gebhart/patrepeval huggingface dataset:
Using GIS to enhance agricultural planning: The example of inter‐seasonal rainfall variability in Zimbabwe (1996)

Inter‐seasonal rainfall variability is evaluated as a potential source of much needed information for agroecological or agroclimatological classifications. For some food crop production areas, inter‐seasonal rainfall variability appears to dominate decisions in the crop‐production strategy. We constructed 31 years worth of seasonal rainfall surfaces for Zimbabwe using techniques as described by Hutchinson (1995) and his software ANUSPLIN. We evaluated these surfaces in an effort to describe the main rainfall period (October to March) for Zimbabwe in terms of rainfall variability. Our results were then put into the context of an agroecological study which produced a Natural Regions map for Zimbabwe. GIS technology enables the synthesis and integration of many more data than was possible in a pre‐computer era and robust rainfall variability surfaces contribute towards improved agroecological and agroclimatological classifications for planning (natural resource management and agricultural) purposes. GIS technology also enables a shift in the design of such agroecological or agroclimatological studies: dynamic characterization can readily produce objective specific classifications, classifications which use the wealth of data readily accessible in a GIS to produce maps and databases reflecting specific boundary conditions.
Multiple sequence alignment accuracy and evolutionary distance estimation (2005)

The bias in distance estimation appears to be a direct result of the standard greedy progressive algorithm used by many multiple alignment methods. These results have implications for choosing new taxa and genomes to sequence when resources are limited.
Structural studies of spider silk proteins in the fiber (1997)

Although spider silk has been studied for a number of years the structures of the proteins involved have yet to be definitely determined. X-ray diffraction and solid-state nuclear magnetic resonance (NMR) were used to study major ampullate (dragline) silk from Nephila clavipes. The silk was studied in its natural state, in the supercontracted state and in the restretched state following supercontraction. The natural silk structure is dominated by beta-sheets aligned parallel to the fiber axis. Supercontraction is characterized by randomizing of the orientation of the beta-sheet. When the fiber is restretched alignment is regained. However, the same reorientation was observed for wetting of minor ampullate silk which does not supercontract. Thus, the reorientation of beta-sheets alone cannot explain the supercontraction in dragline silk. Cocoon silk showed very little beta-sheet orientation in the natural state and there were no changes upon wetting. NMR and X-ray diffraction data are consistent with the beta-sheets arising from the poly-alanine sequences known to be present in the proteins of major ampullate silk as has been proposed previously.
Induced surface roughness to promote the growth of tilted-AlN films for shear mode resonators (2013)

Two methods currently used to induce surface roughness that promotes the growth of AlN tilted grains to fabricate shear mode resonators have been investigated. The first one involves the use of a rough substrate to provide tilted facets on which the AlN grains will grow with a certain angle. The second method is based on using a thin non-piezoelectric AlN seed layer that exhibits high populations of {10·3} and {10·2} planes. The influence of the power applied to the Al target and the total gas pressure during the deposition process of the AlN seed layer has been studied and correlated with the k <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">shear</sub> of the resonators. The best fabricated devices show a shear mode resonance frequency at around 1.45 GHz, a k <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">shear</sub> up to 3.64% and a Q <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">shear</sub> above 230 when operating in air, which reduces to 108 when operating in liquid.
Efficient isolation of live microglia with preserved phenotypes from adult mouse brain (2012)

Immunomagnetic separation is an efficient method to isolate microglia from the CNS, and is equally suitable for isolating quiescent and activated microglia. This technique allows evaluation of microglial activities ex vivo, which accurately reflects their activities in vivo. Microglia obtained by this method can be used for multiple downstream applications including qRT-PCR, ELISA, Western blotting, and flow cytometry to analyze microglial activities in any number of CNS pathologies or injuries.
Platelet function in sepsis (2002)

Platelets play a complex role in sepsis; they are able to modulate not only their own function but also that of cells around them. Further study is needed to better define the precise mechanisms and effects of platelet activation in sepsis and to determine the benefits and risks of inhibiting platelet function.
Detection of serum free light chains: the problem with antigen excess (2010)

