gebhart/patrepeval huggingface dataset:
A Metal-Accumulator Mutant of Arabidopsis thaliana (1996)

A mutation designated man1 (for manganese accumulator) was found to cause Arabidopsis thaliana seedlings to accumulate a range of metals. The man1 mutation segregated as a single recessive locus located on chromosome 3. When grown on soil, mutant seedlings accumulated Mn (7.5 times greater than wild type), Cu (4.6 times greater than wild type), Zn (2.8 times greater than wild type), and Mg (1.8 times greater than wild type) in leaves. In addition to these metals, the man1 mutant accumulated 2.7-fold more S in leaves, primarily in the oxidized form, than wild-type seedlings. Analysis of seedlings grown by hydroponic culture showed a similar accumulation of metals in leaves of man1 mutants. Roots of man1 mutants also accumulated metals, but unlike leaves they accumulated 10-fold more total Fe (symplasmic and apoplasmic combined) than wild-type roots. Roots of man1 mutants possessed greater (from 1.8- to 20-fold) ferric-chelate reductase activity than wild-type seedings, and this activity was not responsive to changes of Mn nutrition in either genotype. Taken together, these results suggest that the man1 mutation disrupts the regulation of metal-ion uptake or homeostasis in Arabidopsis.
Structural comparison of two highly homologous thermophilic bacterial alcohol dehydrogenases (1996)

Pl3sucl from S. pombe is a member of the QDC28 kinase ~pecific (CKS) class of cell-cycle control proteins, that includes CKS 1 from S. cerevisiae and the human homologues CksHs 1 and CksHs2.P13sucl participates in the regulation ofp34cdc2, a cyclindependent kinase controlling the G 1 -S and the G 2 -M transitions of the cell cycle.The CKS proteins are believed to exert their regulatory activity by binding to the kinase, in which case their function may be governed by their conformation or oligome1ization state._ Analysis of various assemblies of the CKS proteins, as found in different crystal forms, should help to clarify their role in cell cycle control.Previously determined X-ray structures of p13sucl, CksHs 1 and CksHs2 show that these proteins share a common fold but adopt different oligomeric states.P13sucl and CksHs 1 were solved as monomers [1,2].In addition, CksHs2 and pl3sucl were observed in assemblies of strand-exchanged dimers [3,4].We report the X-ray crystal structure ofpJ3sucl to 1.95 A resolution in space group C222J.It is present in the crystals as a strandexchanged dimer.The overall monomeric fold is preserved in each lobe of the dimer but a single B-strand (Ile94 to Aspl02) is exchanged between the central B-sheets of each molecule.Strand exchange, which has been observed for pl3sucl in two different space groups, and for CksHs2, is now confirmed to be an intrinsic feature of the CKS family.A switch between levels of assembly may serve to coordinate the function of the CKS proteins in cell cycle control.
High-throughput assessment of hemoglobin polymer in single red blood cells from sickle cell patients under controlled oxygen tension (2019)

Sickle cell disease (SCD) is caused by a variant hemoglobin molecule that polymerizes inside red blood cells (RBCs) in reduced oxygen tension. Treatment development has been slow for this typically severe disease, but there is current optimism for curative gene transfer strategies to induce expression of fetal hemoglobin or other nonsickling hemoglobin isoforms. All SCD morbidity and mortality arise directly or indirectly from polymer formation in individual RBCs. Identifying patients at highest risk of complications and treatment candidates with the greatest curative potential therefore requires determining the amount of polymer in individual RBCs under controlled oxygen. Here, we report a semiquantitative measurement of hemoglobin polymer in single RBCs as a function of oxygen. The method takes advantage of the reduced oxygen affinity of hemoglobin polymer to infer polymer content for thousands of RBCs from their overall oxygen saturation. The method enables approaches for SCD treatment development and precision medicine.
Development and validation of ELISAs for monitoring bacterial and parasitic infections in laboratory rodents and rabbits (2014)

