gebhart/patrepeval huggingface dataset:
The Design of Rate-Compatible LDPC Codes for IR-HARQ Systems over Erasure Channels (2010)

Application-layer forward error correcting (AL-FEC) codes, providing error protection across blocks of packetized data, are becoming increasingly important in emerging networking applications. In this paper, we investigate AL-FEC solutions based on rate- compatible low-density parity-check (RC LDPC) codes, as they may offer excellent performance with low system complexity. Recent studies on RC LDPC codes are focused on physical layer incremental redundancy hybrid automatic-repeat-request (IR-HARQ) systems and typical wireless channel models. The focus of our study is RC LDPC code design as an AL-FEC solution in packet-level IR-HARQ systems assuming erasure channels between the source and the destination(s). We propose novel design methods for RC LDPC codes over erasure channels motivated by the dependance of finite-length LDPC code performance on the size of the smallest stopping set of its code graph. Simulation experiments demonstrate that the proposed RC LDPC design significantly outperforms the state-of-the-art RC LDPC codes in the error-floor region, and in particular, in the domain of poor channel conditions.
Mechanism of plasmid-mediated quinolone resistance (2002)

Quinolones are potent antibacterial agents that specifically target bacterial DNA gyrase and topoisomerase IV. Widespread use of these agents has contributed to the rise of bacterial quinolone resistance. Previous studies have shown that quinolone resistance arises by mutations in chromosomal genes. Recently, a multiresistance plasmid was discovered that encodes transferable resistance to quinolones. We have cloned the plasmid-quinolone resistance gene, termed qnr, and found it in an integron-like environment upstream from qacE Delta 1 and sulI. The gene product Qnr was a 218-aa protein belonging to the pentapeptide repeat family and shared sequence homology with the immunity protein McbG, which is thought to protect DNA gyrase from the action of microcin B17. Qnr had pentapeptide repeat domains of 11 and 28 tandem copies, separated by a single glycine with a consensus sequence of A/C D/N L/F X X. Because the primary target of quinolones is DNA gyrase in Gram-negative strains, we tested the ability of Qnr to reverse the inhibition of gyrase activity by quinolones. Purified Qnr-His(6) protected Escherichia coli DNA gyrase from inhibition by ciprofloxacin. Gyrase protection was proportional to the concentration of Qnr-His(6) and inversely proportional to the concentration of ciprofloxacin. The protective activity of Qnr-His(6) was lost by boiling the protein and involved neither quinolone inactivation nor independent gyrase activity. Protection of topoisomerase IV, a secondary target of quinolone action in E. coli, was not evident. How Qnr protects DNA gyrase and the prevalence of this resistance mechanism in clinical isolates remains to be determined.
Redox Control of a Ring-Opening Polymerization Catalyst (2011)

The activity of an yttrium alkoxide complex supported by a ferrocene-based ligand was controlled using redox reagents during the ring-opening polymerization of L-lactide. The oxidized complex was characterized by X-ray crystallography and (1)H NMR, XANES, and Mössbauer spectroscopy. Switching in situ between the oxidized and reduced yttrium complexes resulted in a change in the rate of polymerization of L-lactide. Synthesized polymers were analyzed by gel permeation chromatography. Polymerization of trimethylene carbonate was also performed with the reduced and oxidized forms of an indium alkoxide complex. The indium system showed the opposite behavior to that of yttrium, revealing a metal-based dependency on the rate of polymerization.
Mesenteric lymph nodes at the center of immune anatomy (2006)

The surface of the intestinal mucosa is constantly assaulted by food antigens and enormous numbers of commensal microbes and their products, which are sampled by dendritic cells (DCs). Recent work shows that the mesenteric lymph nodes (MLNs) are the key site for tolerance induction to food proteins and that they also act as a firewall to prevent live commensal intestinal bacteria from penetrating the systemic immune system.
Influence of Thermal Processing on the Allergenicity of Peanut Proteins (2005)

