gebhart/patrepeval huggingface dataset:
Autologous Feeder Cells from Embryoid Body Outgrowth Support the Long-Term Growth of Human Embryonic Stem Cells More Effectively than Those from Direct Differentiation (2009)

Autologous feeder cells have been developed by various methods to minimize the presence of xenogenic entities in human embryonic stem cell (hESC) cultures. However, there was no systematic comparison of supportive effects of the feeder cells on hESC growth, nor comparison to the supportive effects of various feeder-free culture systems and standard mouse feeder cells. In this study, we aimed to compare the supportive abilities of autologous feeders derived either directly from H9 hESCs (H9 dF) or from outgrowth of embryoid body predifferentiated in suspension from H9 hESCs (H9 ebF). Mouse feeder system and matrigel-mTeSR1 feeder-free system were used as controls. H9 ebF was found to secrete more basic fibroblast growth factor in the conditioned medium than H9 dF did. The undifferentiated state of H9 hESCs was sustained more stably on H9 ebF than on H9 dF, and the differentiation potential of H9 hESCs on H9 ebF was higher than on H9 dF. We concluded that H9 ebF was an optimal autologous feeder to maintain the long-term undifferentiated state of hESCs in our current culture system. This study helps to standardize the autologous culture of hESCs. It also suggests a more definite direction for future development of xeno-free culture system for hESCs.
Cryptography and Network Security: Principles and Practice (1998)

William Stallings' Cryptography and Network Security: Principles and Practice, 5e is a practical survey of cryptography and network security with unmatched support for instructors and students. In this age of universal electronic connectivity, viruses and hackers, electronic eavesdropping, and electronic fraud, security is paramount. This text provides a practical survey of both the principles and practice of cryptography and network security. First, the basic issues to be addressed by a network security capability are explored through a tutorial and survey of cryptography and network security technology. Then, the practice of network security is explored via practical applications that have been implemented and are in use today. An unparalleled support package for instructors and students ensures a successful teaching and learning experience. The new edition has been updated to include coverage of the latest topics including expanded coverage of block cipher modes of operation, including authenticated encryption; revised and expanded coverage of AES; expanded coverage of pseudorandom number generation; new coverage of federated identity, HTTPS, Secure Shell (SSH) and wireless network security; completely rewritten and updated coverage of IPsec; and a new chapter on legal and ethical issues.
Transthyretin and familial amyloidotic polyneuropathy (2007)

Familial amyloidotic polyneuropathy (FAP) is an inherited autosomal dominant disease that is commonly caused by accumulation of deposits of transthyretin (TTR) amyloid around peripheral nerves. The only effective treatment for FAP is liver transplantation. However, recent studies on TTR aggregation provide clues to the mechanism of the molecular pathogenesis of FAP and suggest new avenues for therapeutic intervention. It is increasingly recognized that there are common features of a number of protein-misfolding diseases that can lead to neurodegeneration. As for other amyloidogenic proteins, the most toxic forms of aggregated TTR are likely to be the low-molecular-mass diffusible species, and there is increasing evidence that this toxicity is mediated by disturbances in calcium homeostasis. This article reviews what is already known about the mechanism of TTR aggregation in FAP and describes how recent discoveries in other areas of amyloid research, particularly Alzheimer's disease, provide clues to the molecular pathogenesis of FAP.
Protein Kinase C-ζ as a Downstream Effector of Phosphatidylinositol 3-Kinase during Insulin Stimulation in Rat Adipocytes (1997)

