gebhart/patrepeval huggingface dataset:
Regret Bounds for Stochastic Shortest Path Problems with Linear Function Approximation (2021)

We propose an algorithm that uses linear function approximation (LFA) for stochastic shortest path (SSP). Under minimal assumptions, it obtains sublinear regret, is computationally efficient, and uses stationary policies. To our knowledge, this is the first such algorithm in the LFA literature (for SSP or other formulations). Our algorithm is a special case of a more general one, which achieves regret square root in the number of episodes given access to a certain computation oracle.
Expression of fibulin-6 in failing hearts and its role for cardiac fibroblast migration (2014)

Fibulin-6, a fibroblast-released ECM protein, may play an important role during MR by imparting an effect on CF migration in close and complementary interplay with TGF-β1 signalling.
First record of the Western Atlantic cocoa damselfish Stegastes variabilis from the Levant (Perciformes: Pomacentridae) (2023)

Abstract In the present paper, we report the collection of a specimen of the West central Atlantic Stegastes variabilis in the shores of Israel, eastern shore of the Mediterranean. This record was preceded by a record of this species from Malta, in the central Mediterranean. The present record suggests that S. variabilis has established a small population in the Mediterranean.
Characterization of Aspergillus fumigatus Isolates from Air and Surfaces of the International Space Station (2016)

One mission of the Microbial Observatory Experiments on the International Space Station (ISS) is to examine the traits and diversity of fungal isolates to gain a better understanding of how fungi may adapt to microgravity environments and how this may affect interactions with humans in a closed habitat. Here, we report an initial characterization of two isolates, ISSFT-021 and IF1SW-F4, of <i>Aspergillus fumigatus</i> collected from the ISS and a comparison to the experimentally established clinical isolates Af293 and CEA10. Whole-genome sequencing of ISSFT-021 and IF1SW-F4 showed 54,960 and 52,129 single nucleotide polymorphisms, respectively, compared to Af293, which is consistent with observed genetic heterogeneity among sequenced <i>A. fumigatus</i> isolates from diverse clinical and environmental sources. Assessment of <i>in vitro</i> growth characteristics, secondary metabolite production, and susceptibility to chemical stresses revealed no outstanding differences between ISS and clinical strains that would suggest special adaptation to life aboard the ISS. Virulence assessment in a neutrophil-deficient larval zebrafish model of invasive aspergillosis revealed that both ISSFT-021 and IF1SW-F4 were significantly more lethal than Af293 and CEA10. Taken together, these genomic, <i>in vitro</i>, and <i>in vivo</i> analyses of two <i>A. fumigatus</i> strains isolated from the ISS provide a benchmark for future investigations of these strains and for continuing research on specific microbial isolates from manned space environments. <b>IMPORTANCE</b> As durations of manned space missions increase, it is imperative to understand the long-term consequence of microbial exposure on human health in a closed human habitat. To date, studies aimed at bacterial and fungal contamination of space vessels have highlighted species compositions biased toward hardy, persistent organisms capable of withstanding harsh conditions. In the current study, we assessed traits of two independent <i>Aspergillus fumigatus</i> strains isolated from the International Space Station. Ubiquitously found in terrestrial soil and atmospheric environments, <i>A. fumigatus</i> is a significant opportunistic fungal threat to human health, particularly among the immunocompromised. Using two well-known clinical isolates of <i>A. fumigatus</i> as comparators, we found that both ISS isolates exhibited normal <i>in vitro</i> growth and chemical stress tolerance yet caused higher lethality in a vertebrate model of invasive disease. These findings substantiate the need for additional studies of physical traits and biological activities of microbes adapted to microgravity and other extreme extraterrestrial conditions.
Evidence for a Size Dependent Nucleation Mechanism in Solid State Polymorph Transformations (2008)

