gebhart/patrepeval huggingface dataset:
MetEx, a Metabolomics Explorer Application for Natural Product Discovery (2021)

Advances in next-generation DNA sequencing technologies, bioinformatics, and mass spectrometry-based metabolite detection have ushered in a new era of natural product discovery. Microbial secondary metabolomes are complex, especially when otherwise silent biosynthetic genes are activated, and there is therefore a need for data analysis software to explore and map the resulting multidimensional datasets. To that end, we herein report the Metabolomics Explorer (MetEx), a publicly available web application for the analysis of parallel liquid chromatography-coupled mass spectrometry (LC-MS)-based metabolomics data. MetEx is a highly interactive application that facilitates visualization and analysis of complex metabolomics datasets, consisting of retention time, <i>m/z</i>, and MS intensity features, as a function of hundreds of conditions or elicitors. The software enables prioritization of leads from three-dimensional maps, extraction of two-dimensional slices from various higher order plots, organization of datasets by elicitor chemotypes, customizable library-based dereplication, and automatically scored lead selection. We describe the application of MetEx to the first UPLC-MS-guided high-throughput elicitor screen in which <i>Burkholderia gladioli</i> was challenged with 750 elicitors, and the resulting profiles were interrogated by UPLC-Qtof-MS and subsequently analyzed with the app. We demonstrate the utility of MetEx by reporting elicitors for several cryptic metabolite groups and by uncovering new natural products that remain to be characterized. MetEx is available at https://mo.princeton.edu/MetEx/.
Ureteral Access for Upper Urinary Tract Disease: The Access Sheath (2001)

Ureteral access with the flexible ureteroscope remains a challenge for the urologist. The routine use of a newly developed, site-specific ureteral access sheath facilitates entry into the ureter for fragmentation and basket extraction of ureteral and renal calculi. The step-by-step technique of ureteral access with the Access Sheath is described.
polyMOF Formation from Kinked Polymer Ligands via ortho‐Substitution (2018)

Abstract Reticular chemistry is an important tool in the crystal engineering of metal‐organic frameworks (MOFs). Isoreticular chemistry allows for the preparation of MOFs of the same topology from ligands with related geometries. In this work, reticular chemistry is used to explore the scope of polyMOFs, which are frameworks synthesized from polymer ligands. “Linked” ortho ‐substituted benzene dicarboxylate polymer ligands with varying length alkyl spacers were used to synthesize polyMOFs and elucidate the effects of polymer architecture on resulting crystal formation. It was found that these “kinked” polymer ligands were able to form polyIRMOF architectures, but did not readily form polyUiO‐66 topologies.
Photoreflectance Study of Interface Roughness in Ge/SiGe Strained-Layer Heterostructures (1994)

Ge/SiGe strained-layer heterostructures have been investigated using photoreflectance (PR) spectroscopy. On the basis of the comparison between the experimental and calculated quantum well-related transition energies formed at the Γ point, band discontinuities at the Ge/SiGe heterojunction are determined and found to vary linearly with Ge content in the SiGe layer. Conduction band offset ratio Q c (= Δ E c /(Δ E c +Δ E v HH )) at the Γ point is evaluated to be 0.68 ±0.08 . From the intrinsic linewidth of the quantum well-related transitions, roughness at the Ge/SiGe heterointerface has been characterized for the first time and is estimated to be ±1 monolayer (ML). In addition, the splittings in the PR spectra are observed in some samples at low temperatures. These splittings are due to the difference in the well width and correspond to the height (or depth) of about 10 ML.
Reactivity of Ph2P(O)py-2 with Platinum(II) Alkyl Derivatives − Building-up of a Chiral Phosphorus Atom through C,N-Cyclometallation (2002)