Insulin provoked rapid increases in enzyme activity of immunoprecipitable protein kinase C-zeta (PKC-zeta) in rat adipocytes. Concomitantly, insulin provoked increases in 32P labeling of PKC-zeta both in intact adipocytes and during in vitro assay of immunoprecipitated PKC-zeta; the latter probably reflected autophosphorylation, as it was inhibited by the PKC-zeta pseudosubstrate. Insulin-induced activation of immunoprecipitable PKC-zeta was inhibited by LY294002 and wortmannin; this suggested dependence upon phosphatidylinositol (PI) 3-kinase. Accordingly, activation of PI 3-kinase by a pYXXM-containing peptide in vitro resulted in a wortmannin-inhibitable increase in immunoprecipitable PKC-zeta enzyme activity. Also, PI-3,4-(PO4)2, PI-3,4,5-(PO4)3, and PI-4,5-(PO4)2 directly stimulated enzyme activity and autophosphoralytion in control PKC-zeta immunoprecipitates to levels observed in insulin-treated PKC-zeta immunoprecipitates. In studies of glucose transport, inhibition of immunoprecipitated PKC-zeta enzyme activity in vitro by both the PKC-zeta pseudosubstrate and RO 31-8220 correlated well with inhibition of insulin-stimulated glucose transport in intact adipocytes. Also, in adipocytes transiently expressing hemagglutinin antigen-tagged GLUT4, co-transfection of wild-type or constitutive PKC-zeta stimulated hemagglutinin antigen-GLUT4 translocation, whereas dominant-negative PKC-zeta partially inhibited it. Our findings suggest that insulin activates PKC-zeta through PI 3-kinase, and PKC-zeta may act as a downstream effector of PI 3-kinase and contribute to the activation of GLUT4 translocation.
A New Sol-Gel Approach to Prepare MgO Thin Films (1999)

MgO thin films were successfully prepared on Si substrate by a novel and simple Sol-Gelmethod. The results indicated that collodion is a key element to form stable MgO sols. Thestructures of MgO films are closely related to the amount of collodion and the annealing temperature. In addition, the microstructures of the MgO thin films were examined with X-ray distraction(XRD), Atomic Force Morphology (AFM) and Transmission Electron Micrograph (TEM).
Thin‐Film Transformation of NH4PbI3 to CH3NH3PbI3 Perovskite: A Methylamine‐Induced Conversion–Healing Process (2016)

Methylamine-induced thin-film transformation at room-temperature is discovered, where a porous, rough, polycrystalline NH<sub>4</sub> PbI<sub>3</sub> non-perovskite thin film converts stepwise into a dense, ultrasmooth, textured CH<sub>3</sub> NH<sub>3</sub> PbI<sub>3</sub> perovskite thin film. Owing to the beneficial phase/structural development of the thin film, its photovoltaic properties undergo dramatic enhancement during this NH<sub>4</sub> PbI<sub>3</sub> -to-CH<sub>3</sub> NH<sub>3</sub> PbI<sub>3</sub> transformation process. The chemical origins of this transformation are studied at various length scales.
Protograph-Based Raptor-Like LDPC Codes (2015)

This paper proposes protograph-based Raptor-like (PBRL) codes as a class of rate-compatible low-density parity-check codes for binary-input AWGN channels. As with the Raptor codes, exclusive-OR operations on precoded bits produce additional parity bits providing extensive rate compatibility. Unlike Raptor codes, each additional parity bit in the protograph is explicitly designed to optimize the density evolution threshold. During the lifting process, approximate cycle extrinsic message degree (ACE) and circulant progressive edge growth (CPEG) constraints are used to avoid undesirable graphical structures. Some density-evolution performance is sacrificed to obtain lower error floors, particularly at short block-lengths. Simulation results are shown for information block sizes of k = 1032 and 16 384. For a target frame error rate of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-5</sup> , at each rate, the k = 1032 and 16 384 code families perform within 1 dB and 0.4 dB of both the Gallager bound and the normal approximation, respectively. The 16 384 code family outperforms the best known standardized code family, namely, the AR4JA codes. The PBRL codes also outperform DVB-S2 codes that have the advantages of longer blocklengths and outer BCH codes. Performance is similar to RC code families designed by Nguyen et al. that do not constrain codes to have the PBRL structure and involve simulation in the optimization process at each rate.
Identification of a Salmonella virulence gene required for formation of filamentous structures containing lysosomal membrane glycoproteins within epithelial cells (1996)