This study applies aimless shooting and likelihood maximization to determine the molecular mechanism in the solid state polymorph transformation in terephthalic acid from over 500 candidate order parameters. The crystals examined here extend the range of crystal sizes considered in our previous work (J. Amer. Chem. Soc. 2007, 129, 4714) and reveal a change in the mechanism with increasing system size. As the crystal size increases beyond that studied in our previous work, the polymorph transformation mechanism changes from a global distortion of the crystal to a local corner nucleation mechanism. In the corner nucleation mechanism, the interfacial area between the two polymorphs is minimized for a given nucleus size. However, this mechanism differs from classical nucleation theory in that the molecular level details are essential to describe the nucleation process, which involves nonspherical domains at the corner of the crystal. These new findings suggest that there is a range of sizes for which corner nucleation is the dominant mechanism of polymorph transitions, thus implying that different mechanistic regimes exist for nucleation based on crystal size. From a computational standpoint, this study demonstrates the utility of aimless shooting and likelihood maximization to identify nonintuitive reaction coordinates in complex systems.
Symbiotic Relations of Sediment‐Agglutinating Nematodes and Bacteria in Detrital Habitats: The Enzyme‐Sharing Concept (2002)

Abstract. A new concept (‘enzyme sharing’) concerning the interaction of marine nematodes and microbes in the degradation of sedimentary detritus is presented. Elements of this concept are (1) the notorious tendency of many aquatic nematodes to agglutinate detrital particles by mucus secretions, (2) new observations on the stimulation of microbial growth by nematodes in agar plates, and (3) literature data on limited endogenous proteolytic capacities of aquatic nematodes. Observations on nematode‐microbe associations in agar plates prompted the conceptual synthesis. In agar medium without the addition of any nutrients a spectacular growth of bacteria was visible on the sinusoidal crawling trails of nematodes only 2 – 3 days after introduction of the worms (species of Adoncholaimus, Anoplostoma and Sabatieria ). Juveniles of Anoplostoma that hatched in the agar cultures left their minute trails in the medium and these were rapidly occupied by bacteria. The nematodes repeatedly visited their bacterial trails, which persisted as a peculiar biotic structure for more than one year and survived the nematodes. In sterile agar preparations containing the fluorogenic methylumbelliferyl‐β‐glucoside in the presence of the nematode Adoncholaimus , an enhanced fluorescence of the medium was visible, indicating β‐glucosidase activity. We therefore assume that oncholaimid nematodes discharge enzymes that alone, or in concert with microbial activities, contribute to the hydrolytic cleavage of refractory polysaccharides containing β‐glucosidic bonds such as agar components and cellulose. The sugars thus produced may then be taken up by the nematodes and concomitantly support the conspicuous growth of microbes. Since we did not observe any feeding of the nematodes on the associated microbes in agar plates, we question the nutritive potential of intact microbial cells for a number of nematodes abounding in detrital habitats, and call attention to the significance of ambient dissolved or adsorbed organic monomeric nutrients. Consequently, we perceive the puzzling perpetual accretion of detrital organic particles to sediment agglutinations by nematodes as an adaptation for operating an ‘enzymatic reactor’ for the production of dissolved nutrients. We hypothesise a relationship of mutual commensalism of nematodes and heterotrophic microbes in detrital habitats and propose the term ‘enzyme sharing’ for this relationship. Both parties invest in a common enzyme pool that decomposes organic detritus for their nutrition. We present here evidence that nematodes contribute β‐glucosidase, which is involved in the cellulase system. Data from the literature suggest that microbial enzymatic processing of detrital proteins yields amino acids available to nematodes, which apparently have no efficient proteolytic enzyme system in their intestines.
ChemInform Abstract: STUDIES ON THE SYNTHESES OF HETEROCYCLIC COMPOUNDS. 749. A SIMPLE SYNTHESIS OF 4‐THIAZOLIDINONES, TETRAHYDRO‐1,3‐THIAZIN‐4‐ONE AND HEXAHYDRO‐1,3‐THIAZEPIN‐4‐ONES FROM AMIDE THIOLS (1978)

Abstract Bei der Umsetzung der Mercaptoamide (III) mit Aldehyden (IV) erhält man in guten Ausbeuten die cyclischen Thioaminale (V), mit Ketonen (II) die offenkettigen Thioketale (I).
Different Properties of Erbium Silicides on Si(100) and Si(551) Orientation Surfaces (2011)

The electrical and physical properties of ErSix on n-type Si(100) and Si(551) surfaces are reported. The Schottky barrier heights (SBHs) depend on the Si substrate orientation. On a Si(100) surface, a low electron SBH around 0.3 eV is obtained and the obtained SBH is larger than 0.4 eV on a Si(551) surface, while this difference is caused by the quantity of Si atoms in ErSix and on Si(100) this is less than on Si(551). These silicidation reactions are very important to develop the future high current drivability devices using any surface orientation.
High Speed Silicon Microring Modulator Based on Carrier Depletion (2010)

