gebhart/patrepeval huggingface dataset:
A fusion protein between serum amyloid A and staphylococcal nuclease—synthesis, purification, and structural studies (1998)

We developed a recombinant DNA system to overexpress a fusion protein between the small, minimally soluble acute phase serum protein, serum amyloid A (SAA), and the bacterial enzyme staphylococcal nuclease (SN). This fusion protein is very soluble and is immunoreactive to polyclonal anti-SAA antibodies. Tryptophan fluorescence shows smooth denaturation curves for the fusion protein in guanidinium HCl or potassium thiocyanate. Fluorescence also indicates that only a single tryptophan residue (of the four present) is accessible to iodide quenching and, presumably, is exposed on the surface of the fusion protein. Circular dichroism (CD) shows a significant signal indicating alpha-helix, which can be attributed to the SAA portion of the molecule; these are the first CD spectral data available for SAA. pH titration shows persistence of helix domains for the fusion protein at pH 3.0, in contrast to the denaturation of SN under the same conditions. (The entire fusion protein shows a random coil pattern below pH 3.0.) By exploiting the structural and solubility properties of SN, this fusion protein has provided the first structural data about SAA-the precursor of the amyloid deposits in secondary amyloidosis. This fusion protein should be useful for further physical and physiologic studies of SAA.
Study of stress measurement using polariscope (2010)

The goal of this research was to investigate an experimental infrared transmission technique to extract the full stress components of the in-plane residual stresses in thin multi crystalline silicon wafer, and try to meet the need of photovoltaic industry to in situ measure residual stress for large cast wafers.
Analysis of Ruminant Respiratory Syncytial Virus Isolates by RNAse Protection of the G Glycoprotein Transcripts (1999)

Two different respiratory syncytial virus (RSV) radiolabeled probes were used to characterize the genetic heterogeneity of 25 ruminant RSV isolates by the ribonuclease protection assay. A 32P-radiolabeled antisense RNA probe was transcribed from cloned ovine and bovine RSV G glycoprotein genes and then hybridized with total RNA isolated from infected cells with various ruminant RSV isolates. The results of this study, along with previously published nucleotide sequence data of the ovine RSV G glycoprotein gene, suggest the presence of at least 2 ruminant RSV subgroups. One subgroup is represented by RSV isolated from respiratory disease outbreaks from calves and goats, and the other is represented by RSV isolated from sheep.
New Alkaloids from Cephalotaxus fortunei (2002)

Four new cephalotaxus alkaloids, cephalotaxine alpha-N-oxide (1), cephalotaxine beta-N-oxide (2), 11-beta-hydroxycephalotaxine beta-N-oxide (3), and isocephalotaxine (4), were isolated, together with several known alkaloids from an EtOAc extract of the fruits of Cephalotaxus fortunei. The structures were determined by spectral analysis including mass spectrometry and 2D NMR. Compounds 1, 2, 3, and 4 displayed cytotoxicity against nasopharynx KB cells with IC50 values of 30, 14, 31, and 15 micro g/mL, respectively.
Facial rejuvenation with botulinum neurotoxin: An anatomical and experiential perspective (2007)

The utilization of botulinum neurotoxin for facial rejuvenation has been progressively expanding into multiple upper, mid, and lower facial and neck applications. Success in these areas is dependent upon a number of factors, above all a sophisticated understanding of the underlying facial anatomy. In addition, although published consensus recommendations can guide dosing and injection site placement, expert technical application is critical, as is individualized treatment for each patient, based on an aesthetic assessment. This includes an evaluation of the patient's unique functional anatomy and a frank discussion of the patient's desires and goals. Only by addressing these considerations can the best possible outcomes be consistently achieved.
X-band multi-beam klystron design and progress report (2015)

Progress on the development of a 5MW 16 beam x-band multi-beam klystron is presented. The power from each of the 16 klystrons is combined using a matched waveguide network. Mechanical and electric models and simulations are discussed. The status of procuring and assembling parts is presented.
Integrated Circuits Based on Amorphous Indium-Gallium-Zinc-Oxide-Channel Thin-Film Transistors (2006)

