gebhart/patrepeval huggingface dataset:
23S rRNA domain V, a fragment that can be specifically methylated in vitro by the ErmSF (TlrA) methyltransferase (1994)

The DNA sequence that encodes 23S rRNA domain V of Bacillus subtilis, nucleotides 2036 to 2672 (C. J. Green, G. C. Stewart, M. A. Hollis, B. S. Vold, and K. F. Bott, Gene 37:261-266, 1985), was cloned and used as a template from which to transcribe defined domain V RNA in vitro. The RNA transcripts served as a substrate in vitro for specific methylation of B. subtilis adenine 2085 (adenine 2058 in Escherichia coli 23S rRNA) by the ErmSF methyltransferase, an enzyme that confers resistance to the macrolide-lincosamide-streptogramin B group of antibiotics on Streptomyces fradiae NRRL 2702, the host from which it was cloned. Thus, neither RNA sequences belonging to domains other than V nor the association of 23S rRNA with ribosomal proteins is needed for the specific methylation of adenine that confers resistance to the macrolide-lincosamide-streptogramin B group of antibiotics.
High efficiency oxide confined vertical cavity surface emitting lasers (1995)

Optical loss is studied in devices with either two aligned apertures above and below the active region or with a single effective aperture above the active region. The latter exhibit slope efficiencies of up to 1 W/A.
On the road toward calcium-based batteries (2018)

This article reviews the progress in the development of a possible battery technology based on calcium, which is an abundant element and has an interesting standard reduction potential. The main bottleneck has been to find electrolytes enabling reversible plating and stripping of calcium, which has been overcome recently. Ongoing efforts focus in optimizing them to enable effective operation of calcium anodes at room temperature and within a large redox potential operation window, despite the formation of a passivation layer at the electrolyte/anode interface. In parallel, researchers are looking for suitable cathode materials enabling reasonably fast insertion and de-insertion of Ca2+ ions, which need to be probed using diverse complementary characterization techniques to avoid biased interpretation of results derived from possible side reactions.
Inhibition of NF-κB Activity in Human T Lymphocytes Induces Caspase-Dependent Apoptosis Without Detectable Activation of Caspase-1 and -3 (1999)

Abstract NF-κB is involved in the transcriptional control of various genes that act as extrinsic and intrinsic survival factors for T cells. Our findings show that suppression of NF-κB activity with cell-permeable SN50 peptide, which masks the nuclear localization sequence of NF-κB1 dimers and prevents their nuclear localization, induces apoptosis in resting normal human PBL. Inhibition of NF-κB resulted in the externalization of phosphatidylserine, induction of DNA breaks, and morphological changes consistent with apoptosis. DNA fragmentation was efficiently blocked by the caspase inhibitor Z-VAD-fmk and partially blocked by Ac-DEVD-fmk, suggesting that SN50-mediated apoptosis is caspase-dependent. Interestingly, apoptosis induced by NF-κB suppression, in contrast to that induced by TPEN (N,N,N′,N′-tetrakis [2-pyridylmethyl]ethylenediamine) or soluble Fas ligand (CD95), was observed in the absence of active death effector proteases caspase-1-like (IL-1 converting enzyme), caspase-3-like (CPP32/Yama/apopain), and caspase-6-like and without cleavage of caspase-3 substrates poly(ADP-ribose) polymerase and DNA fragmentation factor-45. These findings suggest either low level of activation is required or that different caspases are involved. Preactivation of T cells resulting in NF-κB nuclear translocation protected cells from SN50-induced apoptosis. Our findings demonstrate an essential role of NF-κB in survival of naive PBL.
Reversible Supramolecular Assembly at Specific DNA Sites: Nickel‐Promoted Bivalent DNA Binding with Designed Peptide and Bipyridyl–Bis(benzamidine) Components (2014)

Abstract At specific DNA sites, nickel(II) salts promote the assembly of designed components, namely a bis(histidine)‐modified peptide that is derived from a bZIP transcription factor and a bis(benzamidine) unit that is equipped with a bipyridine. This programmed supramolecular system with emergent properties reproduces some key characteristics of naturally occurring DNA‐binding proteins, such as bivalence, selectivity, responsiveness to external agents, and reversibility.
The Challenges of Electronic Cooling: Past, Current and Future (2003)

