gebhart/patrepeval huggingface dataset:
Genetic Engineering of the Major Timothy Grass Pollen Allergen, Phl p 6, to Reduce Allergenic Activity and Preserve Immunogenicity (2007)

On the basis of IgE epitope mapping data, we have produced three allergen fragments comprising aa 1-33, 1-57, and 31-110 of the major timothy grass pollen allergen Phl p 6 aa 1-110 by expression in Escherichia coli and chemical synthesis. Circular dichroism analysis showed that the purified fragments lack the typical alpha-helical fold of the complete allergen. Superposition of the sequences of the fragments onto the three-dimensional allergen structure indicated that the removal of only one of the four helices had led to the destabilization of the alpha helical structure of Phl p 6. The lack of structural fold was accompanied by a strong reduction of IgE reactivity and allergenic activity of the three fragments as determined by basophil histamine release in allergic patients. Each of the three Phl p 6 fragments adsorbed to CFA induced Phl p 6-specific IgG Abs in rabbits. However, immunization of mice with fragments adsorbed to an adjuvant allowed for human use (AluGel-S) showed that only the Phl p 6 aa 31-110 induced Phl p 6-specific IgG Abs. Anti-Phl p 6 IgG Abs induced by vaccination with Phl p 6 aa 31-110 inhibited patients' IgE reactivity to the wild-type allergen as well as Phl p 6-induced basophil degranulation. Our results are of importance for the design of hypoallergenic allergy vaccines. They show that it has to be demonstrated that the hypoallergenic derivative induces a robust IgG response in a formulation that can be used in allergic patients.
BMX tyrosine kinase gene is expressed in granulocytes and myeloid leukaemias (1996)

The growth and maturation of haemopoietic cells is regulated by signal transduction through tyrosine protein kinases. Recently, a novel cytoplasmic tyrosine kinase gene in chromosome X, called Bmx, was identified in human bone marrow RNA. Bmx belongs to a subfamily of tyrosine kinases which are expressed in various haemopoietic cell lineages. We studied Bmx expression using RT-PCR of RNA from fractionated peripheral blood leucocytes, progenitor-enriched fractions of cord blood and from bone marrow or peripheral blood samples from leukaemia patients. Bmx was strongly expressed in haemopoietic tissues and enhanced in neutrophilic granulocytes. Bmx mRNA was also found in CD34-positive progenitor cells from cord blood. All samples (10/10) of patients with acute myeloid leukaemia and (4/4) with chronic myeloid leukaemia showed expression of Bmx. In contrast, none of the samples of acute lymphoid leukaemia (0/8) and only one out of six samples of chronic lymphoid leukaemia expressed Bmx. In conclusion, Bmx expression seems to be associated with myelopoiesis.
Heisenberg, Bell, and experimental quantum cryptography (1994)

When single photons are used to code for individual bits, security can be guaranteed by exploiting Heisenberg's uncertainty principle. Binary information can be coded into two orthogonal states, such as polarization or relative phase (in an interferometer). To receive this information we require an analyzer able to discriminate between the two states in an error-free way. In a linear-polarization system a polarizing beam splitter is used with its axes aligned to the two possible polarization directions. However, using a polarizer at 45° to these directions will ensure a random output uncorrelated to the single-photon-coded bit stream. The principle of secure key sharing, or quantum cryptography, is that a random bit stream is encoded onto individual photons while randomly switching the coding basis between the 0° and 45° polarization bases (in general, any non-orthogonal measurement bases). The receiver also randomly switches between these basis, and information is shared only when a photon is received and the same basis is used for coding and for measurement. An initial experiment of this type was carried out by using faint pulses of polarized visible light over a 40-cm transmission distance.1
A Bias-Reducing Loss Function for CT Image Denoising (2021)

