gebhart/patrepeval huggingface dataset:
Wandering out of the GWAS wilderness: a new pathway paradigm for complex disease genetics (2019)

A genetic contribution to asthma susceptibility has long been recognised.1 Despite multiple approaches, from candidate genes to genome-wide association studies (GWAS), a large proportion of this heritability remains unexplained.2 The reasons for this are myriad and are largely generalisable to similar approaches in other complex diseases and phenotypes. Candidate gene studies are well based in known pathophysiology and can be powered to identify small effect sizes, but often provide limited insight into new biology or therapeutic opportunities. GWAS are largely unbiased (tagging single-nucleotide polymorphism (SNP) selection not withstanding) and provide opportunities for discovery, but identifying the biologically functional variant can prove daunting, and other important variants likely do not survive genome-wide significance corrections where sample sizes, and hence statistical power, are limited. Both of these approaches in isolation are also likely to miss the influence of genetics on the complex phenotypic response to environmental exposures. In this issue of Thorax , Dizier et al report an interesting pathway-based approach to a gene by environment (G×E) analysis of a well-established epidemiological association between environmental tobacco smoke (ETS) exposure and bronchial hyper-responsiveness (BHR).3 This hybrid method has some of the benefits of multiple modalities and may provide a new avenue for further clarifying the genetic underpinnings of other complex diseases.

The basis for the current study …
Plant Water Consumption of SIIRT Pistachio using Blaney Cridlle and Penman - Monteith Methods (2021)

<strong>Abstract</strong><strong>—</strong> Pistachio cultivation is carried out in many provinces of Turkey; however, it is mainly concentrated in the southeastern Anatolia Region due to the suitability of the climate. The pistachio is intensively grown in Gaziantep and Şanlıurfa, Adıyaman, Mardin and Siirt provinces of southeastern Anatolia, and has a significant impact on the economy of the region. Local varieties are mostly grown in Gaziantep and Şanlıurfa provinces, while Siirt variety is mainly grown in Siirt region. The continental climate of the Siirt province causes the summer to be extremely hot and the precipitation regime to be irregular. Therefore, irrigation in the region along with other cultural practices is important in pistachio cultivation. The increase in population and development of industrialization caused a significant decrease in natural resources; therefore, water resources have to be used as most economical and efficient way as possible. Sustainable use of limited water resources and continuous, high-level benefit from water can only be achieved by determining the amount of crop water consumption in accordance with the climatic conditions, and by creating appropriate irrigation programs considering the crop growing periods. This study was carried out to calculate the crop water consumption for Siirt Pistachio plant using modified Blaney Criddle and modified Penman–Monteith methods.
Differential Functions of Splicing Factors in Breast-Cancer Initiation and Metastasis (2019)

SUMMARY Misregulation of alternative splicing is a hallmark of human tumors; yet to what extent and how it contributes to malignancy are only beginning to be unraveled. Here, we define which members of the splicing factor SR and SR-like families contribute to breast cancer, and uncover differences and redundancies in their targets and biological functions. We first identify splicing factors frequently altered in human breast tumors, and then assay their oncogenic functions using breast organoid models. Importantly we demonstrate that not all splicing factors affect mammary tumorigenesis. Specifically, upregulation of either SRSF4, SRSF6 or TRA2β promotes cell transformation and invasion. By characterizing the targets of theses oncogenic factors, we identify a shared set of spliced genes associated with well-established cancer hallmarks. Finally, we demonstrate that the splicing factor TRA2β is regulated by the MYC oncogene, plays a role in metastasis maintenance in vivo , and its levels correlate with breast-cancer-patient survival.
Controllable Edge Oxidation and Bubbling Exfoliation Enable the Fabrication of High Quality Water Dispersible Graphene (2016)

