gebhart/patrepeval huggingface dataset:
Autotaxin Expression in Non–Small-Cell Lung Cancer (1999)

Autotaxin (ATX) is one of the newly discovered autocrine motility-stimulating factors with peptide sequences identical to those of the brain-type phosphodiesterase I (PD-Ialpha). Although ATX/PD-Ialpha is believed to play a role in tumor progression, its expression in various human cancers has not been extensively studied. We have studied the expression of ATX messenger RNA (mRNA) in normal human bronchial epithelial cell (HBEC) and non-small-cell lung cancer (NSCLC) cell lines, and in primary NSCLC with their corresponding normal lung tissues, using reverse transcription-polymerase chain reaction, Northern blot analysis, and in situ hybridization. ATX mRNA was commonly expressed in these cell lines and tissues. The predominantly expressed mRNA species corresponded to the ATX complementary DNA isolated from a human teratocarcinoma cell line. Overexpression of ATX mRNA was detected in seven of 12 (58%) tumor cell lines; however, there was no correlation between the levels of expression of ATX mRNA and the spontaneous motility of these cells. In situ hybridization localized ATX mRNA expression to the basal cells of normal bronchial epithelium, stromal B lymphocytes, and tumor cells. An overexpression of ATX mRNA as compared with its expression in normal bronchial epithelium was mainly found in poorly differentiated carcinomas. Our findings suggest that ATX may have roles additional to its motility-stimulating function in undifferentiated NSCLC.
Gastric Motility Disorders (2004)

Gastric motility disorders are relatively common, and treatment is often challenging. Various etiologies account for numerous clinical sequelae, with weight loss and severe protein-calorie malnutrition often seen in advanced stages of these disorders. In addition to gastrointestinal motor function, an appreciation of visceral sensation is essential to better understand the symptoms found in these patients, as well as possible therapeutic alternatives. This article provides an overview of gut motor and sensory function, techniques available for diagnosing motor disorders, and the principles of nutritional and medical management. Specific nutritional recommendations and a review of pharmacologic agents and novel treatment modalities are provided.
Synthesis and physical properties ofanti-HIV antisense oligonucleotides bearing terminal lipophilic groups (1992)

A number of phosphoramidite monomers have been prepared and used in the synthesis of antisense phosphorothioate oligonucleotides bearing 5'-polyalkyl and cholesterol moieties. Similar groups have also been attached to the 3'-end of oligonucleotides by means of functionalised CPG. Melting temperatures of duplexes formed between phosphorothioate oligonucleotides with lipophilic end-groups and complementary DNA strands were found to be identical to those formed by the equivalent unmodified phosphorothioates.
Ribosome Biogenesis and Control of Cell Proliferation: p53 Is Not Alone (2012)

Cell growth is a prerequisite for cell proliferation, and ribosome biogenesis is a limiting factor for cell growth. In mammalian cells, the tumor suppressor p53 has been shown to induce cell-cycle arrest in response to impaired ribosome biogenesis. Recently, p53-independent mechanisms of cell-cycle arrest in response to alterations of ribosome biogenesis have been described. These findings provide a rational basis for the use of drugs that specifically impact ribosome biogenesis for the treatment of cancers lacking active p53 and extend the scenario of mechanisms involved in the relationship between cell growth and cell proliferation.
Derivation of formulae used to calculate energy expenditure in man. (1987)

The origins of the data used to construct some of the formulae in current usage for the calculation of energy expenditure are discussed. The differences in expenditure calculated by the various formulae cover a range of about 3 per cent. This error is large in relation to long-term studies of energy balance, and to the accuracy attainable with modern respiration chambers. The differences stem in part from the use of inappropriate original values and in part from errors in arithmetic. A new set of source data and a derived formula are presented.
Analysis of Two-Phase Tests in Large-Diameter Flow Lines in Prudhoe Bay Field (1981)

