gebhart/patrepeval huggingface dataset:
Diffuse backscattering Mueller matricesof highly scattering media (1997)

We report on the development of a method that records spatially dependent intensity patterns of polarized light that is diffusely backscattered from highly scattering media. It is demonstrated that these intensity patterns can be used to differentiate turbid media, such as polystyrene-sphere and biological-cell suspensions. Our technique employs polarized light from a He-Ne laser (l=543nm), which is focused onto the surface of the scattering medium. A surface area of approximately 4x4 cm centered on the light input point is imaged through polarization-analysis optics onto a CCD camera. One can observe a large variety of intensity patterns by varying the polarization state of the incident laser light and changing the analyzer configuration to detect different polarization components of the backscattered light. Introducing the Mueller-matrix concept for diffusely backscattered light, a framework is provided to select a subset of measurements that comprehensively describe the optical properties of backscattering media.
In vitro characterization of echogenic liposomes by acoustic scattering at 3.5–15.0 MHz (2004)

Echogenic liposomes (ELIP) are phospholipid vesicles that are being developed as ultrasound contrast agents and as vehicles for drug delivery. These particles, when conjugated with antibodies or peptides, can be used for targeted diagnostic imaging and therapy. Evaluating the acoustic properties of ELIP will allow for optimization of its utility as an ultrasound contrast agent. The diameter of the liposomes ranges from 0.25–10.0 μm. In order to measure the backscattering coefficient in vitro, the backscattered power was compared to that reflected from a perfect reflector, a planar air–water interface. The backscatter coefficient and attenuation of ELIP were evaluated as a function of concentration (0.8–9.9×108/ml) and frequency (3.5–15.0 MHz). By comparing the values of measured backscatter coefficient to a theoretical model that treats the gas within the liposomes as a free air bubble, a size estimate of the encapsulated gas is provided. Finally, calculation of the scattering to attenuation ratio (STAR) gives a value with which to evaluate the efficacy of ELIP as a contrast agent in cardiovascular ultrasound imaging. The backscatter coefficient shows promise as a sensitive method for determining whether the liposomes are left intact or if they are destroyed during imaging.
Organic Crystal Templating of Hollow Silica Fibers (1999)

The incipient crystallization of needlelike forms of organic salts, such as ammonium dl-tartrate or ammonium oxalate, has been used for the templating of sol−gel reactions to produce hollow silica fibers and filaments with geometrically shaped channels. By judicious control of both the crystallization and hydrolysis−condensation processes, flexible tubes with continuous wall structures, often only 30 nm in thickness, can be produced.
Adaptation of Population Structure in Socio-cognitive Particle Swarm Optimization (2016)

In the paper a modification of a Socio-cognitive Particle Swarm Optimization algorithm, recently proposed by the authors, is presented. This modification consists in devising a mechanism for dynamic adaptation of the population structure of the swarm. Besides the design and rationale for the approach, referring to the state-of-the-art PSO original algorithm and several of its modifications, experimental results tackling popular benchmark functions are presented and discussed in detail.
Pharmacotherapy for prevention of post-traumatic stress disorder (2006)

This is the protocol for a review and there is no abstract. The objectives are as follows: 1) To provide an estimate of the efficacy of medication in preventing the development of post-traumatic stress disorder following exposure to a traumatic event. The efficacy of medication in reducing symptom severity for those individuals who subsequently develop PTSD will also be considered. 2) To determine whether particular classes of medication are more effective and/or acceptable than others in the prevention of PTSD. 3) To assess whether depression is a predictor of treatment response in the prevention of PTSD. Copyright © 2006 The Cochrane Collaboration. Published by John Wiley &amp; Sons, Ltd.
Experimental and Kinetic Investigation of CO2and H2O/N2Gasification of Biomass Fuels (2011)

