gebhart/patrepeval huggingface dataset:
Structure and Dynamics of Imidazolium- and Pyridinium-Substituted η3-Cycloheptatrienide-Pd Complexes (2014)

A range of imidazolium- and pyridinium-substituted η3-cycloheptatrienide-Pd complexes was synthesized by nucleophilic attack of different N-donors on cycloheptatrienylidene-Pd complexes. Their full characterization is reported along with DFT studies of their formation and special properties. The target compounds represent the first crystallographically characterized monomeric allyl complexes of a Pd dihalide. The cationic substituents on the cycloheptatrienide ring form strong intramolecular H-bonds to one bromide ligand. The Pd–allyl bond was found to be highly fluxional, showing a continuous migration of the metal along the seven-membered ring even at low temperatures. The exchange of one bromide for a weakly coordinating anion yields dimeric structures and improves the poor solubility of these complexes, allowing their further synthetic utilization.
In Vitro Cell Response to a Polymer Surface Micropatterned by Laser Interference Lithography (2005)

This presentation will introduce laser interference lithography to prepare a periodic line and point micropatterns for study of cell-surface interactions. This process provides a straightforward micropatterning technique based on selective laser ablation of polymers utilizing the periodic energy distribution of two or more beam interference patterns. The micropatterns were characterized by atomic force microscopy, while the surface chemical modification was analyzed using X-ray photoelectron spectroscopy. Human pulmonary fibroblasts cultured on the surface of polycarbonate bearing line micropatterns were elongated, spindlelike, and oriented themselves along the line patterns with all different groove widths. In contrast, cells cultured on point patterns were also bipolar but showed no orientation. Further investigations demonstrated that human pulmonary fibroblast cells cultured on line and point micropatterns showed inflammatory response.
Distributed Prefix Assignment Algorithm (2015)

This document specifies a distributed algorithm for dividing a set of
prefixes in a manner that allows for automatic assignment of sub-
prefixes that are unique and non-overlapping. Used in conjunction with
a protocol that provides flooding of information among a set of
participating nodes, prefix configuration within a network may be
automated.
New staining tools and developments for 3D soft tissue CT imaging (2019)

The application of 3D X-ray imaging for biological samples (e.g. biopsies) to gain a deeper understanding of microscopic structures on a (sub)cellular level is restricted by the weak attenuation contrast of soft tissue. The development of novel staining tools for X-ray soft-tissue imaging will overcome these challenges. Here, we present the application of a recently developed method combining a laboratory-based nanoscopic X-ray CT setup enabling resolutions down to 100 nm with a target-specific X-ray staining protocol. The results clearly show that the X-ray attenuation contrast in the samples is remarkably improved by our staining method and detailed tissue (sub)structures are apparent, which cannot be visualized without the staining. The nanoscopic CT data reproduce the tissue morphology with a similar level of detail as the corresponding histological light microscopy images in 2D and enable pathological characterization of the crucial structures. Beyond that, the applied method allows for visualization of the 3D tissue architecture, offering deeper insights into the 3D microscopic structure of soft-tissue. Moreover, we demonstrate the compatibility of the X-ray stain with standard histological staining methods. Beside medical research, the methodology has the potential to contribute to advances in zoology and developmental biology.
Polyhedral Tensor Schedulers (2019)

Compiler optimizations based on the polyhedral model are able to automatically parallelize and optimize loop-based code. We acknowledge that while polyhedral techniques can represent a broad set of program transformations, important classes of programs could be parallelized just as well using less general but more tractable techniques. We apply this general idea to the polyhedral scheduling phase, which is one of the typical performance bottlenecks of polyhedral compilation.We focus on a class of programs in which enough parallelism is already exposed in the source program, and which includes Deep Learning layers and combinations thereof, as well as multilinear algebra kernels. We call these programs “tensor codes and consequently call “tensor schedulers” the tractable polyhedral scheduling techniques presented here.The general idea is that we can significantly speed up polyhedral scheduling by restricting the set of transformations considered. As an extra benefit, having a small search space allows us to introduce non-linear cost models, which fills a gap in polyhedral cost models.
ChemInform Abstract: Allylboronates in Organic Synthesis: Design of an Improved Chiral Auxiliary and Synthesis of the Trioxadecalin Nucleus of Mycalamides A and B (1995)