According to the FELASA recommendations for the health monitoring of rodent and rabbit breeding and experimental colonies (Kraft et al. 1994; Rehbinder et al. 1996) bacterial and parasitic infections are monitored by culture and microscopy respectively whereas viral infections are monitored by serology. The recommendation on the breeding colonies states that serological methods exist for the detection of antibodies to various bacterial pathogens e.g. Bacillus piliformis (now Clostridium piliforme), mycoplasmas and Leptospira spp. and suggests the possible use of serology for these infections as well as for Treponema cuniculi, Encephalitozoon cuniculi and Toxoplasma gondii. Since 1985 we have explored the utility of serology, notably the enzyme-linked immunosorbent assay (ELISA), for the monitoring of animal colonies. Serology avoids the killing of animals and large numbers of animals can be more easily tested than by culture and results can be obtained within hours. Here we give a brief overview of our work and some experiences. Details can be found in a series of papers published between 1993 and 1999 in Laboratory Animals (LA) and the Journal of Experimental Animal Science (JEAnS) (Table 1). We started with non-X (hemin) and non-V (NADP) factor requiring Pasteurellaceae as such bacteria frequently occurred in all animal species. Later we extended our studies to growth factor requiring members of the family (Haemophilus sp) and bacterial species belonging to other families. The development and validation of the assays were done similarly for bacterial species or groups studied (Figure 1).
Structure of the Human Type II 3β-Hydroxysteroid Dehydrogenase/Δ <sup>5</sup> -Δ <sup>4</sup> Isomerase (3β-HSD) Gene: Adrenal and Gonadal Specificity (1991)

While classical 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4 isomerase deficiency (3 beta-HSD) is a known cause of adrenal hyperplasia resulting in ambiguous genitalia and adrenal insufficiency at birth, nonclassical or late-onset 3 beta-HSD deficiency is found in an important proportion of women with androgen excess. We have previously isolated and sequenced the cDNA and gene for the human type I 3 beta-HSD, which represents the main species expressed in the placenta and skin. Recently, we isolated, sequenced, and expressed the functional cDNA encoding type II 3 beta-HSD, which is the predominant 3 beta-HSD expressed in human adrenals and gonads. The present study describes the isolation and complete sequence of the corresponding type II 3 beta-HSD gene, which is the form most likely responsible for human 3 beta-HSD deficiency. The structural gene contains four exons of 57, 231, 165, and 1,214 bp, respectively, separated by introns of 128, 3,383, and 2,162 bp. DNA sequence analysis of the 5'-flanking region reveals the existence of two putative TATA boxes situated 28 and 140 nucleotides upstream from the transcription start site whereas two putative CAAT boxes are located 57 and 38 nucleotides upstream from the TATA boxes, respectively. A restriction fragment length pattern specific for each gene has been characterized. The present findings should provide the tools required for detailed analysis of the molecular basis of 3 beta-HSD deficiency as well as of normal sex steroid biosynthesis.
Factors Controlling Erythropoiesis in Birds (1966)

Abstract 1. Erythropoiesis in birds is stimulated by bleeding and environmental hypoxia and is suppressed by induced polycythemia, indicating that the physiologic response is similar to that in mammals. 2. This response is mediated through a humoral factor which stimulates erythropoiesis of birds but not of mammals. Similarly, the erythropoietin of mammals does not stimulate the erythropoiesis of birds. 3. Although both the erythropoiesis stimulating factor of birds and of mammals appear to require an intact protein structure for biological activity, the erythropoietin of birds differs from that of mammals in that it is not destroyed by sialidase and does not lose its activity when reacted with antibody to human urinary erythropoietin.
A 1-µW 10-bit 200-kS/s SAR ADC With a Bypass Window for Biomedical Applications (2012)