Abstract A total of 29 two-phase flow tests was conducted in two 3-mile-long flow lines in the Prudhoe Bay field of Alaska. Of these, 11 were for a 12-in.-diameter line and 18 were for a 16-in. line. Nine of the tests were in slug flow, and 20 were in froth flow. Flow rates, inlet and outlet pressures, and temperatures were measured for each test. Gamma densitometers were used to monitor flow pattern and to determine mixture densities and slug characteristics. It was found that a modified Beggs-Brill1 pressure-loss correlation predicted culled data to within − 1.5% on the average compared with + 11.4% for a modified Dukler-Eaton2,3 correlation. Very little scatter was observed with either method. Analysis of flow-pattern observations showed that none of the slug-flow tests were in the Schmidt4 severe slug region characterized by extremely long slugs. It also was found that the slug/froth (dispersed) flow-pattern boundary existed at a much lower liquid flow rate than predicted by either Mandhane et al.5 or Taitel and Dukler.6 Four of the slug-flow tests in 16-in. lines lasted for a sufficient time to permit statistical analysis of slug-length distributions. Sixteen additional tests on 4- and 7-in.-diameter pipe reported by Brainerd and Hedquist* were analyzed statistically. It was found that slug lengths could be represented by a log-normal distribution. A regression analysis approach was successful for estimating the mean slug length for stabilized flow as a function of superficial mixture velocity and pipe diameter. The extreme percentiles of the slug-length distribution then can be computed using standard probability tables, making possible probability statements about expected maximum slug length. A mechanistic analysis of the slug-flow tests resulted in equations for predicting slug velocities, liquid holdup in both the liquid slug and the gas bubble, and the volumes of liquid that are produced and overrun. These parameters are important for predicting liquid-slug effects on separator performance.
Characterization of Esterases Involved in the Hydrolysis of Dipivefrin Hydrochloride (1993)

We characterized the interaction of the prodrug dipivefrin hydrochloride (DPE) with esterase activity in the rabbit cornea. The esterases which were identified included: (1) cholinesterase, (2) acetylcholinesterase, (3) a mixture containing carboxylesterase, acetylesterase and arylesterase, and (4) a non-specific esterase. DPE suppressed all of their activities as well as that of the mixture containing carboxylesterase, acetylesterase and arylesterase, and a nonspecific esterase. However, its effect on cholinesterase was larger than on any of the other activities, suggesting that DPE is a better substrate for cholinesterase than for any of the other esterases. These measurements along with those of substrate-dependent inhibition of 14C-DPE hydrolysis indicated that the DPE-esterase interaction was competitive based on changes in the apparent Km values which were extracted from Lineweaver-Burk plots of esterase activity. The substrate for cholinesterase competed with DPE most strongly among substrates. These results seem to suggest that DPE is hydrolyzed by various corneal esterases, mainly cholinesterase.
The Configurations of N-Methyl- and N-t-Butyl-α-methoxycarbonylmethanimine N-Oxides (1983)

Abstract N-Methyl-α-methoxycarbonylmethanimine N-oxide, Z configuration in crystal, was found to exhibit a facile equilibration with its E-isomer in solution. The configuration of N-t-butyl derivative was always Z.
A Combination of Gabapentin and Morphine Mediates Enhanced Inhibitory Effects on Dorsal Horn Neuronal Responses in a Rat Model of Neuropathy (2002)

After spinal nerve ligation, the inhibitory effects of systemic morphine on evoked dorsal horn neuronal responses are reduced compared with control, whereas the effectiveness of systemic gabapentin is enhanced. In combination with low-dose gabapentin, significant improvement in the effectiveness of morphine is observed, which demonstrates a clinical potential for the use of morphine and gabapentin combinational treatment for neuropathic pain.
An epigenetic breeding system in soybean for increased yield and stability (2018)