Despite significant progresses made on mass production of chemically exfoliated graphene, the quality, cost and environmental friendliness remain major challenges for its market penetration. Here, we present a fast and green exfoliation strategy for large scale production of high quality water dispersible few layer graphene through a controllable edge oxidation and localized gas bubbling process. Mild edge oxidation guarantees that the pristine sp<sup>2</sup> lattice is largely intact and the edges are functionalized with hydrophilic groups, giving rise to high conductivity and good water dispersibility at the same time. The aqueous concentration can be as high as 5.0 mg mL<sup>-1</sup>, which is an order of magnitude higher than previously reports. The water soluble graphene can be directly spray-coated on various substrates, and the back-gated field effect transistor give hole and electron mobility of ~496 and ~676 cm<sup>2</sup> V<sup>-1</sup> s<sup>-1</sup>, respectively. These results achieved are expected to expedite various applications of graphene.
Performance evaluation of heterogeneously integrated 3J InGaP/GaAs/Si tandem solar cells on Si substrate for concentrated photovoltaics (2014)

Integration of III-V multijunction solar cells on Si substrate is highly sought for achieving lower levelized cost of energy by unifying the high-efficiency merits of III-V materials with low-cost and abundance of Si. Triple-junction (3J) InGaP/GaAs/Si solar cells with an active Si bottom cell are investigated for concentrated photovoltaic (CPV) operation under AM1.5d spectrum. We present key insight into the design of GaAs buffer architecture for the optimal down-selection of the buffer doping and thickness to maximize the photon flux penetration to the bottom Si subcell. Ideal case scenario employing dislocations free III-V solar cells directly integrated onto the Si subcell without a buffer layer yielded current-matched 1-sun 3J efficiency of 32.13% and 36.39% under AM1.5d and AM1.5g spectra, respectively. Under AM1.5d the efficiency dropped to 29.30% and 27.32% at a threading dislocation density (TDD) of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> and 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> , respectively, when 0.5 μm thick GaAs buffer was employed between the III-V subcells and the bottom Si subcell. Finally, we present a novel design for heterogeneously integrated 3J InGaP/GaAs/Si tandem solar cell incorporating a TDD of 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> with an efficiency exceeding 33% at 200 suns, indicating a promising future for III-V on Si photovoltaics for CPV operation.
Evaluation of stability and viscosity of [C2mim][DCA] based ionanocolloids (2021)

Abstract In the search for the optimization of heat transfer systems, Ionanocolloids (INCs) as we have termed here, have revealed as very attractive choices due to their increasingly potential applications in thermal energy areas. By definition, INCs are suspensions of nanoparticles (NPs) into Ionic Liquids (ILs). Besides a high degree of versatility and enhanced thermal properties, these new class of fluids are considered as green solvents due to their negligible vapor pressure, non-flammability and recyclability. Despite the great advantages of using these INCs, their industrial application is still a challenge due to low stability and high viscosity issues attributed to them. In this work, different Ionanocolloids were prepared by two-step method, using 1-ethyl-3-methylimidazolium dicyanamide ([C 2 mim][DCA]) together with deionized water as base fluids and 3 different NPs: Titanium(IV) Oxide, Silicon Oxide and Aluminum Oxide. The stability and viscosity of these mixtures were then evaluated and the results are reported.
Numerical linear stability analysis of three-dimensional anisotropic-pressure stellarator plasmas (1985)

A set of linearized equations describing the macroscopic motion of a plasma with anisotropic pressure, obtained originally by Grossmann, Hameiri and Weitzner, from the double adiabatic equations of Chew, Goldberger and Low, is solved numerically as an initial boundary value problem. Any three-dimensional anisotropic pressure equilibrium can be employed. The equilibrium is specified on a toroidal mesh in three dimensions so magnetic surfaces do not necessarily have to exist. The stability of the plasma in the stellarator experiments Proto-CLEO/CLEO, IMS, Wendelstein VII-A, and Heliotron-E is studied as a function of beta, defined in terms of energy density, and as a function of the ratio of parallel to perpendicular pressure, γ. In these devices, equilibrium and stability considerations both imply that the highest β may be obtained with p⊥ > p||.
Retinitis pigmentosa. A symposium on terminology and methods of examination. (1983)

