gebhart/patrepeval huggingface dataset:
Activation of the CPP32 protease in apoptosis induced by 1-beta-D- arabinofuranosylcytosine and other DNA-damaging agents (1996)

The response of human myeloid leukemia cells to treatment with 1-beta-arabinofuranosylcytosine (ara-C) includes the induction of apoptosis. Ara-C induced apoptosis is associated with proteolytic cleavage of poly(ADP-ribose) polymerase (PARP) and protein kinase C (PKC) delta. However, the signals involved in this response are unknown. The present studies show that ara-C treatment of U-937 cells is associated with induction of a protease activity that cleaves the tetrapeptides Ac-DEVD-pNA and Ac-DMOD-pNA found at the cleavage sites of PARP and PKC delta, respectively. The ara-C-induced protease activity was sensitive to overexpression of the anti-apoptotic protein Bcl-xL and the baculovirus protein p35. By contrast, overexpression of the cowpox virus protein CrmA blocked apoptosis induced by engagement of the Fas receptor but not that induced by ara-C. CrmA overexpression also had no detectable effect on ara-C-induced cleavage of PKC delta. The results further show that ara-C induces activation of the CPP32 protease by a CrmA-insensitive and p35-sensitive mechanism. Similar results were obtained with cisplatinum, etoposide, and camptothecin. These findings indicate that ara-C and other DNA-damaging agents activate a CrmA-insensitive apoptotic pathway involving CPP32 and that these signals differ from those associated with apoptosis induced by the Fas receptor.
Identification of logically related heap regions (2009)

This paper introduces a novel set of heuristics for identifying logically related sections of the heap such as recursive data structures, objects that are part of the same multi-component structure, and related groups of objects stored in the same collection/array. When combined with lifetime properties of these structures, this information can be used to drive a range of program optimizations including pool allocation, object co-location, static deallocation, and region-based garbage collection. The technique outlined in this paper also improves the efficiency of the static analysis by providing a compact normal form for the abstract models (speeding the convergence of the static analysis).
Remote-controlled insect navigation using plasmonic nanotattoos (2020)

Developing insect cyborgs by integrating external components (optical, electrical or mechanical) with biological counterparts has a potential to offer elegant solutions for complex engineering problems. 1 A key limiting step in the development of such biorobots arises at the nano-bio interface, i.e. between the organism and the nano implant that offers remote controllability. 1,2 Often, invasive procedures are necessary that tend to severely compromise the navigation capabilities as well as the longevity of such biorobots. Therefore, we sought to develop a non-invasive solution using plasmonic nanostructures that can be photoexcited to generate heat with spatial and temporal control. We designed a ‘nanotattoo’ using silk that can interface the plasmonic nanostructures with a biological tissue. Our results reveal that both structural and functional integrity of the biological tissues such as insect antenna, compound eyes and wings were preserved after the attachment of the nanotattoo. Finally, we demonstrate that insects with the plasmonic nanotattoos can be remote controlled using light and integrated with functional recognition elements to detect the chemical environment in the region of interest. In sum, we believe that the proposed technology will play a crucial role in the emerging fields of biorobotics and other nano-bio applications.
HARKBird: Exploring Acoustic Interactions in Bird Communities Using a Microphone Array (2017)

[abstFig src='/00290001/20.jpg' width='300' text='Bird songs recorded and localized by HARKBird' ] Understanding auditory scenes is important when deploying intelligent robots and systems in real-world environments. We believe that robot audition can better recognize acoustic events in the field as compared to conventional methods such as human observation or recording using single-channel microphone array. We are particularly interested in acoustic interactions among songbirds. Birds do not always vocalize at random, for example, but may instead divide a soundscape so that they avoid overlapping their songs with those of other birds. To understand such complex interaction processes, we must collect much spatiotemporal data in which multiple individuals and species are singing simultaneously. However, it is costly and difficult to annotate many or long recorded tracks manually to detect their interactions. In order to solve this problem, we are developing HARKBird, an easily-available and portable system consisting of a laptop PC with open-source software for robot audition HARK (Honda Research Institute Japan Audition for Robots with Kyoto University) together with a low-cost and commercially available microphone array. HARKBird enables us to extract the songs of multiple individuals from recordings automatically. In this paper, we introduce the current status of our project and report preliminary results of recording experiments in two different types of forests – one in the USA and the other in Japan – using this system to automatically estimate the direction of arrival of the songs of multiple birds, and separate them from the recordings. We also discuss asymmetries among species in terms of their tendency to partition temporal resources.
Synthesis, Kinase Inhibitory Potencies, and in Vitro Antiproliferative Evaluation of New Pim Kinase Inhibitors (2009)