We present a high-speed silicon microring modulator with a low voltage swing and ultralow energy consumption, with the refractive index modulation achieved by carrier depletion in a lateral pn diode embedded in the ring.
Assembling Photoluminescent Silicon Nanocrystals into Periodic Mesoporous Organosilica (2012)

A contemporary question in the intensely active field of periodic mesoporous organosilica (PMO) materials is how large a silsesquioxane precursor can be self-assembled under template direction into the pore walls of an ordered mesostructure. An answer to this question is beginning to emerge with the ability to synthesize dendrimer, buckyball, and polyhedral oligomeric silsesquioxane PMOs. In this paper, we further expand the library of large-scale silsesquioxane precursors by demonstrating that photoluminescent nanocrystalline silicon that has been surface-capped with oligo(triethoxysilylethylene), denoted as ncSi:(CH(2)CH(2)Si(OEt)(3))(n)H, can be self-assembled into a photoluminescent nanocrystalline silicon periodic mesoporous organosilica (ncSi-PMO). A comprehensive multianalytical characterization of the structural and optical properties of ncSi-PMO demonstrates that the material gainfully combines the photoluminescent properties of nanocrystalline silicon with the porous structure of the PMO. This integration of two functional components makes ncSi-PMO a promising multifunctional material for optoelectronic and biomedical applications.
Murein biosynthesis during a synchromous cell cycle of Escherichia coli B (1978)

The last stages of murein biosynthesis were studied in relation to the division cycle of Escherichia coli in cells synchronized by amino acid starvation (Ron et al., J. Bacteriol. 123:374--376, 1975). Murein synthesis and the activities of the D-alanine carboxypeptidase and transpeptidase were found to vary significantly during the cell cycle. Maximal synthesis and transpeptidation were observed immediately after cell division, whereas maximal D-alanine carboxypeptidase activity was detected before cell division. These results are in agreement with our earlier findings that before cell division there is a stage of increased hydrolysis of the C-terminal D-alanine moiety of newly synthesized murein strands.
Measurement of the branching ratio (1997)

We report a measurement of the branching ratio B(D+ → ϱ0ℓ+νℓ)B(D+ → K∗0ℓ+νℓ) from the Fermilab charm hadroproduction experiment E791. Based on signals of 49 ± 17 events in the D+ → ϱ0e+νe mode and 54 ± 18 events in the D+ → ϱ0μ+νμ mode, we measure. B(D+ → ϱ0e+νe)B(D+ → e+νe) = 0.014 ± 0.014 ± 0.009,B(D+ → ϱ0μ+νμ)B(D+ → μ+νμ) = 0.051 ± 0.015 ± 0.009. Combining the results from both the electronic and muonic modes, we obtain B(D+ → ϱ0ℓ+νℓ)B(D+ → ℓ+νℓ) = 0.047 ± 0.013. This result is compared to theoretical predictions.
Behavioral modeling of WCDMA transceiver with VHDL-AMS language (2006)

This article presents the behavioral modeling of a WCDMA transceiver. The model has been developed in VHDL-AMS language. The WCDMA behavioral model is made of RF parameters like gain, impedance, IIP, leakages. The methodology used to develop this model is included in a top-down design flow. The model has been validated by the comparisons between simulation results and measurements on a silicon prototype
Methods for mRNA and Protein Expression Analysis in situ and in vivo (2002)

