gebhart/patrepeval huggingface dataset:
Experimental results from the Los Alamos FEL photoinjector (1991)

The authors report some initial measurements of electron beam properties from the new photoinjector installed as the front end on the Los Alamos free-electron laser (FEL). The FEL is being rebuilt with the photoinjector, added acceleration to 40 MeV, new diagnostics, and a beam line designed to minimize emittance growth. The authors measured the spatial and temporal properties of the beam at energies of about 15 MeV as a function of several parameters and the results have been compared to simulations. The operational characteristics of the important elements of the system and the theoretical comparisons are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Anomaly Detection in Nanofibrous Materials by CNN-Based Self-Similarity (2018)

Automatic detection and localization of anomalies in nanofibrous materials help to reduce the cost of the production process and the time of the post-production visual inspection process. Amongst all the monitoring methods, those exploiting Scanning Electron Microscope (SEM) imaging are the most effective. In this paper, we propose a region-based method for the detection and localization of anomalies in SEM images, based on Convolutional Neural Networks (CNNs) and self-similarity. The method evaluates the degree of abnormality of each subregion of an image under consideration by computing a CNN-based visual similarity with respect to a dictionary of anomaly-free subregions belonging to a training set. The proposed method outperforms the state of the art.
The Ratiometric Transcript Signature MX2/GPR183 Is Consistently Associated With RTS,S-Mediated Protection Against Controlled Human Malaria Infection (2020)

The RTS,S/AS01 vaccine provides partial protection against <i>Plasmodium falciparum</i> infection but determinants of protection and/or disease are unclear. Previously, anti-circumsporozoite protein (CSP) antibody titers and blood RNA signatures were associated with RTS,S/AS01 efficacy against controlled human malaria infection (CHMI). By analyzing host blood transcriptomes from five RTS,S vaccination CHMI studies, we demonstrate that the transcript ratio MX2/GPR183, measured 1 day after third immunization, discriminates protected from non-protected individuals. This ratiometric signature provides information that is complementary to anti-CSP titer levels for identifying RTS,S/AS01 immunized people who developed protective immunity and suggests a role for interferon and oxysterol signaling in the RTS,S mode of action.
Architectural design of a multi-agent system for handling metadata streams (2001)

We have designed a multi-agent architecture to deliver metadata streams synchronously with multimedia streams over a wide-area network. To this end, we have devised a simple protocol for synchronising agents to a media clock. This protocol defines the concept of deadline, after which servers can drop data because it can no longer reach clients in time. We also introduce a new concept of contract as a first-class entity representing a successful subscription; a contract is used by agents as a session identifier during the navigation of streams. Quality of service is a vital element of this architecture because of the need to deliver metadata on time. As a result, our architecture supports various communication protocols, including UDP, RMI, SSL, or multicast. This resulted in a return to a more declarative form of speech acts, totally orthogonal to a notion of virtual communication channel used to manage the quality of service of communication.
Establishment of a retinal hypoxia organ culture model (2017)

Hypoxia plays an important role in several retinal diseases, especially in central retinal artery occlusion (CRAO). Although CRAO has been known for over a hundred years, no cure or sufficient treatment is available. Potential therapies are being evaluated in several <i>in vivo</i> models or primary cultures. However, <i>in vivo</i> models or primary cultures are very time-consuming, expensive, and furthermore several therapies or agents cannot be tested. Therefore, we aimed to develop a standardized organotypic <i>ex vivo</i> retinal hypoxia model. A chamber was developed in which rat retinal explants were incubated for different hypoxia durations. Afterwards, the retinas were adjusted to normal air and incubated for 24, 48 or 72 h under standard conditions. To analyze the retinal explants, and in particular the retinal ganglion cells (RGC) immunohistology, western blot and optical coherence tomography (OCT) measurements were performed. To compare our model to a standardized degeneration model, additional retinal explants were treated with 0.5 and 1 mM glutamate. Depending on hypoxia duration and incubation time, the amount of RGCs decreased and accordingly, the amount of TUNEL-positive RGCs increased. Furthermore, β-III-tubulin expression and retinal thickness significantly decreased with longer-lasting hypoxia. The reduction of RGCs induced by 75 min of hypoxia was comparable to the one of 1 mM glutamate treatment after 24 h (20.27% versus 19.69%) and 48 h (13.41% versus 14.41%) of incubation. We successfully established a cheap, standardized, easy-to-use organotypic culture model for retinal hypoxia. We selected 75 min of hypoxia for further studies, as approximately 50% of the RGC died compared to the control group after 48 h.
Fetal bovine serum (FBS): Past – present – future (2017)