Peanuts are one of the most common and severe food allergens. Nevertheless, the occurrence of peanut allergy varies between countries and depends on both the exposure and the way peanuts are consumed. Processing is known to influence the allergenicity of peanut proteins. The aim of this study was to assess the effect of thermal processing on the IgE-binding capacity of whole peanut protein extracts and of the major peanut allergens Ara h 1 and Ara h 2. Whole proteins, Ara h 1, and Ara h 2 were extracted and purified from raw, roasted and boiled peanuts using selective precipitation and multiple chromatographic steps, and were then characterized by electrophoresis and mass spectrometry. The immunoreactivity of whole peanut extracts and purified proteins was analyzed by the enzyme allergosorbent test (EAST) and EAST inhibition using the sera of 37 peanut-allergic patients. The composition of the whole protein extracts was modified after heat processing, especially after boiling. The electrophoretic pattern showed protein bands of low molecular weight that were less marked in boiled than in raw and roasted peanuts. The same low-molecular-weight proteins were found in the cooking water of peanuts. Whole peanut protein extracts obtained after the different processes were all recognized by the IgE of the 37 patients. The IgE-binding capacity of the whole peanut protein extracts prepared from boiled peanuts was 2-fold lower than that of the extracts prepared from raw and roasted peanuts. No significant difference was observed between protein extracts from raw and roasted peanuts. It is noteworthy that the proteins present in the cooking water were also recognized by the IgE of peanut-allergic patients. IgE immunoreactivity of purified Ara h 1 and Ara h 2 prepared from roasted peanuts was higher than that of their counterparts prepared from raw and boiled peanuts. The IgE-binding capacity of purified Ara h 1 and Ara h 2 was altered by heat treatment and in particular was increased by roasting. However, no significant difference in IgE immunoreactivity was observed between whole protein extracts from raw and roasted peanuts. The decrease in allergenicity of boiled peanuts results mainly from a transfer of low-molecular-weight allergens into the water during cooking.
Platelet activation by CD9 monoclonal antibodies is mediated by the F<sub>Cγ</sub>II receptor (1990)

The function of the human cell surface CD9 antigen is not known, yet monoclonal antibodies (mAbs) of the IgG1 subclass in the CD9 cluster induce activation of platelets. Previously it had been shown that this activation pathway is comparable both in kinetics and extent to physiological agonists such as thrombin. Here it is demonstrated that activation with CD9 mAbs depends on interaction of the Fc part of the CD9 antibody molecule with Fc receptors on the platelet surface, since: (i) mAb directed against the Fc receptor totally blocked the platelet response to CD9 mAb; and (ii) F(ab')2 fragments of the CD9 mAb SYB-1 which bound to platelets, as demonstrated by flow cytometry, failed to activate them. Furthermore, platelet activation by CD9 mAb closely paralleled the activation caused by cross-linking Fc receptors when comparing: (i) kinetics and extent of aggregation; (ii) thromboxane synthesis; (iii) calcium flux; and (iv) the cytoplasmic alkalinization response. Thus it is concluded that CD9 antigen itself does not necessarily participate in stimulus-response coupling leading to platelet activation by CD9 mAbs, and that this activation can be entirely accounted for by the Fc receptor pathway mechanism. The results suggest a possible novel mechanism for platelet consumption in cases of immune thrombocytopenia.
Efficacy and Immunogenicity of Acellular Pertussis Vaccine by Manufacturer and Patient Age (1989)

Acellular pertussis vaccines, which have been used in Japan since 1981, vary in antigenic constituents among manufacturers. First, to assess the immunogenicity by manufacturer and patient age, 161 children aged 3 months to 2 years were immunized by acellular pertussis vaccine from one of three Japanese manufacturers, Biken, Takeda, or Kitasato. Anti-pertussis toxin antibody responses for children immunized with Takeda and Kitasato vaccines were comparable with patients with pertussis in the convalescent stage, and anti-pertussis toxin antibody response for Biken vaccine was far higher than those of convalescing patients. Anti-filamentous hemagglutinin antibody responses for the children given the three vaccines were far higher than those of the patients. Weak serotype 1.3 agglutinin responses were observed only in children administered the Takeda vaccine. Comparing these antibody responses among various age groups, the immunogenicity of acellular vaccines in children aged 3 to 6 months was comparable with children aged 2 years. Second, to assess the manufacturer-specific efficacy, 495 households of patients with pertussis were surveyed from 1981 to 1988. The estimated efficacy of the acellular pertussis vaccines in children aged 2 to 8 years was 82%, and there were no major differences in the secondary attack rates among children immunized with acellular pertussis vaccine from each manufacturer, ie, 12.5% (1/8) for Biken, 11.1% (2/18) for Takeda, and 5.9% (1/17) for Kitasato. We conclude from these two studies that similar efficacy was observed in children aged 2 years or older for acellular pertussis vaccines from the three manufacturers, which produced anti-pertussis toxin antibody responses comparable with patients with pertussis and far higher antifilamentous hemagglutinin antibody responses than in the convalescing patients, and that age did not affect the immunogenicity of acellular vaccines.
Isolation and biochemical characterization of a zona pellucida‐binding glycoprotein of boar spermatozoa (1991)

