gebhart/patrepeval huggingface dataset:
Avidin-biotin affinity chromatography: application to the isolation of human placental insulin receptor. (1984)

The ligand N alpha, B1-(6-biotinylamido)hexanoyl-insulin was attached noncovalently to Sepharose 4B immobilized succinoylavidin to form an insulin-affinity resin. This resin was used to isolate highly purified insulin receptor from human placental tissue by a four step process involving (i) preparation of a crude membrane fraction, (ii) solubilization with Triton X-100, (iii) wheat germ agglutinin purification, and (iv) insulin-affinity chromatography. NaDodSO4/PAGE of the purified 125I-labeled receptor under nonreducing conditions showed the presence of a major component with an approximate molecular weight of 350,000 and a minor component with a molecular weight of approximately equal to 166,000. Based on the assumption that the degree of labeling is comparable in both components, the material corresponding to the Mr 350,000 peak represents approximately equal to 94% of the receptor preparation as determined by scanning the autoradiograms. The specific insulin binding capacity of the preparation is 18 +/- 6 micrograms of 125I-labeled insulin per mg of protein as determined by the polyethylene glycol assay and analyzed by Scatchard plot. Insulin binding activity was stable at 4 degrees C and pH 7.6 for at least 12 weeks but was destroyed by freezing and thawing. The availability of highly purified receptor afforded the opportunity to explore its precipitability by polyethylene glycol under assay conditions. Whereas trichloroacetic acid precipitated 95% of the 125I-labeled receptor, polyethylene glycol precipitated only 30%. If the specific activity of the receptor is corrected for incomplete precipitability by polyethylene glycol, the apparent specific binding would be 3.5 +/- 1.2 mol of insulin per mol of receptor. These results are in disagreement with the current receptor model, which postulates that 1 mol of receptor (Mr, 350,000) binds 2 mol of insulin. Clearly, the problems associated with the method available for determining insulin binding are sufficiently serious to preclude their use in determining receptor valence.
Nucleotide sequence of the thrA gene of Escherichia coli. (1980)

The thrA gene of Escherichia coli codes for a single polypeptide chain having two enzymatic activities required for the biosynthesis of threonine, aspartokinase I and homoserine dehydrogenase I. This gene was cloned in a bacterial plasmid and its complete nucleotide sequence was established. It contains 2460 base pairs that encode for a polypeptide chain of 820 amino acids. The previously determined partial amino acid sequence of this protein is in good agreement with that predicted from the nucleotide sequence. The gene contains an internal sequence that resembles the structure of bacterial ribosome-binding sites, with an AUG preceded by four triplets, each of which can be converted to a nonsense codon by a single mutation. This suggests that the single polypeptide chain was formed by the fusion of two genes and that initiation of translation may occur inside the gene to give a protein fragment having only the homoserine dehydrogenase activity.
Optimizing wound healing. A practice within nursing's domain. (1990)

Clinicians could be overwhelmed with all that needs to be done to advance the clinical care of tissue wounds. This is not the time to be discouraged, however. Perhaps there has been no period in the history of health care when the possibility of influencing future trends in wound care was greater. Generally speaking, nurses are increasing their understanding of their place in healing activities and are involved in tending wounds that demand greater direct care. Simultaneously, some manufacturers of wound care products seek the input of clinicians as they attempt to produce sound and usable products. Articles appear that delimit scientifically based approaches to wound care and debunk those based solely on tradition. Levine reminded us that "perhaps no worker can influence the success of the healing process more than the nurse." I encourage the readers of this article to take Levine's statement to heart, to latch onto the current momentum, and to force the next decade in health care to be referred to not as the "era of the wound" but rather as the "era of healing."
Flavivirus Capsid Is a Dimeric Alpha-Helical Protein (2003)

