gebhart/patrepeval huggingface dataset:
A TCP (Transmission Control Protocol)/IP (Internet Protocol) Gateway Interconnecting AX.25 Packet Radio Networks to the Defense Data Network (1988)

The packet radio, in recent years has been gaining popularity as a transmission medium for digital traffic. It provides its user with the capability of accessing computer resources while in a mobile configuration or in a remote location where access to cable based computer networks are either unreliable or non existent. As with any communications network, communications protocols must be in place to manage the transmission of data. Currently, the Transmission Control Protocol (TCP) and Internet Protocol (IP) are used in the cable-based network, Department of Defense network (DDN). With the capability that the packet radio provides, this effort's objective was to implement the TCP/IP protocols within a packet radio network and build a gateway through the Air Force Institute of Technology Network (AFIT-NET) to the DDN. Research for the project revealed that the software package, The KA9Q Internet Software Package, had already implemented TCP/IP and associated protocols such as Telnet and FTP for the packet radio. Unfortunately, when using the Telnet protocol within this package to communicate with a mainframe computer, passwords are transmitted in the clear. Any station monitoring the frequency can acquire a user's password to a particular mainframe. In order to protect the integrity of a user's computer resources, a method of a passwordless login is necessary. This effort undertook implementing the Data Encryption Standard (DES) within the KA9Q software, such that, encrypted strings are used to validate users. Theses.
Normal intrinsic Th1/Th2 balance in patients with chronic phase chronic myeloid leukemia not treated with interferon-alpha or imatinib. (2003)

In the absence of leukemia and accessory cells, the intrinsic cytokine-producing capacity of CML T helper cells is normal. A Th2 shift was not detected, and the predominant presence of an IL-10-producing, immunosuppressive T helper cell subset could be excluded.
Isolation, identification and phylogenetic analysis of a heterotrophic nitrifier (2003)

A heterotrophic nitrifier, named strain HN, was isolated from the greenhouse soil. The cells of isolates were Gram positive, rod or coccus. The colonies of the strain were orange-red. Strain HN could ammonize organic nitrogen compounds and nitrify ammonia itself when it grew on acetamide companying the formation of ammonia and nitrite. It also could denitrify nitrate companying the formation of nitrite. The phylogentic analysis based on 16S rRNA suggested strain HN was the closest relative of Rhococcus ruber with 99% sequence identity. The phylogenetic analysis of strain HN was performed by PHYLIPS and the phylogenetic tree of strain HN and the neighbouring nitrifiers was given. This paper first reported Rhococcus sp. strain HN is a heterotrophic nitrifier.
Nonlinear refractive index of a rare-earth-doped fiber laser (2004)

An expression is derived for the intensity-dependent index of refraction of a rare-earth-doped fiber laser by use of a Kramers-Kronig relation and simple rate equations. The solution is applied to examine the properties of the nonlinear index of an ytterbium-doped silicate fiber laser at 975-nm pump and 1080-nm laser wavelengths.
TLR3 Can Directly Trigger Apoptosis in Human Cancer Cells (2006)

TLRs function as molecular sensors to detect pathogen-derived products and trigger protective responses ranging from secretion of cytokines that increase the resistance of infected cells and chemokines that recruit immune cells to cell death that limits microbe spreading. Viral dsRNA participate in virus-infected cell apoptosis, but the signaling pathway involved remains unclear. In this study we show that synthetic dsRNA induces apoptosis of human breast cancer cells in a TLR3-dependent manner, which involves the molecular adaptor Toll/IL-1R domain-containing adapter inducing IFN-beta and type I IFN autocrine signaling, but occurs independently of the dsRNA-activated kinase. Moreover, detailed molecular analysis of dsRNA-induced cell death established the proapoptotic role of IL-1R-associated kinase-4 and NF-kappaB downstream of TLR3 as well as the activation of the extrinsic caspases. The direct proapoptotic activity of endogenous human TLR3 expressed by cancerous cells reveals a novel aspect of the multiple-faced TLR biology, which may open new clinical prospects for using TLR3 agonists as cytotoxic agents in selected cancers.
B- and T-cell Development Both Involve Activity of the Unfolded Protein Response Pathway (2008)