The supplementation of culture medium with fetal bovine serum (FBS, also referred to as "fetal calf serum") is still common practice in cell culture applications. Due to a number of disadvantages in terms of quality and reproducibility of in vitro data, animal welfare concerns, and in light of recent cases of fraudulent marketing, the search for alternatives and the development of serum-free medium formulations has gained global attention. Here, we report on the 3rd Workshop on FBS, Serum Alternatives and Serum-free Media, where regulatory aspects, the serum dilemma, alternatives to FBS, case-studies of serum-free in vitro applications, and the establishment of serum-free databases were discussed. The whole process of obtaining blood from a living calf fetus to using the FBS produced from it for scientific purposes is de facto not yet legally regulated despite the existing EU-Directive 2010/63/EU on the use of animals for scientific purposes. Together with the above-mentioned challenges, several strategies have been developed to reduce or replace FBS in cell culture media in terms of the 3Rs (Refinement, Reduction, Replacement). Most recently, releasates of activated human donor thrombocytes (human platelet lysates) have been shown to be one of the most promising serum alternatives when chemically-defined media are not yet an option. Additionally, new developments in cell-based assay techniques, advanced organ-on-chip and microphysiological systems are covered in this report. Chemically-defined serum-free media are shown to be the ultimate goal for the majority of culture systems, and examples are discussed.
Localization of Alexa-conjugated cisplatin in cisplatin-resistant cell lines (2004)

1218 Resistance to cisplatin, one of the most widely used anticancer chemotherapeutic agents, is a major clinical problem. The exact mechanism of cisplatin resistance is still unknown. In KB-CP-r cells, multidrug resistance is accompanied by decreased accumulation of platinum compounds and membrane protein mislocalization, which is caused mainly by a defect of plasma membrane protein recycling as shown by pulse-chase labeling and pulse-chase biotinylation analysis. We have hypothesized that the mislocalization of a cisplatin-binding protein or proteins is responsible for the decreased drug uptake. To study distribution of cisplatin in parental and KB-CP-r cells, a fluorescent platinum compound, Alexa Fluo-546 cisplatin, was used. Using digital fluorescence confocal microscopy, the fluorescent cisplatin was readily internalized by the parental KB-3-1 cells and localized throughout the cells after 2 hours. In contrast, only punctate cytoplasmic staining was observed in KB-CP-r cells after incubation, with little or no fluorescence observed in the nucleus. In parental cells, Alexa-546 cisplatin entered cells partially by pinocytosis similar to that seen with Dextran-10, after which it localized in the Golgi apparatus as detected by colocalization with NBD-C6-ceramide, followed by nuclear localization. The overall fluorescence accumulated in the cells decreased in the KB-CP-r cells compared with sensitive KB-3-1 cells, as observed by Flow Cytometry (FACS) and confocal fluorescence microscopy, consistent with decreased uptake of the platinum complex in KB-CP-r cells. To identify the punctate compartment in which Alexa-488 cisplatin localized in CP-r cells, we examined cell extracts by iodixanol gradient centrifugation. As detected by antibodies to Alexa-488, the fluorescent cisplatin was mostly in a low density membrane fraction in both sensitive and resistant cells. Some Alexa-488 cisplatin binding proteins (CBPs) were not labeled in KB-3-1 cells after treatment with 10mg/ml cisplatin, suggesting specific labeling. We conclude that failure of appropriate trafficking of cell membrane binding protein(s) for cisplatin may result in resistance to cisplatin in cultured cancer cells, presumably because putative CP-r cell surface receptors/ transporters/ channels are not properly located on the cell surface in these cells.
Energy component analysis for dilute aqueous solutions of Li+, Na+F−, and Cl− ions (1984)

