gebhart/patrepeval huggingface dataset:
Mechanistic model of nutrient uptake explains dichotomy between marine oligotrophic and copiotrophic bacteria (2021)

Marine bacterial diversity is immense and believed to be driven in part by trade-offs in metabolic strategies. Here we consider heterotrophs that rely on organic carbon as an energy source and present a molecular-level model of cell metabolism that explains the dichotomy between copiotrophs-which dominate in carbon-rich environments-and oligotrophs-which dominate in carbon-poor environments-as the consequence of trade-offs between nutrient transport systems. While prototypical copiotrophs, like Vibrios, possess numerous phosphotransferase systems (PTS), prototypical oligotrophs, such as SAR11, lack PTS and rely on ATP-binding cassette (ABC) transporters, which use binding proteins. We develop models of both transport systems and use them in proteome allocation problems to predict the optimal nutrient uptake and metabolic strategy as a function of carbon availability. We derive a Michaelis-Menten approximation of ABC transport, analytically demonstrating how the half-saturation concentration is a function of binding protein abundance. We predict that oligotrophs can attain nanomolar half-saturation concentrations using binding proteins with only micromolar dissociation constants and while closely matching transport and metabolic capacities. However, our model predicts that this requires large periplasms and that the slow diffusion of the binding proteins limits uptake. Thus, binding proteins are critical for oligotrophic survival yet severely constrain growth rates. We propose that this trade-off fundamentally shaped the divergent evolution of oligotrophs and copiotrophs.
Stress Release Behaviors of Amorphous SiC/Si Structure during Annealing (2001)

An amorphous SiC/Si crystal structure is annealed at 950°C for 30 min in hydrogen gas atmosphere. Shrinkage of the amorphous SiC film during the annealing results in stress at the SiC/Si interface. Release behaviors of the stress depend on both the thickness of the film and the orientation of the Si substrate. When the stress is more than the fracture limits of the film and the substrate, release of the stress results in breaks in the SiC/Si structure. On the other hand, when the stress is smaller than one of the two fracture limits, no break occurs. If the fracture limit of the film is smaller than that of the substrate, the breaks are straight lines and their direction depends on the orientation of the substrate. Moreover, if the fracture limit of the film is more than that of the substrate, the breaks become curved. Also, the density of the breaks, length per unit area on the substrate, depends on shrinkage of the film and orientation of the substrate. The effects of residual oxygen in the substrate are also discussed.
Estimation of Power Integrity Impact to Low Power Processor Performance Through Pre-Silicon Simulation and Post-Silicon Measurements (2011)

The impact of power integrity on processor performance is critical in nano-scale era. We proposed the enhanced pre-silicon simulation to accurately capture the power delivery quality. The post silicon performance measurements correlates well with pre-silicon analysis and demonstrate that power integrity could impact performance up to 15% in low and high frequencies.
General-purpose Tagging of Freesound Audio with AudioSet Labels: Task Description, Dataset, and Baseline (2018)

This paper describes Task 2 of the DCASE 2018 Challenge, titled "General-purpose audio tagging of Freesound content with AudioSet labels". This task was hosted on the Kaggle platform as "Freesound General-Purpose Audio Tagging Challenge". The goal of the task is to build an audio tagging system that can recognize the category of an audio clip from a subset of 41 diverse categories drawn from the AudioSet Ontology. We present the task, the dataset prepared for the competition, and a baseline system.
A programmable routing controller for flexible communications in point-to-point networks (2002)

Modern parallel and distributed applications have a wide range of communication characteristics and performance requirements. This paper presents programmable routing controller (PRC), a custom ASIC that supports flexible network policies to accommodate diverse application requirements. By dedicating a small programmable processor to each incoming link, the PRC can implement wormhole, virtual cut-through, and packet switching, as well as hybrid schemes, under a variety of unicast and multicast routing algorithms. The PRC can support several applications or traffic types simultaneously by implementing multiple routing-switching microcode routines.
Analysis of Neutral B -Meson Decays into Two Muons (2021)