Members of the Pim kinase family have been identified as promising targets for the development of antitumor agents. After a screening of pyrrolo[2,3-a]- and [3,2-a]carbazole derivatives toward 66 protein kinases, we identified pyrrolo[2,3-a]carbazole as a new scaffold to design potent Pim kinase inhibitors. In particular, compound 9 was identified as a low nM selective Pim inhibitor. Additionally, several pyrrolo[2,3-a]carbazole derivatives showed selectivity for Pim-1 and Pim-3 over Pim-2. In vitro antiproliferative activities of 9 and 28, the most potent Pim inhibitors identified, were evaluated toward three human solid cancer cell lines (PA1, PC3, and DU145) and one human fibroblast primary culture, revealing IC50 values in the micromolar range. Finally, the crystal structure of Pim-1 complexed with lead compound 9 was determined. The structure revealed a non-ATP mimetic binding mode with no hydrogen bonds formed with the kinase hinge region and explained the selectivity of pyrrolo[2,3-a]carbazole derivatives for Pim kinases.
Efficacy of Kaolin-Based Particle Films to Control Apple Diseases (2001)

Studies were conducted from 1997 to 1999 to evaluate the effect of processed kaolin-based particle film applications on the incidence and severity of apple (Malus domestica Borkh.) diseases. Greenhouse and field studies demonstrated that pre-emptive application of hydrophobic and hydrophilic particles reduced the incidence of fire blight (Erwinia amylovora (Burrill) Winslow et al.) in blossoms and injured shoots. Hydrophobic and hydrophilic particles suppressed sooty blotch (Gloeodes pomigena (Schwein.)) and flyspeck (Schizothyrium pomi (Mont. &amp; Fr.) Arx: anamorph Zygophiala jamaicensis Mason) to levels equivalent to conventional fungicides. In field studies, apple scab (Venturia inaequalis (Cooke) Wint.: anamorph Spilocaea pomi Fr.) was not suppressed by hydrophilic particles. Hydrophilic particles did not interfere with the action of conventional fungicides or the activity of calcium hydroxide to suppress apple scab. Hydrophilic particles did reduce powdery mildew (Podosphaera leucotricha (Ell. &amp; Ev.) E.S. Salmon (anamorph Oidium farinosum Cooke)) russetting on fruit, but leaf infection was extensive. Accepted for publication 27 July 2001. Published 23 August 2001.
Pathogen-specific antigen target for production of antibodies produced by comparative genomics (2014)

Abstract: Listeria monocytogenes continues to be a major public health risk and there is a need for improved rapid detection methods. New and highly specific L. monocytogenes antibodies are needed to advance current detection and meet the needs of industry. This research compared the L. monocytogenes genome with that of L. innocua (a nonpathogenic species of Listeria ) and identified nine surface proteins specific to L. monocytogenes . Protein sequences were collected from the database and properties such as hydropathy profile and transmembrane topology were analyzed using TMpred software. Nine peptide sequences were chosen, and synthetic peptides were made and administered to rabbits for antibody production. All nine antibodies were screened against a panel of L. monocytogenes , nonpathogenic Listeria , and non- Listeria bacteria. Two of the nine antibodies, ie, the Lm404 and LmC639 polyclonal antibodies, showed a specific reaction to L. monocytogenes internalin B and actin polymerization protein, respectively, and were characterized further by enzyme-linked immunosorbent assay, Western blot, and transmission electron microscopy. In Western blot, both antibodies reacted with the targeted protein and did not cross-react with other Listeria spp. The Lm404 polyclonal antibody showed a high reaction with the panel of 41 L. monocytogenes strains while the LmC639 polyclonal antibody showed a weak reaction. Both the Lm404 and LmC639 polyclonal antibodies showed potential for use in immunoassays for specific detection of L. monocytogenes . This study further indicates that comparative genomics could be used to select pathogen-specific antigen for antibody production. Keywords: comparative genomics, Listeria monocytogenes , polyclonal antibodies, internalin B, actin polymerization protein, proteomics
Measurement of Dijet Azimuthal Decorrelations inppCollisions ats=7  TeV (2011)

