gebhart/patrepeval huggingface dataset:
The <i>puh</i> structural gene coding for the H subunit of the <i>Rhodospirillum rubrum</i> photoreaction center (1991)

The Rhodospirillum rubrum structural gene puh, coding for the photoreaction center H polypeptide, and three other putative genes that surround puh were cloned and sequenced. The deduced 257 amino acid H polypeptide has a molecular weight of 27,909, in close agreement with polyacrylamide gel electrophoresis determination. Hydropathy plots predict a single hydrophobic alpha helix. The H polypeptide of Rhodospirillum rubrum shares only 23% of its residues with all three of the H polypeptides from Rhodopseudomonas viridis, Rhodobacter capsulatus, and Rhodobacter sphaeroides. Despite this apparent low degree of similarity, statistical analysis leaves no doubt about their close relatedness. Interspecies evolutionary distance, assessed by this analysis, confirms the closeness of the two Rhodobacter species, Rhodospirillum rubrum and Rhodopseudomonas viridis being approximately equidistant from them. Three regions of the H polypeptide are highly conserved in all four species. They correspond to known contact points of H with the complex of the other two (L and M) subunits on the cytoplasmic side of the membrane. A glutamic acid residue (H polypeptide residue 177), conserved in the other bacteria and suggested to be involved in the binding of secondary quinone QB, is replaced by serine in Rhodospirillum rubrum. The open reading frames G115, I2372, and I3087 are predicted to, respectively, encode polypeptides of 480, 224, and 155 residues coiled in 10, 2, and 1 transmembrane helices. Open reading frame G115 shares 56% identical residues with F1696, a sequence arranged in the genome of Rhodobacter capsulatus. The gene product of ORF I3087 is predicted to share highly similar sequences with nitrogenase reductase (encoded by nifH) of 11 different bacterial species and is suggested to have a regulatory function.
Genotoxicity of retroviral hematopoietic stem cell gene therapy (2011)

Continued research on virus-host interactions and next-generation vectors should further improve the safety of future HSC gene therapy vectors and protocols.
Enhanced Heat Transport in Environmental Systems Using Microencapsulated Phase Change Materials (1992)

<div class="htmlview paragraph">The thermal management of avionic environmental systems is a growing concern to engineers. Increased heating loads and systems weight coupled with reduced volume present challenging problems to designers. This paper will outline a methodology for enhanced heat transport and storage that uses a new two-component fluid mixture consisting of a microencapsulated phase change material (microPCM) for enhanced latent heat transport. SBIR investigations for NASA, USAF, SDIO, and NSF since 1983 have demonstrated the effectiveness of this novel coolant in significantly enhancing the carrier fluid's effective thermal capacitance, increasing the exchanger heat transfer coefficient, providing essentially isothermal heat transport, and reducing pumping power requirements.</div>
A recombinant murine retrovirus for simian virus 40 large T cDNA transforms mouse fibroblasts to anchorage-independent growth (1986)

A recombinant murine retrovirus containing the intact cDNA sequence for the simian virus 40 (SV40) large T antigen (T) was constructed by using the pZIPNeo SV(X)1 vector. Psi 2 packaging cells were then transfected, and G418-resistant clones were used to generate helper-free viral stocks. NIH 3T3 mouse fibroblasts infected by the recombinant T cDNA retrovirus were selected fro G418 resistance. Such cultures synthesized authentic SV40 T and were transformed to anchorage-independent growth at high efficiency. Therefore, this vector has allowed the study of the transformation properties of T under conditions of neutral drug selection and in the absence of SV40 small t antigen.
Water recovery from brines and salt‐saturated solutions: operability and thermodynamic efficiency considerations for desalination technologies (2017)

Due to the high osmotic pressures of the brine concentrates, reverse osmosis, the most common desalination technology, is impractical. Mechanical vapor compression which, like reverse osmosis, utilizes mechanical work to operate, is reported to have the highest thermodynamic efficiency of the desalination technologies for treatment of salt-saturated brines. Thermally-driven processes, such as flash evaporation and distillation, are technically able to process saturated salt solutions, but suffer from low thermodynamic efficiencies. This inefficiency could be offset if an inexpensive source of waste or renewable heat could be used. Overarching issues posed by high salinity solutions include corrosion and the formation of scales/precipitates. These issues limit the materials, conditions, and unit operation designs that can be used.
Decreased insulin secretion in type 2 diabetes: a problem of cellular mass or function? (2001)

