gebhart/patrepeval huggingface dataset:
Immunisation with gamma globulin to Murray Valley encephalitis virus and with an inactivated Japanese encephalitis virus vaccine as prophylaxis against Australian encephalitis: Evaluation in a mouse model (2000)

In northwestern Australia, the flavivirus Murray Valley encephalitis (MVE) poses a significant health risk to infants in some aboriginal communities, particularly during each wet season. While there are too few cases to warrant the development of a vaccine against MVE, a safe, effective prophylaxis for these children is still urgently required. The use of passive transfer of human gamma globulin to MVE or immunisation with a vaccine to the closely related Japanese encephalitis (JE) virus were investigated as potential strategies. When 40 microg of IgG was purified from MVE-immune human sera and transferred to 3-week-old mice, the animals were protected from lethal IP inoculation with MVE virus while still producing a detectable immune response to the virus. Similarly, sera from adult mice infected sublethally with MVE or JE virus provided significant protection against MVE infection. However, sera from mice sublethally infected with the related Kunjin or immunised with the inactivated JE vaccine (Biken) provided no protection against MVE challenge. In fact, mice immunised passively with the latter appeared to succumb to MVE challenge more rapidly than mice that received serum from unimmunised animals, suggesting that antibody to the vaccine had accelerated the progression of disease. These preliminary trials in mice indicate that passive immunisation with human gamma globulin has the greatest potential as a strategy for MVE prophylaxis, whilst the apparent enhancement of MVE by antibodies to the JE vaccine requires further investigation, with particular reference to current vaccination programs in areas of Australia and Papua New Guinea, where both JE and MVE occur.
Fluorine-18 labeling of monoclonal antibodies and fragments with preservation of immunoreactivity (1991)

A new method is reported for labeling proteins with the positron-emitting nuclide 18F. Initially, 4-[18F]-fluorobenzylamine was prepared in two steps from aqueous [18F]fluoride in high yield. The 18F acylation agent was formed by reaction of this product with disuccinimidyl suberate. Overall yields for the 4-[18F]fluorobenzylamine succinimidyl ester ([18F]SFBS), decay corrected to the end of cyclotron bombardment, were about 30% in a synthesis time of 60 min. After a 15-min reaction, 30-45% (decay corrected) of the [18F]SFBS could be coupled to intact antibodies and their F(ab')2 and Fab fragments. Coupling yields were dependent on protein concentration but not reaction time. HPLC purification of [18F]SFBS was necessary to obtain optimal coupling efficiency and immunoreactivity. The immunoreactivities of 18F-labeled F(ab')2 and Fab fragments of an antimyosin antibody were 89 +/- 5% and 75 +/- 9%, respectively. Biodistribution studies in normal mice demonstrated similar in vivo behavior of 18F-labeled antibody fragments and those labeled with 125I by using N-succinimidyl 3-[125I]iodobenzoate. These results indicate that this method may be useful for labeling monoclonal antibodies and other proteins and peptides with 18F.
Dietary Polyphenols Promote Growth of the Gut Bacterium Akkermansia muciniphila and Attenuate High-Fat Diet–Induced Metabolic Syndrome (2015)

Dietary polyphenols protect against metabolic syndrome, despite limited absorption and digestion, raising questions about their mechanism of action. We hypothesized that one mechanism may involve the gut microbiota. To test this hypothesis, C57BL/6J mice were fed a high-fat diet (HFD) containing 1% Concord grape polyphenols (GP). Relative to vehicle controls, GP attenuated several effects of HFD feeding, including weight gain, adiposity, serum inflammatory markers (tumor necrosis factor [TNF]α, interleukin [IL]-6, and lipopolysaccharide), and glucose intolerance. GP lowered intestinal expression of inflammatory markers (TNFα, IL-6, inducible nitric oxide synthase) and a gene for glucose absorption (Glut2). GP increased intestinal expression of genes involved in barrier function (occludin) and limiting triglyceride storage (fasting-induced adipocyte factor). GP also increased intestinal gene expression of proglucagon, a precursor of proteins that promote insulin production and gut barrier integrity. 16S rRNA gene sequencing and quantitative PCR of cecal and fecal samples demonstrated that GP dramatically increased the growth of Akkermansia muciniphila and decreased the proportion of Firmicutes to Bacteroidetes, consistent with prior reports that similar changes in microbial community structure can protect from diet-induced obesity and metabolic disease. These data suggest that GP act in the intestine to modify gut microbial community structure, resulting in lower intestinal and systemic inflammation and improved metabolic outcomes. The gut microbiota may thus provide the missing link in the mechanism of action of poorly absorbed dietary polyphenols.
Characterization of the major polypeptides of the rat liver nuclear envelope. (1983)

