gebhart/patrepeval huggingface dataset:
Anatomy of herpes simplex virus DNA: evidence for four populations of molecules that differ in the relative orientations of their long and short components. (1975)

Intact DNA molecules extracted from HSV-1 (herpes simplex virus 1, human herpes virus 1) strain MP virions have a molecular weight of approximately 97 X 10(6), but cleavage with the HinIII restriction enzyme yields fourteen fragments with summed molecular weights of 160 X 10(6). Six "major" fragments occur once in every molecule in the population and account for 60% of the genetic information. Four "minor" fragments are present in amounts equivalent to one copy for every two genomes (0.5 molar ratio) and the other four occur only once in every four molecules (0.25 molar ratio). The minor fragments can be arranged into four equimolar sets, each with summed molecular weights that account for the remaining 40% of the genome. Treatment with lambda 5' exonuclease revealed that all molecules contain 0.5 molar ratio fragments at both termini. These observations and the results of similar analyses of the EcoRI and double HinIII/EcoRI digests indicate that there are four distinct structural forms of HSV DNA which differ only in the relative orientations of two subregions, designated L and S. The L and S segments consist of 82 and 18% of the sequences, respectively, and each has inverted terminally redundant regions that correspond to the internal duplications observed by electron microscopy. The DNA from other strains of HSV-1 and 2 also consists of equal proportions of all four possible permutations of the L and S segments. These unusual features of HSV DNA molecules have novel implications with regard to the genetic map and the mode of replication and evolution of herpes simples viruses.
Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome (2016)

The ribosome is one of the major targets for therapeutic antibiotics; however, the rise in multidrug resistance is a growing threat to the utility of our current arsenal. The orthosomycin antibiotics evernimicin (EVN) and avilamycin (AVI) target the ribosome and do not display cross-resistance with any other classes of antibiotics, suggesting that they bind to a unique site on the ribosome and may therefore represent an avenue for development of new antimicrobial agents. Here we present cryo-EM structures of EVN and AVI in complex with the Escherichia coli ribosome at 3.6- to 3.9-Å resolution. The structures reveal that EVN and AVI bind to a single site on the large subunit that is distinct from other known antibiotic binding sites on the ribosome. Both antibiotics adopt an extended conformation spanning the minor grooves of helices 89 and 91 of the 23S rRNA and interacting with arginine residues of ribosomal protein L16. This binding site overlaps with the elbow region of A-site bound tRNA. Consistent with this finding, single-molecule FRET (smFRET) experiments show that both antibiotics interfere with late steps in the accommodation process, wherein aminoacyl-tRNA enters the peptidyltransferase center of the large ribosomal subunit. These data provide a structural and mechanistic rationale for how these antibiotics inhibit the elongation phase of protein synthesis.
Investigation of SSEA-4 Binding Protein in Breast Cancer Cells (2013)

SSEA-4, a sialyl-glycolipid, has been commonly used as a pluripotent human embryonic stem cell marker, and its expression is correlated with the metastasis of some malignant tumors. However, there is no in-depth functional study related to the receptor and the role of this glycolipid. Here, we report the identification of an SSEA-4-binding protein in a breast cancer cell line, MCF-7. By using affinity capture and glycan microarray techniques, the intracellular FK-506 binding protein 4 (FKBP4) was identified to bind directly to SSEA-4. The biological significance of SSEA-4/FKBP4 interaction was investigated.
Overexpression of lysosomal-type sialidase leads to suppression of metastasis associated with reversion of malignant phenotype in murine B16 melanoma cells (2001)