Abstract Background: In recent years, measurement of serum immunoglobulin free light chains (FLCs) has greatly facilitated diagnosis and monitoring of various plasma cells dyscrasias, including multiple myeloma. Detection of FLCs by nephelometry depends on the formation of immune complexes. However, it is known that if the antigen (free light chain) is present in great excess, non-precipitating immune complexes can be formed and be detected poorly. This may lead to inaccurate test results. Methods: Serum samples from 91 patients were subjected prospectively to the detection of free κ and λ light chains by automated nephelometry. A standard dilution of 1:100 was paralleled by a 1:2000 dilution. In addition, samples with values below the effective range (1:100) were subjected to a 1:20 dilution in order to calculate the κ/λ ratio. Results: Here, we report the incidence of antigen excess in a cohort of 91 patients with a high proportion of monoclonal abnormalities. A standard dilution (1:100) of free light κ chains from a patient with monoclonal immunoglobulin A κ gammopathy were missed repeatedly. In a second patient (with myeloproliferative disease and an apparent incidental FLC monoclonal gammopathy of undetermined significance) free λ chains were also substantially underestimated in the standard dilution. Hence, the incidence of erroneously low test results due to antigen excess was 2.20%. Conclusions: We found a significantly higher incidence of falsely low test results due to antigen excess than reported previously. Antigen excess may result in erroneous interpretations in sera subjected to nephelometric analysis. Therefore, clinical decisions should not be based solely on a single assay, especially if FLC testing includes only one dilution of the serum sample. Instead, several parallel dilutions should be recommended for screening of patients. Clin Chem Lab Med 2010;48:1419–22.
Gas in scattering media absorption spectroscopy – from basic studies to biomedical applications (2013)

Abstract The recently introduced Gas in Scattering Media Absorption Spectroscopy (GASMAS) technique provides novel possibilities for analysis in biophotonics. Free gas in pores or cavities is monitored with narrow‐band laser radiation, which can discern the gas absorptive imprints which are typically several orders of magnitude more narrow than the features of the surrounding tissue through which the diffusely scattered light emerges to the detector. Important gases monitored are oxygen and water vapour. Applications include diagnosis of human sinus cavities and surveillance of neonatal children, but also characterization of food‐stuffs, food packages and pharmaceutical preparations. Non‐biological applications include the study of construction materials such as wood, polystyrene foams and ceramics. For nano‐porous materials, information on the pore sizes can be obtained from observed line broadening. Apart from concentration measurements, the GASMAS technique also allows the study of gas transport and diffusion, and pressure and temperature information can also be obtained.
Antibody redesign by chain shuffling from random combinatorial immunoglobulin libraries. (1991)

A number of experiments on the shuffling of heavy and light chains from antibodies of defined specificity for the transition-state analogue hapten nitrophenyl phosphonamidate are described. The experiments report on the promiscuity of heavy and light chains in binding antigen and the feasibility of antibody redesign by this shuffling process. The concepts of incestuous and extraclonal promiscuous association are described. Shuffling opens the possibility of generating panels of antibodies with related specificity but of distinct idiotypic composition that may have significance in the use of human monoclonal antibodies in therapy.
Plastic Scintillators. III. The Synthesis of Some Anthracene Derivatives as Wavelength Shifters in Plastic Scintillators (1966)

Abstract Fifteen anthracene derivatives have been synthesized, and their absorption and fluorescence spectra have been measured. The spectra will be discussed in this paper. According to the spectra, some of anthracene derivatives synthesized here are better wavelength shifters than the compounds previously described in the literature.
Recent Studies of Port Dredging and Offshore Spoil Dumps (1990)