There is growing interest in the use of deep neural network (DNN) based image denoising to reduce patient’s X-ray dosage in medical computed tomography (CT). An effective denoiser must remove noise while maintaining the texture and detail. Commonly used mean squared error (MSE) loss functions in the DNN training weight errors due to bias and variance equally. However, the error due to bias is often more egregious since it results in loss of image texture and detail. In this paper, we present a novel approach to designing a loss function that penalizes variance and bias differently. Our proposed bias-reducing loss function allows us to train a DNN denoiser so that the amount of texture and detail retained can be controlled through a user adjustable parameter. Our experiments verify that the proposed loss function enhances the texture and detail in denoised images with only a slight increase in the MSE.
Time‐lapse PS‐wave time‐shifts and quantitative pressure‐saturation discrimination applications (2023)

Abstract We show that time‐lapse (4D) time‐shifts from PS‐wave data are valuable as they are very sensitive to pressure changes, whereas 4D time‐shifts from PP‐wave data are sensitive to both pressure and saturation changes. This gives another opportunity from using 4D amplitudes alone to understand and discriminate areas of pressure changes from areas of saturation changes in field data. 4D PS time‐shifts sense transmission related changes taking into consideration propagation through the altered medium, whereas amplitude changes are reflection or backscattered signals from the boundary. Therefore, these two attributes will be complimentary in 4D interpretation. Rock‐physics‐based time‐shift cross‐plots are generated to analyse how pressure and saturation changes in a reservoir impact PP‐ and PS‐wave time‐shifts. The developments of 4D time‐shifts are shown fixing the reservoir properties and varying reservoir layer thickness. Synthetic seismic data from a wedge is modelled to understand differences between 4D amplitude and time‐shift changes and the value of PS time‐shifts. Cases with pressure changes only and saturation changes only are also analysed with the wedge model. The method is next applied to two 4D field data sets. One is in the North Sea and the other offshore Brazil. In these field data sets, with different levels of noise in the 4D data, we see interpretable results from PS‐wave time‐shifts that can help in 4D signal understanding and improve reservoir characterization and monitoring practices. We believe that with modern acquisition and processing, this technology is realizable and provides quantitative and accurate 4D interpretations. It is shown that the use of PS‐wave data can lead to a larger chance of success in placing development wells.
Evidence That Multiple Defects in Lipid Regulation Occur before Hyperglycemia during the Prodrome of Type-2 Diabetes (2014)

Defects in adipocyte function from excess energy storage as relatively hypoxic visceral and hepatic fat, and impaired mitochondrial fatty acid oxidation may initiate the observed perturbations in lipid metabolism. Together with evidence from the failure of glucose-directed treatments to improve cardiovascular outcomes, these data and those of others indicate that a new, quite different definition of type-2 diabetes is required. This definition would incorporate disturbed lipid metabolism prior to hyperglycemia.
Sensors for Continuous Monitoring of Surgeon’s Cognitive Workload in the Cardiac Operating Room (2020)

Monitoring healthcare providers' cognitive workload during surgical procedures can provide insight into the dynamic changes of mental states that may affect patient clinical outcomes. The role of cognitive factors influencing both technical and non-technical skill are increasingly being recognized, especially as the opportunities to unobtrusively collect accurate and sensitive data are improving. Applying sensors to capture these data in a complex real-world setting such as the cardiac surgery operating room, however, is accompanied by myriad social, physical, and procedural constraints. The goal of this study was to investigate the feasibility of overcoming logistical barriers in order to effectively collect multi-modal psychophysiological inputs via heart rate (HR) and near-infrared spectroscopy (NIRS) acquisition in the real-world setting of the operating room. The surgeon was outfitted with HR and NIRS sensors during aortic valve surgery, and validation analysis was performed to detect the influence of intra-operative events on cardiovascular and prefrontal cortex changes. Signals collected were significantly correlated and noted intra-operative events and subjective self-reports coincided with observable correlations among cardiovascular and cerebral activity across surgical phases. The primary novelty and contribution of this work is in demonstrating the feasibility of collecting continuous sensor data from a surgical team member in a real-world setting.
Controlling charility and pinhole defects in Ni catalyst for synthesis of graphene (2011)