Salmonella species are facultative intracellular pathogens that invade epithelial cells and reside within lysosomal membrane glycoprotein (lgp)-containing vacuoles. Coincident with the onset of bacterial replication inside these vacuoles, Salmonella induce the formation of stable lgp-containing filamentous structures that connect with the Salmonella-containing vacuoles. Salmonella typhimurium SL1344::Tn l0dCm mutant strains unable to induce these structures were isolated. All contained insertions within a novel Salmonella induced filament gene A (sifA). sifA is present only in Salmonella species and encodes a protein with a predicted molecular mass of 38 kDa and an apparent molecular mass of 35 kDa. sifA is flanked by 300 base pairs, and sifA and its flanking DNA show no homology to sequences in DNA databases. sifA is located within the potABCD operon, a housekeeping locus involved in periplasmic transport of polyamines. Fourteen-base-pair direct repeats mark the probable site of integration of sifA and its flanking DNA have a significantly reduced G+C content (41%) when compared with the potABCD operon (51%) and the Salmonella genome (52-54%). Deletion mutant strains in sifA or in the downstream potC were constructed. Delta sifA does not produce Salmonella-induced filaments in epithelial cells, and is attenuated in mice. Delta potC produces Salmonella-induced filaments in epithelial cells, and was fully virulent. Collectively, these results suggest that sifA arose by horizontal gene transfer into Salmonella and its product is involved in a virulence-associated intracellular phenotype related to Salmonella-induced filament formation.
Improved Lysosomal Trafficking Can Modulate the Potency of Antibody Drug Conjugates (2017)

Antibody drug conjugates (ADCs) provide an efficacious and relatively safe means by which chemotherapeutic agents can be specifically targeted to cancer cells. In addition to the selection of antibody targets, ADCs offer a modular design that allows selection of ADC characteristics through the choice of linker chemistries, toxins, and conjugation sites. Many studies have indicated that release of toxins bound to antibodies via noncleavable linker chemistries relies on the internalization and intracellular trafficking of the ADC. While this can make noncleavable ADCs more stable in the serum, it can also result in lower efficacy when their respective targets are not internalized efficiently or are recycled back to the cell surface following internalization. Here, we show that a lysosomally targeted ADC against the protein APLP2 mediates cell killing, both in vitro and in vivo, more effectively than an ADC against Trop2, a protein with less efficient lysosomal targeting. We also engineered a bispecific ADC with one arm targeting HER2 for the purpose of directing the ADC to tumors, and the other arm targeting APLP2, whose purpose is to direct the ADC to lysosomes for toxin release. This proof-of-concept bispecific ADC demonstrates that this technology can be used to shift the intracellular trafficking of a constitutively recycled target by directing one arm of the antibody against a lysosomally delivered protein. Our data also show limitations of this approach and potential future directions for development.
Solid Halide Electrolytes with High Lithium‐Ion Conductivity for Application in 4 V Class Bulk‐Type All‐Solid‐State Batteries (2018)

New lithium halide solid-electrolyte materials, Li<sub>3</sub> YCl<sub>6</sub> and Li<sub>3</sub> YBr<sub>6</sub> , are found to exhibit high lithium-ion conductivity, high deformability, and high chemical and electrochemical stability, which are required properties for all-solid-state battery (ASSB) applications, particularly for large-scale deployment. The lithium-ion conductivities of cold-pressed powders surpass 1 mS cm<sup>-1</sup> at room temperature without additional intergrain or grain boundary resistances. Bulk-type ASSB cells employing these new halide solid electrolyte materials exhibit coulombic efficiencies as high as 94% with an active cathode material of LiCoO<sub>2</sub> without any extra coating. These superior electrochemical characteristics, as well as their material stability, indicate that lithium halide salts are another promising candidate for ASSB solid electrolytes in addition to sulfides or oxides.
Concurrent production of interleukin-2, interleukin-10, and gamma interferon in the regional lymph nodes of mice with influenza pneumonia (1994)

Cytokine production has been assessed at the single-cell level (ELISPOT assay) for freshly isolated mediastinal lymph node cells from C57BL/6 mice with primary, nonfatal influenza pneumonia. The mediastinal lymph node populations were also secondarily stimulated in vitro, and culture supernatants were assayed by enzyme-linked immunosorbent assay. Both approaches showed minimal evidence of protein secretion for interleukin-4 (IL-4), IL-5, and tumor necrosis factor, while IL-2, IL-10, and gamma interferon (IFN-gamma) were prominent throughout the response. The numbers of IL-2- and IFN-gamma-producing cells were maximal at 7 days after infection, while the total counts for cells secreting IL-10 were fairly constant from day 3 to 7. The cultures that were stimulated with virus in vitro showed in inverse relationship between IL-10 and IFN-gamma production, with IL-10 peaking on day 3 and IFN-gamma peaking on day 7. Lymphocytes secreting IL-2, IL-10, and/or IFN-gamma were present in CD4+ and CD8+ populations separated by fluorescence-activated cell sorting, although the CD8+ T cells produced less cytokine and were at a relatively lower frequency. Addition of recombinant IL-10 to the virus-stimulated cultures decreased the amount of IFN-gamma that could be detected, while incorporation of a monoclonal antibody to IL-10 had the opposite effect. A neutralization experiment also indicated that IL-2 was the principal mediator of lymphocyte proliferation. These experiments thus show that the developing T-cell response in the regional lymph nodes of mice with influenza cannot be rigidly categorized on the basis of a TH1 or TH2 phenotype and suggest possible regulatory mechanisms.
DNA ligase III is the major high molecular weight DNA joining activity in SV40-transformed human fibroblasts: normal levels of DNA ligase III activity in Bloom syndrome cells (1993)