Lectin-like molecules on the sperm surface are implicated in the process of gamete recognition and adhesion. We have isolated and biochemically characterized a 15 kDa glycoprotein from ejaculated boar sperm which possess zona pellucida-binding- and haemagglutinating-activity. The zona/15 kDa protein interaction is inhibited by fucoidan, suggesting that the glycoprotein is one of the sperm components which participate in the initial gamete interaction. N-Terminal sequence analysis of the isolated 15 kDa glycoprotein showed that it may belong to the same sperm/egg recognition-mediating protein family as the sea urchin sperm protein binding.
How Does the Hydrogen Bonding Interaction Influence the Properties of Furan-Based Epoxy Resins (2017)

A biobased epoxy 2,5-bis[(2-oxiranylmethoxy)methyl]-furan (BOF) together with its petroleum-based analogues, 1,4-bis[(2-oxiranylmethoxy)methyl]-benzene (p-BOB) and 1,3-bis[(2-oxiranylmethoxy)methyl]-benzene (m-BOB), have been synthesized. After their chemical structures were identified by nuclear magnetic resonance (1H NMR and 13C NMR), they were cured by the petroleum-based 4,4′-diaminodiphenylmethane and biobased 5,5′-methylenedifurfurylamine, respectively. Thermal and mechanical properties of the cured resins were investigated by differential scanning calorimetry, thermogravimetric analyzer and dynamic mechanical analysis. Especially, hydrogen bonding interactions in the different cured systems were studied by Fourier transform infrared spectroscopy. Based on the structure–properties relationship investigation, it could be concluded that it was the hydrogen bonding interaction playing a key role in determining the thermal properties of the furan-based epoxy resins.
Anti‐kinetochore staining for single laser, bivariate flow sorting of Indian muntjac chromosomes (1991)

Flow cytometric chromosome sorting typically relies upon dual-laser, bivariate analysis after staining with two different base pair-specific dyes for resolution of chromosomes with similar DNA content. The availability of FITC-conjugated antibodies offers the possibility of single-laser bivariate analysis when combined with propidium iodide (PI) DNA staining, but requires exploitable antigenic differences between chromosomes of interest. A technique was developed for indirect immunofluorescent anti-kinetochore staining of Indian muntjac chromosomes in suspension. Primary antibody binding within permeabilized whole cells minimized centrifugation-induced loss of chromosomal integrity. Subsequent FITC-conjugated second antibody binding was not affected by concurrent PI-counterstaining. Anti-kinetochore staining facilitated resolution of chromosomes No. 2 and X, which formed a doublet peak upon univariate DNA content analysis, as well as recognition of the Y2 peak which was indistinguishable from debris by univariate analysis. The technique allowed greater than 90% purification of each Indian muntjac chromosome.
Joint source-channel decoding of entropy coded Markov sources over binary symmetric channels (2003)

This paper proposes an optimal joint source-channel, maximum a posteriori, decoder for entropy coded Markov sources transmitted over noisy channels. We introduce the concept of incomplete and complete states to deal with the problem of variable length source codes in the decoder. The proposed decoder is sequential, thereby making the expected delay finite. When compared to the traditional decoder, the proposed decoder shows a maximum improvement, of about 4 dB in a modified signal to noise ratio and an improvement of 21.95% in percentage of bits that are received in an out of synchronization condition, for a simple test source.
Self-assembly in aqueous solutions of a non-ionic hydrotrope (2012)