Rat liver nuclear envelopes have been isolated using a newly developed method.Purified nuclei were digested with DNase I and RNase A and then extracted with 1.6 M NaCl in the presence of a reducing agent.This method, which is rapid and simple, yielded predominantly intact nuclear envelope spheres.After correction for phospholipid recovery (40-50%), these nuclear envelopes contained 13, 3, and 4 % of the total
Advanced Polymorphic Worms: Evading IDS by Blending in with Normal Traffic (2005)

Abstract. Normal traffic can provide worms with a very good source of information to camouflage themselves. In this paper, we explore the concept of polymorphic worms that mutate based on normal traffic. We assume that a worm has already penetrated a system and is trying to hide its presence and propagation attempts from an IDS. We focus on stealthy worms that cannot be reliably detected by increases in traffic because of their low propagation factor. We first give an example of a simple polymorphic worm. Such worms can evade a signature-based IDS but not necessarily an anomaly-based IDS. We then show that it is feasible for an advanced polymorphic worm to gather a normal traffic profile and use it to evade an anomaly-based IDS. We tested the advanced worm implementation with three anomaly IDS approaches: NETAD, PAYL and Service-specific IDS. None of the three IDS approaches were able to detect the worm reliably. We found that Payload Execution. The goal of this paper is to advance the science of IDS by analyzing techniques polymorphic worms can use to hide themselves. By showing that polymorphic worms are a practical threat, we hope to stimulate further research to improve existing IDS. 1
A prospective study of the clinical utility of ApoE genotype in the prediction of outcome in patients with memory impairment (1996)

Given the relationship between the presence of ApoE epsilon 4 and Alzheimer's disease (AD), were studied whether knowledge of epsilon 4 status would predict which memory-impaired patients would develop AD over time. One hundred seven patients who presented with memory impairment but not dementia were referred to the study by their family physicians. These patients were followed prospectively over a 2-year period. Twenty-nine patients developed AD, while 78 did not develop dementia. We found that ApoE genotype was a reliable prognostic indicator of who developed AD in this group only when memory test performance was included in the predictive model. These findings indicate that limitations of ApoE genotyping in isolation as a prognostic indicator of AD. Because this study included prospectively selected patients who were followed longitudinally, our findings are likely to have more relevance in the clinical setting than those obtained from currently available retrospective studies.
A comprehensive study of the phase diagram of KxNa1−xNbO3 (2009)

The phase diagram of lead-free piezoelectric KxNa1−xNbO3 has been studied, with particular focus on the proposed morphotropic phase boundaries, by powder and single crystal x-ray diffraction. The tilt system and cation displacement has been mapped out as a function of temperature and composition, highlighting changes in the oxygen octahedra at x=0.2 and x=0.4 at room temperature. The orthorhombic to monoclinic boundary at x=0.5 has been investigated, with a subtle change in the structure observed. The conclusion is that KxNa1−xNbO3 does not display a morphotropic phase boundary comparable with that in lead zirconate titanate, and that the most significant structural change as a function of composition occurs at x=0.2 because of the change of the tilt system.
On the Optimality of Uniform Pulse Amplitude Modulation (2006)

We characterize the optimal M-ary pulse amplitude modulation (PAM) constellation under a general energy constraint. It is shown that uniform M-ary PAM may not always yield the best signal design, e.g., under the average energy constraint. We also identify situations where uniform PAM is optimal, e.g., the peak energy constraint
Online Motion Estimation from Image and Inertial Measurements (2018)

We present two algorithms for estimating sensor motion from image and inertial measurements, which are suitable for use with inexpensive inertial sensors and in environments without known fiducials. The first algorithm is a batch method, which produces optimal estimates of the sensor motion, scene structure, and other parameters using measurements from the entire observation sequence simultaneously. The second algorithm recovers sensor motion, scene structure, and other parameters in an online manner, is suitable for use with long or “infinite” sequences, and handles sequences in which no feature is always visible. We also describe initial results from running each algorithm on a sequence for which ground truth is available. We show that while image measurements alone are not sufficient for accurate motion estimation from this sequence, both batch and online estimation from image and inertial measurements produce accurate estimates of the sensors’ motion.
Spliceosome mutations involving SRSF2, SF3B1, and U2AF35 in chronic myelomonocytic leukemia: Prevalence, clinical correlates, and prognostic relevance (2012)