The capsid proteins of two flaviviruses, yellow fever virus and dengue virus, were expressed in Escherichia coli and purified to near homogeneity suitable for biochemical characterization and structure determination by nuclear magnetic resonance. The oligomeric properties of the capsid protein in solution were investigated. In the absence of nucleic acid, both proteins were predominantly dimeric in solution. Further analysis of both proteins with far-UV circular dichroism spectroscopy indicated that they were largely alpha-helical. The secondary structure elements of the dengue virus capsid were determined by chemical shift indexing of the sequence-specific backbone resonance assignments. The dengue virus capsid protein devoid of its C-terminal signal sequence was found to be composed of four alpha helices. The longest alpha helix, 20 residues, is located at the C terminus and has an amphipathic character. In contrast, the N terminus was found to be unstructured and could be removed without disrupting the structural integrity of the protein.
Anharmonic adlayer vibrations on the Si(111):H surface (1999)

Using infrared absorption spectroscopy, the frequency and linewidth of the H-stretching vibration on the Si(111):H-(1\ifmmode\times\else\texttimes\fi{}1) surface has been measured over a temperature range of 14--350 K. An ab initio calculation of the temperature dependence of the anharmonic frequency shift and the intrinsic linewidth of this mode has been carried out, which fully accounts for the quantum nature of the atomic vibrations by using interacting phonon theory. The theoretical results show that at temperatures greater than 200 K, both line shift and linewidth of the stretching mode are primarily due to strong anharmonic coupling to the bending modes, which suffer decay into substrate modes via cubic anharmonicity. At low temperatures, direct coupling to various phonon modes of the substrate dominates the temperature dependence of the line shift. In addition, predictions are made for the frequency shift due to zero-point motion of the atoms. A strong sensitivity of the frequency on the shape of the Si-H potential has been found that makes quantitative predictions of the influence of zero-point motion very difficult. As a byproduct, the temperature dependence of the interatomic distances near the surface has been obtained and a decrease of the H-Si distance with increasing temperature is predicted.
Architectural tradeoffs for survivor sequence memory management in Viterbi decoders (1993)

In a Viterbi decoder, there are two known memory organization techniques for the storage of survivor sequences from which the decoded information sequence is retrieved, namely, register exchange method and traceback method. This work extends previously known traceback approaches, describes two new traceback algorithms, and compares various traceback methods with each other. Memory size, latency, and implementational complexity of the survivor sequence management are analyzed for both uniprocessor and multiprocessor realizations of Viterbi decoders. A new, one-pointer traceback method is shown to be better than previously known traceback methods.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Psychological aspects of diabetic neuropathic foot complications: an overview (2004)

Despite recent advances in understanding and major efforts to control the biomedical risk factors for neuropathic foot complications, the rates of foot ulceration and amputation remain unacceptably high. As the current focus on physical factors alone has not led to a substantial decline in foot complications in persons with diabetes, we propose a more balanced approach with the consideration of potentially important psychological factors. Until recently, psychosocial research in diabetes has almost exclusively focused on self-care behaviours and the burdens associated with the management of glycaemia, almost to the total neglect of the effects of chronic complications including neuropathy. As the burdens associated with the complications of diabetes begin to overshadow those specific to the control of glycaemia, it is important to develop social and psychological concepts and measures that capture how patients perceive and respond to specific threats such as that of neuropathy. There is now some progress in this area as evidenced by emerging patient-centred, theory-based methods to identify psychological factors influencing adherence behaviours, emotional status and quality of life in diabetic patients at high risk of developing foot ulcers. The development of a conceptual model of patient's common-sense representations or beliefs about foot complications and the type and source of their emotional distress should allow clinicians and behavioural investigators to share ideas for the assessment of patient beliefs and behaviour, and the development of educational methods that should improve clinicians' ability to empower patients to manage their neuropathy more efficiently.
Role of annexins in endocytosis of antigens in immature human dendritic cells (1997)