The unfolded protein response (UPR) signaling pathway regulates the functional capacity of the endoplasmic reticulum for protein folding. Beyond a role for UPR signaling during terminal differentiation of mature B cells to antibody-secreting plasma cells, the status or importance of UPR signaling during hematopoiesis has not been explored, due in part to difficulties in isolating sufficient quantities of cells at developmentally intermediate stages required for biochemical analysis. Following reconstitution of irradiated mice with hematopoietic cells carrying a fluorescent UPR reporter construct, we found that IRE1 nuclease activity for XBP1 splicing is active at early stages of T- and B-lymphocyte differentiation: in bone marrow pro-B cells and in CD4(+)CD8(+) double positive thymic T cells. IRE1 was not active in B cells at later stages. In T cells, IRE activity was not detected in the more mature CD4(+) T-cell population but was active in the CD8(+) cytotoxic T-cell population. Multiple signals are likely to be involved in activating IRE1 during lymphocyte differentiation, including rearrangement of antigen receptor genes. Our results show that reporter-transduced hematopoietic stem cells provide a quick and easy means to identify UPR signaling component activation in physiological settings.
Crystal Structures of Cyclohexanone Monooxygenase Reveal Complex Domain Movements and a Sliding Cofactor (2009)

Cyclohexanone monooxygenase (CHMO) is a flavoprotein that carries out the archetypical Baeyer-Villiger oxidation of a variety of cyclic ketones into lactones. Using NADPH and O(2) as cosubstrates, the enzyme inserts one atom of oxygen into the substrate in a complex catalytic mechanism that involves the formation of a flavin-peroxide and Criegee intermediate. We present here the atomic structures of CHMO from an environmental Rhodococcus strain bound with FAD and NADP(+) in two distinct states, to resolutions of 2.3 and 2.2 A. The two conformations reveal domain shifts around multiple linkers and loop movements, involving conserved arginine 329 and tryptophan 492, which effect a translation of the nicotinamide resulting in a sliding cofactor. Consequently, the cofactor is ideally situated and subsequently repositioned during the catalytic cycle to first reduce the flavin and later stabilize formation of the Criegee intermediate. Concurrent movements of a loop adjacent to the active site demonstrate how this protein can effect large changes in the size and shape of the substrate binding pocket to accommodate a diverse range of substrates. Finally, the previously identified BVMO signature sequence is highlighted for its role in coordinating domain movements. Taken together, these structures provide mechanistic insights into CHMO-catalyzed Baeyer-Villiger oxidation.
RREB-1, a Novel Zinc Finger Protein, Is Involved in the Differentiation Response to Ras in Human Medullary Thyroid Carcinomas (1996)

An activated ras oncogene induces a program of differentiation in the human medullary thyroid cancer cell line TT. This differentiation process is accompanied by a marked increase in the transcription of the human calcitonin (CT) gene. We have localized a unique Ras-responsive transcriptional element (RRE) in the CT gene promoter. DNase I protection indicates two domains of protein-DNA interaction, and each domain separately can confer Ras-mediated transcriptional inducibility. This bipartite RRE was also found to be Raf responsive. By affinity screening, we have cloned a cDNA coding for a zinc finger transcription factor (RREB-1) that binds to the distal RRE. The consensus binding site for this factor is CCCCAAACCACCCC. RREB-1 is expressed ubiquitously in human tissues outside the adult brain. Overexpression of RREB-1 protein in TT cells confers the ability to mediate increased transactivation of the CT gene promoter-reporter construct during Ras- or Raf-induced differentiation. These data suggest that RREB-1 may play a role in Ras and Raf signal transduction in medullary thyroid cancer and other cells.
Effect of L-Triiodothyronine on Radiation-Induced Pulmonary Fibrosis in Dogs (1966)

