gebhart/patrepeval huggingface dataset:
An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data (2009)

The parts of the genome transcribed by a cell or tissue reflect the biological processes and functions it carries out. We characterized the features of mammalian tissue transcriptomes at the gene level through analysis of RNA deep sequencing (RNA-Seq) data across human and mouse tissues and cell lines. We observed that roughly 8,000 protein-coding genes were ubiquitously expressed, contributing to around 75% of all mRNAs by message copy number in most tissues. These mRNAs encoded proteins that were often intracellular, and tended to be involved in metabolism, transcription, RNA processing or translation. In contrast, genes for secreted or plasma membrane proteins were generally expressed in only a subset of tissues. The distribution of expression levels was broad but fairly continuous: no support was found for the concept of distinct expression classes of genes. Expression estimates that included reads mapping to coding exons only correlated better with qRT-PCR data than estimates which also included 3' untranslated regions (UTRs). Muscle and liver had the least complex transcriptomes, in that they expressed predominantly ubiquitous genes and a large fraction of the transcripts came from a few highly expressed genes, whereas brain, kidney and testis expressed more complex transcriptomes with the vast majority of genes expressed and relatively small contributions from the most expressed genes. mRNAs expressed in brain had unusually long 3'UTRs, and mean 3'UTR length was higher for genes involved in development, morphogenesis and signal transduction, suggesting added complexity of UTR-based regulation for these genes. Our results support a model in which variable exterior components feed into a large, densely connected core composed of ubiquitously expressed intracellular proteins.
Global optimization by suppression of partial redundancies (1979)

The elimination of redundant computations and the moving of invariant computations out of loops are often done separately, with invariants moved outward loop by loop. We propose to do both at once and to move each expression directly to the entrance of the outermost loop in which it is invariant. This is done by solving a more general problem, i.e. the elimination of computations performed twice on a given execution path. Such computations are termed partially redundant. Moreover, the algorithm does not require any graphical information or restrictions on the shape of the program graph. Testing this algorithm has shown that its execution cost is nearly linear with the size of the program, and that it leads to a smaller optimizer that requires less execution time.
Design of a diode-laser sensor to monitor water vapor in high-pressure combustion gases (1997)

The design of a diode-laser sensor to monitor water vapor in high-pressure combustion gases is described. The sensor, which employs a multiple-fixed-wavelength absorption strategy, has the potential to simultaneously monitor the water mole fraction and the temperature and pressure in high-pressure and high-temperature environments. The conventional scanned-wavelength strategy, employed in previous diode-laser sensors, is shown to be ill-suited for high-pressure applications. The application of impact and additive approximations in the modeling of H(2)O absorption features at high pressures is validated experimentally for number densities as high as 18 amagats. Criteria to select optimum wavelength combinations for the fixed-wavelengths strategy are discussed. Optimum wavelength combinations that meet these criteria are identified for different temperature and pressure ranges of interest to combustion applications. The proposed sensor configuration and a strategy to obtain the baseline (zero absorption intensity) in high-pressure environments are also described. Line-shape models that are appropriate for different temperature and pressure regimes are identified.
Topical tretinoin for treatment of photodamaged skin. A multicenter study. (1991)

The clinical and histologic effects of a new emollient cream formulation of topical tretinoin at concentrations of 0.05% and 0.01% were examined in 251 subjects with mild to moderate photodamaged facial skin in a randomized, double-blind, vehicle-controlled, multicenter study. Seventy-nine percent of the subjects who received 0.05% tretinoin for 24 weeks showed overall improvement in photodamaged skin compared with improvement in 48% of the vehicle-treated control subjects. Significant reductions were found in fine wrinkling, mottled hyperpigmentation, roughness, and laxity after 0.05% tretinoin therapy when compared with controls. In addition, histologic changes of increased epidermal thickness, decreased melanin content, and stratum corneum compaction provide independent evidence supporting clinical improvement. Side effects of erythema, peeling, and stinging were usually mild and well tolerated.
Nucleotides, Part LXII, Pyridinium Salts - An Effective Class of Catalysts for Oligonucleotide Synthesis (1999)

Various pyridinium salts (see 1 – 9) have been tested as catalysts for the condensation step in the phosphoramidite approach of oligonucleotide synthesis. Pyridinium chloride (1) turned out to be the most effective activator, speeding up the condensation tremendously. Pyridinium bromide (2) and 4-methylbenzenesulfonate (4) can also be regarded as powerful substitutes for the commonly used 1H-tetrazole. The acidic pKa of the pyridinium cation provides an optimal range for phosphoramidite activation, which is followed by a nucleophilic attack of the pyridine ring to give the P-pyridinio intermediate 11 as the most likely precursor of phosphite ester formation (Scheme). 31P-NMR Studies support this proposal indirectly.
Structural determination of oligosaccharides from recombinant iduronidase released with peptide N‐glycanase F using fluorophore‐assisted carbohydrate electrophoresis (1998)

