gebhart/patrepeval huggingface dataset:
Genetic studies of body mass index yield new insights for obesity biology (2015)

Obesity is heritable and predisposes to many diseases. To understand the genetic basis of obesity better, here we conduct a genome-wide association study and Metabochip meta-analysis of body mass index (BMI), a measure commonly used to define obesity and assess adiposity, in upto 339,224 individuals. This analysis identifies 97 BMI-associated loci (P &lt;5 x 10(-8)), 56 of which are novel. Five loci demonstrate clear evidence of several independent association signals, and many loci have significant effects on other metabolic phenotypes. The 97 loci account for similar to 2.7% of BMI variation, and genome-wide estimates suggest that common variation accounts for &gt;20% of BMI variation. Pathway analyses provide strong support for a role of the central nervous systemin obesity susceptibility and implicate new genes and pathways, including those related to synaptic function, glutamate signalling, insulin secretion/action, energy metabolism, lipid biology and adipogenesis.
Waveform Design for Wireless Power Transfer with Limited Feedback (2017)

Waveform design is a key technique to jointly exploit a beamforming gain, the channel frequency-selectivity and the rectifier nonlinearity, so as to enhance the end-to-end power transfer efficiency of Wireless Power Transfer (WPT). Those waveforms have been designed assuming perfect channel state information at the transmitter. This paper proposes two waveform strategies relying on limited feedback for multi-antenna multi-sine WPT over frequency-selective channels. In the waveform selection strategy, the Energy Transmitter (ET) transmits over multiple timeslots with every time a different waveform precoder within a codebook, and the Energy Receiver (ER) reports the index of the precoder in the codebook that leads to the largest harvested energy. In the waveform refinement strategy, the ET sequentially transmits two waveforms in each stage, and the ER reports one feedback bit indicating an increase/decrease in the harvested energy during this stage. Based on multiple one-bit feedback, the ET successively refines waveform precoders in a tree-structured codebook over multiple stages. By employing the framework of the generalized Lloyd's algorithm, novel algorithms are proposed for both strategies to optimize the codebooks in both space and frequency domains. The proposed limited feedback-based waveform strategies are shown to outperform a set of baselines, achieving higher harvested energy.
Nannocystin A: an Elongation Factor 1 Inhibitor from Myxobacteria with Differential Anti‐Cancer Properties (2015)

Cultivation of myxobacteria of the Nannocystis genus led to the isolation and structure elucidation of a class of novel cyclic lactone inhibitors of elongation factor 1. Whole genome sequence analysis and annotation enabled identification of the putative biosynthetic cluster and synthesis process. In biological assays the compounds displayed anti-fungal and cytotoxic activity. Combined genetic and proteomic approaches identified the eukaryotic translation elongation factor 1α (EF-1α) as the primary target for this compound class. Nannocystin A (1) displayed differential activity across various cancer cell lines and EEF1A1 expression levels appear to be the main differentiating factor. Biochemical and genetic evidence support an overlapping binding site of 1 with the anti-cancer compound didemnin B on EF-1α. This myxobacterial chemotype thus offers an interesting starting point for further investigations of the potential of therapeutics targeting elongation factor 1.
A router architecture for flexible routing and switching in multihop point-to-point networks (1999)

Modern parallel and distributed applications have a wide range of communication characteristics and performance requirements. These diverse characteristics affect the performance and suitability of particular routing and switching policies in multihop point-to-point networks. In this paper, we identify a core set of architectural features necessary for flexible selection and implementation of multiple routing and switching schemes. Using this, we present a flexible router whose routing and switching policies can be tailored to the application, allowing the network to meet these diverse needs. By dedicating a small programmable processor to each incoming link, we can implement wormhole, virtual cut-through, and packet switching, as well as hybrid switching schemes, each under a variety of unicast and multicast routing algorithms. In addition, a flexible router can support several applications or traffic types simultaneously, enabling better support of applications with multiple traffic classes. We have designed, implemented, and fabricated the Programmable Routing Controller (PRG). Cycle-level simulations of mesh-connected PRCs also demonstrate that flexible routing and switching can significantly enhance application performance.
Psoriasis Patients Are Enriched for Genetic Variants That Protect against HIV-1 Disease (2012)