We have evaluated the uptake of a soluble protein antigen, denitrophenylated human serum albumin (DNP-HSA), and two different intracellular bacteria; Chlamydia trachomatis serovar L2 and Mycobacterium tuberculosis strain H37Ra, by immature human dendritic cells. These were generated by culturing progenitor cells from blood in the presence of cytokines (granulocyte-macrophage colony-stimulating factor and interleukin-4). Dendritic cells play a crucial part in antigen presentation for the induction of T-cell-dependent immune responses in various tissues. Recently, macropinocytic and phagocytic activity has been shown for immature dendritic cells of mouse, rat and human origin. In the present study, macropinocytosis characterized the uptake of the soluble protein-antigen DNP-HSA, whereas the C. trachomatis were ingested via receptor-mediated endocytosis in coated pits, and opsonized M. tuberculosis via phagocytosis. To follow the intracellular routes of the antigens, their positions were compared with the localization of annexins, a family of Ca(2+)-and phospholipid-binding proteins, involved in membrane fusion, aggregation and transport of different vesicles. To elucidate further the intracellular pathway of the antigens, two other proteins, lysosome-associated membrane protein-1 (LAMP-1) and cathepsin D, were labelled. They are known to colocalize with major histocompatibility complex class II compartments in the immature dendritic cells. We observed a distinct translocation of annexin V to DNP-HSA containing endosomes, and annexin III to vesicles with C. trachomatis. Furthermore, annexin III, IV and V redistributed to phagosomes with M. tuberculosis. Both LAMP-1 and cathepsin D colocalized with DNP-HSA endosomes, and with phagosomes with M. tuberculosis. Thus, immature human dendritic cells have the capacity to phagocytose. Moreover, the handling of these antigens by dendritic cells may represent three distinct intracellular pathways, albeit some properties and compartments are shared.
Are Our Systems Really Integrated? (2000)

To develop a true integrated delivery system, the CEO must articulate the purpose, measure the progress toward the vision, and keep the focus of the mission before all staff. An inability to develop and implement a true integrated delivery system could be caused by sporadic changes in the financing of health care. The challenges remain, and doing what is right for the patient is most important.
II. Synthesis and Biological Evaluation of Some Bioisosteres and Congeners of the Antitumor Agent, 2-{4-[(7-Chloro-2-quinoxalinyl)oxy]phenoxy}propionic Acid (XK469) (2002)

XK469 (1) is among the most highly and broadly active antitumor agents to have been evaluated in our laboratories. Subsequent developmental studies led to the entry of (R)-(+) 1 (NSC 698215) into phase 1 clinical trials (NIH UO1-CA62487). The antitumor mechanism of action of 1 remains to be elucidated, which has prompted a sustained effort to elaborate a pharmacophoric pattern of 1. The present study focused on a strategy of synthesis and biological evaluation of topologically based, bioisosteric replacements of the quinoxaline moiety in the lead compound (1) by quinazoline (4a−d), 1,2,4-benzotriazine (12a−18b), and quinoline (21a−g) ring systems. The synthetic approach to each of the bioisosteres of 1 utilized the methodology developed in previous work (see Hazeldine, S. T.; Polin, L.; Kushner, J.; Paluch, J.; White, K.; Edelstein, M.; Palomino, E.; Corbett, T. H.; Horwitz, J. P. Design, Synthesis, and Biological Evaluation of Analogues of the Antitumor Agent 2-{4-[(7-Chloro-2-quinoxalinyl)oxy]phenoxy}propionic acid (XK469). J. Med. Chem. 2001, 44, 1758−1776.), which is extended to the procurement of the benzoxazole (23a,b), benzthiazole (23c,d), pyridine (25a,b), and pyrazine (27) congeners of 1. Only quinoline analogues, bearing a 7-halo (21a,b,d,e) or a 7-methoxy substituent (21g), showed antitumor activities (Br > Cl > CH3O > F ≈ I), at levels comparable to or greater than the range of activities manifested by 1 and corresponding analogues. At high individual dosages, the (S)-(−) enantiomers of 1 and 21b,d all produce a reversible slowing of nerve−conduction velocity in the mice, the onset of which is characterized by a distinctive dysfunction of the hind legs, causing uncoordinated movements. The condition resolves within 5−10 min. However, at higher dosages, which approach a lethal level, the behavior extended to the front legs, lasting from 20 min to 1 h. By contrast, the (R)-(+) forms of these same agents did not induce the phenomenon of slowing of nerve−conduction velocity.
‘Paradisus Oculorum’: the comparison of two linen damask designs of formal gardens (1986)

