gebhart/patrepeval huggingface dataset:
Determination of the melanocortin-4 receptor structure identifies Ca 2+ as a cofactor for ligand binding (2020)

The melanocortin-4 receptor (MC4R) is involved in energy homeostasis and is an important drug target for syndromic obesity. We report the structure of the antagonist SHU9119-bound human MC4R at 2.8-angstrom resolution. Ca<sup>2+</sup> is identified as a cofactor that is complexed with residues from both the receptor and peptide ligand. Extracellular Ca<sup>2+</sup> increases the affinity and potency of the endogenous agonist α-melanocyte-stimulating hormone at the MC4R by 37- and 600-fold, respectively. The ability of the MC4R crystallized construct to couple to ion channel Kir7.1, while lacking cyclic adenosine monophosphate stimulation, highlights a heterotrimeric GTP-binding protein (G protein)-independent mechanism for this signaling modality. MC4R is revealed as a structurally divergent G protein-coupled receptor (GPCR), with more similarity to lipidic GPCRs than to the homologous peptidic GPCRs.
OOF3D: An Image-Based Finite Element Solver for Materials Science (2012)

Recent advances in experimental techniques (micro CT scans, automated serial sectioning, electron back-scatter diffraction, synchrotron radiation x-rays) have made it possible to characterize the full, three dimensional structure of real materials. Such new experimental techniques have created a need for software tools that can model the response of these materials under various kinds of loads. OOF (Object Oriented Finite Elements) is a desktop software application for studying the relationship between the microstructure of a material and its overall mechanical, electromagnetic, or thermal properties using finite element models based on real or simulated micrographs. OOF provides methods for segmenting images, creating meshes of complex geometries, solving PDEs using finite element models, and visualizing 3D results. We discuss the challenges involved in implementing OOF in 3D and use finite element simulations of trabecular bone as an illustrative example.
Supplementary Tables 1-3 from Colocalization of the Tetraspanins, CO-029 and CD151, with Integrins in Human Pancreatic Adenocarcinoma: Impact on Cell Motility (2023)

Supplementary Tables 1-3 from Colocalization of the Tetraspanins, CO-029 and CD151, with Integrins in Human Pancreatic Adenocarcinoma: Impact on Cell Motility
Analysis of NB-IoT Deployment in LTE Guard-Band (2017)

In 3GPP Rel-13, a narrowband wide-area cellular system, named Narrowband Internet of Things (NB-IoT), has been introduced to provide low-cost, low-power connectivity for the Internet of Things. This system, based on Long Term Evolution (LTE) technology, can be deployed in three operation modes - in-band within LTE carrier, in the guard-band of LTE carrier, and stand-alone. Guard-band deployment allows the operator to support NB-IoT without requiring new spectrum and with minimal impact to LTE. This paper provides an overview and presents a study of NB-IoT deployment in LTE guard band. An analysis of coexistence of NB-IoT with LTE is presented and demonstrates that while there is mutual interference between NB-IoT and LTE on the uplink, the impact on either system is small. A performance analysis of NB-IoT is also presented. The link budget analysis demonstrates how the coverage target can be achieved for the uplink and downlink data channels. Illustrative uplink and downlink link-level simulation results are provided. The analysis in the paper shows that guard-band operation of NB-IoT is feasible and can provide support for massive number of low-throughput IoT devices.
Towards Individuated Reading Experiences: Different Fonts Increase Reading Speed for Different Individuals (2022)

In our age of ubiquitous digital displays, adults often read in short, opportunistic interludes. In this context of Interlude Reading , we consider if manipulating font choice can improve adult readers’ reading outcomes. Our studies normalize font size by human perception and use hundreds of crowdsourced participants to provide a foundation for understanding, which fonts people prefer and which fonts make them more effective readers. Participants’ reading speeds (measured in words-per-minute (WPM)) increased by 35% when comparing fastest and slowest fonts without affecting reading comprehension. High WPM variability across fonts suggests that one font does not fit all. We provide font recommendations related to higher reading speed and discuss the need for individuation, allowing digital devices to match their readers’ needs in the moment. We provide recommendations from one of the most significant online reading efforts to date. To complement this, we release our materials and tools with this article.
Hybrid Effect of Micropatterned Lithium Metal and Three Dimensionally Ordered Macroporous Polyimide Separator on the Cycle Performance of Lithium Metal Batteries (2020)