Five-stage ring oscillators (ROs) composed of amorphous In-Ga- Zn-O (a-IGZO) channel TFTs were fabricated at room temperature with no post-deposition annealing. We observed oscillation of ROs with a variety of channel lengths and channel widths. A RO with channel lengths of 10 um operated at 21.5 kHz (propagation delay of 4.7 us / stage), when the external voltage of +18 V was supplied. A circuit simulation reproduced the measured output characteristics of ROs qualitatively, and also the simulated propagation delays agreed with the measured ones approximately.
Lentiviral vector‐mediated insertional mutagenesis screen identifies genes that influence androgen independent prostate cancer progression and predict clinical outcome (2015)

Prostate cancer (PC) is the second leading cause of cancer related deaths in US men. Androgen deprivation therapy (ADT) improves clinical outcome, but tumors often recur and progress to androgen independent prostate cancer (AIPC) which no longer responds to ADT. The progression to AIPC is due to genetic alterations that allow PC cancer cells to grow in the absence of androgen. Here we performed an insertional mutagenesis screen using a replication-incompetent lentiviral vector (LV) to identify the genes that promote AIPC in an orthotopic mouse model. Androgen sensitive PC cells, LNCaP, were mutagenized with LV and injected into the prostate of male mice. After tumor development, mice were castrated to select for cells that proliferate in the absence of androgen. Proviral integration sites and nearby dysregulated genes were identified in tumors developed in an androgen deficient environment. Using publically available datasets, the expression of these candidate androgen independence genes in human PC tissues were analyzed. A total of 11 promising candidate AIPC genes were identified: GLYATL1, FLNA, OBSCN, STRA13, WHSC1, ARFGAP3, KDM2A, FAM83H, CLDN7, CNOT6, and B3GNT9. Seven out the 11 candidate genes; GLYATL1, OBSCN, STRA13, KDM2A, FAM83H, CNOT6, and B3GNT6, have not been previously implicated in PC. An in vitro clonogenic assay showed that knockdown of KDM2A, FAM83H, and GLYATL1 genes significantly inhibited the colony forming ability of LNCaP cells. Additionally, we showed that a combination of four genes, OBSCN, FAM83H, CLDN7, and ARFGAP3 could significantly predicted the recurrence risk in PC patients after prostatectomy (P = 5.3 × 10<sup>-5</sup> ). © 2015 Wiley Periodicals, Inc.
AAV-Mediated Delivery of the Caspase Inhibitor XIAP Protects Against Cisplatin Ototoxicity (2006)

Hypothesis: Delivery of the gene encoding X-linked inhibitor of apoptosis (XIAP) using an adeno-associated viral (AAV) vector can protect against cisplatin-mediated ototoxicity. Background: Cisplatin is a widely used chemotherapeutic agent with significant ototoxic side effects. One possible mechanism of toxicity is apoptotic death of many cochlear cell types. Acute treatment with inhibitors of caspases- enzymes critical for apoptosis- has been shown to prevent hearing loss in vivo, but is too short-acting for therapeutic use. Gene therapy provides a specific and chronic means of delivering potential therapeutic gents. Introducing an anti-apoptotic gene into the cochlea could provide long-term prophylaxis against the ototoxic effects of cisplatin. Method: Two groups of rats were treated with unilateral injection into the round window of AAV harboring a gene encoding either XIAP or green fluorescent protein (GFP). After at least two months of gene expression, auditory-brainstem-response (ABR) threshold shifts and outer-hair-cell (OHC) number were measured in these two groups of animals after 72-hour treatment with cisplatin. Results: Consistent with previous reports, uninjected and AAV.GFP-injected ears displayed profound ABR threshold elevations and OHC loss after cisplatin treatment. Ears that had been injected with AAV encoding XIAP, however, were significantly protected from these effects: cisplatin-induced ABR-threshold shift and hair-cell loss were attenuated by as much as 78% and 45%, respectively, when compared with contralateral (untreated) ears. Conclusion: XIAP delivery to the cochlea can protect against the audiometric changes and hair-cell loss associated with cisplatin ototoxicity. The efficacy, specificity, and duration of the protective effects make this a potentially attractive therapeutic paradigm.
The Australian Health System: Can We Do Better? (2002)

