gebhart/patrepeval huggingface dataset:
A High-Throughput Assay for siRNA-Based Circadian Screens in Human U2OS Cells (2008)

The advent of siRNA-based screens has revolutionized the efficiency by which functional components of biological processes are identified. A notable exception has been the field of mammalian circadian rhythms. Here, we outline a medium- to high-throughput siRNA-based approach that, in combination with real-time bioluminescence measurement of a circadian reporter gene, can be utilized to elucidate the effects of gene knockdown across several days in human cells.
Cloud-Based Vehicle Ride-Height Control (2019)

We present a novel approach for a cloud-based ride-height control for vehicles equipped with an air suspension. The objective of this approach is to improve both efficiency and comfort, especially on single obstacles, by including vehicle-to-vehicle or vehicle-to-infrastructure (V2X) information on the road ahead in the control algorithm. The focus of this paper is the methodology of data processing on a cloud backend and includes three steps: pre-processing, clustering and allocation of streets to the clusters. In the first step, the database is reduced to obstacles relevant for driving comfort. The second step is to find clusters with a high density of obstacles on a road condition map. Finally, the probability of hitting an obstacle is calculated for each road in the area of a cluster, taking the characteristics and the topology of the road network into account. Example data is used to proof the functionality of the method. The proposed method seems to be a suitable approach for big data applications and might improve a vehicle ride-height control with regard to comfort and efficiency.
Direct Observation of Intramolecular Hydrogen Bonds in Peptide 310 Helices by 3hJN,C′ Scalar Couplings (2004)

Zur Unterscheidung von Helices kann die direkte Beobachtung von Wasserstoffbrücken anhand von skalaren 3hJN,C′-Kopplungen (siehe Bild) dienen. Diese Beobachtung gelingt nicht nur bei α-Helix- und β-Faltblattpeptiden und -proteinen, sondern auch bei 310-helicalen Peptiden. Außerdem liefert das Verfahren Informationen über das Ausfransen am Helixende und erlaubt die Unterscheidung zwischen α- und 310-Helices.
Use of Patch Clamp Electrophysiology to Identify Off-Target Effects of Clinically Used Drugs (2012)

Most drugs have effects attributed to actions at sites other than those that are intended. In many cases these off-target effects have adverse consequences, though in some instances these effects may be neutral or even beneficial. Many off-target effects involve either direct or indirect actions on ion channels. Hence, electrophysiological approaches can be employed to screen drugs for effects on ion channels and thereby predict their off-target actions. The pharmaceutical industry routinely uses cellular expression systems and cloned channels to quickly screen thousands of compounds to eliminate those that have well known adverse ion channel effects, such as inhibition of the Kv11.1 potassium channel encoded by the human Ether-a-go-go related gene (hERG). However, these methods are not well-suited to predicting many other off-target effects mediated by actions on ion channels natively expressed in specific tissues. We have employed a more directed electrophysiological approach to evaluate a small number of compounds (e.g. drugs with known or predicted adverse effects) to identify ion channel targets that might explain their actions. This chapter will describe this approach in some detail and illustrate its use with some specific examples.
Making Large-Scale SVM Learning Practical (2006)

Training a support vector machine SVM leads to a quadratic optimization problem with bound constraints and one linear equality constraint. Despite the fact that this type of problem is well understood, there are many issues to be considered in designing an SVM learner. In particular, for large learning tasks with many training examples on the shelf optimization techniques for general quadratic programs quickly become intractable in their memory and time requirements. SVM light is an implementation of an SVM learner which addresses the problem of large tasks. This chapter presents algorithmic and computational results developed for SVM light V 2.0, which make large-scale SVM training more practical. The results give guidelines for the application of SVMs to large domains.
Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction (2020)

The emergence of SARS-CoV-2 has led to the current global coronavirus pandemic and more than one million infections since December 2019. The exact origin of SARS-CoV-2 remains elusive, but the presence of a distinct motif in the S1/S2 junction region suggests the possible acquisition of cleavage site(s) in the spike protein that promoted cross-species transmission. Through plaque purification of Vero-E6 cultured SARS-CoV-2, we found a series of variants which contain 15-30-bp deletions (Del-mut) or point mutations respectively at the S1/S2 junction. Examination of the original clinical specimen from which the isolate was derived, and 26 additional SARS-CoV-2 positive clinical specimens, failed to detect these variants. Infection of hamsters shows that one of the variants (Del-mut-1) which carries deletion of 10 amino acids (30bp) does not cause the body weight loss or more severe pathological changes in the lungs that is associated with wild type virus infection. We suggest that the unique cleavage motif promoting SARS-CoV-2 infection in humans may be under strong selective pressure, given that replication in permissive Vero-E6 cells leads to the loss of this adaptive function. It would be important to screen the prevalence of these variants in asymptomatic infected cases. The potential of the Del-mut variants as an attenuated vaccine or laboratory tool should be evaluated.
Mining Negatives Association Rules Using Constraints (2018)