Branching fraction and effective lifetime measurements of the rare decay B_{s}^{0}→μ^{+}μ^{-} and searches for the decays B^{0}→μ^{+}μ^{-} and B_{s}^{0}→μ^{+}μ^{-}γ are reported using proton-proton collision data collected with the LHCb detector at center-of-mass energies of 7, 8, and 13 TeV, corresponding to a luminosity of 9 fb^{-1}. The branching fraction B(B_{s}^{0}→μ^{+}μ^{-})=(3.09_{-0.43-0.11}^{+0.46+0.15})×10^{-9} and the effective lifetime τ(B_{s}^{0}→μ^{+}μ^{-})=2.07±0.29±0.03 ps are measured, where the first uncertainty is statistical and the second systematic. No significant signal for B^{0}→μ^{+}μ^{-} and B_{s}^{0}→μ^{+}μ^{-}γ decays is found and upper limits B(B^{0}→μ^{+}μ^{-})<2.6×10^{-10} and B(B_{s}^{0}→μ^{+}μ^{-}γ)<2.0×10^{-9} at the 95% C.L. are determined, where the latter is limited to the range m_{μμ}>4.9 GeV/c^{2}. The results are in agreement with the standard model expectations.
Use of enzymes as catalysts to promote key transformations in organic synthesis (1989)

Abstract The field of biotransformations has developed rapidly over the past eight years. The use of esterases and lipases is now widespread; these enzymes are of particular importance in the production of optically active building blocks for organic synthesis as well as in large-scale processes involving the transesterification of fats. The latter area (i.e. the catalysis of esterification processes) has stimulated research into the properties of immobilized enzymes and the use of enzymes in low-water systems. In related work, enzymes have been used for the preparation of peptides and small proteins. Redox enzymes have been investigated extensively, particularly with regard to the stereocontrolled reduction of ketones to secondary alcohols. The methods for using commercially available enzymes of this type have become increasingly ‘userfriendly’. The controlled oxidation of hydrocarbon units is another area that has deserved increased attention. For example, oxidation of benzene and simple derivatives by Pseudomonas sp. has been researched by a number of U.K. groups. These recent advances in enzyme-catalysed reactions (using both whole-cell systems and partly purified protein) for the transformation of unnatural substrates is discussed and some areas of interest for the future are outlined.
Carotid Endarterectomy (2014)

The transverse skin incision for CEAs is not associated with an increased risk of CNI (P =.42). In this study, the incidence of CNI associated with the transverse incision was 3% (n = 5) vs 5% (n = 3) for longitudinal incisions. All CNIs were temporary.
Word-As-Image for Semantic Typography (2023)

A word-as-image is a semantic typography technique where a word illustration presents a visualization of the meaning of the word, while also preserving its readability. We present a method to create word-as-image illustrations automatically. This task is highly challenging as it requires semantic understanding of the word and a creative idea of where and how to depict these semantics in a visually pleasing and legible manner. We rely on the remarkable ability of recent large pretrained language-vision models to distill textual concepts visually. We target simple, concise, black-and-white designs that convey the semantics clearly. We deliberately do not change the color or texture of the letters and do not use embellishments. Our method optimizes the outline of each letter to convey the desired concept, guided by a pretrained Stable Diffusion model. We incorporate additional loss terms to ensure the legibility of the text and the preservation of the style of the font. We show high quality and engaging results on numerous examples and compare to alternative techniques. Code and demo will be available at our project page.
New step towards the future perennial high capacity optical recording medium (2011)

Three-dimensional optical recording by laser-induced fluorescent silver clusters is demonstrated in glass. The fluorescence properties of these stable clusters can be altered, depending on the glass recording exposure conditions. A "Blu-ray"-like drive enables readout of the information inside the glass without cross-talk and photobleaching. This original recording medium can provide an answer to the societal problem of long-term high-density data storage.
Mechanical parts orienting: the case of a polyhedron on a table (2002)

The problem of orienting a part resting on a table by tilting the table is considered. The initial orientation of the part is assumed to be completely unknown. The objective is to tilt the table in a manner that reduces the uncertainty in the part's orientation. This work focuses on three-dimensional polyhedral parts, with finite friction between the parts and the table, and for which all transitions between different face-table contacts may be regarded as rotations across edges. A planner that determines a sequence of tilting operations designed to minimize the uncertainty in the part's orientation is proposed. The planner runs in time O(n/sup 4/), where n is the number of faces of the polyhedron. The planner produces a sequence of O(n) distinct tilts.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Three Serious Drug Interactions that Every Dentist Should Know About. (2015)