This paper represents my personal recapitualation of my 4 decades of continuous involvement in all phases of electronic cooling, from conceptual design, through engineering development to product implementation. The cooling designs that we applied successfully in the past are reviewed chronologically. The challenges we are currently facing are also discussed and an attempt is made to forecast the challenges that will confront the electronics cooling community in the near and distant future. The paper includes a summary of IBM sponsored research spanning a period of 25 years at 12 universities on a wide range of topics related to electronic cooling technology.
Smooth-bitrate adaptation method for HTTP streaming in vehicular environments (2014)

Recent years have seen a fast growth of video on-demand (VOD) services over HTTP. In order to improve service quality, video services are required to support different network conditions. For vehicular environments, this study proposes a novel adaptation method that improves quality of experience (QoE) by 1) reducing the number of bitrate switches and 2) avoiding sudden quality changes. The experiment shows that proposed method can provide a smooth video even under highly fluctuating network conditions.
Identification of a Chitinase-modifying Protein from Fusarium verticillioides (2011)

Chitinase-modifying proteins (cmps) are proteases secreted by fungal pathogens that truncate the plant class IV chitinases ChitA and ChitB during maize ear rot. cmp activity has been characterized for Bipolaris zeicola and Stenocarpella maydis, but the identities of the proteases are not known. Here, we report that cmps are secreted by multiple species from the genus Fusarium, that cmp from Fusarium verticillioides (Fv-cmp) is a fungalysin metalloprotease, and that it cleaves within a sequence that is conserved in class IV chitinases. Protein extracts from Fusarium cultures were found to truncate ChitA and ChitB in vitro. Based on this activity, Fv-cmp was purified from F. verticillioides. N-terminal sequencing of truncated ChitA and MALDI-TOF-MS analysis of reaction products showed that Fv-cmp is an endoprotease that cleaves a peptide bond on the C-terminal side of the lectin domain. The N-terminal sequence of purified Fv-cmp was determined and compared with a set of predicted proteins, resulting in its identification as a zinc metalloprotease of the fungalysin family. Recombinant Fv-cmp also truncated ChitA, confirming its identity, but had reduced activity, suggesting that the recombinant protease did not mature efficiently from its propeptide-containing precursor. This is the first report of a fungalysin that targets a nonstructural host protein and the first to implicate this class of virulence-related proteases in plant disease.
AMP: Authentication of Media via Provenance (2020)

Advances in graphics and machine learning have led to the general availability of easy-to-use tools for modifying and synthesizing media. The proliferation of these tools threatens to cast doubt on the veracity of all media. One approach to thwarting the flow of fake media is to detect modified or synthesized media through machine learning methods. While detection may help in the short term, we believe that it is destined to fail as the quality of fake media generation continues to improve. Soon, neither humans nor algorithms will be able to reliably distinguish fake versus real content. Thus, pipelines for assuring the source and integrity of media will be required---and increasingly relied upon. We propose AMP, a system that ensures the authentication of media via certifying provenance. AMP creates one or more publisher-signed manifests for a media instance uploaded by a content provider. These manifests are stored in a database allowing fast lookup from applications such as browsers. For reference, the manifests are also registered and signed by a permissioned ledger, implemented using the Confidential Consortium Framework (CCF). CCF employs both software and hardware techniques to ensure the integrity and transparency of all registered manifests. AMP, through its use of CCF, enables a consortium of media providers to govern the service while making all its operations auditable. The authenticity of the media can be communicated to the user via visual elements in the browser, indicating that an AMP manifest has been successfully located and verified.
Table S2 from MFF Regulation of Mitochondrial Cell Death Is a Therapeutic Target in Cancer (2023)

&lt;p&gt;Mutant peptides derived from MFF1 peptide #8 used in this study&lt;/p&gt;
Designing artificial two-dimensional landscapes via atomic-layer substitution (2021)