This chapter contains sections titled: Introduction In situ hybridisation, immunocytochemistry and immunohistochemistry Introduction In situ hybridisation Immunocytochemistry and immunohistochemistry Advanced techniques Application in the study of drug efficacy and toxicity Visualising RNA in living cells Introduction Fluorescence in vivo hybridisation Alternative methods for visualising RNA in vivo MRI – Magnetic resonance imaging Introduction Imaging mRNA with magnetic switches Imaging proteins with targeted probes High-throughput imaging Magnetic resonance-sensitive marker genes MRS – Magnetic resonance spectroscopy Introduction Principles and basics In vivo spectroscopy of mRNA and protein expression Discussion PET – Positron emission tomography Introduction From clinical PET to quantitative small laboratory animal tomography Examples of molecular imaging and imaging of gene expression with PET Quantitative imaging in oncology Quantitative imaging of transgene and endogenous gene expression Discussion and conclusions SPECT – Single photon emission computed tomography Introduction Principles and basics Direct imaging of gene expression Indirect imaging via expressed proteins Conclusions Optical in vivo imaging Introduction Fluorescent proteins Bioluminescence NIRF – Near-infrared fluorescent imaging Enzyme-sensing, activatable NIRF probes Summary References
Image Media Technology for Virtual Reality Applications. Generation of Images with Different Focus and Disparity by Using Multiple Differently Focused Images. (1998)

In this paper, we propose a novel method for generating arbitrarily focused disparity images that uses multiple differently focused images. Given the assumption that the depth of the scene changes stepwise, we derive a formula for the reconstruction between the desired arbitrarily focused disparity image and multiple acquired images; we can reconstruct the arbitrarily focused disparity image by using the formula iteratively. We show that we can reconstruct arbitrarily focused disparity images of natural scenes. Our method requires only the point spread functions of the acquired images for reconstruction, it does not require any spatial segmentation.
Vasculitis-Related Respiratory Disorders (2018)

This quick reference provides the latest information on the diagnosis and management of many common respiratory disorders seen in day-to-day practice, as well as a wide array of rarer pulmonary and sleep disorders. Content is presented in a concise, bulleted template featuring algorithms, tables, and figures that make it easy to find key information to aid in diagnosis and treatment.
Features for segmenting and classifying long-duration recordings of "personal" audio (2004)

A digital recorder weighing ounces and able to record for more than ten hours can be bought for a few hundred dollars. Such devices make possible continuous recordings of "personal audio" - storing essentially everything heard by the owner. Without automatic indexing, however, such recordings are almost useless. In this paper, we describe some experiments with recordings of this kind, focusing on the problem of segmenting the recordings into different "episodes" corresponding to different acoustic environments experienced by the device. We describe several novel features to describe 1-minute-long frames of audio, and investigate their effectiveness at reproducing hand-labeled ground-truth segment boundaries.
Enlarged Range and Filter-Tuned Reception in Photonic Time-Stretched Microwave Radar (2018)

We have previously demonstrated a photonic time-stretched coherent radar (PTS-CR) with central-frequency programmable and bandwidth-tailorable agility. The sampling bandwidth in the reception was essentially compressed by the photonic time-stretched process. However, in the PTS-CR, the reception aperture suffering dead zone was hardly tuned by the fiber delay line and the measurement range was restricted by the pulse repetition rate (PRR) of the mode-locked laser. Here, we report a novel scheme to overcome the restrictions. The reception aperture can be simply tuned by adjusting the center wavelength of an optical filter and the PRR is reduced for enlargement of the measurement range by use of a photonic switch in the transmitter. In the experiment, a tenfold enlargement of measurement range is demonstrated to identify two neighboring targets separated by ~4 cm.
Improving Temperature-Stability of CMOS Rotary Encoders Using a Parallel-Connected MAGFET Array (2006)

Temperature stability is one of the major concerns of sensors for practical applications. This paper presents a method for improving the temperature stability of CMOS magnetic rotary encoders. The main factor of the offset drift is the piezo-resistive effect due to the stress induced by packaging. A connection of four MAGFET elements offers a good offset drift cancellation capability while keeping the sensitivity. Using the proposed method, the offset drift is reduced from 0.4 % without the cancellation to 0.15 % with cancellation under the temperature range of 5°C to 80°C.
Targeted killing of a mammalian cell based upon its specialized metabolic state (2011)