Patients with complex medical and drug histories are becoming more commonplace in dental practice. This article reviews three serious adverse drug interactions that are well supported by the literature and can impact dental practice. Nonsteroidal anti-inflammatory drugs (NSAIDs) inhibit the renal excretion of lithium and lead to lithium toxicity. Metronidazole and fluconazole inhibit the metabolism of warfarin by blocking cytochrome P-450 2C9 (CYP-2C9), the major metabolic pathway of warfarin, with the end result being dramatic increases in patients' international normalized ratios (INRs) and potentially fatal bleeding. Propranolol and other nonselective beta-adrenergic blocking agents can inhibit the vasodilatory effect of epinephrine in dental local anesthetic solutions, leading to hypertensive reactions and a concomitant reflex bradycardia. It is important for clinicians to recognize and avoid these serious drug interactions. By doing so, they will provide the safest and best treatment for their patients.
Aspirin versus Placebo in Pregnancies at High Risk for Preterm Preeclampsia (2017)

Treatment with low-dose aspirin in women at high risk for preterm preeclampsia resulted in a lower incidence of this diagnosis than placebo. (Funded by the European Union Seventh Framework Program and the Fetal Medicine Foundation; EudraCT number, 2013-003778-29 ; Current Controlled Trials number, ISRCTN13633058 .).
Large-scale stabilized FE computational analysis of nonlinear steady state transport/reaction systems. (2004)

The solution of the governing steady transport equations for momentum, heat and mass transfer in fluids undergoing non-equilibrium chemical reactions can be extremely challenging. The difficulties arise from both the complexity of the nonlinear solution behavior as well as the nonlinear, coupled, non-symmetric nature of the system of algebraic equations that results from spatial discretization of the PDEs. In this paper, we briefly review progress on developing a stabilized finite element ( FE) capability for numerical solution of these challenging problems. The discussion considers the stabilized FE formulation for the low Mach number Navier-Stokes equations with heat and mass transport with non-equilibrium chemical reactions, and the solution methods necessary for detailed analysis of these complex systems. The solution algorithms include robust nonlinear and linear solution schemes, parameter continuation methods, and linear stability analysis techniques. Our discussion considers computational efficiency, scalability, and some implementation issues of the solution methods. Computational results are presented for a CFD benchmark problem as well as for a number of large-scale, 2D and 3D, engineering transport/reaction applications.
Des composés de type polyanioniques à l’électrode positive de batteries Na-ion (2021)

Ce chapitre présente le potentiel des matériaux polyanoniques Na3V2(PO4)3 et Na3V2(PO4)2F3, de structures différentes, à l'électrode positive de batteries Na-ion. Sont notamment discutés les voies de synthèse les plus adaptées pour les obtenir, le contrôle de la relation composition - structure – propriétés, mais aussi le défi que représente leur stabilisation lors de l’extraction du troisième sodium de la structure, celle-ci se faisant aujourd’hui au détriment des performances électrochimiques.
Quantitative evaluation of unrestrained human gait on change in walking velocity (2014)

In human gait motion analysis, which is one useful method for efficient physical rehabilitation to define various quantitative evaluation indices, ground reaction force, joint angle and joint loads are measured during gait. To obtain these data as unrestrained gait measurement, a novel gait motion analysis system using mobile force plates and attitude sensors has been developed. On the other hand, a human maintains a high correlation among the motion of all joints during gait. The analysis of the correlation in the recorded joint motion extracts a few simultaneously activating segmental coordination patterns, and the structure of the intersegmental coordination is attracting attention to an expected relationship with a control strategy. However, when the evaluation method using singular value decomposition has been applied to joint angles of the lower limb as representative kinematic parameters, joint moments related to the rotational motion of the joints have not yet been considered. In this paper, joint moments as kinetic parameters applied on the lower limb during gait of a normal subject and a trans-femoral amputee are analyzed under change in walking velocity by the wearable gait motion analysis system, and the effectiveness for quantitatively evaluate the rotational motion pattern in the joints of the lower limb by using joint moments is validated.
Assembly of quasicrystalline photonic heterostructures (2023)