Type 2 diabetes is characterized by diminished or inappropriate secretion of insulin, which could be a defect of either islet cell function or beta-cell mass. Quantitation of islet cell populations in postmortem pancreas demonstrates little change of beta-cell mass in type 2 diabetes. Reduction of islet cell mass (up to 30%) is associated largely with islet amyloid deposition, and the degree of amyloidosis is independent of the duration of the disease. Insulin secretory capacity is dependent on both function and mass of cells. beta-Cell secretion is heterogeneous; increasing glucose concentrations result in recruitment of beta-cells into the secretory pool, indicating a large reserve of secretory capacity that can be recruited in insulin resistant conditions. The Starling curve of islet function describes the relationship of insulin secretion to increasing levels of insulin resistance and hyperglycemia in type 2 diabetes. Longitudinal studies in Macaca mulatta monkeys show that insulin resistance is accompanied by increased islet mass and onset of diabetes is associated with deposition of amyloid and reduction of beta-cells. Increasing the function of unresponsive beta-cells rather than the mass of cells may be a more effective therapeutic target for type 2 diabetes.
Variation in Arsenic Speciation and Concentration in Paddy Rice Related to Dietary Exposure (2005)

Ingestion of drinking water is not the only elevated source of arsenic to the diet in the Bengal Delta. Even at background levels, the arsenic in rice contributes considerably to arsenic ingestion in subsistence rice diets. We set out to survey As speciation in different rice varieties from different parts of the globe to understand the contribution of rice to arsenic exposure. Pot experiments were utilized to ascertain whether growing rice on As contaminated soil affected speciation and whether genetic variation accounted for uptake and speciation. USA long grain rice had the highest mean arsenic level in the grain at 0.26 microg As g(-1) (n = 7), and the highest grain arsenic value of the survey at 0.40 microg As g(-1). The mean arsenic level of Bangladeshi rice was 0.13 microg As g(-1) (n = 15). The main As species detected in the rice extract were AsIII, DMAV, and AsV. In European, Bangladeshi, and Indian rice 64 +/- 1% (n = 7), 80 +/- 3% (n = 11), and 81 +/- 4% (n = 15), respectively, of the recovered arsenic was found to be inorganic. In contrast, DMAV was the predominant species in rice from the USA, with only 42 +/- 5% (n = 12) of the arsenic being inorganic. Pot experiments show that the proportions of DMAV in the grain are significantly dependent on rice cultivar (p = 0.026) and that plant nutrient status is effected by arsenic exposure.
MicroRNA-466l Upregulates IL-10 Expression in TLR-Triggered Macrophages by Antagonizing RNA-Binding Protein Tristetraprolin-Mediated IL-10 mRNA Degradation (2010)

MicroRNAs (miRNAs) are generally recognized as regulating gene expression posttranscriptionally by inhibiting translation or inducing target mRNA degradation. New mechanisms for miRNAs to regulate gene expression also still attract much attention. More and more novel miRNAs are discovered by the advanced sequencing technology, but yet their biological functions are largely unknown. Up to now, the function of miR-466l, a miRNA discovered in mouse embryonic stem cells, remains unclear. In this study, we report that miR-466l can upregulate both mRNA and protein expression of IL-10 in TLR-triggered macrophages. Furthermore, we show that miR-466l can competitively bind to the IL-10 3' untranslated region AU-rich elements, which is a typical binding site for RNA-binding protein (RBP). Tristetraprolin is a well-known RBP, and mediates rapid degradation of IL-10 mRNA. miRNA always mediates target mRNA degradation or translation repression modestly; thus, the net effect of miR-466l's binding to IL-10 AU-rich elements is to prevent IL-10 mRNA degradation mediated by tristetraprolin, resulting in extended t(1/2) of IL-10 mRNA and elevated IL-10 expression. Thus, competitive binding with RBP to the same target mRNA and subsequent stabilization of target mRNA is an alternative mechanism for gene regulation by miRNAs. Also, a mechanism for regulation of IL-10 by miRNAs is outlined.
Seq2Sick: Evaluating the Robustness of Sequence-to-Sequence Models with Adversarial Examples (2020)

