gebhart/patrepeval huggingface dataset:
A continuous hyperchromicity assay to characterize the kinetics and thermodynamics of DNA lesion recognition and base excision (2008)

We report a continuous hyperchromicity assay (CHA) for monitoring and characterizing enzyme activities associated with DNA processing. We use this assay to determine kinetic and thermodynamic parameters for a repair enzyme that targets nucleic acid substrates containing a specific base lesion. This optically based kinetics assay exploits the free-energy differences between a lesion-containing DNA duplex substrate and the enzyme-catalyzed, lesion-excised product, which contains at least one hydrolyzed phosphodiester bond. We apply the assay to the bifunctional formamidopyrimidine glycosylase (Fpg) repair enzyme (E) that recognizes an 8-oxodG lesion within a 13-mer duplex substrate (S). Base excision/elimination yields a gapped duplex product (P) that dissociates to produce the diagnostic hyperchromicity signal. Analysis of the kinetic data at 25 degrees C yields a K(m) of 46.6 nM for the E.S interaction, and a k(cat) of 1.65 min(-1) for conversion of the ES complex into P. The temperature dependence reveals a free energy (DeltaG(b)) of -10.0 kcal.mol(-1) for the binding step (E + S <--> ES) that is enthalpy-driven (DeltaH(b) = -16.4 kcal.mol(-1)). The activation barrier (DeltaG) of 19.6 kcal.mol(-1) for the chemical step (ES <--> P) also is enthalpic in nature (DeltaH = 19.2 kcal.mol(-1)). Formation of the transition state complex from the reactants (E + S <--> ES), a pathway that reflects Fpg catalytic specificity (k(cat)/K(m)) toward excision of the 8-oxodG lesion, exhibits an overall activation free energy (DeltaG(T)) of 9.6 kcal.mol(-1). These parameters characterize the driving forces that dictate Fpg enzyme efficiency and specificity and elucidate the energy landscape for lesion recognition and repair.
Atrophy-centered subtyping of mild cognitive impairment (2020)

Abstract Mild cognitive impairment (MCI) is considered as the transitional phase between normal cognitive aging and Alzheimer’s disease (AD). Nevertheless, trajectories of cognitive decline vary considerably among individuals with MCI. To address this heterogeneity, subtyping approaches have been developed, with the objective of identifying more homogenous subgroups and ultimately improving prognostic outcomes. To date, subtyping of MCI has been based primarily on cognitive performance measures, often resulting in indistinct boundaries between the proposed subgroups and limited validity. The degree to which markers of neurodegeneration such as brain atrophy can be used to subtype MCI into biologically and clinically meaningful subgroups remains unclear. Here we introduce and validate a data-driven subtyping method for MCI based solely upon measures of atrophy derived from structural magnetic resonance imaging (MRI). We trained a dense convolutional neural network to differentiate between patients with AD and age-matched cognitively normal (CN) subjects based on whole brain MRI features. We then deployed the trained model to classify individuals with MCI, as MCI-CN or MCI-AD, based on the degree to which their whole brain gray matter volume resembles CN-like or AD-like patterns. We subsequently validated the model-based subgroups using cognitive, clinical, fluid biomarker, and molecular neuroimaging data. Namely, we observed marked differences between the MCI-CN and MCI-AD groups in baseline and longitudinal cognitive and clinical rating scales, disease-free survival, cerebrospinal fluid (CSF) levels of amyloid beta and tau, fluorodeoxyglucose (FDG) and amyloid PET. Overall, the results suggest that patterns of atrophy in MCI are sufficiently distinct and heterogeneous, and can thus be used to subtype individuals into biologically and clinically meaningful subgroups.
Clinical and functional characteristics of patients with unclassifiable interstitial lung diseases (uILD) from eurIPFreg (2020)