Hydrotropes are amphiphilic molecules, too small to cause spontaneous self-assembly towards equilibrium mesoscale structures in aqueous solutions, but they form dynamic, noncovalent assemblies, which may create microscopic regions of lowered polarity. This enhances the solubilization of hydrophobic compounds, also known as solubilizates, in aqueous solutions and may cause further aggregation to larger structures. In this work, unusual mesoscopic properties of aqueous solutions of a non-ionic hydrotrope, namely tertiary butyl alcohol (TBA) have been investigated by light scattering, microscopy, and chromatography. Aqueous TBA solutions show anomalous thermodynamic and structural properties in the range of concentrations 3-8 mol % TBA and temperatures 0 - 25 °C. These anomalies appear to be associated with short-lived, short-ranged micelle-like structural fluctuations, distinctly different from usual concentration fluctuations in non-ideal solutions. Molecular dynamics simulations and neutron-scattering experiments show clustering of TBA molecules on a nanometer scale, interacting through hydrogen bonds with a shell of water molecules. In this concentration range, TBA aqueous solutions, although macroscopically homogeneous, occasionally show the presence of "mysterious" inhomogeneities on a 100 nm scale. We have found that the emergence of such inhomogeneities strongly correlates with impurities present in commercial TBA samples. Experiments with controlled addition of a third component, such as propylene oxide, isobutyl alcohol, or cyclohexane, reveal the mechanism of formation of these inhomogeneities through stabilization of micelle-like fluctuations by a solubilizate. These structures are long-lived, i.e., stable from a few days up to many months. We have confirmed that mesoscale structures in aqueous solutions can be generated from self-assembly of small molecules, without involvement of surfactants or polymers. This kind of self-assembly may potentially result in the development of novel nanomaterials.
Real-Time Strong-Motion Broadband Displacements from Collocated GPS and Accelerometers (2011)

We present a new solution to the classical problem of deriving displacements from seismic data that is suitable for real-time monitoring. It relies on an optimal combination of collocated high-rate GPS displacements and very high-rate strong-motion accelerometer data using a Kalman filter that takes advantage of the individual strengths of seismic and geodetic networks while minimizing their weaknesses. The result is a more accurate broadband estimate of velocities and displacements at the higher rate provided by accelerometers. In contrast to displacements inferred through integration of seismic data alone, which are degraded by the presence of unphysical drifts and limited dynamic ranges, broadband displacements do not drift and will not clip. Furthermore, they are more accurate and robust than those obtained solely from GPS receivers. We establish the accuracy and precision of the new solution using earthquake engineering data from the University of California, San Diego’s Large High-Performance Outdoor Shake Table. Then we estimate broadband displacements for the 2010 M w 7.2 El Mayor–Cucapah earthquake using 1 Hz GPS displacements and 100 Hz accelerometer data from collocated sensors in southern California. We also reconstruct velocity measurements equivalent to those of broadband seismometers, which clipped at stations hundreds of kilometers from the epicenter during the earthquake. The ability to obtain broadband displacement waveforms in three dimensions with millimeter precision is a breakthrough for a number of areas ranging from earthquake source physics to the response of long-period engineered structures. To do so in real time from a dense monitoring network provides distinct advantages for earthquake early warning and rapid earthquake response.
Bone Marrow Transplantation Can Attenuate the Progression of Mesangial Sclerosis (2005)