Mouse ES cells use a mitochondrial threonine dehydrogenase (TDH) enzyme to catabolize threonine into glycine and acetyl-CoA. Measurements of mRNA abundance have given evidence that ES cells express upwards of 1,000-fold higher levels of TDH mRNA than any of seven other mouse tissues tested. When cell culture medium is deprived of threonine, ES cells rapidly discontinue DNA synthesis, arrest cell division, and eventually die. Such studies led to the conclusion that mouse ES cells exist in a threonine-dependent metabolic state. Proceeding with the assumption that the active TDH enzyme should be essential for the growth and viability of mouse ES cells, we performed a drug screen in search of specific inhibitors of the purified TDH enzyme. Such efforts led to the discovery of a class of quinazolinecarboxamide (Qc) compounds that inhibit the ability of the TDH enzyme to catabolize threonine into glycine and acetyl-CoA. Administration of Qc inhibitors of TDH to mouse ES cells impeded cell growth and resulted in the induction of autophagy. By contrast, the same chemicals failed to affect the growth of HeLa cells at concentrations 300-fold higher than that required to kill mouse ES cells. It was likewise observed that the Qc class of TDH inhibitors failed to affect the growth or viability of ES cell-derived embryoid body cells known to have extinguished TDH expression. These studies demonstrate how it is possible to kill a specific mammalian cell type on the basis of its specialized metabolic state.
Bounds on a gramian-based Interaction Measure for robust control structure selection (2011)

This paper reviews a method for approximating the bounds on a gramian-based Interaction Measure (IM) for systems described by uncertain parametric models. The considered IM is the Participation Matrix. The reviewed method is based on analyzing the uncertainty in the area enclosed by the Nyquist curve. Conditions for the exactitude of this method are derived, and implementation issues are discussed.
Accurate Estimation of Transmitter I/Q Skew for High-Rate Spectrally Efficient Optical Transponders (2018)

We present a phase noise canceler to improve the accuracy of transmitter I/Q skew estimation for high baud-rate optical transponders using high-order modulation formats. The proposed technique reduces the probability of failure due to estimation errors by an order of magnitude.
Une formalisation des reseaux a propagation guidee pour la conception d'un modele de lecture (1998)

Cette these presente une etude formelle des reseaux a propagation guidee (rpg) pour definir une architecture de reconnaissance. Cette architecture a ete appliquee a la realisation d'un systeme de lecture. L'architecture developpee a pour but d'integrer les mecanismes de robustesse et de facilitation offerts par les rpg. D'une part, la robustesse permet a la reconnaissance de s'affranchir d'une partie des distorsions pouvant survenir dans les donnees traitees. D'autre part, la facilitation autorise des traitements de haut niveau a influencer ceux de plus bas niveau. Des methodes de construction ont ete etudiees pour la mise en uvre de cette architecture dans un systeme de reconnaissance. Le systeme de lecture realise est compose de trois niveaux de traitement. A la peripherie, deux reconnaissances sont effectuees en parallele a partir des lettres, l'une precise, l'autre globale et plus rapide. Leurs resultats sont integres dans le module central d'identification des mots. Deux traitements de haut niveau sont effectues a partir de ces mots, portant respectivement sur la syntaxe et la semantique. Les experimentations realisees avec ce systeme de lecture ont permis l'etude de la taille du systeme en fonction de celle des connaissances representees. Elles ont aussi confirme les capacites de reconnaissance robuste de l'architecture et ont illustre l'influence des traitements de haut niveau sur ceux plus peripheriques, qui peut conduire a rendre ceux-ci inutiles. En outre, les traitements peripheriques sont complementaires : la reconnaissance precise n'est utile que quand celle globale, eventuellement appuyee d'information de haut niveau, est insuffisante pour identifier le mot. Enfin, une application reconnaissant du texte braille a partir d'une image capturee par camera a ete realisee. Ce prototype a permis d'illustrer l'utilisation de l'architecture proposee avec des donnees reelles.
Small molecule kinase inhibitor LRRK2-IN-1 demonstrates potent activity against colorectal and pancreatic cancer through inhibition of doublecortin-like kinase 1 (2014)

Given DCLK1's tumor stem cell marker status, a strong understanding of its biological role and interactions in gastrointestinal tumors may lead to discoveries that improve patient outcomes. The results of this study suggest that small molecule inhibitors of DCLK1 kinase should be further investigated as they may hold promise as anti-tumor stem cell drugs.
Raven: A 28nm RISC-V vector processor with integrated switched-capacitor DC-DC converters and adaptive clocking (2015)

This article consists of a collection of slides from the authors' conference presentation. The topics discussed included: Motivation/Raven Project Goals; On-Chip Switched Capacitor DC-DC Converters; Raven3 Chip Architecture; Raven3 Implementation; Raven3 Evaluation; and RISC-V Chip Building at UC Berkeley.