gebhart/patrepeval huggingface dataset:
Polycystic Kidney Disease with Hyperinsulinemic Hypoglycemia Caused by a Promoter Mutation in Phosphomannomutase 2 (2017)

Hyperinsulinemic hypoglycemia (HI) and congenital polycystic kidney disease (PKD) are rare, genetically heterogeneous disorders. The co-occurrence of these disorders (HIPKD) in 17 children from 11 unrelated families suggested an unrecognized genetic disorder. Whole-genome linkage analysis in five informative families identified a single significant locus on chromosome 16p13.2 (logarithm of odds score 6.5). Sequencing of the coding regions of all linked genes failed to identify biallelic mutations. Instead, we found in all patients a promoter mutation (c.-167G>T) in the phosphomannomutase 2 gene (<i>PMM2</i>), either homozygous or <i>in trans</i> with <i>PMM2</i> coding mutations. <i>PMM2</i> encodes a key enzyme in N-glycosylation. Abnormal glycosylation has been associated with PKD, and we found that deglycosylation in cultured pancreatic <i>β</i> cells altered insulin secretion. Recessive coding mutations in <i>PMM2</i> cause congenital disorder of glycosylation type 1a (CDG1A), a devastating multisystem disorder with prominent neurologic involvement. Yet our patients did not exhibit the typical clinical or diagnostic features of CDG1A. <i>In vitro,</i> the <i>PMM2</i> promoter mutation associated with decreased transcriptional activity in patient kidney cells and impaired binding of the transcription factor ZNF143. <i>In silico</i> analysis suggested an important role of ZNF143 for the formation of a chromatin loop including <i>PMM2</i> We propose that the <i>PMM2</i> promoter mutation alters tissue-specific chromatin loop formation, with consequent organ-specific deficiency of PMM2 leading to the restricted phenotype of HIPKD. Our findings extend the spectrum of genetic causes for both HI and PKD and provide insights into gene regulation and <i>PMM2</i> pleiotropy.
The Design and Evaluation of Transparent User Interfaces. From Theory to Practice (1996)

The central research issue addressed by this dissertation is how we can design systems where information on user interface tools is overlaid on the work product being developed with these tools. The interface tools typically appear in the display foreground while the data or work space being manipulated typically appear in the perceptual background. This represents a trade-off in focused foreground attention versus focused background attention. By better supporting human attention we hope to improve the fluency of work, where fluency is reflected in a more seamless integration between task goals, user interface tool manipulations to achieve these goals, and feedback from the data or work space being manipulated. This research specifically focuses on the design and evaluation of transparent user interface'layers'applied to graphical user interfaces. By allowing users to see through windows, menus, and tool palettes appearing in the perceptual foreground, an improved awareness of the underlying workspace and preservation of context are possible. However, transparent overlapping objects introduce visual interference which may degrade task performance, through reduced legibility. This dissertation explores a new interface technique (i.e., transparent layering) and, more importantly, undertakes a deeper investigation into the underlying issues that have implications for the design and use of this new technique. We have conducted a series of experiments, progressively more representative of the complex stimuli from real task domains. This enables us to systematically evaluate a variety of transparent user interfaces, while remaining confident of the applicability of the results to actual task contexts. We also describe prototypes and a case study evaluation of a working system using transparency based on our design parameters and experimental findings. Our findings indicate that similarity in both image color and in image content affect the levels of visual interference. Solid imagery in either the user interface tools (e.g., icons) or in the work space content (e.g., video, rendered models) are highly interference resistant and work well up to 75% transparent (i.e., 25% of foreground image and 75% of background content). Text and wire frame images (or line drawings) perform equally poorly but are highly usable up to 50% transparent, with no apparent performance penalty. Introducing contrasting outlining techniques improves the usability of transparent text menu interfaces up to 90% transparency. These results suggest that transparency is a usable and promising interface alternative. We suggest several methods of overcoming today's technical challenges in order to integrate transparency into existing applications.
Automated measurements of atmospheric visibility (1983)

Abstract The concept of using a solid-state, linear-array imaging device coupled with computerized scene analysis and display to measure daytime atmospheric visibility is described. Computer software is implemented for routine conversion of observed target and sky radiances into measurements of horizon contrast, visual range, target color impairment, and target modulation depth, i.e., target texture and clarity. An assembled, working instrument has been applied to field measurements. Several examples of field measurements are presented. The instrument is fully automated, and is available for visibility research; its applicability to routine visibility monitoring and as an operational tool for aircraft operations is explored.
A Comparative Study on Fetal Heart Rates Estimated from Fetal Phonography and Cardiotocography (2017)

