gebhart/patrepeval huggingface dataset:
Click chemistry as a means to functionalize macroporous PolyHIPE (2008)

The surface functionalization of macroporous polyHIPE (pHIPE) was achieved by Huisgen-type ‘click’ chemistry. In the first step a 600–800 nm thick layer of poly(glycidyl methacrylate) (pGMA) was grafted from the pHIPE surface by atom transfer radical polymerization (ATRP). Near quantitative azidation of the pGMA layer was achieved by the ring-opening reaction of the epoxide groups with sodium azide. The influence of the reaction conditions on the uniformity of the ‘click’ reaction on the three-dimensional macroporous materials was shown in model reactions with propargyl alcohol. Under optimized conditions, azide conversions of around 80% were estimated from IR-spectra. Visualization of the homogeneous functionalization was achieved by the attachment of a fluorescent molecule. Moreover, the first proof of the versatility for biofunctionalization of pHIPE by this method was provided by the attachment of several protected amino acids. The hydrolytic stability of the triazole ring allows for the successful deprotection of the amino acids on the pHIPE.
Dynamically evaluated gravity compensation for the RAVEN surgical robot (2014)

Using an accelerometer on the base of a robot, it is possible to calculate the torque required from each actuator in order to maintain a known pose regardless of base orientation with respect to the direction or magnitude of gravity. A simple and novel method has been developed and implemented for overcoming gravity induced torques on the RAVEN <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">TM</sup> surgical research robot. This innovation will allow for accurate control of serial robot manipulators with re-orientable bases or for those operating in non-stationary environments such as boats, space stations, or moving vehicles.
Base‐Free Palladium‐Catalyzed Sonogashira Coupling Using Organogold Complexes (2011)

Turn to gold: An effective protocol for base-free Sonogashira coupling reactions using organogold complexes as nucleophilic partners has been developed. The palladium-catalyzed methodology offers a general synthesis of aryl–alkynes under operationally simple conditions in good to excellent yields.
Predicting the velocity discrimination function (1988)

Velocity discrimination is not affected by random trial-to-trial variations in contrast, indicating that observers do not confuse changes in contrast with changes in velocity. By analogy with color vision, perceived velocity could be based on the ratio of the contrast energies in two or more temporal mechanisms, producing a velocity percept invariant with contrast changes. 1 The velocity Weber fraction (Δ V / V ) would then be inversely proportional to the derivative of this ratio. Velocity discrimination for sinusoidal gratings is a simple U-shaped function of temporal frequency for all velocities. Using Anderson and Burr's 2 estimate of the two temporal mechanisms for motion, we accurately predicted the shape of this empirical function at low contrasts (&lt;6%) from the ratio model. At higher contrasts, the velocity function flattens because performance is limited to a Weber fraction no better than 0.03–0.05. Thus the velocity function depends on a ratio of contrast energies plus another source of noise which sets a limit on best performance.
NANO HIGHLIGHT Functionalized Nanowires for Electromechanical Detection of Molecules (2005)

Nano-electromechanical systems (NEMS) are emerging as processes are being developed for fabricating structures in the nanometer dimensional range. While offering vastly expanded capabilities such as unprecedented sensitivity to force or to added mass, NEMS present engineers with unprecedented challenges in materials processing, device design, fabrication and integration. Two approaches are utilized for accessing the nanometer domain, the top-down (derived from standard microfabrication paradigm of thin-film deposition, lithography and etching) and bottom-top (synthetic approach). By merging the top-down and bottom-top approaches, we have been able to achieve lateral growth of silicon nanowires with controlled size and density. In one approach, galvanic displacement is combined with microemulsion techniques to selectively deposit catalyst nanoparticles on Si, followed by vapor-liquid-solid growth of Si nanowires [1]. In the second approach, size-selected gold clusters are deposited followed by the VLS growth [2]. Combining these with microfabricated trenches exposing two opposite vertical Si(111) sidewalls, we have obtained singly and doubly clamped beam-like suspended nanostructures, with controlled diameter, density and lengths (Fig. 1). These are important steps towards the realization of a number of NEMS-based devices, including mechanical resonant sensors, nanoseparation devices and thermoelectric generation. Atomic force microscopy is employed to characterize the mechanical elasticity of these suspended Si nanowires [3]. Our experiments provide direct evidence of the mechanical rigidity of the clamping ends of these self-assembled nanowire-in-trench structures. We have also demonstrated the beam-like mechanical behavior of these nanostructures by measuring linear elastic deflections of the nanowires under normal forces applied by the microscope tip and then comparing the results with the theoretical behavior of singly and doubly clamped elastic beams.
Clomazone Does Not Inhibit the Conversion of Isopentenyl Pyrophosphate to Geranyl, Farnesyl, or Geranylgeranyl Pyrophosphate in Vitro (1992)