For many years radiologists and radiobiologists have been concerned with the changes in the lung as sequellae to radiation to the chest. Radiation pneumonitis, frequently accompanied by pulmonary infection, and fibrosis have been recognized since 1922, and their occurrence is well documented in the literature. Englestad (1) has characterized into four stages the development of the reaction of the lung after irradiation of rabbits. In the first stage, which begins 1 to 2 hours after exposure and lasts 1 to 2 days, there is degeneration of the lymph follicles; the bronchial epithelium undergoes changes with abundant mucus secretion, hyperemia, an increase in transudation, and moderate infiltration of leukocytes. The second, or latent, stage is of 2 to 3 weeks' duration. The main reaction occurs in stage 3, with marked degenerative and inflammatory changes. The inflammation may be more or less acute and if often fulminant after very large doses. One to two months postirradiation the acute inflammation reaches its maximum. The leukocyte infiltration diminishes slowly. Large quantities of macrophages appear, and often a great number of giant cells. Stage 4 is one of regenerative changes, with proliferation of connective tissue and sclerosis. At this time there is slight proliferation of the bronchial epithelium, and it is not uncommon to find bone production. Attempts to reverse or modify these effects have met with little success. In man, efforts have been made to minimize the radiation reactions by using as low a dose as
Models of neoplasia and their diagnostic implications: a historical perspective (1993)

In comparison with normal cells, cancer cells have an enhanced ability to trap both nitrogen and energy; an enhanced operation of the glycolytic and direct oxidative pathways, leading to accumulation of lactate and increased production of NADPH; and a greater content of lysosomal hydrolases. These changes represent a reprogramming of gene expression, which, at its most specific, is accompanied by the reappearance in the cell and ultimately in the body fluids of oncodevelopmental proteins not normally found in mature adult tissues. The most florid stage of this reprogramming leads to the metastatic phenotype, which confers upon the cancer cell the ability to stimulate angiogenesis, invade the bloodstream and lymphatic vessel, and arrest and proliferate in distant tissues. The diagnostic implications of these phenotypic changes are illustrated for cancer of the cervix uteri and cancer of the colon. We also review the classical theories of neoplasia, including the cellular anoxia concept of Warburg, the deletion hypothesis of Potter, and various other mechanisms emphasizing genomic derepression and impaired immunity. The critical steps in chemical carcinogenesis are described, and the Vogelstein-Lane model is presented, emphasizing the stepwise and cumulative genomic changes affecting chromosomes 5q, 17p, 18q, and gene amplification of chromosome 12 as well as genomic instability resulting from reduced DNA methylation. The main consequences of these genomic alterations include overexpression or activation of oncogenes such as c-myc and k-ras, together with mutation or functional inactivation of suppressor genes such as p53. Finally, the implications of these findings for diagnosis and management are illustrated by reference to recent investigations in cancers of the breast, colon, and bladder, in which these genomic alterations can be detected by examination of appropriate cellular material and by detection in serum of antibodies to the p53 gene product.
Association of elevated transcript levels of interferon-inducible chemokines with disease activity and organ damage in systemic lupus erythematosus patients (2008)

The combined transcription level of interferon-inducible chemokines in peripheral blood leucocytes is closely associated with disease activity, degree of organ damage, and specific autoantibody patterns in SLE. The chemokine score may serve as a new biomarker for active and severe disease in SLE.
Osteoclasts control reactivation of dormant myeloma cells by remodelling the endosteal niche (2015)

Multiple myeloma is largely incurable, despite development of therapies that target myeloma cell-intrinsic pathways. Disease relapse is thought to originate from dormant myeloma cells, localized in specialized niches, which resist therapy and repopulate the tumour. However, little is known about the niche, and how it exerts cell-extrinsic control over myeloma cell dormancy and reactivation. In this study, we track individual myeloma cells by intravital imaging as they colonize the endosteal niche, enter a dormant state and subsequently become activated to form colonies. We demonstrate that dormancy is a reversible state that is switched 'on' by engagement with bone-lining cells or osteoblasts, and switched 'off' by osteoclasts remodelling the endosteal niche. Dormant myeloma cells are resistant to chemotherapy that targets dividing cells. The demonstration that the endosteal niche is pivotal in controlling myeloma cell dormancy highlights the potential for targeting cell-extrinsic mechanisms to overcome cell-intrinsic drug resistance and prevent disease relapse.
Emerging Issues in AAV-Mediated In Vivo Gene Therapy (2017)