Characterization of the thermal decomposition of various woods, grasses and the biomass structural components, lignin and cellulose, was performed using a TGA with online GC analysis in both CO2 and H2O/N2 gasification environments. CO2 was observed to be a more efficient gasification environment that resulted in improved bio-char conversion during gasification. Introduction of CO2 as co-feed into the gasification environment resulted in enhanced CO and depressed H2 and CH4 concentrations enabling greater control in the syngas ratio produced by adjustment of the level of CO2 introduced. Mass decomposition and H2, CO, CO2 and CH4 gas evolution studies were performed for the various feedstocks at heating rates of from 1–100°C min-1 in both gasification media. When comparing the residual mass fractions of lignin and cellulose gasified in CO2 subjected to slow (1°C min-1) and fast (100°C min-1) heating rates, greater differential processing of the two components was possible with 65%, rather than 42%, of the lignin remaining following cellulose decomposition at the slow heating rate. Selective isolation of the thermally resistant lignin, retaining a greater residual fraction of this structural component, was observed during CO2 gasification at the lowest heating rates. While cellulose thermal decomposition was observed to occur over a narrow temperature window, ~275–425°C, thermal degradation of lignin occurs over a much wider range beginning about 175°C and finishing after 700°C with more than a 35% mass loss after 700°C in a CO2 gasification environment. A least squares best fit analysis for the global kinetic parameters gave an average pyrolysis activation energy for lignin and cellulose in CO2 as 43 and 211 kJ mol-1, while that for lignin and cellulose in H2O/N2 was 53 and 203 kJ mol-1, respectively. The analysis showed a pyrolysis best fit reaction order of three for lignin and one for cellulose. The various biomass feedstocks showed activation energies between 28–72 kJ mol-1 and reaction orders of one or two, with samples high in cellulose content showing correspondingly higher energies and lower reaction order.
Morphological processing for UCIR detection (2003)

A study was conducted on the use of morphological processing for detection in Uncooled Infra Red (UCIR) data using the Clutter type 1 and Clutter type 2 databases. The CMO algorithm was used with various modifications. A fixed minimum peak value was used rather than a fraction of the maximum peak per image. This is much more realistic, since many real scenes will not contain targets. One-dimensional directional structuring elements (SEs) were used for the Close Minus Open algorithm. We used the range of gray levels within the output blob peaks (blob analysis) and larger windows in peak sorting to reduce false alarms. A new dilation minus erosion morphological algorithm gave the best result.
Phenotypic selection for high resistance to Fusarium head blight after introgression of quantitative trait loci (QTL) from exotic spring wheat and verification by simple sequence repeat markers a posteriori (2008)

Abstract Fusarium head blight (FHB) has become an important disease of wheat. We introgressed three resistance quantitative trait loci (QTL) alleles on chromosomes 3B, 5A (from CM82036) and 3A (from ‘Frontana’) into European elite spring wheat and performed phenotypic selection among double‐cross (DC) derived progeny in generations DCF 2 and DCF 3 . After recombination and selfing, we analysed 135 phenotypically selected progeny by simple sequence repeat (SSR) markers linked to the QTL. In a second experiment, we forwarded the best 20 progeny for a further two generations by pedigree selection. Progeny were inoculated at two to four locations with Fusarium culmorum and the percentage of infected spikelets per plot was estimated. Both experiments show that phenotypic selection was highly effective. One‐hundred out of 135 phenotypically selected DCF 1:3 progeny had the combination of donor‐QTL alleles (3B + 5A + 3A, 3B + 5A) with the highest effects on FHB resistance. In the subsequent generations, sufficient genotypic variance was detected. The best F 5:7 bulks had similar resistance to the donor CM82036. The FHB rating was reduced in total by 45% points compared to the parental mean. QTL with high effects can be detected solely by phenotypic selection after targeted introgression.
Evolution along the crassulacean acid metabolism continuum (2010)

Crassulacean acid metabolism (CAM) is a specialised mode of photosynthesis that improves atmospheric CO2 assimilation in water-limited terrestrial and epiphytic habitats and in CO2-limited aquatic environments. In contrast with C3 and C4 plants, CAM plants take up CO2 from the atmosphere partially or predominantly at night. CAM is taxonomically widespread among vascular plants and is present in many succulent species that occupy semiarid regions, as well as in tropical epiphytes and in some aquatic macrophytes. This water-conserving photosynthetic pathway has evolved multiple times and is found in close to 6% of vascular plant species from at least 35 families. Although many aspects of CAM molecular biology, biochemistry and ecophysiology are well understood, relatively little is known about the evolutionary origins of CAM. This review focuses on five main topics: (1) the permutations and plasticity of CAM, (2) the requirements for CAM evolution, (3) the drivers of CAM evolution, (4) the prevalence and taxonomic distribution of CAM among vascular plants with emphasis on the Orchidaceae and (5) the molecular underpinnings of CAM evolution including circadian clock regulation of gene expression.
Rice chitinases: sugar recognition specificities of the individual subsites (2006)