The Australian health system is trapped under bureaucratic regulation and Commonwealth-state conflicts that constrain effective patient-doctor relationships, says Kerryn Phelps.
Antibody Epitopes on the Neuraminidase of a Recent H3N2 Influenza Virus (A/Memphis/31/98) (2002)

We have characterized monoclonal antibodies raised against the neuraminidase (NA) of a Sydney-like influenza virus (A/Memphis/31/98, H3N2) in a reassortant virus A/NWS/33(HA)-A/Mem/31/98(NA) (H1N2) and nine escape mutants selected by these monoclonal antibodies. Five of the antibodies use the same heavy chain VDJ genes and may not be independent. Another antibody, Mem5, uses the same V(H) and J genes with a different D gene and different isotype. Sequence changes in escape mutants selected by these antibodies occur in two loops of the NA, at amino acid 198, 199, 220, or 221. These amino acids are located on the opposite side of the NA monomer to the major epitopes found in N9 and early N2 NAs. Escape mutants with a change at 198 have reduced NA activity compared to the wild-type virus. Asp198 points toward the substrate binding pocket, and we had previously found that a site-directed mutation of this amino acid resulted in a loss of enzyme activity (M. R. Lentz, R. G. Webster, and G. M. Air, Biochemistry 26:5351-5358, 1987). Mutations at residue 199, 220, or 221 did not alter the NA activity significantly compared to that of wild-type NA. A 3.5-A structure of Mem5 Fab complexed with the Mem/98 NA shows that the Mem5 antibody binds at the sites of escape mutation selected by the other antibodies.
Establishment of mouse colonic carcinoma cell lines with different metastatic properties. (1980)

Tumorigenic cell lines were established in culture from three transplantable mouse colonic carcinomas designated CT 26, CT36, and CT 51. The cultured lines were characterized for the retention of the biological characteristics of the parental lines. All three cultured lines retained the ability to form tumors in vivo. Serially transplanted parental lines CT 26 and CT 51 grew at a faster rate than did CT 36 and showed a greater propensity for the formation of lung metastases. Similar characteristics were exhibited by the tumors formed from the injection of cultured cells. The cultured cell lines were also evaluated with respect to a number of in vitro markers for cancer. Cultured CT 26 and CT 51 cells formed tumors at lower inocula than did CT 36. CT 26 and CT 51 showed anchorage-independent growth and lack of contact inhibition, while CT 36 grew as a strict monolayer and did not form colonies in 0.27% agarose. CT 26 had the highest saturation density of the cell lines when grown in media supplemented with either 10 or 2.5% fetal bovine serum, while CT 51 had the lowest saturation density under these conditions. The varying degrees of malignancy exhibited by the three cell lines and the overall retention of the biological characteristics of the parental lines by the cultured lines suggest that the cultured cells (without the contaminating stromal elements present in the serially transplanted lines) will provide suitable material for the investigation of the molecular bases of these malignant characteristics.
Cellular Encapsulation in 3D Hydrogels for Tissue Engineering (2009)

The 3D encapsulation of cells within hydrogels represents an increasingly important and popular technique for culturing cells and towards the development of constructs for tissue engineering. This environment better mimics what cells observe in vivo, compared to standard tissue culture, due to the tissue-like properties and 3D environment. Synthetic polymeric hydrogels are water-swollen networks that can be designed to be stable or to degrade through hydrolysis or proteolysis as new tissue is deposited by encapsulated cells. A wide variety of polymers have been explored for these applications, such as poly(ethylene glycol) and hyaluronic acid. Most commonly, the polymer is functionalized with reactive groups such as methacrylates or acrylates capable of undergoing crosslinking through various mechanisms. In the past decade, much progress has been made in engineering these microenvironments - e.g., via the physical or pendant covalent incorporation of biochemical cues - to improve viability and direct cellular phenotype, including the differentiation of encapsulated stem cells (Burdick et al.). The following methods for the 3D encapsulation of cells have been optimized in our and other laboratories to maximize cytocompatibility and minimize the number of hydrogel processing steps. In the following protocols (see Figure 1 for an illustration of the procedure), it is assumed that functionalized polymers capable of undergoing crosslinking are already in hand; excellent reviews of polymer chemistry as applied to the field of tissue engineering may be found elsewhere (Burdick et al.) and these methods are compatible with a range of polymer types. Further, the Michael-type addition (see Lutolf et al.) and light-initiated free radical (see Elisseeff et al.) mechanisms focused on here constitute only a small portion of the reported crosslinking techniques. Mixed mode crosslinking, in which a portion of reactive groups is first consumed by addition crosslinking and followed by a radical mechanism, is another commonly used and powerful paradigm for directing the phenotype of encapsulated cells (Khetan et al., Salinas et al.).
Tunneling Anisotropic Magnetoresistance-Based Devices (2007)