In recent years, the number of clinical trials in which adeno-associated virus (AAV) vectors have been used for <i>in vivo</i> gene transfer has steadily increased. The excellent safety profile, together with the high efficiency of transduction of a broad range of target tissues, has established AAV vectors as the platform of choice for <i>in vivo</i> gene therapy. Successful application of the AAV technology has also been achieved in the clinic for a variety of conditions, including coagulation disorders, inherited blindness, and neurodegenerative diseases, among others. Clinical translation of novel and effective "therapeutic products" is, however, a long process that involves several cycles of iterations from bench to bedside that are required to address issues encountered during drug development. For the AAV vector gene transfer technology, several hurdles have emerged in both preclinical studies and clinical trials; addressing these issues will allow in the future to expand the scope of AAV gene transfer as a therapeutic modality for a variety of human diseases. In this review, we will give an overview on the biology of AAV vector, discuss the design of AAV-based gene therapy strategies for <i>in vivo</i> applications, and present key achievements and emerging issues in the field. We will use the liver as a model target tissue for gene transfer based on the large amount of data available from preclinical and clinical studies.
Reversible gas-phase redox processes catalyzed by Co-exchanged MFU-4l(arge) (2011)

Postsynthetic metal ion exchange in a benzotriazolate-based MFU-4l(arge) framework leads to a Co(II)-containing framework with open metal sites showing reversible gas-phase oxidation properties.
Synthesis of 3,4-bis-Acetoxymethyl-Furan (1979)

Abstract There are available in the literature1–3 a very limited number of useful routes for the preparation of 3,4-bis-acetoxymethyl-furan in general purpose manufacturing plant because they are either too long and/or they use specialized reagents or techniques. Our attempts to provide a solution to this problem have provided a simple short practical route to the title compound which may have more general application in the synthesis of furans. Additionally both starting materials and reagents are cheap and readily available.
Synergistically constructed polyamine/nanosilica/graphene composites: preparation, features and removal of Hg2+ and dyes from contaminated water (2014)

A simple method was developed to construct graphene–nanosilica composites. Polyethyleneimine (PEI), which is a synthetic polyamine functionally analogous to bio-polyamines in organisms, was used as a template/scaffold/catalyst to direct nanostructured silica formation, i.e., PEI hybridised silica (PEI@SiO2). Due to the cationic nature and reducibility of PEI, the hybrid PEI@SiO2 surface instantly adsorbs the negatively charged graphene oxide (GO) at room temperature, leading to PEI@SiO2@GO composites. The GO was further reduced in situ into reduced grapheme oxide (rGO) to form PEI@SiO2@rGO at 90 °C. The PEI@SiO2@GO showed a high removal efficiency of 96% for Hg2+ from a 10 ppm solution; PEI@SiO2@rGO could decolorise organic dyes (rhodamine B or methyl blue) from solution after 30 min. Unlike previously published methods for producing graphene–inorganic composites, this method is general to other polyamine–silica (or metal oxide) systems and has the synergistic efficiency to target GO without additional surface modification and reductants.
Interplay between evolving surface morphology, atomic-scale growth modes, and ordering duringSixGe1−xepitaxy (1993)

Atomic-scale compositional ordering in ${\mathrm{Si}}_{\mathit{x}}$${\mathrm{Ge}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$ alloys is directly linked to the formation of coherent islands during Stranski-Krastanow growth. The vicinal surfaces associated with nonequilibrium island shapes induce a bilayer step flow growth mode, and the ordering results from Ge segregation at ${\mathit{D}}_{\mathit{B}}$ kinks.
Large-swing CMOS buffer amplifier (1989)

A circuit configuration for a CMOS buffer amplifier is described. The circuit, which is an enhancement of a previously reported buffer amplifier, features a large output voltage swing and a well-controlled quiescent current. A buffer amplifier of this type has been implemented in a 1.5- mu m CMOS technology. The prototype occupies an area of 275 mil/sup 2/. It works with a 5-V supply and can drive more than 4.2 V (peak to peak) in to 300 Omega with a total harmonic distortion of less than 0.025%.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Biosynthesis of the lantibiotic subtilin is regulated by a histidine kinase/response regulator system (1993)