The reaction of Ph2P(O)py-2 (HL) with methyl- and dimethylplatinum(II) derivatives afforded a series of six-membered C,N-cyclometallated species, [PtX(L′)(L)] (X=halide or Me; L′ = neutral ligand, e.g. SMe2, SOMe2, CO, PAr3) arising from activation of one C(sp2)−H bond of a phenyl substituent. The metallation entailed elimination of methane and caused the phosphorus atom to become chiral. The series includes the complex [Pt(Me)(CO)(L)] where the platinum atom is bonded to three different carbon atoms (C, C, Csp). From the neutral species cationic derivatives [Pt(L′)(L′′)(L)]+ (L′ = SMe2, L′′ = CH3CN; L′−L′′ = dppe; L′ = SMe2 or SOMe2, L′′ = H2O) could be obtained. The new complexes were isolated and fully characterised by elemental analyses and spectroscopic techniques (IR, NMR, FAB-MS). The solid-state structures of [PtCl(SMe2)(L)], [PtCl(CO)(L)], [Pt(Me)(SOMe2)(L)], and [Pt(SMe2)(H2O)(L)][BF4] were determined by single-crystal X-ray diffraction.
Stability Assessment of Regenerated Hierarchical ZSM-48 Zeolite Designed by Post-Synthesis Treatment for Catalytic Cracking of Light Naphtha (2017)

Hierarchical ZSM-48, a one-dimensional pore system zeolite with the presence of mesopores, was obtained by post-synthesis alkaline and acid treatments. Hierarchical ZSM-48 exhibited excellent hexane cracking activity compared to parent ZSM-48, which can be attributed to better diffusion as a result of the created mesoporosity. Moreover, the post-synthesis treatment allowed for manipulation of the distribution of active sites. Consequently, better stability and higher propylene selectivity were accomplished. The spent catalyst was regenerated by removing the deposited coke from the pores, and the regenerated catalyst was characterized again to investigate the recyclability of the hierarchical structure achieved. Parent ZSM-48 showed the same textural and acidic properties after regeneration, while the structure of the post-treated sample suffered from serious defects. The defects severely decreased the number of active sites as measured by pyridine Fourier transform infrared spectroscopy and caused major structural collapse as observed by scanning electron microscopy and transmission electron microscopy.
X-linked acro-gigantism (X-LAG): a new form of infant-onset pituitary gigantism (2015)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Interpretation of Unusual Absorption Bandwidths and Resonance Raman Intensities in Excited State Mixed Valence (2005)

Excited state mixed valence (ESMV) occurs in molecules in which the ground state has a symmetrical charge distribution but the excited state possesses two or more interchangeably equivalent sites that have different formal oxidation states. Although mixed valence excited states are relatively common in both organic and inorganic molecules, their properties have only recently been explored, primarily because their spectroscopic features are usually overlapped or obscured by other transitions in the molecule. The mixed valence excited state absorption bands of 2,3-di-p-anisyl-2,3-diazabicyclo[2.2.2]octane radical cation are well-separated from others in the absorption spectrum and are particularly well-suited for detailed analysis using the ESMV model. Excited state coupling splits the absorption band into two components. The lower energy component is broader and more intense than the higher energy component. The absorption bandwidths are caused by progressions in totally symmetric modes, and the difference in bandwidths is caused by the coordinate dependence of the excited state coupling. The Raman intensities obtained in resonance with the high and low energy components differ significantly from those expected based on the oscillator strengths of the bands. This unexpected observation is a result of the excited state coupling and is explained by both the averaging of the transition dipole moment orientation over all angles for the two types of spectroscopies and the coordinate-dependent coupling. The absorption spectrum is fit using a coupled two-state model in which both symmetric and asymmetric coordinates are included. The physical meaning of the observed resonance Raman intensity trends is discussed along with the origin of the coordinate-dependent coupling. The well-separated mixed valence excited state spectroscopic components enable detailed electronic and resonance Raman data to be obtained from which the model can be more fully developed and tested.
A Self-Calibrated Hybrid Thermal-Diffusivity/Resistor-Based Temperature Sensor (2021)