Recently, several Port Authorities in Queensland have instigated detailed studies of their dredging and dumping operations associated with Port dredging works, with methodologies derived and actual studies carried out by Connell Wagner. These studies are aimed at determining whether current practices satisfy stringent Federal Government environmental requirements, and whether any change in dredging or dumping methods are required. This paper examines various stages of investigations, including general field data collection, specialised drogue tracking techniques, plume monitoring equipment and methods including use of nephelometers, and temperature and salinity probes, laboratory testing of spoil, and flume studies on erodability. The physics of dredge and dump plume formation and movement will be discussed, as well as the factors governing long term movement of spoil from dump sites. Other areas addressed include:- - Numerical modelling of dredge and dump plume generation and dispersion. - Advanced statistical analysis of long term current, wave and wind data. - The use of two-dimensional unsteady flow modelling in the study of dredging and dumping of spoil, and the determination of most suitable dump sites. - The modelling of sediment movements in the general area of the spoil dump.
Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA (1997)

A quantitative molecular technique was developed for rapid analysis of microbial community diversity in various environments. The technique employed PCR in which one of the two primers used was fluorescently labeled at the 5' end and was used to amplify a selected region of bacterial genes encoding 16S rRNA from total community DNA. The PCR product was digested with restriction enzymes, and the fluorescently labeled terminal restriction fragment was precisely measured by using an automated DNA sequencer. Computer-simulated analysis of terminal restriction fragment length polymorphisms (T-RFLP) for 1,002 eubacterial sequences showed that with proper selection of PCR primers and restriction enzymes, 686 sequences could be PCR amplified and classified into 233 unique terminal restriction fragment lengths or "ribotypes." Using T-RFLP, we were able to distinguish all bacterial strains in a model bacterial community, and the pattern was consistent with the predicted outcome. Analysis of complex bacterial communities with T-RFLP revealed high species diversity in activated sludge, bioreactor sludge, aquifer sand, and termite guts; as many as 72 unique ribotypes were found in these communities, with 36 ribotypes observed in the termite guts. The community T-RFLP patterns were numerically analyzed and hierarchically clustered. The pattern derived from termite guts was found to be distinctly different from the patterns derived from the other three communities. Overall, our results demonstrated that T-RFLP is a powerful tool for assessing the diversity of complex bacterial communities and for rapidly comparing the community structure and diversity of different ecosystems.
Gadolinium neutron capture therapy for brain tumors: A computer study (1992)

A Monte Carlo computer study of the total dose distribution from neutrons and prompt gamma emissions (but excluding the contribution from conversion and Auger electrons) for gadolinium neutron capture therapy of brain tumors has been carried out in order to test the theoretic feasibility of this modality using commercially available magnetic resonance contrast media. The three-dimensional dose distribution calculations were performed in a spherical head phantom with a spherical tumor at the center. Potentially achievable gadolinium concentrations of 150 micrograms/g of tissue in tumor and 3 micrograms/g in normal tissue were assumed with enrichment to 79.9% gadolinium-157, as supplied by Oak Ridge National Laboratory. Irradiation was assumed to be with a 2-keV monoenergetic cylindrical epithermal neutron beam having a radius of 4 cm. The three-dimensional thermal neutron fluence resulting from the 2-keV beam propagation through the tissue was modeled. For a single neutron beam, the maximum dose is delivered within the tumor but the dose is very inhomogeneous across the tumor volume due to rapid decrease of thermal neutron fluence with depth. Two parallel opposed neutron beams deliver to the interface of normal and malignant tissue 70%-80% of the maximum dose received at the center of the tumor. To deliver an average tumor dose of 500 cGy in 10 min would require a 2-keV source neutrons number of 8.0 x 10(11) per s within the geometry of the beam.
Ocular regeneration by stem cells: present status and future prospects (2008)

Despite the present limitations, it has been progressively accepted that various stem cells may have potential use for the development of cell-based therapies to restore retinal function. AREAS FOR RESEARCH DEVELOPMENT: There is need to understand the cell requirements and environmental conditions that may promote functional integration and long-term survival of stem cells within the diseased retina. At present, this constitutes a major area of research.
6. Testing, Testing, Testing (1998)