<b>Background:</b> In up to 20% of ILD patients a specific diagnosis cannot be established. We analyzed clinical characteristics, progression factors and outcomes of the Giessen uILD cohort within the eurIPFreg. <b>Methods:</b> 140 uILD subjects were recruited between 11/2009-01/2019 (26.4% of the whole ILD cohort). The diagnosis uILD was applied only when a conclusive diagnosis could not be reached with reasonable certainty. <b>Results:</b> At baseline, uILD patients showed a mean age of 68.25 years. 81% were male, 50.7% were previous or current smokers, mean FVC was 67.77% ± 22.12% pred, DLco was 43.75% ± 26.27% pred. Of all patients, 13.57% received pirfenidone, 16.43% azathioprine, 32.86% prednisolone. In 46.43%, the uILD diagnosis was due to conflicting clinical, radiological and pathological data. By applying the diagnostic criteria of UIP based on CT patterns (Fleischner Society), 22.22% of the patients showed a typical UIP pattern, 11.12 % a probable UIP pattern, 12.82 % an indeterminate UIP pattern and 53.84 % CT features most consistent with a non-IPF diagnosis. A multivariate analysis revealed the following risk factors for lung function decline and mortality: smoking (p=0.033), FVC &lt; 50% pred. at baseline (p=0.057), alongside with an annual FVC decline &gt;10% p.a. (p=0.008), and a DLCO &lt;55% pred. at baseline (p=0.002). <b>Conclusions:</b> Similar to IPF, the most important prognostic determinants in uILD are a decline in lung function and smoking. The use of Fleischner diagnostic criteria might allow further differentiation together with new therapeutic options for patients, who currently have no established approach to therapy.
Zákonodárný proces ČR (2009)

Cílem bakalářské práce je seznámit s průběhem a samotným legislativním procesem v České republice. Pro co nejlepší názornost a představu je vybrán jako příklad procesu a jeho jednotlivých kroků Antidiskriminační zákon, který je zajímavý svým obsahem i charakterem projednávání.
Reluctance network modeling tubular linear alternator considering iron nonlinearities (2009)

This paper presents a nonlinear reluctance network modeling a tubular surface mounted permanents magnets linear alternator. The ferromagnetic materials saturation is considered. The topology and the reluctance values of the network are automatically computed. The linkage between rotor and stator network is modified for each rotor position. The model allows a transient study and presents a good accordance with finites elements method considering the magnetic fluxes view by the stator windings. The proposed model is developed to be used in a systemic modeling of a generator set to optimize the alternator for a low frequency application.
Solving the Two-Connected Network with Bounded Meshes Problem (2000)

We study the problem of designing at minimum cost a two-connected network such that the shortest cycle to which each edge belongs (a “mesh”) does not exceed a given length K. This problem arises in the design of fiber-optic-based backbone telecommunication networks. A Branch-and-Cut approach to this problem is presented for which we introduce several families of valid inequalities and discuss the corresponding separation algorithms. Because the size of the problems solvable to optimality by this approach is too small, we also develop some heuristics. The computational performances of these exact and approximate methods are then thoroughly assessed both on randomly generated instances as well as instances suggested by real applications.
Analyzing the performance of pseudo-random single photon counting ranging Lidar (2018)

The detection principle and performance of the pseudo-random single photon counting ranging (PSPCR) Lidar system are investigated. The detection probability and single photon detection efficiency (SPDE) of the macro code for the PSPCR Lidar system are derived based on statistical theory. The effects of the echo primary electrons number and the dead time on the detection probability and SPDE are analyzed. The detection probability increases with the increase of the primary electron number and tends toward saturation. The change of dead time length has little effect on the detection probability of the macro code, especially when the number of echo primary electrons is large. However, the length of dead time is inversely proportional to the number of detected codes. The longer the dead time, the fewer the number of detected codes, and the worse the ranging performance. The signal-to-noise ratio (SNR) of the PSPCR Lidar is analyzed based on the cross-correlation function. The Monte Carlo simulation results show that the PSPCR Lidar has a satisfactory SNR even in a high noise level. As the number of signal primary electrons increases, the SNR gradually increases and tends to be saturated. As the noise increases, the SNR gradually decreases, and the greater the noise, the more severe the SNR decreases. At the same time, based on the assumption that the power of the single code in Gaussian distribution and the time resolution of the photon counting module are less than the code width, the theoretical formula of the range error is deduced. The effects of the echo signal primary electron number and code width on the range error are analyzed. The results show that the fewer the primary electron numbers or the narrower the code width, the smaller the range error of the PSPCR Lidar system. The range error of the PSPCR Lidar system is verified by Monte Carlo simulation. The simulation results are in good agreement with the theoretical analysis.
Flat Panel Displays: Advanced Organic Materials (2000)