Increased sialylation in cell surface glycoproteins is one characteristic feature of cancer cells, particularly related to their metastatic potential and invasiveness. Expression of lysosomal-type sialidase, which plays a major role in hydrolysis of such sialo-glycoproteins, is therefore considered to have a great influence on malignant properties of cancer cells. To investigate whether the sialidase expression level is linked to the malignant phenotype, we transfected B16-BL6 murine melanoma cells, a highly invasive and metastatic line, with an expression vector harboring a rat lysosomal sialidase cDNA; then clones were isolated and examined for changes in biological character. Sialidase-overexpressing cells showed suppression of experimental pulmonary metastasis and tumor progression. The transfectants exhibited diminished cell growth, anchorage-independent growth and increased sensitivity to apoptosis induced by suspension culture or serum depletion in vitro, but no significant alterations in invasiveness, cell motility and cell attachment to fibronectin, collagen IV and laminin. Flow cytometric analysis with either peanut agglutinin (PNA) or Ricinus communis agglutinin (RCA) lectin revealed that desialylated forms of glycoproteins on the cell surfaces were increased. In particular, a desialylated form of a cell surface glycoprotein of 83 kDa was prominent in the transfectants, as determined by galactose oxidase labeling. These observations indicate that sialidase expression is inversely associated with metastatic potential and tumor growth in cancer cells, probably through a regulation mechanism that suppresses cell growth and anchorage-independent growth and promotes apoptosis with deprivation of cell anchorage.
Synthesis of Molecular Brushes by “Grafting onto” Method:  Combination of ATRP and Click Reactions (2007)

Molecular brushes (densely grafted polymers or bottle-brush macromolecules) were synthesized by the "grafting onto" method via combination of atom transfer radical polymerization (ATRP) and "click" reactions. Linear poly(2-hydroxyethyl methacrylate) (PHEMA) polymers were synthesized first by ATRP. After esterification reactions between pentynoic acid and the hydroxyl side groups, polymeric backbones with alkynyl side groups on essentially every monomer unit (PHEMA-alkyne) were obtained. Five kinds of azido-terminated polymeric side chains (SCs) with different chemical compositions and molecular weights were used, including poly(ethylene glycol)-N3 (PEO-N3), polystyrene-N3, poly(n-butyl acrylate)-N3, and poly(n-butyl acrylate)-b-polystyrene-N3. All click coupling reactions between alkyne-containing polymeric backbones (PHEMA-alkyne) and azido-terminated polymeric SCs were completed within 3 h. The grafting density of the obtained molecular brushes was affected by several factors, including the molecular weights and the chemical structures of the linear SCs, as well as the initial molar ratio of linear chains to alkynyl groups. When linear polymers with "thinner" structure and lower molecular weight, e.g., PEO-N3 with Mn = 775 g/mol, were reacted with PHEMA-alkyne (degree of polymerization = 210) at a high molar ratio of linear chains to alkynyl groups in the backbone, the brush copolymers with the highest grafting density were obtained (Y(grafting) = 88%). This result indicates that the average number of SCs was ca. 186 per brush molecule and the average molecular weight of the brush molecules was ca. 190 kg/mol.
Optimal control of energetically efficient ladder decent motion with internal stress adjustment using key joint method (2012)

For multi-contact robot motion, a closed chain is formed by robot links and the environment. This paper proposes a new methodology named “key joint method” for reducing the energy cost by adjusting an internal stress inside a closed chain. Firstly, we analyze the internal stress theoretically taking the degrees of freedom (DOF) and the number of position actuated joints into consideration, then a practical key joint method is proposed by changing a suitable redundant position controlled joint to be force control. After that, a parametric family is introduced for representing various of possible motions subjected to the robot dynamics and other constraints. Finally, a general optimization method is proposed for planning an energetically efficient multi-contact robot motion taking the motion trajectories and internal stress into consideration. As an example, the pace gait ladder decent motion is taken to explain the principle and realization of the proposed method. As experimental evaluation shows, the key joint method is effective for reducing the energy cost in the multi-contact motion.
Activation of the Epidermal Platelet-Activating Factor Receptor Results in Cytokine and Cyclooxygenase-2 Biosynthesis (1998)