Azimuthal decorrelations between the two central jets with the largest transverse momenta are sensitive to the dynamics of events with multiple jets. We present a measurement of the normalized differential cross section based on the full data set (∫Ldt=36 pb(-1)) acquired by the ATLAS detector during the 2010 sqrt(s)=7 TeV proton-proton run of the LHC. The measured distributions include jets with transverse momenta up to 1.3 TeV, probing perturbative QCD in a high-energy regime.
A Pulse-Pattern-Based Phase-Locking Method for Multi-cavity Coherent Pulse Stacking (2017)

A novel phase-locking method, which locks cavity phase based on the pulse patterns detected from each cavity, has stabilized the output pulse intensity in a four-cavity Coherent Pulse Stacking experiment.
Small Molecule Inhibitors of Metabolic Enzymes Repurposed as a New Class of Anthelmintics (2018)

The enormous prevalence of infections caused by parasitic nematodes worldwide, coupled to the rapid emergence of their resistance to commonly used anthelmintic drugs, presents an urgent need for the discovery of new drugs. Herein, we have identified several classes of small molecules with broad spectrum activity against these pathogens. Previously, we reported the identification of carnitine palmitoyltransferases (CPTs) as a representative class of enzymes as potential targets for metabolic chokepoint intervention that was elucidated from a combination of chemogenomic screening and experimental testing in nematodes. Expanding on these previous findings, we have discovered that several chemical classes of known small molecule inhibitors of mammalian CPTs have potent activity as anthelmintics. Cross-clade efficacy against a broad spectrum of adult parasitic nematodes was demonstrated for multiple compounds from different series. Several analogs of these initial hit compounds were designed and synthesized. The compounds we report represent a good starting point for further lead identification and optimization for development of new anthelmintic drugs with broad spectrum activity and a novel mechanism of action.
Functionalizable Nanomorphology Gradients via Colloidal Self-Assembly (2007)

We present a novel approach for the fabrication of tailored nanomorphology gradients on metal oxide surfaces. We first show the direct formation of a nanocolloidal density gradient by a dip-coating process. The obtained silica nanoparticle gradients are then subjected to a heat treatment. Control of this sintering step allows the precise tailoring of the particle morphology on the surface. Both these processes together provide a new tool to form precise, tunable, and material-independent nanomorphology gradients.
Allelopathic Activity and Characterization of Allelopathic Substances from Elaeocarpus floribundus Blume Leaves for the Development of Bioherbicides (2021)

To help protect the environment as well as increase agricultural production, the use of synthetic herbicides must be reduced and replaced with plant-based bioherbicides. Elaeocarpus floribundus is a perennial, evergreen, and medium-sized plant grown in different areas of the world. The pharmaceutical properties and various uses of Elaeocarpus floribundus have been reported, but its allelopathic potential has not yet been explored. Thus, we carried out the present study to identify allelopathic compounds from Elaeocarpus floribundus. Aqueous MeOH extracts of Elaeocarpus floribundus significantly suppressed the growth of the tested species (cress and barnyard grass) in a dose- and species-dependent way. The three most active allelopathic substances were isolated via chromatographic steps and characterized as (3R)-3-hydroxy-β-ionone, cis-3-hydroxy-α-ionone, and loliolide. All three substances significantly limited the seedling growth of cress, and the compound (3R)-3-hydroxy-β-ionone had stronger allelopathic effects than cis-3-hydroxy-α-ionone and loliolide. The concentrations of the compounds required for 50% growth inhibition (I50 value) of the cress seedlings were in the range of 0.0001–0.0005 M. The findings of this study indicate that all three phytotoxic substances contribute to the phytotoxicity of Elaeocarpus floribundus.
Joint iterative detection and decoding using spatially coupled LDPC codes (2016)

