gebhart/patrepeval huggingface dataset:
A Molecularly Cloned Schwarz Strain of Measles Virus Vaccine Induces Strong Immune Responses in Macaques and Transgenic Mice (2003)

Live attenuated RNA viruses make highly efficient vaccines. Among them, measles virus (MV) vaccine has been given to a very large number of children and has been shown to be highly efficacious and safe. Therefore, this vaccine might be a very promising vector to immunize children against both measles and other infectious agents, such as human immunodeficiency virus. A vector was previously derived from the Edmonston B strain of MV, a vaccine strain abandoned 25 years ago. Sequence analysis revealed that the genome of this vector diverges from Edmonston B by 10 amino acid substitutions not related to any Edmonston subgroup. Here we describe an infectious cDNA for the Schwarz/Moraten strain, a widely used MV vaccine. This cDNA was constructed from a batch of commercial vaccine. The extremities of the cDNA were engineered in order to maximize virus yield during rescue. A previously described helper cell-based rescue system was adapted by cocultivating transfected cells on primary chicken embryo fibroblasts, the cells used to produce the Schwarz/Moraten vaccine. After two passages the sequence of the rescued virus was identical to that of the cDNA and of the published Schwarz/Moraten sequence. Two additional transcription units were introduced in the cDNA for cloning foreign genetic material. The immunogenicity of rescued virus was studied in macaques and in mice transgenic for the CD46 MV receptor. Antibody titers and T-cell responses (ELISpot) in animals inoculated with low doses of rescued virus were identical to those obtained with commercial Schwarz MV vaccine. In contrast, the immunogenicity of the previously described Edmonston B strain-derived MV clone was much lower. This new molecular clone will allow for the production of MV vaccine without having to rely on seed stocks. The additional transcription units allow expressing heterologous antigens, thereby providing polyvalent vaccines based on an approved, safe, and efficient MV vaccine strain that is used worldwide.
Location-aided routing (LAR) in mobile ad hoc networks (1998)

A mobile ad hoc network consists of wireless hosts that may move often. Movement of hosts results in a change in routes, requiring some mechanism for determining new routes. Several routing protocols have already been proposed for ad hoc networks. This report suggests an approach to utilize location information (for instance, obtained using the global positioning system) to improve performance of routing protocols for ad hoc networks.
Poly-beta-hydroxybutyrate membrane structure and its relationship to genetic transformability in Escherichia coli (1986)

The effects of competence-inducing treatments on the composition and organization of membrane lipids in Escherichia coli K-12, DH1, DH5, HB101, and RR1 were investigated for two widely used protocols in which transformability is developed at low temperatures in Ca2+ buffers. At stages during each procedure, the lipid compositions of the cells were determined, and the thermotropic lipid phase transitions were observed in whole cell culture by fluorescence assay with the hydrophobic probe N-phenyl-1-naphthylamine. Competence was evaluated by determining transformation efficiencies with plasmid pBR322 DNA. The competence-inducing procedures effected only slight changes in phospholipid compositions which did not correlate with transformability. However, the induction of competence was coincident with de novo synthesis and incorporation of poly-beta-hydroxybutyrate into the cytoplasmic membranes and with the appearance of a sharp lipid phase transition above physiological temperatures. Transformation efficiencies correlated with poly-beta-hydroxybutyrate concentrations and with the intensity of the new phase transition. Transformability, poly-beta-hydroxybutyrate synthesis and the new phase transition were not significantly affected by inhibition of protein synthesis with chloramphenicol or inhibition of respiration or ATP synthesis with azide, cyanide, arsenate, or 2,4-dinitrophenol; however, when poly-beta-hydroxybutyrate synthesis was inhibited with acetaldehyde, the new phase transition was not observed, and competence failed to develop. These studies suggest that genetic transformability in E. coli may be physiologically regulated.
Glycosylation Site-Specific Analysis of Clade C HIV-1 Envelope Proteins (2009)