An important paradigm in evolutionary genetics is that of a delicate balance between genetic variants that favorably boost host control of infection but which may unfavorably increase susceptibility to autoimmune disease. Here, we investigated whether patients with psoriasis, a common immune-mediated disease of the skin, are enriched for genetic variants that limit the ability of HIV-1 virus to replicate after infection. We analyzed the HLA class I and class II alleles of 1,727 Caucasian psoriasis cases and 3,581 controls and found that psoriasis patients are significantly more likely than controls to have gene variants that are protective against HIV-1 disease. This includes several HLA class I alleles associated with HIV-1 control; amino acid residues at HLA-B positions 67, 70, and 97 that mediate HIV-1 peptide binding; and the deletion polymorphism rs67384697 associated with high surface expression of HLA-C. We also found that the compound genotype KIR3DS1 plus HLA-B Bw4-80I, which respectively encode a natural killer cell activating receptor and its putative ligand, significantly increased psoriasis susceptibility. This compound genotype has also been associated with delay of progression to AIDS. Together, our results suggest that genetic variants that contribute to anti-viral immunity may predispose to the development of psoriasis.
Probabilistically-constrained Estimation of Random Parameters with Unknown Distribution (2006)

The problem of estimating random unknown signal parameters in a noisy linear model is considered. It is assumed that the covariance matrices of the unknown signal parameter and noise vectors are known and that the noise is Gaussian, while the distribution of the random signal parameter vector is unknown. Instead of the traditional minimum mean squared error (MMSE) approach, where the average is taken over both the random signal parameters and noise realizations, we propose a linear estimator that minimizes the MSE which is averaged over the noise only. To make our design pragmatic, the minimization is performed for signal parameter realizations whose probability is sufficiently large, while "discarding" low-probability realizations. It is shown that the obtained linear estimator can be viewed as a generalization of the classical Wiener filter
ChemInform Abstract: Palladium‐Catalyzed Synthesis of Anellated Indoles. (1992)

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.
Evaluation of Solute Permeation through the Stratum Corneum: Lateral Bilayer Diffusion as the Primary Transport Mechanism (1997)

Solute permeation across human stratum corneum (SC) was examined in terms of the fundamental bilayer transport properties. A mathematical model was developed to describe the macroscopic SC permeation via the interkeratinocyte lipid domain in terms of (i) the structure and dimensions of the SC, and (ii) the microscale lipid bilayer transport properties, which include the bilayer/water partition coefficient, the lateral diffusion coefficient, the interfacial transbilayer mass transfer coefficient, and the intramembrane transbilayer mass transfer coefficient. The relative importance of the diffusive resistances associated with the bilayer transport properties was evaluated with the model and experimental data. Lateral diffusion coefficients in SC lipid bilayers were calculated from 120 human skin permeability measurements, and compared with previously reported measurements made in SC-extracted lipids. Good qualitative and quantitative agreement was observed, indicating that, in the context of the model, the diffusive resistance associated with lateral diffusion is sufficient to explain the overall resistance of solute permeation through the SC. A similar analysis shows that the diffusive resistance associated with interfacial transbilayer transport is not capable of explaining the experimental permeation values, thus supporting this finding. The lateral diffusion analysis also revealed a bifunctional size dependence of transport within the SC, with a strong size dependence for small solutes (<300 Da) and a weak size dependence for larger solutes.
Free-breathing volumetric fat/water separation by combining radial sampling, compressed sensing, and parallel imaging (2016)

