gebhart/patrepeval huggingface dataset:
Electrical charge of the antigen determines intraarticular antigen handling and chronicity of arthritis in mice. (1984)

We studied the influence of antigenic charge on the handling of intraarticular antigen by the joint and on the ability of the antigen to induce chronic arthritis. Three different antigens were used: anionic native bovine serum albumin (BSA), and charge modified BSA made cationic (pI 8.5) either by methylation (mBSA), or amidation (aBSA). 125I-labeled antigen was injected into the knee joints of nonimmune mice and of mice immunized with antigen in Freund's complete adjuvant. Intraarticular antigen retention of the cationic antigens mBSA and aBSA was significantly increased compared with native BSA, both in immune and non-immune mice. In vitro studies indicated the electrostatic character of the binding of the cationic antigens to joint tissues and confirmed the large difference in antigen retention of the antigens found in vivo. A 100-fold amount of cationic antigen could be bound to non-cartilaginous collagenous tissue of the joint compared with antibody-mediated trapping of native BSA, and for hyaline articular cartilage, this difference was even greater. In immunized mice, chronic arthritis only developed after intraarticular injection of the cationic antigens. This phenomenon was apparently related to increased retention of mBSA and aBSA compared with BSA, since delayed hypersensitivity and humoral immunity were comparable for the three antigens used. Our data indicate that antigenic charge is an important determinant of antigen handling by the joint and, in addition, support the concept that the development of chronic arthritis depends on the amount of antigen retained in the joint.
Plasma-Enhanced ALD of Platinum with O<sub>2</sub>, N<sub>2</sub>and NH<sub>3</sub>Plasmas (2012)

Platinum thin films were grown by plasma-enhanced atomic layer deposition (PEALD) using (methylcyclopentadienyl)-trimethylplatinum (MeCpPtMe3) as precursor and respectively an oxygen, nitrogen and ammonia plasma as reactant. For each process the film thickness was found to be linearly dependent on the number of reaction cycles. Saturation curves and temperature windows were defined and growth rates of 0.45 Å cycle−1, 0.30 Å cycle−1 and 0.40 Å cycle−1 were obtained for the oxygen, nitrogen and ammonia process respectively. All the films were metallic platinum, crystalline, uniform and closed, with low surface roughness and low impurity levels. At a pressure of 1 × 10−3 mbar, nucleation on SiO2 was remarkably faster with the NH3 and N2 processes than with the O2 process. In-situ OES and MS measurements showed a fundamental difference between the NH3 and N2 processes and the O2 process. Based on these measurements we propose a reaction mechanism for the N2 and NH3 PEALD processes where nitrogen will unstably adsorb on the substrate during the plasma pulse and be used during the subsequent precursor pulse to remove part of the precursor ligands.
Epidemiology of dialysis induced hypotension. (1981)

Factors associated with an excessive rate of dialysis induced symptomatic hypotension (SH) were analysed in a population of 1110 patients treated by chronic haemodialysis in 32 French dialysis centres. Significant risk factors for SH were female sex, diabetic nephropathy as the primary renal disease, two weekly dialysis schedule instead of three, use of Coil type dialysers instead of parallel-flow or hollow-fibre dialysers, low dialysate osmolarity, low dialysate K, high body weight subtraction during sessions, low predialysis plasma proteins, high predialysis blood urea, and low nerve conduction velocity. On a statistical basis, the results show the predominance of volume depletion over dialysate composition or neuropathy.
Pore cross-talk in colloidal filtration (2017)

Blockage of pores by particles is found in many processes, including filtration and oil extraction. We present filtration experiments through a linear array of ten channels with one dimension which is sub-micron, through which a dilute dispersion of Brownian polystyrene spheres flows under the action of a fixed pressure drop. The growth rate of a clog formed by particles at a pore entrance systematically increases with the number of already saturated (entirely clogged) pores, indicating that there is an interaction or "cross-talk" between the pores. This observation is interpreted based on a phenomenological model, stating that a diffusive redistribution of particles occurs along the membrane, from clogged to free pores. This one-dimensional model could be extended to two-dimensional membranes.
Unexplained Persistent Lymphadenopathy in Homosexual Men and the Acquired Immune Deficiency Syndrome (1985)