This paper presents an energy efficient successive-approximation-register (SAR) analog-to-digital converter (ADC) for biomedical applications. To reduce energy consumption, a bypass window technique is used to select switching sequences to skip several conversion steps when the signal is within a predefined small window. The power consumptions of the capacitive digital-to-analog converter (DAC), latch comparator, and digital control circuit of the proposed ADC are lower than those of a conventional SAR ADC. The proposed bypass window tolerates the DAC settling error and comparator voltage offset in the first four phases and suppresses the peak DNL and INL values. A proof-of-concept prototype was fabricated in 0.18-μm 1P6M CMOS technology. At a 0.6-V supply voltage and a 200-kS/s sampling rate, the ADC achieves a signal-to-noise and distortion ratio of 57.97 dB and consumes 1.04 μW, resulting in a figure of merit of 8.03 fJ/conversion-step. The ADC core occupies an active area of only 0.082 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Iterative Tomographic Image Reconstruction Using Fourier-Based Forward and Back-Projectors (2004)

Iterative image reconstruction algorithms play an increasingly important role in modern tomographic systems, especially in emission tomography. With the fast increase of the sizes of the tomographic data, reduction of the computation demands of the reconstruction algorithms is of great importance. Fourier-based forward and back-projection methods have the potential to considerably reduce the computation time in iterative reconstruction. Additional substantial speed-up of those approaches can be obtained utilizing powerful and cheap off-the-shelf fast Fourier transform (FFT) processing hardware. The Fourier reconstruction approaches are based on the relationship between the Fourier transform of the image and Fourier transformation of the parallel-ray projections. The critical two steps are the estimations of the samples of the projection transform, on the central section through the origin of Fourier space, from the samples of the transform of the image, and vice versa for back-projection. Interpolation errors are a limitation of Fourier-based reconstruction methods. We have applied min-max optimized Kaiser-Bessel interpolation within the nonuniform FFT (NUFFT) framework and devised ways of incorporation of resolution models into the Fourier-based iterative approaches. Numerical and computer simulation results show that the min-max NUFFT approach provides substantially lower approximation errors in tomographic forward and back-projection than conventional interpolation methods. Our studies have further confirmed that Fourier-based projectors using the NUFFT approach provide accurate approximations to their space-based counterparts but with about ten times faster computation, and that they are viable candidates for fast iterative image reconstruction.
Solid Phase Microextraction for Quantitative Headspace Sampling of Apple Volatiles (1996)

Solid phase microextraction (SPME) was evaluated for use in the quantification of aroma volatile production by Granny Smith apples during cool storage. Particular attention was paid to quantifying alpha-farnesene (3,7,11-trimethyldodeca-1,3(E),6(E),10-tetraene) due to its involvement in superficial scald, a disorder of cool stored apples. Comparison between SPME and solid phase extraction (SPE) showed that the SPME fiber had greater adsorption of high molecular weight (MW) volatiles such as alpha-farnesene. When sampling by SPME, these higher MW volatiles did not equilibrate between apples, headspace, and fiber within sampling times as long as 90 min, while lower MW volatiles equilibrated within 5 min. This behavior was also shown by a simple model system consisting of five selected volatiles dissolved in an involatile, lipophilic liquid (squalane). The less volatile high MW aroma compounds evaporated slowly from the surface of the apples and were depleted from the headspace because of very rapid adsorption by the SPME fiber. The amount of alpha-farnesene adsorbed by the fiber increased with air movement through the system. In a static headspace system, the amount of alpha-farnesene adsorbed by the fiber decreased nonlinearly with increasing distance from the apples, due to adsorption onto the glass walls. While SPME is ideal for rapid, qualitative determination of apple headspace volatiles, the slower equilibration of higher MW volatiles limits its use for quantification in more complex systems.
A magnesium/amorphous silicon passivating contact for <i>n</i>-type crystalline silicon solar cells (2016)