This article describes a hybrid temperature sensor in which an accurate, but energy-inefficient, thermal diffusivity (TD) sensor is used to calibrate an inaccurate, but efficient, resistor-based sensor. The latter is based on silicided polysilicon resistors embedded in a Wien-bridge (WB) filter, while the former is based on an electrothermal filter (ETF) made from a p-diffusion/metal thermopile and an n-diffusion heater. The use of an on-chip sensor for calibration obviates the need for an external temperature reference and a temperature-stabilized environment, thus reducing the cost. To mitigate the area overhead of the TD sensor, it reuses the WB filter’s readout circuitry. Realized in a 180-nm CMOS technology, the hybrid sensor occupies 0.2 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . After calibration at room temperature (~25 °C) and at an elevated temperature (~85 °C), it achieves an inaccuracy of 0.25 °C (3 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\sigma $ </tex-math></inline-formula> ) from −55 °C to 125 °C. The WB sensor dissipates 66 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{W}$ </tex-math></inline-formula> from a 1.8-V supply and achieves a resolution of 450 <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\mu \text{K}_{\mathrm {rms}}$ </tex-math></inline-formula> in a 10-ms conversion time, which corresponds to a resolution figure-of-merit (FoM) of 0.13 pJ <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\cdot \text{K}^{2}$ </tex-math></inline-formula> . The sensor also achieves a sub-10-mHz 1/ <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$f$ </tex-math></inline-formula> noise corner, which is comparable to that of bipolar junction transistor (BJT)-based temperature sensors.
Molecular mechanisms of trauma-induced neuronal degeneration. (1993)

Recent studies suggest that various neuron-specific responses, including activation of glutamate receptors, muscarinic receptors, and oxidative stress, contribute to the events leading to brain and spinal cord neuronal degeneration after trauma. These specific mechanisms and possible future treatments are highlighted in this review.
Tris[2-(2-methoxyethoxy)ethyl]amine (2003)

[70384-51-9] C15H33NO6 (MW 323.43) InChI = 1S/C15H33NO6/c1-17-10-13-20-7-4-16(5-8-21-14-11-18-2)6-9-22-15-12-19-3/h4-15H2,1-3H3 InChIKey = XGLVDUUYFKXKPL-UHFFFAOYSA-N (reagent used as a phase-transfer catalyst in a wide variety of reactions) Alternate Name: tris(3,6-dioxaheptyl)amine, TDA-1. Physical Data: bp 160 °C/0.5 mm Hg; d 1.011 g cm−3. Solubility: soluble in water, alcohol, ethers, and most organic solvents. Form Supplied in: yellow liquid. Analysis of Reagent Purity: NMR, GC. Preparative Methods: prepared by the reaction of 2-(2-methoxy-ethoxy)ethanol with a mixture of ammonia gas and hydrogen gas in the presence of catalytic amounts of Raney nickel. The reagent is also available for purchase in bulk quantities. Purification: can be purified by distillation. Handling, Storage, and Precautions: can be stored at room temperature and can be handled with appropriate skin and eye protection. The toxicological properties have not been thoroughly investigated.
Securing Email (2018)

While email is the most ubiquitous and interoperable form of online communication today, it was not conceived with strong security guarantees, and the ensuing security enhancements are, by contrast, lacking in both ubiquity and interoperability. This situation motivates our research. We begin by identifying a variety of stakeholders who have an interest in the current email system and in efforts to provide secure solutions. We then use differing priorities among stakeholders to help explain the evolution of fragmented secure email solutions undertaken by industry, academia, and independent developers. We also evaluate the building blocks of secure email---cryptographic primitives, key management schemes, and system designs---to identify their support for stakeholder properties. We conclude with a fresh look at the state of secure email and discuss open problems in the area.
Corticotropin-releasing factor binding protein dimerizes after association with ligand. (1994)

We have suggested recently that the fall in plasma CRF-binding protein (BP) during the last few weeks of pregnancy is a direct effect of association with its ligand because of the rapid decrease in plasma BP concentration seen in normal males reaching a nadir some 15 min after a bolus injection of synthetic CRF. In the present study, we have investigated the physicochemical properties of both natural and recombinant BP by gel filtration under physiological conditions and have shown that association of human CRF to this BP results in an increase in molecular weight consistent with the formation of a dimer form of the BP ligand complex. The dimer is more stable when the interaction occurs in the presence of serum or if a peptide with a higher affinity for the BP is substituted as ligand. Experimental evidence would also suggest that the dimer BP has a higher affinity for ligand than the monomeric form. We suggest that this dimerization occurs in vivo when CRF is released into the bloodstream and provides the trigger that causes the uptake of the complex at specific receptor sites.
Supplementary Figure S21 from Evolution of Castration-Resistant Prostate Cancer in ctDNA during Sequential Androgen Receptor Pathway Inhibition (2023)