Pattern discovery techniques, such as association rule discovery is one of the fundamental problem in data mining. Usually the task is limited to positive rules of the form X → Y when X and Y are susbets of items. To enlarge the knowledge discovery from data. Many works pointed out that other rules can be mined linking the present items in transactions with the missing ones designed as negative rules. To mine the most relevant negative rules, the mining task of negative association rules is often coupled with new measure such as lift or conviction to limit the set of extracted association rules. In this work we address the problem of mining strong negative rules by extending the SAT-Based approach proposed in [1]. We show that the conviction constraint leads to a non-linear constraints that have to be managed efficiently to prune the search space. Experiments results explore the efficiency of our new approach.
Scintillation properties of a Cs2LiLa(Br6)90%(Cl6)10%:Ce (CLLBC) crystal (2014)

In investigations of Ce<sup>3+</sup>-doped Cs<sub>2</sub>LiLa(Br6)<sub>90%</sub>(Cl6)<sub>10%</sub> (CLLBC) elpasolite crystals, the crystals show an excellent neutron and gamma (n/&gamma;) radiation response. The results of our studies on the scintillation properties of CLLBC viz. radioluminescence, energy resolution, light yield, decay times, and nonproportionality are discussed. The CLLBC detector can provide energy resolution as good as 4.1% at 662 keV (FWHM), which is better than that of NaI:Tl. Because the crystal contains <sup>6</sup>Li, CLLBC can also detect thermal neutrons. In the energy spectra, the full energy thermal neutron peak appears near or above 3 MeV gamma equivalent energy. This high-energy signature for the thermal neutron peak means that very effective pulse height discrimination is possible. Unfortunately, because the core-to-valence luminescence observed in other elpasolites that can be exploited for effective pulse shape discrimination (PSD) is not observed in the CLLBC, other strategies for obtaining the PSD of CLLBC are needed. The n/&gamma; discrimination capability of CLLBC detectors may be optimized by tuning the cerium doping content for maximum effect on n/&gamma; pulse shape differences. The value of adding a chlorine component to the nominal CLLB crystal is discussed. Because the crystal contains chlorine, its sensitivity to fast neutrons is better than that of Cs<sub>2</sub>LiLaBr<sub>6 </sub>(CLLB). Further, an array of three of these CLLBC detectors may be able to perform directional detection in both the neutron and gamma channels simultaneously.
Supplementary Methods and References from Integrative Radiogenomic Profiling of Squamous Cell Lung Cancer (2023)

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SEA‐AD: Scientific analysis and open access resources targeting early changes in Alzheimer’s disease (2023)

Abstract Background Alzheimer’s disease (AD) is the most common form of dementia, representing ∼70% of all dementia cases, and affecting much of the aged population. Currently our understanding of AD neuropathology is largely centered on characteristic deposition of certain neuropathological proteins and identification of histologically defined neuronal populations. Molecular tools to characterize the transcriptome, epigenome, and spatial organization of single cells in complex brain tissues allow a more refined look at how the neurotypical brain changes in AD than had been possible previously. Linking molecular, cellular, genomic, cognitive, and pathological indicators of AD progression will be essential for understanding disease mechanisms. Methods The Seattle Alzheimer’s Disease Brain Cell Atlas (SEA‐AD) brings together experts in AD research and large‐scale molecular/anatomical brain mapping to modernize AD tissue banking methods, and to combine traditional and quantitative neuropathology with emerging genotyping, single nucleus transcriptomics, single nucleus epigenomics, and spatial transcriptomics technologies. Applied to multiple brain regions in donors spanning different stages of AD pathology, these techniques will identification of cell type specific molecular pathways and yield valuable insights into selective vulnerability or resistance to pathology. Two well characterized cohorts (Adult Changes in Thought (ACT) and the University of Washington ADRC) provided 84 subjects of varying degrees of AD severity, including cognitively normal subjects. Results The initial focus of SEA‐AD was on integrating and interpreting relationships between all collected multimodal data in middle temporal gyrus (MTG). Identified cell types and molecular pathways of interest are presented separately and are both consistent with and expand upon results found from ROSMAP and other cohorts. The complete SEA‐AD MTG atlas is now freely and publicly available at brain‐map.org and includes access to all data and associated donor metadata, tools for visualization and exploration of molecular data, exploration of pathology images, a tool for assigning cell types to community‐based ‐omics datasets, comprehensive documentation, and user support. Conclusions SEA‐AD has developed a high resolution, high‐quality, publicly accessible atlas of aging and AD, and is designed to better understand the complex and likely heterogenous nature of AD.
Effects of Payments on the Riskiness of Returns to Cellulosic Ethanol Feedstock Production (2021)