The lysosomal storage disorder mucopolysaccharidoses I (MPS I) is caused by a deficiency in the production of alpha-L-iduronidase. Recently, a recombinant alpha-L-iduronidase has been produced in Chinese hamster ovary (CHO) cells. It is thought that for alpha-L-iduronidase to be correctly targeted to the lysosomal vesicle a particular oligosaccharide make-up must be present, and characterization of the carbohydrates is critical. Oligosaccharides from alpha-L-iduronidase were analyzed using fluorophore-assisted carbohydrate electrophoresis (FACE). The FACE system uses polyacrylamide gel electrophoresis to separate, quantify, and determine the sequence of oligosaccharides released from glycoproteins. Asparagine-linked oligosaccharides were released from alpha-L-iduronidase using the enzyme peptide N-glycanase F (PNGase F). Released oligosaccharides were labeled with a fluorophore at the reducing termini by reductive amination. A total of nine bands were sequenced from the released pool of oligosaccharides. The pool of fluorescently labeled oligosaccharides was then electrophoresed in preparative gels and each band individually excised and extracted. Isolated bands were treated with a series of exoenzymes to determine the sequence of monosaccharides that make up a particular oligosaccharide. A total of eighteen different oligosaccharides were identified from the original pool of oligosaccharides. A majority of the oligosaccharides, over 73%, were found to be of the sialylated complex type. Four of the oligosaccharides were phosphorylated, making up approximately 11% of the carbohydrate pool, and the remaining 15% were of the oligomannose type.
Kinetics and Mechanisms for the Cleavage and Isomerization of the Phosphodiester Bonds of RNA by Brønsted Acids and Bases (1998)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetics and Mechanisms for the Cleavage and Isomerization of the Phosphodiester Bonds of RNA by Brønsted Acids and BasesMikko Oivanen, Satu Kuusela, and Harri LönnbergView Author Information Department of Chemistry, University of Turku, FIN-20014 Turku, Finland Cite this: Chem. Rev. 1998, 98, 3, 961–990Publication Date (Web):April 1, 1998Publication History Received24 June 1997Revised2 September 1997Published online1 April 1998Published inissue 7 May 1998https://pubs.acs.org/doi/10.1021/cr960425xhttps://doi.org/10.1021/cr960425xresearch-articleACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views3897Altmetric-Citations368LEARN 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 SUBJECTS:Crystal cleavage,Genetics,Ions,Isomerization,Phosphates Get e-Alerts
Soluble complement receptor 1 preserves endothelial barrier function and microcirculation in postischemic pancreatitis in the rat (2004)

Components of the activated complement cascade are considered to play a pivotal role in ischemia-reperfusion-induced organ injury. With the use of intravital epifluorescence microscopy, we investigated the effect of complement inhibition by the recombinant soluble complement receptor 1 (sCR1; TP10) on the effect of macromolecular microvascular permeability, functional capillary perfusion, and leukocyte endothelium interaction in postischemic pancreatitis. Anaesthetized Sprague-Dawley rats were subjected to 60 min of normothermic pancreatic ischemia induced by microclipping of the blood-supplying arteries of the organ. Rats who received sCR1 (15 mg/kg body wt iv; n = 7) during reperfusion showed a significant reduction of permeability (1.77 +/- 1.34 x 10(-8) cm/s; n = 7) of tetramethylrhodamine isothiocyanate-labeled albumin injected 90 min after the onset of reperfusion compared with vehicle-treated animals (6.95 +/- 1.56 x 10(-8) cm/s; n = 7). At 120 min after the onset of reperfusion, the length of red blood cell-perfused capillaries (functional capillary density) was significantly improved (from 279 +/- 15.7 to 330 +/- 3.7 cm(-1); n = 7) and the number of leukocytes adherent to postcapillary venules was significantly reduced (from 314 +/- 87 to 163 +/- 71 mm(-2); n = 7) by sCR1 compared with vehicle treatment. Complement inhibition by sCR1 effectively ameliorates pancreatic ischemia-reperfusion-induced microcirculatory disturbances and might be considered for treatment of postischemic pancreatitis.
Diarrhea associated with severe hypoalbuminemia (1988)