We show that a joint iterative detection and decoding algorithm with spatially-coupled (SC) LDPC codes achieves excellent performance in 100Gbps 16-QAM optical systems with high phase noise. We also demonstrate that complexity and latency of JIDD can be significantly reduced by using SC-LDPC.
Wetting of native and acetylated cellulose by water and organic liquids from atomistic simulations (2023)

Abstract Wetting of cellulose by different liquids is interesting from the point of view of the processing of cellulose-based nanomaterials. Here, the contact angles formed by water and several organic liquids on both native and acetylated cellulose were calculated from molecular dynamics simulations. It was found that liquid surface tension was crucial for their wetting behavior. Acetylation decreases the work of adhesion to most liquids investigated, even non-polar ones, while others are not affected. Water has the highest affinity to cellulose, both native and acetylated. The results have implications for liquid infiltration of nanocellulose networks and the interaction of cellulose with different liquids in general.
Structural and geothermal changes mapped by drone-based photogrammetry and thermal infrared during the 2021 volcanic crisis of Vulcano Island, Sicily&#160; (2022)

&amp;lt;p&amp;gt;Vulcano is an active volcanic island located in the south-central sector of the Aeolian Archipelago (Tyrrhenian Sea, Italy). The most recent active edifice is the La Fossa crater located in the center of the island, neighboring the main settlement Vulcano Porto. Its eruptive history is characterized by frequent transitions from phreatomagmatic to minor magmatic activity. The last eruption occurred in 1888&amp;amp;#8211;90 with strong phreatic (&amp;amp;#8220;Vulcanian&amp;amp;#8221;) eruption pulses. During the last decades, it has undergone several periods of volcanic unrest, accompanied by increasing degassing, rising fumarole temperatures, changing gas compositions, or increasing groundwater- and soil temperatures. Major unrest periods were reported in the 1920s, 1940s, and 1990s. Here we report on the ongoing crisis that initiated in September 2021. Rapidly increasing degassing levels and fumarole temperatures, accompanied by seismic activity and surface deformation were detected and monitored by the monitoring network (INGV bulletin reports). The fast evolution and dynamics of the crisis caused authorities to raise the alert level to orange and led to temporary evacuations in Vulcano Porto. We monitored this crisis from the beginning by monthly drone-based optical and thermal infrared overflights. The drone data was processed by using the Structure-from-Motion approach, allowing to generate spatially dense optical and thermal infrared maps. This way we captured the response of the hydrothermal system at the surface in great detail, were able to monitor the spatio-temporal evolution of the high-temperature fumarole field but also associated mean and low-temperature anomalies of diffuse degassing areas. We compared observations to a previous study considering in detail the structure and thermal expression of the La Fossa fumarole field, and the hydrothermal alteration associated (M&amp;amp;#252;ller et al., 2021, JVGR). Major aspects of changes observed at the surface during the crisis that could be constrained are (i) an increase of fumarole temperatures, (ii) the development of new fumarole vents, (iii) the evolution of a thermal aureole surrounding the major fumarole field at a distance, and (iv) the formation of a net-shaped thermal anomaly network. Changes are presented on a spatial and temporal scale and highlight the dynamics of degassing systems at the surface with implications for volcanic monitoring and hydrothermal alteration research and suggest that unrest is detectable at fumaroles but also at diffuse degassing zones elsewhere affecting a larger region of the La Fossa cone.&amp;amp;#160;&amp;lt;/p&amp;gt;
High-Q bandpass filters using hybrid acoustic-wave-lumped-element resonators (AWLRs) for UHF applications (2015)