Short cycle life of the lithium metal secondary battery (LMSB) is largely ascribed to the dendritic growth of lithium metal during the charging process followed by continuous electrolyte decomposition. To make up for this intrinsic drawback of lithium metal, two pioneering techniques, micropatterning on lithium metal and three dimensionally ordered microporous polyimide (3DOM PI) separator, are combined to ascertain their hybrid effect on the cycle performance of LMSB. When a unit cell consisting of LiNi0.6Mn0.2Co0.2O2/3DOM PI separator/patterned lithium metal is cycled at the charging and discharging c-rates of 0.3C and 1C (1C = 2.5 mA), respectively, above 80% of the initial discharge capacity is maintained even after 400 cycles, while a control cell with polyethylene separator survives only for 130 cycles. This tremendous improvement is ascribed to the combination effect of inducing preferential lithium electrodeposition reaction into the micropattern and the uniform distribution of lithium ions on the nonpatterned lithium surface region by the 3DOM PI separator. Thus, combining these two technologies is very promising for LMSB commercialization in the future.
Advances in Photochemistry, Volume 27 (2002)

edited by Albert Noyes, Jr., George S. Hammond, and J.N. Pitts, Jr.
Semi-automatic assembly of real cross-cut shredded documents (2012)

This paper introduces a semi-automatic approach for cross-cut shredded document reassembly. Automatic algorithms are proposed for segmenting and orienting individual shreds from a scanned shred image, as well as for computing features and ranking potential matches for each shred. Additionally, a human-computer interface is designed to allow semi-automatic assembly of the shreds using the computed feature and match information. Our document de-shredding system was tested on puzzles from the DARPA Shredder Challenge, allowing successful reconstruction of multiple shredded documents and demonstrating the effectiveness of the automatic algorithms.
The Propagation of a Fuel-Air Ratio Disturbance in a Simple Premixer and its Influence on Pressure Wave Amplification (2000)

The propagation of a fuel concentration disturbance in a premixer is studied analytically with a 3-D spatio-temporal mixing model. A simple analytical method is introduced which permits the frequency response characteristics of multiple points of fuel injection in simple (yet meaningful) premixer passage geometries to be obtained. The results provide physical insight into some of the design parameters that may affect the amplitude of FAR fluctuations coming out of a premixer when it is subjected to finite amplitude pressure waves. The possibility of a given design to lead to amplification of pressure waves (Rayleigh’s criteria) can be influenced by the characteristics of the mixing processes in a premixer channel. Results obtained in this paper may affect the design implementation of some of the proposals made for the control of combustion instability such as introduction of multiple time delays through selective fuel placement in a premixer.
Posterior mini-incision (2014)

The incision a surgeon should use for total hip replacement is the one that he/she has confidence in and is skilled at. However, a small posterior incision is a superior incision for patients when scientific data are used as the criteria. It was first described by Sculco et al. [1]. A direct anterior incision has more blood loss, longer operating time and a femur fracture rate three-times that of the posterior incision [2]. It does not have a superior recovery [3]. Compared with the two incision anterior approach, the small posterior incision had better recovery and was favored by patients [4]. Gait analysis shows equality of functional healing by 6 weeks, so there is no advantage for muscle function with the anterior approach [5]. Finally, in 2013, the dislocation rates were very similar for all approaches since the advent of large femoral heads and posterior capsular closure.
Mobile-aware scheduling for low latency backhaul over DOCSIS (2017)

In this paper, we discuss latency reduction techniques for mobile backhaul over Data Over Cable Service Interface Specifications (DOCSIS®) networks. When the latencies from both the wireless and the DOCSIS networks are added together, it can result in noticeable end-to-end system latency, particularly under network congestion. Previously, we proposed a method to improve upstream user-to-mobile core latency by coordinating the LTE and DOCSIS scheduling. The method reduces the impact on system latency from the DOCSIS network's request-grant-data loop, which is the main contributor of backhaul upstream latency. Since the method reduces latency on the DOCSIS data path, it will therefore improve performance of latency sensitive applications, particularly if TCP is used as the transport protocol, especially when the link is congested. In this paper, we investigate the effect of HARQ failure on system performance. Through simulation, we show that despite the uncertainty introduced by the LTE protocol, coordinated scheduling improves overall system latency.
Guest Editorial on Microstructured Fibers (2009)