The described framework provides a viable approach for motion-robust fat/water separation and promises particular value for clinical applications that are currently limited by the breath-holding capacity or cooperation of patients. Magn Reson Med 78:565-576, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Internal Structure of Porous Silica: A Model System for Characterization by Nuclear Magnetic Resonance (1989)

Nuclear magnetic resonance (NMR) relaxation methods have been used to investigate the internal structure of porous silica gelled from colloidal silica and potassium silicate mixtures. These materials possess a narrow pore size distribution with average pore diameter ranging from 470 to 2400 Å (47 to 240 nm) as determined from mercury intrusion porosimetry. NMR relaxation measurements were performed on deionized water impregnated into the pore space. These results determine the distribution of local surface‐to‐volume ratios and show that all of the silica samples are very uniform on a length scale greater than 5 μ. NMR relaxation measurements performed on silica samples partially filled with water provide a precise confirmation of the theoretical model upon which the NMR pore structure analysis is based. Measurements of the relaxation strength at the water—silica interface were found to depend systematically on the initial composition of the material. The self‐diffusion coefficient of water, saturated in the pore space, is reduced by 14% from its bulk value.
Security Analysis and Extensions of the PCB Algorithm for Distributed Key Generation (2005)

Poovendran, Corson and Baras presented a distributed cryptographic key generation algorithm that was suitable for wireless networking environment.However, the security as well as the computational complexity of their scheme were never analyzed.In this work, we present information theoretic analysis of their work and derive the properties of the cryptographic keys that are generated by their scheme.We also present efficient computational schemes that would require only logarithmic number of steps in group size to compute the common keys.
Different‐sized mRNAs from GH4C1 cells induce a TRH‐dependent electrical response in Xenopus laevis oocytes (1990)

Poly(A)+ RNA from the GH4C1 rat pituitary cell line elicited a thyrotropin releasing hormone response in Xenopus laevis oocytes which could be measured as a change in membrane current by the voltage-clamp method. Oocytes injected with Poly(A)+ RNA from GH12C1 cells which do not bind thyrotropin releasing hormone or with buffer solution alone did not show this response. Size fractionation of total poly(A)+ RNA by sucrose density-gradient centrifugation shows two response maximal representing various mRNA fractions larger than 18S. These results indicate the presence of thyrotropin releasing hormone receptor mRNA heterogeneity where the smallest mRNA is at least 2 kb.
Counteracting age-related VEGF signaling insufficiency promotes healthy aging and extends life span (2021)

Aging is an established risk factor for vascular diseases, but vascular aging itself may contribute to the progressive deterioration of organ function. Here, we show in aged mice that vascular endothelial growth factor (VEGF) signaling insufficiency, which is caused by increased production of decoy receptors, may drive physiological aging across multiple organ systems. Increasing VEGF signaling prevented age-associated capillary loss, improved organ perfusion and function, and extended life span. Healthier aging was evidenced by favorable metabolism and body composition and amelioration of aging-associated pathologies including hepatic steatosis, sarcopenia, osteoporosis, "inflammaging" (age-related multiorgan chronic inflammation), and increased tumor burden. These results indicate that VEGF signaling insufficiency affects organ aging in mice and suggest that modulating this pathway may result in increased mammalian life span and improved overall health.
Human lung fibroblasts produce proresolving peroxisome proliferator-activated receptor-γ ligands in a cyclooxygenase-2-dependent manner (2016)