The aim of this study is to investigate that fetal heart rates (fHR) extracted from fetal phonocardiography (fPCG) could convey similar information of fHR from cardiotocography (CTG). Four-channel fPCG sensors made of low cost (<$1) ceramic piezo vibration sensor within 3D-printed casings were used to collect abdominal phonogram signals from 20 pregnant mothers (>34 weeks of gestation). A novel multi-lag covariance matrix-based eigenvalue decomposition technique was used to separate maternal breathing, fetal heart sounds (fHS) and maternal heart sounds (mHS) from abdominal phonogram signals. Prior to the fHR estimation, the fPCG signals were denoised using a multi-resolution wavelet-based filter. The proposed source separation technique was first tested in separating sources from synthetically mixed signals and then on raw abdominal phonogram signals. fHR signals extracted from fPCG signals were validated using simultaneous recorded CTG-based fHR recordings.The experimental results have shown that the fHR derived from the acquired fPCG can be used to detect periods of acceleration and deceleration, which are critical indication of the fetus' well-being. Moreover, a comparative analysis demonstrated that fHRs from CTG and fPCG signals were in good agreement (Bland Altman plot has mean = -0.21 BPM and ±2 <i>SD</i> = ±3) with statistical significance (<i>p</i> < 0.001 and Spearman correlation coefficient ρ = 0.95). The study findings show that fHR estimated from fPCG could be a reliable substitute for fHR from the CTG, opening up the possibility of a low cost monitoring tool for fetal well-being.
Scanning and transmission electron microscopy of ovine mesenteric arteries infected with first-generation meronts of Sarcocystis tenella (1982)

First-generation meronts of Sarcocystis tenella were found within subendothelial cells between the endothelium and internal elastic membrane of mesenteric arteries. At 14 and 16 days postinoculation (DPI), host cells with mature meronts were enlarged, measuring 25.6 × 22 μm (16.4–35 × 4.4–28.5 μm; n = 17), which caused the endothelium to protrude into the vessel lumen. In mesenteric arteries, protuberances measured 37.4 × 29.7 μm (32–57 × 16.5–47 μm; n = 15) and extended 16.8 μm (12–27 μm; n = 12) into the vessel lumen. Merozoites in meronts measured 5.3 × 1.7 μm (4.5–5.5 × 1.5–1.8 μm; n = 20); free merozoites were 5.5 × 1.5 μm (4.8–6 × 1.3–1.7 μm; n = 18). At 16 DPI many of the endothelial cells covering protuberances as well as many of the host cells had sloughed from the tunica intima of the mesenteric arteries which exposed relatively large areas, 189.5 μm (50–350 μm; n = 15) in diameter, of the internal elastic membrane.
Coal Desulfurization during Gaseous Treatment (1977)

Sulfur removal from coal during treatment with gaseous atmospheres at elevated temperatures is of interest both because such a treatment might serve as a basis for a coal desulfurization process (1,2,3) and because knowledge of the fate of sulfur when coal is heated has application during carbonization or gasification. Early interest in desulfurization under these conditions concentrated mainly on the production of metallurgical coke. The various approaches included pretreatment of the coal before carbonization, carbonization of the coal in various gases to remove sulfur compounds, or treatment of the coke to reduce its sulfur content. Only recently has interest turned to desulfurization of coal or char for use as a power plant fuel. Sulfur removal from coal during carbonization has been investigated both with and without the addition of reactive gases such as hydrogen and oxygen. During carbonization in the presence of only the gases derived from the coal, hydrogen
CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9 (2018)

Here we describe a method for robust directed evolution using mutagenesis of large sequence spaces in their genomic contexts. The method employs error-prone PCR and Cas9-mediated genome integration of mutant libraries of large-sized donor variants into single or multiple genomic sites with efficiencies reaching 98-99%. From sequencing of genome integrants, we determined that the mutation frequency along the donor fragments is maintained evenly and successfully integrated into the genomic target loci, indicating that there is no bias of mutational load towards the proximity of the double strand break. To validate the applicability of the method for directed evolution of metabolic gene products we engineered two essential enzymes in the mevalonate pathway of Saccharomyces cerevisiae with selected variants supporting up to 11-fold higher production of isoprenoids. Taken together, our method extends on existing CRISPR technologies by facilitating efficient mutagenesis of hundreds of nucleotides in cognate genomic contexts.
Towards End to End head-free gaze classification (2019)