Risk and Uncertainty, Environmental Economics and Policy, Agricultural and Food Policy
Azimuthal anisotropy using shear dipole sonic: insights from the AIG 10 well, Corinth Rift Laboratory (2004)

Within the Corinth Rift Laboratory, dipole sonic data have been acquired in the AIG 10 well between depths 711 and 1004 m during three passes of a sonic logging tool at three different borehole fluid pressures. Specific sections of the well reveal clear characteristics of either moderate-to-large azimuthal anisotropy (9–25%) below the Aigion Fault, e.g., 779–784 and 809–816 m, with a fast-shear azimuth directed 105°, or homogeneous isotropic medium (i.e., 735–753 m) between the casing shoe and the fault. The presence of the fault is coincident with the identification of lower velocities over an interval of approximately 12–14 m. Analysis of the data reveals that the formation is not acoustically stress-sensitive to the 3 MPa differential pressure applied. Interpretation of the sonic data with complementary image logs suggests the anisotropy is due to intrinsic fractures and bedding, and the fast-shear direction 105° is consistent with the regional maximum horizontal stress.
Improved optical outcoupling of OLED microdisplays by nanostructured substrates (2011)

We present optical simulations of the light outcoupling efficiency of an OLED-anode design which allows the integration of a grating with high refractive index contrast into a topemitting OLED with standard CMOS technology. We demonstrate the effective coupling of the grating with the confined organic modes and therefore changing the outcoupling efficiency with respect to the planar OLED-stack.
Structural Health Monitoring of Aerospace Structures with Sol-Gel Spray Sensors (2007)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Quasi-resonant enhancement of a grazing diffracted wave and deep suppression of specular reflection on shallow metal gratings in terahertz (2015)

We report on a previously unexamined anomaly at diffraction of THz radiation on metal gratings. This anomaly consists in a nearly complete redirection of energy to a non-specular homogeneous diffraction order propagating at a specific grazing angle and deep suppression of the specular reflection. We show that this anomaly is located far enough from the well-known one caused by the resonant excitation of the surface plasmon-polariton. The effect under consideration is of general nature and can exist in all spectrum regions; however, it is especially pronounced in THz region, where it should be taken into account when analyzing relevant experimental results.
Spin chains, defects, and quantum wires for the quantum-double edge (2021)

Non-Abelian defects that bind Majorana or parafermion zero modes are prominent in several topological quantum computation schemes. Underpinning their established understanding is the quantum Ising spin chain, which can be recast as a fermionic model or viewed as a standalone effective theory for the surface-code edge -- both of which harbor non-Abelian defects. We generalize these notions by deriving an effective Ising-like spin chain describing the edge of quantum-double topological order. Relating Majorana and parafermion modes to anyonic strings, we introduce quantum-double generalizations of non-Abelian defects. We develop a way to embed finite-group valued qunits into those valued in continuous groups. Using this embedding, we provide a continuum description of the spin chain and recast its non-interacting part as a quantum wire via addition of a Wess-Zumino-Novikov-Witten term and non-Abelian bosonization.
A Hybrid Scheduling Algorithm for Data Intensive Workloads in a MapReduce Environment (2012)

The specific choice of workload task schedulers for Hadoop MapReduce applications can have a dramatic effect on job workload latency. The Hadoop Fair Scheduler (FairS) assigns resources to jobs such that all jobs get, on average, an equal share of resources over time. Thus, it addresses the problem with a FIFO scheduler when short jobs have to wait for long running jobs to complete. We show that even for the FairS, jobs are still forced to wait significantly when the MapReduce system assigns equal sharing of resources due to dependencies between Map, Shuffle, Sort, Reduce phases. We propose a Hybrid Scheduler (HybS) algorithm based on dynamic priority in order to reduce the latency for variable length concurrent jobs, while maintaining data locality. The dynamic priorities can accommodate multiple task lengths, job sizes, and job waiting times by applying a greedy fractional knapsack algorithm for job task processor assignment. The estimated runtime of Map and Reduce tasks are provided to the HybS dynamic priorities from the historical Hadoop log files. In addition to dynamic priority, we implement a reordering of task processor assignment to account for data availability to automatically maintain the benefits of data locality in this environment. We evaluate our approach by running concurrent workloads consisting of the Word-count and Terasort benchmarks, and a satellite scientific data processing workload and developing a simulator. Our evaluation shows the HybS system improves the average response time for the workloads approximately 2.1x faster over the Hadoop FairS with a standard deviation of 1.4x.
Analysis of subcellular location of bestrophin in transfected RPE cell lines (2000)