The phenotypes of cultured cell lines established from individuals with Bloom syndrome (BLM), including an elevated spontaneous frequency of sister chromatid exchanges (SCEs), are consistent with a defect in DNA joining. We have investigated the levels of DNA ligase I and DNA ligase III in an SV40-transformed control and BLM fibroblast cell line, as well as clonal derivatives of the BLM cell line complemented or not for the elevated SCE phenotype. No differences in either DNA ligase I or DNA ligase III were detected in extracts from these cell lines. Furthermore, the data indicate that in dividing cultures of SV40-transformed fibroblasts, DNA ligase III contributes > 85% of high molecular weight DNA joining activity. This observation contrasts with previous studies in which DNA ligase I was reported to be the major DNA joining activity in extracts from proliferating mammalian cells.
Apathy: a neuropsychiatric syndrome (1991)

Traditionally, apathy has been viewed as a symptom indicating loss of interest or emotions. This paper evaluates evidence that neuropsychiatric disorders also produce a syndrome of apathy. Both the symptom and the syndrome of apathy are of conceptual interest because they signify loss of motivation. An apathy syndrome is defined as a syndrome of primary motivational loss, that is, loss of motivation not attributable to emotional distress, intellectual impairment, or diminished level of consciousness. Loss of motivation due to disturbance of intellect, emotion, or level of consciousness defines the symptom of apathy. Neuropsychiatric literature dealing with apathy is reviewed within the framework of three approaches to defining the concept of a syndrome. Clinical and investigative approaches for evaluating apathy when it occurs in association with other syndromes are described.
Development of Short Antimicrobial Peptides Derived from Host Defense Peptides or by Combinatorial Libraries (2002)

Recent increase of antibiotic-resistant pathogens demands exploration of novel antimicrobial molecules with unexploited mechanisms. Several hundred host defense peptides have been isolated from natural sources and their functions characterized. As host defense peptides have several advantages over classic antibiotics for resistant pathogens, there are many efforts to develop host defense peptides as therapeutic agents. In this review, focusing on the development of short antimicrobial peptides (< or = 18-mer), several examples are introduced that identify the active fragment from cyclic host peptides, or novel antimicrobial peptides derived from combinatorial libraries. Moreover, structure-activity relationships of short antimicrobial peptides are discussed, and several methods for improving bioavailability as well as specificity of the peptides, such as D-amino acid replacements, unnatural amino acid replacements, and backbone modifications, are discussed.
Miniaturized independently controllable multichamber thermal cycler (2003)

This paper presents the design, fabrication, and characterization of a miniaturized multichamber thermal cycler that is independently controllable with multiplex thermal protocols for the polymerase chain reaction (PCR) of nucleic acids. Thermal isolation between multiple chambers is achieved by an etch-through slot on a silicon membrane containing the reaction chambers, while keeping the silicon substrate unheated by directly contacting the substrate with a bottom heat sink. The thermal response is very fast due to reduced parasitic thermal mass. Typical ramping and cooling rates achieved are 15-100°C/s and 10-70°C/s, respectively. In contrast to uniform heating, as reported by other research groups, a side-heating scheme is used in this study to improve the temperature uniformity inside the reaction chamber. Finite-element-analysis (FEA) is used to predict and optimize the thermal performance. A temperature uniformity of <± 0.15°C in the reaction chamber filled up with water has been measured at 95°C, while keeping the substrate temperature as low as 0.4°C above the room temperature. This ensures independent controllability of multichamber thermal multiplexing on the same chip with low thermal cross talk between chambers. Experiments are in agreement with FEA predictions. The developed device can be used for quick optimization of PCR protocols and multiplexing of numbers of PCR reactions simultaneously in a short time.
Myristoylation as a target for inhibiting HIV assembly: Unsaturated fatty acids block viral budding (2002)

