gebhart/patrepeval huggingface dataset:
Therapy of Lupus Nephritis (1986)

We evaluated renal function in 107 patients with active lupus nephritis who participated in long-term randomized therapeutic trials (median follow-up, seven years). For patients taking oral prednisone alone, the probability of renal failure began to increase substantially after five years of observation. Renal function was better preserved in patients who received various cytotoxic-drug therapies, but the difference was statistically significant only for intravenous cyclophosphamide plus low-dose prednisone as compared with high-dose prednisone alone (P = 0.027). The advantage of treatment with intravenous cyclophosphamide over oral prednisone alone was particularly apparent in the high-risk subgroup of patients who had chronic histologic changes on renal biopsy at study entry. Patients treated with intravenous cyclophosphamide have not experienced hemorrhagic cystitis, cancer, or a disproportionate number of major infections. We conclude that, as compared with high-dose oral prednisone alone, treatment of lupus glomerulonephritis with intravenous cyclophosphamide reduces the risk of end-stage renal failure with few serious complications.
HIV-1 isolation from small amounts of whole blood: a technical evaluation. (1992)

We have evaluated a simple and sensitive culture technique for isolation of Human Immunodeficiency Virus Type-1 (HIV-1) from small amounts of whole blood. Data shown in the paper demonstrate that: 1) cell cultures from small amounts of heparinized whole blood (HWB) allow a high isolation rate in infected subjects at all stages of diseases; 2) among asymptomatic subjects the HIV-1 isolation rate is increased in cell cultures from HWB, with respect to cell cultures from peripheral blood mononuclear cells; 3) cultural results from HWB are not influenced by the presence of detectable serum p24 antigen, but a good correlation was found with the titre of anti p24 antibodies in serum; 4) continuous cell lines (such as Molt-3 cells) instead of peripheral blood mononuclear cells can be used, obtaining good results, for HIV-1 isolation from HWB; 5) frozen samples of HWB can be used in cell cultures for HIV-1 isolation; 6) the type of anticoagulant (Heparin or EDTA) used for the collection of blood does not influence viral replication in cell cultures from whole blood; 7) viral isolation from HWB is highly sensitive; amounts so small as five microliters of whole blood are sufficient, in some cases, to obtain viral replication in cell cultures; 8) the minimal dose of HWB sufficient to infect cell cultures (HWB M.D.I.) varied among different patients. Although this work failed to establish a correlation between this parameter and the clinical and immunological status of patients, it is conceivable that HWB M.D.I. could give information about viral load in blood and have a prognostic significance; 9) the HWB M.D.I. rise in patients treated with Zidovudine, suggesting that this method could be employed in the virological evaluation of trials with antiretroviral drugs.
Oligomeric Structures Required for Complement Activation of Serum Mannan- Binding Proteins (1995)

Serum mannan-binding protein (S-MBP) comprises a series of homooligomers, and activates complement when it binds to appropriate carbohydrate ligands. In this study, the structural requirements necessary for complement activation were examined for rat, rabbit, and human S-MBPs. On SDS-PAGE under non-reducing conditions, the S-MBPs gave three major bands: large, middle, and small oligomers. Since three subunits (23-25 kDa) form a triple helix (the base structural unit) at the collagen-like domain within the S-MBP molecule, it was estimated that human and rabbit S-MBPs comprise a mixture of pentamers, tetramers, and trimers of the respective structural units. In contrast, rat S-MBP is composed of tetramers, trimers, and dimers. The large and middle oligomers were almost equal in their ability to activate complement, whereas the small oligomers had very low or no activity. Upon digestion with bacterial collagenase, the large and small oligomers were degraded almost completely. In contrast, the middle oligomers remained largely intact, and the surviving middle oligomers retained complete ability to activate complement. The degraded product, trimers of the carbohydrate recognition domain (CRD), did not show any complement activating activity. These data indicate that not only the structural integrity of the S-MBP collagen-like domain and CRD, but also a unique conformational structure present in the middle oligomers are critically important for carbohydrate-mediated complement activation.
Optical Feedback Interferometry (2006)