The 21 papers in this special issue on microstructured fibers cover most recent advances in designs, fabrication and applications in the area of photonic crystal fibers (PCF), photonic band-gap fibers (PBGF), nanostructured fibers and hole assisted fibers (HAF), including high speed DWDM transmission over PCF, nonlinear properties and applications, microstructured fiber lasers and amplifiers, nanostructure core fibers and devices, HAF with zero dispersion in the near infrared and visible wavelength regions, fluid-filled solid core PBGF, gas and pressure sensors using PBGF, chirped PCF for guiding sub-100-fs pulses, microstructured fiber gratings, PCF for THz transmission, linear core array microstructured fibers, and polymer microstructured fibers.
Perspective from Aberrant Crypt Foci in the Adenoma Prevention with Celecoxib Trial (2023)

Perspective from Aberrant Crypt Foci in the Adenoma Prevention with Celecoxib Trial
Waveguide-coupled Localized Excitons From a WSe2 monolayer on a Silicon Nitride Photonic Platform (2019)

We demonstrate the coupling of localized excitons from a WSe2 monolayer into a silicon nitride waveguide by measuring the waveguide-coupled fluorescence, paving the way towards scalable fabrication of on-chip single photon sources.
Structural characterization of a follicle-stimulating hormone action inhibitor in porcine ovarian follicular fluid. Its identification as the insulin-like growth factor-binding protein. (1990)

Recently, an inhibitory polypeptide that could block the follicle-stimulating hormone-induced estradiol and progesterone production in rat ovary granulosa cells has been isolated from porcine ovarian follicular fluid. Amino-terminal sequence analysis of the purified inhibitor suggests that it could be the porcine congener of the 53-kDa subunit of the growth hormone-dependent insulin-like growth factor binding protein (IGF-BP3). Using amino acid sequence information derived from the purified inhibitor to construct oligonucleotide probes, we have now identified the complementary deoxyribonucleic acids (cDNAs) encoding the inhibitory polypeptide from a porcine liver and a porcine ovary library. The nucleotide and predicted amino acid sequences revealed that the cDNAs indeed encode the porcine homolog of the recently characterized human IGF-BP3. The mature polypeptide consists of 266 amino acids, which is 2 amino acids longer than the human sequence. Between the two species, there are 42 amino acid substitutions, but the 18 cysteines and the three Asn-linked glycosylation sites are totally conserved. A single mRNA species of 2.6 kilobases encoding the IGF-BP3 was detected in porcine gonadal, brain, and liver tissues by Northern analysis.
SMRT repression of nuclear receptors controls the adipogenic set point and metabolic homeostasis (2008)

The nuclear receptor corepressor, silencing mediator of retinoid and thyroid hormone receptors (SMRT), is recruited by a plethora of transcription factors to mediate lineage and signal-dependent transcriptional repression. We generated a knockin mutation in the receptor interaction domain (RID) of SMRT (SMRT(mRID)) that solely disrupts its interaction with nuclear hormone receptors (NHRs). SMRT(mRID) mice are viable and exhibit no gross developmental abnormalities, demonstrating that the reported lethality of SMRT knockouts is determined by non-NHR transcription factors. However, SMRT(mRID) mice exhibit widespread metabolic defects including reduced respiration, altered insulin sensitivity, and 70% increased adiposity. The latter phenotype is illustrated by the observation that SMRT(mRID)-derived MEFs display a dramatically increased adipogenic capacity and accelerated differentiation rate. Collectively, our results demonstrate that SMRT-RID-dependent repression is a key determinant of the adipogenic set point as well as an integrator of glucose metabolism and whole-body metabolic homeostasis.
ChemInform Abstract: Palladium‐Catalyzed Arylation of Polar Organometallics Mediated by 9‐ Methoxy‐9‐borabicyclo(3.3.1)nonane: Suzuki Reactions of Extended Scope. (1996)