A method and system for assembling a quasicrystalline heterostructure. A plurality of particles is provided with desirable predetermined character. The particles are suspended in a medium, and holographic optical traps are used to position the particles in a way to achieve an arrangement which provides a desired property.
Collection of High Pedigree AM Data for Data Analysis and Correlation. CRADA Final Report (2019)

ORNL worked with Senvol to develop and evaluate a standard operating procedure for collection of pedigree data for Additive Manufacturing using the Concept Laser XLine 1000r using an Al-Si-Mg alloy. ORNL independently evaluated and provided feedback to Senvol regarding the standard operating procedure document. Those edits were incorporated in the document that was then used to fabricate builds on the Concept Laser XLine 1000r to evaluate the efficacy of the document in collecting pedigreed data. The builds were done with varying build parameters, and the samples were subjected to tensile testing. The tensile data was used as an input for an artificial intelligence-based data analytics framework to determine the correlation between the build parameters and resulting tensile strength.
Toward an energy function for the contact map representation of proteins (2000)

We analyzed several energy functions for predicting the native state of proteins from an energy minimization procedure. We derived the parameters of a given energy function by imposing the basic requirement that the energy of the native conformation of a protein is lower than that of any conformation chosen from a set of decoys. Our work is motivated by a recent result which proved that the simple pairwise contact approximation of the energy is insufficient to satisfy simultaneously such a basic requirement for all the proteins in a database. Here, we investigate the reasons of such negative results and show how to improve the predictive power of methods based on energy minimization. We generated decoys by gapless threading, and we derive energy parameters by perceptron learning. We first considered hydrophobic contributions to the energy, defined in several ways, and showed that the additional hydrophobic terms enlarge slightly the number of proteins that can be stabilized together. Next, we performed various modifications of the pairwise energy term. We introduced (1) a distinction between inter-residue contacts on the surface and in the core of a protein and (2) a simple distance-dependent pairwise interaction in which a two-tier definition of contact replaces the original (single-tier) one. Our results suggest that a detailed treatment of the pairwise potential is likely to be more relevant than the consideration of other forces. Proteins 2000;40:237–248. © 2000 Wiley-Liss, Inc.
A Novel Route to Alkenoyl- and Cinnamoylketene Dithioacetals (1991)

2-Acetyl(ethoxycarbonyl)methylene-1,3-dithietane and -dithiane (1) were condensed with various aldehydes or ketones to afford high yields of the corresponding substituted 2-(1-carboxy-2-oxo-3-butenylidene)-1,3-dithietanes and -dithianes 4, which upon heating decarboxylated smoothly to give the title compounds in high yield.
A follow-up linkage study supports evidence for a bipolar affective disorder locus on chromosome 21q22 (2001)

Evidence for linkage between bipolar affective disorder (BP) and 21q22 was first reported by our group in a single large pedigree with a lod score of 3.41 with the PFKL locus. In a subsequent study, with denser marker coverage in 40 multiplex BP pedigrees, we reported supporting evidence with a two-point lod score of 2.76 at the D21S1260 locus, about 6 cM proximal to PFKL. For cost-efficiency, the individuals genotyped in that study comprised a subset of our large pedigree sample. To augment our previous analysis, we now report a follow-up study including a larger sample set with an additional 331 typed individuals from the original 40 families, improved marker coverage, and an additional 16 pedigrees. The analysis of all 56 pedigrees (a total of 862 genotyped individuals vs. the 372 genotyped previously), the largest multigenerational BP pedigree sample reportedly analyzed to date, supports our previous results, with a two-point lod score of 3.56 with D21S1260. The 16 new pedigrees analyzed separately gave a maximum two-point lod score of 1.89 at D21S266, less than 1 cM proximal to D21S1260. Our results are consistent with a putative BP locus on 21q22.
Activation and Deactivation of the Polymerization of Ethylene over rac‐EtInd2ZrCl2 and (nBuCp)2ZrCl2 on an Activating Silica Support (2014)