Bone marrow (BM) transplantation has been shown to provide beneficial effects in injured organs, including heart, liver, and kidney. We explored the therapeutic potential of BM transplantation (BMT) in Wilms' tumor suppressor 1 (Wt1) heterozygous mice, which represent a model of mesangial sclerosis. After transplantation of wild-type BM, there is statistically significantly lower urinary albumin and increased survival in Wt1+/- recipients. Control BMT using Wt1+/- donors showed no significant beneficial effects. The long-term beneficial effect of BMT was dependent on the dose of irradiation applied to the recipients before BMT. At a lethal dose of 1,000 cGy, the decrease in albuminuria and prolongation of lifespan in Wt1+/- mice were transient, with maximal amelioration at 12 weeks and resumption of albuminuria by 24 weeks after BMT. This was, at least in part, due to irradiation and not Wt1 heterozygosity because wild-type recipients also developed albuminuria within 24 weeks of BMT with 1,000 cGy. In contrast, Wt1+/- mice transplanted after 400 cGy showed long-term improvement in albuminuria and lifespan. Approximately 0.4% of podocytes were marrow derived, a level that is unlikely to be responsible for the therapeutic effects. In addition, donor BM cells formed rings surrounding the glomeruli, and approximately one third of the cells in these rings were macrophages. In conclusion, transplantation of wild-type BM attenuates progression of mesangial sclerosis in the Wt1+/- model of renal disease, and the mechanism by which this occurs may involve engraftment of BM-derived cells in the renal parenchyma.
A convenient synthesis of 2,3,5,6-tetrahalogenopyridines and of 3,5-bis(alkylthio)pyridines from 2,6-diaminopyridine (1980)

Controlled chlorination of 2,6-diaminopyridine (1) affords 2,6-diamino-3,5-dichloropyridine (2a) which is then bis(diazotised) to give 2,3,5,6-tetrachloropyridine (3a); similarly prepared are other 2,3,5,6-tetra(chloro/bromo)pyridines and 2,6-dichloro-3,5-bis(thiocyanato)pyridine (3h), from which 3,5-bis(alkylthio)pyridines are easily obtained.
<title>New technology for raster document image compression</title> (1999)

This paper describes in detail the LuraDocument technique, a recently developed, high performance technique for compressing and archiving scanned documents, particularly those containing text and image. LuraDocument offers higher compression rates and quality in comparison to traditional document compression methods, preserving text legibility even at extremely high compression rates. This various stages of LuraDocument compression are described in detail, including image quantization and text detection procedures.
High-precision diode-laser-based temperature measurement for air refractive index compensation (2011)

We present a laser-based system to measure the refractive index of air over a long path length. In optical distance measurements, it is essential to know the refractive index of air with high accuracy. Commonly, the refractive index of air is calculated from the properties of the ambient air using either Ciddor or Edlén equations, where the dominant uncertainty component is in most cases the air temperature. The method developed in this work utilizes direct absorption spectroscopy of oxygen to measure the average temperature of air and of water vapor to measure relative humidity. The method allows measurement of temperature and humidity over the same beam path as in optical distance measurement, providing spatially well-matching data. Indoor and outdoor measurements demonstrate the effectiveness of the method. In particular, we demonstrate an effective compensation of the refractive index of air in an interferometric length measurement at a time-variant and spatially nonhomogeneous temperature over a long time period. Further, we were able to demonstrate 7 mK RMS noise over a 67 m path length using a 120 s sample time. To our knowledge, this is the best temperature precision reported for a spectroscopic temperature measurement.
In Vitro Studies of 5-Fluorocytosine Resistance in <i>Candida albicans</i> and <i>Torulopsis glabrata</i> (1972)

Spontaneous mutants of Candida albicans resistant to 5-fluorocytosine (5-FC) were isolated from a strain susceptible to 5-FC. These mutants were compared with 5-FC-resistant strains of C. albicans and Torulopsis glabrata isolated from patients treated with the drug and from untreated patients. Resistance to 5-FC was in all cases followed by a decreased susceptibility to 5-fluorouracil. Most strains were also more resistant to 5-fluorouridine and had a lowered incorporation of uridine. In one spontaneous mutant totally resistant to all three 5-fluoropyrimidines, the uridine monophosphate pyrophosphorylase activity was greatly decreased. The 5-FC-resistant strains were of two main phenotypic classes. Class one was unaffected by 5-FC at the highest concentration tested. The growth rate of strains belonging to the other class was markedly decreased by low concentrations of 5-FC, but these strains were still able to form colonies after 7 days of incubation on plates containing very high concentrations of the drug (2,000 mug/ml). The frequency of spontaneous mutation of a susceptible strain to 5-FC resistance was fairly high. The number of mutants growing on media containing 5-FC was unchanged by concentrations ranging from 25 to 500 mug/ml.