Sugar recognition specificities of class III (OsChib1a) and class I (OsChia1cDeltaChBD) chitinases from rice, Oryza sativa L., were investigated by analyzing (1)H- and (13)C-nuclear magnetic resonance spectra of the enzymatic products from partially N-acetylated chitosans. The reducing end residue of the enzymatic products obtained by the class III enzyme was found to be exclusively acetylated, whereas both acetylated and deacetylated units were found at the nearest neighbor to the reducing end residue. Both acetylated and deacetylated units were also found at the nonreducing end residue and its nearest neighbor of the class III enzyme products. Thus, only subsite (-1) among the contiguous subsites (-2) to (+2) of the class III enzyme was found to be specific to an acetylated residue. For the class I enzyme, the reducing end residue was preferentially acetylated, although the specificity was not absolute. The nearest neighbor to the acetylated reducing end residue was specifically acetylated. Moreover, the nonreducing end residue produced by the class I enzyme was exclusively acetylated, although there was a low but significant preference for deacetylated units at the nearest neighbor to the nonreducing end. These results suggest that the three contiguous subsites (-2), (-1), and (+1) of the class I enzyme are specific to three consecutive GlcNAc residues of the substrate. In rice plants, the target of the class I enzyme might be a consecutive GlcNAc sequence probably in the cell wall of fungal pathogen, whereas the class III enzyme might act toward an endogenous complex carbohydrate containing GlcNAc residue.
Density, Electrical Conductivity, and Dynamic Viscosity of N-Alkyl-4-methylpyridinium Bis(trifluoromethylsulfonyl)imide (2012)

Two air and water stable hydrophobic ionic liquids N-alkyl-4-methylpyridinium bis(trifluoromethylsulfonyl)imide ([Cn4mpy][NTf2], n = 2, 4) were synthesized and characterized. The density, electrical conductivity, and dynamic viscosity were measured and estimated in the range of T = (278.15 to 363.15) K. The melting temperature, glass transition temperature, and decomposition temperature of the two ILs were determined according to the differential scanning calorimetry (DSC) and thermogravimetric analyzer (TG). The molecular volume, standard molar entropy, and lattice energy were estimated in terms of empirical equations on the basis of the density values. The electrical conductivity and dynamic viscosity values dependence on temperature were fitted by the Vogel–Fulcher–Tamman equation. The molar conductivity was calculated by the density and electrical conductivity.
Nanoporous Glass as a Model System for a Consistency Check of the Different Techniques of Diffusion Measurement (2011)

The remarkable differences in the guest diffusivities in nanoporous materials commonly found with the application of different measuring techniques are usually ascribed to the existence of a hierarchy of transport resistances in addition to the diffusional resistance of the pore system and their differing influence due to the differing diffusion path lengths covered by the different measuring techniques. We report diffusion measurements with nanoporous glasses where the existence of such resistances could be avoided. Molecular propagation over diffusion path lengths from hundreds of nanometers up to millimeters was thus found to be controlled by a uniform mechanism, appearing in coinciding results of microscopic and macroscopic diffusion measurement.
Hypertrophic chondrocytes undergo further differentiation to osteoblast-like cells and participate in the initial bone formation in developing chick embryo (1994)

Differentiation of hypertrophic chondrocytes to an osteoblast-like phenotype occurs in vivo in the hypertrophic cartilage of chick embryo tibiae underneath early or prospective periosteum and in cartilage around vascular canals. Synthesis of type I collagen by hypertrophic chondrocytes was shown by immunolocalization of the C propeptide. By enzyme cytochemistry it was instead shown that, in vivo, further differentiating hypertrophic chondrocytes express alkaline phosphatase at the time of initial mineral deposition. Evidence that hypertrophic chondrocytes may resume proliferation was obtained by BrdU labeling. A monoclonal antibody (LA5) was isolated and characterized that recognizes a hypertrophic chondrocyte membrane protein. In addition to staining hypertrophic chondrocytes surrounded by a type II and type X collagen-stainable matrix, the LA5 antibodies also stained elongated chondrocytes at the cartilage/bone collar interface and cells incorporated in the first layer of bone and osteoid matrix.
Establishing the involvement of the novel geneAGBL5in retinitis pigmentosa by whole genome sequencing (2016)