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.
Characterization of Adsorbate-Induced Ordering Transitions of Liquid Crystals within Monodisperse Droplets (2009)

The ordering of liquid crystals (LCs) within micrometer-sized droplets is known to depend strongly on the presence of interfacial adsorbates, although the exact sequence of ordered equilibrium states that accompany a change in interfacial anchoring from tangential to perpendicular has not been established. In this paper, we report use of a methodology that permits the preparation of monodisperse LC droplets in aqueous phases to investigate ordering transitions in the LC droplets that accompany the adsorption of amphiphiles at the aqueous-LC droplet interface. By using an amphiphile that undergoes reversible adsorption at the aqueous-LC interface (sodium dodecylsulfate, SDS), we identified six distinct topologically ordered states of the LC droplets as a function of increasing concentration of SDS. We exploited the reversible adsorption of the SDS to LC droplets with diameters of 8.0+/-0.2 microm to confirm that these topological states are equilibrium ones. We also exposed LC droplets to a continuous gradient in concentration of SDS to document the continuous transitions between topological states and to confirm the absence of additional, intermediate topological states. The formation of the LC droplets as aqueous dispersions also enabled an investigation of ordering transitions in LC droplets driven by biomolecular interactions. Surprisingly, enzymatic hydrolysis of the phospholipid L-dipalmitoyl phosphatidylcholine (L-DLPC) by phospholipase A2 at the interfaces of the LC droplets was observed to trigger the same progression of topologically ordered states of the LC as was observed with SDS. Overall, the results presented in this paper resolve prior conflicting data in the literature by providing an unambiguous set of observations regarding topologically ordered states encountered in LC droplets. This paper provides a data set against which future theories and simulations of LCs can be compared to develop a fundamental understanding of the competition between volumetric and interfacial effects in droplets. The results also suggest that topological ordering transitions in LC droplets can be exploited to report interfacial enzymatic reactions.
Demonstration: Enabling closed-loop neurostimulation with downloadable firmware upgrades (2015)

The first demo provides a detailed overview of the key building blocks required for implementing an investigational closed-loop neurostimulator. Fig 1 illustrates the demo set-up for prototyping and testing closed-loop DBS paradigms, which was designed to simulate the conditions of a neural environment. DBS leads are immersed in a saline tank, into which a DAQ device outputs appropriately scaled voltages from previously recorded neural signals. Leads sense the representative signals and adapt their stimulation settings in response to the sensed signals. The parameter updates are controlled in real-time by the embedded closed-loop algorithm, while the algorithm parameters can be configured with external telemetry commands. Finally, using the API released with the investigational Nexus-E system, data can be streamed to MATLAB to monitor operation. Neural signals, algorithm states, and stim settings are visualized with the GUI.
High frequency EMI sensing for estimating depleted uranium radiation levels in soil (2018)

This paper studies high (100 kHz up to 15 MHz) frequency electromagnetic responses (HFEMI) for DU metallic pieces and DU contaminated soils and derives a simple empirical expression from the measured HFEMI data for estimating DU contamination levels in soil. Depleted uranium (DU) is the byproduct of uranium enrichment and contains 33% less radioactive isotopes than natural uranium. There are at least thirty facilities at fourteen separate locations in the US, where munitions containing DU have been evaluated or used for training. At these sites, which vary in size, evaluation studies have been conducted with and without catch boxes. In addition, the DoD used DU at open firing ranges as large as thousands of acres (hundreds of hectares), for both artillery and aircraft training. These activities have left a legacy of DU contamination. Currently at military sites where DU munitions have been or are being used, cleanup activities mainly are done by excavating and shipping large volumes of site soil and berm materials to a hazardous material radiation disposal site. This approach is very time consuming, costly, and associated with the potential for exposure of personnel performing excavation and transportation. It also limits range use during the operation. So, there is an urgent need for technologies for rapid surveying of large areas to detect, locate, and removal of DU contaminants at test sites. Additionally, the technologies are needed to detect material at a depth of at least 30 cm as well as discriminate between DU metals and oxides from natural uranium and from other conductive metals such as natural and man-made range clutter. One of the potential technologies for estimating DU radiation levels in soils is HFEMI sensing. In this paper, HFEMI signals are collected for DU metal pieces, sodium diunarate (Na<sub>2</sub>U<sub>2</sub> O<sub>3</sub>) and tri-uranium octoxide (U<sub>3</sub>O<sub>8</sub>). The EMI signal’s sensitivity with respect to DU material composition and conditions are illustrated and analyzed. A new scheme for extracting near-surface soil’s EM parameters is formulated.
Accurate determination of thermal resistance of FETs (2005)