Crafting adversarial examples has become an important technique to evaluate the robustness of deep neural networks (DNNs). However, most existing works focus on attacking the image classification problem since its input space is continuous and output space is finite. In this paper, we study the much more challenging problem of crafting adversarial examples for sequence-to-sequence (seq2seq) models, whose inputs are discrete text strings and outputs have an almost infinite number of possibilities. To address the challenges caused by the discrete input space, we propose a projected gradient method combined with group lasso and gradient regularization. To handle the almost infinite output space, we design some novel loss functions to conduct non-overlapping attack and targeted keyword attack. We apply our algorithm to machine translation and text summarization tasks, and verify the effectiveness of the proposed algorithm: by changing less than 3 words, we can make seq2seq model to produce desired outputs with high success rates. We also use an external sentiment classifier to verify the property of preserving semantic meanings for our generated adversarial examples. On the other hand, we recognize that, compared with the well-evaluated CNN-based classifiers, seq2seq models are intrinsically more robust to adversarial attacks.
Carbohydrates in protein. 4. The determination of mannose in hen's-egg albumin by radioisotope dilution (1962)

EMULSIN GLUCOSIDASE AND GALACTOSIDASE 335 3. No separation of the two activities was achieved by ammonium sulphate fractionation or by partial heat inactivation.
Zinc ions modulate protein tyrosine phosphatase 1B activity (2014)

A novel mechanism by which Zn<sup>2+</sup>modulates PTP1B activity encompasses the binding to the closed and phospho-intermediate forms only.
Turismo de negócios: a opinião de hóspedes sobre as ações de marketing de relacionamento da rede hoteleira de São José dos Campos (SP) (2013)

Este trabalho buscou analisar o Marketing de Relacionamento utilizado na rede hoteleira de São José dos Campos, voltada para o turismo de negócios. O Marketing de Relacionamento é o processo contínuo de identificação e criação de novos valores, com clientes individuais, o compartilhamento de seus benefícios durante uma vida toda de parceria e uma vertente do marketing adequada ao setor hoteleiro. O objetivo geral deste trabalho foi identificar a opinião dos clientes em relação às práticas de Marketing de Relacionamento usadas pela rede hoteleira de São José dos Campos (SP). A metodologia utilizada neste estudo consistiu em uma pesquisa empírica de campo, na qual foram aplicados questionários a 90 clientes dos hotéis de São José dos Campos. Os resultados indicaram que o público, que é parcialmente composto por estrangeiros e, portanto, possui referências internacionais da rede hoteleira, identificou algumas das ações realizadas pela rede hoteleira. Fica evidente que as grandes redes hoteleiras que trabalham na cidade de São José dos Campos conduzem o seu negócio aplicando alguns elementos de Marketing de Relacionamento, o que faz com que, de maneira geral, o público atendido opine positivamente sobre os serviços prestados.
Infection of neonatal swine with Clostridium difficile (2000)

Clostridium difficile is an established cause of antibiotic-associated diarrhea and pseudomembranous colitis in humans and domestic and laboratory animals. Diagnostic findings support a role for C. difficile in neonatal enteritis of pigs. A typical case will occur in a piglet 1–7 days of age, with diarrhea beginning soon after birth. Pathology includes moderate to severe mesocolonic edema, sometimes accompanied by hydrothorax and/or ascites, with scattered foci of suppuration in the colonic lamina propria and accumulation of neutrophils in the mesocolon. Exudation of neutrophils and fibrin into the lumen gives rise to socalled “volcano” lesions. Cultures of affected tissues commonly yield heavy growth of C. difficile, and toxin testing almost invariably reveals the presence of toxins A and B. Treatment with antimicrobials and use of probiotics has yielded mainly unsatisfactory results, but bacitracin methylene disalicylate may be useful for prevention. The lack of commercially available immunoprophylactic products may cause producers to turn to autogenous bacterin/toxoids, but their effectiveness is uncertain.
Adsorção de corantes têxteis utilizando a estrutura metal-orgânica [Cu3(BTC)2(H2O)3]n obtida por síntese eletroquímica (1970)