While more than 250 genes are known to cause inherited retinal degenerations (IRD), nearly 40-50% of families have the genetic basis for their disease unknown. In this study we sought to identify the underlying cause of IRD in a family by whole genome sequence (WGS) analysis. Clinical characterization including standard ophthalmic examination, fundus photography, visual field testing, electroretinography, and review of medical and family history was performed. WGS was performed on affected and unaffected family members using Illumina HiSeq X10. Sequence reads were aligned to hg19 using BWA-MEM and variant calling was performed with Genome Analysis Toolkit. The called variants were annotated with SnpEff v4.11, PolyPhen v2.2.2, and CADD v1.3. Copy number variations were called using Genome STRiP (svtoolkit 2.00.1611) and SpeedSeq software. Variants were filtered to detect rare potentially deleterious variants segregating with disease. Candidate variants were validated by dideoxy sequencing. Clinical evaluation revealed typical adolescent-onset recessive retinitis pigmentosa (arRP) in affected members. WGS identified about 4 million variants in each individual. Two rare and potentially deleterious compound heterozygous variants p.Arg281Cys and p.Arg487* were identified in the gene ATP/GTP binding protein like 5 (AGBL5) as likely causal variants. No additional variants in IRD genes that segregated with disease were identified. Mutation analysis confirmed the segregation of these variants with the IRD in the pedigree. Homology models indicated destabilization of AGBL5 due to the p.Arg281Cys change. Our findings establish the involvement of mutations in AGBL5 in RP and validate the WGS variant filtering pipeline we designed.
Chaphamaparvovirus antigen and nucleic acids are not detected in kidney tissues from cats with chronic renal disease or immunocompromised cats (2021)

Chronic kidney disease (CKD) is a common cause of morbidity and mortality in domestic cats, but the cause is still largely elusive. While some viruses have been associated with this disease, none have been definitively implicated as causative. Recently, <i>Rodent chaphamaparvovirus 1</i> was recognized as the cause of murine inclusion body nephropathy, a disease reported for over 40 years in laboratory mice. A novel virus belonging to the same genus, <i>Carnivore chaphamaparvovirus</i> 2, was recently identified in the feces of cats with diarrhea. The goal of this study was to investigate the possible role of chaphamaparvoviruses including members of <i>Rodent chaphamaparvovirus 1</i> and <i>Carnivore chaphamaparvovirus 2</i> in the development of feline CKD. The presence of these viruses was retrospectively investigated in formalin-fixed paraffin-embedded feline kidney samples using polymerase chain reaction, in situ hybridization, and immunohistochemistry. Cats were divided into 3 groups: normal (<i>N</i> = 24), CKD (<i>N</i> = 26), and immunocompromised (<i>N</i> = 25). None of the kidney tissues from any of the 75 cats revealed the presence of chaphamaparvovirus DNA, RNA, or antigen. We conclude that viruses belonging to the chaphamaparvovirus genus are unlikely to contribute to the occurrence of feline CKD.
Characterization of crystals of the Hjc resolvase fromArchaeoglobus fulgidusgrown in gel by counter-diffusion (2005)

Holliday junction-resolving enzymes are ubiquitous proteins that play a key role in DNA repair and reorganization by homologous recombination. The Holliday junction-cutting enzyme (Hjc) from the archaeon Archaeoglobus fulgidus is a member of this group. The first Hjc crystals were obtained by conventional sparse-matrix screening. They exhibited an unusually elongated unit cell and their X-ray characterization required special care to avoid spot overlaps along the c* axis. The use of an arc appended to the goniometric head allowed proper orientatation of plate-like crystals grown in agarose gel by counter-diffusion. Thus, complete diffraction data were collected at 2.7 Å resolution using synchrotron radiation. They belong to space group P3121 or P3221, with unit-cell parameters a = b = 37.4, c = 271.8 Å.
Integrated Simulation and State Estimation for Precision Landing on Titan (2020)

This paper reports on a study of the application of a ram-air parafoil to Entry, Descent, and Landing (EDL) on Titan. A comprehensive simulation was constructed to enable simulation of EDL state estimation performance from 10 minutes before entry (E-10 min) to touchdown on the surface of Titan. EDL performance is characterized assuming an entry phase starting at E-10 min followed by a parafoil guided phase for descent and landing to enable precise landing on a predetermined target. Guided descent during the parafoil phase is achieved using the parafoil steering capability while state estimation is accomplished using vision-based Terrain Relative Navigation (TRN). The simulation is used in this study to conduct Monte Carlo analysis of TRN state estimation for a full entry phase sequence followed by a straight line flight path descent and landing.
Mammalian brain and erythrocyte carboxyl methyltransferases are similar enzymes that recognize both D-aspartyl and L-isoaspartyl residues in structurally altered protein substrates. (1984)