Technology advancements in history have often been propelled by material innovations. In recent years, two-dimensional (2D) materials have attracted substantial interest as an ideal platform to construct atomic-level material architectures. In this work, we design a reaction pathway steered in a very different energy landscape, in contrast to typical thermal chemical vapor deposition method in high temperature, to enable room-temperature atomic-layer substitution (RT-ALS). First-principle calculations elucidate how the RT-ALS process is overall exothermic in energy and only has a small reaction barrier, facilitating the reaction to occur at room temperature. As a result, a variety of Janus monolayer transition metal dichalcogenides with vertical dipole could be universally realized. In particular, the RT-ALS strategy can be combined with lithography and flip-transfer to enable programmable in-plane multiheterostructures with different out-of-plane crystal symmetry and electric polarization. Various characterizations have confirmed the fidelity of the precise single atomic layer conversion. Our approach for designing an artificial 2D landscape at selective locations of a single layer of atoms can lead to unique electronic, photonic, and mechanical properties previously not found in nature. This opens a new paradigm for future material design, enabling structures and properties for unexplored territories.
Electron Beam Lithography (2017)

Electron beam lithography (EBL) is a specialized technique for creating the extremely fine patterns (much smaller than can be seen by the naked eye) required by the modern electronics industry for integrated circuits. Derived from the early scanning electron microscopes, the technique in brief consists of scanning a beam of electrons across a surface covered with a resist film sensitive to those electrons, thus depositing energy in the desired pattern in the resist film. The process of forming the beam of electrons and scanning it across a surface is very similar to what happens inside the everyday television or CRT display, but EBL typically has three orders of magnitude better resolution. The main attributes of the technology are 1) it is capable of very high resolution, almost to the atomic level; 2) it is a flexible technique that can work with a variety of materials and an almost infinite number of patterns; 3) it is slow, being one or more orders of magnitude slower than optical lithography; and 4) it is expensive and complicated — electron beam lithography tools can cost many millions of dollars and require frequent service to stay properly maintained.
Design, Implementation, and Field Testing of a Portable Fluorescence-Based Vapor Sensor (2009)

The design and implementation of a portable fluorescence-based vapor sensing system are described. The system incorporates previously developed microsensor array technology into a compact, low-power device capable of collecting and delivering ambient vapor samples to the array while monitoring and recording the fluorescent responses of the sensors. The sensors respond differentially when exposed to a sample vapor and, when processed using a support vector machine (SVM) pattern recognition algorithm, are shown to discriminate between three classes of petroleum distillates. The system was characterized using sample vapors prepared under several different conditions in three sensing scenarios. The first scenario demonstrates the basic operational capability of the device in the field by presenting high concentration vapors to the array. The second scenario introduces the potential for a greater degree of variability in both sample vapor concentration and composition in an effort to emulate real-world sensing conditions. The third scenario uses an on-board trained pattern recognition algorithm to identify unknown vapors as their responses are collected. The device demonstrated high classification accuracy throughout the field tests and is capable of improving its classification accuracy when challenged with samples presented under variable ambient conditions by enhancing the signal-to-noise ratio of the array response.
Cloud Computing Resources Utilization and Cost Optimization for Processing Cloud Assets (2020)

In the field of Cloud Content Platform, where a user can store varieties of cloud assets (e.g. PDF documents) and can access them on any other platform such as Web, Desktop or Mobile. A creative content application may create different types of assets and store them on cloud content platform. A corresponding micro-service or cloud-worker should be present to handle asset processing request. Multiple cloud-workers should be present to handle different kind of asset processing requests. Most of the times, cloud computing resources are under utilized and cost spent on them for handling such requests is not optimized. Also, for a large and complex asset, the overall response time may increase due to high asset processing time. In this paper, we present novel method and system to predict cloud computing resources to serve input asset processing request. The method and system are designed in such a way to maximize resource utilization, minimize cost spent and minimize processing time by such computing resources. The method includes training of supervised learning based predictive model with historic data which includes asset processing requests, asset properties and their corresponding cloud computing resource utilization. The method also includes greedy approach to identify appropriate number of cloud computing resources required to process input asset processing job requests.
Nanomotor-based biocatalytic patterning of helical metal microstructures (2012)