Controlling the growth of proper crystal morphology and defect density in Ni catalyst are necessary ingredients for achieving precision number of graphene layers [1] and good yields in CMOS transistor device fabrication. The size of grains can be controlled during sputter deposition but the apparent effects in charility are not apparent until after the high temperature annealing process. XRD analysis has been utilized to show degrees of transformation due to controlling variations in sputter gas pressure and temperature. These parameters can accelerate or postponed the final the preferred orientation of the film. The final grain size of the annealed Ni affects the minimum amount of H2 needed to prevent oxidation during the graphene synthesis.
Measurement of the photorefractive phase shift by polarization interferometry (1993)

We present a new approach to measure the phase shift between the photorefractive grating and the interference pattern in two-wave-mixing experiments. This approach is based on using two polarizations for one of the input beams and making them interfere after propagation through the crystal. The real and imaginary parts of the exponential gain are determined independently during grating buildup and erasure. Active stabilization of the optical paths based on this technique is also described and is shown to provide optimal grating formation. The method is applied to an undoped BaTiO3 crystal in which the contribution of traps grating is found negligible.
Development of [18F]FPy-WL12 as a PD-L1 Specific PET Imaging Peptide (2019)

Expression of programmed cell death ligand 1 (PD-L1) within tumors is an important biomarker for guiding immune checkpoint therapies; however, immunohistochemistry-based methods of detection fail to provide a comprehensive picture of PD-L1 levels in an entire patient. To facilitate quantification of PD-L1 in the whole body, we developed a peptide-based, high-affinity PD-L1 imaging agent labeled with [<sup>18</sup>F]fluoride for positron emission tomography (PET) imaging. The parent peptide, WL12, and the nonradioactive analog of the radiotracer, <sup>19</sup>FPy-WL12, inhibit PD-1/PD-L1 interaction at low nanomolar concentrations (half maximal inhibitory concentration [IC<sub>50</sub>], 26-32 nM). The radiotracer, [<sup>18</sup>F]FPy-WL12, was prepared by conjugating 2,3,5,6-tetrafluorophenyl 6-[<sup>18</sup>F]fluoronicotinate ([<sup>18</sup>F]FPy-TFP) to WL12 and assessed for specificity in vitro in 6 cancer cell lines with varying PD-L1 expression. The uptake of the radiotracer reflected the PD-L1 expression assessed by flow cytometry. Next, we performed the in vivo evaluation of [<sup>18</sup>F]FPy-WL12 in mice bearing cancer xenografts by PET imaging, ex vivo biodistribution, and blocking studies. In vivo data demonstrated a PD-L1-specific uptake of [<sup>18</sup>F]FPy-WL12 in tumors that is reduced in mice receiving a blocking dose. The majority of [<sup>18</sup>F]FPy-WL12 radioactivity was localized in the tumors, liver, and kidneys indicating the need for optimization of the labeling strategy to improve the in vivo pharmacokinetics of the radiotracer.
SAT-304 Pituitary Stem Cells May Drive Adenomas Causing Cushing’s Disease (2020)

