gebhart/patrepeval huggingface dataset:
Marine Magnetic Surveying and Disturbance Field Monitoring by Autonomous Marine Vehicles (2014)

Abstract Directional drilling uses measurement while drilling (MWD) to infer the inclination and azimuth of the drill bit. The accuracy of the measured azimuth critically depends on the local direction and strength of the geomagnetic field. Lateral uncertainties in the bottomhole location can typically be reduced by 50% if the local geomagnetic field is known accurately. This requires both the mapping of spatial crustal anomalies as well as the continuous monitoring of "space weather" disturbance field variations during drilling operations. Traditionally, these tasks are carried out by aircraft, ships and onshore geomagnetic observatories. A novel study employed autonomous marine vehicles for geomagnetic surveying. Two autonomous marine vehicles were equipped with towed magnetometers and were deployed for 2 months offshore the Hawaiian Islands. To investigate the accuracy of the measurements, the two vehicles surveyed exact-repeat profiles. The measurements of the two vehicles agreed to within 2nT, exceeding even the stringent 5nT standard for geomagnetic observatories. To avoid entangling the towed magnetometer, the autonomous vehicles had to be in continuous motion. They demonstrated their ability to circulate around a given target. This "base station" mode allows them to monitor the time variations of the disturbance field. After correcting for spatial gradients of the crustal field, the measured disturbance field variations were found to be in excellent agreement with the Honolulu observatory. In the final phase of the study, one of the vehicles acted as a base station, while the other surveyed a regular pattern. A total of 700 line kilometers were flawlessly surveyed by one vehicle within 14 days. The resulting crustal magnetic anomaly map agrees to within 10nT with previous, lower-quality ship-borne magnetic surveys. This study demonstrates the utility of autonomous marine vehicles to carry out crustal magnetic surveys and monitor disturbance fields in support of offshore directional drilling operations. These new capabilities improve well placement for increased oil and gas recovery. Accurate geomagnetic reference values further enable tighter quality control of MWD equipment, enhancing safety and reducing nonproductive time.
Organisational trails through software systems (2002)

The use of three dimensional software visualisation techniques has the power to transform the way that tacit knowledge gathering and retrieval takes place during many software maintenance activities. The focus of this work is the understanding and management of software from various perspectives and therefore it is the visualisation of these software artefacts that is of greatest interest. This work moves towards providing a generic visualisation that is applicable to the management of many software systems within the bounds of the organisation, with the ability to view various artefacts over time (and thus their evolution) and also to incorporate lower level visualisations in three dimensions.
The Role of Homogeneous Catalysis in the Conversion of Biomass and Biomass Derived Platform Chemicals (2017)

Various methods are available to convert biomass into chemicals. In this chapter, the biomass is converted either thermally or via fermentation into a limited number of platform chemicals that can be used as raw material for further, mostly catalytic conversions into the desired products. Heterogeneous catalysis has a long history in converting hydrocarbons into functionalized molecules, but in the chemistry presented in the chapter, where deoxygenation is often the first step, heterogeneous catalysis often struggles with catalyst deactivation and homogeneous catalysis is the method of choice for many transformations. This is aided by the fact that homogeneous catalysis often works at much lower temperatures than heterogeneous catalysis, which is highly advantageous when it comes to avoiding side reactions such as condensation reactions. The chapter divides along the lines of the most important groups of raw materials: the sugars and their polymers cellulose and hemicellulose, lignin and fatty acids.
Mapping the multimerization domains of the Gag protein of yeast retrotransposon Ty1 (1997)

The two-hybrid system was used to define regions of the Ty1 Gag protein responsible for multimerization. Gag truncations lacking the first 146 or the last 97 amino acids (Gag is 440 amino acids in length) interact. A severely C-terminally truncated molecule (lacking the last 207 amino acids) was the smallest truncation to interact, suggesting that some protein-protein interactions between Gag molecules are mediated through the first 233 amino acids. However, an internal deletion of amino acids 147 to 233 does not abolish Gag-Gag interaction, indicating that more than one region can mediate Gag interaction. Surprisingly, we found that a truncation lacking the last 97 amino acids interacts with itself but not with full-length Gag. This is apparently due to an artifact of the two-hybrid assay, since these same molecules coassemble with wild-type Gag into Ty1 virus-like particles.
Field-Evolved Resistance: Assessing the Problem and Ways to Move Forward (2013)