Metal-Organic Framework (MOF) é uma rede de coordenação com ligantes orgânicos e estrutura porosa. O objetivo dessa pesquisa foi sintetizar por via eletroquímica a MOF [Cu3(BTC)2(H2O)3]n e aplicá-la como material adsorvente para a remoção de corantes de tecidos nos efluentes. A MOF foi síntizada eletroquimicamente e por via amperométrica, fixando-se o potencial em 12 V durante 17 min, resultando em 73% de rendimento de um sólido azul. O produto final foi usado na sua forma bruta e caracterizado por FTIR e voltametria cíclica. Essa MOF, quando em contato com uma mistura que simulou um efluente de indústria têxtil, permitiu sua descoloração, acompanhada da decantação de um sólido colorido. Essa despigmentação também foi observada através da análise do sobrenadante por espectroscopia UV-Vis. O espectro de FTIR do sólido decantado após a mistura da MOF com o corante, evidenciou a adsorção dos pigmentos da solução pela MOF. Esse resíduo sólido de MOF apresentou-se ambientalmente vantajoso, por ter sido facilmente separado do efluente tratado e por ser regenerável e reutilizável. Isso o diferencia do lodo gerado nos processos de coagulação/floculação tradicionais, que pode ser danoso ao meio ambiente.
Size and cohesion metrics as indicators of the long method bad smell (2015)

Source code bad smells are usually resolved through the application of well-defined solutions, i.e., refactorings. In the literature, software metrics are used as indicators of the existence and prioritization of resolving bad smells. In this paper, we focus on the long method smell (i.e. one of the most frequent and persistent bad smells) that can be resolved by the extract method refactoring. Until now, the identification of long methods or extract method opportunities has been performed based on cohesion, size or complexity metrics. However, the empirical validation of these metrics has exhibited relatively low accuracy with regard to their capacity to indicate the existence of long methods or extract method opportunities. Thus, we empirically explore the ability of size and cohesion metrics to predict the existence and the refactoring urgency of long method occurrences, through a case study on java open-source methods. The results of the study suggest that one size and four cohesion metrics are capable of characterizing the need and urgency for resolving the long method bad smell, with a higher accuracy compared to the previous studies. The obtained results are discussed by providing possible interpretations and implications to practitioners and researchers.
Structural Basis for Inhibition of Translation by the Tumor Suppressor Pdcd4 (2006)

The tumor suppressor function of Programmed Cell Death 4 (Pdcd4) is achieved through interactions between Pdcd4 and components of the translation initiation complex, namely, the RNA helicase eIF4A and the scaffolding protein eIF4G. These interactions are mediated through two MA3 domains on the Pdcd4 molecule and result in inhibition of protein synthesis. We have solved the high-resolution crystal structure of the C-terminal MA3 (cMA3) domain of Pdcd4 in several crystal forms and demonstrated its similarity to the MA3 domain of eIF4G. As predicted by the structure, the cMA3 domain competes with eIF4Gc for binding to eIF4A and surprisingly is sufficient to inhibit translation initiation. Mutations that abolish eIF4A binding negate both functions of the cMA3. Interestingly mutations in the Akt phosphorylation site influenced neither cMA3 binding to eIF4A nor its ability to inhibit translation initiation. Finally, our structural analysis reveals MA3 domains to be a novel subfamily of VHS domains.
Vectorized Delivery of Alpha-GalactosylCeramide and Tumor Antigen on Filamentous Bacteriophage fd Induces Protective Immunity by Enhancing Tumor-Specific T Cell Response (2018)

We have exploited the properties of filamentous bacteriophage <i>fd</i> to deliver immunologically active lipids together with antigenic peptides. Filamentous bacteriophages resemble for size, capability to be permeable to blood vessels, and high density antigen expression, a nature-made nanoparticle. In addition, their major coat protein pVIII, which is arranged to form a tubular shield surrounding the phage genome, has a high content of hydrophobic residues promoting lipid association. We conjugated bacteriophages to alpha-GalactosylCeramide (α-GalCer), a lipid antigen-stimulating invariant natural killer T (iNKT) cells and capable of inducing their anti-tumoral activities. We found that bacteriophage fd/α-GalCer conjugates could repeatedly stimulate iNKT cells <i>in vitro</i> and <i>in vivo</i>, without inducing iNKT anergy. Moreover, co-delivery of α-GalCer and a MHC class I restricted tumor-associated antigenic determinant to antigen-presenting cells <i>via</i> bacteriophages strongly boosted adaptive CD8<sup>+</sup> T cell response and efficiently delayed tumor progression. Co-delivery of a tumor antigen and iNKT-stimulatory lipid on the surface of filamentous bacteriophages is a novel approach to potentiate adaptive anti-cancer immune responses, overcoming the current limitations in the use of free α-GalCer and may represent an attractive alternative to existing delivery methods, opening the path to a potential translational usage of this safe, inexpensive, and versatile tool.
Initial Problems with Polynomials on Right-hand Sides (2009)