Among the metals, magnesium has one of the lowest work functions, with a value of 3.7 eV. This makes it very suitable to form an electron-conductive cathode contact for silicon solar cells. We present here the experimental demonstration of an amorphous silicon/magnesium/aluminium (a-Si:H/Mg/Al) passivating contact for silicon solar cells. The conduction properties of a thermally evaporated Mg/Al contact structure on n-type crystalline silicon (c-Si) are investigated, achieving a low resistivity Ohmic contact to moderately doped n-type c-Si (∼5 × 1015 cm−3) of ∼0.31 Ω cm2 and ∼0.22 Ω cm2 for samples with and without an amorphous silicon passivating interlayer, respectively. Application of the passivating cathode to the whole rear surface of n-type front junction c-Si solar cells leads to a power conversion efficiency of 19% in a proof-of-concept device. The low thermal budget of the cathode formation, its dopant-less nature, and the simplicity of the device structure enabled by the Mg/Al contact open up possibilities in designing and fabricating low-cost silicon solar cells.
Excitation of transversely excited CO2 waveguide lasers (1975)

Using a preionization scheme based on the Malter effect, small-signal gains ≳5%/cm at 10.6 μm ahve been produced in a 1-mm2-cross-section waveguide CO2 amplifier at total operating pressures of 100–760 Torr. Comparisons are made between this preionization scheme and those using electron beams.
Water‐Soluble Polymers Coupled with Glycopeptide Antigens and T‐Cell Epitopes as Potential Antitumor Vaccines (2013)

Highly decorated: Tumor-associated MUC1 glycopeptide and tetanus toxoid T-cell epitope P2 can be attached to water-soluble poly(N-(2-hydroxypropyl)methacrylamide) carriers by orthogonal ligation techniques. Fully synthetic vaccine A with additional nanostructure-promoting domains induced antibodies that exhibit high affinity to tumor cells.
A method, system, and tools for intelligent interruption management (2005)

Interrupting users engaged in tasks typically has negative effects on their task completion time, error rate, and affective state. Empirical research has shown that these negative effects can be mitigated by deferring interruptions until more opportune moments in a user's task sequence. However, existing systems that reason about when to interrupt do not have access to task models that would allow for such finer-grained temporal reasoning. We outline our method of finding opportune moments that links a physiological measure of workload with task modeling techniques and theories of attention. We describe the design and implementation of our interruption management system, showing how it can be used to specify and monitor practical, representative user tasks. We discuss our ongoing empirical work in this area, and how the use of our framework may enable attention aware systems to consider a user's position in a task when reasoning about when to interrupt.
Structure of the reovirus cell-attachment protein: a model for the domain organization of sigma 1 (1990)

This report describes a model for the structure of the reovirus cell-attachment protein sigma 1. S1 gene nucleotide sequences were determined for prototype strains of the three serotypes of mammalian reoviruses. Deduced amino acid sequences of the S1-encoded sigma 1 proteins were then compared in order to identify conserved features of these sequences. Discrete regions in the amino-terminal two-thirds of sigma 1 sequence share characteristics with the fibrous domains of other cellular and viral proteins. Most of the amino-terminal one-third of sigma 1 sequence is predicted to form an alpha-helical coiled coil like that of myosin. The middle one-third of sigma 1 sequence appears more heterogeneous; it is predicted to form a large region of beta-sheet that is followed by a region which contains two short alpha-helical coiled coils separated by a smaller region of beta-sheet. The two beta-sheet regions are each proposed to form a cross-beta sandwich like that suggested for the rod domain of the adenovirus fiber protein (N. M. Green, N. G. Wrigley, W. C. Russell, S. R. Martin, and A. D. McLachlan, EMBO J. 2:1357-1365, 1983). The remaining carboxy-terminal one-third of sigma 1 sequence is predicted to form a structurally complex globular domain. A model is suggested in which the discrete regions of sigma 1 sequence are ascribed to morphologic regions seen in computer-processed electron micrographic images of the protein (R. D. B. Fraser, D. B. Furlong, B. L. Trus, M. L. Nibert, B. N. Fields, and A. C. Steven, J. Virol. 64:2990-3000, 1990.
Magnetic multilayers on nanospheres (2006)