Human lung fibroblasts (HLFs) act as innate immune sentinel cells that amplify the inflammatory response to injurious stimuli. Here, we use targeted lipidomics to explore the hypothesis that HLFs also play an active role in the resolution of inflammation. We detected cyclooxygenase-2 (COX-2)-dependent production of both proinflammatory and proresolving prostaglandins (PGs) in conditioned culture medium from HLFs treated with a proinflammatory stimulus, IL-1β. Among the proresolving PGs in the HLF lipidome were several known ligands for peroxisome proliferator-activated receptor-γ (PPARγ), a transcription factor whose activation in the lung yields potent anti-inflammatory, antifibrotic, and proresolving effects. Next, we used a cell-based luciferase reporter to confirm the ability of HLF supernatants to activate PPARγ, demonstrating, for the first time, that primary HLFs activated with proinflammatory IL-1β or cigarette smoke extract produce functional PPARγ ligands; this phenomenon is temporally regulated, COX-2- and lipocalin-type PGD synthase-dependent, and enhanced by arachidonic acid supplementation. Finally, we used luciferase reporter assays to show that several of the PGs in the lipidome of activated HLFs independently activate PPARγ and/or inhibit NFκB. These results indicate that HLFs, as immune sentinels, regulate both proinflammatory and proresolving responses to injurious stimuli. This novel endogenous resolution pathway represents a new therapeutic target for globally important inflammatory diseases such as chronic obstructive pulmonary disease.
Iterative Time-Variant Channel Estimation for 802.11p Using Generalized Discrete Prolate Spheroidal Sequences (2012)

This paper deals with channel estimation for orthogonal frequency-division multiplexing (OFDM) in time-variant wireless propagation channels. We particularly consider the challenges of the IEEE 802.11p standard, which is the worldwide dominant system for vehicular communications. For historic reasons, 802.11p uses a pilot pattern that is identical to the pattern used in 802.11a, which was initially designed for the estimation of indoor channels with little or no time variations. Therefore, this pilot pattern violates the sampling theorem for channels with both large delay spread and large Doppler spread, as often occurs in vehicular communications. To remedy this problem, we design a robust iterative channel estimator based on a 2-D subspace spanned by generalized discrete prolate spheroidal sequences. Due to the tight subspace design, the iterative receiver is able to converge to the same bit error rate (BER) as a receiver with perfect channel knowledge. Furthermore, we propose a backward compatible modification of the 802.11p pilot pattern such that the number of iterations sufficient for convergence can be reduced by a factor of 2-3, strongly reducing implementation complexity.
Molecular-scale features that govern the effects of O-glycosylation on a carbohydrate-binding module (2015)

Protein glycosylation is a ubiquitous post-translational modification in all kingdoms of life. Despite its importance in molecular and cellular biology, the molecular-level ramifications of <i>O</i>-glycosylation on biomolecular structure and function remain elusive. Here, we took a small model glycoprotein and changed the glycan structure and size, amino acid residues near the glycosylation site, and glycosidic linkage while monitoring any corresponding changes to physical stability and cellulose binding affinity. The results of this study reveal the collective importance of all the studied features in controlling the most pronounced effects of <i>O</i>-glycosylation in this system. Going forward, this study suggests the possibility of designing proteins with multiple improved properties by simultaneously varying the structures of <i>O</i>-glycans and amino acids local to the glycosylation site.
Hierarchical scheduling for diverse datacenter workloads (2013)

There has been a recent industrial effort to develop multi-resource hierarchical schedulers. However, the existing implementations have some shortcomings in that they might leave resources unallocated or starve certain jobs. This is because the multi-resource setting introduces new challenges for hierarchical scheduling policies. We provide an algorithm, which we implement in Hadoop, that generalizes the most commonly used multi-resource scheduler, DRF [1], to support hierarchies. Our evaluation shows that our proposed algorithm, H-DRF, avoids the starvation and resource inefficiencies of the existing open-source schedulers and outperforms slot scheduling.
Angular filtering of spatial modes in a vertical-cavity surface-emitting laser by a Fabry–Perot étalon (1999)

A low-finesse Fabry–Perot étalon is employed as an angularly selective filter to discriminate against the high-order spatial modes of a vertical-cavity surface-emitting laser (VCSEL) in the near field. Single-transverse-mode operation is obtained over a wide region for a 15 μm diam VCSEL.
21.3: Mode separation in a magnetron with diffraction output driven by a transparent cathode (2010)