Subtilin is a lanthionine-containing peptide antibiotic (lantibiotic) which is produced by Bacillus subtilis ATCC 6633. Upstream from the structural gene of subtilin, spaS, three genes (spaB, spaT, and spaC) which are involved in the biosynthesis of subtilin have been identified (C. Klein, C. Kaletta, N. Schnell, and K.-D. Entian, Appl. Environ. Microbiol. 58:132-142, 1992). By using a hybridization probe specific for these genes, the DNA region downstream from spaS was isolated. Further subcloning revealed a 5.2-kb KpnI-HindIII fragment on which two open reading frames, spaR and spaK, were identified approximately 3 kb downstream from spaS. The spaR gene encodes an open reading frame of 220 amino acids with a predicted molecular mass of 25.6 kDa. SpaR shows 35% similarity to positive regulatory factors OmpR and PhoB. The spaK gene encodes an open reading frame of 387 amino acids with a predicted molecular mass of 44.6 kDa and was highly similar to histidine kinases previously described (PhoM, PhoR, and NtrB). Hydrophobicity blots suggested two membrane-spanning regions. Thus, spaR and spaK belong to a recently identified family of environmentally responsive regulators. These results indicated a regulatory function of spaR and spaK in subtilin biosynthesis. Indeed, batch culture experiments confirmed the regulation of subtilin biosynthesis starting in the mid-logarithmic growth phase and reaching its maximum in the early stationary growth phase. Gene deletions within spaR and spaK yielded subtilin-negative mutants, which confirms that subtilin biosynthesis is under the control of a two-component regulatory system.(ABSTRACT TRUNCATED AT 250 WORDS)
Uptake of neoglycoproteins via membrane lectin(s) of L1210 cells evidenced by quantitative flow cytofluorometry and drug targeting (1984)

The presence and the sugar specificity of membrane lectins on the cell surface of mouse L1210 leukemia cells were demonstrated by using various neoglycoproteins (glycosylated serum albumin) substituted with fluorescein or methotrexate. Neoglycoproteins were prepared by reaction of glycosidophenylisothiocyanates with bovine serum albumin. The binding of neoglycoproteins to L1210 cells depends on the nature of the carried sugar and on the number of bound sugar residues per neoglycoprotein molecule. The best results were obtained with fucosylated serum albumin containing 25 +/- 5 residues of fucose. The amount of cell-associated fluorescein-labeled neoglycoproteins was several fold higher at 37 degrees C than at 4 degrees C suggesting a specific endocytotic process. The membrane lectin-mediated endocytosis was further demonstrated by showing that the cell-associated fluorescence upon cell incubation in the presence of fluorescein-labeled neoglycoproteins at 37 degrees C increased several fold after addition of monensin, a proton/sodium ionophore known to raise the pH of endosomes and lysosomes. The analysis of fluorescein-labeled neoglycoproteins association to the L1210 cells were achieved by quantitative flow cytofluorometry after standardization with calibrated polystyrene sulfonate beads carrying various amounts of 1-(fluoresceinylthioureido)-4,8-diazalicosane. In addition, the cytotoxicity of neoglycoprotein-bound methotrexate was shown to be related to the presence and to the nature of the carried sugar: fucosylated serum albumin was shown to be the most efficient neoglycoprotein carrier, and to have a cytotoxicity close to that of anti L1210 cell IgM monoclonal antibody carrying methotrexate.
Error analysis in acoustic elastography. II. Strain estimation and SNR analysis (1997)

Accurate displacement estimates are required to obtain high-quality strain estimates in elastography. In this paper the strain variance is derived from the statistical properties of the displacement field to define a point signal-to-noise ratio for elastography (SNR0). Displacements caused by compressional forces applied along the axis of the transducer beam are modeled by scaling and shifting the axial reflectivity profile of the tissue. The strain variance is given as a function of essential experimental parameters, such as the amount of tissue compression, echo waveform window length, and the amount of window overlap. SNR0 is defined in terms of applied compression and strain variance and normalized by the input signal-to-noise ratio (SNRi) for echo signals, to formulate the performance metric SNR0/SNRi. This quantity characterizes the noise properties, dynamic range, and sensitivity of strain images based on the spatial resolution requirements. The results indicate that low noise, high sensitivity, and limited dynamic range strain images are obtained for high-frequency bandpass signals when the applied strain is small. For large strains, however, one strategy for low-noise strain imaging employs base-band signals to obtain images with large dynamic range but limited peak sensitivity and noise figure. A better strategy includes companding, which eliminates the average strain in the echo signal before cross-correlation to reduce the dynamic range requirement and increase peak sensitivity for strain estimates.
Privacy-preserving network forensics (2011)

Privacy-preserving attribution of IP packets can help balance forensics with an individual's right to privacy.