Two purified isozymes of protein carboxyl methyltransferase from bovine brain catalyze the substoichiometric transfer of methyl groups in vitro from S-adenosyl-L-[methyl-3H]methionine to several erythrocyte membrane proteins, which include bands 2.1, 3, and 4.1, as well as several integral membrane polypeptides. D-Aspartic acid beta-[3H]methyl ester has been isolated from proteolytic digests of these methylated proteins, suggesting that protein D-aspartyl residues can serve as methyl-acceptor sites for the two brain enzymes. This formation of D-aspartic acid beta-[3H]methyl ester is competitively inhibited by the peptide L-Val-L-Tyr-L-Pro-L-isoAsp-Gly-L-Ala, which contains an L-aspartyl residue in an unusual beta-peptide linkage. Since this peptide is a stoichiometric substrate for the brain methyltransferases, it appears that one enzymatic activity can catalyze methyl ester formation at both D-aspartyl and L-isoaspartyl sites. In these respects, the activity of both brain isozymes closely resembles those previously described for the erythrocyte enzyme. The results are discussed in terms of a model in which derivatized aspartyl residues in proteins, arising by either racemization or isomerization, are recognized by the methyltransferase; the enzyme may function in either the metabolism or correction of the altered structures. The presence of a similar enzyme in both translationally active (brain) and inactive (erythrocyte) tissues suggests that the reactions are of general importance to cellular integrity.
Hypofractionated accelerated high-dose radiotherapy (RT) in non-small cell lung cancer (NSCLC) (2008)

7527 Background: Dose escalation and RT intensification may improve local control in NSCLC but may potentially increase late toxicity. We postulated that accelerated hypofractionated RT is safe and efficacious with use of 3D-CRT and application of strict dose volume constraints (DVC). Methods: 50 patients with stage I–III medically inoperable/unresectable NSCLC, with weight loss less than 10% and KPS >70% were enrolled on a phase 1/11 clinical trial (ICORG 99–09) with a schedule of 72 Gy in 24 fractions, once daily, five fractions per week, over 32 days. Median age = 65 years (Range: 45–82 yrs). 39 patients were male and 11 female. 31 patients had induction chemotherapy. No elective lymph node irradiation was used. Primary endpoints were acute and late esophageal (RTOG/EORTC scale) and pulmonary toxicity (SWOG). Secondary endpoints were response rate at 3 months, time to tumor progression (TTP), time to tumor local progression (TTLP), time to distant progression (TTDP), progression-free survival (PFS) and overall survival (OS). Results: 45 patients were treated with median f/u =11 months (range 3–73 mos). Acute toxicity was as follows: acute pneumonitis (20 pts: Grade (Gr) 1=19 pts, Gr2=1 pt); acute esophagitis (20 pts: Gr1=14pts, Gr2=3 pts, Gr3=3 pts) with one 4 day treatment interruption. 12 pts had late pneumonitis (Gr1=10 pts, Gr2=2 pts). A previous analysis presented at ASCO 2004 reported 2 pts with Gr 5 late esophagitis. Therefore, we introduced an additional esophageal DVC where <1 cm of circumferential esophagus was within the 98% isodose. Since then 8 patients were treated with no grade 5 toxicity and Gr1 = 1pt, Gr2 = 1pt, Gr3=1pt, with median f/u = 9 mos. Tumor response rate at 3 mos: (18% CR, 29% PR, 15% SD, 17% PD and 20 % non-evaluable). Median TTP = 12 mos, median TTLP =21 mos, and median TTDP = 11 mos. 1 yr PFS=81%, 3 yr PFS=28%. Median OS=17 mos with 1 yr OS=81%, 3 yr OS=25%. Conclusions: The toxicity profile is favorable apart from initial unexpected esophageal late toxicity. We continue to evaluate the safety of our esophageal DVC. The median survival and TTLP results are encouraging as 40% pts had Stage III disease. No significant financial relationships to disclose.