Flat Panel Displays Liquid Crystals and Liquid Crystal Displays (LCDs) Liquid Crystal Displays Using Nematic Liquid Crystals Photoluminescence and Electroluminescence from Organic Materials Organic Light-Emitting Diodes Using Low-Molar-Mass Materials (LMMMs) Organic Light-Emitting Diodes Using Light-Emitting Polymers Conclusions and Outlook Subject Index.
Improving College Students' Success In Gateway Science Courses: Lessons Learned From An Anatomy And Physiology Workshop (2012)

In this study, we evaluated the effectiveness of a two-week pre-anatomy and physiology workshop intended to contribute to student success in anatomy and physiology. The study showed that workshop participants had significantly higher post-test scores, better study habits, and generally felt more confident or prepared for anatomy and physiology. The workshop participants also reported that they understood membrane transport the least and organization of the body the most, information that may be useful in anatomy and physiology curriculum development. Preliminary studies also show that students that participated in the workshop performed significantly better than the general student body, with lower attrition rates in anatomy and physiology.
Brokering algorithms for data replication and migration across cloud-based data stores (2017)

Cloud computing provides users with highly reliable, scalable and flexible computing and storage resources in a pay-as-you-go manner.Data storage services are gaining increasing popularity and many organizations are considering moving data out of their in-house data centers to the so-called Cloud Storage Providers (CSPs).However, reliance on a single CSP introduces challenges in terms of service unavailability, vendor lock-in, high network latency to the end users, and a non-affordable monetary cost to application providers.These factors are vital for the data-intensive applications which experience a time-varying workload, and the providers of these applications require to offer users storage services at an affordable monetary cost within the required Quality of Service (QoS).The utilization of multiple CSPs is a promising solution and provides the increment in availability, the enhancement in mobility, the decline in network latency, and the reduction in monetary cost by data dispersion across CSPs offering several storage classes with different prices and performance metrics.The selection of these storage classes is a non-trivial problem.This thesis presents a set of algorithms to address such problem and facilitates application providers with an appropriate selection of storage services so that the data management cost of data-intensive applications is minimized while the specified QoS by users is met.The thesis advances this field by making the following key contributions:1. Data placement algorithms that select storage services for replication non-stripped and stripped objects respectively, with the given availability to minimize storage cost and with the given budget to maximize availability.2. A dual cloud-based storage architecture for data placement, which optimizes data management cost (i.e,storage, read, write, and potential migration costs) and considers user-perceived latency for reading and writing data as a monetary cost.3. The optimal offline algorithm and two online algorithms with provable performance guarantees for data placement, which exploit pricing differences across storage classes owned by different CSPs to optimize data management cost for a given number of replicas of the object while respecting the user-perceived latency.4. A lightweight object placement algorithm that utilizes Geo-distributed storage classes to optimize data management cost for a number of replicas of the object that is dynamically determined.5. Design and implementation of a prototype system for empirical studies in latency evaluation in the context of a data placement framework across two cloud providers services (Amazon S3 and Microsoft Azure).
Identification of 55,000 Replicated DNA Methylation QTL (2017)