A number of companies have found testing materials through sophisticated equipment and methods to guarantee construction quality to be a successful practice. Laboratorio Tecnologico Mantovano (LTM) and Tecnotest, two firms involved in guaranteeing the quality of construction, are profiled. Objectives and methodologies are examined, such as LTM's aims of identifying effective subjects of tests and their meanings, as well as having a comprehensive suite of equipment on hand to offer complete service. Equipment is examined, including the roller compactor.
Rib spreader laceration: a confusing artifact of emergency thoracotomy. (1983)

During emergency thoracotomy, an artifactual injury complex consisting of laceration, abrasion, and, rarely, contusion may be formed by application of a surgical instrument called a rib spreader. Six cases demonstrating this confusing injury are presented, and its formation is discussed.
Induction of Hypoxia-inducible Factor-1α by Transcriptional and Translational Mechanisms (2002)

Hypoxia-inducible factor-1 (HIF-1) regulates the transcription of many genes induced by low oxygen conditions. Recent studies have demonstrated that non-hypoxic stimuli can also activate HIF-1 in a cell-specific manner. Here, we define two key mechanisms that are implicated in increasing the active subunit of the HIF-1 complex, HIF-1alpha, following the stimulation of vascular smooth muscle cells (VSMC) with angiotensin II (Ang II). We show that, in contrast to hypoxia, the induction of HIF-1alpha by Ang II in VSMC is dependent on active transcription and ongoing translation. We demonstrate that stimulation of VSMC by Ang II strongly increases HIF-1alpha gene expression. The activation of diacylglycerol-sensitive protein kinase C (PKC) plays a major role in the increase of HIF-1alpha gene transcription. We also demonstrate that Ang II relies on ongoing translation to maintain elevated HIF-1alpha protein levels. Ang II increases HIF-1alpha translation by a reactive oxygen species (ROS)-dependent activation of the phosphatidylinositol 3-kinase pathway, which acts on the 5'-untranslated region of HIF-1alpha mRNA. These results establish that the non-hypoxic induction of the HIF-1 transcription factor via vasoactive hormones (Ang II and thrombin) is triggered by a dual mechanism, i.e. a PKC-mediated transcriptional action and a ROS-dependent increase in HIF-1alpha protein expression. Elucidation of these signaling pathways that up-regulate the vascular endothelial growth factor (VEGF) could have a strong impact on different aspects of vascular biology.
Physics of Electric Propulsion (1969)

Book on physics of electric propulsion covering gas acceleration principles, flow heating and space thrustor design
Nuclear envelope proteins and neuromuscular diseases (2002)

Several neuromuscular diseases are caused by mutations in emerin and A-type lamins, proteins of the nuclear envelope. Emery-Dreifuss muscular dystrophy is caused by mutations in emerin (X-linked) or A-type lamins (autosomal dominant). Mutations in A-type lamins also cause limb-girdle muscular dystrophy type 1B, dilated cardiomyopathy with conduction defect, and Charcot-Marie-Tooth disorder type 2B1. They also cause partial lipodystrophy syndromes. The functions of emerin and A-type lamins and the mechanisms of how mutations in these proteins cause tissue-specific diseases are not well understood. The mutated proteins may cause structural damage to cells but may also affect processes such as gene regulation. This review gives an overview of this topic and describes recent advances in identification of disease-causing mutations, studies of cells and tissues from subjects with these diseases, and animal and cell culture models.
Inhibition of hepatitis B virus by retroviral vectors expressing antisense RNA (1997)