The accurate determination of the channel temperature in field-effect transistors (FETs) and monolithic microwave integrated circuits is critical for reliability. An original accurate closed-form expression is presented for the thermal resistance of multifinger FET structures. The model is based on the solution of Laplace's equations in prolate spheroidal coordinates and elliptical cylinder coordinates. The model's validity is verified by comparing the results with finite-element simulations, and experimental observations from liquid-crystal measurements and spatially resolved photoluminescence measurements. Very close agreement is observed in all cases.
N,N-Diarylanilinosquaraines and Their Application to Organic Photovoltaics (2011)

We report new derivatives of symmetric squaraine dyes with N,N-diarylanilino substituents that have high solubility and high absorptivity (ε = 0.71–4.1 × 105 M–1 cm–1) in the red solar spectral region (λmax = 645–694 nm) making them promising candidates for application in organic photovoltaics (OPVs). Unsymmetrical N,N-diisobutylanilino- and N,N-diphenylanilino(diphenylamino)squaraines have also been prepared that give blue-shifted absorption spectra (λmax = 529–535 nm) relative to their symmetric counterparts. Compared to bis(N,N-diisobutylanilino)squaraine, both symmetrical and unsymmetrical N,N-diarylanilino squaraines show markedly broader absorption bands in solution than their N,N-dialkylanilino squaraine counterparts: the full width at half-maximum (fwhm) for N,N-diarylanilino squaraines range from 1280–1980 cm–1, while the fwhm value for the N,N-diisobutylanilino squarine is only 630 cm–1. The absorption bands for thin films of N,N-diarylanilino squaraines broaden further to 2500–3300 cm–1. N,N-Diarylanilino squaraines are fluorescent, albeit with lower quantum yields than bis(N,N-diisobutylanilino)squaraine (ϕPL = 0.02–0.66 and 0.80, respectively). OPVs were prepared with solution processed squaraine layers using the following structure: ITO/squaraine (66–85 Å)/C60 (400 Å)/BCP (100 Å)/Al (1000 Å), BCP = bathocuproine. Devices using thin films of the bis(N,N-diarylanilino)squaraines as donor layers show improved performance relative to OPVs prepared with bis(N,N-dialkylanilino)squaraines, i.e. bis(N,N-diisobutylanilino)squaraine: open-circuit voltage Voc = 0.59 ± 0.05 V, short-circuit current Jsc = 5.58 ± 0.16 mA/cm2, fill factor FF = 0.56 ± 0.03, and power conversion efficiency η = 1.8 ± 0.2% under 1 sun, AM1.5G simulated illumination, compared with bis(N,N-diphenylanilino)squaraine: Voc = 0.82 ± 0.02 V, Jsc = 6.71 ± 0.10 mA/cm2, FF = 0.59 ± 0.01, and η = 3.2 ± 0.1%. Morphological studies of thin films suggest that the solubility of bis(N,N-diarylanilino)squaraines plays an important role in controlling the optoelectronic properties of the OPVs.
P2X4-Receptor-Mediated Synthesis and Release of Brain-Derived Neurotrophic Factor in Microglia Is Dependent on Calcium and p38-Mitogen-Activated Protein Kinase Activation (2009)