DNA methylation plays an important role in the regulation of transcription. Genetic control of DNA methylation is a potential candidate for explaining the many identified SNP associations with disease that are not found in coding regions. We replicated 52,916 cis and 2,025 trans DNA methylation quantitative trait loci (mQTL) using methylation measured on Illumina HumanMethylation450 arrays in the Brisbane Systems Genetics Study (n=614 from 177 families) and the Lothian Birth Cohorts of 1921 and 1936 (combined n = 1366). The trans mQTL SNPs were found to be over-represented in 1Mbp subtelomeric regions, and on chromosomes 16 and 19. There was a significant increase in trans mQTL DNA methylation sites in upstream and 5’ UTR regions. No association was observed between either the SNPs or DNA methylation sites of trans mQTL and telomere length. The genetic heritability of a number of complex traits and diseases was partitioned into components due to mQTL and the remainder of the genome. Significant enrichment was observed for height (p = 2.1x10 −10 ), ulcerative colitis (p = 2x10 −5 ), Crohn’s disease (p = 6x10 −8 ) and coronary artery disease (p = 5.5x10 −6 ) when compared to a random sample of SNPs with matched minor allele frequency, although this enrichment is explained by the genomic location of the mQTL SNPs.
Time-reversed ultrasonically encoded optical focusing into tissue-mimicking media with thickness up to 70 mean free paths (2011)

In turbid media such as biological tissue, multiple scattering hinders direct light focusing at depths beyond one transport mean free path. As a solution to this problem, time-reversed ultrasonically encoded (TRUE) optical focusing is proposed based on ultrasonic encoding of diffused laser light and optical time reversal. In TRUE focusing, a laser beam of long coherence length illuminates a turbid medium, where the incident light undergoes multiple scattering and part of it gets ultrasonically encoded within the ultrasonic focal zone. A conjugated wavefront of the ultrasonically encoded light is then generated by a phase conjugate mirror outside the medium, which traces back the trajectories of the ultrasonically encoded diffused light and converges light to the ultrasonic focal zone. Here, we report the latest experimental improvement in TRUE optical focusing that increases its penetration in tissue-mimicking media from a thickness of 3.75 to 7.00 mm. We also demonstrate that the TRUE focus depends on the focal diameter of the ultrasonic transducer.
IFN-Gamma Inhibits JC Virus Replication in Glial Cells by Suppressing T-Antigen Expression (2015)

Our results suggest a novel role for IFN-γ in the regulation of JCV gene expression via downregulation of the major viral regulatory protein, T-antigen, and provide a new avenue of research to understand molecular mechanisms for downregulation of viral reactivation that may lead to development of novel strategies for the treatment of PML.
Magnet optimization for pulsed energy conversion (1979)

A flux compression generator called PULSAR is being developed to meet power requirements for future fusion reactors. Key components of the generator are superconducting magnet, generator coil of normal metallic conductor, and an armature, either a metallic conductor or plasma. Chemical energy is used to increase the mutual inductance between the armture and nested generator coil and superconducting magnet. Flux compression occurs and electrical energy is transferred to a load inductance. This paper will present the results of a study that was conducted to design a suitable superconducting magnet for the PULSAR device.
Rituximab treatment in patients with primary Sjögren's syndrome: An open‐label phase II study (2005)

Findings of this phase II study suggest that rituximab is effective in the treatment of primary SS. The high incidence of HACAs and associated side effects observed in this study needs further evaluation.
COMMUNICATION IN NOISE: SUCCESS RELATED TO THREE DEGREES OF EMPHASIS ON VERBAL CONTEXT. (1954)

The purpose of the experiment was to investigate what effect minimizing or emphasizing attention to an objective verbal context will have upon the intelligibility of spoken words when the amount of information and signal-to-noise ratio are held constant. The subjects were administered multiple-choice intelligibility tests under noise conditions by the following methods: (1) The subject checked the words heard among four alternatives for each test item. (2) The subject whispered four alternatives before the test word was spoken. (3) The subject did not see the alternatives before the word was spoken by the experimenter. The data collected in this study indicate that listener scores are improved under the condition in which verbal context of the test items is stressed; on the other hand, listener scores are lessened under the condition in which the verbal context is minimized. The broad implication of the study is that time spent by listener-talkers in studying the nomenclature they must communicate will be repaid by more efficient communications. (Author)
Toward Stationary Concentrator Photovoltaic Panels (2017)