Recent studies suggest that the lipid mediator platelet-activating factor (PAF) is involved in keratinocyte function and skin inflammation. Indeed, PAF is found in association with inflammatory skin diseases, intradermal injections of PAF induce inflammation, and keratinocytes express functional PAF receptors (PAF-R). One mechanism by which the keratinocyte PAF-R could contribute to epidermal functions and inflammatory states would be through the synthesis of inflammatory regulators, such as PAF, PGs, and cytokines. The ability of the epidermal PAF-R to induce the synthesis of these immunomodulators was tested using a model system created by transduction of the PAF-R-negative human epidermal cell line KB with the PAF-R. Activation of this epidermal PAF-R resulted in arachidonic acid release, and the biosynthesis of PAF and PGE2. In addition, the KB PAF-R triggered increased levels of mRNA and protein for the inducible isozyme of cyclooxygenase (COX-2) as well as IL-6 and IL-8, both of which have been implicated in skin inflammatory processes. Studies with the human keratinocyte-derived epidermal cell line HaCaT revealed that activation of the endogenous PAF-R led to the increased accumulation of COX-2, IL-6, and IL-8 mRNA similar to that seen with the KB PAF-R model system. Finally, treatment of HaCaT keratinocytes with IL-8 resulted in PAF biosynthesis, indicating the existence of a positive feedback loop between IL-8 and PAF in epidermal cells. These studies suggest involvement of PAF and the PAF-R in the epidermal cytokine network.
Quality improvement of paper from bamboo and hardwood furnish through fiber fractionation (2005)

This study is aimed to improve the quality of paper made from hardwoods (70-80%) and bamboo furnish (20-30%) through fractionation process. The fiber fractionation followed by selective processing of each fraction proved to be a better option to produce paper of improved quality in terms of strength, optical and printing properties. The paper also discusses the machine runnability with fractionated pulp samples based on Wet web properties and fines content of fractionated pulp. The possibilities of using different fractions in different grades were also explored. This is a good opportunity for mills having multiple paper machines and making different varieties of paper.
An Experimental Service for Adaptable Data Reconfiguration (1972)

The ARPA computer network (ARPANET) is a nationwide network of diverse autonomous computers connected via a message-switching store-and-forward communications subnet using leased wide-band (50-kbit/s) telephone lines. A primary objective of the ARPANET is to share preexisting programs and data. Many of the difficulties of using remotely generated programs and data are found to be simple format incompatibilities requiring data manipulations like character set conversion, header prefacing and stripping, packing and unpacking of repeated data, generating counters and flags, and field transposition. The data reconfiguration service (DRS) is an attempt to provide a convenient way of performing these data manipulations in order to mediate between superficially incompatible data streams connecting existing programs in the ARPANET. Desiring to match two incompatible input-output streams, an applications programmer specifies a data stream transformation (called a form) written in the data reconfiguration language (DRL). Associating the appropriate form name with the connection between his two programs, the programmer causes the DRS to follow his instructions on how the specified data streams are to be manipulated in the communication required to make the two programs cooperate over the ARPANET. Components of the DRS include the specification of its special-purpose data reconfiguration language, a form compiler to translate forms into fast-running transformation programs, an interpreter to perform high-speed data transformations at application program run time, and a standard set of ARPANET protocols for the routine handling of connections and form specifications between operating systems.
Synthesis of Silicon Nanowires with Wurtzite Crystalline Structure by Using Standard Chemical Vapor Deposition (2007)

Silicon nanowires—filamentary crystals with a very high ratio of length to diameter (see figure)—allow growth of the wurtzite crystalline phase, which is also semiconducting for silicon. The association of this phenomenon with the competition between surface energy and pressure effects occurring at diameters below 150 nm is shown.
Methodological problems in genetic association studies of longevity--the apolipoprotein E gene as an example (2004)