"Field-evolved resistance" is defined as a "genetically based decrease in susceptibility of a population to a toxin caused by exposure to the toxin in the field." The key component of "field-evolved" resistance is that it does confer decreased susceptibility to an insecticide in the field. Another key component is that the decrease in susceptibility to the insecticide is because of previous exposure of the target insect to the toxin in the field. Several studies have reported field-evolved resistance to crops engineered to express proteins from the bacterium, Bacillus thuringiensis (Bt). However, there has not been a consistent standard in the application of the definition of field-evolved resistance for Bt crops. The inconsistency in applying the definition arises from differences in the methods used to detect resistance, the ecology of the interaction between the pest and the Bt crop, and the effective dose the pest encounters while feeding on the Bt crop. Using case studies of reported resistance to Bt crops, it is demonstrated resistance does not come in a single form, and that in most cases, resistance can still be managed.
Three‐dimensional multi‐ribbon interconnection for back‐contact solar cells (2021)

Abstract Back‐contact solar cells are an interesting technology with advantages over traditional two‐sided cells. A lack of standardized and low‐cost interconnection methods inhibits their market penetration. In an attempt to overcome this obstacle, this work introduces an interconnection technology, based on a fabric of encapsulant with incorporated metal ribbons. The encapsulant is tailored for this application by adding glass fibres to a thermoplastic polyolefin. For this tailored encapsulant, characterization experiments were conducted and results on viscosity and coefficient of thermal expansion are shown. Initial reliability testing on sample‐size modules with high‐efficiency interdigitated back‐contact (IBC) cells shows promising results, passing up to four times the IEC 61215 standard for thermal cycling.
Remodeling of the Human Retina in Choroideremia: Rab Escort Protein 1 (REP-1) Mutations (2006)

The CHM disease sequence involves detectable retinal thickening, which may be due to Müller cell activation and hypertrophy from photoreceptor stress. Photoreceptor degeneration, RPE depigmentation, and retinal remodeling follow. The results represent in vivo evidence in humans for retinal remodeling and provide a marker for the earliest stage of this response to genetic retinal disease. For CHM and other candidate human retinopathies considered for therapy, there is now a framework for making informed decisions about timing, retinal location, and potential value of treatment.
Spinning up the polymorphs of calcium carbonate (2014)

Controlling the growth of the polymorphs of calcium carbonate is important in understanding the changing environmental conditions in the oceans. Aragonite is the main polymorph in the inner shells of marine organisms, and can be readily converted to calcite, which is the most stable polymorph of calcium carbonate. Both of these polymorphs are significantly more stable than vaterite, which is the other naturally occurring polymorph of calcium carbonate, and this is reflected in its limited distribution in nature. We have investigated the effect of high shear forces on the phase behaviour of calcium carbonate using a vortex fluidic device (VFD), with experimental parameters varied to explore calcium carbonate mineralisation. Variation of tilt angle, rotation speed and temperature allow for control over the size, shape and phase of the resulting calcium carbonate.
Abstract 2442: XPO1 is selinexor prime target: validation by mutating cysteine 528 on both XPO1 alleles using CRISPR/Cas9 genome editing (2015)