Ninety-three homosexual men with persistent lymphadenopathy were followed at the Memorial Sloan-Kettering Cancer Center for a mean period of 20.8 months. Histories and serologic evidence of a number of previous infections were common, but the lymphadenopathy was not due to recognizable infections or neoplastic disease. Leukopenia, lymphopenia, granulocytopenia, monocytopenia, decreased ratios of T-helper to T-suppressor cells, decreased natural killer cell activity and increased serum immunoglobulin concentrations were common. Lymph node biopsies showed reactive hyperplasia without any unique histopathologic features. Antibody to the human T-lymphotropic virus-III (HTLV-III or LAV), a newly described retrovirus believed to be the etiologic agent of the acquired immune deficiency syndrome (AIDS), was detected in 91.4%. Over a 3-year period, 11 cases of AIDS were recognized in these patients: Kaposi's sarcoma developed in 7 and opportunistic infections in 4. The lymphadenopathy resolved in six patients and the others remained unchanged. Although most of these patients are asymptomatic and remain well, the risk of AIDS in this group of men was higher than in other groups of homosexual men in New York.
Designing for Multi-Tasking Environments: Multiple Monitors vs. Multiple Windows (1997)

Complex semi-automated processes, from aircraft flight management to command and control, typically require a large number of displays. Multiple, overlapping windows provide one method of coping with multiple displays. Multiple monitors provide another method. With the advent of good flat panel displays for real monitors and with the advent of Head Mounted Display (HMD) technology for creating virtual monitors, multiple monitors become a promising possibility even in cramped environments like cockpits and shipboard control rooms. To determine the true value of multiple monitors (real or virtual) we must understand their capabilities and integration with human cognitive and perceptual abilities, then design for their ultimate use. In the first experiment, we found that accessing information distributed across an array of monitors was at least as effective as locating and managing windows on a single monitor. In the second experiment, we found that a task that requires only infrequent monitoring can be moved to a secondary, peripheral monitor without disrupting performance on that or any other concurrent task. In future experiments, we plan to compare these results to results from HMD-based systems.
ChemInform Abstract: SUBSTITUENTENEFFEKTE AUF (1)H‐NMR‐SPEKTREN VON AROMATEN 6. MITT. ((2)H6)BENZOL‐INDUZIERTE LOESUNGSMITTEL‐VERSCHIEBUNGEN FUER 4,4′‐DISUBSTITUIERTE 2,2′,6,6′‐TETRAMETHYL‐BIPHENYLE UND VERWANDTE VERBINDUNGEN (1970)

Abstract Anhand der 1 H‐NMR‐Spektren der Aromaten (I)‐(III) in Tetrachlorkohlenstoff und Perdeuterobenzol werden die Differenzen Ader chemischen Verschiebungen bestimmt.
Robust recognition of zinc binding sites in proteins (2007)

Metals play a variety of roles in biological processes, and hence their presence in a protein structure can yield vital functional information. Because the residues that coordinate a metal often undergo conformational changes upon binding, detection of binding sites based on simple geometric criteria in proteins without bound metal is difficult. However, aspects of the physicochemical environment around a metal binding site are often conserved even when this structural rearrangement occurs. We have developed a Bayesian classifier using known zinc binding sites as positive training examples and nonmetal binding regions that nonetheless contain residues frequently observed in zinc sites as negative training examples. In order to allow variation in the exact positions of atoms, we average a variety of biochemical and biophysical properties in six concentric spherical shells around the site of interest. At a specificity of 99.8%, this method achieves 75.5% sensitivity in unbound proteins at a positive predictive value of 73.6%. We also test its accuracy on predicted protein structures obtained by homology modeling using templates with 30%-50% sequence identity to the target sequences. At a specificity of 99.8%, we correctly identify at least one zinc binding site in 65.5% of modeled proteins. Thus, in many cases, our model is accurate enough to identify metal binding sites in proteins of unknown structure for which no high sequence identity homologs of known structure exist. Both the source code and a Web interface are available to the public at http://feature.stanford.edu/metals.
Question Answering Using Word Associations (2009)