Clomazone, an herbicide that reduces the levels of leaf carotenoids and chlorophylls, is thought to act by inhibiting isopentenyl pyrophosphate isomerase or the prenyltransferases responsible for the synthesis of geranylgeranyl pyrophosphate. Cell-free extracts prepared from the oil glands of common sage (Salvia officinalis) are capable of converting isopentenyl pyrophosphate to geranylgeranyl pyrophosphate. Clomazone at 250 micromolar (a level that produced leaf bleaching) had no detectable effect on the activity of the relevant enzymes (isopentenyl pyrophosphate isomerase and the three prenyltransferases, geranyl, farnesyl, and geranylgeranyl pyrophosphate synthases). Thus, inhibition of geranylgeranyl pyrophosphate biosynthesis does not appear to be the mode of action of this herbicide.
SWNT Networks with Polythiophene Carboxylate Links for High-Performance Silicon Monoxide Electrodes (2018)

Carboxylated polythiophenes, such as poly[3-(potassium-4-butanoate) thiophene] (PPBT), play a critical role in securely connecting single-walled carbon nanotube (SWNT) electrical networks onto the surface of carbon-coated silicon monoxide (c-SiOx). These connections are a function of the materials’ surface chemistries and resultant physical/chemical bonding through favorable molecular interactions. Specifically, the PPBT π-conjugated backbone and alkyl side chain carboxylate moieties (COO−), respectively, physically interact with the SWNT and c-SiOx carbon layer π-electron-rich surfaces, and chemically bind to surface hydroxyl (−OH) species of the c-SiOx electroactive materials to form a carboxylate bond. This approach effectively captured pulverized particles that form during battery operation and beneficially suppressed the thickness change that electrodes typically undergo. The resultant electrodes exhibited superior electrochemical performance, which was ascribed to stable SEI layer formation, reduced electrode resistance, and improved electrode kinetics. Moreover, electrodes fabricated by blending 30 wt % of c-SiOx with graphite using <3 wt % binder exhibited remarkable performance in both coin-type half-cell and pouch-type full-cell systems. The concept that introduces robust SWNT electrical networks with PPBT carboxylate linkages suggests a feasible approach for the design of practical, high-performance, and high-capacity anodes for battery applications.
Search for Higgs boson production in association with a high-energy photon via vector-boson fusion with decay into bottom quark pairs at $$ \sqrt{s} $$ = 13 TeV with the ATLAS detector (2021)

A bstract A search is presented for the production of the Standard Model Higgs boson in association with a high-energy photon. With a focus on the vector-boson fusion process and the dominant Higgs boson decay into b -quark pairs, the search benefits from a large reduction of multijet background compared to more inclusive searches. Results are reported from the analysis of 132 fb − 1 of pp collision data at $$ \sqrt{s} $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> </mml:math> = 13 TeV collected with the ATLAS detector at the LHC. The measured Higgs boson signal yield in this final-state signature is 1 . 3 ± 1 . 0 times the Standard Model prediction. The observed significance of the Higgs boson signal above the background is 1 . 3 standard deviations, compared to an expected significance of 1 . 0 standard deviations.
Cancer cells employ an evolutionarily conserved polyploidization program to resist therapy (2020)

Unusually large cancer cells with abnormal nuclei have been documented in the cancer literature since 1858. For more than 100 years, they have been generally disregarded as irreversibly senescent or dying cells, too morphologically misshapen and chromatin too disorganized to be functional. Cell enlargement, accompanied by whole genome doubling or more, is observed across organisms, often associated with mitigation strategies against environmental change, severe stress, or the lack of nutrients. Our comparison of the mechanisms for polyploidization in other organisms and non-transformed tissues suggest that cancer cells draw from a conserved program for their survival, utilizing whole genome doubling and pausing proliferation to survive stress. These polyaneuploid cancer cells (PACCs) are the source of therapeutic resistance, responsible for cancer recurrence and, ultimately, cancer lethality.
Quantitative input–output dynamics of a c-di-GMP signal transduction cascade in Vibrio cholerae (2022)