Abstract In the second half of the seventeenth century, the enthusiasm for gardens often became an obsession: no more so than in France, where Louis XIV expended not simply huge sums of money but also a great deal of time and energy. Their creation involved the talents of architects, sculptors and hydraulic engineers and reflected the current philosophical and political ideas, often with poetic and mythological allusions. Their upkeep necessitated armies of gardeners, and their use the skills of playwrights and devisers of masques and varied theatrical spectaculars. Their truest records are found in several brilliant series of contemporary engravings, and their spirit in paintings, journals and poems, for today the actual gardens are pale reflections of their former glory.
Regulation of Em Gene Expression in Rice (1992)

Expression of the Em gene was characterized in rice (Oryza sativa L.) suspension cultures following exposure of the cultures to various combinations of abscisic acid (ABA) and salt. Response-saturating concentrations of either ABA (50 micromolar) or NaCl (0.4 molar) rapidly induced (by 60 minutes) the accumulation of Em mRNA, with a maximum accumulation occurring 12 to 24 hours after treatment. NaCl-induced Em expression was accompanied by a doubling of endogenous ABA levels as determined by immunoassay. Inhibition of ABA biosynthesis by fluridone during NaCl treatment reduced the levels of endogenous ABA by fourfold and Em expression by 50%. Desiccation of the cultures to 12 to 15% of their initial fresh weight increased endogenous ABA more than twofold and was accompanied by an increase in Em mRNA levels. Exposure of the cultures to heat shock temperatures, chilling, or ultraviolet light neither increased endogenous ABA levels nor induced Em expression. When a subthreshold or saturating level of NaCl was added in combination with increasing levels of ABA, Em transcripts were detected at ABA concentrations that alone did not induce expression of Em. Treatment with saturating levels of both NaCl and ABA resulted in a doubling of Em transcript levels over the maximum signal for each treatment alone. Hence, our data suggested that salt interacted synergistically with ABA, in part because of the increased sensitivity of rice cells to ABA. The effect of salt stress on Em gene expression in rice suspension cells appeared to operate through two pathways: one is mediated through increases in the level of ABA; the other is via a unique salt response pathway that includes an intermediate that is common to both the salt and ABA response chains.
[Effects of STAT3 antisense oligodeoxynucleotides on apoptosis and proliferation of mouse melanoma cell line B16]. (2006)

STAT3 is highly expressed and activated in all the tumor cells detected. STAT3 ASODN can abrogate the activity of STAT3 protein, inhibit proliferation and induce apoptosis of B16 cells, which support that STAT3 may be a potential molecular target for tumor therapy.
Surface codes: Towards practical large-scale quantum computation (2012)

This article provides an introduction to surface code quantum computing. We first estimate the size and speed of a surface code quantum computer. We then introduce the concept of the stabilizer, using two qubits, and extend this concept to stabilizers acting on a two-dimensional array of physical qubits, on which we implement the surface code. We next describe how logical qubits are formed in the surface code array and give numerical estimates of their fault tolerance. We outline how logical qubits are physically moved on the array, how qubit braid transformations are constructed, and how a braid between two logical qubits is equivalent to a controlled-not. We then describe the single-qubit Hadamard, $\stackrel{\ifmmode \hat{}\else \^{}\fi{}}{S}$ and $\stackrel{\ifmmode \hat{}\else \^{}\fi{}}{T}$ operators, completing the set of required gates for a universal quantum computer. We conclude by briefly discussing physical implementations of the surface code. We include a number of Appendices in which we provide supplementary information to the main text.
Label-free flow-enhanced specific detection of Bacillus anthracis using a piezoelectric microcantilever sensor (2008)