Comparaison des valeurs calculees par une methode de Monte-Carlo avec les donnees experimentales
Varying the Alkali-Metal Radii in (KxRb1–x)n[GaH2]n (0 ≤ x ≤ 1) Reorients a Stable Polyethylene-Structured [GaH2]nn– Anionic Chain (2013)

The stability of a negatively charged polyethylene-structured [GaH2]n(n-) cluster ion was investigated by varying the K(+)/Rb(+) ratio in ((K(x)Rb(1-x))n[GaH2]n (0 ≤ x ≤ 1). Neutron, X-ray, and IR spectroscopies were used to characterize the new phases. Between the limiting compositions Kn[GaH2]n and Rbn[GaH2]n, the [GaH2]n(n-) chains remained almost identical, indicating a stable specie. For rubidium-rich samples up to a potassium content corresponding to (K0.5Rb0.5)n[GaH2]n, two phases coexist in the samples, RbGaH2 and (K0.5Rb0.5)n[GaH2]n, with a ratio mirroring the relative alkali-ion content. The two phases have a different alignment of the [GaH2]n(n-) chains. For potassium-rich samples beyond (K0.5Rb0.5)n[GaH2]n, the samples were single-phased. The unit cell volume of the new (K0.5Rb0.5)n[GaH2]n structure type shrinks according to Vegard's law as smaller K(+) ions substitute for larger Rb(+) ions. The [GaH2]n(n-) chains remained, however, almost identical. IR spectra from the different phases were very similar, exhibited stretching, scissoring, and rocking modes similar to those in ordinary polyethylene, but shifted to lower frequencies, reflecting weaker Ga-H bonds. The existence of stable Kn[GaH2]n and Rbn[GaH2]n, would help to dehydrogenate KGaH4 and RbGaH4 upon heating. If this could be transferred to lighter alanates and borohydrides, it could be possible to develop more functional hydrogen-storage systems.
ESTIMATING THE FRACTAL DIMENSION OF THE S&P 500 INDEX USING WAVELET ANALYSIS (2004)

S&amp;P 500 index data sampled at one-minute intervals over the course of 11.5 years (January 1989–May 2000) is analyzed, and in particular the Hurst parameter over segments of stationarity (the time period over which the Hurst parameter is almost constant) is estimated. An asymptotically unbiased and efficient estimator using the log-scale spectrum is employed. The estimator is asymptotically Gaussian and the variance of the estimate that is obtained from a data segment of N points is of order [Formula: see text]. Wavelet analysis is tailor-made for the high frequency data set, since it has low computational complexity due to the pyramidal algorithm for computing the detail coefficients. This estimator is robust to additive non-stationarities, and here it is shown to exhibit some degree of robustness to multiplicative non-stationarities, such as seasonalities and volatility persistence, as well. This analysis suggests that the market became more efficient in the period 1997–2000.
HIV Sequence Compendium 2018 (2018)

This compendium is an annual summary of the data contained in the HIV sequence database. We try to present a judicious selection of the data in such a way that it is of maximum utility to HIV researchers. Each of the alignments attempts to display the genetic variability within the different species, groups and subtypes of the virus.
Principled Optimization Of Dynamic Neural Networks (2020)

Thesis (Ph.D.)--University of Washington, 2020
1‐Benzenesulfinyl Piperidine (BSP)/Triflic Anhydride: An Effective Combination for the Hydrolysis of Dithioacetals. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
On the automatic establishment of security relations for devices (2013)

The deployment of devices at remote or distributed locations is a typical scenario e.g. in large enterprise networks or industrial applications. In the deployment of a device identification of the device and the establishment of security relations (trust) between the device and other elements of the infrastructure is crucial. Usually, the process requires either to pre-configure the device or to let administrators physically access the device for configuration. Both options induce costs. For functional configurations and software distribution zero configuration solutions are available. One important step hereby is the establishment of trust into the individual device by the device owner. This trust establishment requires in typical schemes a large organizational involvement of the device owner resp. operator. The approach presented in this paper addresses the step of initial trust establishment.
ChemInform Abstract: Time‐Resolved Resonance Raman Study of the δδ* Excited State of Re2Cl2‐ 8 and Re2Br2‐ 8 (1991)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Exploring edge-based input techniques for handheld text entry (2004)