Microglia in the dorsal horn of the spinal cord are increasingly recognized as being crucial in the pathogenesis of pain hypersensitivity after injury to a peripheral nerve. It is known that P2X4 purinoceptors (P2X4Rs) cause the release of brain-derived neurotrophic factor (BDNF) from microglia, which is necessary for maintaining pain hypersensitivity after nerve injury. However, there is a critical gap in understanding how activation of microglial P2X4Rs leads to the release of BDNF. Here, we show that stimulating P2X4Rs with ATP evokes a biphasic release of BDNF from microglia: an early phase occurs within 5 min, whereas a late phase peaks 60 min after ATP stimulation. Concomitant with the late phase of release is an increased level of BDNF within the microglia. Both phases of BDNF release and the accumulation within the microglia are dependent on extracellular Ca(2+). The late phase of BDNF release and accumulation, but not the early phase of release, are suppressed by inhibiting transcription and translation, indicating that activation of P2X4R causes an initial release of a pre-existing pool of BDNF followed by an increase in de novo synthesis of BDNF. The release of BDNF is abolished by inhibiting SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor)-mediated exocytosis. Furthermore, we find that the P2X4R-evoked release and synthesis of BDNF are dependent on activation of p38-mitogen-activated protein kinase (MAPK). Together, our findings provide a unifying mechanism for pain hypersensitivity after peripheral nerve injury through P2X4R-evoked increase in Ca(2+) and activation of p38-MAPK leading to the synthesis and exocytotic release of BDNF from microglia.
Failure of sheep–goat hybrid conceptuses to develop to term in sheep–goat chimaeras (1993)

Six hybrid pregnancies were established: three in sheep-goat chimaeras, one in a sheep-(sheep-goat)hybrid chimaera and two in does. Pregnancies were monitored weekly by ultrasonography and peripheral concentrations of pregnancy specific protein B (PSPB) were measured. Placental development as detected by ultrasonography appeared to be slower in hybrid-in-goat pregnancies than in hybrid-in-chimaera pregnancies, although this difference was not reflected in PSPB concentrations. Time of fetal death could not be predicted from PSPB concentrations. Chimaeras appeared to carry hybrid pregnancies longer than ewes and does usually carry hybrid pregnancies, but none was carried to term.
Time-Varying Convex Optimization: Time-Structured Algorithms and Applications (2020)

Optimization underpins many of the challenges that science and technology face on a daily basis. Recent years have witnessed a major shift from traditional optimization paradigms grounded on batch algorithms for medium-scale problems to challenging dynamic, time-varying, and even huge-size settings. This is driven by technological transformations that converted infrastructural and social platforms into complex and dynamic networked systems with even pervasive sensing and computing capabilities. This article reviews a broad class of state-of-the-art algorithms for time-varying optimization, with an eye to performing both algorithmic development and performance analysis. It offers a comprehensive overview of available tools and methods and unveils open challenges in application domains of broad range of interest. The real-world examples presented include smart power systems, robotics, machine learning, and data analytics, highlighting domain-specific issues and solutions. The ultimate goal is to exemplify wide engineering relevance of analytical tools and pertinent theoretical foundations.
Biomechanical Evaluation of an Adjustable Loop Suspensory Anterior Cruciate Ligament Reconstruction Fixation Device: The Value of Retensioning and Knot Tying (2016)

Retensioning and knot tying after initial reduction of the tendon graft with an adjustable loop ACL fixation device may help to further reduce concerns of loop slippage and displacement with cyclic loading during postoperative rehabilitation.
Design of a Fluorescence-Activated Cell Sorting-Based Mammalian Protein–Protein Interaction Trap (2004)

The mammalian protein-protein interaction trap (MAPPIT) is a two-hybrid assay based on insights in type I cytokine signal transduction. Bait and prey polypeptides are tethered to mutant cytokine receptor chimeras which are impaired in signaling. On bait-prey interaction and after ligand stimulation, the JAK-STAT signaling cascade is initiated leading to transcription of a reporter or marker gene under the control of the STAT3-responsive rPAP1 promoter. In addition to a physiologically relevant context for mammalian protein-protein interactions this method provides separation of interactor and effector zones, and can be applied for both analytical and screening purposes. In the protocol described here, a cytokine receptor derived surface tag is used as a selectable marker. After an initial presort step using magnetic-activated cell sorting (MACS), "positive" cells are selected by fluorescence-activated cell sorting (FACS).
Motion-Induced Overestimation of the Number of Items in a Display (2004)