Epigenetic variation has been associated with a wide range of adaptive phenotypes in plants, but there exist few direct means for exploiting this variation. RNAi suppression of the plant-specific gene, MutS HOMOLOG1 (MSH1), in multiple plant species produces a range of developmental changes accompanied by modulation of defence, phytohormone and abiotic stress response pathways along with methylome repatterning. This msh1-conditioned developmental reprogramming is retained independent of transgene segregation, giving rise to transgene-null 'memory' effects. An isogenic memory line crossed to wild type produces progeny families displaying increased variation in adaptive traits that respond to selection. This study investigates amenability of the MSH1 system for inducing agronomically valuable epigenetic variation in soybean. We developed MSH1 epi-populations by crossing with msh1-acquired soybean memory lines. Derived soybean epi-lines showed increase in variance for multiple yield-related traits including pods per plant, seed weight and maturity time in both glasshouse and field trials. Selected epi-F<sub>2:4</sub> and epi-F<sub>2:5</sub> lines showed an increase in seed yield over wild type. By epi-F<sub>2:6,</sub> we observed a return of MSH1-derived enhanced growth back to wild-type levels. Epi-populations also showed evidence of reduced epitype-by-environment (e × E) interaction, indicating higher yield stability. Transcript profiling of epi-lines identified putative signatures of enhanced growth behaviour across generations. Genes related to cell cycle, abscisic acid biosynthesis and auxin response, particularly SMALL AUXIN UP RNAs (SAURs), were differentially expressed in epi-F<sub>2:4</sub> lines that showed increased yield when compared to epi-F<sub>2:6</sub> . These data support the potential of MSH1-derived epigenetic variation in plant breeding for enhanced yield and yield stability.
BIOCHEMICAL, CELLULAR, AND PHARMACOLOGICAL ASPECTS OF THE MULTIDRUG TRANSPORTER (1999)

Considerable evidence has accumulated indicating that the multidrug transporter or P-glycoprotein plays a role in the development of simultaneous resistance to multiple cytotoxic drugs in cancer cells. In recent years, various approaches such as mutational analyses and biochemical and pharmacological characterization have yielded significant information about the relationship of structure and function of P-glycoprotein. However, there is still considerable controversy about the mechanism of action of this efflux pump and its function in normal cells. This review summarizes current research on the structure-function analysis of P-glycoprotein, its mechanism of action, and facts and speculations about its normal physiological role.
Treatment of Chronic Infection (2006)

Failure of an acute inflammatory response to resolve a wound infection heralds a cascade of events that affects the host and pathogens, culminating in a chronic, refractory condition. The factors contributing to this outcome include immune compromise of the host, antimicrobial resistance, wound-healing deficiencies, and the adherence of pathogens to themselves and wound surfaces via an impenetrable, resistant biofilm. To eradicate chronic infection, the pathogens, biofilm, surfaces available for adherence, and compromised tissue must be removed.
Formation of High Quality InP and InAs Nanocrystals in a Noncoordinating Solvent (2002)

High quality InP nanocrystals without any size sorting were synthesized in a noncoordinating solvent by strictly controlling the reaction parameters. This synthetic method is much faster, less expensive, and “greener” than any current methods for the synthesis of high quality InP nanocrystals. Fatty acids with well-defined chain lengths as the ligands, a noncoordinating solvent, and a thorough degassing process are critical factors for the formation of high quality InP nanocrystals. The growth of nearly monodisperse InAs nanocrystals through a similar scheme was also observed.
Plasma VEGF and soluble VEGF receptor FLT-1 in proliferative retinopathy: relationship to endothelial dysfunction and laser treatment. (2000)

In this pilot study, patients with proliferative retinopathy demonstrate elevated peripheral markers of angiogenesis and endothelial dysfunction, suggesting a role for these processes in the pathogenesis of this condition. A fall in levels of VEGF after successful laser treatment may provide an opportunity for monitoring disease progression or relapse via a blood sample.
Characterization of the Mouse Bile Salt Export Pump Overexpressed in the Baculovirus System (2001)

The bile salt export pump (Bsep), a member of the ATP-binding cassette superfamily of transporters, mediates the ATP-dependent canalicular secretion of bile salts. We have cloned and expressed the mouse Bsep (mBsep) protein in Sf9 insect cells, and characterized its transport and ATPase properties. Because its deduced amino acid sequence predicts multiple phosphorylation sites for protein kinase A, protein kinase C (PKC) and Ca(2+)-calmodulin dependent kinase II, we have also tested whether mBsep undergoes phosphorylation. MBsep transports both glycine and taurine conjugated bile salts. Sf9 cell membranes that express mBsep exhibit higher basal ATPase activity than control membranes, and this is further stimulated by bile salts and inhibited by vanadate. Taurochenodeoxycholate is transported with the highest affinity and is the most potent inducer of ATPase activity. Cyclosporin A, glibenclamide and rifamycin SV, all competitive inhibitors of Bsep transport, also reduced the bile salt-stimulated ATPase activity. MBsep exists as a phospho-protein when expressed in Sf9 cells and the immunoprecipitated mBsep complex is a substrate for the catalytic subunit of PKC. When mBsep and the alpha-isoform of mouse PKC are co-expressed in Sf9 cells, a ninefold stimulation of phosphorylation occurs. This is further increased to 18-fold after activation by phorbol ester. Given that bile salts activate selected PKC isoforms in hepatocytes, including the alpha isoform, the phosphorylation of mBsep by PKCalpha may represent a point of regulation for this transporter that is mediated by its own substrate.
Artificial microvascular network: a new tool for measuring rheologic properties of stored red blood cells (2011)