Abstract Introduction:Cell rests of self-renewing Sox2+ progenitor cells have been identified in the normal pituitary glands1, however their role in human pituitary tumorigenesis is not understood. Adrenocorticotropic hormone (ACTH) producing microadenomas that cause Cushing’s disease frequently (~70%) lack pathogenic genetic mutations.2 In mice, targeted expression of oncogenic β-catenin in Sox2+ cells generate microadenomas. Interestingly, the Sox2+ cells reside within the adjacent normal gland and drive adenomas in a paracrine fashion.3 We hypothesized that Sox2+ progenitors in human pituitary gland may drive the formation of microadenomas that cause Cushing’s disease (CD). Methods:Four ACTH producing adenomas and two non-functional adenomas (NFPA) with separately annotated adjacent normal tissue (henceforward called ‘microenvironment’) were procured for this study (NCT00060541). We performed RNA deep sequencing (RNAseq) and compared expression of lineage-specific markers and progenitor markers using two-sample T-tests after testing for variance equality and using Welch’s approximation for degrees of freedom. Results:We found expected overexpression of ACTH preprohormone POMC in CD adenomas compared to adjacent microenvironment (?-fold) and NFPA (?-fold). The microenvironment in Cushing’s disease showed increased expression of progenitor markers including SOX2, SOX9, CDH1, GRFA2, and KLF4 compared with microenviroment in NFPA. Likewise, the Cushing’s disease microenvironment showed increased expression ofPOMC (26.98 - fold, P = 0.004) as well as PRLR (FC 17.39, P = 0.006) and GH1 (FC 29.91, P = 0.003) implying that increased Sox2+ progenitors contribute to terminally differentiated corticotrope, lactotroph and somatotroph lineages in-vivo. Conclusions:We report increased expression of several progenitor markers and concomitant elevation in tissues-specific markers in the microenvironment of Cushing’s disease patients. Our results indicate that increased pituitary progenitors in the microenvironment of human corticotropinomas may signal in paracrine fashion and may contribute to the pathogenesis of Cushing’s disease. References:1. Cox, B. et al. J. Endocrinol.234, R135-R158 (2017).2. Bi, W. L. et al. Clin. Cancer Res.23, 1841-1851 (2017).3. Andoniadou, C. L. et al. Cell Stem Cell13, 433-445 (2013).
Callisto (2018)

Sexual misconduct is prevalent in workplace and education settings but stigma and risk of further damage deter many victims from seeking justice. Callisto, a non-profit that has created an online sexual assault reporting platform for college campuses, is expanding its work to combat sexual assault and harassment in other industries. In this new product, users will be invited to an online "matching escrow" that will detect repeat perpetrators and create pathways to support for victims. Users submit encrypted data about their perpetrator, and this data can only be decrypted by the Callisto Options Counselor (a lawyer), when another user enters the identity of the same perpetrator. If the perpetrator identities match, both users will be put in touch independently with the Options Counselor, who will connect them to each other (if appropriate) and help them determine their best path towards justice. The client relationships with the Options Counselors are structured so that any client-counselor communications would be privileged. A combination of client-side encryption, encrypted communication channels, oblivious pseudo-random functions, key federation, and Shamir Secret Sharing keep data confidential in transit, at rest, and during the matching process with the guarantee that only the lawyer ever has access to user submitted data, and even then only when a match is identified.
Tonic and burst spinal cord stimulation waveforms for the treatment of chronic, intractable pain: study protocol for a randomized controlled trial (2016)

ClinicalTrials.gov, NCT02011893 . Registered on 10 December 2013.
Monolayer formation of 6-deoxy-6-thiol-β-cyclodextrin on a Au(111) surface studied by scanning tunneling microscopy (2001)

Mono(6-deoxy-6-thiol) β-cyclodextrins (β-CyD–SH) were grown on a Au(111) surface in ethanol solution, and monolayer formation process of which was studied by scanning tunneling microscopy for the first time. At the initial stage, β-CyD–SH molecules were adsorbed on the Au(111) surface not only randomly, but also partially in a linear ordering. In the following stage, islands were formed and resulted in a uniform monolayer. The observed mechanism is completely different from the model predicted on the basis of the macroscopic result, the Langmuir model. An attractive interaction exists between β-CyD–SHs, contrary to the prediction by the model. The observed growth processes are quite similar to what was previously observed for lipoamide–β-cyclodextrin (LP–β-CyD). However, in the case of β-CyD–SH, the islands did not grow in size as compared to the case of LP–β-CyD, and the number of the islands increased to form a uniform monolayer. This characteristic indicates that the interaction strength ratio of CyD–Au to CyD–CyD is larger for β-CyD–SH than that for LP–β-CyD.
Excitation of lower hybrid waves in a plasma by electron beams (1975)