Thin-film technology is widely implemented in numerous applications. Although flat substrates are commonly used, we report on the advantages of using curved surfaces as a substrate. The curvature induces a lateral film-thickness variation that allows alteration of the properties of the deposited material. Based on this concept, a variety of implementations in materials science can be expected. As an example, a topographic pattern formed of spherical nanoparticles is combined with magnetic multilayer fi lm deposition. Here we show that this combination leads to a new class of magnetic material with a unique combination of remarkable properties: The so-formed nanostructures are monodisperse, magnetically isolated, single-domain, and reveal a uniform magnetic anisotropy with an unexpected switching behaviour induced by their spherical shape. Furthermore, changing the deposition angle with respect to the particle ensemble allows tailoring of the orientation of the magnetic anisotropy, which results in tilted nanostructure material.
Hydrophobic Chromatography: Use for Purification of Glycogen Synthetase (1973)

A homologous series of omega-aminoalkylagaroses [Sepharose-NH(CH(2))(n)NH(2)] that varied in the length of their hydrocarbon side chains was synthesized. This family of agaroses was used for a new type of chromatography, in which retention of proteins is achieved mainly through lipophilic interactions between the hydrocarbon side chains on the agarose and accessible hydrophobic pockets in the protein. When an extract of rabbit muscle was subjected to chromatography on these modified agaroses, the columns with short "arms" (n = 2 and n = 3) excluded glycogen synthetase (EC 2.4.1.11), but the enzyme was retained on delta-aminobutyl-agarose (n = 4), from which it could be eluted with a linear NaCl gradient. Higher members of this series (e.g., n = 6) bind the synthetase so tightly that it can be eluted only in a denatured form. A column of delta-aminobutyl-agarose, which retained the synthetase, excluded glycogen phosphorylase (EC 2.4.1.1), which in this column series and under the same conditions requires side chains 5-(or 6)-carbon-atoms long for retention. Therefore, it is possible to isolate glycogen synthetase by passage of muscle extract through delta-aminobutyl-agarose, then to extract phosphorylase by subjecting the excluded proteins to chromatography on omega-aminohexyl-agarose (n = 6). On a preparative scale, the synthetase (I form) was purified 25- to 50-fold in one step. This paper describes some basic features and potential uses of hydrophobic chromatography. The relevance of the results presented here to the design and use of affinity chromatography columns is discussed.
Vascular endothelial growth factor plasma levels before and after treatment of neovascular age‐related macular degeneration with bevacizumab or ranibizumab (2011)

Intravitreal bevacizumab significantly reduced VEGF plasma levels until 28 days after intravitreal injection in patients with exudative AMD. Ranibizumab did not achieve a significant plasma VEGF reduction at the same time-point. These findings alert to the potential systemic safety differences between the two drugs after intravitreal administration.
Determination of thermal conductivity of sands under varying moisture, drainage/wetting, and porosity conditions - applications in near-surface soil moisture distribution analysis (2009)

A class of problems in hydrology and remote sensing requires improved understanding of how water and heat flux boundary conditions affect the soil moisture processes in the shallow subsurface near the land/atmospheric interface. In these systems, a clear understanding of how variations in water content, soil drainage/wetting and porosity conditions affect the soil's thermal behavior is needed for the accurate detection of buried objects such as landmines, however, very few experimental data showing the effects of these variations are available. In this study, the effect of soil moisture, soil hysteretic behavior and porosity on the thermal conductivity of some sandy soils was investigated. For this experimental investigation, a Tempe cell was modified to have a network of sampling ports, continuously monitoring water saturation, capillary pressure, temperature, and soil thermal properties. The water table was established at mid elevation of the cell and then lowered slowly. The initially saturated soil sample was subjected to slow drainage, wetting, and secondary drainage cycles. After liquid water drainage ceased, evaporation was induced at the surface to remove soil moisture from the sample to obtain thermal conductivity data below the residual saturation. For the test soils studied, thermal conductivity increased with increasing soil density and moisture content while thermal conductivity values were similar for soil drying/wetting behavior. Thermal properties measured in this study were then compared with independent estimates made using empirical models from literature. These soils will be used in a proposed set of experiments in intermediate scale test tanks to obtain data to validate methods and modeling tools used for landmine detection.