The measurements performed using the AMVN device confirm a significant decline in the rheologic properties of RBCs in units nearing expiration and demonstrate the sensitivity of the device to these storage-induced changes. The AMVN device may be useful for testing the effect of new storage conditions, additive solutions, and rejuvenation strategies on the rheologic properties of stored RBCs in vitro.
SEGCloud: Semantic Segmentation of 3D Point Clouds (2017)

3D semantic scene labeling is fundamental to agents operating in the real world. In particular, labeling raw 3D point sets from sensors provides fine-grained semantics. Recent works leverage the capabilities of Neural Networks(NNs), but are limited to coarse voxel predictions and do not explicitly enforce global consistency. We present SEGCloud, an end-to-end framework to obtain 3D point-level segmentation that combines the advantages of NNs, trilinear interpolation(TI) and fully connected Conditional Random Fields (FC-CRF). Coarse voxel predictions from a 3D Fully Convolutional NN are transferred back to the raw 3D points via trilinear interpolation. Then the FC-CRF enforces global consistency and provides fine-grained semantics on the points. We implement the latter as a differentiable Recurrent NN to allow joint optimization. We evaluate the framework on two indoor and two outdoor 3D datasets (NYU V2, S3DIS, KITTI, Semantic3D.net), and show performance comparable or superior to the state-of-the-art on all datasets.
CO2 hydration by immobilized carbonic anhydrase (2003)

The enzyme carbonic anhydrase (isoform II) from bovine and human erythrocytes was immobilized using different covalent coupling methods on inert matrices. Immobilized carbonic anhydrase may enable concentration of CO2 for Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase)-catalysed fixation in bioreactors. In the present study the activity of carbonic anhydrase with respect to hydration of CO2 using soluble and immobilized enzymes was determined. The stability of the immobilization matrix, the properties of the immobilized enzymes subjected to a variation in operation variables and the activity profile with respect to storage are reported. Immobilization imparted greater thermal and storage stability and enhanced reusability.
Two Proteins for the Price of One: The Design of Maximally Compressed Coding Sequences ⋆ (2010)

Abstract. The emerging field of synthetic biology moves beyond conventional genetic manipulation to construct novel life forms which do not originate in nature. We explore the problem of designing the provably shortest genomic sequence to encode a given set of genes by exploiting alternate reading frames. We present an algorithm for designing the shortest DNA sequence simultaneously encoding two given amino acid sequences. We show that the coding sequence of naturally occurring pairs of overlapping genes approach maximum compression. We also investigate the impact of alternate coding matrices on overlapping sequence design. Finally, we discuss an interesting application for overlapping gene design, namely the interleaving of an antibiotic resistance gene into a target gene inserted into a virus or plasmid for amplification. 1
Genetic Progression From Melanocyte to Malignant Melanoma (2007)

Melanocytes can give rise to a variety of benign and malignant neoplasms that differ in their appearance and, more importantly, in their biological behavior. Melanocytic nevi are self-limited proliferations of melanocytes, whereas melanocytes in melanoma continue to proliferate and therefore constitute a severe threat to the host. There is emerging evidence that the initiating events, such as mutations in oncogenes, such as BRAF and RAS, may be similar in nevi and melanoma. However, the exact nature of the mechanism that restricts proliferation in nevi that presumably fails in melanoma is currently unclear. Among melanomas, clinical and histopathological presentation can vary significantly. Several factors, such as anatomic location, sun-exposure patterns, and patient age have been associated with different histopathological and clinical patterns of melanoma (,). In this chapter, I review genetic changes in different types of nevi and melanomas and discuss potential biological consequences and possible impacts on classification and therapy.
Molecular Epidemiology of HTLV-I in the World (1996)