The linear theory of excitation of electrostatic lower hybrid waves by electron beams is presented. The importance of such waves in tokamaks with runaway electrons is discussed.
Kidney stone, by near-ambient pressure XPS (2019)

Near-ambient pressure X-ray photoelectron spectroscopy (NAP-XPS) is a less traditional form of XPS that allows samples to be analyzed at relatively high pressures, i.e., greater than 2500 Pa. With NAP-XPS, XPS can be used to probe moderately volatile liquids, biological samples, porous materials, and/or polymeric materials that outgas significantly. In this submission, we show O 1s, C 1s, and Ca 2p narrow scans and a survey NAP-XPS spectrum from a human urolith, i.e., a kidney stone, which is a biomaterial that could not be analyzed at moderate pressures by conventional approaches.
Antioxidant diffusion in polyethylene hot‐water pipes (1997)

Abstract This paper presents oxidation induction time (OIT) data for samples taken from a range of polyethylene hot‐water pipes before and after hydrostatic pressure testing with internal stagnant water and external air. Linear relationships between OIT and antioxidant concentration were established for the antioxidants/polymers used. A model assuming Fickian diffusion of the antioxidant to the surrounding media and chemical consumption of the antioxidant (Regime B model) was applied to the OIT‐profile data. The Regime B model was successfully applied to OIT‐profile data except for in the case of a pipe with a substantial scatter in the OIT data, indicative of compositional heterogeneity. The choice of initial conditions for the modeling was critical. The use of initial conditions based on insufficiently exposed pipes led to an overestimate of the diffusivities caused by the combined action of Regimes A (internal precipitation) and B loss mechanisms. The time period associated with Regime A constituted up to 25% of the lifetime for the pipes studied. Antioxidants with sterically accessible polar groups showed a higher melting point and greater interaction with dissolved water and carbon black. Obtained radial dependences of the antioxidant diffusivities ( D ) indicate that the water concentration in the polymer influenced D primarily through cluster formation involving water and antioxidant molecules and by competition between water and antioxidant molecules about adsorption sites on carbon black particles and to a much lesser extent by plasticization. Antioxidant concentration profiles calculated for the failure time interval in pressure testing appeared in the same concentration range, and fracture initiation occurs in the regions in the pipe wall first reaching depletion of the antioxidant system.
From biomass to feedstock: one-step fractionation of lignocellulose components by the selective organic acid-catalyzed depolymerization of hemicellulose in a biphasic system (2011)

A concept for a highly integrated fractionation of lignocellulose in its main components (cellulose-pulp, soluble hemicellulose sugars and lignin) is described, based on the selective catalytic depolymerization of hemicellulose in a biphasic solvent system. This leads to an effective disentanglement of the compact lignocellulose structure, liberating and separating the main components in a single step. At mild temperatures (80–140 °C), oxalic acid catalyzes selectively the depolymerization of hemicellulose to soluble sugars in aqueous solution, whereas the more crystalline cellulose-pulp remains solid and inaccessible to the acid catalysis. In the presence of a second organic phase consisting of bio-based 2-methyltetrahydrofuran (2-MTHF), lignin is directly separated from the pulp and the soluble carbohydrates by in situextraction. The oxalic acid catalyst can be crystallized from the aqueous solution, recovered and re-used. The delignified cellulose-pulp obtained from this biphasic system can be directly subjected to enzymatic depolymerization, affording soluble oligomers and glucose at rates almost comparable to those observed for the hydrolysis of commercial microcrystalline Avicel®. Overall, the concept may offer a promising approach for an efficient and selective pre-treatment of lignocellulosic materials under mild and environmentally-friendly conditions.