Abstract Human Exportin-1 (XPO1) is the key nuclear-cytoplasmic transport protein that exports a variety of different cargo proteins out of the cell's nucleus. Inhibition of XPO1-mediated protein export results in nuclear retention of cargo proteins including tumour suppressor proteins and is a novel therapeutic strategy for cancer. Selinexor, an orally bioavailable XPO1 inhibitor, effectively demonstrates potent activity against multiple types of cancer. Here we directly demonstrate the high selectivity of selinexor for XPO1 inside living cells. Selinexor binds to the cargo-binding pocket of XPO1 and inhibits the formation of XPO1-cargo complex. The binding of selinexor to XPO1 involves a slowly reversible Michael addition type interaction of its acrylate moiety with cysteine 528 residue of XPO1. Using CRISPR/Cas9 genome editing we have now created a homozygous Jurkat T-ALL cell line carrying a Cys528Ser mutation in XPO1. This cell line was used to study the specificity of selinexor for XPO1 inside the cancer cell. Selinexor was highly toxic to wild-type Jurkat cells in the low nanomolar range while the mutant cells were resistant up to micromolar concentrations. These results were confirmed by resistance to induction of caspase dependent apoptosis as well as cell cycle arrest in mutant cells. The single Cys528Ser mutation thus confers resistance to selinexor. In addition, selinexor failed to accumulate cargo proteins in the nucleus of mutant cells. Moreover, the Cys528Ser substitution conferred resistance to the direct interaction of this drug to XPO1 in cells. In conclusion, these results validate XPO1 as the selinexor's prime target and pinpoint its unique selectivity to the Cys528 residue of XPO1. Our findings also demonstrate the general utility of CRISPR/Cas9 genome editing for introducing point mutations in the genome of cancer cells for drug-target specificity validation. Citation Format: Jasper E. Neggers, Thomas Vercruysse, Maarten Jacquemyn, Els Vanstreels, Erkan Baloglu, Sharon Shacham, Marsha Crochiere, William Senapedis, Yosef Landesman, Dirk Daelemans. XPO1 is selinexor prime target: validation by mutating cysteine 528 on both XPO1 alleles using CRISPR/Cas9 genome editing. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2442. doi:10.1158/1538-7445.AM2015-2442
Novel cleaning technology for nanoparticle removal (2019)

It’s generally said that the management of particles is important. In DUV lithography, it’s needed to remove particles on photomask surface not to induce patterning defects on wafer. Moreover, in Nanoimprint lithography (NIL), particles on template cause not only patterning defects on wafer but also its own pattern collapse. Therefore, these particles have to be entirely removed from substrate surface with cleaning technology. In this paper, we proposed ‘Freeze Cleaning’ which has more than 99% PRE for 40nm SiN standard nanoparticle without pattern collapse and critical dimension (CD) shift. And it was also demonstrated that soft defects on template which remained after conv. cleaning could be removed with Freeze Cleaning. These results predict that Freeze Cleaning will contribute to progress of photomask and template technology to next stage.
Serum proteomic profiling of rheumatoid arthritis–interstitial lung disease with a comparison to idiopathic pulmonary fibrosis (2022)

Although interstitial lung disease (ILD) causes significant morbidity and mortality in rheumatoid arthritis (RA), it is difficult to predict the development or progression of ILD, emphasising the need for improved discovery through minimally invasive diagnostic tests. Aptamer-based proteomic profiling was used to assess 1321 proteins from 159 patients with rheumatoid arthritis with interstitial lung disease (RA-ILD), RA without ILD, idiopathic pulmonary fibrosis and healthy controls. Differential expression and gene set enrichment analyses revealed molecular signatures that are strongly associated with the presence and severity of RA-ILD and provided insight into unexplored pathways of disease. These warrant further study as non-invasive diagnostic tools and future therapeutic targets.
Electromagnetic Breast Imaging: Results of a Pilot Study in Women with Abnormal Mammograms (2007)

Results from EM breast examinations provide statistical evidence of a mean increase in image contrast of 150%-200% between abnormal (benign and malignant) and normal breast tissue.
Ultraviolet laser-induced poling inhibition produces bulk domains in MgO-doped lithium niobate crystals (2014)

We report the realization of high-resolution bulk domains achieved using a shallow, structured, domain inverted surface template obtained by UV laser-induced poling inhibition in MgO-doped lithium niobate. The quality of the obtained bulk domains is compared to those of the template and their application for second harmonic generation is demonstrated. The present method enables domain structures with a period length as small as 3 μm to be achieved. Furthermore, we propose a potential physical mechanism that leads to the transformation of the surface template into bulk domains.
Microfluidics-based point-of-care test for serodiagnosis of Lyme Disease (2016)