This chapter presents an overview of the self-mixing effect in lasers for sensing purposes. The basic theory of the self-mixing effect is presented for a weak feedback. The influence of a moderate and a strong feedback are then discussed before examining some specific cases:\n• multiple optical feedback due to an asymmetric external\ncavity\n• multiple mode lasing by laser diode\n• influence of the speckle effect on self-mixing interferometry\nThe main representative sensing applications are then presented and discussed including displacement, velocity, profile, vibration measurements and correlated applications\nlike measurements for medicine, sound reproduction, modal\nanalysis, angle measurements, 3-D vision or even massmarket\nmobile telephones.
Interrogation of the Plasma Proteome with Differential Scanning Calorimetry (2007)

Human plasma is a complex fluid that contains more than 3000 individual proteins and peptides in quantities ranging from nanograms to tens of grams per liter (1)(2). The plasma proteome and peptidome(3) hold great promise for disease diagnosis and therapeutic monitoring(4)(5). In recent years proteomics has focused primarily on analysis of low-abundance proteins by use of high-resolution methods such as 2-dimensional electrophoresis(6) and mass spectrometry(7). These methods have identified changes in the composition of low-abundance proteins and peptides in plasma that correlate with particular diseases. Typically no single protein emerges from such analyses as a wholly reliable biomarker. Instead changes in the pattern of proteins and peptides often serve as the best diagnostic indicator for a particular disease. In addition, many components of the peptidome were found to be complexed with more abundant serum proteins, especially human serum albumin and immunoglobulins. These findings led to the concept of the “interactome”(8).

Currently, the routine clinical laboratory procedures that are used to assess major components of the proteome include protein electrophoresis (PE) and immunofixation electrophoresis. Modern differential scanning calorimetry (DSC) provides a direct means for detecting what is perhaps the most fundamental property of biochemical reactions, heat changes, and can reliably measure heat changes of 0.1 μcal. In a typical DSC experiment, an aqueous solution of protein is heated at a constant rate in the sample cell alongside an identical reference cell that contains only the solvent (buffer). Thermal balance between the sample and reference cells is maintained by electrically powered feedback heaters. Any chemical process in the sample cell that absorbs or releases heat results in a thermal imbalance. The power applied by the feedback heaters provides a direct measure of heat capacity changes accompanying thermally induced denaturation and dissociation reactions …
Binding of NF-Y Transcription Factor to One of the Cis-elements in the Myeloperoxidase Gene Promoter That Responds to Granulocyte Colony-stimulating Factor (1997)

The expression of the myeloperoxidase (MPO) gene is restricted to cells of the myeloid cell lineage and is induced by granulocyte colony-stimulating factor (G-CSF). In this study, a series of deletion mutations was introduced in the promoter of the human MPO gene, which was then fused to the chloramphenicol acetyltransferase gene. The G-CSF-induced promoter activity was examined in mouse myeloid precursor FDC-P1 transformants that constitutively express the G-CSF receptor. A G-CSF-responsive element (GRE) in the MPO gene was found approximately 800 base pairs upstream from the transcription initiation site. When the 5'-flanking region of the human MPO gene contained this element, it yielded promoter activity in cells cultured with G-CSF but not in cells cultured with interleukin 3. Gel shift assays with the element showed that a specific nuclear factor(s) (NF/G-CSF) binds to the element. The NF/G-CSF was purified by affinity chromatography using an oligonucleotide of GRE. Protein sequence analysis of the purified NF/G-CSF indicated that NF/G-CSF is a ubiquitous transcription factor, NF-Y, which is composed of three subunits. The recombinant NF-Y was then shown to bind to GRE in a combination of the three subunits.
An experimental investigation of creep and viscoelastic properties using depth-sensing indentation techniques (1997)