To demonstrate a relationship between diarrheal incidence and the onset of hypoalbuminemia developing as a result of acute protein-calorie malnutrition and severe catabolism, we initially studied two patients who had developed severe hypoalbuminemia (less than 2.5 g/dl) and diarrhea on a variety of enteral diets. Each patient was placed on a peptide enteral formula at a rate of infusion equivalent to that used during the previous 24 h. Diarrheal volumes decreased significantly from greater than 1500 to less than 100 ml/day and from greater than 4000 to 800 ml/day. We subsequently studied 12 patients in a randomized, prospective fashion to confirm our previous observations. Seven patients received a peptide enteral formula, and five received a standard isotonic enteral formula as a control. The patients were monitored for a minimum of 2 wk or until serum albumin levels reached 3 g/dl. Nutritional variables were measured initially and every 4 days for the duration of the study. Of the patients receiving the isotonic feeding, only one of five completed the study period without diarrhea. Two patients died unrelated to the feeding, and three patients developed severe diarrhea within 48 h of institution of the study. Of the seven patients receiving the peptide feeding, six completed the study period without diarrhea. One patient had a large stool volume initially which decreased by day 2 of the study. We conclude that a peptide enteral formula is well tolerated in patients with severe hypoalbuminemia when compared to a standard isotonic enteral formula. The ability to provide enteral nutrition in a form that is well tolerated in hypoalbuminemia patients may obviate the need for parenteral nutrition routinely in these patients.
Isolation and partial characterization of pancreatic polypeptide-like material in the brain of the blowfly Calliphora vomitoria (1981)

Using 10(6) flies (5 kg of heads) a pancreatic polypeptide-like material has been partially purified from the blowfly Calliphora vomitoria. The isolated material was eluted on Sephadex G-50 similarly to bovine pancreatic polypeptide and had an RF on polyacrylamide-gel electrophoresis that was identical with that of the bovine hormone. The material diluted linearly and showed parallelism with bovine standards in a bovine pancreatic polypeptide immunoassay. In specificity controls the immunoreactivity was not abolished by trasylol and no cross-reactivity was discerned in assay for glucagon, proangiotensin and cyclic AMP. These data suggest that the pancreatic polypeptide material in the brain of the blowfly has close structural similarity to the mammalian hormone.
Capillary Electrophoresis of Sugar Acids (2008)

This chapter illustrates the usefulness of capillary electrophoresis (CE) for the analysis of sugar acids, that is, monosaccharides and lower oligosaccharides carrying carboxylate, sulphate or phosphate groups. In order to provide a general description of the main results and challenges in the field, some relevant applications and reviews on CE of such saccharidic compounds are tabulated. Furthermore, some detailed experimental procedures are shown, regarding the CE analysis of sugar acids released upon hydrolysis of acidic polysaccharides and of glycans linked to glycoproteins. In particular, the protocols will deal with the following compounds: (i) unsaturated, underivatized oligosaccharides from lyase-treated alginate; (ii) oligosaccharides derivatized with 4-aminobenzonitrile, arising from chemical hydrolysis of alginate; (iii) sialic acid derivatized with 2-aminoacridone, released from human serum immunoglobulin G.
Characteristics of new cell lines derived from Burkitt lymphomas (1969)

Thirty-five cell lines were established from 47 Burkitt lymphoma biopsies. In different biopsies the modal cell size was found to vary and the tumor was often built up by larger cells if the patients received chemotherapy. In all cases the predominant cell size shifted towards larger values during cultivation. All cells in three biopsies from one patient and in the culture lines derived showed surface reactivity with anti-IgM and antikappa light chain reagents. This trait was maintained in all three lines for about 21 weeks but was lost thereafter. A fourth biopsy—taken after the patient had been treated with cytosine arabinoside—did not have this immunoglobulin reactivity. Chromosomal analysis revealed that one of the IgM reactive lines had 46 as stemline number and normal diploid karyotype, while the nonreactive line had 47 as stemline number with an extra C chromosome in addition to the normal male karyotype. One or two C chromosomes, corresponding in size with pair 10 were formed as markers with subterminal constriction on their long arms. The unusual cellular trait—IgM specificity—being present on both the biopsy and its derived cell line, indicates the representativeness of the culture line for the in-vivo tumor in this case.
Naive, Effector, and Memory CD8 T Cells in Protection Against Pulmonary Influenza Virus Infection: Homing Properties Rather Than Initial Frequencies Are Crucial (1999)