The geographic distribution of human T-cell lymphotropic/leukemia virus type I (HTLV-I) was initially believed to be limited to southwestern Japan, the Caribbean basin, and Africa. However, extensive searches in recent years have discovered its existence in other areas of the world as well as in isolated, ethnic populations such as South Amerindians, Australo-Melanesian aborigines, religiously segregated Jews, and Pygmies. Previous genetic analyses indicated that HTLV-I can be phylogenetically classified into three major lineages: Melanesian, Central African, and Cosmopolitan groups. Recently, more detailed characterization using long terminal repeat sequences (the most variable genomic region) has revealed that the Cosmopolitan group consists of four subtypes: (A) Transcontinental, (B) Japanese, (C) West African, and (D) North African. Most HTLV-I isolates of the same ethnic group from distant locations and those from different groups inhabiting the same area showed phylogenetic similarities. These observations indicate the present distribution of this virus should be interpreted from the anthropological backgrounds of the virus-possessing populations as well as spatial contact among them. Thus, the molecular epidemiology of HTLV-I and its simian counterpart, STLV-I, provides us with important clues for understanding not only the origin and dissemination of this retrovirus but past human movements over the globe.
Immune complexes as therapy for autoimmunity (2005)

For several decades, intravenous Ig has been used as treatment for a variety of immune-related diseases, including immune thrombocytopenic purpura (ITP), autoimmune neuropathies, systemic lupus erythematosus, myasthenia gravis, Guillain-Barré syndrome, skin blistering syndromes, and Kawasaki disease. Despite years of use, its mechanism of immunomodulation is still unclear. Recent studies using mouse models of ITP and arthritis, including one reported in this issue of the JCI, now provide some insights into this mechanism and the rationale for the development of Fcγ receptor–targeted therapeutics.
c-ets-2 protooncogene has mitogenic and oncogenic activity. (1989)

An expression vector containing the murine c-ets-2 protooncogene cDNA was introduced into NIH 3T3 cells by DNA transfection. The cells transfected with this construct showed foci of densely growing, morphologically altered cells, when grown either in low-serum (0.05%) or in serum-free medium. The c-ets-2-derived foci contained additional copies of the c-ets-2 gene, Northern blot analysis demonstrated overexpression of a c-ets-2-specific 2.5-kilobase RNA, and ets-specific antiserum recognized a 56-kDa protein. Overexpression of the c-ets-2-encoded protein stimulated cell proliferation and abolished their serum requirement. The c-ets-2 transfected cells formed colonies in semisolid medium and induced tumors in nude mice, indicating that c-ets-2 can be a transforming gene when overexpressed in these cells. This work demonstrates that a member of the c-ets gene family has transforming and mitogenic activity. In addition, the role of c-ets-2 in cell proliferation and its location in the minimal Down syndrome region on chromosome 21 implicates its involvement in the phenotypic changes associated with Down syndrome.
Comparative reactivities of esters of oncogenic and nononcogenic purine N-oxides and evidence of the oxidation-reduction reactivity of aromatic nitrenium ions. (1980)

Studies on the relative reactivities of esters of oncogenic and nononcogenic members of the purine N-oxide series indicate that, despite similarities in rates of reaction with the solvent, electrophilic cations from oncogenic derivatives are 10- to 100-fold more reactive toward added nucleophiles in vitro than are cations from nononcogenic compounds. The studies provide strong confirmation of an earlier proposal that nitrenium ion contributors of delocalized aromatic cations from 3-acyloxypurines, rather than radical intermediates, are the agents responsible for the oxidizing reactivity of these esters. They demonstrate further that delocalized aromatic nitrenium ions are highly susceptible to reduction by common nucleophiles that are not usually associated with oxidation-reduction reactions. Examples of such behavior with "soft" bases and other oncogenic arylamines indicate the generality of this little recognized property of aromatic nitrenium ions.