Currently, diagnostic testing for Lyme disease is done by determination of the serologic responses to Borrelia burgdorferi antigens, with the exception of the early localized phase of disease where diagnosis must be done clinically. Here, we describe the use of microfluidics technology to develop a multiplexed rapid lab-on-a-chip point of care (POC) assay for the serologic diagnosis of human Lyme disease. Following ELISA screening of 12 candidate antigens, we tested 8 on a microfluidic diagnostic system, called mChip-Ld, using a set of 60 serological samples. The mChip-Ld test, which can be performed in 15 minutes at the point of care, showed promising performance for detection of antibodies to B. burgdorferi using the PPO triplex test (rP100 + PepVF + rOspC-K, AUC of 0.844) compared to a gold-standard reference of culture confirmed clinical samples. The performance is comparable to the commonly used C6 peptide by lab-based ELISA. In addition, the mChip-Ld test showed promising performance for early-stage diagnosis of the disease using the antigen OspC-K (sensitivity and specificity of 84% and 92%, respectively; AUC of 0.877). Overall, this study underscores the potential of using microfluidics to aid the diagnosis of Lyme disease at the point of care.
A comparative study on iron sources for mitochondrial haem synthesis including ferritin and models of transit pool species (1986)

The rates of reaction of various exogenic iron(III) complexes with deuteroporphyrin IX in isolated mitochondria to form deuterohaem were measured. Ferritin was shown to supply iron readily for haem synthesis if the ferritin iron was reductively mobilised by the mitochondrial respiratory chain with succinate as substrate and FMN as mediator. In contrast, polynuclear complexes of iron(III) were able to form deuterohaem without added FMN. Rates of haem formation are about five times higher for the lowest polynuclear units than for ferritin. Sorbitol, gluconate, and bovine serum albumin were used as scavengers for polynuclear complexes with restricted size. Strong chelators of iron(II) compete favourably for deuterohaem formation, which supports the multistep mechanism for haem formation suggested by a priori arguments. Rates of deuterohaem formation were measured in homologous and heterologous systems of ferritins and mitochondria. Slightly differing rates of haem formation were shown to originate in different rates of iron mobilisation from the ferritins. The lack of species specificity in the interaction of ferritin with mitochondria also shows up in the linear dependence of ferritin binding on its bulk concentration as measured using 3H-labeled ferritin. Rates of haem formation are virtually the same in mitoplasts and mitochondria which indicates insignificant influences of the outer membrane. The hypothesis of low polynuclears as major components of the intracellular transit iron pool implies that both ferritin and transit iron pool species are largely equivalent sources of iron for mitochondrial haem synthesis.
Evidence of intrinsic silicon nanostructure formation in SiN matrix deposited by various low temperature CVD techniques (2007)

Abstract In this work, we report the intrinsic formation of silicon nanostructures (ns‐Si) in non‐stoechiometric amorphous hydrogenated silicon nitride (SiN x :H) obtained by different deposition techniques (UltraViolet photo‐assisted Chemical Vapour Deposition and Low‐Frequency Plasma‐Enhanced CVD using two different reactors). No post‐deposition treatment was needed. The obtained layers were characterized by photoluminescence (PL) and photocurrent (PC) spectroscopy, revealing emission/absorption mechanisms dominated by confined excitons within ns‐Si. Transmission electron microscopy (TEM) confirmed the presence of these ns‐Si, in a crystalline form, for SiN x :H layers obtained by both LF‐PECVD reactors. Thus, quantum confinement effect could be identified for every deposition techniques involved, revealing the formation of intrinsic ns‐Si in the amorphous SiN matrix. (© 2007 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Influence of pH, Precursor Concentration, Growth Time, and Temperature on the Morphology of ZnO Nanostructures Grown by the Hydrothermal Method (2011)