A new nanomotor-based surface-patterning technique based on the movement of a magnetically powered enzyme-functionalized flexible nanowire swimmer offers the ability to create complex helical metal microstructures.
ChemInform Abstract: An Expedient Radical Based Approach to Difluorophosphonate Analogues of Thionucleosides. (1998)

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.
Session details: Medical applications of genetic and evolutionary computation workshop (MedGEC) (2012)

Welcome to MedGEC 2012
Cool white light-emitting three stack OLED structures for AMOLED display applications (2016)

This paper demonstrates 2-stack and 3-stack white organic light-emitting diodes (WOLEDs) with fluorescent blue and phosphorescent yellow emissive units. The 2-stack and 3-stack WOLED comprises blue-yellow and blue-blue-yellow (blue-yellow-blue) combinations. The position of the yellow emitter and possible cavity lengths in different stack architectures are theoretically and experimentally investigated to reach Commission Internationale de L'Eclairage (CIE) coordinates of near (0.333/0.333). Here, a maximum external quantum efficiency (EQE) of 23.6% and current efficiency of 62.2 cd/A at 1000 cd/m<sup>2</sup> as well as suitable CIE color coordinates of (0.335/0.313) for the blue-blue-yellow 3-stack hybrid WOLED structure is reported. In addition, the blue-yellow-blue 3-stack architecture exhibits an improved angular dependence compared to the blue-blue-yellow structure at a decreased EQE of 19.1%.
(Invited) Completely Organic Carbon Nanostructured Thermoelectric Thin Films with Power Factors Exceeding Bismuth Telluride (2016)

Low electrical conductivity (s) and thermopower (S) have long excluded polymers from thermoelectric applications. Adding carbon nanotubes produces polymer nanocomposites that exhibit thermoelectric behavior (i.e., generate electricity via a thermal gradient). These nanocomposites exhibit electrical conductivity as high as 200,000 S/m, with a reasonable S (35 – 70 mV/K). 1,2 This high electrical conductivity is paired with low thermal conductivity (k ~ 0.3 W m -1 K -1 ). Power factors (PF = S 2 s) are as high as 500 mW m -1 K -2 ) for these composites, containing carbon nanotubes stabilized by porphines and poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate), making them competitive with inorganic semiconductors (e.g., lead telluride) in terms of conversion efficiency. These composites are lightweight and relatively flexible when compared with traditional semiconductor thermoelectrics (e.g., bismuth telluride). Very recent work using layer-by-layer (LbL) assembly will also be described. Sequential layering of PANi, graphene, and double walled carbon nanotubes (DWNT) produces films with increased carrier mobility, originating from strong π-π interactions between PANi and DWNT and the higher electrical conductivity of graphene. In this investigation of the thermoelectric behavior of an LbL-assembled film, the resulting multilayer thin films exhibit a remarkable power factor (1825 mW m -1 K -2 ) that exceeds lead telluride and is more than half the value of bulk bismuth telluride. 3 Additionally, these water-based systems can be applied like ink or paint, which should further improve their usefulness in harnessing waste heat from a variety of sources (e.g., exhaust manifolds or the human body through clothing). For more information about the Polymer Nanocomposites Lab visit: http://nanocomposites.tamu.edu. References 1. Moriarty, G. P.; Briggs, K.; Stevens, B.; Yu, C.; Grunlan J. C. Energy Technology 2013 , 1 , 265-272. 2. Kim, D.; Kim, Y. S.; Choi, K.; Grunlan J. C.; Yu, C. ACS Nano 2010 , 4 , 513-523. 3. Cho, C.; Stevens, B.; Hsu, J.-H.; Bureau, R.; Hagen, D. A.; Regev, O.; Yu, C.; Grunlan J. C. Advanced Materials 2015 , 27 , 2996-3001.
Optimizing the memory bandwidth with loop fusion (2004)