Best macular dystrophy is an autosomal dominant disease leading to macular degeneration and subsequent impaired vision. The disease has juvenile onset and affects the retinal pigment epithelium and adjacent photoreceptors. There are histopathological similarities between Best macular dystrophy (BMD) and age-related macular degeneration (AMD) with accumulation of lipofuscin in the outer retina. Recently, we identified the gene VMD2 causing Best macular dystrophy. The VMD2 gene has unknown function and there are no similarities between the VMD2 product, called bestrophin, and other proteins with known function. In order to gain more knowledge about the function of bestrophin we investigated its subcellular localization. DNA constructs encoding the bestrophin protein fused to the green fluorescent protein (GFP) or a c-myc tag were transiently expressed in COS-7 cells or retinal pigment epithelium cells. The observed pattern of bestrophin fusion protein was spotted and mainly perinuclear, well corresponding to the endoplasmic reticulum (ER), which was also suggested when counterstaining with an ER probe. Probes for other organelles had a different localization pattern compared to bestrophin. In conclusion, the results indicate that bestrophin is located to the endoplasmic reticulum.
Does Erythropoietin Regulate TRPC Channels in Red Blood Cells? (2017)

Our results allow concluding that Epo and PGE2 regulation of the Ca2+ homeostasis is distinctly different between murine and human RBCs and that changes in intracellular Ca2+ upon Epo treatment is a primary rather than a compensatory effect. In human RBCs, Epo itself has no effect on Ca2+ fluxes but inhibits the PGE2-induced Ca2+ entry. In murine mature RBCs functional evidence indicates TRPC4/C5 mediated Ca2+ entry activated by Epo whereas PGE2 leads to a TRPC independent Ca2+ entry.
Analysis of Cardiovascular Phenotype and Genotype-Phenotype Correlation in Individuals With a JAG1 Mutation and/or Alagille Syndrome (2002)

More than 90% of individuals with a JAG1 mutation or AGS have cardiovascular anomalies, with branch PA stenosis the most common abnormality. Cardiovascular phenotype does not correlate with the type or location of JAG1 mutation.
A Novel Pore-Forming Toxin in Type A Clostridium perfringens Is Associated with Both Fatal Canine Hemorrhagic Gastroenteritis and Fatal Foal Necrotizing Enterocolitis (2015)

A role for type A Clostridium perfringens in acute hemorrhagic and necrotizing gastroenteritis in dogs and in necrotizing enterocolitis of neonatal foals has long been suspected but incompletely characterized. The supernatants of an isolate made from a dog and from a foal that died from these diseases were both found to be highly cytotoxic for an equine ovarian (EO) cell line. Partial genome sequencing of the canine isolate revealed three novel putative toxin genes encoding proteins related to the pore-forming Leukocidin/Hemolysin Superfamily; these were designated netE, netF, and netG. netE and netF were located on one large conjugative plasmid, and netG was located with a cpe enterotoxin gene on a second large conjugative plasmid. Mutation and complementation showed that only netF was associated with the cytotoxicity. Although netE and netG were not associated with cytotoxicity, immunoblotting with specific antisera showed these proteins to be expressed in vitro. There was a highly significant association between the presence of netF with type A strains isolated from cases of canine acute hemorrhagic gastroenteritis and foal necrotizing enterocolitis. netE and netF were found in all cytotoxic isolates, as was cpe, but netG was less consistently present. Pulsed-field gel electrophoresis showed that netF-positive isolates belonged to a clonal population; some canine and equine netF-positive isolates were genetically indistinguishable. Equine antisera to recombinant Net proteins showed that only antiserum to rNetF had high supernatant cytotoxin neutralizing activity. The identifica-tion of this novel necrotizing toxin is an important advance in understanding the virulence of type A C. perfringens in specific enteric disease of animals.
A two-photon fluorescent turn-on probe for nitroxyl (HNO) and its bioimaging application in living tissues (2015)

The first two-photon fluorescent probe for specific detection of nitroxyl is designed and synthesized, and we have further demonstrated that the new two-photon fluorescent probe could be employed to image nitroxyl in living cells and tissues.
High Strength and Electrical Conductivity of UFG Copper Alloys (2010)

Copper based materials are still the most attractive low resistivity materials for microelectronics and electrotechnics applications, though, all variants developed to combine strength and conductivity, such as solid solutions and composites, suffer from decay in electric conductivity while strength is increased . In a addition, linear decay was also conjectured for pure copper when grain size is refined below the UFG and nanostructured domains (except when grain boundaries are pure twins). Copper alloys with low content of silver and chromium were prepared by high pressure torsion (HPT) with various annealing conditions. Vickers hardness and electric resistivity in the temperature range of 4K-340K, were measured as well as microstructural characterizations were performed using quantitative X-ray diffraction. Depending on the annealing conditions the alloys exhibit from 25% to 75% of IACS electric conductivity at room temperature and hardness in the range of 200 Hv. Origins of both high strength and high electric conductivity were investigated from microstructures analysis, using transmission electron microscopy and mechanical testing.