Text mining systems such as categorizers and query retrievers of the first generation were largely hinged on word level statistics and provided a wonderful first-cut approach. However systems based on simple word-level statistics quickly saturate in performance, despite the best data mining and machine learning algorithms. This problem can be traced to the fact that, typically, naive, word-based feature representations are used in text applications, which prove insufficient in bridging two types of chasms within and across documents, viz. lexical chasm and syntactic chasm . The latest wave in text mining technology has been marked by research that will make extraction of subtleties from the underlying meaning of text, a possibility. In the following two chapters, we pose the problem of underlying meaning extraction from text documents, coupled with world knowledge, as a problem of bridging the chasms by exploiting associations between entities. The entities are words or word collocations from documents. We utilize two types of entity associations, viz. paradigmatic (PA) and syntagmatic (SA). We present first-tier algorithms that use these two word associations in bridging the syntactic and lexical chasms. We also propose second-tier algorithms in two sample applications, viz., question answering and text classification which use the first-tier algorithms. Our contribution lies in the specific methods we introduce for exploiting entity association information present in WordNet, dictionaries, corpora and parse trees for improved performance in text mining applications.
Activation of nuclear factor-κ B is linked to resistance to neoadjuvant chemotherapy in breast cancer patients (2006)

The nuclear factor (NF)-kappaB system is a promising anticancer target due to its role in oncogenesis and chemoresistance in preclinical models. To provide evidence in a clinical setting on the role of NF-kappaB in breast cancer, we aimed to study the value of basal NF-kappaB/p65 in predicting resistance to neoadjuvant chemotherapy, and to characterise the pharmacodynamic changes in NF-kappaB/p65 expression following chemotherapy in patients with locally advanced breast cancer. Pre- and post-chemotherapy tumour specimens from 51 breast cancer patients treated with anthracycline- and/or taxane-containing neoadjuvant chemotherapy were assayed by immunohistochemistry for NF-kappaB/p65 subcellular expression. We studied NF-kappaB/p65, a well-characterised member of the NF-kappaB family that undergoes nuclear translocation when NF-kappaB is activated. Activation of NF-kappaB (i.e. nuclear NF-kappaB/p65 staining in pre-therapy specimens) was linked to chemoresistance. Patients with NF-kappaB/p65 nuclear staining in pre-treatment samples had a 20% clinical response rate, while patients with undetected nuclear staining had a 91% response rate to chemotherapy (P = 0.002). Notably, four patients achieved a complete histological response and none of them had pre-treatment NF-kappaB/p65 nuclear staining. Moreover, the number of patients with NF-kappaB/p65 activation increased after chemotherapy exposure. It is concluded that NF-kappaB/p65 activation assayed by immunohistochemistry is a predictive factor of resistance to neoadjuvant chemotherapy in breast cancer patients. Moreover, NF-kappaB activation was inducible following chemotherapy in a proportion of breast cancer patients. These novel clinical findings strengthen the rationale for the use of NF-kappaB inhibitors to prevent or overcome chemoresistance in breast cancer.
New method for determining emitter resistance (1992)

A new method is described to determine the emitter resistance of bipolar transistors. With this method the emitter resistance can directly be extracted from the Gummel plot. It is based on the fact that the base current is zero at a certain collector-base voltage due to impact ionisation.
The value of forecasting BYDV in autumn sown cereals (2000)

Crop Food Research has developed a model to forecast the occurrence of severe barley yellow dwarf virus (BYDV) incidence in autumnsown wheat crops in Canterbury based on alate aphid flights This information is potentially valuable to growers in Canterbury who can modify their inputs each year according to the risk of BYDV This paper uses expected gross margins to estimate the financial benefit of the Crop Food Research BYDV Forecast Service to arable growers in Canterbury Results suggest that the value of the BYDV Forecast Service is positive but varies greatly depending upon forecast accuracy and adoption rate
β-Scission of C-3 (β-Carbon) Alkoxyl Radicals on Peptides and Proteins:  A Novel Pathway Which Results in the Formation of α-Carbon Radicals and the Loss of Amino Acid Side Chains (2000)