The memory bandwidth largely determines the performance and energy cost of embedded systems. At the compiler level, several techniques improve the memory bandwidth at the scope of a basic block, but often fail to exploit all. We propose a technique to optimize the memory bandwidth across the boundaries of a basic block. Our technique incrementally fuses loops to better use the available bandwidth. The resulting performance depends on how the data is assigned to the memories of the memory layer. At the same time, the assignment also strongly influences the energy cost. Therefore, we combine in our approach the fusion and assignment decisions. Designers can use our output to trade-off the energy cost with the system’s performance.
INTRAVASCULAR STRAIN IMAGING: EXPERIMENTS ON AN (1996)

stiffness of atherosclerotic lesions can help In coronary arteries, knowing the relative physicians select the most appropriate therapeutic modality. Because soft material supports larger can distinguish tissue of differing stiffness. In a strains than hard, measurements of this quantity previous paper, we described techniques for computing displacements and strains in coronary imaging catheter. Here, we demonstrate that arteries using an integrated angioplasty and hard and soft materials in a tissue-mimicking phantom can be differentiated with this device. Because tissue motion cannot be distinguished from catheter motion a priori, we perform a0 computations in the coordinate system centered at the balloon’s geometric center. This reference frame depends only on balloon shape and is independent of catheter motion. A correlationbased, phase-sensitive speckle tracking algorithm has been developed to compute strain. Maximum phantom displacement was greater than 25 pm, and the maximum radial, normal strain was about 4.0 percent.
Challenges and constraints when applying few shot learning to a real-world scenario: In-the-wild camera-trap species classification (2023)

Few shot learning (FSL) describes the challenge of learning to classify when there are only few labeled examples. The goal is to be able to adapt to a new classification task using a minimum amount of new data. However, when applying FSL to real-world problems, a number of constraints and challenges are encountered: model selection, training data selection, hyper-parameter and cost function, and final decision making. In this paper, we consider a realistic problem that fits perfectly with the narratives of FSL: our goal is to classify animal species that appear in our in-the-wild camera traps located in Senegal, when these species have yet to appear in popular animal datasets. Using the philosophy of FSL, we first train a FSL network to learn to separate animal species, using popular, large animal datasets, and then evaluate the network with our data, for which there are few labeled images. Using this framework, we conduct a comparison between FSL models, parameter selection, training strategy, etc. We also discuss a weakness of the current FSL framework &#x2013; lack of the option &#x201C;does not belong to any of the classes&#x201D;. This is a common problem in real-world systems due to false positives when detecting bounding boxes that contain, in our case, animals. We then propose an additional constraint to overcome this weakness.
Stochastic Resonance (2014)

Abstract Noise is usually considered a nuisance or a laboratory curiosity, better avoided, in most practical applications. However, certain nonlinear dynamic systems in nature (the most ubiquitous of these being, of course, the central nervous system) appear to utilize the background noise as an aid to the analysis of low‐intensity signals embedded in the noise floor. A phenomenon known as stochastic resonance (SR) has been studied in the context of this amplification of weak signals in a noise background; the effect is only one of a plethora of diversified behavior that is displayed by nonlinear dynamic systems in the presence of noise, and can actually lead to an energy transfer from the noise floor to the signal feature (in the response), under the appropriate operating conditions.
Measurement of the production cross section of an isolated photon associated with jets in proton-proton collisions ats=7  TeVwith the ATLAS detector (2012)

A measurement of the cross section for the production of an isolated photon in association with jets in proton-proton collisions at a center-of-mass energy ffiffi ffi s p 7 TeV is presented. Photons are reconstructed in the pseudorapidity range j j < 1:37 and with a transverse energy E T > 25 GeV. Jets are reconstructed in the rapidity range jy jet j < 4:4 and with a transverse momentum p jet T > 20 GeV. The differential cross section d=dE T is measured, as a function of the photon transverse energy, for three different rapidity ranges of the leading-p T jet: jy jet j < 1:2, 1:2 jy jet j < 2:8 and 2:8 jy jet j < 4:4. For each rapidity configuration the same-sign y jet ! 0 and opposite-sign y jet < 0 cases are studied separately. The results are based on an integrated luminosity of 37 pb 1 , collected with the ATLAS detector at the LHC. Next-to-leading order perturbative QCD calculations are found to be in fair agreement with the data, except for E