SRSF2, SF3B1, and U2AF35 (U2AF1) are the three most frequent genes involved with spliceosome mutations in myeloid malignancies. SF3B1 mutations are most frequent (~80%) in myelodysplastic syndromes (MDS) with ring sideroblasts (RS) but lack prognostic relevance. SRSF2 mutations are associated with shortened overall (OS) and leukemia-free survival (LFS) in both MDS and myelofibrosis. In this study of 226 patients with chronic myelomonocytic leukemia (CMML), mutational frequencies were 40% for SRSF2 (all affecting P95), 6% for SF3B1 (primarily K700E) and 9% for U2AF35 (mostly S34F and Q157P/R). These mutations were mutually exclusive and 54% of the patients displayed at least one mutation. The three mutation groups were phenotypically similar, with the exception of higher RS% (P < 0.0001) in patients with SF3B1 mutations. At a median follow-up of 15 months, 176 (78%) deaths and 32 (14%) leukemic transformations were documented. OS (median survivals of 17, 16, 17, and 20 months; P = 0.48) and LFS (leukemic transformation rates of 17, 13, 15, and 5%; P = 0.63) were similar among patients with none of the three mutations, SRSF2, SF3B1, or U2AF35 mutations, respectively. We conclude that SRSF2 is the most frequently mutated spliceosome gene in CMML but neither it nor SF3B1 or U2AF35 mutations are prognostically relevant.
Microencapsulation of Enzymes, Cells, and Genetically Engineered Microorganisms (2003)

Microencapsulation of biologically active material in the form of artificial cell was reported as early as 1964 (1-4). However, it is only in the past 10 yr that many centers have extensively developed this (5). More recently, we have concentrated on three areas of artificial cells for blood substitutes, enzyme therapy, and cell therapy. Space allows only a few examples to be given here.
Cardiotoxicity Induced by Chemotherapy and Antibody Therapy (2006)

Modern cancer therapy employs a combination of chemotherapy, antibody-based therapy, radiotherapy, and surgery to prolong life and provide cure. However, many of the chemotherapy agents and antibodies, either singly or in combination, can affect the cardiovascular system. Common cardiovascular manifestations of these therapies include heart failure, ischemia, hypotension, hypertension, edema, QT prolongation, bradyarrhythmia, and thromboembolism. The patient's age, underlying cardiovascular status, and genetic background, as well as the route of drug administration and dosage, can all contribute to the development of cardiotoxicity. Strategies to monitor for and to manage these effects are discussed in this review.
A VMM security kernel for the VAX architecture (1990)

The development of a virtual-machine monitor (VMM) security kernel for the VAX architecture is described. Particular focus is on how the system's hardware, microcode, and software are aimed at meeting A1-level security requirements while maintaining the standard interfaces and applications of the VMS and ULTRIX-32 operating systems. The VAX security kernel supports multiple concurrent virtual machines on a single VAX system, providing isolation and controlled sharing of sensitive data. Rigorous engineering standards were applied during development to comply with the assurance requirements for verification and configuration management. The VAX security kernel was developed with a heavy emphasis on performance and on system management tools. The kernel performs sufficiently well that all of its development can be now carried out in virtual machines running on the kernel itself, rather than in a conventional time-sharing system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Immunotherapy of Recurrent Genital Herpes with Recombinant Herpes Simplex Virus Type 2 Glycoproteins D and B: Results of a Placebo‐Controlled Vaccine Trial (1997)

