. In addition, I review apoptosis, especially via death receptor pathway, in naive and various memory subsets of CD4(+) and CD8(+) T cells (with primary emphasis on CD8(+) naive and memory subsets) in human aging and discuss the role of apoptosis in immune senescence.
Adjustable access electronic books (2003)

Describes a tested electronic book publishing and adjustable reading system that provides books in special media for print-disabled users, i.e. books on tape, printed braille, and large print. The system converts printed books into portable, single volume computer bookfiles that have the exact text function and access as the original book. The software enables print-disabled persons to read these bookfiles in their preferred special medium using their computers and adaptive computer devices. They can turn pages, jump instantly to the top of any original printed page, leave personal bookmarks and notes and instantly jump to and from the original table of contents and index. Reading is fully user-adjustable to any adaptive device or even simultaneous combinations like speech and magnified print together. Each user receives a unique key device and software. Books ordered are uniquely encrypted for their key only.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>