The study of gaze behavior benefits from the classification of the time series into distinct movement types, or events, such as saccade, pursuit, and fixation. Because the manual identification of events is time consuming and subjective, there is a need for automated classifiers. Although there are several solutions for the classification of the eye-in-head signal, there are no established solutions for classification of the coordinated movements of the eyes and head that will occur in less constrained contexts, for example, when wearing a virtual or augmented reality display. Our approach involves training various temporal classifiers on our new Gaze-in-Wild dataset, recorded from over 20 unrestrained participants and hand-coded by 5 practiced labellers. Subjects were instrumented with a 6-axis 100 Hz inertial measurement unit (mean drift: 0.03 deg/sec), a 30 Hz ZED stereo camera, and a 120Hz Pupil labs eye tracker (mean calibration AngError < 1 deg within 10 degrees from calibration pattern center) to record eye and head orientation. The effort culminated in over 2 hours and 20 minutes of hand labelled head-free gaze behavior data, with approximately 20000 detected fixational movements, 18000 saccades, 1400 pursuit events, and 4000 blinks. We use this hand labelled data to benchmark our dataset using standard machine learning classifiers and train our recurrent network model which leverages multiple Neural Arithmetic Logic Units to classify gaze behavior directly from raw, unfiltered eye-in-head and head vectors. Activation map of various hidden units provides insight on learned representations of eye and head coordination and velocity based feature representations which are directly comparable with hand-crafted features. The performance of our classifier is evaluated using various event based metrics and shows that it can attain near-human level classification (>kappa 0.70, event F1> 0.85).
Test of lepton universality with $$ {\Lambda}_b^0\to {pK}^{-}{\mathrm{\ell}}^{+}{\mathrm{\ell}}^{-} $$ decays (2020)

A bstract The ratio of branching fractions of the decays $$ {\Lambda}_b^0 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msubsup> <mml:mi>Λ</mml:mi> <mml:mi>b</mml:mi> <mml:mn>0</mml:mn> </mml:msubsup> </mml:math> → pK − e + e − and $$ {\Lambda}_b^0 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msubsup> <mml:mi>Λ</mml:mi> <mml:mi>b</mml:mi> <mml:mn>0</mml:mn> </mml:msubsup> </mml:math> → pK − μ + μ − , $$ {R}_{pK}^{-1} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msubsup> <mml:mi>R</mml:mi> <mml:mi>pK</mml:mi> <mml:mrow> <mml:mo>−</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msubsup> </mml:math> , is measured for the first time using proton-proton collision data corresponding to an integrated luminosity of 4 . 7 fb − 1 recorded with the LHCb experiment at center-of-mass energies of 7, 8 and 13 TeV. In the dilepton mass-squared range 0 . 1 &lt; q 2 &lt; 6 . 0 GeV 2 /c 4 and the pK − mass range m ( pK − ) &lt; 2600 MeV /c 2 , the ratio of branching fractions is measured to be $$ {R}_{pK}^{-1}={1.17}_{-0.16}^{+0.18}\pm 0.07 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msubsup> <mml:mi>R</mml:mi> <mml:mi>pK</mml:mi> <mml:mrow> <mml:mo>−</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msubsup> <mml:mo>=</mml:mo> <mml:msubsup> <mml:mn>1.17</mml:mn> <mml:mrow> <mml:mo>−</mml:mo> <mml:mn>0.16</mml:mn> </mml:mrow> <mml:mrow> <mml:mo>+</mml:mo> <mml:mn>0.18</mml:mn> </mml:mrow> </mml:msubsup> <mml:mo>±</mml:mo> <mml:mn>0.07</mml:mn> </mml:math> , where the first uncertainty is statistical and the second systematic. This is the first test of lepton universality with b baryons and the first observation of the decay $$ {\Lambda}_b^0 $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msubsup> <mml:mi>Λ</mml:mi> <mml:mi>b</mml:mi> <mml:mn>0</mml:mn> </mml:msubsup> </mml:math> → pK − e + e − .
Tessera: Scalable, shade robust module (2015)