&lt;p&gt;Supplementary Figure S21 shows per patient absolute AR gene copy number and number of mutant AR copies at different cell-free DNA collection timepoints&lt;/p&gt;
indranilsinharoy/PyZDDE: Release version v2.0.3 (2016)

See https://github.com/indranilsinharoy/PyZDDE/wiki/08.-News-and-updates
Contraction-related variation in frequency dependence of acoustic properties of canine myocardium (1989)

Results of experiments performed in several laboratories indicate that contracting myocardium exhibits a cyclic variation of the magnitude of ultrasonic backscatter, with maxima occurring at end-diastole and minima at end-systole. The mechanisms responsible for this variation are not well understood. The purpose of the present study was to determine whether the frequency dependence of backscatter exhibits systematic variation throughout the cardiac cycle, analysis of which may facilitate improved understanding of biologic factors responsible for the cyclic variation of the magnitude of backscatter. In this study, the myocardial backscatter coefficient, as a function of frequency, was measured throughout the cardiac cycle in nine open-chest dogs. The frequency dependence of the backscatter coefficient was computed from a least-squares linear fit to log backscatter coefficient versus log frequency data. A cyclic variation of frequency dependence of backscatter was found with maximum near end-diastole (f2.6 +/- 0.1) and minimum near end-systole (f2.2 +/- 0.1), a significant variation (p less than 0.01). These results suggest that mechanisms responsible for the cyclic variation of backscatter may include changes in the effective size of the dominant scatterers throughout the cardiac cycle. An alternative explanation for the observed variation is an increase in the myocardial attenuation coefficient during systole followed by a decrease in diastole.
Irregular high frequency patterns decrease the effectiveness of deep brain stimulation in a rat model of Parkinson's disease (2011)

Deep brain stimulation (DBS) is an effective treatment of Parkinson's disease, but its mechanisms are still unclear. To test the hypothesis that DBS alleviates motor symptoms by regularizing neuronal firing, we applied regular frequency stimulation between 5-260 Hz as well as irregular high frequency stimulation with an average rate of 130Hz to rats with unilateral 6-hydroxydopamine (6-OHDA) lesions. We found that high frequency regular stimulation above 130Hz was more effective than both low frequency stimulation and high frequency irregular stimulation at normalizing pathological circling behavior. Our results support the hypothesis that DBS is effective because it is able to mask pathological firing patterns within the basal ganglia, and highlight the importance of the temporal pattern in addition to the rate of stimulation.
A Topological Model for the Blockchain (2018)

As it was mostly developed in a non-academic context, the literature on the blockchain often lacks of mathematical rigour. Therefore, fundamental computational problems of this new technology such as consensus, Byzantine fault tolerance and self-stabilization can not be fully looked into. In this work we use the principles of distributed computing to introduce a topological structure with the purpose of facilitating the study of the blockchain. Our model exploits classical topological tools used in the context of distributed systems to describe the evolution of a blockchain. Different assumptions on the input assignments, number of generated blocks and latency of the system are considered in our analysis. Furthermore, we define a probabilistic structure to enrich our model and to add also a predictive capability.
Correction: Electronic conductance and thermopower of single-molecule junctions of oligo(phenyleneethynylene) derivatives (2021)

Correction for ‘Electronic conductance and thermopower of single-molecule junctions of oligo(phenyleneethynylene) derivatives’ by Hervé Dekkiche <italic>et al.</italic>, <italic>Nanoscale</italic>, 2020, <bold>12</bold>, 18908–18917, DOI: 10.1039/D0NR04413J.
Performance Comparison of LMNO Cathodes Produced with Pullulan or PEDOT:PSS Water-Processable Binders (2022)