Subjects were asked to report the number of items in a display as the items moved along a circular path around the fixation point. As the rotation speed increased, the apparent number of items also increased. This motion-induced overestimation (MIO) effect was investigated in three experiments. In the first experiment, the effect of rotation speed and set size was explored with an enumeration task. The overestimation error increased with an increase in speed or number of items in the display. In the second experiment, we used an adjustment paradigm to measure the speed threshold of MIO effect onset. Temporal rate of the display, which was defined as product of rotation speed and the number of rotating items, was the determining factor of MIO onset. In the third experiment, moving items were marked with different colours. Surprisingly, the number of perceived items was still overestimated even though the number of perceived colours was not.
Supplementary Figure 3 from A Novel Experimental Heme Oxygenase-1–Targeted Therapy for Hormone-Refractory Prostate Cancer (2023)

Supplementary Figure 3 from A Novel Experimental Heme Oxygenase-1–Targeted Therapy for Hormone-Refractory Prostate Cancer
Longitudinal study of people learning to use continuous voice-based cursor control (2009)

We conducted a 2.5 week longitudinal study with five motor impaired (MI) and four non-impaired (NMI) participants, in which they learned to use the Vocal Joystick, a voice-based user interface control system. We found that the participants were able to learn the mapping between the vowel sounds and directions used by the Vocal Joystick, and showed marked improvement in their target acquisition performance. At the end of the ten session period, the NMI group reached the same level of performance as the previously measured "expert" Vocal Joystick performance, and the MI group was able to reach 70% of that level. Two of the MI participants were also able to approach the performance of their preferred device, a touchpad. We report on a number of issues that can inform the development of further enhancements in the realm of voice-driven computer control.
Conceptual Specification of Forest Utility Balers for Wody Biomass (2016)

<abstract> Abstract. A new class of modular woody biomass baler is designed to maximize recovery of forest residuals from small/remote/stranded landings, scattered roadside windrows and piles, thinnings from hand crews, and forest management prunings. The baler module is designed to be incorporated onto a wide range of undercarriages and prime movers. The baler module can be mounted on and powered by a forestry log forwarder when in-woods mobility is needed. Such configuration takes advantage of the forwarder‘s mobility, onboard log crane, and hydraulic power capacity. Balers may also be mounted on highway or forestry trailers, with self-contained power and loading. The bale size for the utility baler was established to be easily lifted by small-log loaders, skid-steer loaders with forks, and the like.
Environmental stress cracking of 3D-printed polymers exposed to concrete (2022)

Increasing demand for complex concrete shapes in architecture has triggered the use of digital fabrication methods for producing non-standard formworks. To this end, polymer extrusion 3D printing has already shown promising results in a range of research projects. However, 3D-printed polymer formworks can suffer from sudden failures during casting, which are generally associated with the pressure exerted by the wet concrete on the thin plastic formworks. Such failures can however be substantially accelerated by the corrosive effects of the wet concrete paste on some 3D-printed thermoplastics, a phenomenon that has not been studied in depth so far. This paper first reviews the state of the art of 3D-printed polymer formworks and their applications in architecture. It focuses on the failures caused by formwork pressure and synthesizes the various solutions to this problem reported in the literature. Beyond this, additional results are introduced to provide a guideline for thermoplastic selection in 3D-printed formworks. Common thermoplastics are presented, and their behaviour during concrete casting is documented. This behaviour can be analysed through ultimate strength and creep tests performed in three-point bending on 4 × 10 × 100 mm 3D-printed polymer samples, both in dry state and exposed to an alkaline solution of pH 13, typical for cementitious materials. The tests show that contact with the alkaline solution leads to a rapid strength loss in some thermoplastics. This effect is particularly pronounced with PLA and its blends, for which the strength loss over 10 min is more than 80 % compared to dry samples. Other thermoplastics, such as ABS, ASA, HIPS, Nylon, PVA and ABS/PC have shown more limited or in some cases no deterioration under the same conditions. The material-specific mechanism of deterioration is environmental stress cracking in contact with the alkaline solutions and it occurs in all 3D printing orientations and loading directions where tensile stresses occur.