The validity of case-control type studies of the genetic basis of longevity based on the above assumptions is questionable, especially when considerable differences exist in allele frequency by population and when the genes in question interact with environmental factors, which vary by time and place.
Cloning and characterization of cDNA sequences corresponding to myosin light chains 1, 2, and 3, troponin-C, troponin-T, alpha-tropomyosin, and alpha-actin. (1982)

A library of cDNA clones was constructed from adult rat skeletal muscle mRNA, from which a set of contractile protein clones was selected. These clones were identified by sequencing the cDNA inserts and comparing the derived amino acid sequences with published sequences of rabbit contractile proteins. In this manner, clones corresponding to myosin light chains 1, 2, and 3, troponin-C, troponin-T, alpha-tropomyosin, and alpha-actin were identified. A high degree of amino acid sequence conservation was found upon comparison of the rat and rabbit proteins. Using the cDNA clone panel, we analyzed the expression of abundant rat muscle mRNAs. We show that abundant rat muscle mRNAs can be classified into four developmentally regulated groups, based upon their expression at different stages of myogenesis. One class of mRNAs is expressed during all stages of muscle development. Since these mRNAs are also present in nonmuscle tissues, we conclude that they code for housekeeping proteins. The second class of mRNAs is present in both embryonic and adult muscle, while a third class of mRNAs is expressed only in adult muscle. A small number of mRNAs, which are present at greater levels in undifferentiated myoblasts than in adult muscle, comprise a fourth class. These results suggest the existence of at least four modes of gene control during myogenesis.
Recoverin and Hsc 70 are found as autoantigens in patients with cancer-associated retinopathy. (1999)

These observations suggest that humoral autoimmune reactions against recoverin and hsc 70 might be involved in the pathogenesis of CAR.
Optimal one-wafer cyclic scheduling analysis of hybrid multi-cluster tools with one-space buffering module (2014)

A multi-cluster tool with both single and dual-arm individual cluster tools is called a hybrid multi-cluster tool. To operate it, one needs to coordinate different types of robots for accessing the shared buffering modules. Aiming at finding a one-wafer periodic schedule such that the lower bound of cycle time can be reached, this work studies its scheduling when its bottleneck individual tool is process-bound. With a timed Petri net model, the scheduling problem is reduced to determine the waiting time of robots. Then, the conditions are presented, under which a one-wafer periodic schedule exists such that the lower bound of cycle time can be reached. Based on them, an efficient algorithm is given to check whether such a one-wafer periodic schedule exists. If so, it is found via simple calculation. An example is given to show its effectiveness.
A microcellular processing study of poly(ethylene terephthalate) in the amorphous and semicrystalline states. Part II: Cell growth and process design (1996)

Abstract Microcellular semicrystalline polymers such as poly(ethylene terephthalate) show great promise for engineering applications because of their unique properties, particularly at higher densities. Recent studies have shown that some high density microcellular polymers have longer fatigue lives and/or equivalent strengths relative to the neat polymer. Relatively few microcellular processing studies of semicrystalline polymers have been presented. In general, semicrystalline polymers are relatively difficult to microcellular process compared to amorphous polymers. In this paper, the microcellular processing of poly(ethylene terephthalate) in the amorphous and semicrystalline states is studied in order to quantify the processing differences. Particular emphasis is given to the cell growth stage of microcellular processing comparing the processing characteristics of semicrystalline and amorphous PET. Based on the results of this study, a number of critical process parameters are identified. Another goal of this analysis is to derive robust microcellular process design strategies for the amorphous and semicrystalline materials. Process design strategies are given for both semicrystalline and amorphous PET.
Relative Effectiveness of Various Ions on the Solubility and Crystal Growth of Lysozyme (1989)