The aim of this paper is to demonstrate lithium metal battery cells assembled with high potential cathodes produced by sustainable processes. Specifically, LiNi0.5Mn1.5O4 (LMNO) electrodes were fabricated using two different water-processable binders: pullulan (PU) or the bifunctional electronically conductive poly(3,4-ethylenedioxythiophene)-poly(styrene sulfonate) (PEDOT:PSS). The cell performance was evaluated by voltammetric and galvanostatic charge/discharge cycles at different C-rates with 1M LiPF6 in 1:1 (v:v) ethylene carbonate (EC):dimethyl carbonate (DMC) (LP30) electrolyte and compared to that of cells assembled with LMNO featuring poly(vinylidene difluoride) (PVdF). At C/10, the specific capacity of LMNO-PEDOT:PSS and LMNO-PU were, respectively, 130 mAh g−1 and 127 mAh g−1, slightly higher than that of LMNO-PVdF (124 mAh g−1). While the capacity retention at higher C-rates and under repeated cycling of LMNO-PU and LMNO-PVdF electrodes was similar, LMNO-PEDOT:PSS featured superior performance. Indeed, lithium metal cells assembled with PEDOT:PSS featured a capacity retention of 100% over 200 cycles carried out at C/1 and with a high cut-off voltage of 5 V. Overall, this work demonstrates that both the water-processable binders are a valuable alternative to PVdF. In addition, the use of PEDOT:PSS significantly improves the cycle life of the cell, even when high-voltage cathodes are used, therefore demonstrating the feasibility of the production of a green lithium metal battery that can exhibit a specific energy of 400 Wh kg−1, evaluated at the electrode material level. Our work further demonstrates the importance of the use of functional binders in electrode manufacturing.
SARS-CoV-2 VOC type and biological sex affect molnupiravir efficacy in severe COVID-19 dwarf hamster model (2022)

SARS-CoV-2 variants of concern (VOC) have triggered infection waves. Oral antivirals such as molnupiravir promise to improve disease management, but efficacy against VOC delta was questioned and potency against omicron is unknown. This study evaluates molnupiravir against VOC in human airway epithelium organoids, ferrets, and a lethal Roborovski dwarf hamster model of severe COVID-19-like lung injury. VOC were equally inhibited by molnupiravir in cells and organoids. Treatment reduced shedding in ferrets and prevented transmission. Pathogenicity in dwarf hamsters was VOC-dependent and highest for delta, gamma, and omicron. All molnupiravir-treated dwarf hamsters survived, showing reduction in lung virus load from one (delta) to four (gamma) orders of magnitude. Treatment effect size varied in individual dwarf hamsters infected with omicron and was significant in males, but not females. The dwarf hamster model recapitulates mixed efficacy of molnupiravir in human trials and alerts that benefit must be reassessed in vivo as VOC evolve.
Controlling van der Waals Contacts in Complexes of Fullerene C60 (2003)

An impurity aids in the purification of C60. A 1:1 complex of C60 and calix[5]arene crystallizes from toluene (see picture) with the fullerenes organized in a one-dimensional zigzag array shrouded by a sheath of calixarenes. The complex forms in the presence of other globular molecules including C70, the major impurity in fullerite.
N-Halamine Biocidal Materials with Superior Antimicrobial Efficacies for Wound Dressings (2017)

This work demonstrated the successful application of N-halamine technology for wound dressings rendered antimicrobial by facile and inexpensive processes. Four N-halamine compounds, which possess different functional groups and chemistry, were synthesized. The N-halamine compounds, which contained oxidative chlorine, the source of antimicrobial activity, were impregnated into or coated onto standard non-antimicrobial wound dressings. N-halamine-employed wound dressings inactivated about 6 to 7 logs of <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i> bacteria in brief periods of contact time. Moreover, the N-halamine-modified wound dressings showed superior antimicrobial efficacies when compared to commercially available silver wound dressings. Zone of inhibition tests revealed that there was no significant leaching of the oxidative chlorine from the materials, and inactivation of bacteria occurred by direct contact. Shelf life stability tests showed that the dressings were stable to loss of oxidative chlorine when they were stored for 6 months in dark environmental conditions. They also remained stable under florescent lighting for up to 2 months of storage. They could be stored in opaque packaging to improve their shelf life stabilities. In vitro skin irritation testing was performed using a three-dimensional human reconstructed tissue model (EpiDerm™). No potential skin irritation was observed. In vitro cytocompatibility was also evaluated. These results indicate that N-halamine wound dressings potentially can be employed to prevent infections, while at the same time improving the healing process by eliminating undesired bacterial growth.