We investigated the influence of the pH value, precursor concentration ( C ), growth time and temperature on the morphology of zinc oxide (ZnO) nanostructures. The pH of the starting solution was varied from 1.8 to 12.5. It was found that the final pH reaches an inherent value of 6.6 independently of the initial pH solution. Various ZnO structures of nanotetrapod-like, flower-like, and urchin-like morphology were obtained at alkaline pH (8 to 12.5) whereas for pH solution lower than 8 rod-like nanostructures occurred. Moreover, we observed the erosion of the nanorods for a pH value less than 4.6. By changing the concentrations the density and size were also varied. On going from a high (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>C</mml:mi><mml:mo>&gt;</mml:mo><mml:mn>400</mml:mn></mml:math> mM) to lower (<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>C</mml:mi><mml:mo>&lt;</mml:mo><mml:mn>25</mml:mn></mml:math> mM) C , the resulted ZnO nanostructures change from a film to nanorods (NRs) and finally nanowires (NWs). It was also found that the length and diameter of ZnO NRs follow a linear relation with time up to 10 hours, above which no further increase was observed. Finally the effect of growth temperature was seen as an influence on the aspect ratio.
Linear oligopeptides. Part 406.1 Helical screw sense of peptide molecules: the pentapeptide system (Aib)4/L-Val[L-(αMe)Val] in solution (1998)

A variety of N α-blocked pentapeptide esters, each containing four helicogenic, achiral α-aminoisobutyric acid residues and one chiral L-valine or C α-methyl-L-valine residue in the N-terminal, internal or C-terminal position of the sequence, have been synthesized by solution methods and fully characterized. The results of a solution conformational analysis, performed by using FTIR absorption and 1H NMR techniques, favour the conclusion that all of the pentapeptides examined fold into a 310-helical structure. In addition, a CD study of the N α-para-bromobenzoylated peptides strongly supports the view that the prevailing screw sense of the 310-helical structure that is formed is strongly dependent upon the position in the sequence of the single chiral C α-tri- or C α-tetrasubstituted α-amino acid.
Iodine-promoted one-pot synthesis of 1,3,4-oxadiazole scaffolds via sp3 C–H functionalization of azaarenes (2019)

An efficient metal-free one-pot protocol has been developed for the construction of 1,3,4-oxadiazole derivatives <italic>via</italic> iodine-mediated oxidative amination of benzylic C–H bonds of azaarenes.
Low Frequency of Autoantibodies to the Human Na+/I−Symporter in Patients with Autoimmune Thyroid Disease1 (2000)

Several studies suggest that the sodium-iodide symporter (NIS) may represent a major autoantigen in autoimmune diseases of the thyroid. The aim of the present paper was to investigate the importance of autoantibodies to human NIS (hNIS-Ab) in patients suffering from Hashimoto's thyroiditis (HT) and Graves' disease (GD). Full-length human NIS (hNIS) was cloned from thyroid tissue, expressed by in vitro transcription and translation in the presence of [(35)S]methionine, and used to analyze autoantibodies in a direct binding assay. The structurally similar glucose transporter, GLUT-2, was produced in the same system as control protein. Autoradiography revealed that full-length hNIS was expressed, recognized by a NIS monoclonal antibody, and strongly bound by some sera from patients with autoimmune thyroid disease, which did not react with the GLUT-2 control protein. Using the 95.2th percentile of healthy controls as threshold for positivity, 19 of 177 (10.7%) patients with GD and 15 of 72 (20.8%) patients with HT had hNIS-Ab, respectively. Applying more stringent cut-off criteria (99.4th percentile of normal controls), hNIS-Ab were found in only 5.6% of patients with GD and 6. 9% of patients with HT. In HT significantly higher hNIS-Ab levels were observed compared with GD and normal controls (P: < 0.001). There was no correlation between hNIS-Ab and TSH receptor antibodies and only a weak correlation to thyroid peroxidase antibodies (P: < 0. 05). Comparison of hNIS-Ab, thyroid peroxidase, and TSH receptor antibodies in individual sera revealed that the additional detection of hNIS-Ab did not increase the diagnostic power for GD or HT. Our data indicate that hNIS is not a major antigen in autoimmune thyroid disease, as it is the target of humoral autoimmunity in only a few patients with GD and HT. The frequency of hNIS-Ab may be lower than that reported in previous studies.