We demonstrate using particle-in-cell (PIC) computer simulations that symmetric axial extraction of radiation from a magnetron driven by a transparent cathode provides good separation of eigenmodes switched by the applied axial magnetic field, even for a large number of identical cavities. In addition, high efficiency magnetron operation and stable π-mode generation over a wide region of magnetic field and for various cathode radii are demonstrated.
Stress Analysis of Unbonded and Bonded Prestressed CFRP-strengthened Steel Plates (2016)

Numerous research studies are available in the literature on strengthening of steel members using carbon fiber reinforced polymer (CFRP) composites. Although it is clear that strengthening using prestressed CFRP plates has several advantages over non-prestressed reinforcements, less attention has been paid in the literature to develop theoretical formulations. Consequently, in this paper, unbonded and bonded prestressed CFRP-strengthened steel plates are analyzed and stresses in CFRP and steel substrate are analytically formulated. Furthermore, the effect of single-side retrofit, which is usually neglected in stress calculations, has been studied. Analytical formulations were then verified by the results of static tests on CFRP-strengthened steel plates under tensile loading. The primary results show that prestressing could considerably reduce the tensile stresses in steel. Consequently, strengthening with prestressed CFRP laminates could be used as an efficient technique for strengthening of steel members, especially those prone to fatigue. However, the available capacity of the prestressed bonded reinforcements before debonding is much less than the developed mechanically anchored, prestressed unbonded reinforcements. Moreover, analytical modeling and experimental results of the current study show that neglecting the eccentricity in single-side CFRP-strengthened steel plates could result in an unsafe stress prediction in steel substrate.
Textural and sensory qualities of muffins prepared with fermented rice bran (2013)

Rice is one of the most popular cereal grains in the world. Rice bran, a by-product of the rice milling process, contains an abundance of nutrients including protein, fiber, vitamin B complex, vitamin E, and other nutraceuticals. However, rice bran is underutilized in the food industry. In this project muffins were prepared with varying concentrations (2.5%, 5.0%, 7.5%, 10.0%, 15.0%, 20.0%, and 25.0%) of 60 mesh (250 µm) fermented rice bran (60 mFRB) and 80 mesh (180 µm) fermented rice bran (80 mFRB). A cappuccino muffin formulation was used as flavor for all the samples. The control sample was prepared without the fermented rice bran for comparison. Initial taste evaluations using student panelists demonstrated muffins incorporated with 80 mFRB were too dense, unacceptable, and discontinued for further study while the muffins prepared with 60 mFRB were found to be acceptable. The sensory qualities (texture, color, mouthfeel, aroma) and overall consumer acceptability of the muffins with 2.5%, 5.0%, 7.5%, and 10.0% 60 mFRB have lower firmness values in comparison to the control representing a softer texture. Three out of five sensory panelists considered muffins with 20.0% and 25.0% 60 mFRB to be acceptable in terms of color, texture, mouthfeel, and aroma. Hence, this project demonstrates that fermented rice bran products can be used in the preparation of breakfast food products like muffins. This innovative ingredient formulation concept can be useful in creating successful commercial bakery products that will provide protein, fiber and other nutrients.
<title>Infrared measurement of thermal constants in laser-irradiated scleral tissue</title> (1996)

Laser scleral buckling (LSB) experiments were performed by irradiating human cadaver eyes with a focused beam from a 2.1-micrometer Ho:YAG laser. Spatially and temporally resolved temperature maps of the sclera were inferred from infrared images of the tissue's thermal radiation. An infrared focal-plane camera operating in the 3- to 5-micrometer wavelength interval was used for the measurements, from which we derived absorption and thermal diffusivity coefficients of the scleral tissue, along with the temperature dependence of these coefficients. A thermal-response model was developed, which describes the tissue surface temperature in response to a train of laser pulses, given the pulse repetition rate, beam fluence, spot size, and total energy delivered. This model provides guidance for optimization of laser-irradiation parameters for LSB treatment.