Broad band, quasi-static and frequency specific dynamic techniques adapted to depth-sensing indentation testing have been utilized to measure both time dependent plasticity (creep) at both room and elevated temperatures as well as time dependent elasticity (viscoelasticity) at room temperature. Indentation Creep Using a variety of depth-sensing indentation techniques at both room and elevated temperatures, the dependency of the indentation hardness on the variables of indentation strain rate (stress exponent for creep, n) and temperature (apparent activation energy for creep, Q), and the existence of a steady state behavior in an indentation creep test with a Berkovich indenter were investigated. The indentation creep response of five materials, Pb-65 at% In (at RT), high purity indium (from RT to 75°C), high purity aluminum (from RT to 250°C), a vapor deposited amorphous alumina f ilm (at RT), and single crystal alumina (sapphire) (at RT), was measured. It was shown for the first time that the indentation strain rate, def ined as it/h, could be held constant during an experiment using a Berkovich indenter by controlling the loading rate such that the loading rate divided by the load, Pip, remained constant. This technique yields the most unambiguous determination of the stress exponent for creep and seems to most closely approximate the steady state results fr om uniaxial testing. The results from the constant P / p experiments were compared to the results from conventional indentation creep experiments where the load is ramped on at a high rate and then held constant for a period of time. It was shown that the transition from the loading segment to hold
The osteoporosis-pseudoglioma syndrome locus is on chromosome 11q (1994)

The osteoporosis-pseudoglioma syndrome (OPS), is a rare autosomal recessive disorder characterized by severe osteoporosis with multiple fractures and blindness, both occurring in childhood. The precise pathogenic mechanism for OPS is unknown. Insights into its cause may be useful towards understanding the pathophysiology of more common disorders, such as senile osteoporosis, persistent hyperplasia of the primary vitreous, and retinopathy of prematurity, whose features have some similarity with OPS. As a first step in determining the cause of OPS, we have mapped the locus of the disorder to chromosome 11q. This was accomplished by assuming genetic homogeneity and by performing linkage analysis with homozygosity mapping in 18 individuals (7 patients, 5 unaffected siblings, and 7 parents) from 3 different consanguineous kindreds. Since the condition could be caused by an abnormal extracellular matrix component, we began by testing several candidate genes (e.g., COL1A1, COL1A2, Osteopontin, Osteonectin) distributed on 12 different chromosomes. We also initiated a systematic search at 20 cM intervals with highly polymorphic simple sequence tandem repeats. Linkage and homozygosity was detected with marker D11S913 (LOD score 3.8 at {theta} = 0). Additional markers are being tested to confirm this observation. The fibroblast collagenase, fibronectin-like-2 gene and rod outer segment protein-1 (ROMmore » 1) also map to chromosome 11q and are candidate genes.« less
Structures of a minimal human CFTR first nucleotide-binding domain as a monomer, head-to-tail homodimer, and pathogenic mutant (2010)

Upon removal of the regulatory insert (RI), the first nucleotide binding domain (NBD1) of human cystic fibrosis transmembrane conductance regulator (CFTR) can be heterologously expressed and purified in a form that remains stable without solubilizing mutations, stabilizing agents or the regulatory extension (RE). This protein, NBD1 387-646(Delta405-436), crystallizes as a homodimer with a head-to-tail association equivalent to the active conformation observed for NBDs from symmetric ATP transporters. The 1.7-A resolution X-ray structure shows how ATP occupies the signature LSGGQ half-site in CFTR NBD1. The DeltaF508 version of this protein also crystallizes as a homodimer and differs from the wild-type structure only in the vicinity of the disease-causing F508 deletion. A slightly longer construct crystallizes as a monomer. Comparisons of the homodimer structure with this and previously published monomeric structures show that the main effect of ATP binding at the signature site is to order the residues immediately preceding the signature sequence, residues 542-547, in a conformation compatible with nucleotide binding. These residues likely interact with a transmembrane domain intracellular loop in the full-length CFTR channel. The experiments described here show that removing the RI from NBD1 converts it into a well-behaved protein amenable to biophysical studies yielding deeper insights into CFTR function.
Developments in the Field of Bioorthogonal Bond Forming Reactions—Past and Present Trends (2014)

In response to the ever increasing need of chemical biology for new tools, a wide variety of new, highly selective reactions have been described. Herein we report a summary of recent developments and the historical background on bioorthogonal ligation reactions.
Synthesis of load-independent DC drive system (2003)