We are investigating how handheld devices like Palm PDAs and PocketPCs can be used as assistive technologies for computer access by people with motor impairments such as Muscular Dystrophy and Cerebral Palsy. As part of this research, we are developing new input techniques for handheld text entry. People with motor impairments suffer from symptoms that affect their ability to use conventional text entry methods. One symptom is a lack of stability in stylus movements caused by tremor or spasm. In an effort to create a more stable means of text entry, we are researching how to leverage elevated physical edges in our development of new text entry techniques. We present three edge-based techniques: Edge Keyboards, CornerSlide, and EdgeWrite.
Long-term culture of patient-derived cardiac organoids recapitulated Duchenne muscular dystrophy cardiomyopathy and disease progression (2022)

Duchenne Muscular Dystrophy (DMD) is an X-linked neuromuscular disease which to date is incurable. The major cause of death is dilated cardiomyopathy however, its pathogenesis is unclear as existing cellular and animal models do not fully recapitulate the human disease phenotypes. In this study, we generated cardiac organoids from patient-derived induced pluripotent stem cells (DMD-COs) and isogenic-corrected controls (DMD-Iso-COs) and studied if DMD-related cardiomyopathy and disease progression occur in the organoids upon long-term culture (up to 93 days). Histological analysis showed that DMD-COs lack initial proliferative capacity, displayed a progressive loss of sarcoglycan localization and high stress in endoplasmic reticulum. Additionally, cardiomyocyte deterioration, fibrosis and aberrant adipogenesis were observed in DMD-COs over time. RNA sequencing analysis confirmed a distinct transcriptomic profile in DMD-COs which was associated with functional enrichment in hypertrophy/dilated cardiomyopathy, arrhythmia, adipogenesis and fibrosis pathways. Moreover, five miRNAs were identified to be crucial in this dysregulated gene network. In conclusion, we generated patient-derived cardiac organoid model that displayed DMD-related cardiomyopathy and disease progression phenotypes in long-term culture. We envision the feasibility to develop a more complex, realistic and reliable <i>in vitro</i> 3D human cardiac-mimics to study DMD-related cardiomyopathies.
Enhanced Kerr optical nonlinearity of integrated waveguides incorporating layered GO films (2019)

We experimentally demonstrate enhanced optical Kerr nonlinearity of hybrid integrated waveguides coated with layered graphene oxide (GO) films. Owing to the high Kerr nonlinearity of GO and strong mode overlap between GO and waveguide, up to ~9.5-dB enhancement of four wave mixing (FWM) conversion efficiency is achieved.
Ultrasound-based cell sorting with microbubbles: A feasibility study (2018)

The isolation and sorting of cells is an important process in research and hospital labs. Most large research and commercial labs incorporate fluorescently or magnetically labeled antibodies adherent to cell surface antigens for cell identification and separation. In this paper, a process is described that merges biochemical labeling with ultrasound-based separation. Instead of lasers and fluorophore tags, or magnets and magnetic particle tags, the technique uses ultrasound and microbubble tags. Streptavidin-labeled microbubbles were mixed with a human acute lymphoblastic leukemia cell line, CCL 119, conjugated with biotinylated anti-CD7 antibodies. Tagged cells were forced under ultrasound, and their displacement and velocity quantified. Differential displacement in a flow stream was quantified against erythrocytes, which showed almost no displacement under ultrasound. A model for the acoustic radiation force on the conjugated pairs compares favorably with observations. This technology may improve on current time-consuming and costly purification procedures.
Sequential robot imitation learning from observations (2021)