This paper describes the development and output measurements on a new shade robust module, named the Tessera module. This module uses a novel electrical configuration, comprised of shade independent blocks protected by in-laminate diodes, with a mixture of series and parallel connections. By using ECN's existing back contact technology [1], no significant additional manufacturing costs occur. The design, method and manufacturing technology will be explained. The module leads to an increased annual output in case of shading and an increase in system safety due to lower heat dissipation: of 40°C instead of 130°C compared to standard diodes, and reduced failure of components. Annual yield has been calculated showing significant gains.
Chick Embryo Experimental Platform for 3D Tissue Engineering Modelling of Cancer Micrometastases for Tumor Biology, Drug Development and Nanomaterials Testing (2021)

Colonization of distant organs by tumor cells is a critical step of cancer progression. The initial avascular stage of this process (micrometastasis) remains almost inaccessible to study due to the lack of relevant experimental approaches. Here, we introduce an in vitro/in vivo model of organ-specific micrometastases of triple-negative breast cancer (TNBC) that is fully implemented in a cost-efficient chick embryo (CE) experimental platform. The model is built as three-dimensional (3D) tissue engineering constructs (TECs) combining human MDA-MB-231 cells and decellular-ized CE organ-specific scaffolds. TNBC cells colonized CE organ-specific scaffolds in 2-3 weeks, forming tissue-like structures. The feasibility of this methodology for basic cancer research, drug development and nanomedicine was demonstrated on a model of hepatic micrometastasis of TNBC. We revealed that MDA-MB-231 differentially colonize parenchymal and stromal com-partments of the liver-specific extracellular matrix (LS-ECM) and become more resistant to the treatment with molecular Doxorubicin (Dox) and Dox-loaded mesoporous silica nanoparticles than in monolayer cultures. When grafted on CE chorioallantoic membrane, LS-ECM-based TECs induced angiogenic switch. These findings may have important implications for the diag-nosis and treatment of TNBC. The methodology established here is scalable and adaptable for pharmacological testing and cancer biology research of various metastatic and primary tumors.
Development of a dynamic finite element computer code for the inelastic analysis of cask structures -- PRONTO 3D (1989)

The Engineering Analysis Department at Sandia National Laboratories has developed a three-dimensional transient solid dynamics computer code, PRONTO 3D, that can simulate and analyze radioactive material packaging impact and puncture events. Sphere and cask impact example problems demonstrated the contact surface algorithm and other aspects of the code PRONTO 3D has proven to be a powerful tool for analyzing problems in impact dynamics, rock blasting, and accident analyses. 4 refs., 5 figs.
Apple polyphenols inhibit plasma CETP activity and reduce the ratio of non‐HDL to HDL cholesterol (2008)

Previous reports demonstrated that hypocholesterolemic activity of apple was associated with its pectin and fiber. This report was to investigate the effect of apple polyphenols (AP) on blood cholesterol level and gene expression of cholesterol-regulating enzymes in Golden Syrian hamsters maintained on a 0.1% cholesterol diet. It was found that dietary supplementation of 0.3 or 0.6% of AP did not affect plasma total cholesterol (TC), but it increased HDL cholesterol (HDL-C) and decreased non-HDL-C, thus leading to a lower ratio of non-HDL-C to HDL-C. Plasma total triacylglycerol (TG) level was also significantly reduced when hamsters were fed a diet supplemented with 0.6% AP. Western blot analysis did not find any effect of AP on sterol regulatory element-binding protein 2 (SREBP-2), LDL receptor (LDLR), 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR), and cholesterol-7alpha-hydroxylase (CYP7A). Most interesting was that supplementation of AP had no effect on protein abundance of plasma cholesteryl ester transport protein (CETP), but it suppressed plasma CETP activity. A series of in vitro assays confirmed that AP inhibited CETP in a dose dependent manner. It was concluded that AP favorably improved distribution of cholesterol in lipoproteins, most likely, by its inhibition on CETP activity.
Ecological interaction of a biocontrol Pseudomonas fluorescens strain producing 2,4-diacetylphloroglucinol with the soft rot potato pathogen Erwinia carotovora subsp. atroseptica (2006)