Bacterial biofilms are multicellular communities that collectively overcome environmental threats and clinical treatments. To regulate the biofilm lifecycle, bacteria commonly transduce sensory information via the second messenger molecule cyclic diguanylate (c-di-GMP). Using experimental and modeling approaches, we quantitatively capture c-di-GMP signal transmission via the bifunctional polyamine receptor NspS-MbaA, from ligand binding to output, in the pathogen Vibrio cholerae. Upon binding of norspermidine or spermidine, NspS-MbaA synthesizes or degrades c-di-GMP, respectively, which, in turn, drives alterations specifically to biofilm gene expression. A long-standing question is how output specificity is achieved via c-di-GMP, a diffusible molecule that regulates dozens of effectors. We show that NspS-MbaA signals locally to specific effectors, sensitizing V. cholerae to polyamines. However, local signaling is not required for specificity, as changes to global cytoplasmic c-di-GMP levels can selectively regulate biofilm genes. This work establishes the input-output dynamics underlying c-di-GMP signaling, which could be useful for developing bacterial manipulation strategies.
<title>Smart pixel designs for image-processing</title> (1994)

Image Processing is widely regarded as a successful application of electronic technology. However, there is a wide gap between commercially successful image processing implementations and system design that have been proposed by the research community. Of particular interest are image processing architectures that use large number of densely interconnected processors to compute and transmit image date in parallel 2-D format. The interconnect density and packaging constraints of electronic packaging technology preclude efficient implementation of such architectures. In contrast, optoelectronic integrated circuits combined with surface-normal optical interconnects offer the promise of a technology platform that is inherently better suited for the implementation of interconnect intensive image processing applications.
The potential of carbocyclic nucleosides for the treatment of AIDS: synthesis of some diphosphorylphosphonates possessing potent activity against HIV-coded reverse transcriptase (1992)

The phosphonates 19, 20, 24, 27 and the diphosphorylphosphonates 10 and 11 have been prepared as mimics of nucleoside-phosphates and -triphosphates respectively. The compounds 10 and 11 were found to be potent inhibitors of human immunodeficiency virus reverse transcriptase (HIV-rt).
Linkage analysis of a DNA polymorphism proximal to the Duchenne and Becker muscular dystrophy loci on the short arm of the X chromosome. (1985)

The inheritance of a restriction fragment length polymorphism (RFLP) detected by a cloned DNA sequence (p754) from the short arm of the X chromosome has been studied in 14 Duchenne muscular dystrophy kindreds and six Becker muscular dystrophy kindreds. The linkage data obtained suggest that both the DMD and BMD loci are located in the same region (p21) on the short arm of the X chromosome at a distance of about 15 to 20 cM from the 754 locus. Data from families informative for both the p754 and L1.28 polymorphisms suggest that p754 is closer to the disease loci than is L1.28.
Ga doped ZnO thin films deposited by RF sputtering for NO2 sensing (2019)

Ga doped ZnO thin films have been deposited by Radio-Frequency (RF) magnetron sputtering on fused silica substrates. The structural analysis of the n-type sensitive material showed a preferential orientation in the [001] direction. The microstructure of the thin film indicated an increasing grain size with the increase of the thicknesses. The micro sensor platforms have been fabricated with ZnO:Ga thin film deposited using a reliable stencil mask onto interdigitated electrodes containing micro-hotplates. The as fabricated micro sensor allowed to sense sub-ppm concentration (500 ppb) of nitrogen dioxide under cycled temperature mode. This system revealed promising sensing performance with a response R/R0 up to 18 at low temperature step (50 °C).
Rhenium, Palladium, and Copper Pyridylalkoxide Complexes:  Synthesis, Structural Characterization, and Catalytic Application in Epoxidation Reactions (2007)