The extensive glycosylation of HIV-1 envelope proteins (Envs), gp120/gp41, is known to play an important role in evasion of host immune response by masking key neutralization epitopes and presenting the Env glycosylation as "self" to the host immune system. The Env glycosylation is mostly conserved but continues to evolve to modulate viral infectivity. Thus, profiling Env glycosylation and distinguishing interclade and intraclade glycosylation variations are necessary components in unraveling the effects of glycosylation on Env's immunogenicity. Here, we describe a mass spectrometry-based approach to characterize the glycosylation profiles of two rVV-expressed clade C Envs by identifying the glycan motifs on each glycosylation site and determining the degree of glycosylation site occupancy. One Env is a wild-type Env, while the other is a synthetic "consensus" Env (C.CON). The observed differences in the glycosylation profiles between the two clade C Envs show that C.CON has more unutilized sites and high levels of high mannose glycans; these features mimic the glycosylation profile of a Group M consensus immunogen, CON-S. Our results also reveal a clade-specific glycosylation pattern. Discerning interclade and intraclade glycosylation variations could provide valuable information in understanding the molecular differences among the different HIV-1 clades and in designing new Env-based immunogens.
A Dispatching Method for Automated Guided Vehicles to Minimize Delays of Containership Operations (1999)

There is a worldwide trend to automate the handling operations in port container terminals in an effort to improve productivity and reduce labor cost. This study iscusses how to apply an AGV(automated guided vehicle) system to the handling of containers in the yard of a port container ter-minal. The main issue of this paper is how to assign tasks of container delivery to AGVs during ship operations in an automated port container terminal. A dual-cycle operation is assumed in which the loading and the discharging operation can be performed alternately. Mixed integer linear program-ming formulations are suggested for the dispatching problem. The completion time of all the dis-charging and loading operations by a quayside crane is minimized, and the minimization of the total travel time of AGVs is also considered as a secondary objective. A heuristic method using useful properties of the dispatching problem is suggested to reduce the computational time. The perfor-mance of the heuristic algorithm is evaluated in light of solution quality and computation time.
Neutralizing IL‐21 and IL‐15 Inhibits Pro‐inflammatory Cytokine Production in Rheumatoid Arthritis (2008)

Interleukin IL-21 and IL-15 belong to the common gamma-chain receptor family. IL-15 represents a novel therapeutic target in rheumatoid arthritis (RA), whereas less is known about the role of IL-21 in human inflammatory diseases. We have analysed the effects of blocking IL-21 and IL-15 on spontaneous production of pro-inflammatory cytokines in RA synovial cell cultures. RA synovial membrane cells were cultured in the presence of an IL-21R-Fc chimera or a neutralizing IL-15 antibody and production of tumour necrosis factor (TNF)alpha, IL-6 and IL-1beta was measured by enzyme-linked immunosorbent assay (ELISA). Expression of IL-21 and IL-15 in RA synovium was measured by RT-PCR and ELISA. mRNA for IL-21 and IL-21R was detected in the culture cell lysates. Protein for IL-15 was found at detectable levels in the cell lysates. Both the IL-21R-Fc chimera and anti-IL-15 antibody inhibited cytokine release, although substantially more IL-21R-Fc was needed. IL-21R-Fc at the highest dose (100 microg/ml) significantly reduced TNFalpha production by 50%, IL-6 by 57% and IL-1beta by 81%. Anti-IL-15 antibody (5 microg/ml) significantly inhibited TNFalpha release by 51%, IL-6 by 37% and IL-1beta by 82% in line with previous published observations. The data confirm that IL-15 plays a role in RA and suggests that IL-21 is also involved in driving the pro-inflammatory cytokine response in RA.
Solid-Phase Enzymatic Synthesis of a Sialyl Lewis X Tetrasaccharide on a Sepharose Matrix (1998)

Thiopyridyl Sepharoses with different linker arm lengths were prepared from epoxy Sepharose 6B by reaction first with 1,8-diamino-3,6-dioxaoctane and then with, sucessively, diethoxy-3-cyclobutene-1,2-dione (squaric acid diethyl ester) and 1,8-diamino-3,6-dioxaoctane in several cycles, followed by reaction of the obtained amino Sepharoses with, successively, thiobutyrolactone and 2,2'-dithiopyridine. The thiopyridyl Sepharoses were reacted with the glucosamine derivative 2-(3'-mercaptobutyrylamido)ethyl 2-acetamido-2-deoxy-beta-D-glucopyranoside, giving GlcNAc Sepharoses with different linker lengths. Enzymatic galactosylation of these with beta-(1-4)-galactosyltransferase and UDP-galactose gave yields varying between 70 and 98%, and there was a clear correlation between linker length and yield. A GlcNAc Sepharose with a long linker was then used in a solid-phase synthesis of a sialyl Le x tetrasaccharide. The three required enzymes (galactosyl-, sialyl, and fucosyltransferase) and nucleotide sugars were reacted consecutively with the GlcNAc Sepharose, giving, after cleavage from Sepharose with DTT, the free sialyl Le x tetrasaccharide derivative in a 57% total yield after purification.
Osteoclasts are required for bone tumors to grow and destroy bone (1998)