Erwinia carotovora subspecies atroseptica is the agent of soft rot of potato and causes important crop damage in Europe. Synthetic 2,4-diacetylphloroglucinol (DAPG) inhibited the growth of E. carotovora subsp. atroseptica under in vitro conditions and Pseudomonas fluorescens F113, which produces DAPG, was studied for biocontrol of E. carotovora subsp. atroseptica. Wild-type F113 (or the spontaneous rifampicin-resistant mutant F113Rif) inhibited growth of E. carotovora subsp. atroseptica on solid medium, displayed bactericidal activity towards the pathogen in liquid medium, and prevented Erwinia-mediated rotting of wounded potato tuber under in vitro conditions. F113Rif reduced the population size of E. carotovora subsp. atroseptica in soil and on potato tuber dice in competition experiments carried out with unplanted soil and soil planted with diced potato tubers, respectively. Co-inoculation of potato tuber seeds with F113Rif and E. carotovora subsp. atroseptica reduced Erwinia contamination of the seed tubers compared with single inoculation with the pathogen. F113G22 is a Tn5::lacZY-induced DAPG-negative biosynthetic derivative of F113 and showed no antibiosis towards E. carotovora subsp. atroseptica in vitro. In contrast to F113Rif, F113G22 did not inhibit Erwinia-mediated rotting of wounded potato tuber in vitro, did not influence survival of E. carotovora subsp. atroseptica in unplanted soil or soil planted with potato tuber dice and did not reduce Erwinia contamination of potato seed tubers. F113G22(pCU203) is a complemented derivative with restored DAPG-producing ability. F113G22(pCU203) had similar effects against E. carotovora subsp. atroseptica as F113 (or F113Rif) under in vitro conditions and in soil microcosms. The results indicate that P. fluorescens F113 is a promising biocontrol agent against the potato soft rot agent E. carotovora subsp. atroseptica and suggest that the pseudomonad's ability to produce DAPG is a key factor in its inhibition of the pathogen.
HyperRail: Modular, 3D Printed, 1-100 meter, Programmable, and Low-cost Linear Motion System for Imaging and Sensor Suites (2018)

Reliable, accurate, and affordable linear motion systems for agricultural applications are currently not easily accessible due to their elevated cost. Most systems available to the public have price tags in the thousands and their dimensions cannot be easily customized. Current systems have a max length of about ten meters and for a typical greenhouse application, the length may not be sufficient. The price of the system increases with an increase in length and with a base price in the thousands it becomes almost impractical to buy a system for such application. The HyperRail is a modular linear motion system with a repeatability of 2mm and current top speed of 100mm/s. An advantage this system has is its ability to increase or decrease the length of system with minimum effort and nominal increase in price. The HyperRail can be mounted on a set of tripods or directly on the structure of a building such as a greenhouse. The base price for a three-meter system, on tripods, is US$240 and an additional US$45 for each additional one-and-a-half meter. The HyperRail was designed for the use of hyperspectral imaging but can be adapted for other sensor systems. We report on a nine-meter study over pine seedlings infected with a virus. A push-broom hyperspectral camera (Headwall Nano) was mounted on the carriage of the system imaging the seedlings. The rail is currently being adapted to an environmental sensor suite that will monitor CO2, luminosity, humidity, temperature, and the concentration of dust. The HyperRail also includes bidirectional-wireless communication between the drive and the carriage; this means that the sensor suite can operate autonomously and communicate to the HyperRail drive to move to a specific location and take measurements. This system includes a graphical user interface for users who are unfamiliar with programming but could also be used through a command line interface for individuals that want to work the code and see the effects of the changes immediately. This system was developed at Oregon State University’s OPEnS Lab, here is a link to the project page for more detailed information. URL for project page: http://www.open-sensing.org/hyper-rail/
Packaging solution with a 3-dimensional coupling scheme for direct optical interconnects to the chip (2004)

Inter-Chip Optical Interconnects are viable alternatives for conventional copper wires. However, the costly assembly and packaging process is the major obstacle to their commercial breakthrough, where especially the coupling of optical components seems to be the most critical aspect. This paper describes the packaging and 3-D coupling scheme we have developed for a 2-D parallel optical interconnect module with on-chip access. It is a passive index alignment method that measures the coordinates of alignment features to achieve correct alignment. We belief it is a possible low cost solution as full automation is possible.