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.
Continuous Glycoprotein-130–Mediated Signal Transducer and Activator of Transcription-3 Activation Promotes Inflammation, Left Ventricular Rupture, and Adverse Outcome in Subacute Myocardial Infarction (2010)

Background— In patients with myocardial infarction, high serum levels of interleukin-6 cytokines predict a poor outcome. The common receptor of interleukin-6 cytokines, glycoprotein-130 (gp130), signals via janus kinase/signal transducer and activator of transcription (STAT), cytoplasmic protein tyrosine phosphatase/extracellular signal-regulated kinase, and phosphoinositide-3-kinase/Akt pathways, and the regulation of these pathways depends at least in part on the gp130 tyrosine-757 residue. By analyzing cardiomyocyte-specific gp130 Y757F mutant mice, we investigated the effect of disturbed gp130 signaling after myocardial infarction. Methods and Results— The cardiomyocyte-restricted α-myosin heavy chain-Cre-recombinase-loxP system was used to generate mice with gp130 Y757F mutant cardiomyocytes ( αMHC-Cre tg/− ;gp130 fl/Y757F [Y 757 F]); all other cells carried at least 1 functional gp130 gene, ensuring normal gp130 signaling. Y 757 F mice displayed normal cardiac function and morphology at 3 months of age comparable to their nonmutant littermates. In response to myocardial infarction, Y 757 F mice displayed higher mortality associated with increased left ventricular rupture rate, sustained cardiac inflammation, and heart failure. These adverse effects were associated with prolonged and enhanced STAT3 activation and increased expression of interleukin-6 and of the complement-activating mannose-binding lectin C. Pharmacological inhibition of the complement system by cobra venom factor attenuated inflammation, prevented left ventricular rupture, and improved cardiac function in Y 757 F mice. Stronger effects were observed with a genetic reduction of STAT3 (STAT3 flox/+ ) restricted to cardiomyocytes in Y 757 F mice, which prevented extensive upregulation of interleukin-6, complement activation, and sustained inflammation and lowered left ventricular rupture rate, heart failure, and mortality in subacute myocardial infarction. Conclusion— Impaired downregulation of gp130-mediated STAT3 activation in subacute infarction promotes cardiac inflammation, adverse remodeling, and heart failure, suggesting a potential causative role of high interleukin-6 serum levels after myocardial infarction.
Ionic liquids—media for unique phosphorus chemistry (2005)

Ionic liquids have been shown to offer hitherto unseen control as both a storage solvent for PCl3 and POCl3 and reaction media for fluorination and mixed anhydride formation under benign conditions.
Formation and stability of 3–5 atom gold clusters from gold complexes during the catalytic reaction: dependence on ligands and counteranions (2013)

Gold complexes and salts decompose to catalytically active 3-5 atom gold clusters during the one-pot acylation-hydration of propargyl alcohols. Kinetic and spectroscopic studies show that released ligands and counteranions exert a direct effect on the formation and stability of the clusters.
Analysis and optimization of waveguide multiapplicator hyperthermia systems (1993)

A method is proposed for determining the excitation coefficients of an antenna array operating in a large rectangular waveguide and used as a hyperthermia system. The excitation coefficients of the array elements are optimized for attaining an improved specific absorption rate (SAR) distribution around a deep-seated tumor. The method is applied to a two-dimensional problem of a piecewise homogeneous post in a waveguide representing a section of the human torso. The array is operating below the cutoff frequency of the dominant mode of the waveguide. Numerical simulations have been performed to check the effectiveness of this approach. The results show that by using the proposed optimization method, SAR distributions can be improved.
New Jaspamide Derivatives from the Marine Sponge Jaspis splendans Collected in Vanuatu (1998)

Two new jaspamide derivatives (1 and 2) along with jaspamide have been isolated from the marine sponge Jaspis splendans collected in Vanuatu. Their chemical structures were determined from 1D and 2D NMR studies and MS data. These two compounds inhibited the in vitro growth of the NSCLC-N6 human tumor cell lines with IC50 values in the microg/mL range.
A reference based analysis framework for analyzing system call traces (2010)