Two retroviral vectors carrying an antisense gene from the hepatitis B virus (HBV) preS/S or preC/C were constructed and used to infect the human hepatoblastoma cell line 2.2.15, which expresses HBV surface antigen (HBsAg), HBV e antigen (HBeAg) and releases HBV particles. The results showed that the inhibitory effects of antisense gene transfer, mediated by retroviral vectors on the expression of HBV antigens, appeared as early as day 3 after transduction, reached a maximum on day 5 and persisted for at least 11 days. Our data indicate that, on day 5 after introduction, antisense preS/S inhibited HBsAg and HBeAg expression by 71% and 23%, and the antisense preC/C inhibited HBsAg and HBeAg expression by 23% and 59%. HBV DNA production, in the supernatant of the 2.2.15 cells transduced with either antisense preS/S or preC/C, was also reduced on day 5, but the viability of the 2.2.15 cells was not affected. Our results demonstrate that the replication and expression of HBV can be inhibited through antisense gene transfer mediated by retroviral vectors and that the antisense-preC/C or antisense-preS/S may be potentially useful for clinical gene therapy against HBV.
Sexual Function and Satisfaction in the Treatment of Chronic Major Depression With Nefazodone, Psychotherapy, and Their Combination (2002)

Chronic depression is associated with high rates of sexual dysfunction. Treatment with nefazodone, CBASP, and combined treatment improved sexual interest/satisfaction, with greatest improvement observed with combined treatment.
Single‐Layer Transition Metal Dichalcogenide Nanosheet‐Based Nanosensors for Rapid, Sensitive, and Multiplexed Detection of DNA (2014)

Single-layer transition metal dichalcogenide nanosheets, including MoS2, TiS2, and TaS2, are used as novel sensing platforms for sensitive and selective detection of DNA, based on their high fluorescence-quenching ability and different affinities toward single-stranded DNA and double-stranded DNA. Importantly, for the first time, a single-layer TaS2 nanosheet-based multiplexed DNA sensor is also developed.
IL-7 transgenic mice: analysis of the role of IL-7 in the differentiation of thymocytes in vivo and in vitro (1995)

We have generated a high copy number transgenic mouse line in which expression of mouse IL-7 cDNA is under the control of the mouse MHC class II E alpha promoter. These mice were generated in order to see if IL-7 over-production in the thymus altered either thymocyte differentiation or the process of negative selection. Using in situ hybridization, IL-7 transcripts could be detected in the thymic cortex and medulla as well as the spleen and lymph nodes of transgenic mice but was undetectable in normal controls. Phenotypic and molecular analysis of thymocytes from embryonic and adult transgenic mice failed to reveal a dramatic effect of IL-7 on thymocyte differentiation and negative selection of the TCR V beta repertoire appeared to be intact. In peripheral lymph nodes, there was a massive (30-fold) increase in the number of T cells (CD8+ > CD4+) and simultaneous presence of immature (B220+, Ig-) B cells. TCR repertoire analysis showed that the expansion of peripheral T cells was polyclonal. Using the polymerase chain reaction (PCR), transgene-specific IL-7 transcripts could be detected in the thymus from day 14 of fetal development. However, using semi-quantitative PCR, there was no dramatic increase in the degree of TCR beta or TCR alpha gene rearrangements during thymocyte ontogeny in vivo. Similarly, when fetal mouse thymus lobes were cultured with IL-7 in vitro, there was no dramatic increase in the degree of TCR beta or TCR alpha gene rearrangements. We conclude that IL-7 is probably not an important differentiation factor for immature mouse thymocytes.
High Throughput Automated Allele Frequency Estimation by Pyrosequencing (2008)

Pyrosequencing is a DNA sequencing method based on the principle of sequencing-by-synthesis and pyrophosphate detection through a series of enzymatic reactions. This bioluminometric, real-time DNA sequencing technique offers unique applications that are cost-effective and user-friendly. In this study, we have combined a number of methods to develop an accurate, robust and cost efficient method to determine allele frequencies in large populations for association studies. The assay offers the advantage of minimal systemic sampling errors, uses a general biotin amplification approach, and replaces dTTP for dATP-apha-thio to avoid non-uniform higher peaks in order to increase accuracy. We demonstrate that this newly developed assay is a robust, cost-effective, accurate and reproducible approach for large-scale genotyping of DNA pools. We also discuss potential improvements of the software for more accurate allele frequency analysis.