Reaction of bis(alkyl/aryl)-2-pyridylalcoholate ligands (a−g) with [ReOCl4](NBu4) results in the formation of metal-oxo complexes of the general formula [ReOCl3(L)](NBu4) (2, 3) and [ReOCl(L)2] (4, 5), with L = bis(alkyl/aryl)-2-pyridylalcoholate. Molecular structures of the complexes 2a, 4a, and 5a have been determined by single-crystal X-ray diffraction studies. Besides the expected crystal structure of 4a, where an alkoxide site of one of the ligands is coordinated trans to the rhenyloxo fragment, complex 5a shows a rare example of a trans chloro-oxo [ReOCl(L)2] connectivity. Additionally, starting from Pd(OAc)2 and [CuCl2·2(H2O)] complexes of the form [M(L)2] (M = Cu, Pd) (6a−g and 8a) were prepared. For complexes 6a and 8a molecular structures have been determined by single-crystal X-ray diffraction studies, which showed the expected square planar geometry with the pyridine ring nitrogens situated mutually in trans position. Complexes 3, 4, 6, and 8 were tested in the epoxidation reaction of cyclooctene with TBHP (tert-butylhydrogenperoxide).
Complement activation product C4d in oral and oropharyngeal squamous cell carcinoma (2015)

C4d-containing fragments are detected in oral primary tumors and are increased in saliva from patients with OSCC.
Design of a Well-Defined Poly(Dimethylsiloxane)-Based Microbial Nanoculture System (2020)

Organosilanes contain hydrocarbon-like backbones, allowing them to react with silicone-based agents in the presence of a catalyst and polymerize into membranes with tunable transport and mechanical properties. Owing to their high hydrophobicity, Poly(dimethylsiloxane) (PDMS) membranes, and more particularly, Sylgard® 184, have been used for applications including drug delivery, gas separation, and microfluidics fabrication. However, the undefined composition of the material and its ability to leach out uncured oligomers make its functionalization and usage challenging for many biological applications. This article presents the design of a novel culture system generated using PDMS-based membranes to study microbial dynamics. The microbial culture system that is referred to as “nanoculture” serves to encapsulate and grow microbes in semipermeable membranes. The mechanical properties of the membranes are reinforced through osmotic annealing, which enable the nanocultures to withstand high shear stress similar to environmental conditions while maintaining transport properties essential to microbial communication and growth. The present study lays the foundation for a novel microbial culture system that would enable the cultivation of microorganisms in environments other than laboratory conditions.
A New Adaptation Approach for Viewport-adaptive 360-degree Video Streaming (2017)

In this paper, we propose a new adaptation approach for viewport-adaptive streaming of 360-degree videos over the Internet. The proposed approach is able to systematically decide quality levels of tiles according to user head movements and network conditions by taking into account not only prediction errors but also user head movements in each adaptation interval. Experimental results show that the proposed approach can effectively adapt 360-degree videos to both varying network conditions and user head movements. Compared to existing approaches, the proposed approach can improve the average viewport quality by up to 3.9dB and reduce the standard deviation of the viewport quality by up to 50%.
Dynamic viscoelastic measurement of gelatin gel and porcine liver specimen by micro-MRE (2017)

This study aimed to measure a viscoelastic property of gelatin gels and porcine liver by the magnetic resonance elastography using micro-magnetic resonance imaging (micro-MRE). In the experiments, gelatin gel specimens (90 × 70 × 50 mm) made of gelatin solution with 5, 7, 10, 12, and 15 wt% concentration were examined under excitation with longitudinal waves in frequency of 50-250 Hz and amplitude of 0.5 mm. The viscoelastic modulus was obtained as storage shear modulus G’ and loss shear modulus G”. As a result, G’ values increased with the concentration and the excitation frequency. G” value was much smaller than G’. Double-layer specimens composed of 5 and 15 wt% gelatin gels were also examined. The average of G’ in each concentration gel in the double-layer specimens showed no significant difference from the single-material specimens with the same concentration. Furthermore, a porcine liver specimen (150 × 50 × 30 mm) were examined; however, the specimen were not vibrated and the displacement distribution in the specimen was not observed. When porcine liver specimens were embedded in the 15 wt% gel (70 × 70 × 50 mm), the specimens were vibrated deeply and G’ and G” of the liver and gel regions were obtained. As a result, G’ of the gel region was almost the same as the value of the gel specimens. G’ of the liver region increased with the excitation frequency as well as the gel specimens. The viscoelastic modulus of the porcine liver could be measured by embedding it inside gelatin gel using the micro-MRE system. This study demonstrated the application of the MRE system as the dynamic viscoelasticity measurements of gelatin gel and liver specimen.
Deletion of soluble epoxide hydrolase enhances coronary reactive hyperemia in isolated mouse heart: role of oxylipins and PPARγ (2016)