The application of Taylor series has become a standard concept in numerical analysis. Their ability of approximating functions arbitrarily close under certain conditions makes them an ideal tool for the integration of differential equations. Before the appearance of digital computers the analytical determination of Taylor series coefficients, i.e. the calculation of higher derivatives, was regarded as too complicated. In many modern text books on numerical or applied mathematics has even been stated that Taylor series can only be applied as implementation in very special cases. In this paper an outline is presented of establishing Taylor series coefficients of initial problems with polynomials on right-hand sides. The application of recurrent Taylor series to the integration of systems of ordinary differential equations is discussed. The software TKSL for the solution of initial value problems by means of recurrent Taylor series has been developed and many positive results have been obtained.
Uranium(III) Complexes with Bulky Aryloxide Ligands Featuring Metal–Arene Interactions and Their Reactivity Toward Nitrous Oxide (2013)

We report the synthesis and use of an easy-to-prepare, bulky, and robust aryloxide ligand starting from inexpensive precursor materials. Based on this aryloxide ligand, two reactive, coordinatively unsaturated U(III) complexes were prepared that are masked by a metal-arene interaction via δ-backbonding. Depending on solvent and uranium starting material, both a tetrahydrofuran (THF)-bound and Lewis-base-free U(III) precursor can easily be prepared on the multigram scale. The reaction of these trivalent uranium species with nitrous oxide, N2O, was studied and an X-ray diffraction (XRD) study on single crystals of the product revealed the formation of a five-coordinate U(V) oxo complex with two different molecular geometries, namely, square pyramidal and trigonal bipyramidal.
Complete Characterization of Posttranslational Modification Sites in the Bovine Milk Protein PP3 by Tandem Mass Spectrometry with Electron Capture Dissociation as the Last Stage (2003)

A comprehensive approach to protein identification and determination of sites of posttranslational modifications (PTMs) in heavily modified proteins was tested. In this approach, termed "reconstructed molecular mass analysis" (REMMA), the molecular mass distribution of the intact protein is measured first, which reveals the extent and heterogeneity of modifications. Then the protein is digested with one or several enzymes, with peptides separated by reversed-phase HPLC, and analyzed by Fourier transform mass spectrometry (FTMS). Vibrational excitation (collisional or infrared) or electron capture dissociation (ECD) of peptide ions provides protein identification. When a measured peptide molecular mass indicates the possibility of a PTM, vibrational excitation is applied to determine via characteristic losses the type and eventually the structure of the modification, while ECD determines the PTM site. Chromatographic peak analysis continues until full sequence coverage is obtained, after which the molecular mass is reconstructed and compared with the measured value. An agreement indicates that the PTM characterization was complete. This procedure applied to the bovine milk PP3 protein containing 25% modifications by weight yielded all known modifications (five phosphorylations, two O- and one N-glycosylation) as well as the previously unreported NeuNAc-Hex-[NeuNAc]HexNAc group O-linked to Ser60. With the FTMS performance improved, REMMA can serve as the basis for high-throughput, high-sensitivity PTM characterization of biological important proteins, which should speed up the proteomics research.
Synthesis and properties of N<sup>α</sup>‐lauroyl‐L‐arginine dipeptides from collagen‐lauroyl‐L‐arginine dipeptides from collagen (1988)

Abstract In order to obtain protein‐based amphoteric surfactants with antimicrobial properties, N α ‐lauroyl arginine dipeptides have been prepared by condensation between N α ‐lauroyl arginine and amino acids which come from a collagen hydrolysate. Some surfactant properties and the minimum inhibitory concentration against Gram positive and Gram negative bacteria have been evaluated. All types of compounds presented a surfactant‐like behavior. Furthermore, the compounds described in this paper may be considered as mild preservative or protective substances.