A control method and associated circuit for achieving complete load independence in DC drive systems are presented. The system transfer function independent of load is realized while stability and dynamics of the system are controlled by an additional voltage loop. A DC drive system is simulated and evaluated in terms of its load invariance and stability using a synthesis method whose algorithm is shown.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
An Estimate of the Glass Transition Temperature of Transition Metals Alloyed with Metalloids (1979)

Article An Estimate of the Glass Transition Temperature of Transition Metals Alloyed with Metalloids was published on September 1, 1979 in the journal International Journal of Materials Research (volume 70, issue 9).
The construction and use of an X-ray goniometer. Crystal-structure of glyoxaline compounds (With Plate I.) (1926)

In ordinary circumstances crystal-angles are measured by means of light reflected from the crystal-faces. In the partial or complete absence of faces the determination of axial ratios and angles may be impossible. In a recent investigation of certain derivatives of glyoxaline, an example of this was found. It was, in fact, the substance glyoxaline itself, which always occurred as long prisms having four faces in the prism-zone; the ends of the prisms were jagged and rough, and no siglls of optically reflecting-planes could be found on these ends. In such a case, X-ray methods of investigation are now available, and the problem in question is the determination of the dimensions of the unit-cell, not the complete X-ray inveatigation of the structure.
Correlation between quaternary structure and ligand dissociation kinetics for fully liganded hemoglobin (1975)

The quaternary structures of fully liganded adult hemoglobin and hemoglobin Kansas (alpha2beta2 102 Asn-thr) bound by carbon monoxide or nitric oxide were spectroscopically characterized using high-resolution nuclear magnetic resonance (NMR) and ultraviolet circular dichroism (CD). The spectral markers used for the quarternary transition were the line in the NMR spectrum in H2O-14 ppm downfield from 2,2-dimethyl-2-silapentane-5-sulfonate and the negative peak at 285 nm in the ultraviolet CD spectrum. In the nitrosyl derivatives, these two structural markers were compared with the electron paramagnetic resonance (EPR) spectrum at room temperature for the purpose of correlating structural changes in the protein with changes at the heme...
Holographic Dielectric Grating: Theory and Practice (1970)

Lossy dielectric gratings have been analyzed using a Raman-Nath formalism modified to incorporate losses. Four second-order coupled wave equations are retained for computation of the zero, first- and second-order diffracted beams for a multitude of practical cases. Significant differences are found in comparison with computations in which only two coupled waves are retained. The entire range of losses and thicknesses encountered for holograms in film emulsions has been studied using this unified approach. Graphs have been prepared to show the efficiency, i.e., power diffracted in the first-order relative to the total incident power, vs the index modulation for a wide range of thicknesses and losses. At a given thickness, optimum frequency requires a specific exposure. The efficiency for an optimum exposure is plotted vs the loss factor with thickness as a parameter. New experimental data are presented for bleached gratings in which several diffracted orders are measured and compared to our theory for a wide range of index modulation and loss factors.
Adaptive Beamforming Applied to Medical Ultrasound Imaging (2007)

We have applied the minimum variance (MV) adaptive beamformer to medical ultrasound imaging and shown significant improvement in image quality compared to delay-and-sum (DAS). We demonstrate reduced mainlobe width and suppression of sidelobes on both simulated and experimental RF data of closely spaced wire targets, which gives potential contrast and resolution enhancement in medical images. The method is applied to experimental RF data from a heart phantom, in which we show increased resolution and improved definition of the ventricular walls. A potential weakness of adaptive beamformers is sensitivity to errors in the assumed wavefield parameters. We look at two ways to increase robustness of the proposed method; spatial smoothing and diagonal loading. We show that both are controlled by a single parameter that can move the performance from that of a MV beamformer to that of a DAS beamformer. We evaluate the sensitivity to velocity errors and show that reliable amplitude estimates are achieved while the mainlobe width and sidelobe levels are still significantly lower than for the conventional beamformer.
Precision welding cuts downtime at Grand Coulee Dam (1997)