The relationship between soluble epoxide hydrolase (sEH) and coronary reactive hyperemia (CRH) response to a brief ischemic insult is not known. Epoxyeicosatrienoic acids (EETs) exert cardioprotective effects in ischemia/reperfusion injury. sEH converts EETs into dihydroxyeicosatrienoic-acids (DHETs). Therefore, we hypothesized that knocking out sEH enhances CRH through modulation of oxylipin profiles, including an increase in EET/DHET ratio. Compared with sEH<sup>+/+</sup>, sEH<sup>-/-</sup> mice showed enhanced CRH, including greater repayment volume (RV; 28% higher, P < 0.001) and repayment/debt ratio (32% higher, P < 0.001). Oxylipins from the heart perfusates were analyzed by LC-MS/MS. The 14,15-EET/14,15-DHET ratio was 3.7-fold higher at baseline (P < 0.001) and 5.6-fold higher post-ischemia (P < 0.001) in sEH<sup>-/-</sup> compared with sEH<sup>+/+</sup> mice. Likewise, the baseline 9,10- and 12,13-EpOME/DiHOME ratios were 3.2-fold (P < 0.01) and 3.7-fold (P < 0.001) higher, respectively in sEH<sup>-/-</sup> compared with sEH<sup>+/+</sup> mice. 13-HODE was also significantly increased at baseline by 71% (P < 0.01) in sEH<sup>-/-</sup> vs. sEH<sup>+/+</sup> mice. Levels of 5-, 11-, 12-, and 15-hydroxyeicosatetraenoic acids were not significantly different between the two strains (P > 0.05), but were decreased postischemia in both groups (P = 0.02, P = 0.04, P = 0.05, P = 0.03, respectively). Modulation of CRH by peroxisome proliferator-activated receptor gamma (PPARγ) was demonstrated using a PPARγ-antagonist (T0070907), which reduced repayment volume by 25% in sEH<sup>+/+</sup> (P < 0.001) and 33% in sEH<sup>-/-</sup> mice (P < 0.01), and a PPARγ-agonist (rosiglitazone), which increased repayment volume by 37% in both sEH<sup>+/+</sup> (P = 0.04) and sEH<sup>-/-</sup> mice (P = 0.04). l-NAME attenuated CRH in both sEH<sup>-/-</sup> and sEH<sup>+/+</sup> These data demonstrate that genetic deletion of sEH resulted in an altered oxylipin profile, which may have led to an enhanced CRH response.
On the First Insertion of α-Olefins in Hafnium Pyridyl-Amido Polymerization Catalysts (2009)

Reactions of [{N−,N,Cnaphthyl−}HfMe][MeB(C6F5)3] (2) precatalyst with a series of α-olefins have been investigated in order to intercept the active polymerization species generated by an in situ modification of the precursor by insertion of a single monomer unit into the Hf−CAryl bond. In all cases the first migratory insertion of monomer occurs into the Hf−CAryl bond rather than the Hf−CAlkyl bond. A low-temperature polymerization with 170 equiv of 1-hexene activated with tris(pentafluorophenyl)borane (FAB) allows for the complete NMR characterization of a Hf−CAlkylaryl methyl cation. This structure agrees with DFT studies of the kinetically favored diastereomer, although a number of other structures are more stable thermodynamically. Attempts to trap an inserted catalyst through the stoichiometric addition of 2-vinylpyridine or 3-ethoxy-1-propylene led to complicated reactions, but in both cases, experimental and computational data suggest that both processes initiate through insertion of the substrate into the Hf−CAryl bond. In addition, an activated Hf-dibutyl complex is studied in an attempt to minimize differences in the rates of initiation and propagation, as a butyl group is a reasonable mimic for a propagating polymer chain. Tritylborate activation of this complex cleanly generates 1 equiv of 1-butene in close proximity to the Hf-butyl cation via β-hydride abstraction. This reaction results in formation of isotactic poly(1-butene) with a fairly high molecular weight rather than butene oligomers. The observed molecular weight is consistent with a small fraction of active species, and quenching studies show a similar fraction of butene-modified ligand. These results are consistent with slow insertion into the Hf−CAryl bond followed by fast polymerization kinetics, with the latter rate constant being 3 orders of magnitude faster than the former.