This report represents a summary of opinions expressed at a meeting of specialists interested in retinitis pigmentosa (RP) and allied diseases, at which an attempt was made to define some minimum guidelines for ocular evaluation of these disorders. The term RP would be reserved for a group of hereditary disorders that diffusely involve photoreceptor and pigment epithelial function, and should not be used when a secondary cause is suspected. RP may be classified by genetic type (single cases without known affected relatives should be termed isolated or simplex), by the topography of retinal involvement, and by the severity of disease (to identify subtypes with mild or localized disease). Patients should have at least one comprehensive examination that conforms to basic standards, preferable early in the course of the disease. The visual field examination should use both a small and a large test light. Electroretinographic testing should (1) use a full-field stimulus, and (2) routinely document three independent responses (cone, rod, and mixed cone-rod). Patients should be identifiable for future study or therapeutic trials. They should be counseled about the disease and followed regularly. No specific therapy exists at present for most of these diseases, but optical and night vision aids are available. Sunglasses for outdoor use are recommended until more is known about whether long-term exposure to bright sunlight alters the course of these diseases.
Strain effects in the mass flux of methanol in poly(methyl methacrylate) (1980)

Abstract Diffusion of organic solvents into glassy polymers often results in a phase transformation of the hard, solid polymer into a swollen, rubbery material. During the sorption, internal stresses exist in the swollen and glassy parts of the polymer and are thought to contribute significantly to the “anomalous” diffusion observed in many penetrant–polymer systems. In this investigation, isothermal sorption data for the methanol–poly(methyl methacrylate) system have been obtained on plates ranging in thickness from 1/32 to ¼ in. The results show features characteristic of both a strain‐dependent diffusion coefficient and of a stress gradient contribution to the mass flux. An attempt to reproduce these results by combining a strain‐dependent diffusion coefficient model with a stress‐induced contribution to the flux is presented.
Joint uncertainty decoding for noise robust speech recognition (2005)

Background noise can have a significant impact on the performance of speech recognition systems. A range of fast featurespace and model-based schemes have been investigated to increase robustness. Model-based approaches typically achieve lower error rates, but at an increased computational load compared to feature-based approaches. This makes their use in many situations impractical. The uncertainty decoding framework can be considered an elegant compromise between the two. Here, the uncertainty of features is propagated to the recogniser in a mathematically consistent fashion. The complexity of the model used to determine the uncertainty may be decoupled from the recognition model itself, allowing flexibility in the computational load. This paper describes a new approach within this framework, Joint uncertainty decoding. This approach is compared with the uncertainty decoding version ofSPLICE, standardSPLICE, and a new form of front-end CMLLR. These are evaluated on a medium vocabulary speech recognition task with artificially added noise.
Long-Term Inhibition of HIV-1 Infection in Primary Hematopoietic Cells by Lentiviral Vector Delivery of a Triple Combination of Anti-HIV shRNA, Anti-CCR5 Ribozyme, and a Nucleolar-Localizing TAR Decoy (2005)

Combinatorial therapies for the treatment of HIV-1 infection have proven to be effective in reducing patient viral loads and slowing the progression to AIDS. We have developed a series of RNA-based inhibitors for use in a gene therapy-based treatment for HIV-1 infection. The transcriptional units have been inserted into the backbone of a replication-defective lentiviral vector capable of transducing a wide array of cell types, including CD34+ hematopoietic progenitor cells. The combinatorial therapeutic RNA vector harbors a U6 Pol III promoter-driven short hairpin RNA (shRNA) targeting the rev and tat mRNAs of HIV-1, a U6 transcribed nucleolar-localizing TAR RNA decoy, and a VA1-derived Pol III cassette that expresses an anti-CCR5 ribozyme. Each of these therapeutic RNAs targets a different gene product and blocks HIV infection by a distinct mechanism. Our results demonstrate that the combinatorial vector suppresses HIV replication long term in a more-than-additive fashion relative to the single shRNA or double shRNA/ribozyme or decoy combinations. Our data demonstrate the validity and efficacy of a combinatorial RNA-based gene therapy for the treatment of HIV-1 infection.
Positive Heterotropic Cooperativity for Selective Guest Binding via Electronic Communications through a Fused Zinc Porphyrin Array (2005)