The three large 700-MW generators at Grand Coulee Dam--originally built and installed by Canadian General Electric in the late 1970s--are being upgraded using precision welding techniques and leading edge installation technology. These generators suffered from numerous water leaks at and around the bar water connections, resulting in a significant number of forced repair outages that were increasing in frequency. The US Bureau of Reclamation, in conjunction with the Bonneville Power Administration, decided to overhaul these machines. The design from Siemens Power Corp. provided state-of-the-art materials and included a rating increase from 700 to 805 MW, which would make these three machines the highest output single-unit hydrogenerators in the world. The upgrade was to be accomplished with only the replacement of the stator components; there would be no changes to the rotating element. The cost for all three machines is approximately $27.5 million. This project is described in this paper.
Static and Completion Analysis for Planning Knowledge Base Development and Verification (1996)

chien @ aig.jpl.nasa.gov A key obstacle hampering fielding of AI planning applications is the considerable expense of developing, verifying, updating, and maintaining the planning knowledge base (KB). Planning systems must be able to compare favorably in terms of software lifecycle costs to other means of automation such as scripts or rule-based expert systems. Consequently, in order to field real systems, planning practitioners must be able to provide: 1. tools to allow domain experts to create and debug their own planning knowledge bases; 2. tools for software verification, validation, and testing; and 3. tools to facilitate updates and maintenance of the planning knowledge base. This paper describes two types of tools for planning knowledge base development: static KB analysis techniques to detect certain classes of syntactic errors in a planning knowledge base; and completion analysis techniques, to interactively debug the planning knowledge base. We describe these knowledge development tools and describe empirical results documenting the usefulness of these tools. 1.
Mining Privilege Escalation Paths for Network Vulnerability Analysis (2007)

Computer security is an important issue in our society. In order to prevent computer systems and networks from attacks, we should try to find flaws in these systems and evaluate them. Generally researchers and red teams use attack graphs to perform network vulnerability analysis, which tend to suffer scalability problems. In this paper we put forward a mining method to generate privilege escalation paths in networks. With these privilege escalation paths we create net privilege graphs and use them for network vulnerability analysis. Experiments show that our approach is valid and scalable to find the possible vulnerabilities exploitation ways in networks.
Conjugated linoleic acid stimulates an anti-tumorigenic protein NAG-1 in an isomer specific manner (2005)

Conjugated linoleic acids (CLAs), naturally occurring fatty acids in ruminant food products, have anti-tumorigenic and pro-apoptotic properties in animal as well as in vitro models of cancer. However, the cellular mechanism has not been fully understood. NAG-1 (non-steroidal anti-inflammatory drug-activated gene-1) is induced by several dietary compounds and belongs to a TGF-beta superfamily gene associated with pro-apoptotic and anti-tumorigenic activities. The present study was performed to elucidate the molecular mechanism by which CLA stimulates anti-tumorigenic activity in human colorectal cancer (CRC) cells. The trans-10, cis-12-CLA (t10,c12-CLA) repressed cell proliferation and induced apoptosis, whereas linoleic acid or c9,t11-CLA showed no effect on cell proliferation and apoptosis. We also found that t10,c12-CLA induced the expression of a pro-apoptotic gene, NAG-1, in human CRC cells. Inhibition of NAG-1 expression by small interference RNA (siRNA) results in repression of t10,c12-CLA-induced apoptosis. Microarray analysis using t10,c12-CLA-treated HCT-116 cells revealed that activating transcription factor 3 (ATF3) was induced and its expression was confirmed by western analysis. The t10,c12-CLA treatment followed by the overexpression of ATF3 increased NAG-1 promoter activity in HCT-116 cells. We further provide the evidence that t10,c12-CLA inhibited the phosphorylation of AKT and the blockage of GSK-3 by siRNA abolished t10,c12-CLA-induced ATF3 and NAG-1 expression. The current study demonstrates that t10,c12-CLA stimulates ATF3/NAG-1 expression and subsequently induces apoptosis in an isomer specific manner. These effects may be through inhibition of AKT/GSK-3beta pathway in human CRC cells.