It has been hypothesized that bone resorption during tumor osteolysis is performed by osteoclasts. Data supporting this hypothesis have been provided from analysis of human biopsy specimens obtained from sites of tumor osteolysis, as well as from experimentation with in vivo animal models. Experiments in this report take this concept one step further by testing the hypothesis that osteoclasts are required for bone tumors to grow and destroy bone. To test this hypothesis, the influence of an osteolytic sarcoma tumor, NCTC clone 2472 (2472), on bone was studied in animals that are osteoclast deficient (microphthalmic, strain B6C3Fe-a/a-Mitf(mi)) but whose osteoclast deficiency can be reversed following bone marrow transplantation. Femora of these mice and unaffected wild-type siblings were injected with 10(5) 2472 cells, and after 14 days the femora were analyzed by radiographic and histomorphometric analysis. Macroscopic tumor, tumor-induced osteolysis, and increased osteoclast number were noted in femora of normal mice but not in femora of osteoclast-deficient mice (p < 0.001). Bone marrow transplantation converted osteoclast-deficient mice to mice with femora that contained osteoclasts in 4 weeks. Femora of these mice were then injected with 10(5) 2472 tumor cells; after 14 days, in contrast to the findings in the original osteoclast-deficient mice, macroscopic tumor was present, tumor-induced osteolysis was noted on roentgenograms, and osteoclast number was increased when tumor-bearing limbs were compared with sham-injected limbs (p < 0.001). These data prove the hypothesis that osteoclasts are required for 2472 tumor-induced osteolysis, and they introduce the exciting possibility that osteoclasts are also required for tumors to grow in bone.
Selection of a Novel and Highly Specific Tumor Necrosis Factor α (TNFα) Antagonist (2010)

Inhibition of tumor necrosis factor alpha (TNFalpha) is a favorable way of treating several important diseases such as rheumatoid arthritis, Crohn disease, and psoriasis. Therefore, an extensive range of TNFalpha inhibitory proteins, most of them based upon an antibody scaffold, has been developed and used with variable success as therapeutics. We have developed a novel technology platform using C-type lectins as a vehicle for the creation of novel trimeric therapeutic proteins with increased avidity and unique properties as compared with current protein therapeutics. We chose human TNFalpha as a test target to validate this new technology because of the extensive experience available with protein-based TNFalpha antagonists. Here, we present a novel and highly specific TNFalpha antagonist developed using this technology. Furthermore, we have solved the three-dimensional structure of the antagonist-TNFalpha complex by x-ray crystallography, and this structure is presented here. The structure has given us a unique insight into how the selection procedure works at a molecular level. Surprisingly little change is observed in the C-type lectin-like domain structure outside of the randomized regions, whereas a substantial change is observed within the randomized loops. Thus, the overall integrity of the C-type lectin-like domain is maintained, whereas specificity and binding affinity are changed by the introduction of a number of specific contacts with TNFalpha.
Porcine Reproductive and Respiratory Syndrome (1993)