This paper focuses on a new family of narrow-band bandpass filters, along with its coupling-matrix-based design approach which feature quasi-elliptic frequency response, effective quality factors (Qs <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sub> ) of the order of 1,000 and small form factors. Hybrid acoustic-wave-lumped-element resonator (AWLR) architectures are proposed as fundamental elements of these filters leading to low-loss passbands with fractional bandwidth (FBW) that is much broader (3.8-7.5 times) than in all acoustic wave (AW) filters and Qs <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sub> that are 10-20 times larger than in traditional lumped-element filters. Experimental prototypes based on commercially-available surface acoustic wave (SAW) resonators were built and tested at 418 MHz. Measured Qs <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sub> between 750-1550 and bandwidths ranging from 0.65 to 0.94 MHz (i.e., 2-3 times the electromechanical coupling coefficient of the AW resonator) are presented.
The impact of BEOL lithography effects on the SRAM cell performance and yield (2009)

With the feature size shrinking down to 65 nm and beyond, manufacturing process variation starts to signif cantly impact the device and interconnect electrical parameters, and therefore the performance of circuits. Back-end-of-line (BEOL) design for manufacturability concerns such as lithography variation and misalignment are more pronounced in the advanced technology node. Since SRAM cell always "tests" the most advanced technology among all design blocks, SRAM cell yield analysis considering the internal cell interconnect BEOL impact is important and necessary. In this paper, we perform a critical study of the effects of BEOL lithographic variations on SRAM performance and yield analysis. An SRAM simulation model with internal cell interconnect RC parasitics is presented in order to study the BEOL lithographic impact. With our method, the impact of BEOL variations on memory designs are systematically evaluated. First, we study the impact of ideal parasitics assuming no lithographic variations. This is followed by considering worstcase, best-case and nominal lithographic variations. On average, ideal parasitics impact the delay by more than 20-30% and impact the stability yield leading to SRAM minimum operating voltage, Vmin, increase of 100mV. This implies that the power estimation with our BEOL model is more accurate, and a traditional model without interconnect parasitic may be 33% off in terms of accuracy. Additional accounting of the litho variations for BEOL study induces about 4% variation on the SRAM read delay. Finally, when the resistance change due to misalignment is of the same order of magnitude as the nonlinear device resistance, the impact is more severe.
On the sum of the r-th powers of the first n integers (1952)

In this note an explicit expression is obtained for the sum of the r -th powers of the first n integers. The result is equivalent to the well-known result in terms of Bernoulli numbers and the equivalence is not difficult to establish. However, the method given here is elementary and self-contained and provides an excellent exercise on. the manipulation of determinants.
Two-Dimensional Trap for Ultrasensitive Quantification of Transient Protein Interactions (2015)

We present an ultrasensitive technique for quantitative protein-protein interaction analysis in a two-dimensional format based on phase-separated, micropatterned membranes. Interactions between proteins captured to lipid probes via an affinity tag trigger partitioning into the liquid-ordered phase, which is readily quantified by fluorescence imaging. Based on a calibration with well-defined low-affinity protein-protein interactions, equilibrium dissociation constants >1 mM were quantified. Direct capturing of proteins from mammalian cell lysates enabled us to detect homo- and heterodimerization of signal transducer and activator of transcription proteins. Using the epidermal growth factor receptor (EGFR) as a model system, quantification of low-affinity interactions between different receptor domains contributing to EGFR dimerization was achieved. By exploitation of specific features of the membrane-based assay, the regulation of EGFR dimerization by lipids was demonstrated.
False positive PSMA PET for tumor remnants in the irradiated prostate and other interpretation pitfalls in a prospective multi-center trial (2020)

ClinicalTrials.gov Identifiers: NCT02940262 and NCT03353740.
Colonoscopy (1993)

This review highlights the past year's literature that pertains to the appropriate use and effectiveness of colorectal endoscopy for the screening and surveillance of neoplasia. Treatment of colorectal neoplasms by electrothermal, photothermal, and photodynamic techniques is discussed. Technologies to extend our current diagnostic capabilities, such as electronic endoscopy and endoscopic ultrasound, are covered. Studies are summarized on the diagnostic yield of colonoscopy in patients with occult and overt bleeding. New information on tissue sampling, bowel preparation, procedure safety, and patient monitoring is presented.