A study is carried out in order to better understand the kinetic behavior of two different metallocene precursors supported on an activating silica support, and, in particular, to attempt to reduce the significance of catalyst deactivation through the use of different alkylating agents. It is observed that it is difficult to prevent the deactivation of the rac ‐EtInd 2 ZrCl 2 sites on the activating support, and, furthermore, the deactivation is accompanied by the disa­ppearance of sites producing the highest‐molecular‐weight polymer. On the contrary, with the ( n BuCp) 2 ZrCl 2 precursor, it is possible to manipulate the addition of either tri‐isobutylaluminum (TIBA) or triethylaluminum (TEA) to significantly reduce the deactivation of the catalyst on the activating supports. Finally, the molecular‐weight distribution seems to depend much more on the intrinsic properties of the active sites than on how the active sites are treated. image
Synthesis and biological evaluation of nucleosides containing 8‐amino‐imidazo[1,2‐α]pyrazine as an isosteric replacement for adenine (1993)

Abstract A number of novel C ‐nucleosides related to purine derivatives are described in which the purine moiety has been replaced by the isosteric heterocycle, 8‐aminoimidazo[1,2‐α]pyrazine. The nucleosides prepared include the ribo, 3′‐deoxy, 2′,3′‐dideoxy, and 2′,3′‐unsaturated derivatives. These C ‐nucleosides represent derivatives containing acid stable glycosyl bonds and they can be considered as analogs of adenine‐ or 3‐deazaade‐nine‐containing nucleosides. Preparation of the parent ribonucleoside was accomplished by reaction of the C‐l functionalized sugar, (2ξ)‐1‐amino‐3,6‐anhydro‐l‐deoxy‐4,5‐ O ‐isopropylidene‐7‐ O ‐trityl‐D‐ allo ‐heptitol with 2,3‐dichloropyrazine, followed by ring closure to the 8‐chloroimidazo[1,2‐α]pyrazine nucleoside, conversion to the 8‐amino derivative and deblocking. A single crystal X‐ray structure of the parent 8‐amino‐3‐(β‐D‐ribofuranosyl)imidazo[1,2‐α]pyrazine is described and the conformation compared to that of formycin. The sugar‐modified analogs were prepared by subsequent functional group manipulations on the sugar moiety. Biological evaluation against HIV in H9 T‐lymphoid cell culture showed the nucleosides to be devoid of significant antiviral activity compared to DDA. The 3‐deazaadenosine analog also demonstrated weak suppression of mouse splenic NK activity toward YAC cells (mouse lymphoma cell targets). The imidazo[1,2‐α]pyrazine analog of 3‐deazaadenosine showed antiinflammatory activity in vivo in the rat pleurisy carrageenan model in the same range with 3‐deazaadenosine.
The human leukocyte‐adhesion ligand, intercellular‐adhesion molecule 2 (1991)

The leukocyte cell-adhesion receptors, complexes of the cluster of differentiation antigen 11a with cluster of differentiation antigen 18 (CD11a/CD18), cluster of differentiation antigen 11b with cluster of differentiation antigen 18 (CD11b CD18) and cluster of differentiation antigen 11c with cluster of differentiation antigen 18 (CD11c CD18), are of major importance in several leukocyte functions. Previously a cellular ligand named intercellular-adhesion molecule 1 (ICAM-1) was identified, isolated and extensively characterized. Recently a second similar molecule, intercellular-adhesion molecule 2 (ICAM-2), was found by a functional DNA-cloning method. We have now synthesized the ICAM-2 DNA by the polymerase chain reaction (PCR), sequenced it, and transferred it into mammalian and bacterial expression vectors. A functional leukocyte-binding glycoprotein was obtained by transfection of COS-1 cells. A soluble protein-A - ICAM-2 fusion protein was made in Escherichia coli, purified and used for antiserum production. The antiserum precipitated a cell-surface protein with an apparent molecular mass of 55 kDa from ICAM-2 transfected COS-1 cells, leukocytes and endothelial cells, and inhibited leukocyte binding to transfected COS-1 cells. The bacterial fusion protein, lacking carbohydrate, specifically bound to leukocyte receptors.
Stereotactic Heavy-Charged-Particle Bragg-Peak Radiation for Intracranial Arteriovenous Malformations (1990)

Given the natural history of these inaccessible lesions and the high risks of surgery, we conclude that heavy-charged-particle radiation is an effective therapy for symptomatic, surgically inaccessible intracranial arteriovenous malformations. The current procedure has two disadvantages: a prolonged latency period before complete obliteration of the vascular lesion and a small risk of serious neurologic complications.