Outbreaks of undiagnosed reproductive failure occurred in North Carolina, Minnesota, and Iowa during 1987-1988 and were characterized by the presence of both respiratory and reproductive signs in swine herds. 29,35,36 The disease was referred to as mystery swine disease because no definitive cause could be assigned to it. Various other names given to this syndrome were disease 89, pig plague 89, SMEDI-like syndrome, swine reproductive failure syndrome, swine reproductive and respiratory syndrome (SRRS), and swine infertility and respiratory syndrome (SIRS) (Table 1). At the First International Symposium on SIRS/PRRS held at St. Paul, Minnesota, USA, a decision was made to call this syndrome PRRS and its virus PRRSV. By 1990, the disease had been detected in 11 states of the United States and 2 provinces of Canada. It was reported in the Munster area of Germany in late 1990, spread rapidly to other parts of Germany, and was called Seuchenhafter Spatabort der Schweine (SSS; infectious late abortion of pigs) and Epidemisch Spatabort der Schweine (ESS; enzootic late abortion of pigs). It was then detected in other European countries (The Netherlands, France, Belgium, England, and Denmark) and has been diagnosed in over 5,000 North European pig farms since late 1990. Although the disease has not been reported in Italy, Poland, Switzerland, and Australia, antibodies against PRRSV have been detected in swine herds in Italy and Poland. The disease is economically important because of the severe adverse effects on swine production, an increase of 20-30% in the stillbirth rate, and a loss of 1.5-2.0 piglets per sow per year. A loss of $250-500
Electronic Structure Differences in ZrO2 vs HfO2 (2005)

Although ZrO2 and HfO2 are, for the most part, quite similar chemically, subtle differences in their electronic structures appear to be responsible for differing MO2/Si (M = Zr, Hf) interface stabilities. To shed light on the electronic structure differences between ZrO2 and HfO2, we have conducted joint experimental and theoretical studies. Because molecular electron affinities are a sensitive probe of electronic structure, we have measured them by conducting photoelectron spectroscopic experiments on ZrO2(-) and HfO2(-). The adiabatic electron affinity of HfO2 was determined to be 2.14 +/- 0.03 eV, and that of ZrO2 was determined to be 1.64 +/- 0.03 eV. Concurrently, advanced electronic structure calculations were conducted to determine electron affinities, vibrational frequencies, and geometries of these systems. The calculated CCSD(T) electron affinities of HfO2 and ZrO2 were found to be 2.05 and 1.62 eV, respectively. The molecular results confirm earlier predictions from solid state calculations that HfO2 is more ionic than ZrO2. The excess electron in MO2(-) occupies an sd-type hybrid orbital localized on the M atom (M = Zr, Hf). The structural parameters of ZrO2 and HfO2 and their vibrational frequencies were found to be very similar. Upon the excess electron attachment, the M-O bond length increases by ca. 0.04 A, the OMO angle increases by 2-4 degrees, and frequencies of all vibrational modes become smaller, with the stretching modes being shifted by 30-50 cm(-1) and the bending mode by 15-25 cm(-1). Together, these studies unveil significant differences in the electronic structures of ZrO2 and HfO2 but not in their structural or vibrational characteristics.
Quantitative analysis of anastomotic intimal hyperplasia in paired Dacron and PTFE grafts. (1990)

The purpose of this investigation was to compare and contrast the occurrence and progression of anastomotic intimal hyperplasia in two commonly used prosthetic arterial grafts. Twenty paired carotid artery interposition grafts of Dacron and PTFE (polytetrafluoroethylene) were implanted in a canine model. The grafts were electively removed at intervals from one week to seven months or at the time of thrombosis. Areas of hyperplastic growth were determined at each anastomosis using a quantitative histologic technique. The number of grafts quantitatively evaluated was 16 Dacron and 12 PTFE, excluding all thrombosed grafts. In both materials, hyperplasia occurred to a significantly greater degree at the distal or downstream anastomosis as compared with the proximal or upstream anastomosis (Dacron P less than 0.001, PTFE P less than 0.05). Quantitative and qualitative evaluation of these two commonly used but different arterial grafts did not demonstrate a significant difference in the occurrence of anastomotic hyperplasia.
A Benchmark Dataset and Evaluation Methodology for Video Object Segmentation (2016)

Over the years, datasets and benchmarks have proven their fundamental importance in computer vision research, enabling targeted progress and objective comparisons in many fields. At the same time, legacy datasets may impend the evolution of a field due to saturated algorithm performance and the lack of contemporary, high quality data. In this work we present a new benchmark dataset and evaluation methodology for the area of video object segmentation. The dataset, named DAVIS (Densely Annotated VIdeo Segmentation), consists of fifty high quality, Full HD video sequences, spanning multiple occurrences of common video object segmentation challenges such as occlusions, motionblur and appearance changes. Each video is accompanied by densely annotated, pixel-accurate and per-frame ground truth segmentation. In addition, we provide a comprehensive analysis of several state-of-the-art segmentation approaches using three complementary metrics that measure the spatial extent of the segmentation, the accuracy of the silhouette contours and the temporal coherence. The results uncover strengths and weaknesses of current approaches, opening up promising directions for future works.
Passive optical fast frequency-hop CDMA communications system (1999)