Exposure of proteins to radicals in the presence of O(2) brings about multiple changes in the target molecules. These alterations include oxidation of side chains, fragmentation, cross-linking, changes in hydrophobicity and conformation, altered susceptibility to proteolytic enzymes, and formation of new reactive groups, including hydroperoxides. These processes can result in the loss of structural or enzymatic activity. Backbone fragmentation is known to occur via a number of mechanisms, most of which involve hydrogen abstraction from the alpha-carbon site on the backbone. In this study, we demonstrate that initial attack at a side chain site, the beta-position (C-3), can give rise to formation of alpha-carbon radicals, and hence backbone cleavage, via the formation and subsequent beta-scission of C-3 alkoxyl radicals. This beta-scission reaction is rapid (k estimated to be >10(7) s(-)(1)) even with primary alkoxyl radicals derived from Ala residues, and occurs when the alkoxyl radicals are generated from a variety of precursors, including hydroperoxides and nitrate esters. These reactions release the former side chain as a reactive aldehyde or ketone; thus, Ala peptides release high yields of methanal (formaldehyde). This product has been quantified with a number of oxidized peptides and proteins, and can account for up to 64% of the initial attacking radicals with some Ala peptides. When quantified together with the hydroperoxide precursors, these species account for up to 80% of the initial radicals, confirming that this is a major process. Methanal causes cell toxicity and DNA damage and is an animal carcinogen and a genotoxic agent in human cells. Thus, the formation and subsequent reaction of alkoxyl radicals formed at the C-3 position on aliphatic amino acid side chains on peptides and proteins can give rise to both backbone fragmentation and the release of further reactive species which can cause cell toxicity and mutagenicity.
High-resolution two-photon spectroscopy of rubidium within a confined geometry (2013)

We present two-photon spectroscopy of a thermal rubidium vapor confined to the hollow core of a photonic-crystal fiber. Linewidths as narrow as 10 MHz were observed on the $5{S}_{1/2}\ensuremath{\rightarrow}5{D}_{5/2}$ transition enabling the hyperfine splitting of the excited state to be resolved. Very strong nonlinear absorption ($>90%$) was observed, with substantial absorption maintained over large detunings (9 GHz) from an intermediate state. These attributes make this system ideal for many frequency metrology and quantum optics applications.
Butyrylcholinesterase: Overview, Structure, and Function (2011)

This chapter contains sections titled: Introduction Name History Why was Butyrylcholinesterase Rather than Acetylcholinesterase Chosen as a Therapeutic? Function of Butyrylcholinesterase Deduced from Studies In People Function of Butyrylcholinesterase Deduced from the Knockout Mouse Function of Butyrylcholinesterase Deduced from the G117H Transgenic Mouse Function of Butyrylcholinesterase Deduced from the AChE Knockout Mouse Function of Butyrylcholinesterase Deduced from Tissue-Specific Deletions of Acetylcholinesterase and Anchor Proteins Function of Butyrylcholinesterase Deduced from Protection Experiments with Purified Butyrylcholinesterase Butyrylcholinesterase in Human Tissues Summary: Functions of Butyrylcholinesterase Structure of Human Butyrylcholinesterase Conclusions and Future Directions Acknowledgments References
[Studies on the persistence of Clostridium botulinum on a cattle farm (author's transl)]. (1979)

In the winter of 1978-1979, the presence of Clostridium botulinum was studied on a cattle farm, on which botulism caused by feeding the animals contaminated brewers' grains occurred in 1977. Cl. botulinum type B, the cause of mortality among cattle at the time, was detected in grass silage prepared in 1978. This organism was not detectable in a grass silage pit dating from 1977 and made prior to the outbreak of botulism. Investigations showed that proteolytic types of C. botulinum having grass as the substrate may produce large amounts of toxin. The production of toxin in grass silage pits may, however, be prevented by a low pH in conjunction with low water activity. The present study showed that the faeces of cattle were also contaminated with Cl. botulinum type B. The degree of infection ran parallel with the degree of contamination of silage feeding in these cases.
Influence of a Locally Applied Electro-Rheological Fluid Layer on Vibration of a Simple Cantilever Beam (1993)