To determine the safety, immunogenicity, and efficacy of a recombinant herpes simplex virus type 2 glycoprotein D and B vaccine in the treatment of recurrent genital herpes, a randomized, placebo-controlled trial was held at two referral centers. Healthy patients with 4-14 recurrences per year received injections of both glycoproteins in MF59 adjuvant or of MF59 alone at 0, 2, 12, and 14 months. For 18 study months, the rate and number of recurrences, the duration and severity of the first confirmed recurrence, vaccine immunogenicity, and rates of local and systemic reactions were determined. The monthly rate of recurrences was not significantly improved, but the duration and severity of the first study outbreak was reduced significantly by vaccination. Glycoprotein-specific and neutralizing antibodies were boosted by vaccination for the duration of the study. This vaccine is safe and immunogenic and ameliorated an observed first postvaccination genital recurrence, but it does not reduce recurrence frequency.
[The effect of sodium humate on metabolism and resistance in highly productive poultry]. (1991)

Natrium humate introduced into broiler chickens Broiler-6 line increases mass on 5-7% on the average and poultry safety on 3-5%. In chicken tissues the indexes of protein, mineral and lipid metabolism normalize, the organism's protection and adaptation opportunities improve as a result of peat preparation influence on fodder component mastering and regulatory processes.
Colonization and plant growth promoting characterization of endophytic Pseudomonas chlororaphis strain Zong1 isolated from Sophora alopecuroides root nodules (2013)

The endophytic strain Zong1 isolated from root nodules of the legume Sophora alopecuroides was characterized by conducting physiological and biochemical tests employing gfp-marking, observing their plant growth promoting characteristics (PGPC) and detecting plant growth parameters of inoculation assays under greenhouse conditions. Results showed that strain Zong1 had an effective growth at 28 ºC after placed at 4-60 ºC for 15 min, had a wide range pH tolerance of 6.0-11.0 and salt tolerance up to 5% of NaCl. Zong1 was resistant to the following antibiotics (μg/mL): Phosphonomycin (100), Penicillin (100) and Ampicillin (100). It could grow in the medium supplemented with 1.2 mmol/L Cu, 0.1% (w/v) methylene blue and 0.1-0.2% (w/v) methyl red, respectively. Zong1 is closely related to Pseudomonas chlororaphis based on analysis the sequence of 16S rRNA gene. Its expression of the gfp gene indicated that strain Zong1 may colonize in root or root nodules and verified by microscopic observation. Furthermore, co-inoculation with Zong1 and SQ1 (Mesorhizobium sp.) showed significant effects compared to single inoculation for the following PGPC parameters: siderophore production, phosphate solubilization, organic acid production, IAA production and antifungal activity in vitro. These results suggest strains P. chlororaphi Zong1 and Mesorhizobium sp. SQ1 have better synergistic or addictive effect. It was noteworthy that each growth index of co-inoculated Zong1+SQ1 in growth assays under greenhouse conditions is higher than those of single inoculation, and showed a significant difference (p < 0.05) when compared to a negative control. Therefore, as an endophyte P. chlororaphis Zong1 may play important roles as a potential plant-growth promoting agent.
Switching Patients with Non-Dialysis Chronic Kidney Disease from Oral Iron to Intravenous Ferric Carboxymaltose: Effects on Erythropoiesis-Stimulating Agent Requirements, Costs, Hemoglobin and Iron Status (2015)

ClinicalTrials.gov NCT02232906.
Rapid screening of open reading frames by protein synthesis with an in vitro transcription and translation assay. (1995)

The analysis of open reading frames (ORFs) to predict full-length or truncated proteins in genes is conventionally achieved by DNA sequencing. This method becomes labor-intensive when a large number of specimens or when large genes are to be examined. To circumvent this problem, we used an in vitro transcription and translation (TT) assay to identify full-length or truncated proteins in PCR-amplified genes. A total of 47 nef genes from the simian immunodeficiency virus (SIV) were cloned from 13 SIV-infected monkeys and were screened for ORFs by using the TT assay. Of these 47 genes, 20 had an intact ORF and 27 had premature stop codons at variable positions in the nef gene. All 20 nef genes with intact ORFs produced full-length proteins, while truncated proteins of different sizes were synthesized from all 27 nef genes with premature stop codons. In addition, we validated a simplified TT protocol that allows the direct screening of ORFs from transformed bacterial colonies, thus eliminating the need for plasmid preparations. By being rapid, simple and cost-effective, this technique should be widely applicable to examine the integrity of the ORF of any gene.
Associated Continued Fractions-Barycentric Blending Rational Interpolation and Its Application in Image Processing (2012)