The goal of adoptive immunotherapy is to target a high number of persisting effector cells to the site of a virus infection or tumor. In this study, we compared the protective value of hemagglutinin peptide-specific CD8 T cells generated from the clone-4 TCR-transgenic mice, defined by different stages of their differentiation, against lethal pulmonary influenza infection. We show that the adoptive transfer of high numbers of Ag-specific unprimed, naive CD8 T cells failed to clear the pulmonary virus titer and to promote host survival. The same numbers of in vitro generated primary Ag-specific Tc1 effector cells, producing high amounts of IFN-gamma, or resting Tc1 memory cells, generated from these effectors, were protective. Highly activated CD62Llow Tc1 effectors accumulated in the lung with rapid kinetics and most efficiently reduced the pulmonary viral titer early during infection. The resting CD62Lhigh naive and memory populations first increased in cell numbers in the draining lymph nodes. Subsequently, memory cells accumulated more rapidly and to a greater extent in the lung lavage as compared with naive cells. Thus, effector cells are most effective against a localized virus infection, which correlates with their ability to rapidly distribute at the infected tissue site. The finding that similar numbers of naive Ag-specific CD8 T cells are not protective supports the view that qualitative differences between the two resting populations, the naive and the memory population, may play a major role in their protective value against disease.
Regulation of bone marrow stromal cell differentiation by cytokines whose receptors share the gp130 Protein (1994)

The bone marrow stroma consists of a heterogeneous population of cells which participate in osteogenic, adipogenic, and hematopoietic events. The murine stromal cell line, BMS2, exhibits the adipocytic and osteoblastic phenotypes in vitro. BMS2 differentiation was examined in response to cytokines which share the gp130 signal transducing protein within their receptor complex. Four of the cytokines (interleukin 6, interleukin 11, leukemia inhibitory factor, and oncostatin M) inhibited hydrocortisone-induced adipocyte differentiation in a dose dependent manner based on lipid accumulation and lipoprotein lipase enzyme activity. Inhibition occurred only when the cytokines were present during the initial 24 h of the induction period; after 48 h their effects were diminished. Likewise, these cytokines increased alkaline phosphatase enzyme activity twofold in preadipocyte BMS2 cells. Both leukemia inhibitory factor and oncostatin M induced early active gene expression in resting preadipocyte BMS2 cells and decreased the steady state mRNA level of a unique osteoblastic gene marker, osteocalcin. A fifth cytokine whose receptor complex shares the gp130 protein, ciliary neurotrophic factor, did not significantly regulate stromal cell differentiation when added by itself. However, with the addition of a missing component of its receptor complex, ciliary neurotrophic factor receptor alpha protein, this cytokine also inhibited BMS2 adipogenesis. Together, these data indicate that the cytokines whose receptors share the gp130 protein can modulate stromal cell commitment to the adipocyte and osteoblast differentiation pathways.
A Better View of Brain Disorders (2006)

As imaging methods such as functional magnetic resonance imaging and positron emission tomography make their way from lab to clinic, neurologists hope to make earlier and more accurate diagnoses of brain disorders (see related Brevia on p.
 1402
 and Perspective on p.
 1395). (Read more.)
Prospects for Control of Herpes Simplex Virus Disease through Immunization (2000)

Herpes simplex viruses (HSVs) can cause a variety of infections, including genital herpes. Despite effective antiviral therapy, HSV infections remain a significant worldwide public health problem. Vaccines offer the best hope for controlling spread and limiting HSV disease. This article discusses the pathogenesis and immunobiology of mucocutaneous HSV infections, summarizes the spectrum of diseases caused by HSV, and provides a review of the field of HSV vaccine research. This article also discusses what might be realistically expected of a vaccine intended for control of genital herpes and explores the question of whether a vaccine that is effective in controlling genital HSV disease might also be effective in controlling nongenital HSV disease. The efficacy of such vaccines for the full spectrum of HSV disease will eventually determine the timing and targeting of immunization, ranging from selective immunization in preadolescence to universal childhood immunization as part of the routine childhood regimen.
Boosting Image Captioning with Attributes (2017)

Automatically describing an image with a natural language has been an emerging challenge in both fields of computer vision and natural language processing. In this paper, we present Long Short-Term Memory with Attributes (LSTM-A) - a novel architecture that integrates attributes into the successful Convolutional Neural Networks (CNNs) plus Recurrent Neural Networks (RNNs) image captioning framework, by training them in an end-to-end manner. Particularly, the learning of attributes is strengthened by integrating inter-attribute correlations into Multiple Instance Learning (MIL). To incorporate attributes into captioning, we construct variants of architectures by feeding image representations and attributes into RNNs in different ways to explore the mutual but also fuzzy relationship between them. Extensive experiments are conducted on COCO image captioning dataset and our framework shows clear improvements when compared to state-of-the-art deep models. More remarkably, we obtain METEOR/CIDEr-D of 25.5%/100.2% on testing data of widely used and publicly available splits in [10] when extracting image representations by GoogleNet and achieve superior performance on COCO captioning Leaderboard.
Latent herpes simplex virus type 1 DNA contains two copies of the virion DNA joint region (1985)

Southern blot analysis of latent herpes simplex virus DNA detected in mouse brain and digested with a restriction enzyme revealed two copies of the virion DNA joint fragment. Thus, the absence of free ends noted previously in latent herpes simplex virus type 1 DNA is due to joining of the termini.