Crystallization conditions for hen egg white lysozyme in the presence of various ions were determined at pH 4.5 and 18 degrees C. The corresponding solubility curves show that the main effects are due to anions in the following order: SCN- greater than NO3- greater than Cl- greater than citrate2- greater than CH3COO- approximately H2PO4- greater than SO4(2-). This is in the reverse order of the lyotropic series of Hofmeister. As a consequence, SCN- precipitates and crystallizes lysozyme at low concentration, whereas sulfate is ineffective even at high concentrations. Crystals obtained with each salt were characterized by x-ray diffraction. Lysozyme thiocyanate and nitrate crystals belong to the monoclinic system, whereas all the others have a tetragonal lattice.
An object-oriented web test model for testing Web applications (2002)

In recent years, Web applications have grown rapidly. As Web applications become complex, there is a growing concern about their quality and reliability. In this paper we present a methodology that uses an object-oriented Web Test Model (WTM) to support Web application testing. The test model captures both structural and behavioral test artifacts of Web applications and represents the artifacts form the object, behavior and structure perspectives. Based on the test model, both structural and behavioral test cases can be derived automatically to ensure the quality of Web applications. Moreover the model also can be used as a road map to identify change ripple effects and to find cost-effective testing strategies for reducing test efforts required in the regression testing.
Scaling the Stiffness, Strength, and Toughness of Ceramic‐Coated Nanotube Foams into the Structural Regime (2014)

Natural materials such as bone and tooth achieve precisely tuned mechanical and interfacial properties by varying the concentration and orientation of their nanoscale constituents. However, the realization of such control in engineered foams is limited by manufacturing‐driven tradeoffs among the size, order, and dispersion uniformity of the building blocks. It is demonstrated how to manufacture nanocomposite foams with precisely controllable mechanical properties via aligned carbon nanotube (CNT) growth followed by atomic layer deposition (ALD). By starting with a low density CNT forest and varying the ALD coating thickness, we realize predictable ≈1000‐fold control of Young's modulus (14 MPa to 20 GPa, where E ∼ ρ 2.8 ), ultimate compressive strength (0.8 MPa to 0.16 GPa), and energy absorption (0.4 to 400 J cm –3 ). Owing to the continuous, long CNTs within the ceramic nanocomposite, the compressive strength and toughness of the new material are 10‐fold greater than commercially available aluminum foam over the same density range. Moreover, the compressive stiffness and strength equal that of compact bone at 10% lower density. Along with emerging technologies for scalable patterning and roll‐to‐roll manufacturing and lamination of CNT films, coated CNT foams may be especially suited to multifunctional applications such as catalysis, filtration, and thermal protection.
Leukemia Inhibitory Factor–dependent Transcriptional Activation in Embryonic Stem Cells (1997)

STAT transcription factors are induced by a number of growth factors and cytokines. Within minutes of induction, the STAT proteins are phosphorylated on tyrosine and serine residues and translocated to the nucleus, where they bind to their DNA targets. The leukemia inhibitory factor (LIF) mediates pleiotropic and sometimes opposite effects both in vivo and in cultured cells. It is known, for example, to prevent differentiation of embryonic stem (ES) cells in vitro. To get insights into LIF-regulated signaling in ES cells, we have analyzed protein-binding and transcriptional properties of STAT recognition sites in ES cells cultivated in the presence and in the absence of LIF. We have detected a specific LIF-regulated DNA-binding activity implicating the STAT3 protein. We show that STAT3 phosphorylation is essential for this LIF-dependent DNA-binding activity. The possibility that ERK2 or a closely related protein kinase, whose activity is modulated in a LIF-dependent manner, contributes to this phosphorylation is discussed. Finally, we show that the multimerized STAT3-binding DNA element confers LIF responsiveness to a minimal thymidine kinase promoter. This, together with our observation that overexpression of STAT3 dominant-negative mutants abrogates this LIF responsiveness, clearly indicates that STAT3 is involved in LIF-regulated transcriptional events in ES cells. Finally, stable expression of such a dominant negative mutant of STAT3 induces morphological differentiation of ES cells despite continuous LIF supply. Our results suggest that STAT3 is a critical target of the LIF signaling pathway, which maintains pluripotent cell proliferation.