Differentiation between species of similar biological structure is of critical importance in biosensing applications. Here, we report specific detection of Bacillus anthracis (BA) spores from that of close relatives, such as B. thuringiensis (BT), B. cereus (BC), and B. subtilis (BS) by varying the flow speed of the sampling liquid over the surface of a piezoelectric microcantilever sensor (PEMS). Spore binding to the anti-BA spore IgG coated PEMS surface is determined by monitoring the resonance frequency change in the sensor's impedance vs. frequency spectrum. Flow increases the resonance frequency shift at lower flow rates until the impingement force from the flow overcomes the binding strength of the antigen and decreases the resonance frequency shift at higher flow rates. We showed that the change from increasing to decreasing resonance frequency shift occurred at a lower fluid flow speed for BT, BC, and BS spores than for BA spores. This trend reduces the cross reactivity ratio of BC, BS, and BT to the anti-BA spore IgG immobilized PEMS from around 0.4 at low flow velocities to less than 0.05 at 3.8 mm s(-1). This cross reactivity ratio of 0.05 was essentially negligible considering the experimental uncertainty. The use of the same flow that is used for detection to further distinguish the specific binding (BA to anti-BA spore antibody) from nonspecific binding (BT, BC, and BS to anti-BA spore antibody) is unique and has great potential in the detection of general biological species.
Neuronal exosomes reveal Alzheimer's disease biomarkers in Down syndrome (2016)

These early increases in Aβ<sub>1-42</sub>, P-T181-tau, and P-S396-tau in individuals with DS may provide a basis for early intervention as targeted treatments become available.
Purification, Regulation, and Molecular and Biochemical Characterization of Pyruvate Carboxylase from Methanobacterium thermoautotrophicum Strain ΔH (1998)

We discovered that Methanobacterium thermoautotrophicum strain DeltaH possessed pyruvate carboxylase (PYC), and this biotin prototroph required exogenously supplied biotin to exhibit detectable amounts of PYC activity. The enzyme was highly labile and was stabilized by 10% inositol in buffers to an extent that allowed purification to homogeneity and characterization. The purified enzyme was absolutely dependent on ATP, Mg2+ (or Mn2+ or Co2+), pyruvate, and bicarbonate for activity; phosphoenolpyruvate could not replace pyruvate, and acetyl-CoA was not required. The enzyme was inhibited by ADP and alpha-ketoglutarate but not by aspartate or glutamate. ATP was inhibitory at high concentrations. The enzyme, unlike other PYCs, exhibited nonlinear kinetics with respect to bicarbonate and was inhibited by excess Mg2+, Mn2+, or Co2+. The 540-kDa enzyme of A4B4 composition contained a non-biotinylated 52-kDa subunit (PYCA) and a 75-kDa biotinylated subunit (PYCB). The pycB gene was probably monocistronic and followed by a putative gene of a DNA-binding protein on the opposite strand. The pycA was about 727 kilobase pairs away from pycB on the chromosome and was probably co-transcribed with the biotin ligase gene (birA). PYCA and PYCB showed substantial sequence identities (33-62%) to, respectively, the biotin carboxylase and biotin carboxyl carrier + carboxyltransferase domains or subunits of known biotin-dependent carboxylases/decarboxylases. We discovered that PYCB and probably the equivalent domains or subunits of all biotin-dependent carboxylases harbored the serine/threonine dehydratase types of pyridoxal-phosphate attachment site. Our results and the existence of an alternative oxaloacetate synthesizing enzyme phosphoenolpyruvate carboxylase in M. thermoautotrophicum strain DeltaH (Kenealy, W. R., and Zeikus, J. G. (1982) FEMS Microbiol. Lett. 14, 7-10) raise several questions for future investigations.
Determination of an Optimum Initial Cable Tension Force for Cable-Stayed Bridges using the Least Square Method (2005)

This study presents a method of determining the optimum cable tension forces for the proper initial equilibrium state of a cable-stayed bridge using the least square method. The proposed method minimizes the errors, i.e., the differences, such as the deflection and the moments of the girder and the tower, between the target values from a continuous beam by considering the cable anchor point as supports of the girder and the responses obtained from the analysis of the entire cable-stayed bridge system. Especially, the proposed method can selectively control the adjustment of the tower moment, the girder moment, and the deflections by introducing the weighing matrix. Through numerical analysis and comparisons with existing studies, the usefulness and validity of the proposed method was verified.