The paper demonstrates the operation of several devices based on tunneling anisotropic magnetoresistance. This effect, which originates from the interplay between the magnetic and transport properties in magnetic materials with strong spin-orbit coupling such as the ferromagnetic semiconductor (Ga,Mn)As, leads to a dependence of the tunneling resistance of devices with respect to the direction of the magnetization in the (Ga,Mn)As layer. We show that such devices can be operated as either information storage elements or sensors. It was also demonstrated that they can be used in either volatile or nonvolatile mode and that they provide either two-state or multiple state devices in either of these modes. Lastly, we present experimental evidence that they can be coupled to traditional ferromagnetic materials to still further enhance the variety of possible device functionalities
A Workload Recording Method for Clinical Laboratories (1972)

Journal Article A Workload Recording Method for Clinical Laboratories Get access George H. Murphy, M.D. George H. Murphy, M.D. George H. Murphy, M.D., Winchester (Va.) Memorial Hospital, is Chairman of the Subcommittee on Workload Recording, Laboratory Management and Planning Committee, College of American Pathologists. Search for other works by this author on: Oxford Academic PubMed Google Scholar Laboratory Medicine, Volume 3, Issue 7, 1 July 1972, Pages 18–22, https://doi.org/10.1093/labmed/3.7.18 Published: 01 July 1972
Expansion of corn extrudates containing dietary fiber: a microstructure study. (1990)

Corn meal was mixed with dietary fiber and extruded by a twin-screw extruder. The microstructure of the extruded products containing wheat bran (up to 30%) or oat fiber (up to 20%) was examined under a scanning electron microscope. The results indicated that the degree of extrudate expansion was dependent on the source and amount of dietary fiber, and was associated with the size of air cells inside extrudates and with the external structure of products. An increase in screw speed favored longitudinal expansion but decreased transverse puffing
Cross-reacting lipopolysaccharide antigens in Legionella pneumophila serogroups 1 to 14 (1995)

Immunological cross-reactions among Legionella species were investigated with sonicated, proteinase K-digested cell lysates. The antigens separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis were either analyzed for lipopolysaccharides (LPSs) by silver staining or transferred to nitrocellulose membranes for serological characterization with rabbit antibodies directed against Legionella pneumophila serogroups 1 and 5. When antiserum prepared against serogroup 5 was used to probe the LPSs from L. pneumophila serogroups 1 to 14, the antibodies recognized a common epitope harbored by all L. pneumophila serogroups but not by other Legionella species or by the gram-negative bacteria tested as controls. Hence, the serogroup 5 antiserum correctly identified all serogroups of L. pneumophila tested in the LPS immunoblot assay. Moreover, the silver-stained profiles of the isolated LPSs revealed characteristic patterns allowing the identification of the individual serogroups of L. pneumophila.
Quantum key distribution over 67 km with a plug&play system (2002)

We present a fibre-optical quantum key distribution system. It works at 1550nm and is based on the plug &amp;amp; play setup. We tested the stability under field conditions using aerial and terrestrial cables and performed a key exchange over 67 km between Geneva and Lausanne.
Chk1 Kinase Negatively Regulates Mitotic Function of Cdc25A Phosphatase through 14-3-3 Binding (2003)

The order and fidelity of cell cycle events in mammals is intimately linked to the integrity of the Chk1 kinase-Cdc25A phosphatase pathway. Chk1 phosphorylation targets Cdc25A for destruction and, as shown here, inhibits interactions between Cdc25A and its mitotic substrate cyclin B1-Cdk1. Phosphorylation of Cdc25A on serine 178 and threonine 507 facilitates 14-3-3 binding, and Chk1 phosphorylates both residues in vitro. Mutation of T507 to alanine (T507A) enhanced the biological activity of Cdc25A. Cdc25A(T507A) was more efficient in binding to cyclin B1, activating cyclin B1-Cdk1, and promoting premature entry into mitosis. We propose that the Chk1/Cdc25A/14-3-3 pathway functions to prevent cells from entering into mitosis prior to replicating their genomes to ensure the fidelity of the cell division process.
Causes of Death for Patients With Community-Acquired Pneumonia (2002)