Upon binding with C60 and diamines, such as 4,4'-bipyridine (bpy) and N,N,N',N'-tetramethylhexane-1,6-diamine (TMHDA), cyclic host 1 possessing two electronically coupled binding sites displays negative homotropic cooperativity and positive heterotropic cooperativity, and their ternary mixtures preferentially form inclusion complexes with hetero-guest pairs 1 supersetC60*bpy and 1 supersetC60*TMHDA under appropriate conditions. Spectroscopic titration profiles in toluene at 20 degrees C demonstrated that the association constants (Kassoc) of C60 with monodiamine complexes 1 supersetbpy (2.8 x 105 M-1) and 1 supersetTMHDA (1.5 x 105 M-1) are 8.5 and 4.5 times greater than that of C60 with guest-free 1 (3.3 x 104 M-1), respectively. On the other hand, mono-C60 complex 1 supersetC60 was 6.1 times more accessible than guest-free 1 toward TMHDA. Absorption spectroscopy in the absence of 1 indicated no direct interaction between C60 and diamines.
PCR detection of nearly any dengue virus strain using a highly sensitive primer ‘cocktail’ (2011)

PCR detection of viral pathogens is extremely useful, but suffers from the challenge of detecting the many variant strains of a given virus that arise over time. Here, we report the computational derivation and initial experimental testing of a combination of 10 PCR primers to be used in a single high‐sensitivity mixed PCR reaction for the detection of dengue virus. Primer sequences were computed such that their probability of mispriming with human DNA is extremely low. A ‘cocktail’ of 10 primers was shown experimentally to be able to detect cDNA clones representing the four serotypes and dengue virus RNA spiked into total human whole blood RNA. Computationally, the primers are predicted to detect 95% of the 1688 dengue strains analyzed (with perfect primer match). Allowing up to one mismatch and one insertion per primer, the primer set detects 99% of strains. Primer sets from three previous studies have been compared with the present set of primers and their relative sensitivity for dengue virus is discussed. These results provide the formulation and demonstration of a mixed primer PCR reagent that may enable the detection of nearly any dengue strain irrespective of serotype, in a single PCR reaction, and illustrate an approach to the broad problem of detecting highly mutable RNA viruses.
Suppression of Carbon Monoxide Poisoning in Proton Exchange Membrane Fuel Cells via Gold Nanoparticle/Titania Ultrathin Film Heterogeneous Catalysts (2019)

Titania (TiO2)-supported gold (Au) nanoparticles (NPs) have long been considered as a promising solution for carbon monoxide (CO) poisoning in proton exchange membrane fuel cells (PEMFCs) as they can efficiently catalyze CO oxidation reaction. Nevertheless, the actual application in functioning PEMFCs has been rarely reported primarily due to the challenges of synthesizing and incorporating the oxidation catalyst in manners compatible with the structure and fabrication of PEMFCs. Here we successfully incorporate the Au NPs/TiO2 catalyst into PEMFCs and demonstrate an excellent CO elimination function, improving the performance and CO tolerance of PEMFCs; we combine an ultrathin TiO2 layer (<1 nm) deposited on a Nafion membrane via the low-temperature atomic layer deposition (ALD) and a monolayer of Au NPs assembled on the top of the ultrathin TiO2 using the Langmuir–Blodgett method. An over 30% enhanced maximum power output is achieved under the presence of a trace amount of CO. Even under highly concentrated CO (0.1%), a less than 10% performance decrease occurs with the incorporation of Au NPs/TiO2, in contrast to a nearly 70% performance decrease observed in the control device. The results represent the first experimental implementation of Au NPs/TiO2 catalysts in PEMFCs and the confirmation of their effectiveness for mitigating the CO poisoning effect.
Planning, budgeting and performance management at Swiss hospitals – Are Swiss hospitals at a crossroads – Will these medical specialist organisations in future develop into institutions with a business orientation? (2013)