Modification of HIV-1 Gag with myristic acid, a saturated 14-carbon fatty acid (14:0), is essential for HIV-1 assembly. We recently showed that exogenous treatment of cells with unsaturated 14-carbon fatty acids, 5-cis-tetradecenoic acid (14:1n-9) and 5-cis,8-cis-tetradecadienoic acid (14:2n-6), reduces the affinity of some myristoylated proteins for plasma membrane rafts, membrane subdomains that have been shown to be required for efficient assembly of HIV. Here we demonstrate that treatment of cells with 14:1n-9 and 14:2n-6 fatty acids reduced the affinity of Gag for rafts but not membranes in general. Furthermore, treatment of cells with 14-carbon unsaturated fatty acids inhibited Gag-driven particle assembly. These effects most likely reflect covalent modification of Gag with unsaturated fatty acids. Treatment with 14:1n-9 and 14:2n-6 fatty acids did not alter intracellular protein trafficking, nor did it reduce cell viability. These studies suggest a strategy to attack HIV assembly by selectively altering the patterns of fatty acid modification.
RAMAN SPECTROSCOPY OF PROTEIN AND NUCLEIC ACID ASSEMBLIES (1999)

The Raman spectrum of a protein or nucleic acid consists of numerous discrete bands representing molecular normal modes of vibration and serves as a sensitive and selective fingerprint of three-dimensional structure, intermolecular interactions, and dynamics. Recent improvements in instrumentation, coupled with innovative approaches in experimental design, dramatically increase the power and scope of the method, particularly for investigations of large supramolecular assemblies. Applications are considered that involve the use of (a) time-resolved Raman spectroscopy to elucidate assembly pathways in icosahedral viruses, (b) polarized Raman microspectroscopy to determine detailed structural parameters in filamentous viruses, (c) ultraviolet-resonance Raman spectroscopy to probe selective DNA and protein residues in nucleoprotein complexes, and (d) difference Raman methods to understand mechanisms of protein/DNA recognition in gene regulatory and chromosomal complexes.
Haemocompatibility of polymer-coated stainless steel stents as compared to uncoated stents. (2005)

Acute and subacute stent thrombosis still represent an unsolved problem in connection with endovascular stents. For this reason coatings are tested now with the intention to reduce thrombogenicity of stainless steel surfaces. This comparative study examined whether a polymeric stent coating affected the haemocompatibility of a stainless steel stent. For compatibility testing, coated and non-coated stents were implanted in a low-grade thrombogenic closed-loop system perfused with platelet rich plasma at shear rates far below the threshold value at which shear-rate-induced activation of thrombocytes occurs. After 21 circulations of the filling volume (exposure time: 6.2 min), the number of single circulating platelets in the perfusion system with uncoated stainless steel stents decreased almost twice as much as was the case with polymer-coated stents. This is thought to indicate that more thrombocytes had adhered to the uncoated stainless steel stent, or that the thrombocytes were clustered in circulating aggregates. Parallel to the platelet aggregation/adherence, a release reaction took place, as was evident from the TAT complexes indicating the generation of thrombin. In the case of the implantation of uncoated stainless steel stents, both the number of activated circulating thrombocytes and the level of platelet reactivity (number of thrombocytes circulating in the plasma as aggregates) were notably higher than in the system with polymer-coated stents. At the same time it should be noted that the activation or aggregation is almost wholly attributable to the exogenic surface of the implanted stent, since activation due to the tube system or to shear rate can be excluded (as shown by measurements of the system without a stent). In addition to activation of the thrombocytes, a notable increase in the number of receptors per platelet (significant only in the system with the uncoated stent) took place. This supports both the adherence of the thrombocytes and their readiness to aggregate, since more receptors (docking places for ligands) are available. The better haemocompatibility of the polymer-coated stents, as verified in the laboratory, was also evident under microscopic examination of the explanted stents following the perfusion tests.