For patients with community-acquired pneumonia, only half of all deaths are attributable to their acute illness. Differences in the timing of death and risk factors for mortality suggest that future studies of community-acquired pneumonia should differentiate all-cause and pneumonia-related mortality.
Nuclear imaging of the fuel assembly in ignition experiments (2013)

First results from the analysis of neutron image data collected on implosions of cryogenically layered deuterium-tritium capsules during the 2011-2012 National Ignition Campaign are reported. The data span a variety of experimental designs aimed at increasing the stagnation pressure of the central hotspot and areal density of the surrounding fuel assembly. Images of neutrons produced by deuterium–tritium fusion reactions in the hotspot are presented, as well as images of neutrons that scatter in the surrounding dense fuel assembly. The image data are compared with 1D and 2D model predictions, and consistency checked using other diagnostic data. The results indicate that the size of the fusing hotspot is consistent with the model predictions, as well as other imaging data, while the overall size of the fuel assembly, inferred from the scattered neutron images, is systematically smaller than models' prediction. Preliminary studies indicate these differences are consistent with a significant fraction (20%–25%) of the initial deuterium-tritium fuel mass outside the compact fuel assembly, due either to low mode mass asymmetry or high mode 3D mix effects at the ablator-ice interface.
Electrostatic Properties of Molecules from the X-Ray Charge Density. Application to Deuterated Benzene, 1-Alanine and d,l-Histidine (1993)

It has been shown (Z. Su and P. Coppens, Acta Cryst. A 48, 188 (1992)) that the electrostatic potential, the electric field, and the electric field gradient (EFG) can be expressed in closed forms in terms of the positions and the charge-density parameters of individual atoms, whose aspherical density is described by a pseudoatom model (e.g., N. Hansen and P. Coppens, Acta Cryst. A 34, 909 (1978)). A F o r t r a n program Molprop91 based on this method has been written (Z. Su, State Univ. of New York at Buffalo 1991). The method has been applied to the title compounds. Low-temperature X-ray diffraction data of fully deuterated benzene (G. A. Jeffrey, J. R. Ruble, Y. Yeon, and C. Lemann, private communication, 1991), /-alanine (R. Destro, R. E. Marsh, and R. Bianchi, J. Phys. Chem. 92, 966 (1988) and d,/-histidine (N. Li, Ph.D. thesis, State University of New York at Buffalo 1989) were analyzed using the least-squares deformation density refinement program Lsmol90 (a modified version of M o l l y ) . Molprop91 was subsequently used to calculate the electrostatic-potential maps in selected sections, and at the nuclear positions. For the latter, the EFGs were also evaluated. The electrostatic potentials were used to fit net atomic charges and estimate the molecular energies. Errors in the derived quantities are given.
Kraftwerk2—A Fast Force-Directed Quadratic Placement Approach Using an Accurate Net Model (2008)

The force-directed quadratic placer ldquoKraftwerk2,rdquo as described in this paper, is based on two main concepts. First, the force that is necessary to distribute the modules on the chip is separated into the following two components: a hold force and a move force. Both components are implemented in a systematic manner. Consequently, Kraftwerk2 converges such that the module overlap is reduced in each placement iteration. The second concept of Kraftwerk2 is to use the ldquoBound2Boundrdquo net model, which accurately represents the half-perimeter wirelength (HPWL) in the quadratic cost function. Aside from these features, this paper presents additional details about Kraftwerk2. An approach to remove halos (free space) around large modules is described, and a method to control the module density is presented. In order to choose the important tradeoff between runtime and quality, a systematic quality control is shown. Furthermore, plots demonstrating the convergence of Kraftwerk2 are presented. Results using various benchmark suites demonstrate that Kraftwerk2 offers both high quality and excellent computational efficiency.