This article explores the question of how Swiss hospitals can establish a coherent performance management system with a long term orientation. With the introduction of competitive mechanisms (DRG system) in the new Medical Insurance Act, a business orientation with regard to hospital management has become a key factor for market survival. The present study is based on a written survey of all Swiss hospitals in the German-speaking regions of the country. They were asked about the status quo and the targets for their performance management systems, based on a general maturity model for performance management, adapted for hospitals. The descriptive evaluation of the data indicates that most hospitals are on the right road. Planning and Controlling are highly matured (in terms of processes), but the strategic importance of an effective performance management system (Reporting, IT integration) is still widely underestimated. Thus most hospitals already have extensive planning mechanisms, but do not give these mechanisms priority when it comes to IT support. Bivariate analyses (correlation matrices) of the results of the survey show that IT, in particular, plays a central role as a carrier medium or platform for performance management. At the same time, these detailed analyses indicate that (management oriented) hospital planning is the actual driver for the establishment and extension of sound performance management systems. The study shows that well-developed IT infrastructures and clear planning figures will allow for performance management of detailed content. It should also not be forgotten that a well-functioning performance management system also has an organisational component. It is only when the tasks, skills and responsibilities of hospital management as these relate to business outlook, medical treatment and care are coordinated that hospitals can be managed in a more performance-orientated way.
Cartesian Sampling Of FID Data Using Oscillating Gradients (1988)

A new method of fast NMR imaging is proposed which uses oscillating gradients and also collects data on Cartesian coordinates. The method is a heuristic attempt at finding an optimal data collection strategy for NMR imaging. It is described in detail and its advantages and disadvantages compared to other methods are analyzed.
Leaked Expressions Captured with Wearable High Resolution Facial Electromyography (2021)

Facial-expressions play a major role in human communication and provide a window to an individual’s emotional state. While facial expressions can be consciously manipulated to conceal true emotions, very brief leaked expressions may occur, exposing one’s true internal state. Leaked expressions are therefore considered as an important hallmark in deception detection, a field with enormous social and economic impact. Challengingly, capturing these subtle and brief expressions has been so far limited to visual examination (manual or machine-based), with almost no electromyography evidence. In this investigation we set to explore whether electromyography of leaked expressions can be faithfully recorded with specially designed wearable electrodes. Indeed, using soft multi-electrode array based facial electromyography, we were able to record localized and brief signals in individuals instructed to suppress smiles. The electromyography evidence was validated with high-speed video recordings. The recording approach reported here provides a new and sensitive tool for leaked expression investigations and a basis for improved automated systems.
InGaN blue light emitting micro-diodes with current path defined by tunnel junction (2020)

We have fabricated tunnel-junction InGaN micro-LEDs using plasma-assisted molecular beam epitaxy technology, with top-down processing on GaN substrates. Devices have diameters between 5 µm and 100 µm. All of the devices emit light at 450 nm at a driving current density of about 10<i>A</i><i>c</i><i>m</i><sup>-2</sup>. We demonstrate that within micro-LEDs ranging in size from 100 µm down to 5 µm, the properties of these devices, both electrical and optical, are fully scalable. That means we can reproduce all electro-optical characteristics using a single set of parameters. Most notably, we do not observe any enhancement of non-radiative recombination for the smallest devices. We assign this result to a modification of the fabrication process, i.e., replacement of deep dry etching by a tunnel junction for the current confinement. These devices show excellent thermal stability of their light emission characteristics, enabling operation at current densities up to 1<i>k</i><i>A</i><i>c</i><i>m</i><sup>-2</sup>.