This experimental work is concerned with the vibration characteristics of a canti lever beam locally linked by an electro-rheological fluid layer to ground. Such a novel vibration con trol strategy can drastically change the vibration characteristics of the beam system, owing to the mechanism that the locally applied ER fluid layer serves as a complex spring and thus change the stiffness matrix, or the structural configuration, of the original beam system under the electric field. It is found that the vibration characteristics of the cantilever beam with the locally applied ER fluid layer treatment is more sensitive to the electric field than a sandwich beam. The influence of the non linear deformation of the ER fluid due to the presence of the yield stress on the vibration of the canti lever beam is also investigated.
Biochemical parameters of neoplasis. I. "Priming" activity of deoxyribonucleic acid from normal and neoplastic human tissues in a deoxyribonucleic acid polymerase system. (1965)

Summary DNA 2 was isolated from surgical biopsies of human neoplastic tissue and from normal tissue of the same organs in the same patients. In a mammalian DNA polymerase system that depends on the presence of a DNA “primer,” DNA from neoplastic tissue appeared to be a more efficient primer than either DNA from corresponding normal tissue or a standard calf thymus DNA preparation used for comparison in all experiments.
1047. BXD Recombinant Inbred Mice Represent a Novel Immune Response Model to AAV-F.IX (2004)

The immune response to adeno-associated virus vector (AAV) gene therapy using the coagulation factor IX transgene (AAV-F.IX) can lead to either elimination of the vector or production of inhibitor antibodies to the expressed transgene. Interestingly not all individuals treated with F.IX or animal models of AAV-FIX develop such an immune response. AAV-F.IX gene therapy can also elicit a tolerance response, or no immune response to AAV and/or the F.IX transgene. We hypothesize that the combined effects of genetic diversity and multiple redundant pathways lead to a diverse antibody response to AAV and FIX. This was tested using C57BL/6 xDBA/2 (BXD) recombinant inbred (RI) strains derived from high responder DBA/2 and low responder C57BL/6 parental mice. To determine the cellular and genetic basis for this response, we analyzed strains of C57BL/6 X DBA/2 (BXD) RI mice derived from high responder, D2, and low responder, B6, parental mice and have observed three response patterns to AAV-F.IX. An immunogenic response was associated with high expression of CD40 and BAFF receptor (BAFF-R) on B cells and CD40 ligand (CD40L) on T cells. This occurred in BXD strains 12, 28, 31, and 33, as well as in D2 strain. A tolerogenic response was associated with development of a CD4+CD25+ T regulatory population. This population was strongly evident in BXD strains 6 and 25 at days 18 and 40, after AAV-F.IX. In certain strains, including BXD strains 8, 19, 22, and 23, exhibited no immune response, which was associated with low CD40 and low BAFF-R on B cells. Genetic linkage analysis revealed a highly significant locus at D12Mit150 (59 cM, LRS=42.1), near the Igh (59 cM) and CD40 binding protein (Traf3) loci (55 cM), and a suggestive locus at D17Mit36 (23 cM, LRS=18.1), near the MHC locus. These results indicate that the antibody response to AAV-F.IX exhibited: (i) a predictable strain-dependent pattern in BXD RI strains; (ii) a correlation with expression of CD40-CD40L, BAFF-BAFF-R, and % of CD4+CD25+ T cells; and (iii) significant linkage to a locus on Chr 12 near the Traf3/Igh locus, and on Chr 17 near the MHC locus.
<title>Vision-based obstacle detection and path planning for planetary rovers</title> (1999)

NASA's next-generation Mars rovers are capable of capturing panoramic stereo imagery of their surroundings. Three- dimensional terrain maps can be derived from such imagery through stereo image correlation. While 3-D data is inherently valuable for planning a path through local terrain, obstacle detection is not fully reliable due to anomalies and noise in the range data. We present an obstacle-detection approach that first identifies potential obstacles based on color-contrast in the monocular imagery and then uses the 3-D data to project all detected obstacles into a 2-D overhead-view obstacle map where noise originating from the 3-D data is easily removed. We also developed a specialized version of the A* search algorithm that produces optimally efficient paths through the obstacle map. These paths are of similar quality as those generated by the traditional A* , at a fraction of the computational cost. Performance gains by an order of magnitude are accomplished by a two-stage approach that leverages the specificity of obstacle shape on Mars. The first stage uses depth-first A* to quickly generate a somewhat sub-optimal path through the obstacle map. The following refinement stage efficiently eliminates all extraneous way-points. Our implementation of these algorithms is being integrated into NASA's award-winning Web-Interface for Telescience.