The advantages of barycentric interpolation formulations in computation are small number of floating points operations and good numerical stability. Adding a new data pair, the barycentric interpolation formula don't require to renew computation of all basis functions. Associated continued fraction interpolation is a classical nonlinear interpolation. A new kind of blending rational interpolants was constructed by combining barycentric interpolation and associated continued fractions. We discussed the interpolation theorem, error estimation, numerical examples. Applications to image processing are discussed.
An optimal algorithm for approximate nearest neighbor searching fixed dimensions (1998)

Consider a set of S of n data points in real d -dimensional space, R d , where distances are measured using any Minkowski metric. In nearest neighbor searching, we preprocess S into a data structure, so that given any query point q ∈ R d , is the closest point of S to q can be reported quickly. Given any positive real ϵ, data point p is a (1 +ϵ)- approximate nearest neighbor of q if its distance from q is within a factor of (1 + ϵ) of the distance to the true nearest neighbor. We show that it is possible to preprocess a set of n points in R d in O(dn log n ) time and O(dn) space, so that given a query point q ∈ R d , and ϵ &gt; 0, a (1 + ϵ)-approximate nearest neighbor of q can be computed in O ( c d , ϵ log n ) time, where c d,ϵ ≤ d ⌈1 + 6d/ϵ⌉ d is a factor depending only on dimension and ϵ. In general, we show that given an integer k ≥ 1, (1 + ϵ)-approximations to the k nearest neighbors of q can be computed in additional O(kd log n ) time.
Comparative analysis of IRF and IFN-alpha expression in human plasmacytoid and monocyte-derived dendritic cells (2003)

Plasmacytoid dendritic cells (PDC) produce high levels of type I IFN upon stimulation with viruses, while monocytes and monocyte-derived dendritic cells (MDDC) produce significantly lower levels. To find what determines the high production of type I IFN in PDC, we examined the relative levels of IRF transcription factors, some of which play critical roles in the induction of IFN. Furthermore, to determine whether the differences could result from expression of distinct IFNA subtypes, the profile of IFNA genes expressed was examined. PDC responded equally well to stimulation with HSV-1 and Sendai virus (SV) by producing high levels of type I IFN, whereas the MDDC and monocyte response to SV were lower, and neither responded well to HSV-1. All three populations constitutively expressed most of the IRF genes. However, real-time RT-PCR demonstrated increased levels of IRF-7 transcripts in PDC compared with monocytes. As determined by intracellular flow cytometry, the PDC constitutively expressed significantly higher levels of IRF-7 protein than the other populations while IRF-3 levels were similar among populations. Analysis of the profile of IFNA genes expressed in virus-stimulated PDC, monocytes and MDDC demonstrated that each population expressed IFNA1 as the major subtype but that the range of the subtypes expressed in PDC was broader, with some donor and stimulus-dependent variability. We conclude that PDC but not MDDC are uniquely preprogrammed to respond rapidly and effectively to a range of viral pathogens with high levels of IFN-alpha production due to the high levels of constitutively expressed IRF-7.
Molecular and cell biology aspects of plague (2000)

A 70-kb virulence plasmid (sometimes called pYV) enables Yersinia spp. to survive and multiply in the lymphoid tissues of their host. It encodes the Yop virulon, a system consisting of secreted proteins called Yops and their dedicated type III secretion apparatus called Ysc. The Ysc apparatus forms a channel composed of 29 proteins. Of these, 10 have counterparts in almost every type III system. Secretion of some Yops requires the assistance, in the bacterial cytosol, of small individual chaperones called the Syc proteins. These chaperones act as bodyguards or secretion pilots for their partner Yop. Yop proteins fall into two categories. Some are intracellular effectors, whereas the others are "translocators" needed to deliver the effectors across the eukaryotic plasma membrane, into eukaryotic cells. The translocators (YopB, YopD, LcrV) form a pore of 16-23 A in the eukaryotic cell plasma membrane. The effector Yops are YopE, YopH, YpkA/YopO, YopP/YopJ, YopM, and YopT. YopH is a powerful phosphotyrosine phosphatase playing an antiphagocytic role by dephosphorylating several focal adhesion proteins. YopE and YopT contribute to antiphagocytic effects by inactivating GTPases controlling cytoskeleton dynamics. YopP/YopJ plays an anti-inflammatory role by preventing the activation of the transcription factor NF-kappaB. It also induces rapid apoptosis of macrophages. Less is known about the role of the phosphoserine kinase YopO/YpkA and YopM.