This paper presents a framework to learn the sequential structure in the demonstrations for robot imitation learning. We first present a family of task-parameterized hidden semi-Markov models that extracts invariant segments (also called sub-goals or options) from demonstrated trajectories, and optimally follows the sampled sequence of states from the model with a linear quadratic tracking controller. We then extend the concept to learning invariant segments from visual observations that are sequenced together for robot imitation. We present Motion2Vec that learns a deep embedding space by minimizing a metric learning loss in a Siamese network: images from the same action segment are pulled together while being pushed away from randomly sampled images of other segments, and a time contrastive loss is used to preserve the temporal ordering of the images. The trained embeddings are segmented with a recurrent neural network, and subsequently used for decoding the end-effector pose of the robot. We first show its application to a pick-and-place task with the Baxter robot while avoiding a moving obstacle from four kinesthetic demonstrations only, followed by suturing task imitation from publicly available suturing videos of the JIGSAWS dataset with state-of-the-art [Formula: see text]% segmentation accuracy and [Formula: see text] cm error in position per observation on the test set.
Poster (2022)

Contemporary home control systems determine real-time heating/cooling demands utilizing smart sensor devices, giving rise to demand control heating, ventilation, and cooling (DCHVAC) systems, thus improving the home's energy efficiency. The adoption of activity monitoring in the smart home control system further augments the controller efficiency and improves occupants' comfort and productivity, elderly monitoring, and so forth. Additionally, the learned occupants' activity patterns help embed machine learning (ML)-based abnormality detection capability to track inconsistencies among the zone sensor measurements. Hence, the incorporation of an activity monitoring system assists anomaly detection models (ADMs) in detecting false data injection (FDI) attacks that are being glowingly researched due to their massive damage capability. However, in this work, we propose a novel attack strategy that identified that the knowledge of occupants' activities along with indoor air quality (IAQ) and occupancy sensor measurements allows the attackers to launch even more hazardous attack (i.e., significant increment in energy cost/ worsening health conditions for the occupants). Hence, it is crucial to analyze the security of the activity monitoring-based smart home DCHVAC system. Accordingly, we propose a novel formal threat analyzer that analyzes the threat space of the smart home DCHVAC control system, which is modeled by rule-based control policies and ML-based ADMs. The rules from the ADM are extracted through an efficient algorithm. The constraints associated with the rules are solved through a satisfiability module theorem (SMT)-based solver. %We performed our initial evaluation of the proposed threat analyzer's effectiveness on the Center of Advanced Studies in Adaptive Systems (CASAS) dataset using some metrics. We will further experiment with other metrics along experimenting with our collaborator's dataset (KTH live-in lab) and open-source Örebro datasets for assessing the framework with realistic occupants' activity. Moreover, we also created our prototype testbed for evaluating the feasibility of the proposed attack and threat analyzer.
Classification of lymphoma in cats and its relationship with the detection of feline leukemia vírus proviral DNA (2022)

ABSTRACT: In this retrospective and prospective study, histopathological and immunohistochemical analyses of 62 cases of lymphomas in cats were performed to classify the anatomic forms and subtypes, according to the WHO guidelines, and correlate it to FeLV proviral DNA detected using PCR. The most common anatomical form was gastrointestinal (40.3%, 25/62), followed by multicentric (29%, 18/62), mediastinal (17.7%, 11/62) and extranodal (12,9%, 8/62). Among the lymphoma subtypes, diffuse large B-cell lymphoma (DLBCL) (30.6%, 19/62) was the most commonly diagnosed followed by peripheral T-cell lymphoma (PTCL) (29%, 18/62) and enteropathy associated T-cell lymphoma type 2 (14.5%, 9/62). DNA extraction from paraffin-embedded neoplastic tissue was obtained in 28 cases and FeLV proviral DNA was detected by PCR, in 23 of these. Of the cases presenting with FeLV proviral DNA, nine (32%) were of the multicentric form, five (22%) of the mediastinal and extranodal forms and four (17%) of the gastrointestinal form. The most frequent subtypes with FeLV proviral DNA, independent of the anatomical form, were DLBCL (39.1%, 9/23) and PTCL (34.7%, 8/23). The presence of the FeLV proviral DNA in 23 cats of this study, probably had association with the multicentric form of lymphoma and higher occurrence in the DLBCL and PTCL subtypes.