Reference based analysis (RBA) is a novel data mining tool for exploring a test data set with respect to a reference data set. The power of RBA lies in it ability to transform any complex data type, such as symbolic sequences and multi-variate categorical data instances, into a multivariate continuous representation. The transformed representation not only allows visualization of the complex data, which cannot be otherwise visualized in its original form, but also allows enhanced anomaly detection in the transformed feature space. We demonstrate the application of the RBA framework in analyzing system call traces and show how the transformation results in improved intrusion detection performance over state of art data mining based intrusion detection methods developed for system call traces.
Quantum correlations in electron microscopy (2020)

Electron microscopes provide a powerful platform for exploring physical phenomena with nanoscale resolution, based on the interaction of free electrons with the excitations of a sample such as phonons, excitons, bulk plasmons, and surface plasmons. The interaction usually results in the absorption or emission of such excitations, which can be detected directly through cathodoluminescence or indirectly through electron energy loss spectroscopy (EELS). However, as we show here, the underlying interaction of a free electron and an arbitrary optical excitation goes beyond what was predicted or measured so far, due to the interplay of entanglement and decoherence of the electron-excitation system. The entanglement of electrons and optical excitations can provide new analytical tools in electron microscopy. For example, it can enable measurements of optical coherence, plasmonic lifetimes, and electronic length scales in matter (such as the Bohr radius of an exciton). We show how these can be achieved using common configurations in electron diffraction and EELS, revealing significant changes in the electron’s coherence, as well as in other quantum information theoretic measures such as purity. Specifically, we find that the purity after interaction with nanoparticles can only take discrete values, versus a continuum of values for interactions with surface plasmons. We quantify the post-interaction density matrix of the combined electron-excitation system by developing a framework based on macroscopic quantum electrodynamics. The framework enables a quantitative account of decoherence due to excitations in any general polarizable material (optical environment). This framework is thus applicable beyond electron microscopy. Particularly in electron microscopy, our work enriches analytical capabilities and informs the design of quantum information experiments with free electrons, allowing control over their quantum states and their decoherence by the optical environment.
Supplementary Table S3. Agreement between three biomarker IHC-based and intrinsic subtypes: impact of adding tumor grade to distinguish between luminal A and luminal B cases. from Performance of Three-Biomarker Immunohistochemistry for Intrinsic Breast Cancer Subtyping in the AMBER Consortium (2023)

&lt;p&gt;Agreement between IHC-based and RNA-based intrinsic subtyping using tumor grade in addition to ER, PR and HER2 expression&lt;/p&gt;
Julia–Colonna asymmetric epoxidation of furyl styryl ketone as a route to intermediates to naturally-occurring styryl lactones (1999)

The enone 1 was oxidized stereoselectively using urea-hydrogen peroxide with polyeucine as the catalyst to give the epoxide 2 which was used to make (+)-goniotriol 7, (+)-goniofufurone 8, (+)-8-acetylgonitriol 9 and gonio-pypyrone 10.
On the Convergence of SARAH and Beyond (2019)

The main theme of this work is a unifying algorithm, \textbf{L}oop\textbf{L}ess \textbf{S}ARAH (L2S) for problems formulated as summation of $n$ individual loss functions. L2S broadens a recently developed variance reduction method known as SARAH. To find an $ε$-accurate solution, L2S enjoys a complexity of ${\cal O}\big( (n+κ) \ln (1/ε)\big)$ for strongly convex problems. For convex problems, when adopting an $n$-dependent step size, the complexity of L2S is ${\cal O}(n+ \sqrt{n}/ε)$; while for more frequently adopted $n$-independent step size, the complexity is ${\cal O}(n+ n/ε)$. Distinct from SARAH, our theoretical findings support an $n$-independent step size in convex problems without extra assumptions. For nonconvex problems, the complexity of L2S is ${\cal O}(n+ \sqrt{n}/ε)$. Our numerical tests on neural networks suggest that L2S can have better generalization properties than SARAH. Along with L2S, our side results include the linear convergence of the last iteration for SARAH in strongly convex problems.