This paper proposes an all-fiber fast optical frequency-hop code division multiple access (FFH-CDMA) for high-bandwidth communications. The system does not require an optical frequency synthesizer allowing high communication bit rates. Encoding and decoding are passively achieved by Bragg gratings, Multiple Bragg gratings replace a frequency synthesizer, achieving a hopping rate in tens of GHz. A main lobe sine apodization can be used in writing the gratings to enhance the system capacity and the spectrum efficiency. All network users can use the same tunable encoder/decoder design. The simultaneous utilization of the time and frequency domains offers notable flexibility in code selection. Simulations show that the encoder efficiently performs the FFH spread spectrum signal generation and that the receiver easily extracts the desired signal from a received signal for several multiple access interference scenarios. We measure the system performance in terms of bit error rate, as well as auto-to cross-correlation contrast. A transmission rate of 500 Mb/s per user is supported in a system with up to 30 simultaneous users at 10/sup -9/ bit error rate. We compare FFH-CDMA to several direct sequence-CDMA systems in terms of bit error rate versus the number of simultaneous users. We show that an optical FFH-CDMA system requires new design criteria for code families, as optical device technology differs significantly from that of radio frequency communications.
Kα,Kβ, and radiative Auger photon intensities inKx-ray spectra from atoms in the20≤Z≤40region (1986)

Accurate measurements of the x-ray intensity ratio I(K\ensuremath{\beta})/I(K\ensuremath{\alpha}) from electron-capture radionuclides, using Si(Li) detectors of calibrated line shape, eliminate an existing large discrepancy between experiment and relativistic Hartree-Fock predictions. Small systematic discrepancies in the literature ratios for the mechanisms of photoionization, and electron and proton excitation, are attributed to omission of radiative Auger (RA) satellites in spectrum analysis. With the inclusion of RA peaks in the spectrum fitting, the present data support Scofield's predictions of I(K\ensuremath{\beta})/I(K\ensuremath{\alpha}) at the 1% accuracy level, an important conclusion for elemental analysis techniques such as proton-induced x-ray emission and x-ray fluorescence. The resulting radiative Auger intensities also agree quite well with calculations.
The α-Chemokine Receptor CXCR4 Is Expressed on the Megakaryocytic Lineage From Progenitor to Platelets and Modulates Migration and Adhesion (1998)

CXCR4 is the receptor for the alpha-chemokine stromal cell-derived factor 1 (SDF-1) and has been shown to be expressed on a diversity of leukocytes. In this report, the expression of the CXCR4 receptor in cells of megakaryocytic lineage and the role of SDF-1 in megakaryocytopoiesis were investigated. Using flow cytometry in combination with reverse transcriptase-polymerase chain reaction (RT-PCR), we observed that bone marrow CD34(+), CD61(+) cells, blood platelets, and megakaryocytic leukemia cell lines all expressed the CXCR4 receptor. To examine the expression of the CXCR4 receptor on megakaryocyte progenitors (colony-forming units-megakaryocyte [CFU-Meg]), CXCR4-positive and -negative CD34(+) populations were separated from bone marrow and cultured in a plasma clot culture system. A subpopulation of the CFU-Meg was found in the CXCR4-positive fraction. The functional significance of CXCR4 expression on cells of the megakaryocytic lineage was examined by studying the effects of SDF-1alpha on migration and proliferation of megakaryocyte progenitor cells in vitro. We found that SDF-1alpha potently induced megakaryocyte progenitor migration and significantly enhanced adhesion of mature marrow megakaryocytes to endothelium. No marked effects of SDF-1alpha alone or in combination with thrombopoietin and stem cell factor/kit ligand on megakaryocyte production in vitro were noted. These results demonstrate for the first time that the CXCR4 alpha-chemokine receptor is expressed on cells of the megakaryocytic lineage from progenitors to platelets and that its ligand SDF-1alpha may modulate several aspects of megakaryocytopoiesis.