Stationary concentrator PV modules offer the potential for high energy production per unit area at low cost. We have explored two optical architectures toward this goal and report on our progress. A novel singlet lens array design incorporating fluidic self-aligned tracking has been demonstrated; this provides an elegant tracking solution but does not provide a sufficiently large effective acceptance angle to be practical for stationary mounting. A catadioptric design is much more promising in this regard. Initial demonstrations show the wide-angle internal tracking compatible with stationary mounting, and detailed modeling predicts high energy output. Practical issues surrounding actuation and backplane assembly must be solved, but these do not represent fundamental obstacles.
Unravelling the impact of frontal lobe impairment for social dysfunction in myotonic dystrophy type 1 (2022)

Myotonic dystrophy type 1 is an autosomal dominant multisystemic disorder affecting muscular and extra muscular systems, including the central nervous system. Cerebral involvement in myotonic dystrophy type 1 is associated with subtle cognitive and behavioural disorders, of major impact on socio-professional adaptation. The social dysfunction and its potential relation to frontal lobe neuropsychology remain under-evaluated in this pathology. The neuroanatomical network underpinning that disorder is yet to disentangle. Twenty-eight myotonic dystrophy type 1 adult patients (mean age: 46 years old) and 18 age and sex-matched healthy controls were included in the study. All patients performed an exhaustive neuropsychological assessment with a specific focus on frontal lobe neuropsychology (motivation, social cognition and executive functions). Among them, 18 myotonic dystrophy type 1 patients and 18 healthy controls had a brain MRI with T<sub>1</sub> and T<sub>2</sub> Flair sequences. Grey matter segmentation, Voxel-based morphometry and cortical thickness estimation were performed with Statistical Parametric Mapping Software SPM12 and Freesurfer software. Furthermore, T<sub>2</sub> white matter lesions and subcortical structures were segmented with Automated Volumetry Software. Most patients showed significant impairment in executive frontal functions (auditory working memory, inhibition, contextualization and mental flexibility). Patients showed only minor difficulties in social cognition tests mostly in cognitive Theory of Mind, but with relative sparing of affective Theory of Mind and emotion recognition. Neuroimaging analysis revealed atrophy mostly in the parahippocampal and hippocampal regions and to a lesser extent in basal ganglia, regions involved in social navigation and mental flexibility, respectively. Social cognition scores were correlated with right parahippocampal gyrus atrophy. Social dysfunction in myotonic dystrophy type 1 might be a consequence of cognitive impairment regarding mental flexibility and social contextualization rather than a specific social cognition deficit such as emotion recognition. We suggest that both white matter lesions and grey matter disease could account for this social dysfunction, involving, in particular, the frontal-subcortical network and the hippocampal/arahippocampal regions, brain regions known, respectively, to integrate contextualization and social navigation.
Enhanced smart window based on electrochromic (EC) polymers (2003)

A large contrast ratio and rapid switching EC polymer device which consists of a laminated two-layer structure between two electrodes was prepared. The new design consists of an ITO glass electrode, a cathodic EC polymer film, a gel electrolyte and a counter-electrode that replaces the anodic EC polymer and ITO electrode. Several types of EC polymers, such as, poly[3,3-dimethyl-3,4-dihydro-2H-thieno(3,4-b)(1,4)dioxepine] (PProDOT-(CH<sub>3</sub>)<sub>2</sub>) and poly[3,4-(2,2-dimethylpropylenedioxy)-pyrrole] (PProDOP-(CH<sub>3</sub>)<sub>2</sub>) were synthesized as cathodic EC polymers. A carbon-based counter-electrode was prepared for comparison with an Au-based counter-electrode. Screen-printing was utilized for the carbon-based counter-electrode. Lithography and sputtering were used for the Au patterned glass counter-electrodes. Several kinds of polymer gel electrolytes were prepared for solid-state applications. Color change of high contrast ratio of visible light transmittance (&gt;&Delta;&#932;55%)of the device is rapidly obtained (0.5-1s) when even less than 2.5V is applied. The repeatability of color changeable EC polymer windows was estimated by the method of electrochemistry and spectrophotometry. This "smart window" technology can be used in many applications where a rapid color change between transparent and color states is required.